AP Bio Full Year Review

General Notes (no answers on other card)

• REREAD the prompt multiple times for the long frqs. Sometimes they throw in one line details that are used in another part.

• Identify: 1 sentence. DEscribe: 1-2 sentences with detail. Explain/Discsuss: LONG, 3-4 sentences with specifics

• REMEMBER UNITS

• Remember to reference the basics. This like mitosis is used for growth, or the purpose of photosynthesis is to use light to synthesize glucose, or DNA is made up of nucleotides. Don’t get caught up in crazy detail if you didn’t write easy stuff down.

• For the “which question could be best investigated by this study?” type of prompt, make sure to choose the option that best aligns with the exact “lens” the quesiton is looking at. If the question takls about molecular/biochemical stuff, then choose the answer about that, not the answer that talks about behavior or intangible qualities

• Dominance of alleles ≠ frequency of alleles

• Smaller animals have a higher metabolic rate than larger animals (its a SA/V thing)

• Remember that even thought evolution/natural selection happens because of selecting factors and selective pressures, a lot of it is due to random chance, like gene drift or getting a new mutation that ends up being favorable.

Unit 1: Water & pH

1. What are emergent properties?

2. Name the 8 Properties of Water

3. What causes the properties of water?

4. Name effects of the properties of water

5. What is the pH scale based on and what is the range?

1. Properties that show up as an organism gets more diverse (cells becoming tissue, etc)

2. Cohesion, Adhesion, Capillary Action, surface tension, lower density as solid, high heat of vaporization, high specific heat, high solvency (can dissolve stuff)

3. Its polarity/hydrogen bonds

4. Hydration shell (can pull ions apart), evaporative cooling, insulation (water underneat ice is warmer for fish to stay alive), temperature moderation (high specific heat makes it hard to change temperature)

5. Based on -log[H+], powers of 10. <7 is acid, >7 is basic. Goes from 1-14

Unit 1: Carbohydrates

1. Elements (Ratio), Monomers, Bond Type

2. What are the two functions of carbohydates?

3. Examples in animals, plants, fungi

4. What distinguishes whether a carb is made for structure or storage?

1. CHO (1:2:1), monosaccharide, glycosidic linkage

2. Structure and storage of energy

3. Animals have glycogen, plants have starch (storage), cellulsoe (cell wall/structure), plants have chitin (also animals for their exoskeleton)

4. If its structure like cellulose, it has alternating Beta and alpha glucoses (OH are flipped every other monomer so it makes it harder to break apart) whereas starch is only alpha

Unit 1: Lipids

1. Elements, Monomers, Bond Type

2. What is saturation?

1. CHO (much more H), fatty acids and glycerol, (triglycerol) ester bond

2. Saturated if only

Unit 1: Proteins

1. Elements, Monomers, Bond Type

2. What two functional groups

3. What determines the properties of an AA?

4. Discuss the 4 levels of folding

5. Examples of proteins

1. CHON, Amino Acids, peptide bond

2. amine group (NH2) and carboxyl group (COOH)

3. The R group

4. Primary: AA order, Secondary: main chain interactions via hydrogen bonds, forms alpha helixes or beta pleated sheets Tertiary: 3D shape through side chain interactions via hydrogen bonds, hydrophilic/phobic interactions, ionic bonds, disulfide bridges, Quaternary: multiple polypeptides interacting together

5. Hormones, enzymes, transport, structure, antibodies

Unit 1: Nucleic Acids

1. Elements, Monomers, Bond Type

2. What are the three components of the monomer?

3. What are the 4 bases, and what are the two types of bases?

4. What are the differences between the two base pair groups?

5. 2 Types

1. CHONP, Nucleotides, phosphodiester bonds

2. Five-carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base

3. Adenine and thymine bond, Guanine and cytosine bond. Uracil for RNA. Purines (double ring) are AG, pyrimidines (single ring) are TCU

4. 3 hydrogen bonds between G and C (means harder/more energy to break them apart), 2 bonds between A and T

5. DNA and RNA

Unit 2: Basic Cell Stuff

1. 3 Parts of Cell Theory

2. Why does SA/V ratio matter?

3. 8 Life Functions

4. What do prokaryotes and eukaryotes share? What is different?

5. Animal vs Plant Cell

Unit 2

1. All living things are made of cells. Cells are the basic units of structure and function. All cells come from prexisting cells. (exception is virus)

2. Need a large proportion of surface area b/c it determines exchange with environment via membrane to perform metabolic processes. Too big and cell can’t sustain enough transport

3. NETSGRRR (Nutrition, Excretion, Transport, Synthesis, Growth, Reproduction, Respiration, Regulation)

4. Share cytoplasm, ribosomes, genetic material, cell membrane. Eukaryotes have membrane-bound organelles like nucleus while prokaryotes do not

5. Vacuole Size (one large in plants), Chloroplasts, cell wall

Unit 2: Plasma Membrane

1. What is the structure called and what are its properties?

2. What types of molecules can go through the cell membrane?

3. What helps to regulate the cell membrane?

4. What are the proteins/things that are part of the cell membrane?

5. 3 Types of Passive Transport

6. 3 Types of Active Transport

7. How do steroids travel across the membrane? How do hormones? How does cholesterol?

1. Fluid mosaic model, proteins in sea of phospholipids (heads face outward), amipathic, semipermeable

2. NONpolar and small, like CO2 and O2

3. Cholesterol helps maintain membrane fluidity with changing temperatures (especially hotter), also whether or not the phospholipids are bent determines fluidiity (more bent means more fluid)

4. Integral proteins (pass completely through), peripheral (stuck to the inside, usually are enzymes), glycoproteins/glycolipids function as receptors or attach to ECM (extracellular matrix) outside cell

5. Passive diffusion goes from high to low concentraiton, no energy. Includes facilitated diffusion (like aquaporins, note that water can still travel simply), simple diffusion (through membrane if nonpolar/small), osmosis (movement of water)

6. Active transport uses energy, goes against concentration gradient, and usually involves vesicles. Exocytosis (out of the cell), endocytosis (includes phagocytosis (engulfing) and pinocytosis (like cellular drinking)), or carrier proteins like sodium-potassium pump

7. Steroids usually travel across the membrane through simple diffusion while hormones need carrier proteins or receptor-mediated endocytosis (active transport where a vesicle is formed by binding to a membrane receptor)

Unit 2: Organelles

1. What are the functions of the following: nucleus, ribosomes, golgi, mitochondria, vacuole, chloroplast, lysosomes, peroxisomes?

