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Three Quarters Honors Biology Study Guide

Biochemistry 3. Due Monday, March 13

1. What is the atomic number? Atomic weight? An isotope? An ion? 2. Calculate the number of protons, neutrons, and electrons based on the periodic table.

a. What are the number of protons, electrons and neutrons in carbon and Chlorine? 3. What are the number of electron cloud layers and how many electrons are in each?

a. Draw electron cloud configuration for carbon & Chlorine. 4. Identify the reactants and products in a chemical equation 5. What is the difference between an ionic and covalent bond? Give an example of each. 6. What is pH? How does what know if a substance is an acid or base or neutral? 7. Identify which functional groups are present for a given molecule. 8. For carbohydrates, fats, and proteins be able to

a. Identify the monomers for each? How does the molecule progress to be a polymer? b. How does dehydration synthesis work to build a polymer of each group? c. How does hydrolysis work to break down the polymer of each group? d. What are the different functions of each group? e. Which and how are these groups listed on a food label.

9. What are the different forms and functions of polysaccharides: glycogen, starch, cellulose 10. How can you tell the difference between saturated, monounsaturated, and polyunsaturated

fats. 11. What are the 4 types of protein structures? What mechanisms are in place to cause the shape

at each level. 12. Interpret a graph on the effects of an enzyme on energy levels and reaction rates. 13. Explain the induced fit model – such as sucrase on sucrose. 14. How does denaturation occur and affect enzymes.

The Cell 4. Due Tuesday, March 14

1. What is the difference between a plant and animal cell. 2. What is the difference between a prokaryote and eukaryote cell 3. Why is the phospholipid bilayer important – what is it composed of, vesicle formation 4. Diffusion- which way do particles move in an experiment

a. Define diffusion b. What happens at equilibrium c. Define Osmosis

5. Lab safety- no question be familiar with class rules for 6. What is the structure (look like) and function of following parts of cell

a. Nucleus b. Nucleolus c. Endoplasmic Reticulum d. Cell wall e. Ribosomes f. Golgi Apparatus

g. Cilia

h. Flagella

i. Mitochondria

j. Central vacuole

k. Chloroplast

7. What are the principles of cell theory 8. How should one look at a slide on the microscope at high power

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Photosynthesis (6. due Friday, March 17) & Cellular Respiration ( 5. due Block 3/15 or 3/16)

1. Define and give examples of: autotroph, heterotroph, consumer, producer 2. What types of energy conversion occur in photosynthesis 3. Plants absorb light by? appear green because of? 4. Experiment

a. Define the independent variable & dependent variable b. Be able to read a graph- no question c. Apply the process of photosynthesis to a lab scenario

5. What are the equations for photosynthesis and cellular respiration? How are they similar yet different?

6. How is energy released in ATP? 7. What are the products and reactants of cellular respiration 8. Yeast and fermentation – what type aerobic or anaerobic? 9. How do muscle cramps develop? 10. What foods are made from fermentation? 11. Comparison of light reaction and Calvin Cycle: light use, location, reactants, products, and

energy types 12. Comparison of Glycolysis, Krebs cycle, Electron transport chain, & fermentation (2 types): #

ATP, location, need for oxygen, produces carbon dioxide

13. Write the balanced chemical equations for photosynthesis & cell respiration

Cell Division 7. Due Monday, March 20

Identify the phases of mitosis in picture form

a. What is the correct order of mitosis phases? b. Which are longest? What occurs during interphase?

