AP BIO EXAM REVIEW

What are the bond between hydrogen and oxygen in water? Between molecules? Why?

polar covalent; hydrogen; polarity

How do saturated fats compare to nonsaturated ones?

Saturated fats straight C chain, solid; unsaturated kinked (double bond in C chain), liquid

Protein structures:

primary: peptide bonds, secondary: hydrogen bonds AA, tertiary: interaction hydrophilic/phobic R groups, quartenary: multiple polypeptides

Prokaryote DNA? Eukaryotic organelles?

prokaryotes circle chromosome in nucleoid; eukaryotes membrane bound organelles

ER, Golgi, Lysosomes, Centrosomes, Peroxisome, Nucleolus, Cytoskeleton

ER: s for lipid synth, r for protein. Lysosomes digest enzymes. Centrosomes: arrange microtubules in spindle. Peroxisome: breaks down toxins in cell. Nucleolus: where ribosomes assembled, cytoskeleton: shape

Fluid Mosaic Model - types of protein, and what is in it to adjust fluidity? What can easily cross the membrane?

Peripheral somewhat through, surface protein on surface, channel is through. Steroids throughout adjust fluidity. Small, nonpolar, hydrophobic molecules easy cross.

Types of Passive Diffusion? Types of Active Diffusion?

Passive: diffusion, osmosis, facilitated. Active: pump, against concentration/large, endo/exocytosis

Hypertonic, Hypotonic, Isotonic; water potential? Osmoregularity?

Hypotonic: lower solute, hypertonic: higher solute, isotonic: same. Water potential is ability water do work, higher with more. Osmoregularity is concentration of solutes.

Coenzymes vs. cofactors; how do enzymes make reactions more efficient?

Cofactors (inorganic) and coenzymes (organic) help enzymes functuon. Enzymes lower activation energy by putting reactants proper orientation, bending substrate to destable bonds, forming temp. bonds with it.

Endergonic vs. Exergonic Reactions

Endergonic: reactants have products with higher free energy - unfavorable; exergonic favored, reactants have higher free energy

Photosynthesis: What are the two processes, and what do they provide to each other? What else do they need?

The light dependent reactions get photons from the sun, and convert H20 to O2, providing the Calvin Cycle with ATP and NADPH. The Calvin Cycle recieves CO2 and releases sugar, providing NADP⁺ and ADP + P_i to the light dependent reactions.

Where do the light dependent reactions occur? What happens in photophosphorylation and photolysis?

In the thylakoids.

• Light energy excites electons in the chloroplast to higher energy, which is released as they move through the chloroplast.

• ETC: Photon energy excites electrons in PSII chlorophyll, then passed by protein carriers in redox reactions until the final electron donor passes electrons to PSII. As electrons go through ETC, energy used for proton gradient, and H+ ions active transport across thylakoid membrane.

The light dependent reactions: How are electrons in PSII replaced? What occurs in chemiosmosis?

• Electrons in PSII replaced by hydrolysis - splitting water molecules; electrons remove from H for ions and eectrons, also release O2 gas.

• Chemiosmosis: ATP synthase; protons pumped out of thylakid, to diffuse in use, phosphorylation of ADP by energy.

• PSI electrons boosted by another photon, through carriers to NADP+ with a P+ by NADP+ reductase to create NADPH.

Light-Independent Reactions

Occurs in the stroma:

1. Carbon fixation: Enzyme Rubisco adds 1 carbon to 5 carbon RuBP from unstable 6 carbon intermediate that immeadiately forms 2 3C molecules.

2. Reduction: ATP and NADPH reduce 2 3C molecules - energy from ATP, e- from NADPH. 3C G3P produced, used to make sugar or for regeneration.

3. Regeneration of RuBP: 5C, needed to continue Calvin cycle; for every 5 G3P, 15 C present - with ATP, rearrange to form 3 RuBP.

List the steps of aerobic cellular respiration

Glycolysis, the link reactions, the Krebs Cycle, Oxidative Phosphorylation

Cellular Respiration: Glycolysis

In the cytosol. Input: 2 NAD+, 2 ATP, glucose (6C). Output: 2 pyruvate (3C), 2 NADH, 4 ATP

Cellular Respiration: The Link Reaction

The matrix. Input: 2 pyruvate, 2 NAD+. Output: 2 acetyl CoA (4C), 2 CO2 (2C), 2 NADH.

Cellular Respiration: The Krebs Cycle

Matrix. Input: 2 acetyl CoA, 6 NAD+, 2 FAD+, 2 ADP + Pi. Output: 4 CO2, 6 NADH, 2 FADH2, 2 ATP

Oxidative Phosphorylation: Inputs/Outputs, 2 major processes?

Inner mitochondrial membrane. Input: 10 NADH, 2 FADH2; output: about 34 ATP. ETC and Chemiosmosis occur here.

Oxidative Phosphorylation: ETC

NADH, FADH2 brought; hydrogen split to electrons and ions. Electrons pass through embed protein carriers, to final electron acceptor oxygen to make water.

