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Bio logy 10 Introduct ion I. Biology – study of all types of living organisms

a. Zoology – study of animals i. Protista (or Protoctista)

b. Botany – study of plants i. Bacteria/Monera ii. Fungi

II. Allied Sciences a. Anatomy – structure of organisms b. Physiology – function of parts c. Histology – tissues d. Molecular Bio. – cells, cellular activities, biomolecules of living

systems (DNA, proteins) e. Ecology – interaction between organisms and environment f. Genetics – heredity and variation; transmission of traits from

parents to children through chromosomes (containing genes) g. Systematics (sp. Taxonomy) – identification and classification of

organisms; sys.: takes into account the phylogenetic relationships – how close or far two organisms are

h. Developmental Bio. – Embryology: development from the zygote and to the different processes used to achieve the same stage as parent organisms

i. Evolution – genetic change in population j. Mammalogy – mammals k. Herpetology – amphibians and reptiles (vertebrata) l. Ichthyology – fishes m. Ornithology – birds n. Parasitology – parasites

i. Ecto- ii. Endo-

o. Entomology – insects p. Malacology – mollusks

i. With shells 1. Bivalves 2. Single valves

ii. W/o shells 1. Squids, slugs

III. Six (6) Kingdom System

a. Protista i. Dinoflagellates ii. Radiolarians

b. Eubacteria i. Spherical (cocci) ii. Bacillus (rod-like shapes) iii. Spirilla (helical)

c. Archaebacteria i. Thermoplasma ii. Methanogens

IV. Three (3) Domain System

a. Unicellular and Prokaryotic i. Eubacteria ii. Archaebacteria

b. Multicellular and Eukaryotic i. Eukaryotes

V. The Scientific Method a. A systematic way of problem-solving b. Steps:

i. Observation of Natural Phenomenon ii. Define the problem

1. What is the causative agent? What is the driving mechanism?

iii. Formulate hypotheses 1. Null hypothesis

iv. Testing the hypotheses 1. Surveying or experimenting 2. Experiment set-up should contain Control and

Experimental Groups a. Two groups w/ identical conditions except for

the variable that need to be tested i. Independent Variable – condition that

affects or causes the result ii. Dependent Variable – outcome due to the

absence or presence of the independent variable

iii. Extraneous Variable – things that must be kept constant between the different set-ups to ensure that only the independent variable is affecting the result

v. Conclusion 1. Statement that evaluates the hypothesis based on

the test results vi. Publish (journal) or orally present (conference or seminar)

results to share with the scientific community c. Theory – statement supported by numerous evidences and

has been continuously tested by various scientist over a long period of time i. Example: Biogenesis

d. Principle – universal statement that has not yet been disproven despite testing through different methods (biochemical, morphological, etc.)

VI. Unifying Concepts of Life a. Hierarchy of Organization – highly structured

i. Atoms ii. Molecules – a chem’l structure consisting of 2 or more

different elements iii. Organelles – various functional components in a cell iv. Cells – life’s fundamental unit of structure and function; a

single cell can perform all the function of life. 1. An organism can be unicellular or multicellular; in a

multicellular organism there is a division of labor through specialization

v. Tissues – a group of cells that work together to perform a specialized function

vi. Organs & Organ System 1. Organ: a body part which carries out a particular

function 2. Organ System: a team of organs that cooperate in a

larger function vii. Organism – individual living things

Nucleus? Cell

Structure Kingdom Mode of Nutrition

C. W. Composition

Eukaryotic Multicellular

Animalia h: ingestion

Plantea a: self-feeding Cellulose

Fungi h: absorptive - saprotrophs

Chitin

Protista a&h: ingestion and photosynthesis

Prokaryotic Unicellular Eubacteria a: photo- or

chemosynthetic

Peptidoglycan

Archaebacteria

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viii. Population – all the individuals of a species w/in a community’s specified area

ix. Communities – array of species inhabiting an ecosystem x. Ecosystem – biotic and abiotic components which life

interacts with xi. Biosphere – all life on Earth and all the places where life

exists. b. Metabolism – sum total of physical and chemical reactions

i. Involves energetics: endergonic and exergonic ii. Types

1. Anabolism – synthesis of large molecules a. Protein synthesis (from amino acids)

2. Catabolism – breakdown of large molecules a. Digestion

3. Anabolism > Catabolism – growth 4. Catabolism > Anabolism – disease or death

c. Growth and Development i. Development – orderly sequence of changes to form an