2. Define and Identify the centromere and sister chromatids 3. What are the number of human chromosomes in cell – body and sex cell 4. What is the purpose of karyotype 5. Define cytokinesis 6. Cancer cells

a. How do they compare to normal cells b. What are treatments for cancer

7. What are the differences between mitosis and meiosis 8. Define: zygote, gametes 9. Diploid and Haploid number- define each and be able to calculate

Genetics 2. Due Friday, March 10

1. Principles that Mendel came up with

2. Dominant and recessive

Definitions: dominant: recessive, phenotype, genotype, homozygous. heterozygous

Figure out genotypes: Homozygous and Heterozygous of eye color (B)

3. Two trait genotypes and FOIL for possible gametes from parents 4. Sex-linked disorders

a. Interpret punnett square b. Figure out phenotypes

5. Pedigrees

a. Know symbols – what do they mean Square-male, circle-female, horizontal line marriage, vertical line offspring

b. Interpret pedigree

c. Genotypes, Chance of passing on trait, parents who don’t have trait

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Nucleic Acids: DNA& RNA 1. Due Tuesday March 7 1. Compare / contrast prokaryotic and eukaryotic DNA in their respective cells 2. List the people/persons responsible for the current understanding of DNA, its structure, etc. Describe their contributions and why their ideas was so important in understanding DNA 3. Draw a DNA molecule that consists of 6 nucleotides accurately bonded. Number the carbons, phosophodiester bonds, 3’ and 5’ ends (remember ant parallel model). Indicate purines and pyrimidines nitrogen bases in addition to correct number of H bonds. 4. Replication (one of the two jobs of DNA): When does it replicate? Explain the idea of the semi-conservative model. List the enzymes and what their respective jobs are Draw a picture and label: leading strand (with arrow), lagging strand(s) with arrows, three okazaki fragments, where helicase is found, where ligase would be used, etc. 5. Protein synthesis (the second job of DNA) Transcription: a. Where does it occur? How much of the DNA is opened? b. What major enzyme(s) are used their jobs c. what is the ‘end product’? d. what is the start codon? Translation: a. Where does it occur? b. what is the ‘end product’? c. describe the structure of a ribosome d.. Where are two places to find ribosomes in an eukaryotic cell e. describe the type of bond formed when amino acids join together. f. Draw a structural picture of an amino acid (label the functional groups) 6. Review the 4 basic structures of protein structure… Yes, you have to go back to an earlier chapter in your book. 7. Comparison chart of DNA to RNA – list at least 4 differences for each type of nucleic acid 8. Mutations – a. what are they? b. discuss how some are passed to offspring while others are not. (think about the type of cell that they are occurring in..) c. list the major types, define and give an example

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Three Quarters Honors Biology Study Guide ANSWERS

Chemistry

1. What is the atomic number? Atomic weight? An isotope? An ion? Atomic number is the number of protons in an element – it is its identity. Atomic mass is the number of protons and neutrons in an element. Isotope is form of an element that weighs more due to more neutrons. Ion is either a positively or negatively charged element / compound due to gaining or losing electrons.

2. Calculate the number of protons, neutrons, and electrons based on the periodic table. The number of protons is the atomic number. The number of electrons of an element on the periodic table is the atomic number. Neutrons are calculated by the atomic mass minus the atomic number.

a. What are the number of protons, electrons and neutrons in Carbon & Chlorine? Carbon: 6 protons, 6 electrons, 6 neutrons Chlorine: 17 electrons, 17 protons, 18

neutrons

3. What are the number of electron cloud layers and how many electrons are in each? Each row of the periodic table is the number of layers in the electron cloud. Each column (up and down) is the number of electrons in the outer most layer.

a. Draw electron cloud configuration for carbon and Chlorine

4. Identify the reactants and products in a chemical equation- reactants are on the left side of the equation and products are on the right side. Hydrogen and oxygen are reactants that make water. H2 + O2 H2O

5. What is the difference between an ionic and covalent bond? Give an example of each. Ionic bonds are made when an electron leaves the outer layer of one element and goes to another element – creating two ions. The atoms attract due to opposite charge like salt Na+ and Cl-. Covalent bonds are when elements share the electrons in the outermost layer like H2O.

6. What is pH? How does what know if a substance is an acid or base or neutral? pH is the measure of H+ ion concentration in a solution. Scale 0-14. Less than 7 acid, greater than 7 base. & is considered neutral or pure water.