2. Difference in Smooth vs Rough ER

3. What is the cytoskeleton and ECM?

4. What is the Endomembrane system and what organelles are part of it?

5. Cells involved in movement would likely have a lot of what?

6. If an organism lives at lower temperatures, what might its membrane have?

1. Stores genetic info, makes proteins, transports/tags/modifies vescicles (cis/trans sides), make ATP, storage (can store toxins, water, etc and act as contractile vacuole to maintain tonicity), make glucose, break down dead cell parts using hydrolytic enzymes (low pH), detox and break down hydrogen peroxide

2. Smooth ER makes lipids, holds ions, and is involved in detoxificaiton. Rought ER makes secretory proteins for export because it has bound ribosomes

3. network of proteins like microtubules and microfilaments thatare responsible for movement, growth, and structure. Outside the cell it the extracellular matrix which is a complex of proteins and carbs that provides support, movement and communication between cells

4. Endomembrane system is the way things are transported out of the cell. Starts with bound ribosome in ER, travels through ER to golgi where it is modified, then to cell membrane through the use of vesicles (make include lysosome as well)

5. Mitochondria but also a big cytoskeleton and many filaments (ECM)

6. More unsaturated phospholipids and cholesterol because it needs to maintain fluidity. Plants may adjust their fluidity between seasons with these molecules

Unit 2: Water potential

1. Where does water move into?

2. What are the three types of solutions?

3. What are the three states of an animal cell called? Plant Cell?

4. How to find potential

5. How to use -iCRT formula

6. How is osmosis affected by diffusable solutes and nondiffusable solutes?

1. Whatever has the higher osmolarity (amount of solutes) or LOWER water potential

2. Hypertonic (higher solute conc. outside), isotonic (same), hypotonic (less)

3. Animal cell in hypertonic is shriveled, isotonic is normal, hypo is swollen/lysed. Plant is plasmolyzed in shriveled, flaccid in isotonic, turgid in hypo (this is normal state)

4. Water potentai l = pressure potential +solute potential. Pressure potentail is usually given (it’s 0 if its an open container), and solute potencial is calculated using -iCRT. Need to calculate the solute potential of the cell AND the solution and compare the values.

5. This is for SOLUTE potential. i is dissociation amount (something like NaCl splits into 2 ions, but sucrose is not ionic so it doesn’t slit and i = 1, C is concentration in molarity, R is a constant, =. 0821, T is the temperature in KELVIN

6. Water flows to side with higher amount of nondiffusable solutes. Diffusable solute concentration does not matter because it will equalize anyway

Unit 3: Themodynamics

1. What do all metabolic processes give off and why?

2. Exergonic vs endergonic?

3. Catabolic vs anabolic?

4. Which do photosynthesis and respiration fall under?

1. Heat b/c entropy (randomness always increases)

2. Exergonic means it releasese energy Endergonic means energy is required.

3. Anabolic means its a building process, catabolic is a breaking down process

4. Photosnythesis is endergonic and anabolic. Respiration is exergonic and catabolic

Unit 3: Enzymes

1. What is an enzyme?

2. What can be said about enzyme shape to substrate?

3. What are cofactors?

4. What factors affect Rxn Rate?

5. Two types of competition

6. Two types of regulation

7. What is energy coupling?

1. Biological catalyst, not used up when speeding up reactions. Don’t change ∆G of the reaction. Lower the activation energy.

2. Specific, induced fit to substrate at active site. CANNOT write lock and key model

3. helps that can transfer electrons and bind to facilitate the reaction. Biological cofactors are coenzymes

4. Temperature, PH, concentration of substrate/products/enzyme, salinity. For explanations, you can take about particles and effective collisions.,

5. Competitive: inhibitor competes with substrate for active site. Noncompetitive: inhibitor attached at allosteric site to cause shape change to active site

6. Negative feedback: negates the change and brings back to original state. Positive feedback: amplifies the change

7. The process of hydrolyzing ATP is exergonic so it is coupled with another endergonic reaction to power it

Unit 3: Photosynthesis

1. Equation. Is it catabolic or anabolic, exothermic or endothermic?

2. Structure of Chloroplast

3. Types of pigments. What is an action spectrum?

4. Two stages and where they take place

5. Reactants and Products of Light Dependent

6. Explain the ETC and Light Dependent Rxn

7. How is ATP produced?

8. Cyclical Electron Flow

9. Reactants and products of Light Independent

10. How does Calvin Cycle work? How much ATP/NADPH in one cycle?

1. 6CO2+6H2O → C6H12O6+6O2, anabolic, endothermic, 686 kJ/mol

2. Has grana (stacks of thylakoids), inner liquid is called stroma

3. Chlorophyll, but also accessory pigments called carotenoids that absorb other wavelengths of light. An action spectrum is a graph of wavelength of light vs photosynthetic activity rate

4. Light dependent takes place in thylakoid and light independent (Calvin Cycle) takes place in stroma

5. Uses Water and Light to create ATP and NADPH

6. Light is absorbed by PSII (p680 pigment) to excite electrons. Light also hits water molecules and breaks them apart in oxygen, protons and electrons. Oxygen leaves, protons used for gradient, electrons replenish ETC. Electron flows down ETC, providing energy that is used to pump proton out of the thylakoid to create electrochemical gradient. Goes up twice, once in PSII then in PSI. Electron is then taken by electron carrier NADPH (gets reduced)

