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UNIVERSITY OF DAYTON ROADMAP TO THE MCAT:
TRACKING MCAT CONTENT IN YOUR
NATURAL AND BEHAVIORAL SCIENCE COURSES
UNIVERSITY OF DAYTON OFFICE OF PREMEDICAL PROGRAMS
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University of Dayton MCAT Mapping
Introduction: One of the main criteria for selection of students to medical school is their performance on the Medical College Admission Test (MCAT). In 2015, the MCAT will change significantly, for the first time since 1991. The modifications reflect changes in both healthcare and an ever-evolving body of medical knowledge. MCAT 2015 will include a new section focusing on the psychological, social and biological foundations of behavior. The exam will test ways these areas influence various factors such as perception, reactions, and behavior as well as psychological, social and cultural differences that influence well-being. The MCAT also includes a “critical analysis and reasoning skills” section, which will test students’ ability to analyze, evaluate and apply information. Finally, two natural science sections will test concepts typically taught in introductory biology, general and organic chemistry, biochemistry, and physics. Recently the American Association of Medical Colleges (AAMC) released two documents to help institutions plan for these changes and develop course content, which reflect the identified content areas of the new MCAT. The Preview Guide for MCAT 2015 provides a blueprint for the exam in that it describes the exam’s content and format and discusses the exam’s conceptual framework. The “Course-Mapping Tool” provides the MCAT content and skills contained in an Excel spreadsheet so that specific topics and sub-topics can be identified as being covered or not covered in specific courses. The Office of Premedical Programs has recently completed a course-mapping project in which content areas from MCAT 2015 were identified as being covered in specific University of Dayton courses. The following documents were developed as a result of this project involving faculty from the Departments of Biology, Chemistry, Physics, Psychology, and Anthropology, Sociology and Social Work. These faculty were provided the MCAT course-mapping tool and were asked to identify within their courses where specific MCAT content are covered. The results of these analyses were compiled by the Office of Premedical Programs. Specifically, the following MCAT Sections were included in this course-mapping project:
Biological and Biochemical Foundations of Living Systems
Chemical and Physical Foundations of Biological Systems
Psychological, Social, and Biological Foundations of Behavior
The fourth section of the MCAT is titled Critical Analysis and Reasoning Skills (CARS). It includes passages and questions to test the student’s ability to comprehend. Passages are excerpted from authentic materials found in a variety of books, journals and magazines, often from
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disciplines in the social sciences and humanities. The CARS section is NOT included in this course mapping since it tests comprehension and not knowledge typically covered in a specific course. The first document titled “Course List with Associated Topics” (page 4) lists courses from the natural and behavioral science departments along with identified MCAT content areas covered in each of these classes. It is expected that this document will be helpful to students and faculty. Students will be able to track and archive materials relevant to the MCAT as they complete these courses. They can also go back over course materials later and pull and archive these portions of the courses. Clearly, these materials will later be helpful for students as they organize and plan their study schedule for the exam. Faculty may find it useful to use this document to identify areas of focus in their courses and identify to students that these areas are typically included in the MCAT. Faculty often look for MCAT content areas to include in their exams as well. The second document is titled “Topic List with Associated Courses”(page 135). It provides a comprehensive listing of all of the content categories in the three identified sections of the MCAT. For each content category, specific courses are listed that include one or more topics or sub-topics in that content category. The degree to which a specific topic is covered in a particular course will vary greatly and it is important that the reader look at the more detailed description of content in any given course in the main “Course Listing with Associated Topics” section. This compilation is not intended to be the sole resource for preparation for the MCAT. Instead it is intended as a useful tool to assist in organizing and archiving MCAT related course materials and to help students begin their MCAT study as they are introduced to relevant materials, building a personal portfolio of these materials throughout their undergraduate studies.
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Topic List with Associated Courses This document is a list of the main University of Dayton courses from the natural and behavioral sciences that include content from the MCAT 2015 Exam. For each identified course, there is a list of topics typically covered in that course.
Table of Contents Page BIOLOGY 5 CHEMISTRY 68 PHYSICS 96 PSYCHOLOGY 99 SOCIOLOGY and ANTHROPOLOGY 128
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BIOLOGY BIO 151 & BIO 151L. Concepts of Biology I: Cell and Molecular Biology and Concepts of Biology Laboratory: Cell and Molecular Biology
Amino Acids ● Description
○ Absolute configuration at the position
○ Amino acids as dipolar ions
○ Classifications
■ Acidic or basic
■ Hydrophobic or hydrophilic
● Reactions
○ Sulfur linkage for cysteine and cysteine
○ Peptide linkage: polypeptides and proteins
○ Hydrolysis
Protein Structure ● Structure
○ 1° structure of proteins
○ 2° structure of proteins
○ 3° structure of proteins; role of proline, cystine,
hydrophobic bonding
○ 4° structure of proteins
● Conformational stability
○ Denaturing and folding
○ Hydrophobic interactions
● Separation techniques
○ Electrophoresis
Non-Enzymatic Protein Function ● Binding
● Immune system
● Motors
Enzyme Structure and Function ● Function of enzymes in catalyzing biological reaction
● Reduction of activation energy
● Substrates and enzyme specificity
● Induced-fit Model
● Mechanism of catalysis
○ Cofactors
○ Coenzyme
● Effects of local conditions on enzyme activity
Control of Enzyme Activity ● Kinetics
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○ General (catalysis)
○ Cooperativity
● Feedback regulation
● Inhibition – types
○ Competitive
○ Non-competitive
● Regulatory enzymes
○ Allosteric enzymes
○ Covalently-modified enzymes
○ Zymogen
Nucleic Acid Structure and Function ● Description
● Nucleotides and nucleosides
○ Sugar phosphate backbone
○ Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick
model of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information
● DNA denaturation, reannealing, hybridization
DNA Replication ● Mechanism of replication: separation of strands, specific
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA ● Repair during replication
● Repair of mutations
Genetic Code ● Central Dogma: DNA → RNA → protein
● The triplet code
● Codon-anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA)
Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA)
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● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins
(snRNPs), small nuclear RNA
(snRNAs) ● Functional and evolutionary importance of introns
Translation ● Roles of mRNA, tRNA, rRNA
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
Eukaryotic Chromosome Organization ● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-Monod Model
● Gene repression in bacteria
● Positive control in bacteria
Control of Gene Expression in Eukaryotes ● Transcriptional regulation
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing
(introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes,
tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
Recombinant DNA and Biotechnology ● Gene cloning
● Restriction enzymes
● DNA libraries
● Generation of cDNA
● Hybridization
● Expressing cloned genes
● Polymerase Chain Reaction
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● Gel Electrophoresis and Southern Blotting
● DNA sequencing
● Analyzing gene expression
● Determining gene function
● Stem cells
● Practical applications of DNA technology: medical
applications, human gene therapy,
pharmaceuticals, forensic evidence, environmental cleanup, agriculture
● Safety and ethics of DNA technology
Evidence that DNA is Genetic Material Mendelian Concepts
● Phenotype and genotype
● Gene
● Locus
● Allele: single and multiple
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
● Complete dominance
● Co-dominance
● Incomplete dominance
● Hybridization: viability
● Gene pool
Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis
● Important differences between meiosis and mitosis
● Segregation of genes
○ Independent assortment
○ Linkage
○ Recombination
■ Single crossovers
■ Double crossovers
■ Synaptonemal complex
■ Tetrad
○ Sex-linked characteristics
○ Very few genes on Y chromosome
○ Sex determination
○ Cytoplasmic/extranuclear inheritance
● Mutation
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○ General concept of mutation — error in DNA
sequence
○ Types of mutations: random, translation error,
transcription error, base substitution,
inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation
○ Inborn errors of metabolism
○ Relationship of mutagens to carcinogens
● Genetic drift
● Synapsis or crossing-over mechanism for increasing genetic
diversity
Analytic Methods ● Test cross
● Gene mapping: crossover frequencies
Principles of Bioenergetics ● Bioenergetics/thermodynamics
○ Free energy/Keq
■ Equilibrium constant
■ Relationship of the equilibrium constant and
ΔG°
○ Concentration
○ Endothermic/exothermic reactions
○ Free energy: G
○ Spontaneous reactions and ΔG°
● Phosphoryl group transfers and ATP
○ ATP hydrolysis ΔG << 0
○ ATP group transfers
● Biological oxidation-reduction
○ Half-reactions
○ Soluble electron carriers
○ Flavoproteins
Carbohydrates ● Description
○ Nomenclature and classification, common names
○ Absolute configuration
○ Cyclic structure and conformations of hexoses
○ Epimers and anomers
● Hydrolysis of the glycoside linkage
● Monosaccharides
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● Disaccharides
● Polysaccharides
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products
○ Feeder pathways: glycogen, starch metabolism
● Fermentation (anaerobic glycolysis)
● Gluconeogenesis
● Net molecular and energetic results of respiration processes
Principles of Metabolic Regulation ● Regulation of metabolic pathways
○ Maintenance of a dynamic steady state
● Regulation of glycolysis and gluconeogenesis
● Metabolism of glycogen
● Regulation of glycogen synthesis and breakdown
○ Allosteric and hormonal control
● Analysis of metabolic control
Citric Acid Cycle ● Acetyl-CoA production
● Reactions of the cycle, substrates and products
● Regulation of the cycle
● Net molecular and energetic results of respiration processes
Metabolism of Fatty Acids and Proteins ● Description of fatty acids
● Oxidation of fatty acids
○ Saturated fats
○ Unsaturated fats
● Ketone bodies
● Anabolism of fats
Oxidative Phosphorylation
● Electron transport chain and oxidative phosphorylation,
substrates and products, general features of the pathway
● Electron transfer in mitochondria
○ NADH, NADPH
○ Flavoproteins
○ Cytochromes
● ATP synthase, chemiosmotic coupling
○ Proton motive force
● Net molecular and energetic results of respiration processes
● Regulation of oxidative phosphorylation
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● Mitochondria, apoptosis, oxidative stress
Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function
● Tissue specific metabolism
● Hormonal regulation of fuel metabolism
● Obesity and regulation of body mass
Plasma Membrane ● General function in cell containment
● Composition of membranes
○ Lipid components
■ Phospholipids (and phosphatids)
■ Steroids
■ Waxes
○ Protein components
○ Fluid mosaic model
● Membrane dynamics
● Solute transport across membranes
○ Thermodynamic considerations
○ Osmosis
■ Colligative properties, osmotic pressure
○ Passive transport
○ Active transport
■ Sodium/potassium pump
● Membrane channels
● Membrane potential
● Membrane receptors
● Exocytosis and endocytosis
● Intercellular junctions
○ Gap junctions
○ Tight junctions
○ Desmosomes
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
● Defining characteristics of eukaryotic cells: membrane bound
nucleus, presence of organelles,
● mitotic division
● Nucleus
○ Compartmentalization, storage of genetic information
○ Nucleolus: location and function
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○ Nuclear envelope, nuclear pores
● Mitochondria
○ Site of ATP production
○ Inner and outer membrane structure
○ Self-replication
● Lysosomes: membrane-bound vesicles containing hydrolytic
enzymes
● Endoplasmic reticulum
○ Rough and smooth components
○ Rough endoplasmic reticulum site of ribosomes
○ Double membrane structure
○ Role in membrane biosynthesis
○ Role in biosynthesis of secreted proteins
● Golgi apparatus: general structure and role in packaging and
secretion
● Peroxisomes: organelles that collect peroxides
Cytoskeleton ● General function in cell support and movement
● Microfilaments: composition and role in cleavage and
contractility
● Microtubules: composition and role in support and transport
● Intermediate filaments, role in support
● Composition and function of cilia and flagella
● Centrioles, microtubule organizing centers
Tissues Formed From Eukaryotic Cells ● Epithelial cells
● Connective tissue cells
Cell Theory ● History and development
● Impact on biology
Classification and Structure of Prokaryotic Cells ● Prokaryotic domains
○ Archaea
○ Bacteria
● Major classifications of bacteria by shape
○ Bacilli (rod-shaped)
○ Spirilli (spiral shaped)
○ Cocci (spherical)
● Lack of nuclear membrane and mitotic apparatus
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● Lack of typical eukaryotic organelles
● Presence of cell wall in bacteria
● Flagellar propulsion, mechanism
Growth and Physiology of Prokaryotic Cells ● Reproduction by fission
● High degree of genetic adaptability, acquisition of antibiotic
resistance
● Exponential growth
● Existence of anaerobic and aerobic variants
● Parasitic and symbiotic
● Chemotaxis
Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA
● Transformation: incorporation into bacterial genome of DNA
fragments from external medium
● Conjugation
● Transposons (also present in eukaryotic cells)
Virus Structure ● General structural characteristics (nucleic acid and protein,
enveloped and nonenveloped)
● Lack organelles and nucleus
● Structural aspects of typical bacteriophage
● Genomic content--RNA or DNA
● Size relative to bacteria and eukaryotic cells
Viral Life Cycle ● Self-replicating biological units that must reproduce within
specific host cell
● Generalized phage and animal virus life cycles
○ Attachment to host, penetration of cell membrane or
cell wall, and entry of viral genetic
○ material
○ Use of host synthetic mechanism to replicate viral
components
○ Self-assembly and release of new viral particles
● Transduction: transfer of genetic material by viruses
● Retrovirus life cycle: integration into host DNA, reverse
transcriptase, HIV
● Prions and viroids: subviral particles
Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,
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interphase
● Mitotic structures
○ Centrioles, asters, spindles
○ Chromatids, centromeres, kinetochores
○ Nuclear membrane breakdown and reorganization
○ Mechanisms of chromosome movement
● Phases of cell cycle: G0, G1, S, G2, M
● Growth arrest
● Control of cell cycle
● Loss of cell cycle controls in cancer cells
Biosignalling ● Apoptosis
Biosignalling ● Gated ion channels
○ Voltage gated
○ Ligand gated
● Receptor enzymes
● G protein-coupled receptors
Lipids ● Description; structure
○ Steroids
Nucleotides and Nucleic Acids
● Nucleotides and nucleosides: composition
○ Sugar phosphate backbone
○ Pyrimidine, purine residues
● Deoxyribonucleic acid: DNA, double helix
● Chemistry
● Other functions
Enzymes ● Classification by reaction type
● Mechanism
○ Substrates and enzyme specificity
○ Induced-fit model
○ Cofactors, coenzymes and vitamins
● Kinetics
○ General (catalysis)
○ Cooperativity
○ Effects of local conditions on enzyme activity
● Inhibition
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● Regulatory enzymes
○ Allosteric
○ Covalently modified
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BIO152 & BIO 152L. Concepts of Biology II: Evolution and Ecology & Concepts of Biology Laboratory II: Evolution and Ecology
Mendelian Concepts ● Phenotype and genotype
● Gene
● Locus
● Allele: single and multiple
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
● Complete dominance
● Co-dominance
● Incomplete dominance, leakage, penetrance, expressivity
● Hybridization: viability
● Gene pool
Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis
● Important differences between meiosis and mitosis
● Segregation of genes
○ Independent assortment
○ Linkage
○ Recombination
■ Single crossovers
■ Double crossovers
■ Synaptonemal complex
■ Tetrad
○ Sex-linked characteristics
○ Very few genes on Y chromosome
○ Sex determination
○ Cytoplasmic/extranuclear inheritance
● Mutation
○ General concept of mutation — error in DNA
sequence
○ Types of mutations: random, translation error,
transcription error, base substitution,
inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation
○ Inborn errors of metabolism
○ Relationship of mutagens to carcinogens
● Genetic drift
● Synapsis or crossing-over mechanism for increasing genetic
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diversity
Analytic Methods ● Hardy–Weinberg Principle
● Test cross
● Gene mapping: crossover frequencies
● Biometry: statistical methods
Evolution ● Natural selection
○ Fitness concept
○ Selection by differential reproduction
○ Concepts of natural and group selection
○ Evolutionary success as increase in percent
representation in the gene pool of the next
○ generation
● Speciation
○ Polymorphism
○ Adaptation and specialization
○ Inbreeding
○ Outbreeding
○ Bottlenecks
● Evolutionary time as measured by gradual random changes
in genome
Reproductive System ● Gametogenesis by meiosis
● Ovum and sperm
○ Differences in formation
○ Differences in morphology
○ Relative contribution to next generation
● Reproductive sequence: fertilization, implantation,
development, birth
Embryogenesis ● Stages of early development (order and general features of
each)
○ Fertilization
○ Cleavage
○ Blastula formation
○ Gastrulation
■ First cell movements
■ Formation of primary germ layers (endoderm,
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mesoderm, ectoderm)
○ Neurulation
● Major structures arising out of primary germ layers
● Neural crest
● Environment–gene interaction in development
Mechanisms of Development ● Cell specialization
○ Determination
○ Differentiation
○ Tissue types
● Cell–cell communication in development
● Cell migration
● Pluripotency: stem cells
● Gene regulation in development
● Programmed cell death
● Existence of regenerative capacity in various species
● Senescence and aging
Nervous System: Structure and Function (BIO 152) ● Major Functions
○ High level control and integration of body systems
○ Adaptive capability to external influences
● Organization of vertebrate nervous system
● Sensor and effector neurons
● Sympathetic and parasympathetic nervous systems:
antagonistic control
● Reflexes
○ Feedback loop, reflex arc
○ Role of spinal cord and supraspinal circuits
● Integration with endocrine system: feedback control
Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at
cell, tissue, and organ level
● Definitions of endocrine gland, hormone
● Major endocrine glands: names, locations, products
● Major types of hormones
● Neuroendrocrinology ― relation between neurons and
hormonal systems
Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action
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● Transport of hormones: blood supply
● Specificity of hormones: target tissue
● Integration with nervous system: feedback control regulation
by second messengers
Respiratory System ● General function
○ Gas exchange, thermoregulation
○ Protection against disease: particulate matter
● Structure of lungs and alveoli
● Breathing mechanisms
○ Diaphragm, rib cage, differential pressure
○ Resiliency and surface tension effects
● Thermoregulation: nasal and tracheal capillary beds;
evaporation, panting
● Particulate filtration: nasal hairs, mucus/cilia system in lungs
● Alveolar gas exchange
○ Diffusion, differential partial pressure
○ Henry’s Law
● pH control
● Regulation by nervous control
○ CO2 sensitivity
Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions
and fluids, removal of metabolic
waste ● Role in thermoregulation
● Four-chambered heart: structure and function
● Endothelial cells
● Systolic and diastolic pressure
● Pulmonary and systemic circulation
● Arterial and venous systems (arteries, arterioles, venules,
veins)
○ Structural and functional differences
○ Pressure and flow characteristics
● Capillary beds
○ Mechanisms of gas and solute exchange
○ Mechanism of heat exchange
○ Source of peripheral resistance
● Composition of blood
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○ Plasma, chemicals, blood cells
○ Erythrocyte production and destruction; spleen, bone
marrow
○ Regulation of plasma volume
● Coagulation, clotting mechanisms
● Oxygen transport by blood
○ Hemoglobin, hematocrit
○ Oxygen content
○ Oxygen affinity
○ Oxygen transport by blood; modification of oxygen
affinity
● Carbon dioxide transport and level in blood
● Nervous and endocrine control
Lymphatic System ● Structure of lymphatic system
● Major functions
○ Equalization of fluid distribution
○ Transport of proteins and large glycerides
○ Production of lymphocytes involved in immune
reactions
○ Return of materials to the blood
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BIO 301. Evolution Mendelian Concepts ● Phenotype and genotype
● Gene
● Locus