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7. Identify which functional groups are present for a given molecule.

Hydroxyl

Carboxyl

Amino

Aldehyde

Ketone

phosphate

nitrogen lone pair

Sulfhydryl

8. For carbohydrates, fats, and proteins be able to

a. Identify the monomers for each? How does the molecule progress to be a polymer?

b. How does dehydration synthesis work to build a polymer of each group? c. How does hydrolysis work to break down the polymer of each group? d. What are the different functions of each group? e. Which and how are these groups listed on a food label.

Category Carbohydrates Fats Proteins

Monomers

Polymers

Monosaccharide like

glucose or fructose -

polysaccharide

Glycerol & fatty acids

triglyceride.

Amino acids

polypeptide chains

primary, secondary,

tertiary, quarternary

Dehydration

synthesis & bonds

Remove 1 water to

make a disaccharide

from 2

monosaccharides

Remove 3 water

molecules to bind

glycerol with 3 fatty

acids

Remove 1 water

molecule to make a

peptide bond

Hydrolysis (add

water to cut)

Polysaccarides

Monosaccharides

Triglyceride

Glycerol + 3 fatty

acids

4th structure 3rd

structure 2nd

structure polypeptide

chain amino acids

Common names/

food

Sugars, syrups fats, oils meats, legumes

Functions 1.Energy for body

2.Stored energy

1.Stored energy

2.Cell membranes

1.Structures- hair,

muscle, tissues

2.Hormones & enzymes

Food Label Carbohydrates, sugars Fats, saturated,

cholesterol

Proteins

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9. What are the different forms and functions of polysaccharides: glycogen, starch,

cellulose

Glycogen- branched chain stored energy for glucose

Cellulose- structural support in stems of plants

Starch- complex sugar food source found in potatoes, rice, and corn

10. How can you tell the difference between saturated, monounsaturated, and

polyunsaturated fats.

Saturated- have no C=C double bonds and all C are saturated with H atoms. Monounsaturated-

have one C=C double bond, and polyunsaturated has two or more C=C bonds.

11. What are the 4 types of protein structures? What mechanisms are in place to cause the

shape at each level.

Primary- polypeptide; Secondary-alpha helix and beta-pleated sheets; Tertiary- Ionic bonds, sulfur

bridges, hydrophobic reactions, hydrogen bonds; Quarternary- multiple amino acids form protein

structure.

14. Interpret a graph on the effects of an enzyme on energy levels and reaction rates.- Enzymes lower activation energy. They aid in speeding up a chemical reaction but do not change the overall energy of the reaction.

13. Explain the induced fit model – such as sucrase on sucrose

E + S --> ES --> E + P / Sucrase (enzyme) binds to sucrose (substrate) (products) glucose

and fructose +sucrase (enzyme)

15. What is denaturation of an enzyme – how does it occur? Protein breaks down and

unfolds due to extreme temperature and pH changes.

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The Cell

1. What is the difference between a plant and animal cell

Plants possess chloroplasts, central vacuoles, and cell walls while animal cell do not.

Centrioles are found in all animal cells.

2. What is the difference between a prokaryote and eukaryote cell – prokaryotic lacks a nucleus and most other organelles

- eukaryotic cell has a membrane bound nucleus and organelles

3. Why is the phospholipid bilayer important- regulates the transport of substances across it, hydrophilic heads and hydrophobic tails, transport proteins. Oxygen and water diffuse, glucose by proteins. Exocytosis / endocytosis- moving material out or into cell by vesicles made of membrane

4. Diffusion- which way do particles move in an experiment a. Define diffusion- net movement of the particles of a substance from where they are more

concentrated to where they are less concentrated b. What happens at equilibrium- reached when the movement of particles in one

direction is equal to the number of particles moving in the other

c. Define osmosis- passive transport of water across a selectively permeable membrane