adult organism ii. Growth – increase in size and number of cells iii. Adults – capable of reproduction

d. Reproduction – perpetuation of species i. Asexual – division, budding, fragmentation ii. Sexual – Egg Cell + Sperm Cell à zygote

e. Responsiveness – tropism (plants) / taxis (animals) i. Adjustment – short-term response

f. Evolution – genetic changes in population over a long period of time i. Adaptation – long-term response

g. Homeostasis – maintenance of constant internal milieu Chemistry of L i fe VII. Inorganic

a. Elements i. Molecules – made up to of 2 same atoms ii. Compound – made up of 2 or more different elements iii. Fe – present in hemoglobin (responsible for the oxygen

carrying capacity of RBCs) iv. Zn – component of most enzymes v. Bonds

1. Ionic 2. Covalent 3. Hydrophobic – bond between 2 nonpolar molecules

vi. John Dalton – Cell Theory: all elements that make up of matter are composed of atoms

vii. Niels Bohr – system of static rings and electrons b. Water – life began in seas and oceans; 75% of the earth; cells

are 65% water i. Characteristics

1. High polarity – reacts with ions and polar compounds; good solvent a. Forms hydration cells around salts

2. Cohesive and Adhesive a. Cohesive – attraction of 2 similar molecules

i. Cohesion is the bonding of H2O molecules resulting to water heating/cooling more slowly - High specific heat capacity

b. Adhesive – attraction of 2 different molecules i. Adhesion – H2O molecules are attracted to

solid surfaces – capillarity of water

3. Surface Tension – due to cohesion of water molecules; so much so that they aren’t that attracted to air molecules

4. Capillarity – rising of water in narrow tubes; due to adhesion of water molecules a. H2O molecules is attracted to one another à

H2O molecules near the tube are attracted to the tube making the “sides” rise à H2O is still attracted to one another making it rise with the “side” molecules à repeat cycle à water rises!

5. Thermal a. High Specific Heat – important to maintain body

temp and survival of aquatic organism (ocean and sea temperature can be maintained)

b. High Heat of Vaporization – 540 kcal/mole; important for it’s cooling effect: sweating

c. Maximum Density at 4 Celsius – water expands below that temperature because it assumes a crystalline structure (ice)

d. Optimum pH level = 7.35 c. Acid, Base, and Buffer System

i. Acids – substances that dissociate to increase hydrogen ion concentration in solution; a proton donor; an electron pair acceptor 1. Coma: body pH > 7

ii. Bases – substances that dissociate to increase hydronium ion concentration in solution; proton acceptor; electron pair donor 1. Tetany: body pH < 7

iii. Buffer System 1. A solution in equilibrium that contains both hydrogen

and hydronium ions that can counteract the addition of and acid or base so that the system can maintain it’s pH level

2. Carbonate and Bicarbonate system in blood maintains the blood pH at 7.35

d. Our body needs 25 of 92 of natural elements in order to function

VIII. Organic a. C, H, O, N elements compose 92% of living matter b. Functional Groups – dictates the properties and activities of

molecules

c. Carbohydrates – (CH2O)n; glycocidic bonds (bonding of glucose units) i. Monosaccharide

1. Trioses (3 C), tetroses (4 C), pentoses (5 C) 2. Hexoses (6 C): glucose, fructose, and galactose

a. Glucose: primary energy source ii. Disaccharide

H C O N S P

Hydrocarbons

Carbohydrates and lipids

Amino acids and proteins

More amino acids and proteins

Nucleic acid (RNA and DNA)

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1. Formed through dehydration synthesis (joining of 2 molecules and elimination of H2O; opposite of hydrolysis) a. Maltose = glucose + glucose b. Lactose = glucose + galactose c. Sucrose = glucose + fructose

iii. Oligosaccharide 1. Complex carbohydrates composed of proteins and

lipids 2. Glycoprotein/glycolipid – molecular ID of the cell

iv. Polysaccharides 1. Cellulose, glycogen, chitin which are composed of

repeating subunits of glucose v. Function:

1. Immediate source of energy 2. Component of cell membrane 3. Structural component of insect skeleton 4. Cell communication

vi. Sugar 1. Cellulose – unbranched; straight (makes it rigid; for

protection, support, and definite shape) d. Lipids – CHO; insoluble in water since nonpolar

i. Neutral Fats – glycerol (3C compounds) and 1, 2, or 3 fatty acids (composed of hydrocarbon chains)

ii. Phospholipids – glycerol attached to 2 fatty acids and a PO4 group 1. Sphingolipids – myelin sheath neurons

iii. Carotenoids – 5 C monomer (isoprene) 1. Red and yellow pigments in plants 2. If split in half: yields vitamin A or retinol

iv. Waxes – glycerol _ long chains of alcohol 1. Cuticle – made of cutin molecules

v. Steroids – no fatty acid tails 1. Variable functional group 2. 4 interlocking C rings 3. examples: cholesterol, vitamin D, sex hormones, bile

salts vi. Saturated – animals vii. Unsaturated – plants

1. MUFA – olive, canola, peanut, and sesame oil 2. PUFA – corn, walnut, sunflower, soybean

viii. VCO is rich lauric acid à monolaurin found in breast milk ix. Sterols – differ in number, position, and type of their

functional group x. Functions

1. Structural component of cell membrane 2. Insulation – brown (infants) and white adipose (fat

tissues) 3. Reserve energy – blubber (Esp. in sea animals like

seals etc..) 4. Source of se hormones - estrogen

e. Proteins – a hydrocarbon w/ an amino & carboxylic group i. Peptide bonds – link amino acids together ii. Structural Hierarchy of Proteins

1. Primary – specific sequence of amino acids; a protein 2. Secondary – coiling or folding of it’s polypeptide

chains; H-bond formation between carboxyl and amino groups of non-adjacent amino acids – R groups are not involved a. Alpha helix – like keratin

b. Beta – pleated sheets – like silk-fibroid 3. Tertiary – 3D structure resulting from the folding of

secondary structures; stabilized by bonds (disulfide bonds?) formed by R groups and amino acids

4. Quaternary a. Made up of 2 or more polypeptides (tertiary

structures) fused to form hemoglobin (2 alpha helix and 2 polypeptide chains) and collagen (3 polypeptide chains)

iii. Denaturation results in the unfolding of structures iv. Functions:

1. Catalytic proteins/Enzymes 2. Storage (ovalbumin, casein, seed protein) 3. Transport (hemoglobin, myoglobin, serum albumin) 4. Contractile (for muscles; myosin and actin) 5. Protective (fibrinogen and thrombin – clotting of

blood) 6. Toxins 7. Hormones – insulin 8. Structural (collagen, elastin, keratin, glycoprotein)

f. Nucleic Acid – nucleotides i. Sugar – deoxyribose (1 less O atom) ii. Phosphate iii. Nitrogen iv. Structures

1. 2 Ring – Purine: Adenine, Guanine 2. Single Ring – Pyrimidine: Cytosine, Thymine, Uracil

v. N – base + Sugar (neoside) vi. Chargaff’s Rule – ensure the correct base pairing

1. A – T (2 H bonds) 2. G – C (3 H bonds)

vii. Phosphodiester bonds – links nucleotides viii. Derivatives

1. Energy Carrier – ADP, ATP 2. Coenzyme – NAD (Nicotinamide Adenine

Dinucleotide) and FA (Flavin Adenine Dinucleotide) a. Coenzymes carry chemical groups between

enzymes; organic, non-protein, aids in enzyme function i. Cofactors – inorganic, non-protein, enzyme

catalysts 3. Signaling Molecule – CAMP (cyclid adenosine

monophosphate) 4. Nucleic Acid – storage of biological info

IX. Central Dogma of Biology a. DNA à mRNA à proteins à phenotype b. DNA Replication

i. Mirror images – 2 DNA’s formed ii. Semi-conservative type of duplication

The Ce l l X. Basic structural (all living things are made up of cells) and functional

(Exhibits all properties and activities of life) unit. a. Anton van Leeuwenhoek – protozoa, sperm b. Robert Hooke – cork cells (cellula) c. Theodore Schwann – all animal are made up of cells d. Matthias Schleiden – all plants are made up of cells e. Rudolf Virchow – cells arise from the division of pre-existing

cells f. Felix Dujardin – sarcode

XI. The Cell Theory

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a. All living things are composed of cells (X.c. and X.d.) b. Cells are the basic unit of structure and function in living things c. All cell come from pre-existing cells. (X.e.)

