AP Bio Exam Review

Molecular Biology

• Importance of molecules and bonding

Bonds:

Ionic – transfer of electrons, results in charged atoms or ions

Covalent – sharing of electrons; most common in organic molecules

Types of covalent bonds

• Polar – results if one element is more “grabby” for the electrons (oxygen, nitrogen)

ex – Oxygen in the H2O molecule

• Nonpolar – electrons are shared equally, no areas of charge

• Important in shape of molecules

Bonds between molecules

• Hydrogen bonding- “attraction” between H of one molecule and an electronegative element in another molecule

• Van der Waal forces: is the sum of the attractive or repulsive forces between molecules

Organic chemistry – the chemistry of Carbon compounds• Most biochemical macromolecules are

polymers (units linked together)

• For the exam, think about what elements are found in the various macromolecules.

Carbohydrates

• Main energy source

• Made of monosaccharides

• many H and OH

• In water, forms rings

• Can link together to form disaccharides or polysaccharides (starches) with the loss of a water molecule (dehydration synthesis or condensation reaction)

• When polysaccharides are taken apart, water has to be added back in: Hydrolysis

Important polysaccharidesThese are made of glucose units.• Glycogen – animal starch, stored in

liver and muscles

• Cellulose – plant starch (animal can’t digest)

• Amylose – plant starch

• Don’t forget when figuring out formula for the polysaccharides to subtract the water molecules!

• Linking 6 glucose (C6H12O6) units:

Proteins

• Made of amino acids (20)

• Used for structure, enzymes, hormones,

transport molecules, etc.

• Shape very important

R groups?

• Make each amino acid unique

• Can confer polarity to the protein

• Can be hydrophobic or hydrophilic

• Important in secondary and tertiary folding

• Amino acids are linked by peptide bonds in a condensation (dehydration) reaction

Orientationis important –Carboxyl group joined to amino group

Three levels of protein structure

• Primary: chain of amino acids

• Secondary: Beta pleats and alpha helix

due to hydrogen bonding

• Tertiary: interactions betweenR groups due to ionic attractions,

polarity, disulfide bridges, etc.

• Quaternary: attractions between chains

Lipids

• Used for insulation, energy

• Nonpolar (do not dissolve in water)

• Contain fats, oils, waxes, steroids such as cholesterol

Structure of a fat – glycerol and 3 fatty acids

unsaturated

Phospholipids make up cell membranes

Steroids, such as cholesterol,ring structure

Also important in cell membranes

Nucleic Acids

• DNA, RNA

• Made of nucleotides

• Each nucleotide has a sugar, phosphate, and a nitrogenous base (A,T,C,G)

• Nucleotides also found in ATP and GTP, energy transfer molecules

Enzymes

• Protein catalysts

• Very specific

• Affected by temp, pH, competing molecules

• Rate can be altered by amount of substrate/enzyme

• Usually named by what they work on

Enzyme Lab

• Catalase – breaks down hydrogen peroxide into water and oxygen

• Used sulfuric acid to stop reaction

• Titration using KMnO4 to measure amt of H2 O2 left.

• Measured rate

The rate can be defined as the amount of product formed in a period of time.

Or it can be defined as the amount of substrate used in a period of time.

Allosteric Interactions• Another molecule can bind and cause

the enzyme to change shape

Difference in Eukaryotic and Prokaryotic Cells

• Prokaryotic cells do not have membrane-bound organelles such as nuclei, ER, Golgi, etc.

• Their energy reactions are carried on in sections of their cell membrane.

• They do have ribosomes , DNA and some have cell walls.

Developing the eukaryotic cell

• Think about importance of an endomembrane system (endocytosis)

and endosymbiosis.

Cell Organelles

Nucleus – control via DNA making proteinsNucleolus – stores ribosomesER – rough – site of ribosome attachment - smooth – lipid metabolism, toxin removalLysosomes – digestive vacuolesGolgi – packages, modifies proteinsMitochondria – energy (ATP) via aerobic cell. respChloroplasts – photosynthesisCytoskeletal elements – microtubules, microfilaments,

support, make up other structures (centrioles, flagella, etc.)