7. Electrochemical gradient helps to perform chemiosmosis, which creates ATP by allowing protons to travel down their gradient through ATP synthase to create ATP

8. Electron goes back through the ETC instead of being directly taken by NADPH to generate more ATP

9. Uses CO2, NADPH, and ATP to generate G3P (2G3Ps = glucose)

10. CO2 is fixed to RuBP to make Rubisco. Then ATP and NADPH is added and enzymes take the compound and make 6 G3P. 5 G3P are used to regenerate RuBP and rest are used to make glucose. One cycle produces 9 ATP and 6 NADPH

Unit 3: Respiration

1. Is it catabolic or anabolic, exothermic or endothermic?

2. 4 Parts

3. Two types of ATP making and how much ATP is made?

4. Phases of Glycolysis

5. Explain Link Reaction

6. Krebs Cycle

7. How does ETC work?

8. Why is there a range of ATP?

9. What is the purpose of fermentation and what are the 2 types?

1. Anabolic, exothermic, -686 kJ/mol

2. Glycolysis, Link Reaction, Krebs Cycle, ETC

3. Substrate-level phosphorlyation (glycolysis/krebs), oxidative phosphorylation (ETC/chemiosmosis), 36-38 ATP

4. Invests 2 ATP, produces 4 ATP, 2 NADH, and 2 pyruvic acid. Remember the enzyme PFK (phosphofructokinase, which regulates glycolysis

5. Pyruvic acid combines with coenzyme A to make Acetyl coA (gets rid of a CO2 and makes 2 NADH)

6. Makes 1 ATP, 3 NADH, FADH2

7. NADH and FADH2 drop off electrons, whose energy are used to pump in protons to create electrochemical gradient for ATP synthase to generate ATP

8. B/c FADH2 drops electrons off at second level of ETC so it doesn’t create a whole number of ATP

9. Fermentation does NOT produce ATP, only glycolysis is used. Fermentation is used to recycles NADH. Includes lactic acid fermentation (animals) and alcohol fermentation (produces ethanol and co2 in yeast)

Unit 4: Signal Transduction Pathway

1. 3 Steps

2. Cell Communication Types (i.e. local signaling types)

3. How does the pathway start?

4. 4 Types of membrane receptors

5. Explain GCPR

6. Explain TRK

7. Explain intracellular signaling

8. What is quorum sensing?

9. What the two types of cell division inhibition?

10. How does shape determine function in this unit?

1. Signal Reception, Transduciton, Response

2. endocrine (hormones, long distance), local: neurotransmitters, paracrine (local cell communication), autocrine (self-signaling), direct signaling through plasmodesmata holes in plants or tight/gap junctions in animals

3. Ligand binds to cell membrane receptor

4. Ligand-gated ion channel, enzyme-linked receptors, G-protein receptors, TRK (tyrosene) receptor

5. GCPR receptor binds with ligand, causing shape change that leads G-protein to move right, phosphorylating and activating adenylyl cyclase, which then starts a phosphorylation cascade (amplifies signal) and sends out a secondary messenger called cAMP. Pathway inactivate swhen ligand dissociates and proteins called phosphatases inactivate the relay proteins

6. 2 Ligands binds to the dimers. Theres three “tail parts” on the bottom that get phosphorylated and then it leads to multiple different transduction pathways.

7. A ligand like a steroid binds with a receptor. The receptor folds inward and makes a vesicle, which travels inside the nucleus and can act as a transcription factor (activate gene expression)

8. When bacteria communicate with each other to see how big the population is. When there are enough bacteria, they form a biofilm

9. Density dependence: cells stop dividing f they interact/touch each other. Anchor dependence: cells must be anchored to something in order to divide

10. Shape of receptors, hormones, shape of relay proteins and mechanisms to activate responses. Vary based on location and structure in parts of the body to initiate different types of responses

Unit 4: Cell Cycle

1. List the phases in order

2. What are the different G’s?

3. What is S

4. Chromosomes vs chromatids vs chromatin?

5. What are telomeres?

6. Steps of M

   • Prophase

   • Metaphase

   • Anaphase

   • Telophase

7. Cytokinesis

8. Where are the checkpoints?

9. What regulates the cell cycle?

10. How does cancer affect the cell cycle?

1. G1,S,G2,M and so on

2. G0 is no cell growth unless damaged, G1 and G2 are replicating cell parts and growing

3. S is DNA replication

4. Chromosomes is anything that has its own centromere (it is intially both sister chromatids before mitosis, then each sister chromatid becomes its own chromosomes). Chromatid are attached to each other when replicated. Chromatin is loose DNA when not undergoing mitosis

5. Telemores are the ends of the chromosomes that shorten after replication (discussed in next unit) which leads to aging

6. Mitosis Phases: produces two identical daughter cells (asexual)

   1. DNA coils up, nuclear membrane disintegrates, centrioles divide and move to poles

   2. chromosomes move to center (called the metaphase plate), spindle fibers from the centrosomes at the poles attach to centromeres (there are also kinetichore motor proteins and nonspindle fiber kinetichores that push off each other to elongate the cell)

   3. Nonkinetichore spindle fibers push off each other, kinetichores separate the sister chromatids and pull them to each side

   4. Nuclear membrane reforms, DNA uncoils, cells get ready to split

7. NOT a phase of mitosis. In plants, a cell plate is formed and the two cells are formed with a new cell wall forming between them. In animals, a cleavage furrow forms and the two cells split

Unit 4: Cell Cycle Regulation

1. Where are the checkpoints?

2. What regulates the cell cycle?

3. How does cancer function and affect the cell cycle?

4. How does the cell stop growth irregularities/malformations?

1. theres one between G1 and S, and then another between G2 and M, and another in metaphase of M

2. proteins called cyclins and CDKs (cyclin-dependent kinases). An example is MPF (maturation promoting factor), which stimulates the start of mitosis

3. Cancer bypasses the checkpoints, produces its own cyclin, also has telomerase so it can’t age. Mutations in proto-oncogenes (like the brca gene for breast cancer) turns them into oncogenes that promote excessive cell growth

4. DNA repair (nuclase excision), apoptosis (signaled cell death), p53 tumor supressor genes,

Unit 5: Meiosis

1. Haploid vs diploid

2. What are the processes of creating gametes called?

3. What thing/structure in meiosis that is not in mitosis?

4. How many divisions/phases does meiosis involve? Are the cells identical, and are the diploid or haploid after the FIRST division?