● Allele: single and multiple
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
● Complete dominance
● Co-dominance
● Incomplete dominance, leakage, penetrance, expressivity
● Hybridization: viability
● Gene pool
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BIO 312 & BIO 312L. General Genetics & Genetics Laboratory
Amino Acids ● Description
○ Absolute configuration at the position
○ Amino acids as dipolar ions
○ Classifications
■ Acidic or basic
■ Hydrophobic or hydrophilic
● Reactions
○ Sulfur linkage for cysteine and cysteine
○ Peptide linkage: polypeptides and proteins
○ Hydrolysis
Protein Structure ● Structure
○ 1° structure of proteins
○ 2° structure of proteins
○ 3° structure of proteins; role of proline, cystine,
hydrophobic bonding
○ 4° structure of proteins
● Conformational stability
○ Denaturing and folding
○ Hydrophobic interactions
○ Solvation layer (entropy)
● Separation techniques
○ Isoelectric point
○ Electrophoresis
Non-Enzymatic Protein Function ● Binding
● Immune system
● Motors
Nucleic Acid Structure and Function ● Description
● Nucleotides and nucleosides
○ Sugar phosphate backbone
○ Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick
model of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information
● DNA denaturation, reannealing, hybridization
DNA Replication
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● Mechanism of replication: separation of strands, specific
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA ● Repair during replication
● Repair of mutations
Genetic Code ● Central Dogma: DNA → RNA → protein
● The triplet code
● Codon-anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA)
Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA)
● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins
(snRNPs), small nuclear RNA
(snRNAs) ● Functional and evolutionary importance of introns
Translation ● Roles of mRNA, tRNA, rRNA
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
Eukaryotic Chromosome Organization ● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-Monod Model
● Gene repression in bacteria
● Positive control in bacteria
24
Control of Gene Expression in Eukaryotes ● Transcriptional regulation
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing
(introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes,
tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
Recombinant DNA and Biotechnology ● Gene cloning
● Restriction enzymes
● DNA libraries
● Generation of cDNA
● Hybridization
● Expressing cloned genes
● Polymerase Chain Reaction
● Gel Electrophoresis and Southern Blotting
● DNA sequencing
● Analyzing gene expression
● Determining gene function
● Stem cells
● Practical applications of DNA technology: medical
applications, human gene therapy,
pharmaceuticals, forensic evidence, environmental cleanup, agriculture
● Safety and ethics of DNA technology
Evidence that DNA is Genetic Material Mendelian Concepts
● Phenotype and genotype
● Gene
● Locus
● Allele: single and multiple
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
● Complete dominance
● Co-dominance
25
● Incomplete dominance, leakage, penetrance, expressivity
● Hybridization: viability
● Gene pool
Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis
● Important differences between meiosis and mitosis
● Segregation of genes
○ Independent assortment
○ Linkage
○ Recombination
■ Single crossovers
■ Double crossovers
■ Synaptonemal complex
■ Tetrad
○ Sex-linked characteristics
○ Very few genes on Y chromosome
○ Sex determination
○ Cytoplasmic/extranuclear inheritance
● Mutation
○ General concept of mutation — error in DNA
sequence
○ Types of mutations: random, translation error,
transcription error, base substitution,
inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation
○ Inborn errors of metabolism
○ Relationship of mutagens to carcinogens
● Genetic drift
● Synapsis or crossing-over mechanism for increasing genetic
diversity
Analytic Methods ● Hardy–Weinberg Principle
● Test cross
● Gene mapping: crossover frequencies
● Biometry: statistical methods
Evolution ● Natural selection
○ Fitness concept
○ Selection by differential reproduction
26
○ Concepts of natural and group selection
○ Evolutionary success as increase in percent
representation in the gene pool of the next
○ generation
● Speciation
○ Polymorphism
○ Adaptation and specialization
○ Inbreeding
○ Outbreeding
○ Bottlenecks
● Evolutionary time as measured by gradual random changes
in genome
Genetics of Prokaryotic Cells (BIO 312L) ● Existence of plasmids, extragenomic DNA
● Transformation: incorporation into bacterial genome of DNA
fragments from external medium
● Conjugation
● Transposons (also present in eukaryotic cells)
Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,
interphase
● Mitotic structures
○ Centrioles, asters, spindles
○ Chromatids, centromeres, kinetochores
○ Nuclear membrane breakdown and reorganization
○ Mechanisms of chromosome movement
● Phases of cell cycle: G0, G1, S, G2, M
● Growth arrest
● Control of cell cycle
● Loss of cell cycle controls in cancer cells
Biosignalling ● Gated ion channels
○ Voltage gated
○ Ligand gated
● Receptor enzymes
● G protein-coupled receptors
Nucleotides and Nucleic Acids ● Nucleotides and nucleosides: composition
○ Sugar phosphate backbone
27
○ Pyrimidine, purine residues
● Deoxyribonucleic acid: DNA, double helix
● Chemistry
● Other functions
Enzymes ● Classification by reaction type
● Mechanism
○ Substrates and enzyme specificity
○ Active site model
○ Induced-fit model
○ Cofactors, coenzymes and vitamins
● Kinetics
○ General (catalysis)
○ Michaelis-Menten
○ Cooperativity
○ Effects of local conditions on enzyme activity
● Inhibition
● Regulatory enzymes
○ Allosteric
● Covalently modified
28
BIO 403 & BIO 403L. Physiology I & Physiology Laboratory I
Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function
● Tissue specific metabolism
● Hormonal regulation of fuel metabolism
● Obesity and regulation of body mass
Plasma Membrane ● General function in cell containment
● Composition of membranes
○ Lipid components
■ Phospholipids (and phosphatids)
■ Steroids
■ Waxes
○ Protein components
○ Fluid mosaic model
● Membrane dynamics
● Solute transport across membranes
○ Thermodynamic considerations
○ Osmosis
■ Colligative properties, osmotic pressure
○ Passive transport
○ Active transport
■ Sodium/potassium pump
● Membrane channels
● Membrane potential
● Membrane receptors
● Exocytosis and endocytosis
● Intercellular junctions
○ Gap junctions
○ Tight junctions
○ Desmosomes
○
Nerve Cell ● Cell body: site of nucleus, organelles
● Dendrites: branched extensions of cell body
● Axon: structure and function
● Myelin sheath, Schwann cells, insulation of axon
● Nodes of Ranvier: propagation of nerve impulse along axon
● Synapse: site of impulse propagation between cells
● Synaptic activity: transmitter molecules
29
● Resting potential: electrochemical gradient
● Action potential
○ Threshold, all-or-none
○ Sodium/potassium pump
● Excitatory and inhibitory nerve fibers: summation, frequency
of firing
● Glial cells, neuroglia
Electrochemistry ● Concentration cell: direction of electron flow, Nernst
equation
Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at
cell, tissue, and organ level
● Definitions of endocrine gland, hormone
● Major endocrine glands: names, locations, products
● Major types of hormones
● Neuroendrocrinology ― relation between neurons and
hormonal systems
Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action
● Transport of hormones: blood supply
● Specificity of hormones: target tissue
● Integration with nervous system: feedback control regulation
by second messengers
Respiratory System ● General function
○ Gas exchange, thermoregulation
○ Protection against disease: particulate matter
● Structure of lungs and alveoli
● Breathing mechanisms
○ Diaphragm, rib cage, differential pressure
○ Resiliency and surface tension effects
● Thermoregulation: nasal and tracheal capillary beds;
evaporation, panting
● Particulate filtration: nasal hairs, mucus/cilia system in lungs
● Alveolar gas exchange
○ Diffusion, differential partial pressure
○ Henry’s Law
● pH control
30
● Regulation by nervous control
● CO2 sensitivity
Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions
and fluids, removal of metabolic
waste ● Role in thermoregulation
● Four-chambered heart: structure and function
● Endothelial cells
● Systolic and diastolic pressure
● Pulmonary and systemic circulation
● Arterial and venous systems (arteries, arterioles, venules,
veins)
○ Structural and functional differences
○ Pressure and flow characteristics
● Capillary beds
○ Mechanisms of gas and solute exchange
○ Mechanism of heat exchange
○ Source of peripheral resistance
● Composition of blood
○ Plasma, chemicals, blood cells
○ Erythrocyte production and destruction; spleen, bone
marrow
○ Regulation of plasma volume
● Coagulation, clotting mechanisms
● Oxygen transport by blood
○ Hemoglobin, hematocrit
○ Oxygen content
○ Oxygen affinity
○ Oxygen transport by blood; modification of oxygen
affinity
● Carbon dioxide transport and level in blood
● Nervous and endocrine control
Lymphatic System ● Structure of lymphatic system
● Major functions
○ Equalization of fluid distribution
○ Transport of proteins and large glycerides
○ Production of lymphocytes involved in immune
31
reactions
● Return of materials to the blood
Digestive System ● Ingestion
○ Saliva as lubrication and source of enzymes
○ Ingestion, esophagus, transport function
● Stomach
○ Storage and churning of food
○ Low pH, gastric juice, mucal protection against self-
destruction
○ Production of digestive enzymes, site of digestion
○ Structure (gross)
● Liver
○ Structural relationship of liver within gastrointestinal
system
○ Production of bile
○ Role in blood glucose regulation, detoxification
● Bile
○ Storage in gall bladder
○ Function
● Pancreas
○ Production of enzymes
○ Transport of enzymes to small intestine
● Small Intestine
○ Absorption of food molecules and water
○ Function and structure of villi
○ Production of enzymes, site of digestion
○ Neutralization of stomach acid
○ Structure (anatomic subdivisions)
● Large Intestine
○ Absorption of water
○ Bacterial flora
○ Structure (gross)
● Rectum: storage and elimination of waste, feces
● Muscular control
○ Peristalsis
● Endocrine control
○ Hormones
○ Target tissues
32
● Nervous control: the enteric nervous system
Excretory System ● Roles in homeostasis
○ Blood pressure
○ Osmoregulation
○ Acid-base balance
○ Removal of soluble nitrogenous waste
● Kidney structure
○ Cortex
○ Medulla
● Nephron structure
○ Glomerulus
○ Bowman’s capsule
○ Proximal tubule
○ Loop of Henle
○ Distal tubule
○ Collecting duct
● Formation of urine
○ Glomerular filtration
○ Secretion and reabsorption of solutes
○ Concentration of urine
○ Counter-current multiplier mechanism
● Storage and elimination: ureter, bladder, urethra
● Osmoregulation: capillary reabsorption of H2O, amino acids,
glucose, ions
● Muscular control: sphincter muscle
Reproductive System ● Male and female reproductive structures and their functions
○ Gonads
○ Genitalia
○ Differences between male and female structures
● Hormonal control of reproduction
○ Male and female sexual development
○ Female reproductive cycle
○ Pregnancy, parturition, lactation
● Integration with nervous control
Muscle System ● Important functions
○ Support: mobility
33
○ Peripheral circulatory assistance
○ Thermoregulation (shivering reflex)
● Structure of three basic muscle types: striated, smooth,
cardiac
● Muscle structure and control of contraction
○ T-tubule system
○ Contractile apparatus
○ Sarcoplasmic reticulum
○ Fiber type
○ Contractile velocity of different muscle types
● Regulation of cardiac muscle contraction
● Oxygen debt: fatigue
● Nervous control
○ Motor neurons
○ Neuromuscular junction, motor end plates
○ Sympathetic and parasympathetic innervation
○ Voluntary and involuntary muscles
Specialized Cell-Muscle Cell ● Structural characteristics of striated, smooth, and cardiac
muscle
● Abundant mitochondria in red muscle cells: ATP source
● Organization of contractile elements: actin and myosin
filaments, crossbridges, sliding filament model
● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone
● Presence of troponin and tropomyosin
● Calcium regulation of contraction
Skin System ● Structure
○ Layer differentiation, cell types
○ Relative impermeability to water
● Functions in homeostasis and osmoregulation
● Functions in thermoregulation
○ Hair, erectile musculature
○ Fat layer for insulation
○ Sweat glands, location in dermis
○ Vasoconstriction and vasodilation in surface
capillaries
● Physical protection
○ Nails, calluses, hair
34
○ Protection against abrasion, disease organisms
● Hormonal control: sweating, vasodilation, and
vasoconstriction
Circulatory System ● Arterial and venous systems; pressure and flow
characteristics
Enzymes ● Classification by reaction type
● Mechanism
○ Substrates and enzyme specificity
○ Active site model
○ Induced-fit model
○ Cofactors, coenzymes and vitamins
● Kinetics
○ General (catalysis)
○ Michaelis-Menten
○ Cooperativity
○ Effects of local conditions on enzyme activity
● Inhibition
● Regulatory enzymes
○ Allosteric
○ Covalently modified
Memory ● Changes in synaptic connections underlie memory and
learning
○ Neural plasticity
○ Memory and learning
● Long-term potentiation
Emotion ● The role of biological processes in perceiving emotion
○ The role of the limbic system in emotion
○ Emotion and the autonomic nervous system
35
BIO 411 & BIO 411L. General Microbiology & General Microbiology Laboratory
Non-Enzymatic Protein Function ● Binding
● Immune system
● Motors
Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions
Control of Enzyme Activity ● Kinetics
○ General (catalysis)
● Feedback regulation
Repair of DNA ● Repair during replication
● Repair of mutations
Genetic Code ● Central Dogma: DNA → RNA → protein
● Messenger RNA (mRNA)
Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-Monod Model
● Gene repression in bacteria
● Positive control in bacteria
Control of Gene Expression in Eukaryotes ● Transcriptional regulation
Recombinant DNA and Biotechnology ● Gene cloning
● Restriction enzymes
● DNA libraries
● DNA sequencing
● Analyzing gene expression
● Determining gene function
Principles of Bioenergetics ● Bioenergetics/thermodynamics
○ Free energy/Keq
■ Equilibrium constant
■ Relationship of the equilibrium constant and
ΔG°
○ Concentration
■ Le Châtelier’s Principle
○ Endothermic/exothermic reactions
○ Free energy: G
○ Spontaneous reactions and ΔG°
36
● Phosphoryl group transfers and ATP
○ ATP hydrolysis ΔG << 0
○ ATP group transfers
● Biological oxidation-reduction
○ Half-reactions
○ Soluble electron carriers
○ Flavoproteins
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products
○ Feeder pathways: glycogen, starch metabolism
● Fermentation (anaerobic glycolysis)
● Gluconeogenesis
● Pentose phosphate pathway
● Net molecular and energetic results of respiration processes
Principles of Metabolic Regulation ● Regulation of metabolic pathways
○ Maintenance of a dynamic steady state
● Regulation of glycolysis and gluconeogenesis
● Analysis of metabolic control
Citric Acid Cycle ● Acetyl-CoA production
● Reactions of the cycle, substrates and products
● Regulation of the cycle
● Net molecular and energetic results of respiration processes
Metabolism of Fatty Acids and Proteins ● Description of fatty acids
● Oxidation of fatty acids
○ Saturated fats
○ Unsaturated fats
● Metabolism of proteins
Oxidative Phosphorylation ● Electron transport chain and oxidative phosphorylation,
substrates and products, general features of the pathway
● Electron transfer in mitochondria
○ NADH, NADPH
○ Flavoproteins
○ Cytochromes
● ATP synthase, chemiosmotic coupling
○ Proton motive force
● Net molecular and energetic results of respiration processes
37
● Regulation of oxidative phosphorylation
Plasma Membrane ● General function in cell containment
● Composition of membranes
○ Lipid components
■ Phospholipids (and phosphatids)
■ Steroids
■ Waxes
○ Protein components
○ Fluid mosaic model
● Membrane dynamics
● Solute transport across membranes
○ Thermodynamic considerations
○ Osmosis
■ Colligative properties, osmotic pressure
○ Passive transport
○ Active transport
■ Sodium/potassium pump
● Membrane channels
● Membrane potential
● Membrane receptors
Cell Theory ● History and development
● Impact on biology
Classification and Structure of Prokaryotic Cells ● Prokaryotic domains
○ Archaea
○ Bacteria
● Major classifications of bacteria by shape
○ Bacilli (rod-shaped)
○ Spirilli (spiral shaped)
○ Cocci (spherical)
● Lack of nuclear membrane and mitotic apparatus
● Lack of typical eukaryotic organelles
● Presence of cell wall in bacteria
● Flagellar propulsion, mechanism
Growth and Physiology of Prokaryotic Cells ● Reproduction by fission
● High degree of genetic adaptability, acquisition of antibiotic
38
resistance
● Exponential growth
● Existence of anaerobic and aerobic variants
● Parasitic and symbiotic
● Chemotaxis
Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA
● Transformation: incorporation into bacterial genome of DNA
fragments from external medium
● Conjugation
● Transposons (also present in eukaryotic cells)
Virus Structure ● General structural characteristics (nucleic acid and protein,
enveloped and nonenveloped)
● Lack organelles and nucleus
● Structural aspects of typical bacteriophage
● Genomic content--RNA or DNA
● Size relative to bacteria and eukaryotic cells
Viral Life Cycle ● Self-replicating biological units that must reproduce within
specific host cell
● Generalized phage and animal virus life cycles
○ Attachment to host, penetration of cell membrane or
cell wall, and entry of viral genetic
○ material
○ Use of host synthetic mechanism to replicate viral
components
○ Self-assembly and release of new viral particles
● Transduction: transfer of genetic material by viruses
● Retrovirus life cycle: integration into host DNA, reverse
transcriptase, HIV
● Prions and viroids: subviral particles
Lipids ● Description; structure
○ Steroids
Enzymes ● Inhibition
● Regulatory enzymes
○ Allosteric
○ Covalently modified
39
BIO 415. Neurobiology
Nerve Cell ● Cell body: site of nucleus, organelles
● Dendrites: branched extensions of cell body
● Axon: structure and function
● Myelin sheath, Schwann cells, insulation of axon
● Nodes of Ranvier: propagation of nerve impulse along axon
● Synapse: site of impulse propagation between cells
● Synaptic activity: transmitter molecules
● Resting potential: electrochemical gradient
● Action potential
○ Threshold, all-or-none
○ Sodium/potassium pump
● Excitatory and inhibitory nerve fibers: summation, frequency
of firing
● Glial cells, neuroglia
Specialized Cell - Nerve Cell ● Myelin sheath, Schwann cells, insulation of axon
● Nodes of Ranvier: propagation of nerve impulse along axon
Sensory Processing ● Sensation
○ Thresholds
○ Weber’s Law
○ Signal detection theory
○ Sensory adaptation
● Sensory receptors
○ Sensory pathways
● Types of sensory receptors
Vision ● Structure and function of the eye
● Visual processing
○ Visual pathways in the brain
○ Parallel processing
● Feature detection
Hearing ● Auditory processing
○ Auditory pathways in the brain
● Sensory reception by hair cells
Other Senses ● Somatosensation
○ Pain perception
40
● Taste
○ Taste buds/chemoreceptors that detect specific
chemicals
● Smell
○ Olfactory cells/chemoreceptors that detect specific
chemicals
○ Pheromones
○ Olfactory pathways in the brain
● Kinesthetic sense
● Vestibular sense
Cognition ● Information-processing model
● Cognitive development
○ Piaget’s stages of cognitive development
○ Cognitive changes in late adulthood
○ Role of culture in cognitive development
○ Influence of heredity and environment on cognitive
development
● Biological factors that affect cognition
● Problem solving and decision making
○ Types of problem solving
○ Barriers to effective problem solving
○ Approaches to problem solving
○ Heuristics, biases, intuition, and emotion
■ Overconfidence and belief perseverance
● Intellectual functioning
○ Multiple definitions of intelligence
○ Influence of heredity and environment on intelligence
● Variations in intellectual ability
Consciousness ● States of consciousness
○ Alertness
○ Sleep
■ Stages of sleep
■ Sleep cycles and changes to sleep cycles
■ Sleep and circadian rhythms
■ Dreaming
■ Sleep disorders
○ Hypnosis and meditation
41
● Consciousness altering drugs
○ Types of consciousness altering drugs and their
effects on the nervous system and
behavior ● Drug addiction and the reward pathway in the brain
Memory ● Encoding
○ Process of encoding information
○ Processes that aid in encoding memories
● Storage
○ Types of memory storage (e.g., sensory, working,
long-term)
○ Semantic networks and spreading activation
● Retrieval
○ Recall, recognition, and relearning
○ Retrieval cues
○ The role of emotion in retrieving memories
● Forgetting
○ Aging and memory
○ Memory dysfunctions (e.g., Alzheimer’s disease,
Korsakoff’s syndrome)
○ Decay
○ Interference
○ Memory construction and source monitoring
● Changes in synaptic connections underlie memory and
learning
○ Neural plasticity
○ Memory and learning
● Long-term potentiation
Language ● Theories of language development (e.g., learning, Nativist,
Interactionist)
● Influence of language on cognition
● Different brain areas control language and speech
Emotion ● Three components of emotion (i.e., cognitive, physiological,
behavioral)
● Universal emotions (e.g., fear, anger, happiness, surprise, joy,
disgust, sadness)
42
● Adaptive role of emotion
● Theories of emotion
○ James-Lange theory
○ Cannon-Bard theory
○ Schachter-Singer theory
● The role of biological processes in perceiving emotion
○ Generation and experience of emotions involve many
brain regions
○ The role of the limbic system in emotion
○ Emotional experiences can be stored as memories
that can be recalled by similar
○ circumstances
○ Prefrontal cortex is critical for emotional experience,
and is also important in
○ temperament and decision making
○ Emotion and the autonomic nervous system
● Physiological markers of emotion (signatures of emotion)
Stress ● The nature of stress
○ Appraisal
○ Different types of stressors (e.g., cataclysmic events,
personal, etc.)
○ Effects of stress on psychological functions
● Stress outcomes/response to stressors
○ Physiological
○ Emotional
○ Behavioral
● Managing stress (e.g., exercise, relaxation techniques,
spirituality, etc.)