Centrioles – cell division (animal cells), anchor spindle fibers

Cell Membrane

• Made of phospholipids and integral and peripheral proteins (act as carrier molecules, enzymes, gates etc)

• Cholesterol – maintains fluidity

• Have glycoproteins and glycolipids as surface markers (receptors, MHC’s etc)

• Hydrophobic on inside, hydrophilic on outside

Differences in cells

• Cell walls in plant, fungi, bacterial cells

• Cell wall composition varies

- fungi: chitin

- plants: cellulose

- bacteria: peptidoglycan

• Chloroplasts in photosynthetic cells

Connections between cells

• Gap junctions – animals

• Plasmodesmata – plant cells

Movement of materials in and out of cells

• Surface area to volume ratio important in determining the movement of materials

Smaller cells better!

Types of transport

• Diffusion (facilitated uses carrier molecules/channels) – passive

• Osmosis – Water movement – passive

• Active Transport: against conc gradient,

- uses energy and carrier molecules, also includes endocytosis and exocytosis

Osmolarity• Direction of water flow depends on

solute conc

• WATER ALWAYS MOVES INTO A HYPERTONIC (HYPEROSMOTIC) SITUATION!

• Look at solute concentration to gauge water movement.

Water Potential

• Equation for water potential (osmotic potential)

Ψ = ΨP + Ψs

pressure potential + solute potential

(+ or -) (always -)

• Ψ = 0 MPa for pure water• As you add solute, the wp becomes more negative

Our lab: Diffusion

• Used bags of different molarities; weighed water gain

• Determined the solute potential SP of potato cells

• Where graph crossed line (no gain or loss of water) gave molar concentration

- Use SP = -iCRT (to figure out solute potential; C = molar conc)

Cell Cyclecontrolled by checkpoints, CDK, cyclin

Mitosis

• Keeps chromosome no. constant, no genetic diversity

• 2 identical cells

• Stages: PMAT

• Think about what is happening to the DNA during the stages.

Prophase, metaphase, anaphase, telophase

cytokinesis• Actual division of cytoplasm

• Forms cell plate in plant cells

• Cleavage furrow in animal cells

Meiosis

• Purpose: to divide chromosome number in half (diploid – haploid) and to promote diversity.

• Results in 4 NONIDENTICAL cells due to crossing over, different arrangement of chromosomes at Metaphase I.

• Meiosis I: cuts chrom no in half

• Meiosis II: divides chromatids

When does crossing-over occur?

Tetrads

• Meiosis is used to make gametes

• Some organisms such as fungi have complete bodies made of haploid cells

GeneticsRemember ratios.

• One trait

F2 3:1 (Aa x Aa)

• Two trait – Remember each organisms has two alleles for each trait!

ex: tall, green plant TtGg

Each gamete gets ONE of each allele pair. Think of all possibilities.

ex: TG, Tg, tG, tg

F2 9:3:3:1 (AaBb x AaBb)

• Be able to relate crosses to Mendel’s laws:

• Law of Segregation – alleles separate during formation of gametes

Law of Independent Assortment:each allele separates independently of other allele in pair (ie chromosomes in

Metaphase I of meiosis)

• Test cross (backcross): use homozygous recessive to determine the genotype of an organism expressing the dominant trait to see if it is heterozygous.

ex – AA or AA, mate with aa

• Sex-linked: REMEMBER TO USE SEX-CHROMOSOMES….NOTHING ON THE Y.

• Probability: use what you expect from individual crosses

ex: AaBb x AABb

probability of getting AABB?

Pedigrees:

• If skips a generation anywhere, recessive

• If more in males, may be sex-linked

• If dominant, has to appear in one parent

Type of inheritance?