5. Describe prophase I and crossing over

6. The texan nine-banded armadillo has a diploid chromosome number of 64. How many chromatids would be found in an armadillo cell in prohpase I of meiosis

7. Types of error (single or double errors, and examples)

8. How can errors be identified?

1. 2n vs n number of chromosomes. Haploids are sex cells (gametes)

2. gametogenesis, spermatogenesis, oogenesis

3. Homologous chromosomes

4. 2 divisions, meiosis I and II (basically the same) except for some added steps. After the first division, the cells are haploid and NOT identical

5. In prophase I, homologous chromosomes come together to form a tetrad in a synapsis to perform crossing over. This exchanges segments of DNA, meaning the cells are no longer identical. Synapsis is process of creating tetrad at the chiasmata, disjunction is when tetrad separates. Process as a whole is crossing over

6. 128 chromaTIDS (they are sister chromatids). If it said how many chromoSOMES, then it would have just been 64 (always the same). If it says amount of DNA, then yes it does double.

7. Non-disjunction (dont separate) which leads to aneuploidy (abnormal # of chromosomes). If it happens in meiosis I then all four cells are wrong. If it happens in meiosis II, two cells are wrong. Monsomy is only 1 chromosome, trisomy if one extra Examples include Down syndrome, Triple X syndrome, Turner syndrome (monosomy X)

8. Karyotype (images of chromosomes taken during metaphase), aminocentisis (needle into amniotic sac)

Unit 5: Mendelian Genetics

1. What is a single gene called and its location? Names for physical vs genetic traits.

2. What are the 3 Generations?

3. Explain Law of Dominance.

4. Explain Law of Segregation. What is its proof?

5. Explain Law of Independent Assortment. What is its proof?

1. Allele. Loci is the position of the gene. Physical appearance is phenotype, genotype is about alleles.

2. Parent generaiton are pures purebred cross). F1 generation are hybrids (monohybrid cross). F2 Generation are the offspring of F1

3. Crossing purebreds yields all dominant phenotypes.

4. When a monohybrid cross is performed, there is a phenotypic ratio of 3:1 and 1:2:1 (homo dom: hetero: homo recessive). Shown by meiosis I where every gamete gets 1 allele

5. A dihybrid cross (crossing two different traits at once) yields a phenotypic ratio of 9:3:3:1 (D for both, D for trait 1 R for trait 2, R for trait 1 D for trait 2, R for both). Shown by meiosis II where sister chromatids are separated so that each trait is segregated separately

Unit 5: Non-Mendelian Genetics

1. Thomas Hunt Morgan and his rules

2. What is a Linked Genes? What does it violate?

3. How to find determine if genes are linked and frequency of crossing over given a table

4. What are Sex linked traits and how are they represented with letters?

5. What is a barr body?

6. Incomplete dominance vs co-dominance?

7. What is polygenic inheritance

8. What are examples of non-nuclear inheritance?

9. What is it called if the environment influences your phenotype, even if you have the same genotype?

10. What is epistasis?

1. He said that there is a wild type (dominant phenotype) and a mutant type (recessive phenotype). Use the lowercase abbreviation of the mutant trait (NOT the uppercase letter of the wild). For example, a vestigial (mutant) trait is vg, vg+ for wild type. Parental type means it has the same phenotype as the parent. Recombinant means the offspring is a combo of the parent alleles.

2. Genes on the same chromosome, inherited together. violates Law of independent assortmen.

3. they give you a chart of genes and if you take the number of recombinant divided by total x100 you find how far the genes are apart in map units, which is also the frequency of crossing over (genes ar linked if less than 50 map units). Using these map units and the distance between genes, you can gene map

4. Genes on the sex chromosomes not autosomes. Can be X-linked or Y-linked, so frequency of inheritance depends on gender.

5. All but one of the X chromosomes are inactivated and condensed.

6. Incomplete dominance is when traits are blended (red+yellow = orange). Codominance is equal expression (like stripes)

7. When a trait results from the interactions of many different genes that each have a different effect, like height

8. Mitochondrial DNA from mother, chloroplast DNA

9. Phenotypic plasticity (NOT epigenetics b/c epigenetics DOES change gene expression but doesn’t change the DNA sequence). An example of this is the number of stomata on a leaf (less stomata if more CO2 b/c they don’t want too much gas escaping)

10. When another gene controls the expression of a different gene. If an organism does not have a dominant phenotype for the epistatic gene, then it does not matter what the other gene is, the person won’t have that trait. (ex: phenotype is Aarr, where A is dominant gene for red color, a is for white color, R is dominant and means that pigment is shown, r means that pigment is not shown. Since two little r's, no pigment is shown and organism is white despite being homo dom. for red).