Biological Bases of Behavior ● The nervous system
○ Neurons
■ The reflex arc
○ Neurotransmitters
○ Peripheral nervous system
○ Central nervous system
■ The brain
○ The brainstem
○ The cerebellum
43
○ The diencephalon
○ The cerebrum
○ Control of voluntary movement in the
cerebral cortex
○ Information processing in the cerebral
cortex
○ Lateralization of cortical functions
○ Methods of studying the brain
● Neurons communicate and influence behavior
● Influence of neurotransmitters on behavior
● The endocrine system
○ Components of the endocrine system
○ Effects of the endocrine system on behavior
● Behavioral genetics
○ Genes, temperament, and heredity
○ Adaptive value of traits and behaviors
○ Interaction between heredity and environmental
influences
● Genetic and environmental factors contribute to the
development of behaviors
○ Experience and behavior
○ Regulatory genes and behavior
○ Genetically based behavioral variation in natural
populations
● Human physiological development
○ Prenatal development
○ Motor development
● Developmental changes in adolescence
Associative Learning ● Classical conditioning
○ Neutral, conditioned, and unconditioned stimuli
○ Conditioned and unconditioned response
○ Processes: acquisition, extinction, spontaneous
recovery, generalization, discrimination
● Operant conditioning
○ Processes of shaping and extinction
○ Types of reinforcement: positive, negative, primary,
conditional
○ Reinforcement schedules: fixed-ratio, variable-ratio,
44
fixed-interval, variable-interval
○ Punishment
○ Escape and avoidance learning
● Cognitive processes that affect associative learning
● Biological factors that affect associative learning
○ Innate behaviors are developmentally fixed
○ Learned behaviors are modified based on experiences
○ Development of learned behaviors
45
BIO 427. Immunology
Non-Enzymatic Protein Function ● Binding
● Immune system
● Motors
Immune System ● Innate (non-specific) vs. adaptive (specific) immunity
● Adaptive immune system cells
○ T-lymphocytes
○ B-lymphocytes
● Innate immune system cells
○ Macrophages
○ Phagocytes
● Concept of antigen and antibody
● Antigen presentation
● Clonal selection
● Antigen-antibody recognition
● Structure of antibody molecule
● Recognition of self vs. non-self, autoimmune diseases
● Major histocompatibility complex
46
BIO 440. Cell Biology
Amino Acids ● Description
○ Absolute configuration at the position
○ Amino acids as dipolar ions
○ Classifications
■ Acidic or basic
■ Hydrophobic or hydrophilic
● Reactions
○ Sulfur linkage for cysteine and cysteine
○ Peptide linkage: polypeptides and proteins
○ Hydrolysis
Protein Structure ● Structure
○ 1° structure of proteins
○ 2° structure of proteins
○ 3° structure of proteins; role of proline, cystine,
hydrophobic bonding
○ 4° structure of proteins
● Conformational stability
○ Denaturing and folding
○ Hydrophobic interactions
○ Solvation layer (entropy)
● Separation techniques
○ Isoelectric point
○ Electrophoresis
DNA Replication ● Mechanism of replication: separation of strands, specific
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA ● Repair during replication
● Repair of mutations
Plasma Membrane ● General function in cell containment
● Composition of membranes
○ Lipid components
■ Phospholipids (and phosphatids)
47
■ Steroids
■ Waxes
○ Protein components
○ Fluid mosaic model
● Membrane dynamics
● Solute transport across membranes
○ Thermodynamic considerations
○ Osmosis
■ Colligative properties, osmotic pressure
○ Passive transport
○ Active transport
■ Sodium/potassium pump
● Membrane channels
● Membrane potential
● Membrane receptors
● Exocytosis and endocytosis
● Intercellular junctions
○ Gap junctions
○ Tight junctions
○ Desmosomes
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
● Defining characteristics of eukaryotic cells: membrane bound
nucleus, presence of organelles,
● mitotic division
● Nucleus
○ Compartmentalization, storage of genetic information
○ Nucleolus: location and function
○ Nuclear envelope, nuclear pores
● Mitochondria
○ Site of ATP production
○ Inner and outer membrane structure
○ Self-replication
● Lysosomes: membrane-bound vesicles containing hydrolytic
enzymes
● Endoplasmic reticulum
○ Rough and smooth components
○ Rough endoplasmic reticulum site of ribosomes
○ Double membrane structure
48
○ Role in membrane biosynthesis
○ Role in biosynthesis of secreted proteins
● Golgi apparatus: general structure and role in packaging and
secretion
● Peroxisomes: organelles that collect peroxides
Cytoskeleton ● General function in cell support and movement
● Microfilaments: composition and role in cleavage and
contractility
● Microtubules: composition and role in support and transport
● Intermediate filaments, role in support
● Composition and function of cilia and flagella
● Centrioles, microtubule organizing centers
Tissues Formed From Eukaryotic Cells ● Epithelial cells
● Connective tissue cells
Cell Theory ● History and development
● Impact on biology
Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,
interphase
● Mitotic structures
○ Centrioles, asters, spindles
○ Chromatids, centromeres, kinetochores
○ Nuclear membrane breakdown and reorganization
○ Mechanisms of chromosome movement
● Phases of cell cycle: G0, G1, S, G2, M
● Growth arrest
● Control of cell cycle
● Loss of cell cycle controls in cancer cells
Biosignalling ● Oncogenes, apoptosis
Biosignalling ● Gated ion channels
○ Voltage gated
○ Ligand gated
● Receptor enzymes
● G protein-coupled receptors
Specialized Cell-Muscle Cell
49
● Structural characteristics of striated, smooth, and cardiac
muscle
● Abundant mitochondria in red muscle cells: ATP source
● Organization of contractile elements: actin and myosin
filaments, crossbridges, sliding filament model
● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone
● Presence of troponin and tropomyosin
● Calcium regulation of contraction
50
BIO 442 & 442L. Developmental Biology & Developmental Biology Laboratory
Protein Structure ● Separation techniques
○ Isoelectric point
○ Electrophoresis
Non-Enzymatic Protein Function ● Motors
Enzyme Structure and Function ● Substrates and enzyme specificity
Nucleic Acid Structure and Function ● Function in transmission of genetic information
Genetic Code ● Central Dogma: DNA → RNA → protein
● Messenger RNA (mRNA)
Transcription ● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
Translation ● Post-translational modification of proteins
Eukaryotic Chromosome Organization ● Chromosomal proteins
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Eukaryotes ● Transcriptional regulation
● DNA binding proteins, transcription factors
● Post-transcriptional control, basic concept of splicing
(introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes,
tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
Recombinant DNA and Biotechnology ● Gene cloning
● Restriction enzymes
● DNA libraries
● Generation of cDNA
● Hybridization
● Expressing cloned genes
● Polymerase Chain Reaction
● Gel Electrophoresis and Southern Blotting
51
● DNA sequencing
● Analyzing gene expression
● Determining gene function
● Stem cells
● Practical applications of DNA technology: medical
applications, human gene therapy,
pharmaceuticals, forensic evidence, environmental cleanup, agriculture
● Safety and ethics of DNA technology
Mendelian Concepts ● Phenotype and genotype
● Gene
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
Meiosis and Other Factors Affecting Genetic Variability ● Important differences between meiosis and mitosis
● Segregation of genes
○ Recombination
■ Single crossovers
■ Double crossovers
■ Synaptonemal complex
■ Tetrad
○ Sex-linked characteristics
● Mutation
○ General concept of mutation — error in DNA
sequence
● Synapsis or crossing-over mechanism for increasing genetic
diversity
Plasma Membrane ● Membrane receptors
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
● Nucleus
○ Compartmentalization, storage of genetic information
○ Nucleolus: location and function
○ Nuclear envelope, nuclear pores
Cytoskeleton
● General function in cell support and movement
52
● Microfilaments: composition and role in cleavage and
contractility
● Microtubules: composition and role in support and transport
● Intermediate filaments, role in support
● Composition and function of cilia and flagella
● Centrioles, microtubule organizing centers
Tissues Formed From Eukaryotic Cells ● Epithelial cells
● Connective tissue cells
Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,
interphase
● Mitotic structures
○ Centrioles, asters, spindles
○ Chromatids, centromeres, kinetochores
○ Nuclear membrane breakdown and reorganization
○ Mechanisms of chromosome movement
● Phases of cell cycle: G0, G1, S, G2, M
● Growth arrest
● Control of cell cycle
● Loss of cell cycle controls in cancer cells
Biosignalling ● apoptosis
Reproductive System ● Gametogenesis by meiosis
● Ovum and sperm
○ Differences in formation
○ Differences in morphology
○ Relative contribution to next generation
● Reproductive sequence: fertilization, implantation,
development, birth
Embryogenesis ● Stages of early development (order and general features of
each)
○ Fertilization
○ Cleavage
○ Blastula formation
○ Gastrulation
■ First cell movements
■ Formation of primary germ layers (endoderm,
53
mesoderm, ectoderm)
○ Neurulation
● Major structures arising out of primary germ layers
● Neural crest
● Environment–gene interaction in development
Mechanisms of Development ● Cell specialization
○ Determination
○ Differentiation
○ Tissue types
● Cell–cell communication in development
● Cell migration
● Pluripotency: stem cells
● Gene regulation in development
● Programmed cell death
Nervous System: Structure and Function Major Functions
o High level control and integration of body systems o Adaptive capability to external influences
Organization of vertebrate nervous system Sensor and effector neurons Sympathetic and parasympathetic nervous systems: antagonistic
control Reflexes
o Feedback loop, reflex arc o Role of spinal cord and supraspinal circuits
Integration with endocrine system: feedback control
Nerve Cell Cell body: site of nucleus, organelles Dendrites: branched extensions of cell body Axon: structure and function Myelin sheath, Schwann cells, insulation of axon Nodes of Ranvier: propagation of nerve impulse along axon Synapse: site of impulse propagation between cells Synaptic activity: transmitter molecules Resting potential: electrochemical gradient Action potential
o Threshold, all-or-none o Sodium/potassium pump
Excitatory and inhibitory nerve fibers: summation, frequency of firing
Glial cells, neuroglia
Biosignalling Receptor enzymes
54
G protein-coupled receptors Endocrine System: Hormones and Their Sources
● Major endocrine glands: names, locations, products
Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action
● Transport of hormones: blood supply
Respiratory System ● General function
○ Gas exchange, thermoregulation
○ Protection against disease: particulate matter
● Structure of lungs and alveoli
● Breathing mechanisms
○ Diaphragm, rib cage, differential pressure
○ Resiliency and surface tension effects
● Thermoregulation: nasal and tracheal capillary beds;
evaporation, panting
● Particulate filtration: nasal hairs, mucus/cilia system in lungs
Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions
and fluids, removal of metabolic
waste ● Four-chambered heart: structure and function
● Endothelial cells
● Systolic and diastolic pressure
● Pulmonary and systemic circulation
● Arterial and venous systems (arteries, arterioles, venules,
veins)
○ Structural and functional differences
○ Pressure and flow characteristics
● Composition of blood
○ Plasma, chemicals, blood cells
○ Erythrocyte production and destruction; spleen, bone
marrow
○ Regulation of plasma volume
Lymphatic System ● Major functions
○ Equalization of fluid distribution
○ Transport of proteins and large glycerides
○ Production of lymphocytes involved in immune
reactions
55
Immune System ● Adaptive immune system cells
○ T-lymphocytes
○ B-lymphocytes
● Innate immune system cells
○ Macrophages
○ Phagocytes
● Concept of antigen and antibody
● Structure of antibody molecule
Digestive System ● Ingestion
○ Saliva as lubrication and source of enzymes
○ Ingestion, esophagus, transport function
● Stomach
○ Storage and churning of food
○ Low pH, gastric juice, mucal protection against self-
destruction
○ Production of digestive enzymes, site of digestion
○ Structure (gross)
● Liver
○ Structural relationship of liver within gastrointestinal
system
○ Production of bile
○ Role in blood glucose regulation, detoxification
● Bile
○ Storage in gall bladder
○ Function
● Pancreas
○ Production of enzymes
○ Transport of enzymes to small intestine
● Small Intestine
○ Absorption of food molecules and water
○ Function and structure of villi
○ Production of enzymes, site of digestion
○ Neutralization of stomach acid
○ Structure (anatomic subdivisions)
● Large Intestine
○ Absorption of water
○ Bacterial flora
56
○ Structure (gross)
● Rectum: storage and elimination of waste, feces
● Endocrine control
○ Hormones
○ Target tissues
● Nervous control: the enteric nervous system
Excretory System ● Roles in homeostasis
○ Blood pressure
○ Osmoregulation
○ Acid-base balance
○ Removal of soluble nitrogenous waste
● Kidney structure
○ Cortex
○ Medulla
● Nephron structure
○ Glomerulus
○ Bowman’s capsule
○ Proximal tubule
○ Loop of Henle
○ Distal tubule
○ Collecting duct
● Storage and elimination: ureter, bladder, urethra
Reproductive System ● Male and female reproductive structures and their functions
○ Gonads
○ Genitalia
○ Differences between male and female structures
● Hormonal control of reproduction
○ Male and female sexual development
○ Female reproductive cycle
○ Pregnancy, parturition, lactation
Skeletal System ● Functions
○ Structural rigidity and support
○ Calcium storage
○ Physical protection
● Skeletal structure
○ Specialization of bone types, structures
57
○ Joint structures
○ Endoskeleton vs. exoskeleton
● Bone structure
○ Calcium/protein matrix
○ Cellular composition of bone
● Cartilage: structure and function
● Ligaments, tendons
● Endocrine control
Skin System ● Structure
○ Layer differentiation, cell types
○ Relative impermeability to water
● Functions in thermoregulation
○ Hair, erectile musculature
○ Fat layer for insulation
○ Sweat glands, location in dermis
○ Vasoconstriction and vasodilation in surface
capillaries
● Physical protection
○ Nails, calluses, hair
○ Protection against abrasion, disease organisms
Specialized Cell - Nerve Cell ● Myelin sheath
Geometrical Optics Optical Instruments, including the human eye
Stoichiometry Molecular weight Metric units commonly used in the context of chemistry Description of composition by percent mass
Solubility Units of concentration (e.g., molarity)
Separations and Purifications Separation and purification of peptides and proteins
o Electrophoresis o Quantitative analysis o Chromatography
Size-exclusion Ion-exchange Affinity
o Racemic mixtures, separation of enantiomers
Non-Enzymatic Protein Function
58
Motors Vision
Structure and function of the eye Other Senses
Smell o Olfactory cells/chemoreceptors that detect specific
chemicals o Olfactory pathways in the brain
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Psychological Disorders Biological bases of nervous system disorders
o Alzheimer’s disease o Parkinson’s disease o Stem cell-based therapy to regenerate neurons in CNS
59
BIO 462. Molecular Biology
Protein Structure ● Structure
○ 1° structure of proteins
○ 2° structure of proteins
○ 3° structure of proteins; role of proline, cystine,
hydrophobic bonding
○ 4° structure of proteins
● Conformational stability
○ Denaturing and folding
○ Hydrophobic interactions
○ Solvation layer (entropy)
● Separation techniques
○ Isoelectric point
○ Electrophoresis
Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions
● Enzyme classification by reaction type
● Reduction of activation energy
● Substrates and enzyme specificity
● Active Site Model
● Induced-fit Model
● Mechanism of catalysis
○ Cofactors
○ Coenzymes
○ Water-soluble vitamins
● Effects of local conditions on enzyme activity
Control of Enzyme Activity ● Kinetics
○ General (catalysis)
○ Michaelis-Menten
○ Cooperativity
● Feedback regulation
● Inhibition – types
○ Competitive
○ Non-competitive
○ Mixed
○ Uncompetitive
● Regulatory enzymes
○ Allosteric enzymes
60
○ Covalently-modified enzymes
○ Zymogen
Nucleic Acid Structure and Function ● Description
● Nucleotides and nucleosides
○ Sugar phosphate backbone
○ Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick
model of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information
● DNA denaturation, reannealing, hybridization
DNA Replication ● Mechanism of replication: separation of strands, specific
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
Repair of DNA ● Repair during replication
● Repair of mutations
Genetic Code ● Central Dogma: DNA → RNA → protein
● The triplet code
● Codon-anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA)
Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA)
● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins
(snRNPs), small nuclear RNA
(snRNAs) ● Functional and evolutionary importance of introns
Translation ● Roles of mRNA, tRNA, rRNA
61
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
Eukaryotic Chromosome Organization ● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-Monod Model
● Gene repression in bacteria
● Positive control in bacteria
Control of Gene Expression in Eukaryotes ● Transcriptional regulation
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing
(introns, exons)
● Cancer as a failure of normal cellular controls, oncogenes,
tumor suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
62
BIO 470. Cancer Biology
DNA Replication ● Mechanism of replication: separation of strands, specific
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
63
BIO 475 & 475L. Human Anatomy & Human Anatomy Laboratory
Reproductive System ● Gametogenesis by meiosis
● Ovum and sperm
○ Differences in formation
○ Differences in morphology
○ Relative contribution to next generation
● Reproductive sequence: fertilization, implantation,
development, birth
Nervous System: Structure and Function Major Functions
o High level control and integration of body systems o Adaptive capability to external influences
Organization of vertebrate nervous system Sensor and effector neurons Sympathetic and parasympathetic nervous systems: antagonistic
control Reflexes
o Feedback loop, reflex arc o Role of spinal cord and supraspinal circuits
Integration with endocrine system: feedback control
Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at
cell, tissue, and organ level
● Definitions of endocrine gland, hormone
● Major endocrine glands: names, locations, products
● Major types of hormones
● Neuroendrocrinology ― relation between neurons and
hormonal systems
Respiratory System ● General function
○ Gas exchange, thermoregulation
○ Protection against disease: particulate matter
● Structure of lungs and alveoli
● Breathing mechanisms
○ Diaphragm, rib cage, differential pressure
○ Resiliency and surface tension effects
● Thermoregulation: nasal and tracheal capillary beds;
evaporation, panting
● Particulate filtration: nasal hairs, mucus/cilia system in lungs
Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions
and fluids, removal of metabolic waste
64
● Four-chambered heart: structure and function
● Pulmonary and systemic circulation
● Arterial and venous systems (arteries, arterioles, venules,
veins)
○ Structural and functional differences
○ Pressure and flow characteristics
● Capillary beds
○ Mechanisms of gas and solute exchange
○ Mechanism of heat exchange
○ Source of peripheral resistance
Lymphatic System Major functions
o Equalization of fluid distribution o Transport of proteins and large glycerides o Production of lymphocytes involved in immune reactions o Return of materials to the blood
Digestive System ● Ingestion
○ Saliva as lubrication and source of enzymes
○ Ingestion, esophagus, transport function
● Stomach
○ Storage and churning of food
○ Low pH, gastric juice, mucal protection against self-
destruction
○ Production of digestive enzymes, site of digestion
○ Structure (gross)
● Liver
○ Structural relationship of liver within gastrointestinal
system
○ Production of bile
○ Role in blood glucose regulation, detoxification
● Bile
○ Storage in gall bladder
○ Function
● Pancreas
○ Production of enzymes
○ Transport of enzymes to small intestine
● Small Intestine
○ Absorption of food molecules and water
○ Function and structure of villi
65
○ Production of enzymes, site of digestion
○ Neutralization of stomach acid
○ Structure (anatomic subdivisions)
● Large Intestine
○ Absorption of water
○ Bacterial flora
○ Structure (gross)
● Rectum: storage and elimination of waste, feces
● Endocrine control
○ Hormones
○ Target tissues
● Nervous control: the enteric nervous system
Excretory System ● Roles in homeostasis
○ Blood pressure
○ Osmoregulation
○ Acid-base balance
○ Removal of soluble nitrogenous waste
● Kidney structure
○ Cortex
○ Medulla
● Nephron structure
○ Glomerulus
○ Bowman’s capsule
○ Proximal tubule
○ Loop of Henle
○ Distal tubule
○ Collecting duct
● Storage and elimination: ureter, bladder, urethra
Reproductive System ● Male and female reproductive structures and their functions
○ Gonads
○ Genitalia
○ Differences between male and female structures
Muscle System ● Important functions
○ Support: mobility
○ Peripheral circulatory assistance
○ Thermoregulation (shivering reflex)
66
● Structure of three basic muscle types: striated, smooth,
cardiac
● Nervous control
○ Motor neurons
○ Neuromuscular junction, motor end plates
○ Sympathetic and parasympathetic innervation
○ Voluntary and involuntary muscles
Skeletal System ● Functions
○ Structural rigidity and support
○ Calcium storage
○ Physical protection
● Skeletal structure
○ Specialization of bone types, structures
○ Joint structures
● Cartilage: structure and function
● Ligaments, tendons
Skin System ● Structure
○ Layer differentiation, cell types
○ Relative impermeability to water
● Functions in thermoregulation
○ Hair, erectile musculature
○ Fat layer for insulation
○ Sweat glands, location in dermis
○ Vasoconstriction and vasodilation in surface
capillaries
● Physical protection
○ Nails, calluses, hair
○ Protection against abrasion, disease organisms
Geometrical Optics Optical Instruments, including the human eye
Sensory Processing Sensory receptors
o Sensory pathways o Types of sensory receptors
Vision Structure and function of the eye
Hearing Auditory processing
o Auditory pathways in the brain
67
Other Senses Taste
o Taste buds/chemoreceptors that detect specific chemicals Smell
o Olfactory cells/chemoreceptors that detect specific chemicals
o Pheromones o Olfactory pathways in the brain
Vestibular sense
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior
68
CHEMISTRY CHM 123 & 123L. General Chemistry & General Chemistry Laboratory
Work Derived units, sign conventions Mechanical advantage Work Kinetic Energy Theorem
Energy Kinetic Energy: KE = ½ mv2; units Potential Energy
o PE = mgh (gravitational, local) o PE = ½ kx2(spring)
Conservation of energy Conservative forces Power, units
Gas Phase Absolute temperature, (K) Kelvin Scale Pressure, simple mercury barometer Molar volume at 0°C and 1 atm = 22.4 L/mol Ideal gas
o Definition o Ideal Gas Law: PV = nRT o Boyle’s Law: PV = constant o Charles’ Law: V/T = constant o Avogadro’s Law: V/n = constant
Kinetic Molecular Theory of Gases o Heat capacity at constant volume and at constant pressure o Boltzmann’s Constant
Deviation of real gas behavior from Ideal Gas Law o Qualitative o Quantitative (Van der Waals’ Equation)
Partial pressure, mole fraction Dalton’s Law relating partial pressure to composition
Light, Electromagnetic Radiation Concept of Interference; Young Double-slit Experiment Thin films, diffraction grating, single-slit diffraction Other diffraction phenomena, X-ray diffraction Polarization of light Circular polarization Properties of electromagnetic radiation
o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of perpendicularly
oscillating electric and magnetic o fields; direction of propagation is perpendicular to both
