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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)
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
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