Unit 5: Pedigree Charts

1. Circle vs square?

2. What are the 6 different types of traits?

3. How can you tell if a trait is Y-linked?

4. How can you tell if a trait is mitochondrial?

5. How can you tell if a trait is recessive?

6. How to tell apart Autosomal Dominant and X-linked Dominant

1. Circle is woman (XX), square is man (XY) which matters for sex-linked traits

2. Autosomal Dominant, Autosomal Recessive, X-linked Dominant, X-linked Recessive, Y-linked, Mitochondrial

3. Y-linked if only males have it

4. Mitochondrial if the mother gives it to ALL her offspring

5. It “skips” a generation (parents don’t have the trait) its usually recessive

6. If there are way more female that have it, it’s X-linked dominant (has to be much more. If it’s not, the best way is to just plug in either T and t for autosomal or X^N and Xⁿ and check.

Unit 6:

1. What are the extra pieces of DNA in prokaryotes?

2. Describe the structure of molecules inside DNA and its shape

3. Hershey and Chase Experiment

4. What is Chargaff’s Rule?

5. Meselson and Stahl?

6. What did Watson, Crick, and Franklin do?

7. What is epigenetics and how does it work? What are the two types of chromatin?

1. Plasmids are double-stranded circular DNA that can be used as vectors (mediums) to transfer genes in the process of transformation/conjugation (prokaryotes taking in other DNA)

2. Covalently-bonded sugar-phosphate backbone on the outside, hydrogen-bonded nitrogenous bases on the inside. Double helix

3. They found that DNA was the “transforming factor” (genetic material) by experimenting with viruses. They used radioactive sulfur (in proteins) and radioactive phosphorus (in DNA) and saw that when viruses replicated, only the radioactive phosphorus remained in the next gen

4. Since A-T and G-C bond as complementary bases, then proportion of A must be same as T (same for G and C).

5. Franklin took a picture of DNA looking from above and saw that that are equal strands across the center (meaning purine bonds to pyrimidine). Watson and Crick built off her work and made a double-stranded model

6. They found that DNA replicates semiconservatively. This is just the idea that each strand of DNA serves as a template for its compliment strand and that DNA is not just replicated randomly or an entire double strand is just made on its own.

7. When your gene expression is altered even though your DNA sequence is the same. DNA is methylated and wound up it balls of histone proteins called nucleosomes to deactivate it (this is called heterochromatin). DNA is activated to be transcribed if its histones are acetylated (this type of loose chromatin is called euchromatin)

Unit 6: DNA Replication

1. What are the two strands called? Where does replication start?

2. What are the steps of replication with the enzymes?

3. What is the directionality of DNA poly and what does this lead to?

4. What is the purpose of a telomere?

5. What is the Central Dogma of Biology and what is the exception?

6. What are the types of RNA?

1. BOTH strands are templates for a new strand to be formed, from the origin of replication (in prokaryotes) or at a replication bubble, which forms replication forks.

2. Helicase unwinds the DNA helix. Topoisomerase stops the helix from retwisting. Single-stranded binding proteins prevent strands from rebinding. Primase adds RNA primer to DNA. DNA poly III adds free nucleotides starting at the primer. DNA poly I replaces the RNA primer. Ligase attaches the okazaki fragments.

3. DNA poly READS 3’ to 5’ and BUILDS a new strand in 5’ to 3’. (note that 5’ is the side with the phosphate, 3’ is with OH). Because of this, one strand is built continuously (leading) and the other strand is built in pieces (okazaki strands on lagging strand)

4. Telomeres are repeated noncoding sequences on the ends of genes that are shortened over time b/c DNA replication can’t replicate up to the last nucleotide because of its directionality. This leads to aging

5. DNA to RNA to protein. Exception are retroviruses with reverse transcriptase that can go RNA to DNA to RNA to protein.

6. Includes messenger RNA (the copy of DNA), ribosomal RNA (makes up ribosomes), transfer RNA (bring amino acids to ribosome by pairing anticodon to codon)

Unit 6: Gene Expression

1. Describe the steps of transcription

2. Describe RNA processing

3. How does a tRNA bind to an amino acid and then to a codon?

4. Why can the third position change but still result in the same amino acid?

5. Describe the steps of Translation with reference to the ribosome sites

6. Whats different about transcription-translation in prokaryotes?

1. Transcription factors (proteins) bind to promoter site of DNA that is before the gene (this is called a “TATA” box in eukaryotes). Then, RNA poly binds to the promoter site and starts to transcribe (creates pre-mRNA). The strand that is copied is the template (NONcoding strand). The steps are called Initation, Elongation, Termination (same as tRNA). Termination is when a certain nucleotide is hit, leading to a “polyadenylation signal”

2. A GTP cap is added to the 5’ end, a poly A tail is added to the 3’ end (this prevents mRNA from getting degraded) and alternative RNA splicing occurs (exons are KEPT, noncoding introns are cut OUT). This is done by a spliceosome

3. An enzyme called tRNA aminoacyl-synthetase binds the amino acid to the right tRNA. Then the tRNA matches its anticodon to its compliment mRNA codon during translation

4. There’s something called “wobble pairing” where things that don’t normally bind can pair up, so the last nucleotide is the least important

5. There are three sites of the ribosome: E (exit), P (peptidyl), and then A (arrival). Starts with Initiation: AUG start codon codes for Methionine amino acid. The next tRNA binds at the P site and it forms a peptide bond there. The order is that tRNA arrives at A, leaves its AA at P, and exits without AA and E (this is called elongation). Then, when all the necessary amino acids go and a stop codon is hit, this starts termination.

6. Prokaryotes do transcription and translation simultaneously because no transport out of the nucleus and no need for modification

Unit 6: Gene Expression Regulation

1. How is DNA regulation (there are 4 ways)

2. What is an operon?

3. Discuss lac operon.

4. Discuss trp operon.

5. what is eukaryotic regulation?