Classification of electromagnetic spectrum, photon energy E = (hf) Visual spectrum, color
Atomic Nucleus Atomic number, atomic weight Neutrons, protons, isotopes
69
Nuclear forces, binding energy Radioactive decay
o α, β, γ decay o Half-life, exponential decay, semi-log plots
Mass spectrometer
Electronic Structure Orbital structure of hydrogen atom, principal quantum number n,
number of electrons per orbital Ground state, excited states Absorption and emission line spectra Use of Pauli Exclusion Principle Paramagnetism and diamagnetism Conventional notation for electronic structure Bohr atom Heisenberg Uncertainty Principle Effective nuclear charge Photoelectric effect
The Periodic Table - Classification of Elements into Groups by Electronic Structure
Alkali metals Alkaline earth metals: their chemical characteristics Halogens: their chemical characteristics Noble gases: their physical and chemical characteristics Transition metals Representative elements Metals and non-metals Oxygen group
The Periodic Table - Variations of Chemical Properties with Group and Row
Valence electrons First and second ionization energy
o Definition o Prediction from electronic structure for elements in different
groups or rows Electron affinity
o Definition o Variation with group and row
Electronegativity o Definition o Comparative values for some representative elements and
important groups Electron shells and the sizes of atoms Electron shells and the sizes of ions
Stoichiometry Molecular weight Empirical versus molecular formula Metric units commonly used in the context of chemistry Description of composition by percent mass
70
Mole concept, Avogadro’s number NA Definition of density Oxidation number
o Common oxidizing and reducing agents o Disproportionation reactions
Description of reactions by chemical equations o Conventions for writing chemical equations o Balancing equations, including redox equations o Limiting reactants
Theoretical yields
Ions in Solutions Anion, cation: common names, formulas and charges for familiar ions
(e.g., NH4+ ammonium, PO43– phosphate, SO42– sulfate) Hydration, the hydronium ion
Titration Indicators Neutralization Interpretation of the titration curves Redox titration
Covalent Bond Lewis Electron Dot formulas
o Resonance structures o Formal charge o Lewis acids and bases
Partial ionic character o Role of electronegativity in determining charge distribution o Dipole Moment
σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective geometries o Valence shell electron pair repulsion and the prediction of
shapes of molecules (e.g., NH3, H2O, CO2) o Structural formulas for molecules involving H, C, N, O, F, S, P, Si,
Cl o Delocalized electrons and resonance in ions and molecules
Multiple bonding o Affect on bond length and bond energies o Rigidity in molecular structure
Stereochemistry of covalently bonded molecules o Isomers
Structural isomers Stereoisomers (e.g., diastereomers, enantiomers,
cis/trans isomers) Conformational isomers
o Polarization of light, specific rotation o Absolute and relative configuration
Conventions for writing R and S forms o Conventions for writing E and Z forms
Energy Changes in Chemical Reactions - Thermochemistry,
71
Thermodynamics Thermodynamic system – state function Zeroth Law – concept of temperature First Law: ΔE = Q – W (conservation of energy) Second Law – concept of entropy
o Entropy as a measure of “disorder” o Relative entropy for gas, liquid, and crystal states
Measurement of heat changes (calorimetry), heat capacity, specific heat Heat transfer – conduction, convection, radiation Endothermic/exothermic reactions
o Enthalpy, H, and standard heats of reaction and formation o Hess’ Law of Heat Summation
Bond dissociation energy as related to heats of formation Free energy: G Spontaneous reactions and ΔG° Coefficient of expansion Heat of fusion, heat of vaporization Phase diagram: pressure and temperature
72
CHM 124 & 124L. General Chemistry & General Chemistry Laboratory
Electrochemistry o Concentration cell: direction of electron flow, Nernst equation
Equilibrium Concept of force, units Analysis of forces acting on an object Newton’s First Law of Motion, inertia Torques, lever arms
Electrochemistry Electrolytic cell
o Electrolysis o Anode, cathode o Electrolyte o Faraday’s Law relating amount of elements deposited (or gas
liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the electrodes
Galvanic or Voltaic cells o Half-reactions o Reduction potentials, cell potential o Direction of electron flow
Concentration cell Batteries
o Electromotive force, Voltage o Lead-storage batteries o Nickel-cadmium batteries
Acid/Base Equilibria Bronsted-Lowry definition of acid, base Ionization of water
o Kw, its approximate value (Kw = [H+][OH–] = 10-14 at 25°C, 1 atm) o Definition of pH: pH of pure water
Conjugate acids and bases (e.g., NH4+ and NH3) Strong acids and bases (e.g., nitric, sulfuric) Weak acids and bases (e.g., acetic, benzoic)
o Dissociation of weak acids and bases with or without added salt o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids or bases
Equilibrium constants Ka and Kb: pKa, pKb Buffers
o Definition and concepts (common buffer systems) o Influence on titration curves
Solubility Units of concentration (e.g., molarity) Solubility product constant; the equilibrium expression Ksp Common-ion effect, its use in laboratory separations
o Complex ion formation o Complex ions and solubility o Solubility and pH
Titration
73
Indicators Neutralization Interpretation of the titration curves Redox titration
Liquid Phase - Intermolecular Forces Hydrogen bonding Dipole Interactions Van der Waals’ Forces (London dispersion forces)
Energy Changes in Chemical Reactions - Thermochemistry, Thermodynamics
Thermodynamic system – state function Zeroth Law – concept of temperature First Law: ΔE = Q – W (conservation of energy) Second Law – concept of entropy
o Entropy as a measure of “disorder” o Relative entropy for gas, liquid, and crystal states
Measurement of heat changes (calorimetry), heat capacity, specific heat Heat transfer – conduction, convection, radiation Endothermic/exothermic reactions
o Enthalpy, H, and standard heats of reaction and formation o Hess’ Law of Heat Summation
Bond dissociation energy as related to heats of formation Free energy: G Spontaneous reactions and ΔG° Coefficient of expansion Heat of fusion, heat of vaporization Phase diagram: pressure and temperature
Rate Processes in Chemical Reactions - Kinetics and Equilibrium Reaction rate Dependence of reaction rate upon concentration of reactants
o Rate law, rate constant o Reaction order
Rate-determining step Dependence of reaction rate upon temperature
o Activation energy Activated complex or transition state Interpretation of energy profiles showing energies of
reactants, products, activation energy, and ΔH for the reaction
o Use of the Arrhenius Equation Kinetic control versus thermodynamic control of a reaction Catalysts Equilibrium in reversible chemical reactions
o Law of Mass Action o Equilibrium Constant o Application of Le Châtelier’s Principle
Relationship of the equilibrium constant and ΔG°
74
CHM 313 & 313L. Organic Chemistry & Organic Chemistry Laboratory
Molecular Structure and Absorption Spectra Infrared region
o Intramolecular vibrations and rotations o Recognizing common characteristic group absorptions,
fingerprint region Visible region
o Absorption in visible region gives complementary color (e.g., carotene)
o Effect of structural changes on absorption (e.g., indicators) Ultraviolet region
o π-electron and non-bonding electron transitions o Conjugated systems
NMR spectroscopy o Protons in a magnetic field; equivalent protons o Spin-spin splitting
Covalent Bond Lewis Electron Dot formulas
o Resonance structures o Formal charge o Lewis acids and bases
Partial ionic character o Role of electronegativity in determining charge distribution o Dipole Moment
σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective geometries o Valence shell electron pair repulsion and the prediction of
shapes of molecules (e.g., NH3, H2O, CO2) o Structural formulas for molecules involving H, C, N, O, F, S, P, Si,
Cl o Delocalized electrons and resonance in ions and molecules
Multiple bonding o Effect on bond length and bond energies o Rigidity in molecular structure
Stereochemistry of covalently bonded molecules o Isomers
Structural isomers Stereoisomers (e.g., diastereomers, enantiomers,
cis/trans isomers) Conformational isomers
o Polarization of light, specific rotation o Absolute and relative configuration
Conventions for writing R and S forms o Conventions for writing E and Z forms
Separations and Purifications Extraction: distribution of solute between two immiscible solvents Distillation Chromatography
o Basic principles involved in separation process
75
Column chromatography, gas-liquid chromatography High pressure liquid chromatography
o Paper chromatography o Thin-layer chromatography
Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography
Size-exclusion Ion-exchange Affinity
o Racemic mixtures, separation of enantiomers
Alcohols Description
o Nomenclature o Physical properties (acidity, hydrogen bonding)
Important reactions o Oxidation o Protection of alcohol o Preparation of mesylates and tosylates
76
CHM 314 & 314L. Organic Chemistry & Organic Chemistry Laboratory
Amino Acids Description
o Absolute configuration at the position o Amino acids as dipolar ions o Classifications
Acidic or basic Hydrophobic or hydrophilic
Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis
Nucleic Acid Structure and Function Description Nucleotides and nucleosides
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
Base pairing specificity: A with T, G with C Function in transmission of genetic information
o DNA denaturation, reannealing, hybridization
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Hydrolysis of the glycoside linkage Monosaccharides Disaccharides Polysaccharides
Nucleotides and Nucleic Acids Nucleotides and nucleosides: composition
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid: DNA, double helix Chemistry Other functions
Amino Acids, Peptides, Proteins Amino acids: description
o Absolute configuration at the α position o Dipolar ions o Classification
Acidic or basic Hydrophilic or hydrophobic
o Synthesis of α-amino acids Strecker Synthesis
77
Gabriel Synthesis Peptides and proteins: reactions
o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis
General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins o o Isoelectric point
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Hydrolysis of the glycoside linkage Keto-enol tautomerism of monosaccharides Disaccharides Polysaccharides
Aldehydes and Ketones Description
o Nomenclature o Physical properties
Important reactions o Nucleophilic addition reactions at C=O bond
Acetal, hemiacetal Imine, enamine Hydride reagents Cyanohydrin
o Oxidation of aldehydes o Reactions at adjacent positions: enolate chemistry
Keto-enol tautomerism (α-racemization) Aldol condensation, retro-aldol Kinetic versus thermodynamic enolate
General principles o Effect of substituents on reactivity of C=O; steric hindrance
o Acidity of α-H; carbanions
Carboxylic Acids Description
o Nomenclature o Physical properties
Important reactions o Carboxyl group reactions
Amides (and lactam), esters (and lactone), anhydride formation
Reduction Decarboxylation
Reactions at 2-position, substitution
78
Acid Derivatives (Anhydrides, Amides, Esters) Description
o Nomenclature o Physical properties
Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides
General principles o Relative reactivity of acid derivatives o Steric effects o Electronic effects
Strain (e.g., β-lactams) Phenols
Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological 2e- redox centers
Polycyclic and Heterocyclic Aromatic Compounds Biological aromatic heterocycles
Phosphorus Compounds Description, structure of phosphoric acids
79
CHM 420. Biochemistry
Amino Acids Description
o Absolute configuration at the position o Amino acids as dipolar ions o Classifications
Acidic or basic Hydrophobic or hydrophilic
Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis (mentioned without detail)
Protein Structure Structure
o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic
bonding o 4° structure of proteins
Conformational stability o Hydrophobic interactions o Solvation layer (entropy)
Separation techniques o Isoelectric point o Electrophoresis
Non-Enzymatic Protein Function Binding Immune system Motors
Enzyme Structure and Function Function of enzymes in catalyzing biological reactions Reduction of activation energy Substrates and enzyme specificity Active Site Model Induced-fit Model Mechanism of catalysis
o Cofactors o Coenzymes o Water-soluble vitamins
Control of Enzyme Activity Kinetics
o General (catalysis) o Michaelis-Menten o Cooperativity
Feedback regulation Inhibition – types
o Competitive o Non-competitive o Mixed
80
o Uncompetitive Regulatory enzymes
o Allosteric enzymes o Covalently-modified enzymes
Nucleic Acid Structure and Function Description Nucleotides and nucleosides
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
Base pairing specificity: A with T, G with C
Principles of Bioenergetics Bioenergetics/thermodynamics
o Free energy/Keq Equilibrium constant Relationship of the equilibrium constant and ΔG°
o Concentration o Endothermic/exothermic reactions o Free energy: G o Spontaneous reactions and ΔG°
Phosphoryl group transfers and ATP o ATP hydrolysis ΔG << 0 o ATP group transfers
Biological oxidation-reduction o Soluble electron carriers o Flavoproteins
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Monosaccharides Disaccharides Polysaccharides
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway Glycolysis (aerobic), substrates and products Fermentation (anaerobic glycolysis) Gluconeogenesis Pentose phosphate pathway Net molecular and energetic results of respiration processes
Principles of Metabolic Regulation Regulation of metabolic pathways
o Maintenance of a dynamic steady state Regulation of glycolysis and gluconeogenesis Metabolism of glycogen
Citric Acid Cycle
81
Acetyl-CoA production Reactions of the cycle, substrates and products Regulation of the cycle Net molecular and energetic results of respiration processes
Metabolism of Fatty Acids Description of fatty acids Digestion, mobilization, and transport of fats Oxidation of fatty acids
o Saturated fats o Unsaturated fats
Ketone bodies Anabolism of fats Non-template synthesis: biosynthesis of lipids and polysaccharides Metabolism of proteins
Oxidative Phosphorylation Electron transport chain and oxidative phosphorylation, substrates and
products, general features of the pathway Electron transfer in mitochondria
o NADH, NADPH o Flavoproteins o Cytochromes
ATP synthase o Proton motive force
Net molecular and energetic results of respiration processes
Plasma Membrane General function in cell containment Composition of membranes
o Lipid components Phospholipids (and phosphatids) Steroids Waxes
o Protein components o Fluid mosaic model
Membrane dynamics Solute transport across membranes
o Thermodynamic considerations o Osmosis
Colligative properties o Passive transport o Active transport
Sodium/potassium pump Membrane channels Membrane potential Membrane receptors
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles,
82
Nucleus Mitochondria
o Site of ATP production o Inner and outer membrane structure
Lysosomes: membrane-bound vesicles containing hydrolytic enzymes Endoplasmic reticulum
o Rough and smooth components o Rough endoplasmic reticulum site of ribosomes
Golgi apparatus: general structure and role in packaging and secretion Peroxisomes: organelles that collect peroxides
Biosignalling Gated ion channels
o Voltage gated o Ligand gated
Receptor enzymes G protein-coupled receptors
Lipids Types
o Storage Triacyl glycerols Free fatty acids: saponification
o Structural Phospholipids and phosphatids Sphingolipids Waxes
o Signals/cofactors Fat-soluble vitamins Steroids Prostaglandins
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CHM 451. General Biochemistry I
Amino Acids Description
o Absolute configuration at the position o Amino acids as dipolar ions o Classifications
Acidic or basic Hydrophobic or hydrophilic
Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis
Protein Structure Structure
o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic
bonding o 4° structure of proteins
Conformational stability o Denaturing and folding o Hydrophobic interactions o Solvation layer (entropy)
Separation techniques o Isoelectric point o Electrophoresis
Non-Enzymatic Protein Function Binding Immune system Motors
Enzyme Structure and Function Function of enzymes in catalyzing biological reactions Enzyme classification by reaction type Reduction of activation energy Substrates and enzyme specificity Active Site Model Induced-fit Model Mechanism of catalysis
o Cofactors o Coenzymes o Water-soluble vitamins
Effects of local conditions on enzyme activity
Control of Enzyme Activity Kinetics
o General (catalysis) o Michaelis-Menten o Cooperativity
Feedback regulation Inhibition – types
84
o Competitive o Non-competitive o Mixed o Uncompetitive
Regulatory enzymes o Allosteric enzymes o Covalently-modified enzymes
Zymogen
Nucleic Acid Structure and Function Description Nucleotides and nucleosides
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
Base pairing specificity: A with T, G with C Function in transmission of genetic information DNA denaturation, reannealing, hybridization
Evidence that DNA is Genetic Material Principles of Bioenergetics
Bioenergetics/thermodynamics o Free energy/Keq
Equilibrium constant Relationship of the equilibrium constant and ΔG°
o Concentration Le Châtelier’s Principle
o Endothermic/exothermic reactions o Free energy: G o Spontaneous reactions and ΔG°
Phosphoryl group transfers and ATP o ATP hydrolysis ΔG << 0 o ATP group transfers
Biological oxidation-reduction o Half-reactions o Soluble electron carriers o Flavoproteins
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Hydrolysis of the glycoside linkage Monosaccharides Disaccharides Polysaccharides
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway Glycolysis (aerobic), substrates and products
85
o Feeder pathways: glycogen, starch metabolism Fermentation (anaerobic glycolysis) Gluconeogenesis Pentose phosphate pathway Net molecular and energetic results of respiration processes
Principles of Metabolic Regulation Regulation of metabolic pathways
o Maintenance of a dynamic steady state Regulation of glycolysis and gluconeogenesis Metabolism of glycogen Regulation of glycogen synthesis and breakdown
o Allosteric and hormonal control Analysis of metabolic control
Plasma Membrane General function in cell containment Composition of membranes
o Lipid components Phospholipids (and phosphatids) Steroids Waxes
o Protein components o Fluid mosaic model
Membrane dynamics Solute transport across membranes
o Thermodynamic considerations o Osmosis
Colligative properties, osmotic pressure o Passive transport o Active transport
Sodium/potassium pump Membrane channels Membrane potential Membrane receptors Exocytosis and endocytosis Intercellular junctions
o Gap junctions o Tight junctions o Desmosomes
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles,
mitotic division Nucleus
o Compartmentalization, storage of genetic information o Nucleolus: location and function o Nuclear envelope, nuclear pores
Mitochondria
86
o Site of ATP production o Inner and outer membrane structure o Self-replication
Lysosomes: membrane-bound vesicles containing hydrolytic enzymes Endoplasmic reticulum
o Rough and smooth components o Rough endoplasmic reticulum site of ribosomes o Double membrane structure o Role in membrane biosynthesis o Role in biosynthesis of secreted proteins
Golgi apparatus: general structure and role in packaging and secretion Peroxisomes: organelles that collect peroxides
Electrochemistry Concentration cell: direction of electron flow, Nernst equation
Biosignalling Gated ion channels
o Voltage gated o Ligand gated
Receptor enzymes G protein-coupled receptors
Lipids Description; structure
o Steroids Terpenes and terpenoids
Equilibrium Concept of force, units Analysis of forces acting on an object Newton’s First Law of Motion, inertia Torques, lever arms
Electrochemistry Electrolytic cell
o Electrolysis o Anode, cathode o Electrolyte o Faraday’s Law relating amount of elements deposited (or gas
liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the electrodes
Galvanic or Voltaic cells o Half-reactions o Reduction potentials, cell potential o Direction of electron flow
Concentration cell Batteries
o Electromotive force, Voltage o Lead-storage batteries
Nickel-cadmium batteries Acid/Base Equilibria
87
Bronsted-Lowry definition of acid, base Ionization of water
o Kw, its approximate value (Kw = [H+][OH–] = 10-14 at 25°C, 1 atm) o Definition of pH: pH of pure water
Conjugate acids and bases (e.g., NH4+ and NH3) Strong acids and bases (e.g., nitric, sulfuric) Weak acids and bases (e.g., acetic, benzoic)
o Dissociation of weak acids and bases with or without added salt o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids or bases
Equilibrium constants Ka and Kb: pKa, pKb Buffers
o Definition and concepts (common buffer systems) o Influence on titration curves
Titration Indicators Neutralization Interpretation of the titration curves Redox titration
Separations and Purifications Extraction: distribution of solute between two immiscible solvents Distillation Chromatography
o Basic principles involved in separation process Column chromatography, gas-liquid chromatography High pressure liquid chromatography
o Paper chromatography o Thin-layer chromatography
Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography
Size-exclusion Ion-exchange Affinity
Racemic mixtures, separation of enantiomers Nucleotides and Nucleic Acids
Nucleotides and nucleosides: composition o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid: DNA, double helix Chemistry Other functions
Amino Acids, Peptides, Proteins Amino acids: description
o Absolute configuration at the α position o Dipolar ions o Classification
88
Acidic or basic Hydrophilic or hydrophobic
o Synthesis of α-amino acids Strecker Synthesis Gabriel Synthesis
Peptides and proteins: reactions o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis
General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins o o Isoelectric point
The Three-Dimensional Protein Structure Conformational stability
o Hydrophobic interactions o Solvation layer (entropy)
4° quaternary structure Denaturing and Folding
Non-Enzymatic Protein Function Binding Immune system Motor
Lipids Types
o Storage Triacyl glycerols Free fatty acids: saponification
o Structural Phospholipids and phosphatids Sphingolipids Waxes
o Signals/cofactors Fat-soluble vitamins Steroids Prostaglandins
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Hydrolysis of the glycoside linkage Keto-enol tautomerism of monosaccharides Disaccharides Polysaccharides
Enzymes Classification by reaction type
89
Mechanism o Substrates and enzyme specificity o Active site model o Induced-fit model o Cofactors, coenzymes and vitamins
Kinetics o General (catalysis) o Michaelis-Menten o Cooperativity o Effects of local conditions on enzyme activity
Inhibition Regulatory enzymes
o Allosteric o Covalently modified
Principles of Bioenergetics Bioenergetics/thermodynamics
o Free energy/Keq o Concentration
P o ATP hydrolysis ΔG << 0 o ATP group transfers
Biological oxidation–reduction o Half-reactions o Soluble electron carriers o Flavoproteins
90
CHM 452. General Biochemistry II
Non-Enzymatic Protein Function Binding Immune system Motors
Enzyme Structure and Function Function of enzymes in catalyzing biological reactions Enzyme classification by reaction type Reduction of activation energy Substrates and enzyme specificity Active Site Model Induced-fit Model Mechanism of catalysis
o Cofactors o Coenzymes o Water-soluble vitamins
Effects of local conditions on enzyme activity
Control of Enzyme Activity Kinetics
o General (catalysis) o Michaelis-Menten o Cooperativity
Feedback regulation Inhibition – types
o Competitive o Non-competitive o Mixed o Uncompetitive
Regulatory enzymes o Allosteric enzymes o Covalently-modified enzymes