XII. Two Types:

a. Viruses – can’t reproduce outside a host i. An obligate parasite w/ a protein coat and nucleic acid

(DNA and RNA) b. Eukaryotes have compartmentalization via and endomembrane

system and specialization of functions bought about by the presence of membrane-bound organelles

c. Organelles i. Only in animals

1. Centrioles 2. Lysosomes – digestive organelle where

macromolecules are hydrolyzed ii. Only in plants

1. Vacuoles – storage tanks of the cell a. S: membrane – enclosed sac b. F: store H2O, salts, proteins, CH2O

2. Cell Walls 3. Chloroplasts – plastid: organelles that store food and

pigment XIII. Cell Structure and Function

a. Cell Membrane (Singer or Nicholson) i. Fluid Mosaic Model

1. Fluid – phospholipid bilayer: a trilaminar structure a. e- dense protein – clear structure of lipids – e-

dense protein b. Bilipid layer – allows only uncharged, non-polar,

small molecules and water c. Oligosaccharides – glycoproteins and lipids

i. Cell wall recognition/communication ii. Molecular ID of the cell

d. Proteins – extrinsic, integral and trans-proteins that transport molecules in and out of the cell

2. Mosaic – integrated proteins and molecules a. Extrinsic – proteins are outside b. Integral – proteins are inside

ii. Functions: 1. Separates cells from surroundings 2. Regulates the entrance and exit of substances 3. Protects and supports the cell

b. Cell Wall (only in plants) i. Has three (3) layers

1. Primary Cell Wall a. Thin and flexible; fibrous and elastic cellulose

2. Middle lamella a. Thin layer; rich in polysaccharides called pectin b. Acts as the glue

3. Upon maturation cells strengthens its cell walls a. Secretion of hardening substances into the

Primary C.W. b. Addition of a Secondary Cell Wall

i. Plants = cellulose + lignin ii. Fungi = chitin

iii. Prokaryotes = CH2Os + polypeptides c. Nucleus

i. Enclosed by a nuclear envelope 1. Double-membrane with pores

a. 2 bilipid layers with a space of 20-40 nm b. Pores are 100 nm in diameter

2. Nuclear side is line with a Nuclear Lamina a. Netlike array of protein filament for shape and

support b. Nuclear Matrix (?) – network of protein fibers

3. Chromosomes (carry genetic info) made of chromatin (complex of DNA and protein) a. 46 in somatic cells b. 23 in sex cells

ii. Nucleolus 1. Mass of densely stained granules and fibers adjoining

part of the chromatin d. Cytoplasmic Organelles

i. Ribosomes 1. RNA + protein 2. Protein factories

ii. Endoplasmic (w/in the cytoplasm) Reticulum (network) 1. Extensive internal membrane 2. Rough ER

a. Rough due to the presence of ribosomes; connected to the nuclear envelop

b. Protein synthesis and modification 3. Smooth ER

a. Smooth walls b. Synthesis of lipids, packaging of proteins into

vesicles, metabolism of carbohydrates, detoxification (for the liver), storage of calcium ions

iii. Golgi Apparatus – shipping and receiving center 1. Packages and distributes synthesized molecules 2. Has a cis face (the receiving; located near ER) and a

trans face (the transporting) 3. Cisternal Maturation Model

iv. Lysosome 1. Membranous sac of hydrolytic enzymes use for

digestion of macromolecules

Eukaryotic Prokaryotic

0.1 – 10 µm 10 – 100 µm

No membrane bound organelles; no nucleus

Organelles are membrane bound; true nucleus

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a. Endocytosis: cells engulf microscopic particles b. Phagocytosis: cell engulfs particle by wrapping

pseudopodia around it and taking it into the cell c. Autophagy: cell recycles its own materials