6. How is alternative DNA splicing a form of regulation?

7. What are post-translational modifications?

8. What is RNA Regulation? How do miRNAs work?

1. Epigenetics, operons, alternative DNA splicing, post-translational modifications, RNA Regulation

2. An operon is a section of DNA (ONLY prokaryotic) that has a promoter site, operator site, followed by the gene. There is another regulatory gene that codes for a repressor protein. This repressor protein then binds to the promoter region and can prevent RNA poly from binding

3. the lac operon is an inducible operon, meaning it is only activated if necessary. Lactose acts as allosteric inhibitor for the repressor protein. If lactose is present, the repressor protein undergoes a shape change to its active site and cannot bind to the promoter, allowing transcription to happen. Transcription leads to the creation of enzymes that break down lactose. When lactose is broken down, it cannot inhibit the repressor protein and the gene is “off” again. Also important to note there are other mechanisms that regulate the lac operon. For example, when glucose concentration is low, levels of cAMP rise which serves as an enhancer to the RNA poly on the lac operon

4. The trp operon is a repressible operon, meaning it is on unless there is too much product being produced. When there is a lot of tryptophan (an essential amino acid), then the operon is turned off because trp acts as a cofactor for the repressor protein. When there is little tryptophan, then the operon is activated (b/c repressor can’t be activated).

5. Eukaryotes have a bunch of different proteins that work together with transcription factors to allow the RNA poly to bind. These include mediator proteins, enhancers+activators (they fold to help transcription factors bind to promoter), and bending proteins that are specific to certain genes. Also signal transduction pathways (hormones like growth factor)

6. one gene can lead to many different proteins based on which introns are cut out to make specific mRNAs

7. Changes made to a protein’s function, like adding functional groups to the protein or its ends, or even destroying it by using big enzyme complexes called proteasomes

8. RNAi means RNA interference. RNA molecules can pair with mRNA transcripts, and if they match they either repress translation or destroy the mRNA.There are also siRNAs which can degrade mRNA as well. If a gene is doubled then it is “silenced” by RNAi.

Unit 6: Mutation and viruses

1. What can cause mutation?

2. 3 types of point mutations

3. Explain gene rearrangements and framshifts

4. What is a virus and what is its structure?

5. Lytic vs lysogenic cycle

6. What is horizontal gene transfer?

7. What is a hox gene?

1. Chemicals, radiation (UV causes thymine dimers, where thymines in DNA sequence can bind to each other), viruses, meiotic/mitotic errors, replication errors

2. Substitutions can cause nonsense mutation (results in stop codon, worst outcome), nonsense (wrong amino acid), silent (same amino acid, no difference)

3. Genetic rearrangments include insertions and deletions that can cause frameshift, duplications, inversions (part of the cromosome get oriented wrong), translocations (part of a different chromosome attached to a different one)

4. Virus is not technically living, it a protein case with genetic material (could be double or single stranded DNA or RNA). It is a parasite that requires a host to reproduce its proteins/genome

5. Lytic cycle is hen virus immediately uses host cell’s machinery to replicate its genetic info and make its proteins, filling up with copies of itself until it lyses (bursts) the cell. Lysogenic cycle is where virus implants its genetic material into host sequence, laying dormant until it gets triggered by environment to start reproducing itself resulting in a lytic cycle (like HIV). This can result in viral bacteria being transferred through a process called transduction

6. Although bacteria produce asexually by binary fission, they can increase their genetic diversity by conjugation (exchanging DNA with other bacteria) and transformation (taking up outside DNA)

7. A hox gene is a gene that has to do with making sure that body parts are in the correct places (like a ear does not grow on your chest)

Unit 6: Biotechnology

1. What is recombinant DNA technology?

2. What is PCR?

3. What is gel electrophoresis?

1. When a plasmid is removed from a bacteria, cut with a restriction enzyme. Another gene (could be insulin gene from eukaryote that already has introns removed) is then cut with the same restriction enzyme so that is has matching sticky ends which can be attached to the plasmid by using ligase. Then heat shock the bacteria so it takes in the plasmid (transformation) and it will produce the protein

2. PCR is a way of amplifying a DNA sequence by first denaturing the DNA sample (raising heat to break hydrogen bonds), then adding primers, DNA poly, and free nucleotides. Decrease temperature so that the DNA can replicate. Repeat this process again and again.

3. A block that is connected to a battery that supplies a current across the gel (made of a sugar called agarose). It seperates DNA based on charge and size because of the current (remember DNA is negatively charged b/c of the phosphate)

Unit 7: Evolution

1. What is evolution? Who came up with it?

2. What are Darwin’s observations about evolutionary fitness?

3. Who was Lamarck and what was his ideas? Why was he wrong?

4. List the 5 pieces of evidence for Evolution

5. What is the story of the peppered moth?

6. What determines if evolution occurs?

1. Evolution is the accumulation of genetic changes over time that results in an increase to fitness; survival of the fittest. It was developed by Charles Darwin while working with finches on the Galapagos Islands

2. Fitness is measured by how an organism is able to survive AND how much it can reproduce (MUST SAY THIS**). Favorable traits are selected for by the environment and provide differential relative fitness. Species produce more offspring than resources available.

3. Lamarck was the guy who looked at acquired traits (like tattoos or muscles). He thought that these passed on, but he was wrong because acquired traits don’t change genotype of the way genes are expressed (not epigenetic, although stress can alter epigenetics).

4. Comparing anatomy/morphology (includes homologous features or vestigial features), comparative embryology (how organisms develop from birth), comparing DNA, comparing proteins, and biogeography (where the organisms are and how they interact with their environment)

5. The peppered moth were almost all white in allele frequency but the industrial revolution turned trees black, so darker colors were selected for because these organisms were better able to camouflage and not be eaten, thus increasing the proportion of dark alleles.

6. Change in biotic and especially abiotic (environmental) factors

Unit 7: Mechanisms of Evolution

1. What are the three main mechanisms of evolution?

2. What are the 5 types of Natural Selection?

3. What are the types of genetic drift?

4. what is gene flow?