Zymogen
Nucleic Acid Structure and Function Description Nucleotides and nucleosides
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure
Base pairing specificity: A with T, G with C Function in transmission of genetic information DNA denaturation, reannealing, hybridization
DNA Replication Mechanism of replication: separation of strands, specific coupling of
free nucleic acids Semi-conservative nature of replication Specific enzymes involved in replication Origins of replication, multiple origins in eukaryotes Replicating the ends of DNA molecules
91
Repair of DNA Repair during replication Repair of mutations
Genetic Code Central Dogma: DNA → RNA → protein The triplet code Codon-anticodon relationship Degenerate code, wobble pairing Missense, nonsense codons Initiation, termination codons Messenger RNA (mRNA)
Transcription Transfer RNA (tRNA); ribosomal RNA (rRNA) Mechanism of transcription mRNA processing in eukaryotes, introns, exons Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs),
small nuclear RNA (snRNAs)
Translation Roles of mRNA, tRNA, rRNA Role and structure of ribosomes Initiation, termination co-factors Post-translational modification of proteins
Eukaryotic Chromosome Organization Chromosomal proteins Single copy vs. repetitive DNA Supercoiling Heterochromatin vs. euchromatin Telomeres, centromeres
Evidence that DNA is Genetic Material Principles of Metabolic Regulation
Regulation of metabolic pathways o Maintenance of a dynamic steady state
Regulation of glycolysis and gluconeogenesis Metabolism of glycogen Regulation of glycogen synthesis and breakdown
o Allosteric and hormonal control Analysis of metabolic control
Citric Acid Cycle Acetyl-CoA production Reactions of the cycle, substrates and products Regulation of the cycle Net molecular and energetic results of respiration processes
Metabolism of Fatty Acids and Proteins Description of fatty acids Digestion, mobilization, and transport of fats
92
Oxidation of fatty acids o Saturated fats o Unsaturated fats
Ketone bodies Anabolism of fats Non-template synthesis: biosynthesis of lipids and polysaccharides Metabolism of proteins
Oxidative Phosphorylation Electron transport chain and oxidative phosphorylation, substrates and
products, general features of the pathway Electron transfer in mitochondria
o NADH, NADPH o Flavoproteins o Cytochromes
ATP synthase, chemiosmotic coupling o Proton motive force
Net molecular and energetic results of respiration processes Regulation of oxidative phosphorylation Mitochondria, apoptosis, oxidative stress
Hormonal Regulation and Integration of Metabolism Higher level integration of hormone structure and function Tissue specific metabolism Hormonal regulation of fuel metabolism Obesity and regulation of body mass
Lipids Description; structure
o Steroids Terpenes and terpenoids
Nucleotides and Nucleic Acids Nucleotides and nucleosides: composition
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid: DNA, double helix Chemistry Other functions
Lipids Types
o Storage Triacyl glycerols Free fatty acids: saponification
o Structural Phospholipids and phosphatids Sphingolipids Waxes
o Signals/cofactors Fat-soluble vitamins Steroids Prostaglandins
93
Phenols Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological
2e- redox centers
Enzymes Classification by reaction type Mechanism
o Substrates and enzyme specificity o Active site model o Induced-fit model o Cofactors, coenzymes and vitamins
Kinetics o General (catalysis) o Michaelis-Menten o Cooperativity o Effects of local conditions on enzyme activity
Inhibition Regulatory enzymes
o Allosteric o Covalently modified
94
CHM 462L. Biochemistry Laboratory
Protein Structure Structure
o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic
bonding o 4° structure of proteins
Conformational stability o Denaturing and folding o Hydrophobic interactions o Solvation layer (entropy)
Separation techniques o Isoelectric point o Electrophoresis
Enzyme Structure and Function Function of enzymes in catalyzing biological reactions Enzyme classification by reaction type Reduction of activation energy Substrates and enzyme specificity Active Site Model Induced-fit Model Mechanism of catalysis
o Cofactors o Coenzymes o Water-soluble vitamins
Effects of local conditions on enzyme activity Genetic Code
Central Dogma: DNA → RNA → protein The triplet code Codon-anticodon relationship Degenerate code, wobble pairing Missense, nonsense codons Initiation, termination codons Messenger RNA (mRNA)
Recombinant DNA and Biotechnology Gene cloning Restriction enzymes DNA libraries Generation of cDNA Hybridization Expressing cloned genes Polymerase Chain Reaction Gel Electrophoresis and Southern Blotting DNA sequencing Analyzing gene expression Determining gene function Stem cells Practical applications of DNA technology: medical applications, human
95
gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture
Safety and ethics of DNA technology
Separations and Purifications Extraction: distribution of solute between two immiscible solvents Distillation Chromatography
o Basic principles involved in separation process Column chromatography, gas-liquid chromatography High pressure liquid chromatography
o Paper chromatography o Thin-layer chromatography
Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography
Size-exclusion Ion-exchange Affinity
Racemic mixtures, separation of enantiomers
Enzymes Classification by reaction type Mechanism
o Substrates and enzyme specificity o Active site model o Induced-fit model o Cofactors, coenzymes and vitamins
Kinetics o General (catalysis) o Michaelis-Menten o Cooperativity o Effects of local conditions on enzyme activity
Inhibition Regulatory enzymes
o Allosteric Covalently modified
96
PHYSICS PHY 201. General Physics
Translational Motion Units and dimensions Vectors, components Vector addition Speed, velocity (average and instantaneous) Acceleration
Equilibrium Concept of force, units Analysis of forces acting on an object Newton’s First Law of Motion, inertia Torques, lever arms
Work Derived units, sign conventions Mechanical advantage Work Kinetic Energy Theorem
Energy Kinetic Energy: KE = ½ mv2; units Potential Energy
o PE = mgh (gravitational, local) o PE = ½ kx2(spring)
Conservation of energy Conservative forces Power, units
Fluids Density, specific gravity Buoyancy, Archimedes’ Principle Hydrostatic pressure
o Pascal’s Law o Hydrostatic pressure; P = ρgh (pressure versus depth)
Viscosity: Poiseuille Flow Continuity equation (A∙v = constant) Concept of turbulence at high velocities Surface tension Bernoulli’s equation Venturi effect, pitot tube
97
PHY 202. General Physics
Electrostatics Charge, conductors, charge conservation Insulators Electric field E
o Field lines o Field due to charge distribution
Potential difference, absolute potential at point in space Circuit Elements
Current I = ΔQ/Δt, sign conventions, units Electromotive force, voltage Resistance
o Ohm’s Law: I = V/R o Resistors in series o Resistors in parallel o Resistivity: ρ = R•A/L
Capacitance o Parallel plate capacitor o Energy of charged capacitor o Capacitors in series o Capacitors in parallel o Dielectrics
Conductivity o Metallic o Electrolytic
Meters
Sound Production of sound Relative speed of sound in solids, liquids, and gases Intensity of sound, decibel units, log scale Attenuation (Damping) Doppler Effect: moving sound source or observer, reflection of sound
from a moving object Pitch Resonance in pipes and strings Ultrasound Shock waves
Light, Electromagnetic Radiation Concept of Interference; Young Double-slit Experiment Thin films, diffraction grating, single-slit diffraction Other diffraction phenomena, X-ray diffraction Polarization of light Circular polarization Properties of electromagnetic radiation
o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of perpendicularly
oscillating electric and magnetic o fields; direction of propagation is perpendicular to both
Classification of electromagnetic spectrum, photon energy E = (hf)
98
Visual spectrum, color
Geometrical Optics Reflection from plane surface: angle of incidence equals angle of
reflection Refraction, refractive index n, Snell’s law: n1 sin θ1 = n2 sin θ2 Dispersion, change of index of refraction with wavelength Conditions for total internal reflection Spherical mirrors
o Center of curvature o Focal length o Real and virtual images
Thin lenses o Converging and diverging lenses o Use of formula 1/p + 1/q = 1/f, with sign conventions o Lens strength, diopters
Combination of lenses Lens aberration Optical Instruments, including the human eye
Electronic Structure Orbital structure of hydrogen atom, principal quantum number n,
number of electrons per orbital Ground state, excited states Absorption and emission line spectra Use of Pauli Exclusion Principle Conventional notation for electronic structure Bohr atom Effective nuclear charge Photoelectric effect
99
PSYCHOLOGY PSY 101. Introductory Psychology
Sensory Processing Sensation
o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation
Sensory receptors o Sensory pathways o Types of sensory receptors
Vision Structure and function of the eye Visual processing
o Visual pathways in the brain o Parallel processing o Feature detection
Hearing Auditory processing
o Auditory pathways in the brain Sensory reception by hair cells
Other Senses Somatosensation
o Pain perception Taste
o Taste buds/chemoreceptors that detect specific chemicals
Smell o Olfactory cells/chemoreceptors that detect specific
chemicals o Pheromones o Olfactory pathways in the brain
Kinesthetic sense Vestibular sense
Perception Perception
o Bottom-up/Top-down processing o Perceptual organization (e.g., depth, form, motion,
constancy) o Gestalt principles
Attention Selective attention Divided attention
Cognition Information-processing model Cognitive development
o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development
100
o Influence of heredity and environment on cognitive development
Biological factors that affect cognition Problem solving and decision making
o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion
Overconfidence and belief perseverance Intellectual functioning
o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability
Consciousness States of consciousness
o Alertness o Sleep
Stages of sleep Sleep cycles and changes to sleep cycles Sleep and circadian rhythms Dreaming Sleep disorders
o Hypnosis and meditation Consciousness altering drugs
o Types of consciousness altering drugs and their effects on the nervous system and behavior
o Drug addiction and the reward pathway in the brain Memory
Encoding o Process of encoding information o Processes that aid in encoding memories
Storage o Types of memory storage (e.g., sensory, working, long-
term) o Semantic networks and spreading activation
Retrieval o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories
Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease,
Korsakoff’s syndrome) o Decay o Interference o Memory construction and source monitoring
Changes in synaptic connections underlie memory and learning o Neural plasticity
101
o Memory and learning o Long-term potentiation
Language Theories of language development (e.g., learning, Nativist,
Interactionist) Influence of language on cognition
o Different brain areas control language and speech Emotion
Three components of emotion (i.e., cognitive, physiological, behavioral)
Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness)
Adaptive role of emotion Theories of emotion
o James-Lange theory o Cannon-Bard theory o Schachter-Singer theory
The role of biological processes in perceiving emotion o Generation and experience of emotions involve many
brain regions o The role of the limbic system in emotion o Emotional experiences can be stored as memories that
can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional experience,
and is also important in o temperament and decision making o Emotion and the autonomic nervous system o Physiological markers of emotion (signatures of
emotion) Stress
The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events,
personal, etc.) o Effects of stress on psychological functions
Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques,
spirituality, etc.)
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Neurotransmitters o Peripheral nervous system o Central nervous system
102
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
Personality Theories of personality
o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective o Situational approach to explaining behavior
Psychological Disorders Understanding psychological disorders
o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders
Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders
103
o Schizophrenia o Dissociative disorder o Personality disorders
Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-based therapy to regenerate neurons in CNS
Motivation Factors that influence motivation
o Instinct o Arousal o Drives
Negative feedback systems o Needs
Theories that explain how motivation affects human behavior o Drive reduction theory o Incentive theory o Other: cognitive and need based theories
Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.)
o Biological factors in regulation of these motivational processes
o Socio-cultural factors in regulation of these motivational processes
Attitudes Components of attitudes (i.e., cognitive, affective, and
behavioral) The link between attitudes and behavior
o Processes by which behavior influences attitudes (e.g., foot-in-the door phenomenon,
o role-playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory
How the Presence of Others Affects Individual Behavior Social facilitation Deindividuation Bystander effect Social loafing Peer pressure
Group Processes Group polarization Groupthink
Socialization Definition of socialization Norms
104
Agents of socialization (e.g., the family, mass media, peers, workplace)
Stigma and deviance Conformity and obedience
Habituation and Dishabituation Associative Learning
Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous
recovery, generalization, discrimination Operant conditioning
o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary,
conditional o Reinforcement schedules: fixed-ratio, variable-ratio,
fixed-interval, variable-interval o Punishment o Escape and avoidance learning
Cognitive processes that affect associative learning Biological factors that affect associative learning
o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors
Observational Learning Modeling Biological processes that affect observational learning
o Mirror neurons o Role of the brain in experiencing vicarious emotions
Applications of observational learning to explain individual behavior
Theories of Attitude and Behavior Change Elaboration Likelihood Model
o Information processing routes to persuasion (e.g., central and peripheral route processing)
Social Cognitive theory Factors that affect attitude change (e.g., changing behavior,
characteristics of the message and target, social factors)
Self-Concept and Identity Definitions of self-concept, identity, and social identity The role of self-esteem, self-efficacy, and locus of control in self-
concept and self-identity Different types of identities (e.g., race/ethnicity, gender, age,
sexual orientation, class) Formation of Identity
Stages of identity development o Theories of developmental stages (e.g., Erikson,
Vygotsky, Kohlberg, Freud)
105
Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-taking) o Influence of group (e.g., reference group)
Influence of culture and socialization on identity formation Attributing Behavior to Persons or Situations
Attribution theory o Fundamental attribution error o How culture affects attributions
How self-perceptions shape our perceptions of others How perceptions of the environment shape our perceptions of
others Prejudice and Bias
Definition of prejudice Processes that contribute to prejudice
o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice
Stereotypes Ethnocentrism
o In-group and out-group o Ethnocentrism vs. cultural relativism
Processes Related to Stereotypes Self-fulfilling prophecy Stereotype threat
Elements of Social Interaction Statuses Roles Groups Networks Organizations
Self-presentation and Interacting with Others Expressing and detecting emotion
o Gender shapes expression o Culture shapes expression
Impression management o Front stage vs. back stage self (Dramaturgical
approach) Verbal and nonverbal communication Animal signals and communication
Social Behavior Attraction Aggression Attachment Social support Biological explanations of social behavior in animals
o Foraging behavior o Mating behavior and mate choice o Applying game theory
106
o Altruism o Inclusive fitness
Discrimination Individual vs. institutional discrimination The relationship between prejudice and discrimination How power, prestige, and class facilitate discrimination
107
PSY 321. Cognitive Processes
Perception Perception
o Bottom-up/Top-down processing o Perceptual organization (e.g., depth, form, motion,
constancy) o Gestalt principles
Attention Selective attention Divided attention
Cognition Information-processing model Cognitive development
o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive
development Biological factors that affect cognition Problem solving and decision making
o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion
Overconfidence and belief perseverance Intellectual functioning
o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability o
Consciousness States of consciousness
o Alertness o Sleep
Stages of sleep Sleep cycles and changes to sleep cycles Sleep and circadian rhythms Dreaming Sleep disorders
o Hypnosis and meditation Consciousness altering drugs
o Types of consciousness altering drugs and their effects on the nervous system and behavior
o Drug addiction and the reward pathway in the brain Memory
Encoding o Process of encoding information o Processes that aid in encoding memories
Storage
108
o Types of memory storage (e.g., sensory, working, long-term)
o Semantic networks and spreading activation Retrieval
o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories
Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease,
Korsakoff’s syndrome) o Decay o Interference o Memory construction and source monitoring
Changes in synaptic connections underlie memory and learning o Neural plasticity o Memory and learning o Long-term potentiation
Language Theories of language development (e.g., learning, Nativist,
Interactionist) Influence of language on cognition
o Different brain areas control language and speech
Biological Bases of Behavior
The nervous system o Neurons
The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity
109
o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
110
PSY 322. Learning Attention Selective attention Divided attention
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
Habituation and Dishabituation Associative Learning
Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous
recovery, generalization, discrimination
111
Operant conditioning o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary,
conditional o Reinforcement schedules: fixed-ratio, variable-ratio,
fixed-interval, variable-interval o Punishment o Escape and avoidance learning
Cognitive processes that affect associative learning Biological factors that affect associative learning
o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors
Observational Learning Modeling Biological processes that affect observational learning
o Mirror neurons o Role of the brain in experiencing vicarious emotions
Applications of observational learning to explain individual behavior
112
PSY 323. Psychology of Perception
Sensory Processing Sensation
o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation
Sensory receptors o Sensory pathways o Types of sensory receptors
Vision Structure and function of the eye Visual processing
o Visual pathways in the brain o Parallel processing o Feature detection
Hearing Auditory processing
o Auditory pathways in the brain Sensory reception by hair cells
Other Senses Somatosensation
o Pain perception Taste
o Taste buds/chemoreceptors that detect specific chemicals
Smell o Olfactory cells/chemoreceptors that detect specific
chemicals o Pheromones o Olfactory pathways in the brain
Kinesthetic sense Vestibular sense
Perception Perception
o Bottom-up/Top-down processing o Perceptual organization (e.g., depth, form, motion,
constancy) o Gestalt principles
Attention Selective attention Divided attention
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Neurotransmitters o Peripheral nervous system o Central nervous system
113
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
114
PSY 341. Social Psychology
Attitudes Components of attitudes (i.e., cognitive, affective, and
behavioral) The link between attitudes and behavior
o Processes by which behavior influences attitudes (e.g., foot-in-the door phenomenon,
o role-playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory
How the Presence of Others Affects Individual Behavior Social facilitation Deindividuation Bystander effect Social loafing Peer pressure
Group Processes Group polarization Groupthink
Culture Assimilation Multiculturalism Subcultures
Socialization Definition of socialization Norms Agents of socialization (e.g., the family, mass media, peers,
workplace) Stigma and deviance Conformity and obedience
Theories of Attitude and Behavior Change Elaboration Likelihood Model
o Information processing routes to persuasion (e.g., central and peripheral route processing)
Social Cognitive theory Factors that affect attitude change (e.g., changing behavior,
characteristics of the message and target, social factors)
Self Concept and Identity Definitions of self-concept, identity, and social identity The role of self-esteem, self-efficacy, and locus of control in self-
concept and self-identity Different types of identities (e.g., race/ethnicity, gender, age,
sexual orientation, class) Formation of Identity
Stages of identity development o Theories of developmental stages (e.g., Erikson,
Vygotsky, Kohlberg, Freud) Influence of social factors on identity formation
o Influence of individuals (e.g., imitation, role-taking)
115
o Influence of group (e.g., reference group) Influence of culture and socialization on identity formation
Attributing Behavior to Persons or Situations Attribution theory
o Fundamental attribution error o How culture affects attributions
How self-perceptions shape our perceptions of others How perceptions of the environment shape our perceptions of
others Prejudice and Bias
Definition of prejudice Processes that contribute to prejudice
o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice
Stereotypes Ethnocentrism
o In-group and out-group o Ethnocentrism vs. cultural relativism
Processes Related to Stereotypes Self-fulfilling prophecy Stereotype threat
Elements of Social Interaction Statuses Roles Groups Networks Organizations
Self-presentation and Interacting with Others Expressing and detecting emotion
o Gender shapes expression o Culture shapes expression
Impression management o Front stage vs. back stage self (Dramaturgical
approach) Verbal and nonverbal communication Animal signals and communication
Social Behavior Attraction Aggression Attachment Social support Biological explanations of social behavior in animals
o Foraging behavior o Mating behavior and mate choice o Applying game theory o Altruism o Inclusive fitness
116
PSY 351. Child Psychology
Cognition Information-processing model Cognitive development
o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive
development Biological factors that affect cognition Problem solving and decision making
o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion
Overconfidence and belief perseverance Intellectual functioning
o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability
Language Theories of language development (e.g., learning, Nativist,
Interactionist) Influence of language on cognition
o Different brain areas control language and speech
Stress The nature of stress
o Appraisal o Different types of stressors (e.g., cataclysmic events,
personal, etc.) o Effects of stress on psychological functions
Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques,
spirituality, etc.)