• Linked genes will not give expected ratios

• Determined by amount of crossing-over resulting in recombinations of parent-types

• Can use to make chromosome maps

- closer genes are, less recombinations or

cross-overs

Other things

• Pleiotropy: one gene, many effects

• Polygenic Inheritance: many genes determining phenotype, additive effect

• Epistasis: one gene controlling expression of another gene

• Incomplete dominance

• Codominance

Genetic diseases

• May be caused by chromosome abnormalities (number and structural)

Turners 45 female XO

Klinefelters 47 male XXY

Down’s trisomy 21

- may be caused by nondisjunction during cell division

• May be caused by gene mutations

Nondisjunction

Failure of chromosomesto separate normally

Structural abnormalities

• Karyotypes can discern chromosome abnormalities

Our lab: Fruit Flies• Chi-square test used to test validity of

results

Formulas willbe given to youon the exam.

This number or lower to consider your data fits your prediction.

Importance of Free Energy

• Ability to do work in the cell

Energy Transformations

• Laws of thermodynamics: 1st energy, 2nd entropy (confusion)• ATP – energy carrier molecule substrate level phosphorylation – transferring a phosphate from ATP to a molecule to activate it

oxidative phosphorylation – using the movement of electrons to

attach a phosphate to ADP to make ATP

What to expect on the exam….

• You need to know general outcomes, places in the cell these occur, importances, etc.

• Pathways will probably be given for you to interpret.

Photosynthesis vs Cell Respiration

• Photosynthesis – anabolic

• Cellular respiration – catabolic

• 6CO2 + 6H2O ----------- C6H12O6 + 6H2O

photo

cell resp

Do not memorize steps. Diagrams are usually given on the AP exam for interpretation.

Cellular respirationderiving energy (ATP) from food we eat

• Three parts: glycolysis (in cytoplasm); Krebs Cycle (matrix of mitochondria); ETC (cristae membrane) in eukaryotes.

Prokaryotes carry on these processes in specialized membranes near the cell membrane.

• Glycolysis – Glucose to 2 Pyruvates, needs 2ATP to start, makes 4 ATP, net yield 2 ATP

• If aerobic: pyruvate changes to acetyl Co-A (after releasing CO2) to enter the Krebs Cycle

• Krebs Cycle generates (per turn, 2 turns per glucose) 1 ATP, 3 NADH, 1 FADH, 2 CO2

• Krebs cycle generates many intermediaries used in other pathways

NADH and FADH are electron/H carriers

• If anaerobic (no oxygen), fermentation occurs and pyruvate is changed to

- lactic acid in muscle cells

- alcohol and CO2 in yeast cells

No more ATP generated, but does recycle NADH to NAD+ a to be used in glycolysis.

Electron Transport Chain• Basis: electrons (along with H atoms)

are passed from one energy level to next by NADH and FADH2.

• Final acceptor of electrons is OXYGEN!

• Forms water (with H atoms)

How does this make ATP?

• Chemiosmosis: reactions pump H+ into space between mitochondrial inter membrane space. As protons flow back across the inner membrane, ATP is phosphorylated.

• Same type of ETC in photosynthesis in the chloroplasts (different direction of e flow)

• All organisms carry on some phase of cell respiration – maybe only glycolysis!

Photosynthesis

• Occurs in the chloroplast

• Two parts:

• Light-dependent (in thylakoid membranes of the grana) – light separates electrons from chlorophyll and those are passed through a series of carriers to generate ATP and eventually picked up by NADP (P in plants)

• Water is split generating oxygen as a waste product.

• The purpose of splitting water is to supply electrons to those lost in chlorophyll!

• ATP and NADPH go to the Calvin Cycle (light independent part)

• Calvin Cycle – use ATP and NADPH and CO2 to make glucose

Our labs

• Using DPIP as an electron-acceptor (replaces NADP) in the light-dependent reaction, changes color.

• Cell respiration: germinating vs nongerminating pea seeds, measured oxygen uptake in respirometers

Cell Respiration Lab

Some typical results

Photosynthesis Lab

Graph from Photosynthesis Lab:% Transmission of light by chloroplasts in

various conditions

Leaf Float Lab

Rate Calculations

• How do you calculate rate?

• Change in product divided by change in time.

