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 polysaccharides
These 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
Orientation
is 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 proteins
Nucleolus – stores ribosomes
ER – rough – site of ribosome attachment
- smooth – lipid metabolism, toxin removal
Lysosomes – digestive vacuoles
Golgi – packages, modifies proteins
Mitochondria – energy (ATP) via aerobic cell. resp
Chloroplasts – photosynthesis
Cytoskeletal 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 Cycle
controlled 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 crossingover occur?
Tetrads
• Meiosis is used to make gametes
• Some organisms such as fungi have
complete bodies made of haploid cells
Genetics
Remember 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 SEXCHROMOSOMES….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 chromosomes
to separate normally
Structural abnormalities
• Karyotypes can discern chromosome
abnormalities
Our lab: Fruit Flies
• Chi-square test used to test validity of
results
Formulas will
be given to you
on 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 respiration
deriving 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 replication
proceeds in opposite
directions.
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
Fission
asexual
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 – Genes
Codes for
repressor
which can bind to the operator
Lac operon – inducible
lactose 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 and
create 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