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
117
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
Habituation and Dishabituation Associative Learning
Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous
recovery, generalization, discrimination Operant conditioning
o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary,
conditional o Reinforcement schedules: fixed-ratio, variable-ratio,
fixed-interval, variable-interval o Punishment o Escape and avoidance learning
Cognitive processes that affect associative learning Biological factors that affect associative learning
o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors
Observational Learning Modeling Biological processes that affect observational learning
o Mirror neurons
118
o Role of the brain in experiencing vicarious emotions Applications of observational learning to explain individual
behavior
Self Concept and Identity Definitions of self-concept, identity, and social identity The role of self-esteem, self-efficacy, and locus of control in self-
concept and self-identity Different types of identities (e.g., race/ethnicity, gender, age,
sexual orientation, class) Formation of Identity
Stages of identity development o Theories of developmental stages (e.g., Erikson,
Vygotsky, Kohlberg, Freud) Influence of social factors on identity formation
o Influence of individuals (e.g., imitation, role-taking) o Influence of group (e.g., reference group)
Influence of culture and socialization on identity formation
119
PSY 361. Personality Personality Theories of personality
o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective o Situational approach to explaining behavior
Self Concept and Identity Definitions of self-concept, identity, and social identity The role of self-esteem, self-efficacy, and locus of control in self-
concept and self-identity Different types of identities (e.g., race/ethnicity, gender, age,
sexual orientation, class)
Formation of Identity Stages of identity development
o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud)
Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-taking) o Influence of group (e.g., reference group)
Influence of culture and socialization on identity formation
120
PSY 366. Health Psychology
Emotion Three components of emotion (i.e., cognitive, physiological,
behavioral) Universal emotions (e.g., fear, anger, happiness, surprise, joy,
disgust, sadness) Adaptive role of emotion Theories of emotion
o James-Lange theory o Cannon-Bard theory o Schachter-Singer theory
The role of biological processes in perceiving emotion o Generation and experience of emotions involve many
brain regions o The role of the limbic system in emotion o Emotional experiences can be stored as memories that
can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional experience,
and is also important in o temperament and decision making o Emotion and the autonomic nervous system o Physiological markers of emotion (signatures of
emotion)
Stress The nature of stress
o Appraisal o Different types of stressors (e.g., cataclysmic events,
personal, etc.) o Effects of stress on psychological functions
Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques,
spirituality, etc.) Biological Bases of Behavior
The nervous system o Neurons
The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex
121
Information processing in the cerebral cortex
Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
Psychological Disorders Understanding psychological disorders
o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders
Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders o Schizophrenia o Dissociative disorder o Personality disorders
Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-based therapy to regenerate neurons in CNS
Motivation Factors that influence motivation
o Instinct o Arousal o Drives
Negative feedback systems o Needs
122
Theories that explain how motivation affects human behavior o Drive reduction theory o Incentive theory o Other: cognitive and need based theories
Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.)
o Biological factors in regulation of these motivational processes
o Socio-cultural factors in regulation of these motivational processes
Attitudes Components of attitudes (i.e., cognitive, affective, and
behavioral) The link between attitudes and behavior
o Processes by which behavior influences attitudes (e.g., foot-in-the door phenomenon,
o role-playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory
How the Presence of Others Affects Individual Behavior Social facilitation Deindividuation Bystander effect Social loafing Peer pressure
Attributing Behavior to Persons or Situations Attribution theory
o Fundamental attribution error o How culture affects attributions
How self-perceptions shape our perceptions of others How perceptions of the environment shape our perceptions of
others
Health Disparities Race, gender, and class inequalities in health
Healthcare Disparities Race, gender, and class inequalities in healthcare
123
PSY 368. Community Psychology
Culture Symbolic culture
o Language and symbols o Values and beliefs o Norms and rituals
124
PSY 422. Physiological Psychology
Vision Structure and function of the eye Visual processing
o Visual pathways in the brain o Parallel processing o Feature detection
Hearing Auditory processing
o Auditory pathways in the brain Sensory reception by hair cells
Other Senses Somatosensation
o Pain perception Taste
o Taste buds/chemoreceptors that detect specific chemicals
Smell o Olfactory cells/chemoreceptors that detect specific
chemicals o Pheromones o Olfactory pathways in the brain
Kinesthetic sense Vestibular sense
Consciousness States of consciousness
o Alertness o Sleep
Stages of sleep Sleep cycles and changes to sleep cycles Sleep and circadian rhythms Dreaming Sleep disorders
o Hypnosis and meditation Consciousness altering drugs
o Types of consciousness altering drugs and their effects on the nervous system and behavior
o Drug addiction and the reward pathway in the brain
Stress The nature of stress
o Appraisal o Different types of stressors (e.g., cataclysmic events,
personal, etc.) o Effects of stress on psychological functions
Stress outcomes/response to stressors o Physiological o Emotional o Behavioral
125
o Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)
Biological Bases of Behavior The nervous system
o Neurons The reflex arc
o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the
cerebral cortex Information processing in the cerebral
cortex Lateralization of cortical functions Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
Psychological Disorders Understanding psychological disorders
o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders
Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders
126
o Schizophrenia o Dissociative disorder o Personality disorders
Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-based therapy to regenerate neurons in CNS
127
PSY 443. Psychology of Women
Culture Symbolic culture
o Language and symbols o Values and beliefs o Norms and rituals
Evolution and human culture
128
SOCIOLOGY and ANTHROPOLOGY SOC 101. Principles of Sociology
Culture o Assimilation o Multiculturalism o Subcultures
Socialization o Definition of socialization o Norms o Agents of socialization (e.g., the family, mass
media, peers, workplace) o Stigma and deviance
Formation of Identity o Influence of culture and socialization on
identity formation Prejudice and Bias
o Definition of prejudice o Stereotypes o Ethnocentrism
In-group and out-group Ethnocentrism vs. cultural relativism
Elements of Social Interaction o Statuses o Roles o Groups o Networks o Organizations
Discrimination o Individual vs. institutional discrimination o The relationship between prejudice and
discrimination o How power, prestige, and class facilitate
discrimination Theoretical Approaches
o Functionalism o Conflict theory o Symbolic interactionism o Social constructionism
Social Institutions o Education o Family o Religion o Government and economy o Health and medicine
Culture o Material culture o Symbolic culture
Values and beliefs
129
Norms and rituals o Culture and social groups
Demographic Structure of Society o Age o Gender o Race and ethnicity
Demographic Shifts and Social Change o Demographic transition o Fertility, migration, and mortality o Globalization
Spatial Inequality o Global inequalities
Social Class o Aspects of social stratification
Class, status, and power Cultural capital and social capital Social reproduction Privilege and prestige Intersections with race, gender and age
o Patterns of social mobility Intergenerational and intragenerational
mobility Downward and upward mobility Meritocracy
o Poverty Relative and absolute
Social exclusion (segregation and isolation)
130
SOC 303. Modern Social Theory
Theoretical Approaches o Functionalism o Conflict theory o Symbolic interactionism o Social constructionism
SOC 322. Sex Roles and Society Self-presentation and Interacting with Others o Gender shapes expression
Demographic Structure of Society o Sexual orientation
SOC 325. Deviant Behavior Socialization o Stigma and deviance o Conformity and obedience
SOC 328. Racial and Ethnic Relations
Prejudice and Bias o Processes that contribute to prejudice
Power, prestige, and class Demographic Structure of Society
o Race and ethnicity
SOC 330. Perspectives on Aging
Demographic Structure of Society o Age
SOC 331. Marriage & the Family
Social Institutions o Family
SOC 332. Sociology of Women Self-presentation and Interacting with Others o Gender shapes expression
Demographic Structure of Society o Gender
SOC 333. Sociology of Sexualities
Demographic Structure of Society o Sexual orientation
SOC 334. Religion and Society Social Institutions o Religion
SOC 337. Political Sociology Social Institutions o Government and economy
131
SOC 339. Social Inequality Prejudice and Bias o Processes that contribute to prejudice
Power, prestige, and class Discrimination
o Individual vs. institutional discrimination o The relationship between prejudice and
discrimination o How power, prestige, and class facilitate
discrimination Social Class
o Aspects of social stratification Class, status, and power Cultural capital and social capital Social reproduction Privilege and prestige Intersections with race, gender and age
o Patterns of social mobility Intergenerational and intragenerational
mobility Downward and upward mobility Meritocracy
o Poverty Relative and absolute Social exclusion (segregation and
isolation)
132
SOC 340. Social Psychology in Society
How the Presence of Others Affects Individual Behavior o Social facilitation o Deindividuation o Bystander effect o Social loafing o Peer pressure
Group Processes o Group polarization o Groupthink
Socialization o Conformity and obedience
Self-Concept and Identity o Definitions of self-concept, identity, and social
identity Formation of Identity
o Stages of identity development Theories of developmental stages (e.g.,
Erikson, Vygotsky, Kohlberg, Freud) o Influence of social factors on identity formation
Influence of individuals (e.g., imitation, role-taking)
Influence of group (e.g., reference group)
o Influence of culture and socialization on identity formation
Elements of Social Interaction o Statuses o Roles o Groups o Networks o Organizations
Self-presentation and Interacting with Others o Expressing and detecting emotion
Gender shapes expression Culture shapes expression
o Impression management Front stage vs. back stage self
(Dramaturgical approach) o Verbal and nonverbal communication o Animal signals and communication
Culture o Symbolic culture
Language and symbols
133
SOC 341. Self & Society Self-Concept and Identity o Definitions of self-concept, identity, and social
identity o Different types of identities (e.g., race/ethnicity,
gender, age, sexual orientation, class) Formation of Identity
o Influence of social factors on identity formation Influence of individuals (e.g., imitation,
role-taking) Influence of group (e.g., reference
group) Self-presentation and Interacting with Others
o Impression management Front stage vs. back stage self
(Dramaturgical approach)
SOC 342. Collective Behavior Demographic Shifts and Social Change o Social movements
SOC 351. Urban Sociology Demographic Shifts and Social Change o Urbanization
Spatial Inequality o Racial segregation(neighborhoods)
SOC 368. Immigration & Immigrants
Demographic Structure of Society o Immigration status
SOC 435. Economy & Society Demographic Shifts and Social Change o Globalization
Spatial Inequality o Global inequalities
SWK 335. Social Work & Environmental Justice
Spatial Inequality o Environmental justice (location and exposure
to health risks)
134
ANT 150. Cultural Anthropology
Culture o Assimilation o Multiculturalism o Subcultures
Prejudice and Bias o Ethnocentrism
In-group and out-group o Ethnocentrism vs. cultural relativism
Self-presentation and Interacting with Others o Culture shapes expression
Culture o Material culture o Symbolic culture
Values and beliefs Norms and rituals
o Culture and social groups
ANT 300. Evolution of People & Culture
Culture o Evolution and human culture
ANT 315. Language & Culture Self-presentation and Interacting with Others o Verbal and nonverbal communication
Culture o Symbolic culture
Language and symbols
135
Topic List with Associated Courses This document lists the topics that will be found on the MCAT 2015 exam, arranged by content category, along with the University of Dayton course numbers for any course that covers material in that content category. Specifically, content from the following sections of the MCAT are listed:
Biological and Biochemical Foundations of Living Systems – p. 136
Chemical and Physical Foundations of Biological Systems – p. 156
Psychological, Social, and Biological Foundations of Behavior – p. 167
Note that not every listed course covers every topic in a given content category. Every effort has been made to highlight what topics in a given content category are covered or not covered in each course. However, this document should be used in conjunction with the companion “Course Listing with Associated Topics” to fully discern what content may be found in a given course. The list in this document follows the order and organization found in the AAMC publications: Preview Guide for the MCAT 2015 Exam and The Official Guide to the MCAT (MCAT 2015) Exam. The fourth section of the MCAT is titled Critical Analysis and Reasoning Skills. It includes passages and questions to test the student’s ability to comprehend. Passages are excerpted from authentic materials found in a variety of books, journals, and magazines, often from disciplines in the social sciences and humanities. This MCAT section is NOT included in this course mapping since it does not test knowledge typically covered in a specific course.
136
Biological and Biochemical Foundations of Living Systems
Content Category 1A: Structure and function of proteins and their constituent amino acids
Amino Acids ● Description
○ Absolute configuration at the position
○ Amino acids as dipolar ions
○ Classifications
■ Acidic or basic
■ Hydrophobic or hydrophilic
● Reactions
○ Sulfur linkage for cysteine and cysteine
○ Peptide linkage: polypeptides and proteins
○ Hydrolysis
CHM 314, 420, 451 & BIO 151, 151L, 312, 312L, 440
Protein Structure ● Structure
○ 1° structure of proteins
○ 2° structure of proteins
○ 3° structure of proteins; role of proline, cystine,
hydrophobic bonding
○ 4° structure of proteins
● Conformational stability
○ Denaturing and folding (Not CHM 420)
○ Hydrophobic interactions
○ Solvation layer (entropy) (Not BIO 151)
● Separation techniques
○ Isoelectric point (Not BIO 151)
○ Electrophoresis
CHM 420, 451, 462L & BIO 151, 151L, 312, 312L, 440, 442L, 462
Non-Enzymatic Protein Function ● Binding
● Immune system
● Motors
BIO 151, 151L, 312, 312L, 411, 411L, 427,442 & CHM 420, 451, 452
Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions (BIO 411)
● Enzyme classification by reaction type (Not BIO 151) (Not CHM
420)
● Reduction of activation energy
BIO 151, 151L, BIO 411, 442L, 462 & CHM 420, 451, 452
137
● Substrates and enzyme specificity
● Active Site Model (Not BIO 151)
● Induced-fit Model
● Mechanism of catalysis
○ Cofactors (BIO 411)
○ Coenzymes (BIO 411)
○ Water-soluble vitamins (Not BIO 151)
● Effects of local conditions on enzyme activity
Control of Enzyme Activity ● Kinetics
○ General (catalysis) (BIO 411)
○ Michaelis-Menten(Not BIO 151)
○ Cooperativity
● Feedback regulation (BIO 411)
● Inhibition – types
○ Competitive
○ Non-competitive
○ Mixed (Not BIO 151)
○ Uncompetitive(Not BIO 151)
● Regulatory enzymes
○ Allosteric enzymes
○ Covalently-modified enzymes
○ Zymogen (Not CHM 420)
BIO 151, 151L, 411, 462 & CHM 420, 451, 452
Content Category 1B: Transmission of genetic information from the gene to the protein
Nucleic Acid Structure and Function ● Description
● Nucleotides and nucleosides
○ Sugar phosphate backbone
○ Pyrimidine, purine residues
● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model
of DNA structure
● Base pairing specificity: A with T, G with C
● Function in transmission of genetic information (Not CHM 420)
● DNA denaturation, reannealing, hybridization (Not CHM 420)
CHM 314, 420, 451, 452 & BIO 151, 151L, 312, 312L, 442, 462
DNA Replication ● Mechanism of replication: separation of strands, specific
BIO 151, 151L, 312, 312L, 440,
138
coupling of free nucleic acids
● Semi-conservative nature of replication
● Specific enzymes involved in replication
● Origins of replication, multiple origins in eukaryotes
● Replicating the ends of DNA molecules
462, 470 & CHM 452
Repair of DNA ● Repair during replication
● Repair of mutations
BIO 151, 151L, 312, 312L, 411, 411L, 440, 462 & CHM 452
Genetic Code ● Central Dogma: DNA → RNA → protein (BIO 411)
● The triplet code
● Codon-anticodon relationship
● Degenerate code, wobble pairing
● Missense, nonsense codons
● Initiation, termination codons
● Messenger RNA (mRNA) (BIO 411)
BIO 151, 151L, 312, 312L, 411, 442, 462 & CHM 452, 462L
Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA)
● Mechanism of transcription
● mRNA processing in eukaryotes, introns, exons
● Ribozymes, spliceosomes, small nuclear ribonucleoproteins
(snRNPs), small nuclear RNA
(snRNAs) ● Functional and evolutionary importance of introns
BIO 151, 151L, 312, 312L, 442, 462 & CHM 452
Translation ● Roles of mRNA, tRNA, rRNA
● Role and structure of ribosomes
● Initiation, termination co-factors
● Post-translational modification of proteins
BIO 151, 151L, 312, 312L, 442, 462 & CHM 452
Eukaryotic Chromosome Organization ● Chromosomal proteins
● Single copy vs. repetitive DNA
● Supercoiling
● Heterochromatin vs. euchromatin
BIO 151, 151L, 312, 312L, 442, 462 & CHM 452
139
● Telomeres, centromeres
Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-Monod Model
● Gene repression in bacteria
● Positive control in bacteria
BIO 151, 151L, 312, 312L, 411, 411L, 462
Control of Gene Expression in Eukaryotes ● Transcriptional regulation(BIO 411)
● DNA binding proteins, transcription factors
● Gene amplification and duplication
● Post-transcriptional control, basic concept of splicing (introns,
exons)
● Cancer as a failure of normal cellular controls, oncogenes, tumor
suppressor genes
● Regulation of chromatin structure
● DNA methylation
● Role of non-coding RNAs
BIO 151, 151L, 312, 312L, 411, 442, 462
Recombinant DNA and Biotechnology ● Gene cloning (BIO 411)
● Restriction enzymes (BIO 411)
● DNA libraries (BIO 411)
● Generation of cDNA
● Hybridization
● Expressing cloned genes
● Polymerase Chain Reaction(BIO 411)
● Gel Electrophoresis and Southern Blotting
● DNA sequencing (BIO 411)
● Analyzing gene expression (BIO 411)
● Determining gene function (BIO 411)
● Stem cells
● Practical applications of DNA technology: medical applications,
human gene therapy,
pharmaceuticals, forensic evidence, environmental cleanup, agriculture
● Safety and ethics of DNA technology
BIO 151, 151L, 312, 312L, 411, 442, & CHM 462L
140
Content Category 1C: Transmission of heritable information from generation to generation and the processes that increase genetic diversity
Evidence that DNA is Genetic Material
BIO 151, 151L, 312, 312L, & CHM 451, 452
Mendelian Concepts ● Phenotype and genotype
● Gene
● Locus
● Allele: single and multiple
● Homozygosity and heterozygosity
● Wild-type
● Recessiveness
● Complete dominance
● Co-dominance
● Incomplete dominance, leakage, penetrance, expressivity (Not
BIO 151)
● Hybridization: viability
● Gene pool
BIO 151, 151L, 152, 152L, 301, 312, 312L, 442
Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis
● Important differences between meiosis and mitosis
● Segregation of genes
○ Independent assortment
○ Linkage
○ Recombination
■ Single crossovers
■ Double crossovers
■ Synaptonemal complex
■ Tetrad
○ Sex-linked characteristics
○ Very few genes on Y chromosome
○ Sex determination
○ Cytoplasmic/extranuclear inheritance
● Mutation
○ General concept of mutation — error in DNA sequence
○ Types of mutations: random, translation error,
BIO 151, 151L, 152, 152L, 312, 312L, 442, 442L
141
transcription error, base substitution,
inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation
○ Inborn errors of metabolism
○ Relationship of mutagens to carcinogens
● Genetic drift
● Synapsis or crossing-over mechanism for increasing genetic
diversity
Analytic Methods ● Hardy–Weinberg Principle (Not BIO 151)
● Test cross
● Gene mapping: crossover frequencies
● Biometry: statistical methods (Not BIO 151)
BIO 151, 151L, 152, 152L, 312, 312L
Evolution ● Natural selection
○ Fitness concept
○ Selection by differential reproduction
○ Concepts of natural and group selection
○ Evolutionary success as increase in percent
representation in the gene pool of the next
○ generation
● Speciation
○ Polymorphism
○ Adaptation and specialization
○ Inbreeding
○ Outbreeding
○ Bottlenecks
● Evolutionary time as measured by gradual random changes in
genome
BIO 152, 152L, 312, 312L
Content Category 1D: Principles of bioenergetics and fuel molecule metabolism
Principles of Bioenergetics ● Bioenergetics/thermodynamics
○ Free energy/Keq
■ Equilibrium constant
■ Relationship of the equilibrium constant and ΔG°
○ Concentration
BIO 151, 151L, 411, 411L & CHM 420, 451
142
■ Le Châtelier’s Principle (Not BIO 151) (Not CHM
420)
○ Endothermic/exothermic reactions
○ Free energy: G
○ Spontaneous reactions and ΔG°
● Phosphoryl group transfers and ATP
○ ATP hydrolysis ΔG << 0
○ ATP group transfers
● Biological oxidation-reduction
○ Half-reactions (Not CHM 420)
○ Soluble electron carriers
○ Flavoproteins
Carbohydrates ● Description
○ Nomenclature and classification, common names