Oxidative Phosphorylation: Chemiosmosis

Energy from ETC pumps H+ from the matrix to the intermembrane, producing proton gradient. H+ wants to diffuse back to matrix; does so through ATP synthase, ADP is phosphorylated.

Substrate level phosphorylation

Direct phosphorylate without ETC/chemiosmosis, not as much ATP.

Anaerobic: Alcohol Fermentation

2 pyruvate + 2 NADH → 2 ethanol + 2 CO2 + 2 NAD+

Anaerobic: Lactic Acid Fermentation

2 pyruvate + 2 NADH → 2 lactic acid + 2 NAD+

types of cell signaling: autocrine, juxtacrine, paracrine, endocrine. Positive vs, Negative Feedback

autocrine: ligand from self, juxtacrine: touching cells, paracrine is close by, endocrine is by hormone, long distance. Positive Feedback deviates homeostasis; Negative brings return to.

Signal Transduction Pathways:

1. Reception: hydrophilic ligand binds to membrane receptors, otherwise ligand bonds inside. Recpetor changes shape.

2. Transduction: chem. reactions help cell choose response. Siganl cascade: chemical reactions cause molecules trigger, signal amplification. Kinases: active molecules by p-late. Enzymes make secondary messengers.

3. Response

What do cyclin and CDK do in the cell cycle. How do proto-oncogens work - what are oncogens? How about tumor suppresor molecules?

cyclin and cyclin-dependent kinases = mitosis promoting factor. Proto-oncogen propels; oncogen is a mutated. tumor suppresor genes slow/correct mutations.

Name the steps of the cell cycle and give a brief summary of the steps. How does density-dependent inhibition, anchorage dependent? When does recombination happen?

G1: growth, S: grow and DNA replication, G2: growth and prep divide, M: mitosis. If too many cells, stop divide; anchorage: need to be attached to something to divide. Recombination during prophase I.

Mendel’s Law of Segregation? Mendel’s Law of Independent Assortment? Linked genes? Phenotype plasticity?

Segregation: people have 2 copies gene, segregate independent to gametes. Assortment: genes sort seperately into gametes - unless linked (map units). Phenotype plasticity: depends on environment though same genes.

STUDY THIS DNA replication - what is it considered? What does helicase do? What does topimerase do? What does polymerasedo? Leading strand synthesis; lagging strand synthesis?

DNA replication semi-conservative. Helicase unzips; topimerase nicks to release tension before sealing, RNA polymerase makes RNA primers, DNA polymerase synth 3’ to 5’, adds nucleotides in 5’ to 3’. Leading strand 3’ to 5’, adds nucleotides 5 to 3. Lagging strand 5’ to 3’, Dna pol gors oppostie to read 3 to 5, ligase glues Okazaki fragments.

How does RNA transcribe genes? How is mRNA refined to mature mRNA?

RNA pol transcribes by bind promoter, with help transcription factors. TATA box helps identify. Adds new nucleotides 5 to 3, transcribes 3 to 5. mRNA refined 3 ways: Noncoding introns removed from exons by splicosome - alt. splicing. 5’ end protected 5’ GTP cap - allow exit nucleus and initiate translate. 3 pol-A by that polymerase to stop degrade.

Translation: Inititation, Elongation, Termination

Initiation: rRNA pairs with start codon, and tRNA brings corresponding AA. Elongation: ribsomes translocates (move) next codon, new tRNA and peptide bonds AA. Repeat - 1st tRNA released. Termination: stop codon, release factors bind to ribosome to ribsome to dissassemble and release.

What is a promoter? What is a operator? What is a structural gene? Inducible operons vs. repressible operon?

Promoter where RNA polymerase binds. Operator: noncoding seq binding site for repressors. Strucutral genes coding seq. with genes to function. Inducible operons catabolic: turned off unless inducer present, repressor on operator until inducer binds to make ineffective. Repressible: anabolic, on unless product abundant; corepressor helps repressor protein bind to operator sequence.

Eukaryotic Gene Regulation: Promoters, regulatory switches, mediators, epigenetic changes

Promoters, regulatory switches: enhancers - reg. switches where activator proteins/transcription factors, silencers - repressor protein binders. Mediators: connects regulatory proteins and allow communication. Epigenetic changes: reversible mod to DNA nucleotides.

How can differential gene expression help? What are the 4 methods of differential gene expression?

Differential gene expression = different cells.

1. Transformation: uptake naked foreign DNA

2. Transduction: transmission from one organism to another by virus

3. Conjugation: by cell contact, like by pilus

4. Transposition: genes jumping around between/within chromosomes

Intersexual vs. Intrasexual Selection; Interspecific/Intraspecific Competition

Intersexual Selection: one sex picky; Intrasexual Selection: individuals of the same sex compete for mates. Interspecific competition: different species, intraspecific competition: same species

5 conditions for HW

1. Large population

2. No gene flow

3. No mutations

4. No migration

5. No natural selection

extant

a species with living individuals