v. Vacuoles 1. Membrane enclosed sac for storage

e. Mitochondria and Chloroplasts i. Mitochondria’s 2 Layers

1. Outer layer – acts as envelope 2. Inner layer – has many folds to increase surface area 3. Site of cellular respiration

a. Glucose + 6 O2 à 6 CO2 + 6 H2O + ATP i. ATP: Adenosine Triphosphate

4. The power house of the cell ii. Chloroplasts are plant organelles (plastids) that store food

and pigment 1. Site of photosynthesis

a. 6 CO2 + 6 H2O + light à Glucose + 6 O2 f. Cytoskeleton

i. Made up of microtubules 1. Hollow tubes made of protein 2. Cilia – short thread-like structure for cell movement

and movement of substances along cell surface 3. Flagella

ii. Supports cell structure and drives cell movements XIV. Cell Membrane Transport

a. Non-mediated / Passive i. Movement of small molecules from a region of high

concentration to a region of lower concentration ii. Energy is not required

1. Diffusion – dependent on concentration gradient 2. Osmosis – movement of water across cell

membranes a. In animals

i. Hypertonic – high concentration of salt outside of cell à influx of water; causes lysis

ii. Isotonic – cell is normal iii. Hypotonic – high concentration of salt

inside the cell à water rushes out; shriveled

b. In plants i. Hypertonic – turgid (normal) ii. Isotonic – flaccid iii. Hypotonic - plasmolysis

3. Dialysis b. Mediated / Active

i. Movement from low concentration region to a higher concentration

ii. Energy is used up iii. Requires a carrier protein iv. Types

1. Uniport – 1; one direction

2. Symport – 2; one direction 3. Antiport – 2; two directions

c. Facilitated – requires transport proteins d. Bulk Transport – movement of large molecules with the use

of vesicles i. Endocytosis

1. Phagocytosis – cell-eating 2. Pinocytosis – cell-drinking 3. Receptor-mediated endocytosis

ii. Exocytosis XV. The Cell Cycle

a. Important Terms: i. Cell division – the basis of the continuity of life ii. Genome – a cell’s endowment of DNA

1. Prokaryotic – single DNA molecule 2. Eukaryotic – multiple DNA molecules

iii. Chromosomes – structures DNA are packaged into iv. Chromatin – complex of DNA and proteins; is the building

material of chromosomes. v. Somatic Cells – human body cells except reproductive

cells 1. Gametes – reproductive cells; egg and sperm

a. Chromosomes are half of somatic cells vi. Sister Chromatids – duplicated chromosome; attached by

cohesins 1. Centromere – point of greatest attachment

vii. Mitosis – division of genetic material in nucleus 1. Cytokinesis – division of the cytoplasm

viii. Meiosis – a variation of cell division where the number of chromosomes is reduced to half

b. Phases of the Cell Cycle i. Interphase

1. G1 (1st gap)

a. Cell grows b. Duplication of organelles, components,

centrosomes 2. S (synthesis)

a. Duplication of the chromosomes (DNA) 3. G2 (2

nd gap) a. More growth in preparation for M phase b. Complete duplication of centrosomes c. Synthesis of tubulins, aster, and histone proteins d. Nuclear envelope Is developed

ii. Mitotic (M) Phase 1. Mitosis

a. Prophase i. Chromosomes become so tightly packed

they can be seen ii. Nucleoli disappears iii. Mitotic spindle begins to form

1. Made of fibers of microtubules and associated proteins

2. Centrosomes are driven apart b. Prometaphase

i. Nuclear envelope fragments ii. Chromatids each has a kinetochore iii. When a microtubules attaches to the

kinetochore, the kinetochore becomes a kinetochore microtubules

c. Metaphase

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i. Centrosomes are opposite poles ii. Chromosomes have arrived at the

metaphase plate – equidistant to both centrosomes

d. Anaphase i. Starts when cohesion proteins are cleaved ii. Each chromatid, due to separation,

becomes a chromosome iii. Cell elongates as non-kinetochore

microtubules continue to lengthen e. Telophase

i. 2 daughter nuclei form ii. 2 Nuclear envelope form from the

previous envelope’s fragments iii. chromosomes become less condensed iv. Spindle is depolymerized

2. Cytokinesis a. In Animals, formation of a cleavage furrow

which pinches the cell into 2.