5. Lab safety- be familiar with class rules for: fire use, acid use, glass breakage

6. What is the structure (look like) and function of following parts of cell a. Nucleus: center of cell, circular; the part that houses the cell's genetic material in the form

of DNA

b. Nucleolus: ball-like mass of fibers and granules in a cell nucleus

c. Endoplasmic Reticulum: may be smooth or rough ribbon-like; network of membranes

within a cell's cytoplasm that produces a variety of molecules

d. Cell wall: box like structure; strong wall outside a plant cell's plasma membrane that

protects the cell and maintains its shape

e. Ribosomes: small dot structures- cluster of proteins and nucleic acids that constructs

proteins in a cell

f. Golgi apparatus: flattened stack of ovals; cellular organelle that modifies, stores, and

routes cell products

g. Cilia: short hair-like structures from a cell and containing bundles of microtubules that

move a cell through its surroundings or move fluid over the cell's surface

h. Flagella: whip-like structure responsible for movement

i. Mitochondria: powerplant of cell- turns glucose into ATP; bean shaped

j. Central vacuole: large structure (bigger than nucleus) stores water to help hold plants up

k. Chloroplast: green disk structure responsible to turn solar energy into glucose

7. What are the principles of cell theory

- All living things are composed of cells, cells are the basic unit of structure and function in

living things (life legos), cells come from pre-existing cells

8. How should one look at a slide on the microscope at high power: set in on low power and

find the object, go to medium and then high keeping the organism in the center of the field of view,

only use the fine adjustment on high power.

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Photosynthesis / Cell Respiration

1. Define and give and example of:

-autotroph- organism that makes its own food; plant

-heterotroph- organism that obtains food by eating other organisms; animal

-consumer- gains energy from eating another organism

-producer- an organism that makes its own food and produces organic molecules that serve\

as food for other organisms in an ecosystem

2. What types of energy conversion occur in photosynthesis: sun light into chemical energy

3. Plants absorb light by? pigments called chlorophyll and appear green because of?

Chlorophyll / chloroplast

4. Experiment

a. Define the independent variable & dependent variable Independent- the variable being manipulated; dependent- the variable that may change

from the independent variable being manipulated

b. Be able to read a graph c. Apply process of photosynthesis- see chemical equation

5. What are the equations for photosynthesis and cellular respiration? How are they similar

yet different?

Cell respiration: 6O2 + C6H12O6 + 6CO2 + 6H2O + 38 ATP

Photosynthesis: 6CO2 + 6H2O + Solar Energy 6O2 + C6H12O6

6. How is energy released in ATP? When chemical bonds are broken between phosphates

energy is released

7. What are the products and reactants of cellular respiration: in # 5. Products (outputs) are

on the right side of chemical equations, reactants (inputs) are on the left side

8. Yeast and fermentation – what type aerobic or anaerobic? Anaerobic because do not need

oxygen

9. How do muscle cramps develop? Build up of lactic acid during fermentation in muscles due

to lack of oxygen

10. What foods are made from fermentation? Cheese, alcoholic beverages, breads, yogurt.

11. Comparison of light reaction and Calvin Cycle: light use, location, reactants, products,

and energy types

Light Reaction Calvin Cycle

Light use Light-dependent reaction Light-Independent reaction / Dark

Reaction

Location Thylakoid membrane Stroma

Input / Reactant Light + water CO2 + RuP

Output / Product Oxygen G3P C6H12O6

Energy NADP+ NADPH

ADP + P ATP

9 ATP 9 ADP + P per turn

6 NADPH 6 NADH+ per turn

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12. Comparison of Glycolysis, Krebs cycle, Electron transport chain, & fermentation (2

types): # ATP, location, need for oxygen, produces carbon dioxide

Glycolysis Krebs Electron transport

Chain

Fermentation

# ATP 2ATP 2ATP 34 ATP 2 ATP

Location Cytoplasm Mitochondria Mitochondria Yeast / Muscles

Need Oxygen-

Aerobic

No No Yes No

CO2 produced No Yes No Yes- alcohol

13. Write the chemical equations for photosynthesis & cell respiration

Photosynthesis- Carbon dioxide + light + water glucose + oxygen;