5. What are the two theories of how evolution occurs over time?

6. Name all the sources of diversity at the cellular, individual, and population levels.

1. Genetic Drift, Natural Selection, Gene Flow

2. Stabilizing selection (population becomes more centered towards hybrids), Disruptive selection (hybrids become very low in number while homozygous genotypes become more common), Directional (one allele becomes more common than the other), frequency dependent (predators tends to eat the more common phenotype, even if it isn’t the dominant allele, like white colors for worms is a dominant trait but since its more common in the population birds eat it and therefore most worms are black), sexual selection (males compete for females, or females choose their mates, not random)

3. Bottleneck effect: loss of genetic diversity when there is a big natural disaster or extinction that leaves only a couple members of the population alive. Founder effect: usually from birds being blown offcourse of geographic isolation that results in new population forming that is genetically different than the other (also less diverse)

4. Gene flow is immigration and emigration (going out), which can introduce new genes or remove genes from a population

5. One theory about evolution is punctuated equilibrium (long periods of stasis and quick periods of rapid evolution) and gradualism (evolution occurs in small steps over time), neither is wrong (that’s why you see phylogeny charts that look like forks and others that look more like trees)

6. Cellular: segregtion, independent assortment, random fertilization, crossing over, mutations (and environmental mutagens like carcinogens), aging and determination of telomeres, viruses. Population: any mechanism of natural selection, recombination/sexual selection or evolution in general can be discussed.

Unit 7: Speciation and Population Genetics

1. How to use Hardy Weinberg Equations

2. Name the 5 conditions for Hardy Weinberg Equilibrium (for no evolution)

3. What is convergent evolution?

4. What is speciation and what does it mean for two populations?

5. Name the 8 Pre/post-zygotic barriers to fertilization (that lead to speciation)

6. What are allopatric and sympatric speciation?

7. What is the expeirment done about the origins of life on earth that you need to know?

8. What is the RNA-world hypothesis?

1. p²+2pq+q² p² is homozygous dominant, 2pq is heterzygous, q² is homo recessive. p²+2pq represents dominant phenotypes, q² is recessive phenotypes. If they give you that x% show the recessive trait then this is q². From there you can square root to find q and then use the formula 1 = p + q to do the rest

2. Large population (a small popualtion is suspetible to environmental impact), no mutations (this can add new alleles), no gene flow (can introduce new alleles), non-random mating (no sexual selection), no natural selection (environment can’t give preference to a certain allele)

3. Prezygotic: Habitat Isolation, behavioral isolation (like mating dances), Temporal (time/season), mechanical (size/structure of gonads), gametic isolation (gametes can’t fertilze each other).

   Postzygotic: hybrid inviability (hybrid is weak and feeble, die early), hybrid infertility (can’t reproduce, like liger), hybrid breakdown (even if hybrids are able to produce offspring the next generation experiences inviability or infertility)

4. Where two different species develop similar traits because of their environmental pressures (like bats and birds) but the structures of these features are completely different and not due to common ancestry (called analogous features).

5. Creation of new species due to accumulation of genetic change. Means that two populations CANNOT produce fertile or viable offspring (due to the barriers).

6. Allopatric speciation is speciation that results from geographic barriers and interruption of gene flow (can’t interbreed so becomes new species), and sympatric is when other barriers, like behavioral or temporal don’t allow the two groups of a population to meet up and so they speciate

7. Miller-Urey experiment shows that organic compounds like amino acids can be created by early earth conditions (using inorganic compounds, heat, electricity, and no O2)

8. RNA world-hypothesis says that orignal life-forms started with RNA as genetic material and developed from there. A piece of evidence are ribozymes, which are RNA molecules that serve as enzymes.

Unit 7: Phylogeny and Cladograms

1. Differences between the two

2. What is a shared derived character vs ancestral characteristic?

3. What is an outgroup?

4. What is adaptive radiation?

5. r vs k-selected species?

1. phylogeny shows evolutionary relationships over time. Cladograms show common ancestry, and the dashed lines at ht intersection points represent a new defining trait that split the two paths.

2. Shared derived character is a trait that all members of a certain cladogram group has. An ancestral characteristic is a trait that all descending groups of a species have.

3. The group that branches off first from the rest

4. Evolution that occurs rapidly if there is a need to fill empty niches. Like when birds reach a new island with no other birds, they differentiate with food sources, with some birds focusing on being ground birds, others being fish birds, etc. Resource partitioning. Remember that NO TWO species/populations can occupy the same niche in the same area. They must use different resources in different ways or else one would just outcompete the other and would go extinct or have to adapt.

5. R-species is a species that reproduces quickly and produces small offspring in the hopes of prioritizing the increase size of the population. K-selected species reproduce slower, are larger, and take the time to raise their young (quality not quantity)

Unit 8: Ecology of Communication and Environmental Behavior

1. Endotherms vs ectoderms

2. Explain the following instinct, imprinting, pheromones, altruistic behavior.

3. 3 Symbiotic Relationships

4. What are plant hormones and what is tropism?

5. What are the orders of ecological organization?

6. What is net productivity?

1. Endotherms generate their own body heat using metabolism (metabolic processes release heat, 2nd Law of thermodynamics). Ectotherms have a metabolic rate (i.e. respiration rate) that depends on environmental temperature, dont have set body temp.