c. Cell Cycle Control System

i. Checkpoint – stop and go signals regulate the cell cycle 1. G1 Checkpoint – checks cell size, nutrients, growth

factors, DNA damage

2. G2 Checkpoint – checks cell size and success of

DNA duplication 3. Spindle Assembly Checkpoint – checks

chromosomes and spindle attachment ii. Factors that help control the Cell Cycle

1. Growth Factors i. Proteins that stimulates cells to divide

ii. Promotes CDK – cyclin binding (MPF (maturation promoting factor) – the CDK – cyclin complex)

a. Epidermal Growth Factor – stimulates cell proliferation and embryonic cells

b. Erythropoietin – cell proliferation of RBC c. Fibroblast Growth Factor – cell proliferation of

many cells d. Interleukin – triggers the division of T-

lymphocytes e. Nerve Growth Factors – cell proliferation of

neurons 2. Cell Cycle Inhibitors

a. Chalones – counteracts growth factors b. Colchicines – binds with microtubules c. Antibiotics – inhibits protein synthesis in

prokaryotes d. Contact Inhibition – cells strop to divide and join

to heal a wound 3. Regulatory Proteins

a. Cyclins i. A protein whose concentration cyclically

fluctuates ii. Peaks during mitosis

b. CDK (Cyclin dependent Kinases i. Activated by presence of cyclins ii. Activates other necessary proteins

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d. Meiosis i. Reductionist division; highly specialized form of Mitosis ii. Takes place in the gonads and produces gametes that

are haploid (n) iii. Important Terms:

1. Genes – hereditary units of DNA 2. Locus – gene’s specific location in the chromosome 3. Homologous

chromosome – pair of chromosome that have the same length, centromere position, and staining patter

iv. Types of Reproduction 1. Asexual 2. Sexual

v. Stages 1. Interphase 2. Meiosis I – 2n à 2n;

separates homologous chromosomes a. Prophase I

i. Centrosome movement, spindle formation, nuclear envelope breakdown.

ii. Crossing over occurs; chiasmata is formed iii. Substages

1. Leptotene – thin long chromosomes oriented near nuclear membrane form the attachment plaque

2. Zygotene – close pairing of homologous structures (tetrads/bivalent)

3. Pachytene – crossing over; chromosomes become shorter and thicker and appear V, X, or S like

4. Diplotene – Tetrads start to separate (bivalents)

5. Diakinesis – bivalents detached from the attachment plaque

b. Metaphase I i. Homologous chromosomes are now at the

metaphase plate c. Anaphase I

i. The homolog break apart and each one goes to one end

ii. Chromatid cohesion persists. d. Telophase I and Cytokinesis

i. Each half of the cell has a haploid set of duplicated chromosomes

ii. Formation of 2 haploid daughter cells

3. Meiosis II – 2n à n; separates sister chromatids; interphase w/o DNA replication (interkinesis) a. Prophase II

i. Spindle forms; chromosomes condense b. Metaphase II

i. Due to the crossing over in prophase 1 each half of the homolog (2 sister chromatids) are not the same

ii. Attachment of spindles to kinetochore which are at the equatorial plate

c. Anaphase II i. Sister chromatids are driven to opposite

poles (now called, chromosomes) d. Telophase II and Cytokinesis

i. Nuclei forms, chromosomes become uncondensed

B ioenerget ics XVI. Nutritional Types

a. Autotroph – organism that can manufacture its own food from inorganic substances i. Photosynthetic – uses light to produce glucose

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ii. Chemosynthetic – uses energy from oxidation of inorganic compounds

b. Heterotroph – cannot manufacture food, hence, they eat autotrophs

XVII. Photosynthesis – manufacture of glucose from CO2 + H2O + light energy a. Essential Factors

i. Raw Materials 1. Co2 – free and abundant 2. H2O

ii. Energy (Radiant Energy) 1. Sunlight: red and blue are the most effective 2. Light has both wave – and particle – like properties

iii. Pigments – organic molecule which selectively absorbs

light of specific wavelengths 1. Chlorophyll a – direct participation in photosynthesis

a. Absorbs violet and red light and appears green 2. Chlorophyll b – absorbs blue light and appears yellow 3. Carotenoid pigments – accessory pigments; rainbow

harvesters a. Xanthophyll – yellow b. Lycopene – red-orange; like in tomato c. β-carotene – orange d. Anthocyanin – purple or violet e. Zeaxanthin –