Molecular Genetics• DNA vs RNA

sugars (deoxyribose in DNA, ribose RNA

structure (double strand DNA, single RNA) bases (DNA thymine) RNA (uracil)

• Base pairs

3 bonds more stable

DNA replication – semiconservative (Meselsohn-Stahl – used N14 and N15)

• Enzymes involved: (supposedly do not need to know for exam)

helicase – unwinds

single-stranded binding proteins – keeps

strands apart

topoisomerase – allows strands to unravel

RNA primase – attach RNA primers

DNA polymerase – add new DNA bases

Ligase – joins Okasaki fragments

• Chromosomes are protected by telomeres during replication.

Leading and lagging strands

• DNA polymerase moves in 3-5’ direction

• One side copied in one piece

• Other side in pieces called Okasaki fragments

• Pieces joined by ligase

Notice the replicationproceeds in oppositedirections.

DNA polymerase moves in 3-5’ direction

Protein Synthesis

• Central dogma: DNA – RNA – protein

• Two steps

Transcription – mRNA made from DNA in nucleus

Translation – mRNA (codons) match to

tRNA (anticodons) with their amino acids at the ribosomes

EPA sites (probably too specific for exam)

Amino acids joined by peptide bonds

• Transcription steps

1) initiation – RNA polymerase attaches to

promoter regions (TATA box) unzips DNA

2) elongation – by RNA polymerase 5 – 3

3) termination –

RNA processing:

introns removed by snRNP’s

exons stay

end modification; Poly A tail, 5’ cap (from GTP)

• Translation – same steps

initiation – small ribosomal subunit

attaches to mRNA

tRNA carrying methionine attaches P site

next tRNA comes into A site

continues, original tRNA goes to E site

stops at termination (stop codon)

• Energy provided by GTP

• In prokaryotes, both processes occur in the cytoplasm of the cell; no RNA processing

What happens to the proteins that are made?

• Those that are made on attached ribosomes:

• Those that are made on free ribosomes:

Mutations

• Point – change in nucleotide

- silent mutation – does not change

amino acid

- missense mutation – different amino

acid

- nonsense mutation - changes aa to

stop codon• Frame Shift – deletion, addition throws

reading frame off.

DNA organization

• DNA packaged with proteins (histones) to form chromatin in beads called nucleosomes

• Euchromatin – DNA loosely bound, can

be transcribed• Heterochromatin – DNA tightly bound,

due to methylation• Chromatin becomes chromosomes

during cell division.

Viruses• Consist of protein coat and nucleic acid

• Not considered “living”, need a host cell

• Have lytic and lysogenic cycles

• Can be used as vectors to carry genes

• Bacteriophages – used by Hershey and Chase to prove DNA was genetic material

• Retroviruses – contain reverse transcriptase for RNA ----- DNA

Unfortunately DNA from retroviruses such as HIV is not proof-read so many mutations may occur.

Bacterial Genetics

• Bacteria contain plasmids• Most reproduce by binary fission (asex)• Ways for genetic variation

conjugation with sex pili

transduction – during lytic phase of viral infection, some bacterial/viral DNA is mixed

transformation - DNA taken up from

surroundings

Conjugation can result with bacterial cells gaining R plasmids for antibiotic resistance.

Transduction brings new genetic combinations

Binary Fissionasexual

Gene Regulation• All cells in an organism have the same DNA, but not

all of it is turned on• In prokaryotes, have operons that direct a particular

pathway• Remember RPOG

RNA polymerase

binds here

Regulator – Promoter – Operator – GenesCodes for

repressor

which can bind to the operator

Lac operon – induciblelactose acts as an inducer

Tryp operon – repressible - produces enzymes for synthesis of

tryptophan; presence of tryptophan in cell cuts it off

Remember!

• Inducible operons (lac) are off and are turned on by available substrate in the cell to code for enzymes to break down the substrate

• Repressible operons (tryp) are on and are turned off by the product which acts as a corepressor.

Epigenetics• changes in gene expression or cellular

phenotype, caused by mechanisms other than changes in the underlying DNA sequence, some of which are heritable.

• Examples of such modifications are DNA methylation and histone modification

• can modify the activation of certain genes

Examples of epigenetics

• in Development• Somatic epigenetic inheritance through

epigenetic modifications, particularly through DNA methylation and chromatin remodeling, is very important in the development of multicellular eukaryotic organisms. Cells differentiate into many different types, which perform different functions, and respond differently to the environment and intercellular signalling.