Cell Respiration- Glucose + oxygen carbon dioxide + water + ATP

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Cell Reproduction

1. Identify the phases of mitosis in picture form a. What is the correct order of mitosis phases? Prophase, metaphase, anaphase,

telophase, & cytokinesis

b. Which are longest? Interphase between mitotic divisions What occurs during interphase? Cell grows, double chromosomes and organelles

2. Define and identify the centromere- place where sister chromatids are connected and sister chromatids- exact copies of the same chromosome

3. What are the number of human chromosomes in cell – body- 46 and sex cell- 23 4. What is the purpose of karyotype- A map of all the chromosomes in a body cell, can

diagnose some genetic disorders before birth or during life. 5. Define cytokinesis- the cell divides the cytoplasm and organelles between the two daughter

cells 6. Cancer cells

a. How do they compare to normal cells- reproduce more rapidly, larger and use more

nutrients

b. What are treatments for cancer- surgery, chemotherapy, and radiation

7. What are the differences between mitosis and meiosis- mitosis creates exact copies of body cells (diploid); meiosis creates haploid sex cells

8. Define: zygote- form when fertilization of egg with sperm, gametes- sex cells (egg and sperm)

9. Define each and be able to calculate Diploid - # of chromosomes from mom AND dad and Haploid number-number of chromosomes from mom OR dad

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Genetics and DNA

1. Principles that Mendel came up with

-Dominance: one trait is expressed over another when present ( Brown or blue)

-Segregation: 50% of receiving either trait or factor ( B or b)

-Probability: Chance that a given trait will be seen

2. Dominant and recessive

A. Definitions dominant: descriptive of an allele in a heterozygous individual that appears to be the

only one affecting a trait (B)

recessive: descriptive of an allele in a heterozygous individual that does not appear to

affect a trait (b)

phenotype: observable traits of an organism (blue eyes)

genotype: genetic makeup of an organism; an organism's combination of alleles

(BB or Bb or bb)

B. Figure out genotypes: Homozygous and Heterozygous homozygous: having identical alleles for a gene (BB or bb)

heterozygous: having different alleles for a gene (Bb)

C. Two trait genotypes and FOIL for possible gametes from parents First – Outside – Inside – Last BbPp = BP, Bp, bP, bp

3. Sex-linked disorders

a. Interpret punnett square b. Figure out phenotypes H-normal h-hemophilia: 25% male normal, 25% male with disease

25% female normal, 25% carrier

XH Y

XH

XH XH XH Y

Xh XH Xh Xh Y

4. Pedigrees

a. Know symbols – what do they mean Square-male, circle-female, horizontal line marriage, vertical line offspring

b. Interpret pedigree Genotypes, Chance of passing on trait, parents who don’t have trait3. Sex-linked disorders

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Nucleic Acids: DNA& RNA

1. Compare / contrast prokaryotic and eukaryotic DNA in their respective cells Prokaryotic – circular DNA (yes – double helix, too); ribosome in cytoplasm, too Eukaryotic – linear strands of DNA (also double helix shape), ribosomes and many organelles 2. List the people/persons responsible for the current understanding of DNA, its structure, etc. Describe their contributions and why their ideas was so important in understanding DNA 1928 – F. Griffith: mice and two strains of streptococcus—rough (not deadly because immune system recognized it and destroyed it before it produced a toxin; and smooth (in a protein coat so the bacteria was able to ‘hide’ form the immune system, and thus produced a toxin that caused the mouse to die). When denatured smooth and rough strains were injected into mouse together (both individually allowed the mouse to live) caused the mouse to die. This was coined ‘transformation’ Avery, MacLeod and McCarty – used enzymes to prove that DNA was the transforming factor but people still did not believe them. Hershey and Chase – Radioactive sulfur to tag protein coat of a bacteriophage (virus that infects bacteria) and radioactive Phosphorus to tag the DNA inside the virus. Used a blender and centrifuge in two separate experiments to prove that it was indeed DNA that was the transforming factor. Watson, Crick, Wilkins, and Franklin – DNA structure was a double helix in the 1950. Franklin died before the Nobel prize was awarded (probably from breast cancer due to x-ray crystallography). Chargaff: Amount of Adenine = Thymine nitrogen bases Cytosine bases = Guanine bases 3. Draw a DNA molecule that consists of 8 nucleotides accurately bonded. Number the carbons, phosophodiester bonds, 3’ and 5’ ends (remember ant parallel model). Indicate purines and pyrimidines nitrogen bases in addition to correct number of H bonds.