○ Absolute configuration
○ Cyclic structure and conformations of hexoses
○ Epimers and anomers
● Hydrolysis of the glycoside linkage
● Monosaccharides
● Disaccharides
● Polysaccharides
BIO 151, 151L & CHM 314, 420, 451
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products
○ Feeder pathways: glycogen, starch metabolism (Not CHM
420)
● Fermentation (anaerobic glycolysis)
● Gluconeogenesis
● Pentose phosphate pathway (Not BIO 151)
● Net molecular and energetic results of respiration processes
BIO 151, 151L, 411, 411L & CHM 420, 451
Principles of Metabolic Regulation ● Regulation of metabolic pathways
○ Maintenance of a dynamic steady state
● Regulation of glycolysis and gluconeogenesis
● Metabolism of glycogen (Not BIO 411)
● Regulation of glycogen synthesis and breakdown (Not BIO 411)
(Not CHM 420)
BIO 151, 151L, 411, 411L & CHM 420, 451, 452
143
○ Allosteric and hormonal control (Not BIO 411) (Not CHM
420)
● Analysis of metabolic control(Not CHM 420)
Citric Acid Cycle ● Acetyl-CoA production
● Reactions of the cycle, substrates and products
● Regulation of the cycle
● Net molecular and energetic results of respiration processes
BIO 151, 151L, 411, 411L & CHM 420, 452
Metabolism of Fatty Acids and Proteins ● Description of fatty acids
● Digestion, mobilization, and transport of fats (Not BIO 151) (Not
BIO 411)
● Oxidation of fatty acids
○ Saturated fats
○ Unsaturated fats
● Ketone bodies (Not BIO 411)
● Anabolism of fats (Not BIO 411)
● Non-template synthesis: biosynthesis of lipids and
polysaccharides (Not BIO 151) (Not BIO 411)
● Metabolism of proteins (Not BIO 151) (Not CHM 420)
BIO 151, 151L, 411, 411L & CHM 420, 452
Oxidative Phosphorylation ● Electron transport chain and oxidative phosphorylation,
substrates and products, general features of the pathway
● Electron transfer in mitochondria
○ NADH, NADPH
○ Flavoproteins
○ Cytochromes
● ATP synthase, chemiosmotic coupling (Not CHM 420)
○ Proton motive force
● Net molecular and energetic results of respiration processes
● Regulation of oxidative phosphorylation (Not CHM 420)
● Mitochondria, apoptosis, oxidative stress (Not BIO 411) (Not
CHM 420)
BIO 151, 151L, 411, 411L & CHM 420, 452
Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function
● Tissue specific metabolism
● Hormonal regulation of fuel metabolism
BIO 151, 151L, 403, 403L, & CHM 452
144
● Obesity and regulation of body mass
Content Category 2A: Assemblies of molecules, cells, and groups of cells within single cellular and multicellular organisms
Plasma Membrane ● General function in cell containment
● Composition of membranes
○ Lipid components
■ Phospholipids (and phosphatids)
■ Steroids
■ Waxes
○ Protein components
○ Fluid mosaic model
● Membrane dynamics
● Solute transport across membranes
○ Thermodynamic considerations
○ Osmosis
■ Colligative properties, osmotic pressure
○ Passive transport
○ Active transport
■ Sodium/potassium pump
● Membrane channels
● Membrane potential
● Membrane receptors
● Exocytosis and endocytosis(Not BIO 411) (Not CHM 420)
● Intercellular junctions (Not BIO 411) (Not CHM 420)
○ Gap junctions
○ Tight junctions
○ Desmosomes
BIO 151, 151L, 403, 403L, 411, 411L, 440, 442 & CHM 420, 451
Membrane-Bound Organelles and Defining Characteristics of Eukaryotic Cells
● Defining characteristics of eukaryotic cells: membrane bound
nucleus, presence of organelles,
● Mitotic division (Not CHM 420)
● Nucleus (Not CHM 420)
○ Compartmentalization, storage of genetic information
○ Nucleolus: location and function
○ Nuclear envelope, nuclear pores
BIO 151, 151L, 403, 403L, 440, 442 & CHM 420, 451
145
● Mitochondria
○ Site of ATP production
○ Inner and outer membrane structure
○ Self-replication (Not CHM 420)
● Lysosomes: membrane-bound vesicles containing hydrolytic
enzymes
● Endoplasmic reticulum
○ Rough and smooth components
○ Rough endoplasmic reticulum site of ribosomes
○ Double membrane structure (Not CHM 420)
○ Role in membrane biosynthesis (Not CHM 420)
○ Role in biosynthesis of secreted proteins (Not CHM 420)
● Golgi apparatus: general structure and role in packaging and
secretion (Not CHM 420)
● Peroxisomes: organelles that collect peroxides
Cytoskeleton ● General function in cell support and movement
● Microfilaments: composition and role in cleavage and
contractility
● Microtubules: composition and role in support and transport
● Intermediate filaments, role in support
● Composition and function of cilia and flagella
● Centrioles, microtubule organizing centers
BIO 151, 151L, 440, 442
Tissues Formed From Eukaryotic Cells ● Epithelial cells
● Connective tissue cells
BIO 151, 151L, 440, 442
Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses
Cell Theory ● History and development
● Impact on biology
BIO 151, 151L, 411, 411L, 440
Classification and Structure of Prokaryotic Cells ● Prokaryotic domains
○ Archaea
○ Bacteria
● Major classifications of bacteria by shape
BIO 151, 151L, 411, 411L
146
○ Bacilli (rod-shaped)
○ Spirilli (spiral shaped)
○ Cocci (spherical)
● Lack of nuclear membrane and mitotic apparatus
● Lack of typical eukaryotic organelles
● Presence of cell wall in bacteria
● Flagellar propulsion, mechanism
Growth and Physiology of Prokaryotic Cells ● Reproduction by fission
● High degree of genetic adaptability, acquisition of antibiotic
resistance
● Exponential growth
● Existence of anaerobic and aerobic variants
● Parasitic and symbiotic
● Chemotaxis
BIO 151, 151L, 411, 411L
Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA
● Transformation: incorporation into bacterial genome of DNA
fragments from external medium
● Conjugation
● Transposons (also present in eukaryotic cells)
BIO 151, 151L, 312L, 411, 411L
Virus Structure ● General structural characteristics (nucleic acid and protein,
enveloped and nonenveloped)
● Lack organelles and nucleus
● Structural aspects of typical bacteriophage
● Genomic content--RNA or DNA
● Size relative to bacteria and eukaryotic cells
BIO 151, 151L, 411, 411L
Viral Life Cycle ● Self-replicating biological units that must reproduce within
specific host cell
● Generalized phage and animal virus life cycles
○ Attachment to host, penetration of cell membrane or cell
wall, and entry of viral genetic
○ material
○ Use of host synthetic mechanism to replicate viral
components
BIO 151, 151L, 411, 411L
147
○ Self-assembly and release of new viral particles
● Transduction: transfer of genetic material by viruses
● Retrovirus life cycle: integration into host DNA, reverse
transcriptase, HIV
● Prions and viroids: subviral particles
Content Category 2C: Processes of cell division, differentiation, and specialization
Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,
interphase
● Mitotic structures
○ Centrioles, asters, spindles
○ Chromatids, centromeres, kinetochores
○ Nuclear membrane breakdown and reorganization
○ Mechanisms of chromosome movement
● Phases of cell cycle: G0, G1, S, G2, M
● Growth arrest
● Control of cell cycle
● Loss of cell cycle controls in cancer cells
BIO 151, 151L, 312, 312L, 440, 442
Biosignalling ● Oncogenes (Not BIO 151), apoptosis
BIO 151, 151L, 440, 442
Reproductive System ● Gametogenesis by meiosis
● Ovum and sperm
○ Differences in formation
○ Differences in morphology
○ Relative contribution to next generation
● Reproductive sequence: fertilization, implantation,
development, birth
BIO 152, 152L, 442, 475, 475L
Embryogenesis ● Stages of early development (order and general features of
each)
○ Fertilization
○ Cleavage
○ Blastula formation
○ Gastrulation
BIO 152, 152L, 442
148
■ First cell movements
■ Formation of primary germ layers (endoderm,
mesoderm, ectoderm)
○ Neurulation
● Major structures arising out of primary germ layers
● Neural crest
● Environment–gene interaction in development
Mechanisms of Development ● Cell specialization
○ Determination
○ Differentiation
○ Tissue types
● Cell–cell communication in development
● Cell migration
● Pluripotency: stem cells
● Gene regulation in development
● Programmed cell death
● Existence of regenerative capacity in various species
● Senescence and aging
BIO 152, 152L, 442
Content Category 3A: Structure and functions of the nervous and endocrine systems and ways in which these systems coordinate the organ systems
Nervous System: Structure and Function ● Major Functions
○ High level control and integration of body systems
○ Adaptive capability to external influences
● Organization of vertebrate nervous system
● Sensor and effector neurons
● Sympathetic and parasympathetic nervous systems:
antagonistic control
● Reflexes
○ Feedback loop, reflex arc
○ Role of spinal cord and supraspinal circuits
● Integration with endocrine system: feedback control
BIO 152, 442, 442L, 475, 475L
Nerve Cell ● Cell body: site of nucleus, organelles
● Dendrites: branched extensions of cell body
BIO 403, 403L, 415, 442
149
● Axon: structure and function
● Myelin sheath, Schwann cells, insulation of axon
● Nodes of Ranvier: propagation of nerve impulse along axon
● Synapse: site of impulse propagation between cells
● Synaptic activity: transmitter molecules
● Resting potential: electrochemical gradient
● Action potential
○ Threshold, all-or-none
○ Sodium/potassium pump
● Excitatory and inhibitory nerve fibers: summation, frequency of
firing
● Glial cells, neuroglia
Electrochemistry ● Concentration cell: direction of electron flow, Nernst equation
BIO 403, 403L & CHM 124, 451
Biosignalling ● Gated ion channels
○ Voltage gated
○ Ligand gated
● Receptor enzymes
● G protein-coupled receptors
BIO 151, 151L, 312, 312L, 440, 442 & CHM 420, 451
Lipids ● Description; structure
○ Steroids
○ Terpenes and terpenoids (Not BIO 151) (Not BIO 411)
BIO 151, 151L, 411, 411L & CHM 451, 452
Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at cell,
tissue, and organ level
● Definitions of endocrine gland, hormone
● Major endocrine glands: names, locations, products
● Major types of hormones
● Neuroendrocrinology ― relation between neurons and
hormonal systems
BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L
Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action
● Transport of hormones: blood supply
BIO 152, 152L, 403, 403L, 442
150
● Specificity of hormones: target tissue
● Integration with nervous system: feedback control regulation by
second messengers
Content Category 3B: Structure and integrative functions of the main organ systems
Respiratory System ● General function
○ Gas exchange, thermoregulation
○ Protection against disease: particulate matter
● Structure of lungs and alveoli
● Breathing mechanisms
○ Diaphragm, rib cage, differential pressure
○ Resiliency and surface tension effects
● Thermoregulation: nasal and tracheal capillary beds;
evaporation, panting
● Particulate filtration: nasal hairs, mucus/cilia system in lungs
● Alveolar gas exchange
○ Diffusion, differential partial pressure
○ Henry’s Law
● pH control
● Regulation by nervous control
○ CO2 sensitivity
BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L
Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and
fluids, removal of metabolic
waste ● Role in thermoregulation
● Four-chambered heart: structure and function
● Endothelial cells
● Systolic and diastolic pressure
● Pulmonary and systemic circulation
● Arterial and venous systems (arteries, arterioles, venules, veins)
○ Structural and functional differences
○ Pressure and flow characteristics
● Capillary beds
○ Mechanisms of gas and solute exchange
○ Mechanism of heat exchange
○ Source of peripheral resistance
BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L
151
● Composition of blood
○ Plasma, chemicals, blood cells
○ Erythrocyte production and destruction; spleen, bone
marrow
○ Regulation of plasma volume
● Coagulation, clotting mechanisms
● Oxygen transport by blood
○ Hemoglobin, hematocrit
○ Oxygen content
○ Oxygen affinity
○ Oxygen transport by blood; modification of oxygen
affinity
● Carbon dioxide transport and level in blood
● Nervous and endocrine control
Lymphatic System ● Structure of lymphatic system
● Major functions
○ Equalization of fluid distribution
○ Transport of proteins and large glycerides
○ Production of lymphocytes involved in immune reactions
○ Return of materials to the blood
BIO 152, 152L 403, 403L, 475, 475L
Immune System ● Innate (non-specific) vs. adaptive (specific) immunity
● Adaptive immune system cells
○ T-lymphocytes
○ B-lymphocytes
● Innate immune system cells
○ Macrophages
○ Phagocytes
● Concept of antigen and antibody
● Antigen presentation
● Clonal selection
● Antigen-antibody recognition
● Structure of antibody molecule
● Recognition of self vs. non-self, autoimmune diseases
● Major histocompatibility complex
BIO 427, 442, 442L
Digestive System BIO 403, 403L,
152
● Ingestion
○ Saliva as lubrication and source of enzymes
○ Ingestion, esophagus, transport function
● Stomach
○ Storage and churning of food
○ Low pH, gastric juice, mucal protection against self-
destruction
○ Production of digestive enzymes, site of digestion
○ Structure (gross)
● Liver
○ Structural relationship of liver within gastrointestinal
system
○ Production of bile
○ Role in blood glucose regulation, detoxification
● Bile
○ Storage in gall bladder
○ Function
● Pancreas
○ Production of enzymes
○ Transport of enzymes to small intestine
● Small Intestine
○ Absorption of food molecules and water
○ Function and structure of villi
○ Production of enzymes, site of digestion
○ Neutralization of stomach acid
○ Structure (anatomic subdivisions)
● Large Intestine
○ Absorption of water
○ Bacterial flora
○ Structure (gross)
● Rectum: storage and elimination of waste, feces
● Muscular control
○ Peristalsis
● Endocrine control
○ Hormones
○ Target tissues
● Nervous control: the enteric nervous system
442, 442L, 475, 475L
Excretory System BIO 403, 403L,
153
● Roles in homeostasis
○ Blood pressure
○ Osmoregulation
○ Acid-base balance
○ Removal of soluble nitrogenous waste
● Kidney structure
○ Cortex
○ Medulla
● Nephron structure
○ Glomerulus
○ Bowman’s capsule
○ Proximal tubule
○ Loop of Henle
○ Distal tubule
○ Collecting duct
● Formation of urine
○ Glomerular filtration
○ Secretion and reabsorption of solutes
○ Concentration of urine
○ Counter-current multiplier mechanism
● Storage and elimination: ureter, bladder, urethra
● Osmoregulation: capillary reabsorption of H2O, amino acids,
glucose, ions
● Muscular control: sphincter muscle
442, 442L, 475, 475L
Reproductive System ● Male and female reproductive structures and their functions
○ Gonads
○ Genitalia
○ Differences between male and female structures
● Hormonal control of reproduction
○ Male and female sexual development
○ Female reproductive cycle
○ Pregnancy, parturition, lactation
○ Integration with nervous control
BIO 403, 403L, 442, 442L, 475, 475L
Muscle System ● Important functions
○ Support: mobility
○ Peripheral circulatory assistance
BIO 403, 403L, 475, 475L
154
○ Thermoregulation (shivering reflex)
● Structure of three basic muscle types: striated, smooth, cardiac
● Muscle structure and control of contraction
○ T-tubule system
○ Contractile apparatus
○ Sarcoplasmic reticulum
○ Fiber type
○ Contractile velocity of different muscle types
● Regulation of cardiac muscle contraction
● Oxygen debt: fatigue
● Nervous control
○ Motor neurons
○ Neuromuscular junction, motor end plates
○ Sympathetic and parasympathetic innervation
○ Voluntary and involuntary muscles
Specialized Cell-Muscle Cell ● Structural characteristics of striated, smooth, and cardiac
muscle
● Abundant mitochondria in red muscle cells: ATP source
● Organization of contractile elements: actin and myosin
filaments, crossbridges, sliding filament model
● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone
● Presence of troponin and tropomyosin
● Calcium regulation of contraction
BIO 403, 403L, 440
Skeletal System ● Functions
○ Structural rigidity and support
○ Calcium storage
○ Physical protection
● Skeletal structure
○ Specialization of bone types, structures
○ Joint structures
○ Endoskeleton vs. exoskeleton
● Bone structure
○ Calcium/protein matrix
○ Cellular composition of bone
● Cartilage: structure and function
● Ligaments, tendons
BIO 442, 442L, 475, 475L
155
● Endocrine control
Skin System ● Structure
○ Layer differentiation, cell types
○ Relative impermeability to water
● Functions in homeostasis and osmoregulation
● Functions in thermoregulation
○ Hair, erectile musculature
○ Fat layer for insulation
○ Sweat glands, location in dermis
○ Vasoconstriction and vasodilation in surface capillaries
● Physical protection
○ Nails, calluses, hair
○ Protection against abrasion, disease organisms
● Hormonal control: sweating, vasodilation, and vasoconstriction
BIO 403, 403L, 442, 475, 475L
156
Chemical and Physical Foundations of Biological Systems Content Category 4A: Translational motion, forces, work, energy, and equilibrium in living systems
Translational Motion Units and dimensions Vectors, components Vector addition Speed, velocity (average and instantaneous) Acceleration
PHY 201 PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.
Equilibrium Concept of force, units Analysis of forces acting on an object Newton’s First Law of Motion, inertia Torques, lever arms
PHY 201 & CHM 124, 420, 451 PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.
Work Derived units, sign conventions Mechanical advantage Work Kinetic Energy Theorem
PHY 201 & CHM 123 PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.
Energy Kinetic Energy: KE = ½ mv2; units Potential Energy
o PE = mgh (gravitational, local) o PE = ½ kx2(spring)
Conservation of energy Conservative forces Power, units
PHY 201 & CHM 123 PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.
Content Category 4B: Importance of fluids for the circulation of blood, gas movement, and gas exchange
Fluids Density, specific gravity Buoyancy, Archimedes’ Principle Hydrostatic pressure
o Pascal’s Law o Hydrostatic pressure; P = ρgh (pressure versus
depth) Viscosity: Poiseuille Flow Continuity equation (A∙v = constant) Concept of turbulence at high velocities Surface tension Bernoulli’s equation Venturi effect, pitot tube
PHY 201 PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics..
Circulatory System BIO 403, 403L
157
Arterial and venous systems; pressure and flow characteristics
Gas Phase Absolute temperature, (K) Kelvin Scale Pressure, simple mercury barometer Molar volume at 0°C and 1 atm = 22.4 L/mol Ideal gas
o Definition o Ideal Gas Law: PV = nRT o Boyle’s Law: PV = constant o Charles’ Law: V/T = constant o Avogadro’s Law: V/n = constant
Kinetic Molecular Theory of Gases o Heat capacity at constant volume and at constant
pressure o Boltzmann’s Constant
Deviation of real gas behavior from Ideal Gas Law o Qualitative o Quantitative (Van der Waals’ Equation)
Partial pressure, mole fraction Dalton’s Law relating partial pressure to composition
CHM 123
Content Category 4C: Electrochemistry and electrical circuits and their elements
Electrostatics Charge, conductors, charge conservation Insulators Electric field E
o Field lines o Field due to charge distribution
Potential difference, absolute potential at point in space
PHY 202
Circuit Elements Current I = ΔQ/Δt, sign conventions, units Electromotive force, voltage Resistance
o Ohm’s Law: I = V/R o Resistors in series o Resistors in parallel o Resistivity: ρ = R•A/L
Capacitance o Parallel plate capacitor o Energy of charged capacitor o Capacitors in series o Capacitors in parallel o Dielectrics
Conductivity o Metallic o Electrolytic
Meters
PHY 202
158
Electrochemistry Electrolytic cell
o Electrolysis o Anode, cathode o Electrolyte o Faraday’s Law relating amount of elements
deposited (or gas liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the
electrodes Galvanic or Voltaic cells
o Half-reactions o Reduction potentials, cell potential o Direction of electron flow
Concentration cell Batteries
o Electromotive force, Voltage o Lead-storage batteries o Nickel-cadmium batteries
CHM 124, 451
Specialized Cell - Nerve Cell Myelin sheath, Schwann cells, insulation of axon Nodes of Ranvier: propagation of nerve impulse along axon
BIO 415, 442
Content Category 4D: How light and sound interact with matter
Sound Production of sound Relative speed of sound in solids, liquids, and gases Intensity of sound, decibel units, log scale Attenuation (Damping) Doppler Effect: moving sound source or observer, reflection
of sound from a moving object Pitch Resonance in pipes and strings Ultrasound Shock waves
PHY 202
Light, Electromagnetic Radiation Concept of Interference; Young Double-slit Experiment Thin films, diffraction grating, single-slit diffraction Other diffraction phenomena, X-ray diffraction Polarization of light Circular polarization Properties of electromagnetic radiation
o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of
perpendicularly oscillating electric and magnetic o fields; direction of propagation is perpendicular to
both Classification of electromagnetic spectrum, photon energy E
PHY 202 & CHM 123
159
= (hf) Visual spectrum, color
Molecular Structure and Absorption Spectra Infrared region
o Intramolecular vibrations and rotations o Recognizing common characteristic group
absorptions, fingerprint region Visible region
o Absorption in visible region gives complementary color (e.g., carotene)
o Effect of structural changes on absorption (e.g., indicators)
Ultraviolet region o π-electron and non-bonding electron transitions o Conjugated systems
NMR spectroscopy o Protons in a magnetic field; equivalent protons o Spin-spin splitting
CHM 313
Geometrical Optics Reflection from plane surface: angle of incidence equals
angle of reflection Refraction, refractive index n, Snell’s law: n1 sin θ1 = n2 sin θ2 Dispersion, change of index of refraction with wavelength Conditions for total internal reflection Spherical mirrors
o Center of curvature o Focal length o Real and virtual images
Thin lenses o Converging and diverging lenses o Use of formula 1/p + 1/q = 1/f, with sign
conventions o Lens strength, diopters
Combination of lenses Lens aberration Optical Instruments, including the human eye
PHY 202 & BIO 442, 442L, 475, 475L
Content Category 4E: Atoms, nuclear decay, electronic structure, and atomic chemical behavior
Atomic Nucleus Atomic number, atomic weight Neutrons, protons, isotopes Nuclear forces, binding energy Radioactive decay
o α, β, γ decay o Half-life, exponential decay, semi-log plots
Mass spectrometer
CHM 123
Electronic Structure Orbital structure of hydrogen atom, principal quantum
PHY 202 & CHM 123
160
number n, number of electrons per orbital Ground state, excited states Absorption and emission line spectra Use of Pauli Exclusion Principle Conventional notation for electronic structure Bohr atom Effective nuclear charge Photoelectric effect
PHY202 does not cover items in nuclear physics.