2. Instinct is a behavior that is known from birth. Imprinting are traits learned very on as an offspring that carry on in the offspring, pheremones are chemical signals that attract mates. Altruistic behavior are behaviors that benefit the population (like giving warning calls to other species members or worker bees slaving away for the queen)

3. Mutualism (+/+) both organisms benefit, Commensalism (+/0) one organism benefits while the other is unaffected, parasitism (+/-) one organism benefits while host is harmed

4. Plant hormones include ethylene gas (promotes ripening), auxins (promote tropism). Tropism is the tendency of a plant to grow in response to a stimulus, like plants growing towards sunlight is called phototropism

5. Population (group of same species in an area), community (all living things in an area), ecosystem (all living/nonliving things in an are), biosphere (everything on Earth where living things exist)

6. measures how organic materials that are left over after photosynthesis organisms take care of their own needs (what passes on to the next trophic level)

Unit 8: Ecological Relationships and Diversity

1. What are the trophic levels?

2. How to draw a food web properly

3. How much energy is traveled up trophic levels?

4. What is biomass?

5. What is a keystone species?

6. What is Simpson’s Diversity Index? (on reference table)

7. Two types of population growth and what makes them different

8. What are limiting factors, and what are the two different types?

9. Two types of ecological succession

1. Producers (autotrophs), primary consumers (herbivores), secondary consumers (omnivores and carnivores), tertiary, quaternary consumers. Decomposers break down

2. Arrows grow in direction of energy flow (or points to what eats it). Longer arrows from organisms at the bottom, arrows get smaller as you go up. DONT FORGET DECOMPOSERS, all arrow go to the decomposer

3. 10% of energy transfers at each trophic level (be careful if they say 90% lost as heat)

4. the total quantity of dry mass of organic material (living and dead) in an area

5. A keystone species is a species that is so interconnected with an ecosystem that if it were removed all other species would decline or collapse

6. Diversity Index = 1 − Σ(n/N)^2 where n is the number of a certain organism, and N is the total number of organisms in an area. Basically, you just sum up all the types of organisms divided by the total number, square it, then subtract it from 1.

7. Exponential is dN/dt (rate) = rN where r is equal to (birth-death)/total number of organisms. There is no bounds. Logistic curve is where there is an upper bound to the growth, so it grows at a fast rate, then switches to a slow rate. It reaches a maximum population amount (called a carrying capacity K) b/c of limiting factors

8. Limiting factors are resources that are limited in quantity that prevent populations from expanding. Include abiotic and biotic factors like food, space, water. There are density dependent factors that increase in effect as the population grows, like competition, or disease. There are also density independent factors that always limit a population regardless of its size, like weather or droughts.

9. Ecological succession is the progression of plants. Primary succession starts with a pioneer species that creates the soil, and then progresses until a climax community is reached. It can be stopped at different points in different biomes (this is why some forests have deciduous trees, while others are pine trees). If succession is interrupted, like by a fire, then it is secondary succession and it returns to climax community

Unit 8: Threats to Biodiversity

Explain the causes, effects of the following issues:

1. Biological Magnification

2. Global climatic change (DON’T say global warming!!)'

3. Ozone depletion

4. Acid Rain

5. Deforestation

6. Invasive species

7. Eutrophication

1. When a pollutant (like DDT) leaches into the bottom levels of a food chain (like absorbed by plants) and then it travels up and amplifies in effect because the higher levels eat more and more of the bottom levels.

2. Caused by greenhouse effect, pollution, burning of fossil fuels. Increases temperatures which can lead to habitat destruction and harm biodiversity.

3. When the ozone layer of the atmosphere is destroyed by pollutants like CFCs (chlorofluorocarbons), leading to more mutations b/c more UV rays get through the atmoshpere.

4. Caused by pollution of factories. Leads to rain with lower (more acidic pH), which can kill plants and life and destroy environments.

5. Chopping down trees results in habitat destruction (doesn’t really increase carbon emissions like most think b/c oceans produce most of the oxygen by doing photosynthesis, not trees)

6. When a new species is introduced by accident into a new area and since it has no natural predators it disrupts food chains and can destroy ecosystems (spotted lantern fly)

7. When excessive nutrients are dumped into a body of water (like nitrogen fertilizers), leading to huge blooms of algae. These excessive plants then overuse resources like oxygen which can kill animals living in the water

Experimental Design - ALWAYS the first or second question on the test

1. What are all the parts you need?

2. Positive vs negative control groups

3. Fermentation Tube Procedure

4. Respirometer Procedure

5. Catalase Lab Procedure

1. Hypotheses, independent/dependent variable, control groups, factors kept constant, data collection method, need to state repetition or large sample size, and then some sort of statistical analysis to determine significance, like chi square

2. A positive control has a known effect. A negative control is a treatment (or absence of a treatment) that has no effect

3. Fermentation tube: put yeast in the bottom of the tube, fill it will water, add sugar. The rate of fermentation is measured by the number of carbon dioxide bubbles produced at the top, vary the amount of sugar.

4. Not too important but its something like you put an organism in a jar with a stopper that has a tube in it and you measure the pressure difference

5. An enzyme that breaks down hydrogen peroxide to make oxygen gas and water. Use varying concentrations of hydrogen peroxide and measure the number of air bubbles.

Chi Squared Test

1. What are the hypotheses?

2. How to use the formula and calculate expected value

3. How to find degree of freedom

4. How to find the “critical value” When can you reject the hypothesis?

1. Always two hypotheses. Null says that the outcome is due to random chance alone or has no effect, alternative is whatever the experiment wants to find out (like the phenotype is due to nonmendelian genetics not random chance)

2. (o-e)²/e where o is the observed (what they give you in the question), and e is the expected (need to calculate it based on genetics. For example, in mendelian genetics, if you do a monohybrid cross there is a 75% expected value of the dominant phenotype, just use punnett squares)

3. The degree of freedom is (number of outcomes - 1). For mendeliang enetics, there are two outcomes: either you get the dominant phenotype or recessive phenotype, so df = 1. They try to trick you sometimes though, so if its like incomplete dominance and the heterozygote leads to a trait so that there are 3 outcomes, then df = 1. If they are talking about two traits, there are 4 different outcomes then, so df = 3

4. Critical value is the value of the reference table that you see when looking under the degrees of freedom you found. You can reject anytime your calculated value is GREATER than the p = 0.05 value.