4. Granum – stack of thykaloids 5. Composition of Chlorophyll

a. Porphyrin Ring – Mg with 9 C ring surrounding it b. Phytol – 20 C atoms c. Chlorophyll a – ends with a CH3 d. Chlorophyll b – ends with a CHO

6. Photosystem – light harvesting unit composed of the reaction center a. Corresponding reaction center for chlorophyll a

in: i. Photosystem I – P700 ii. Photosystem II – P680

iv. Temperature 1. 5° - 40°

a. Rate increases until 35° and then starts to decrease

v. Essential vi. e- carriers, enzymes

b. Process of Photosynthesis i. Light Reactions – takes place in the thylakoid membrane

of the chloroplastid; Photophosphorylation – synthesis of ATP that is driven by light energy. 1. Noncyclic

a. Involves the cooperation of 2 photosystems b. Excited e- do not return to original position after

excess energy is removed

c. Produces ATP, NADPH, and O2 d. Raw Mat’l Required: H2O e. Photolysis of H2O to O2 occurs to replace lost

e-

2. Cyclic

a. Involves only photosystem I b. Excited e- return to original state after excess

energy is released c. Produces ATP d. Operates when ATP runs low for the next

stage (dark reactions) e. Increase in NADPH may stimulate a temporary

shift from noncyclic to cyclic e- flow until ATP supply catches up with demand

3. ATP synthesis in both types is by chemiososis

a. Chemiosmosis – production of ATP using energy of the H+ gradient across membrane to phosphorylate ADP; osmosis via a chemical gradient

b. Comparison of chemiosmosis in mitochondria and chloroplasts

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i. ATP Synthase – a complex molecule that allows the passage of H+ 1. Required since a build-up of H+ due to

the proton pump will create a gradient but the inner membrane doesn’t allow H+

ii. Dark Reactions – takes place in the stroma and can occur in the absence/presence of light; uses ATP and NADPH to convert CO2 → sugar

1. Calvin / C3 Cycle a. Synthesizes glyceraldehyde 3-phosphate (3C

sugar) and is converted to glucose and ether organic compounds

b. Utilizes 9 ATP molecules & 6 NADPH to form a glyceraldehyde 3-phosphate

c. Plants that utilize C3 – rice, wheat, soybeans d. Occurs in the mesophyll cells of leaves; needs 6

cycles to produce glucose e. It takes 2 G3P molecules to produce 1 glucose;

It takes 3 cycles to produce 1 G3P molecule

2. C4 Pathway

a. Evolved primarily in the tropics (intense light, high temperatures, and dryness)

b. Observed in corn and sugarcane c. Prefaces the Calvin Cycle with an alternate

mode of carbon fixation wherein it produces a 4-C compound

d. Useful when CO2 concentration is relatively lower in comparison with O2.

e. The Calvin Cycle occurs in the bundle-sheath cells while the production of the 4C compound

occurs in the mesophyll cells. The mesophyll cells have a PEP carboxylase, an enzyme, which binds CO2 to PEP can fix carbon efficiently when Rubisco can’t.

f. It is the SPATIAL SEPARATION of biochemical events i. PEP System in the mesophyll cells ii. RuBP System in the bundle sheath cells

g. Photorespiration is the pathway in which Rubisco attaches O2 to RuBP releasing CO2. This occurs when O2 concentration is high. This is where the C4 pathway comes in since the plant cannot efficiently fix carbon.

3. Crassulacean Acid Metabolism (CAM) a. Observed in the crassulacean family, cactus

members, orchids, pineapple families; evolved in areas with arid conditions

b. Everything happens in the mesophyll cells much like the C3 Cycle but the events are similar to the C4 pathway but with the division of the biochemical reactions happening TEMPORALLY.