The Periodic Table - Classification of Elements into Groups by Electronic Structure
Alkali metals Alkaline earth metals: their chemical characteristics Halogens: their chemical characteristics Noble gases: their physical and chemical characteristics Transition metals Representative elements Metals and non-metals Oxygen group
CHM 123
The Periodic Table - Variations of Chemical Properties with Group and Row
Valence electrons First and second ionization energy
o Definition o Prediction from electronic structure for elements in
different groups or rows Electron affinity
o Definition o Variation with group and row
Electronegativity o Definition o Comparative values for some representative
elements and important groups Electron shells and the sizes of atoms Electron shells and the sizes of ions
CHM 123
Stoichiometry Molecular weight Empirical versus molecular formula Metric units commonly used in the context of chemistry Description of composition by percent mass Mole concept, Avogadro’s number NA Definition of density Oxidation number
o Common oxidizing and reducing agents o Disproportionation reactions
Description of reactions by chemical equations o Conventions for writing chemical equations o Balancing equations, including redox equations o Limiting reactants
CHM 123, BIO 442L
161
o Theoretical yields
Content Category 5A: Unique nature of water and its solutions
Acid/Base Equilibria Bronsted-Lowry definition of acid, base Ionization of water
o Kw, its approximate value (Kw = [H+][OH–] = 10-14 at 25°C, 1 atm)
o Definition of pH: pH of pure water Conjugate acids and bases (e.g., NH4
+ and NH3) Strong acids and bases (e.g., nitric, sulfuric) Weak acids and bases (e.g., acetic, benzoic)
o Dissociation of weak acids and bases with or without added salt
o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids
or bases Equilibrium constants Ka and Kb: pKa, pKb Buffers
o Definition and concepts (common buffer systems) o Influence on titration curves
CHM 124, 451
Ions in Solutions Anion, cation: common names, formulas and charges for
familiar ions (e.g., NH4+ ammonium, PO43– phosphate, SO42–
sulfate) Hydration, the hydronium ion
CHM 123
Solubility Units of concentration (e.g., molarity) Solubility product constant; the equilibrium expression Ksp Common-ion effect, its use in laboratory separations
o Complex ion formation o Complex ions and solubility o Solubility and pH
CHM 124, BIO 442L
Titration Indicators Neutralization Interpretation of the titration curves Redox titration
CHM 123, 124, 451
Content Category 5B: Nature of molecules and intermolecular interactions
Covalent Bond Lewis Electron Dot formulas
o Resonance structures o Formal charge o Lewis acids and bases
Partial ionic character o Role of electronegativity in determining charge
CHM 123, 313
162
distribution o Dipole Moment
σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective
geometries o Valence shell electron pair repulsion and the
prediction of shapes of molecules (e.g., NH3, H2O, CO2)
o Structural formulas for molecules involving H, C, N, O, F, S, P, Si, Cl
o Delocalized electrons and resonance in ions and molecules
Multiple bonding o Affect on bond length and bond energies o Rigidity in molecular structure
Stereochemistry of covalently bonded molecules o Isomers
Structural isomers Stereoisomers (e.g., diastereomers,
enantiomers, cis/trans isomers) Conformational isomers
o Polarization of light, specific rotation o Absolute and relative configuration
Conventions for writing R and S forms Conventions for writing E and Z forms
Liquid Phase - Intermolecular Forces Hydrogen bonding Dipole Interactions Van der Waals’ Forces (London dispersion forces)
CHM 124
Content Category 5C: Separation and purification methods Separations and Purifications
Extraction: distribution of solute between two immiscible solvents
Distillation Chromatography
o Basic principles involved in separation process Column chromatography, gas-liquid
chromatography High pressure liquid chromatography
o Paper chromatography o Thin-layer chromatography
Separation and purification of peptides and proteins o Electrophoresis (BIO 442L) o Quantitative analysis o Chromatography
Size-exclusion Ion-exchange Affinity
Racemic mixtures, separation of enantiomers
CHM 313, 451, 462L
163
Content Category 5D: Structure, function, and reactivity of biologically-relevant molecules
Nucleotides and Nucleic Acids Nucleotides and nucleosides: composition
o Sugar phosphate backbone o Pyrimidine, purine residues
Deoxyribonucleic acid: DNA, double helix Chemistry Other functions
BIO 151, 151L, 312, 312L & CHM 314, 451, 452
Amino Acids, Peptides, Proteins Amino acids: description
o Absolute configuration at the α position o Dipolar ions o Classification
Acidic or basic Hydrophilic or hydrophobic
o Synthesis of α-amino acids Strecker Synthesis Gabriel Synthesis
Peptides and proteins: reactions o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis
General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins o o Isoelectric point
CHM 314, 451
The Three-Dimensional Protein Structure Conformational stability
o Hydrophobic interactions o Solvation layer (entropy)
4° quaternary structure Denaturing and Folding
CHM 451
Non-Enzymatic Protein Function Binding Immune system Motor (BIO 442)
CHM 451
Lipids Types
o Storage Triacyl glycerols Free fatty acids: saponification
o Structural Phospholipids and phosphatids Sphingolipids Waxes
o Signals/cofactors
CHM 420, 451, 452
164
Fat-soluble vitamins Steroids Prostaglandins
Carbohydrates Description
o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers
Hydrolysis of the glycoside linkage Keto-enol tautomerism of monosaccharides Disaccharides Polysaccharides
CHM 314, 451
Aldehydes and Ketones Description
o Nomenclature o Physical properties
Important reactions o Nucleophilic addition reactions at C=O bond
Acetal, hemiacetal Imine, enamine Hydride reagents Cyanohydrin
o Oxidation of aldehydes o Reactions at adjacent positions: enolate chemistry
Keto-enol tautomerism (α-racemization) Aldol condensation, retro-aldol Kinetic versus thermodynamic enolate
General principles o Effect of substituents on reactivity of C=O; steric
hindrance o o Acidity of α-H; carbanions
CHM 314
Alcohols Description
o Nomenclature o Physical properties (acidity, hydrogen bonding)
Important reactions o Oxidation o Protection of alcohol o Preparation of mesylates and tosylates
CHM 313
Carboxylic Acids Description
o Nomenclature o Physical properties
Important reactions o Carboxyl group reactions
Amides (and lactam), esters (and lactone), anhydride formation
Reduction
CHM 314
165
Decarboxylation Reactions at 2-position, substitution
Acid Derivatives (Anhydrides, Amides, Esters) Description
o Nomenclature o Physical properties
Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides
General principles o Relative reactivity of acid derivatives o Steric effects o Electronic effects o Strain (e.g., β-lactams)
CHM 314
Phenols Oxidation and reduction (e.g., hydroquinones), ubiquinones:
biological 2e- redox centers
CHM 314, 452
Polycyclic and Heterocyclic Aromatic Compounds Biological aromatic heterocycles
CHM 314
Content Category 5E: Principles of chemical thermodynamics and kinetics
Enzymes Classification by reaction type Mechanism
o Substrates and enzyme specificity o Active site model o Induced-fit model o Cofactors, coenzymes and vitamins
Kinetics o General (catalysis) o Michaelis-Menten o Cooperativity o Effects of local conditions on enzyme activity
Inhibition Regulatory enzymes (BIO 411)
o Allosteric o Covalently modified
BIO 151, 151L, 312, 312L, 403, 403L & CHM 451, 452, 462L
Principles of Bioenergetics Bioenergetics/thermodynamics
o Free energy/Keq o Concentration
o ATP hydrolysis ΔG << 0 o ATP group transfers
Biological oxidation–reduction o Half-reactions o Soluble electron carriers
CHM 451
166
o Flavoproteins
Phosphorus Compounds Description, structure of phosphoric acids
CHM 314
Energy Changes in Chemical Reactions - Thermochemistry, Thermodynamics
Thermodynamic system – state function Zeroth Law – concept of temperature First Law: ΔE = Q – W (conservation of energy) Second Law – concept of entropy
o Entropy as a measure of “disorder” o Relative entropy for gas, liquid, and crystal states
Measurement of heat changes (calorimetry), heat capacity, specific heat
Heat transfer – conduction, convection, radiation Endothermic/exothermic reactions
o Enthalpy, H, and standard heats of reaction and formation
o Hess’ Law of Heat Summation Bond dissociation energy as related to heats of formation Free energy: G Spontaneous reactions and ΔG° Coefficient of expansion Heat of fusion, heat of vaporization Phase diagram: pressure and temperature
CHM 123, 124
Rate Processes in Chemical Reactions - Kinetics and Equilibrium
Reaction rate Dependence of reaction rate upon concentration of
reactants o Rate law, rate constant o Reaction order
Rate-determining step Dependence of reaction rate upon temperature
o Activation energy Activated complex or transition state Interpretation of energy profiles showing
energies of reactants, products, activation energy, and ΔH for the reaction
o Use of the Arrhenius Equation Kinetic control versus thermodynamic control of a reaction Catalysts Equilibrium in reversible chemical reactions
o Law of Mass Action o Equilibrium Constant o Application of Le Châtelier’s Principle
Relationship of the equilibrium constant and ΔG°
CHM 124
167
Psychological, Social, and Biological Foundations of Behavior Content Category 6A: Sensing the environment Sensory Processing
Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation
Sensory receptors o Sensory pathways o Types of sensory receptors
PSY101, 323 & BIO 415, 475
Vision Structure and function of the eye Visual processing
o Visual pathways in the brain o Parallel processing o Feature detection
PSY 101, 323, 422 & BIO 415, 442, 442L, 475, 475L
Hearing Auditory processing
o Auditory pathways in the brain Sensory reception by hair cells
PSY 101, 323, 422 & BIO 415, 475, 475L
Other Senses Somatosensation
o Pain perception Taste
o Taste buds/chemoreceptors that detect specific chemicals
Smell o Olfactory cells/chemoreceptors that detect specific
chemicals o Pheromones o Olfactory pathways in the brain
Kinesthetic sense Vestibular sense
PSY 101, 323, 422 & BIO 415, 442, 475, 475L
Perception Perception
o Bottom-up/Top-down processing o Perceptual organization (e.g., depth, form, motion,
constancy) o Gestalt principles
PSY 101, 321, 323
Content Category 6B: Making sense of the environment Attention
Selective attention Divided attention
PSY 101, 321, 322, 323
Cognition Information-processing model
PSY 101, 321, 351 & BIO 415
168
Cognitive development o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive
development Biological factors that affect cognition Problem solving and decision making
o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion
Overconfidence and belief perseverance Intellectual functioning
o Multiple definitions of intelligence o Influence of heredity and environment on
intelligence o Variations in intellectual ability
Consciousness States of consciousness
o Alertness o Sleep
Stages of sleep Sleep cycles and changes to sleep cycles Sleep and circadian rhythms Dreaming Sleep disorders
o Hypnosis and meditation Consciousness altering drugs
o Types of consciousness altering drugs and their effects on the nervous system and behavior
o Drug addiction and the reward pathway in the brain
PSY 101, 321, 422 & BIO 415
Memory Encoding
o Process of encoding information o Processes that aid in encoding memories
Storage o Types of memory storage (e.g., sensory, working,
long-term) o Semantic networks and spreading activation
Retrieval o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories
Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease,
Korsakoff’s syndrome)
PSY 101, 321 & BIO 415
169
o Decay o Interference o Memory construction and source monitoring
Changes in synaptic connections underlie memory and learning (BIO 403)
o Neural plasticity o Memory and learning o Long-term potentiation
Language Theories of language development (e.g., learning, Nativist,
Interactionist) Influence of language on cognition Different brain areas control language and speech
PSY 101, 321, 351 & BIO 415
Content Category 6C: Responding to the world Emotion
Three components of emotion (i.e., cognitive, physiological, behavioral)
Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness)
Adaptive role of emotion Theories of emotion
o James-Lange theory o Cannon-Bard theory o Schachter-Singer theory
The role of biological processes in perceiving emotion o Generation and experience of emotions involve
many brain regions o The role of the limbic system in emotion (BIO 403) o Emotional experiences can be stored as memories
that can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional
experience, and is also important in o temperament and decision making o Emotion and the autonomic nervous system (BIO
403) o Physiological markers of emotion (signatures of
emotion)
PSY 101, 366 & BIO 415
Stress The nature of stress
o Appraisal o Different types of stressors (e.g., cataclysmic events,
personal, etc.) o Effects of stress on psychological functions
Stress outcomes/response to stressors o Physiological o Emotional o Behavioral
Managing stress (e.g., exercise, relaxation techniques,
PSY 101, 351, 366, 422 & BIO 415
170
spirituality, etc.)
Content Category 7A: Individual influences on behavior Biological Bases of Behavior
The nervous system (BIO , 442, 442L, 475, 475L) o Neurons
The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system
The brain o The brainstem o The cerebellum o The diencephalon o The cerebrum o Control of voluntary movement in
the cerebral cortex o Information processing in the
cerebral cortex o Lateralization of cortical functions o Methods of studying the brain
Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system (BIO 475, 475L)
o Components of the endocrine system o Effects of the endocrine system on behavior
Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental
influences Genetic and environmental factors contribute to the
development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural
populations Human physiological development
o Prenatal development o Motor development o Developmental changes in adolescence
PSY 101, 321, 322, 323, 351, 366, 422 BIO 312, 415
Personality Theories of personality
o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective
Situational approach to explaining behavior
PSY 101, 366
171
Psychological Disorders Understanding psychological disorders
o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders
Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders o Schizophrenia o Dissociative disorder o Personality disorders
Biological bases of nervous system disorders (BIO 442) o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-based therapy to regenerate neurons in
CNS
PSY 101, 366, 422
Motivation Factors that influence motivation
o Instinct o Arousal o Drives
Negative feedback systems o Needs
Theories that explain how motivation affects human behavior
o Drive reduction theory o Incentive theory o Other: cognitive and need based theories
Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.)
o Biological factors in regulation of these motivational processes
o Socio-cultural factors in regulation of these motivational processes
PSY 101, 366
Attitudes Components of attitudes (i.e., cognitive, affective, and
behavioral) The link between attitudes and behavior
o Processes by which behavior influences attitudes (e.g., foot-in-the door phenomenon,
o role-playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory
PSY 101, 341, 366
172
Content Category 7B: Social processes that influence human behavior
How the Presence of Others Affects Individual Behavior Social facilitation Deindividuation Bystander effect Social loafing Peer pressure
PSY 101, 341, 366 & SOC 340
Group Processes Group polarization Groupthink
PSY 101, 341 & SOC 340
Culture Assimilation Multiculturalism Subcultures
PSY 341 & SOC 101
Socialization Definition of socialization Norms Agents of socialization (e.g., the family, mass media, peers,
workplace) Stigma and deviance Conformity and obedience
PSY 101, 341 SOC 101 SOC 101 SOC 101 SOC 101, 325 SOC 325, 340
Content Category 7C: Attitude and behavior change Habituation and Dishabituation
PSY 101, 322, 351
Associative Learning Classical conditioning
o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous
recovery, generalization, discrimination Operant conditioning
o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary,
conditional o Reinforcement schedules: fixed-ratio, variable-ratio,
fixed-interval, variable-interval o Punishment o Escape and avoidance learning
Cognitive processes that affect associative learning Biological factors that affect associative learning
o Innate behaviors are developmentally fixed o Learned behaviors are modified based on
experiences o Development of learned behaviors
PSY 101, 322, 351 BIO 415
Observational Learning Modeling
PSY 101, 322, 351
173
Biological processes that affect observational learning o Mirror neurons o Role of the brain in experiencing vicarious emotions
Applications of observational learning to explain individual behavior
Theories of Attitude and Behavior Change Elaboration Likelihood Model
o Information processing routes to persuasion (e.g., central and peripheral route processing)
Social Cognitive theory Factors that affect attitude change (e.g., changing behavior,
characteristics of the message and target, social factors)
PSY PSY 101, 341
Content Category 8A: Self-identity Self-Concept and Identity
Definitions of self-concept, identity, and social identity The role of self-esteem, self-efficacy, and locus of control in
self-concept and self-identity Different types of identities (e.g., race/ethnicity, gender,
age, sexual orientation, class)
PSY 101, 341, 351, 361 & SOC 340, 341
Formation of Identity Stages of identity development
o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud)
Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-taking) o Influence of group (e.g., reference group)
Influence of culture and socialization on identity formation
PSY 101, 341, 351, 361 SOC 340 SOC 340 SOC 340 & 341 SOC 340 & 341 SOC 101 & 340
Content Category 8B: Social thinking Attributing Behavior to Persons or Situations
Attribution theory o Fundamental attribution error o How culture affects attributions
How self-perceptions shape our perceptions of others How perceptions of the environment shape our perceptions
of others
PSY 101, 341, 366
Prejudice and Bias Definition of prejudice Processes that contribute to prejudice
o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice
Stereotypes Ethnocentrism
o In-group and out-group o Ethnocentrism vs. cultural relativism
PSY 101, 341 & SOC 101, 328PS PSY 101, 341 SOC 101 SOC 328, 339 SOC 101 & ANT 150 SOC 101 & ANT 150
Processes Related to Stereotypes Self-fulfilling prophecy
PSY 101, 341
174
Stereotype threat
Content Category 8C: Social interactions Elements of Social Interaction
Statuses Roles Groups Networks Organizations
PSY 101, 341 & SOC 101, 340
Self-presentation and Interacting with Others Expressing and detecting emotion
o Gender shapes expression (SOC 322,332) o Culture shapes expression (ANT 150)
Impression management o Front stage vs. back stage self (Dramaturgical
approach) Verbal and nonverbal communication (ANT 315) Animal signals and communication
PSY 101, 341 & SOC 340, 341 SOC 322, 332 ANT 150 SOC 341 ANT 315
Social Behavior Attraction Aggression Attachment Social support Biological explanations of social behavior in animals
o Foraging behavior o Mating behavior and mate choice o Applying game theory o Altruism o Inclusive fitness
PSY 101, 341
Discrimination Individual vs. institutional discrimination The relationship between prejudice and discrimination How power, prestige, and class facilitate discrimination
PSY 101 & SOC 101, 339
Content Category 9A: Understanding social structure Theoretical Approaches
Functionalism Conflict theory Symbolic interactionism Social constructionism
SOC 101, 303
Social Institutions Education Family Religion Government and economy Health and medicine
SOC 101 SOC 101, 331 SOC 101, 334 SOC 101, 337 SOC 101
Culture Material culture Symbolic culture
SOC 101 & ANT 150 SOC 101 & ANT 150 & PSY
175
o Language and symbols o Values and beliefs o Norms and rituals
Culture and social groups Evolution and human culture
368, 443 SOC 340 & ANT 315 SOC 101 & ANT 150 SOC 101 & ANT 150 SOC 101 & ANT 150 ANT 300 & PSY 443
Content Category 9B: Demographic characteristics and processes
Demographic Structure of Society Age Gender Race and ethnicity Immigration status Sexual orientation
SOC 101, 330 SOC 101, 332 SOC 101, 328 SOC 368 SOC 333, 322
Demographic Shifts and Social Change Demographic transition Fertility, migration, and mortality Social movements Globalization Urbanization
SOC 101 SOC 101 SOC 342 SOC 101, 435 SOC 351
Content Category 10A: Social inequality Spatial Inequality
Residential segregation (neighborhoods) Environmental justice (location and exposure to health
risks) Global inequalities
SOC 351 SWK 335 SOC 101, 435
Social Class Aspects of social stratification
o Class, status, and power o Cultural capital and social capital o Social reproduction o Privilege and prestige o Intersections with race, gender and age
Patterns of social mobility o Intergenerational and intragenerational mobility o Downward and upward mobility o Meritocracy
Poverty o Relative and absolute o Social exclusion (segregation and isolation)
SOC 101, 339
Health Disparities Race, gender, and class inequalities in health
PSY 366
Healthcare Disparities Race, gender, and class inequalities in healthcare
PSY 366