Epigenetic changes have been observed to occur in response to environmental exposure—for example, mice given some dietary supplements have epigenetic changes affecting expression of the agouti gene, which affects their fur color, weight, and propensity to develop cancer

MicroRNA and RNAi’s

• Non-coding RNA’s that downregulate mRNAs by causing the decay of the targeted mRNA

• some downregulation occurs at the level of translation into protein.

DNA technology

• Recombinant DNA – use restriction enzymes to cut DNA and gene of interest to be inserted

• Gel electrophoresis – sort fragments by size and charte

• DNA fingerprinting – people have different size fragment RFLPS

Plasmid Maps

Be able to read andcreate one.

• Complementary DNA or cDNA made from mRNA using reverse transcriptase

• PCR

Our Labs

• DNA electrophoresis of restriction enzyme fragments

-how to plot graph and read size of fragments

• Transformation experiment with pGLO, inserting plasmid with GFP into E.coli cells.

- calculate transformation efficiency

Evolution

• Darwinian evolution – by means of natural selection based on heritable traits

• Remember populations evolve, not individuals

• Evidences for: homologies, biogeography, fossil record, molecular evidence (DNA, proteins)

Evolution of Populations• Microevolution – looking at changes in

allele frequencies

• Hardy Weinberg Equilibrium says gene frequencies WILL NOT CHANGE if conditions are met:

- no natural selection

- random mating

- large populations

- no gene flow (migration, immigration)

You have to know how to do this!

p = frequency of recessive allele (can be obtained by taking the square root of the number of recessive individuals in the population)

r = frequency of dominant allele (subtract p from 1)

p + q = 1

Substitute in equation

Types of selection

• Directional – drifts to either side

• Stabilizing – stays same

• Disruptive – middle NOT favored

• Sexual (can be combined with other three)

http://schoolworkhelper.net/wp-content/uploads/2011/12/types-of-natural-selection.jpg

Speciation

• populations have to be reproductively isolated (cannot interbreed and produce fertile offspring)

• Allopatric – geographical isolation

• Sympatric – reproductive barriers exist in same location

Allopatric Speciation

Reproductive barriers

• Pre-zygotic

- different mating rituals, mismatch genitals, time of mating, etc.

• Post-zygotic

- failure of zygote to thrive or failure of offspring or grand-offspring to survive and reproduce

Hybrids

• Can complicate the issue of determining if different species

• If hybrids can interbreed with either parent, probably not new species

• Polyploidy (allo and auto) lead to new species in plants

History of Life on Earth

• Hypotheses of how life arose

• RNA hypothesis

• Metabolism first hypothesis

• At some time though abiotic synthesis probably did occur

- Miller, Urey experiment

- protobionts, coacervates

Endosymbiosis

• Important in explaining the origin of eukaryotic cells, particularly mitochondria and chloroplast

endosymbiosis and tree of life

Mass Extinctions• Be able to interpret diagrams and

charts

Do not need to memorize, just interpret

Phylogeny and systematics

• Phylogeny – evolutionary history

• Systematics – classifying and determining evolutionary relationships

• KNOW how to interpret and create cladograms. Expect lots of these!

• Use Bioinformatics (computer programs such as BLAST) to infer phylogeny

Cladogram Analysis

• Look for outgroups (those that have the most differences)

• Those with the least differences are the closest together.

outgroup

Derived characters

Different ways to set-up

Use of parsimony in cladistics• The set-up that involves the least amount of

evolutionary changes

It is considered more likely that trait B evolved only once (right hand cladogram) rather than twice (left-hand cladogram).

Looking at ancestry

• Polyphyletic - A group that does not share a common ancestor,

• Paraphyletic - groups that have a common ancestry but that do not include all descendants

• Monophyletic - includes the most recent common ancestor of a group of organisms, and all of its descendents

What is this one?

What about convergent evolution?

• Traits evolved due to inhabiting similar environments or needed for similar situations. Do not infer ancestry.

Convergent evolution

Three domains