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4. Replication (one of the two jobs of DNA): When does it replicate? – during the S phase of interphase Explain the idea of the semi-conservative model. Both sides of the DNA strand are used as patterns to build identical strands that remain hooked together by a centromere List the enzymes and what their respective jobs Helicase – unzips the DNA – breaking the H bonds RNA primase – puts down RNA nucleotides to allow the strands to build DNA polymerase – adds DNA nucleotides to the 3’ end of the growing strands (both leading and lagging); another kind actually removes the RNA nucleotides Ligase – glues strands together (especially the lagging or Okazaki fragments) Draw a picture & label: leading strand (with arrow), lagging strand(s) with arrows, three okazaki fragments, where helicase is found, where ligase would be used, etc.

5. Protein synthesis (the second job of DNA) Transcription: a. Where does it occur? In the nucleus How much of the DNA is opened? 1 gene b. What major enzyme(s) are used their jobs RNA polymerase adds RNA nucleotides to 3’ end of the growing strand c. what is the ‘end product’? mRNA d. what is the start codon? AUG which codes for methionine (amino acid) Translation: a. Where does it occur? On a ribosome in the cytoplasm b. what is the ‘end product’? Amino acid chain that forms a primary protein structure c. describe the structure of a ribosome. There is a large and small component. On the large component, there is a E (exit), P (peptide forming spot) and A (where need tRNA’s bring in the amino acids to be ADDed to the growing peptide chain. mRNA is read in the 5’ to 3’ direction. d. Where are two places to find ribosomes in a eukaryotic cell – free floating & attached to ER e. describe the type of bond formed when amino acids join together. Peptide f. Draw a structural picture of an amino acid (label the functional groups)

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6. Review the 4 basic structures of protein structure…

7. Comparison chart of DNA to RNA – list at least 4 differences for each type of nucleic acid

DNA RNA

Sugar

Deoxyribose ribose

Nitrogen bases

A, T, C, G A, U, C, G

# of strands

Two one

Found Nucleus Nucleus (mRNA) and cytoplasm (tRNA); in ribosome (rRNA)

8. Mutations –

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a. what are they? the changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations, caused by the alteration of single base units in DNA, or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes. b. discuss how some are passed to offspring while others are not. (think about the type of cell that they are occurring in..) --somatic (body) cells are not passed to offspring so they just stay with the person who has abnormal cells (i.e. skin cancer, stomach cancer, etc. --mutations in gametes (germ cells) are passed to offspring c. list the major types, define and give an example Frameshift: caused by an insertion / deletion of one or more nucleotides. Additions of 1 or 2 cause far more disruption than those of 3(or groups of 3) due to the fact that that grouping would code for and additional amino acid rather than possibly change everything downstream from the change. Deletion mutation results in a lot of missense:

Insertion mutation results here in a lot of missense as well.

Point mutation:

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1. Silent (wobble) when the third nucleotide base codes for the same amino acid

2. Missense – still codes for amino acids but not necessarily the right amino acids sequence

3. Nonsense – usually codes for an early stop ; therefore the amino acid chain makes no

sense at all

1. Silent mutation example:

2. Missense mutation example:

3. Nonsense mutation example:

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