XVIII. Cell Metabolism a. Types

i. Catabolism – synthesis of large molecules; an endergonic reaction

ii. Anabolism – breakdown of large molecules; exergonic; production of ATP 1. ATP = energy currency of the cell

b. Law of Thermodynamics i. Conservation of Energy = energy is constant

1. Energy is neither created nor destroyed; it can only be transformed.

ii. Entropy 1. Decrease in the amount of free (useful) energy

a. Capacity to do work

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XIX. Types of Respiration a. Aerobic Respiration

i. Oxidation: e- are passed on to an e- acceptor molecule like FAD and NAD

ii. Reduction: e- are gained or accepted iii. A controlled combustion of fuel molecules to produce

energy; each reaction is catalyzed by specific enzymes. 1. Combustion is controlled so that the energy released

per stage can be harnessed. iv. A series of reactions produces ATP, which is them used

to drive biosynthetic reactions and other energy-requiring processes in the cell

v. Phases of Respiration 1. Glycolysis – glucose splitting’

a. Energy Investment Phase i. A glucose is made into glucose 6-

Phosphate by hexokinase (uses 1st ATP) à ii. Glucose 6-Phosphate is converted into

Fructose 6-Phosphate à iii. Phosphofructokinase attaches one of an

ATP’s phosphate to the G6P (uses 2nd ATP) à

iv. Fructose – 1,6 – bisphosphate à v. Aldolase cleaves Frucose-1,6-bisphosphate

into 2 3 carbon sugars (Glyceraldehyde 3 – Phosphate [G3P]

b. Energy Payoff Phase i. G3P is oxidized by NAD+ (which becomes

NADH) and a phosphate group attaching to G3P harvests the energy from this exergonic reaction creating a 1,3 – biphosphogylycerate à 1. 2 NADH

ii. The 1-phophate is transferred to ADP (creating ATP) in an exergonic reaction à the carbonyl group is oxidized to a carboxyl group of the organic acid 3-phosphoglyceratenà 1. 2 ATP

iii. Phosphoglyceromutase relocates the remaining phosphate group à 2-phosphoglycerate

iv. Enolase creates a double bond in the substrate by extracting an H2O and yielding a phosphoenolpyruvate (PEP) 1. 2 H2O

v. The last phosphate group in the substate is transferred to an ADP by pyruvate kinase à pyruvate (or pyruvic acid) 1. 2 ATP and 2 Pyruvic Acid

c. ATP Utilization: 2 ATP d. ATP Production: 4 ATP; via substrate-

phosphorylation e. Net Products: 2 Pyruvic Acids, 2 ATP, and 2

NADH

2. Pyruvate Oxidation a. Occurs in the Mitochondrion b. Carbon dioxide diffuses out once Pyruvate is

brought into the mitochondrion by active transport. Pyruvate is oxidized by a NAD+ and Coenzyme attaches to Pyruvate. i. 2 CO2, 2 NADH, 2 Acetyl CoA

© agpcastro  

3. Citric Acid Cycle (Krebs Cycle) a. Occurs in the mitochondria b. Occurs via oxidative decarboxylation c. Products: 2 ATP + 6 NADH + 2 FADH

4. Oxidative Phosphorylation

a. Electrons from NADH and FADH2 are passed to a series of e- acceptors (cytochrome complex)

b. Some of the energy released are used to pump protons from the mitochondrial matrix to the intermembrane space which creates an electrochemical gradient

c. Protons diffuse down the concentration gradient with the aid of the ATP Synthase

d. ATP is produced when a PO4 is added to ADP

by the ATP synthase

i. The chemical formation of ATP is driven by a diffusion force similar to osmosis called

chemiosmosis

e. 7.3 kcal per ATP molecule i. 7.3 kcal/mole x 36 mole ATP = 263 kcal

vi. The efficiency of Aerobic respiration is 263 out of 686 that is about 38%. The rest is released as heat used to maintain the body temperature.

b. Anaerobic Respiration

i. In the absence of O2, H+ form glycolysis is donated to

inorganic molecules in a process called anaerobic respiration. 1. Many cells use fermentation to produce ATP by

substrate-level phosphorylation ii. Uses an Electron Transport Chain

1. The ETC is also called the Respiratory Chain c. Two Types of Fermentation

i. Alcohol Fermentation 1. Pyruvate à Acetaldehyde à Alcohol 2. The Co2 released causes bread with yeast to rise 3. The source of alcohol in beer or wine

ii. Lactic Acid Fermentation

1. Pyruvate à Lactate 2. Occurs in muscle cells