1. DNA, RNA, Proteins and Evolution Flashcards
word for when genes are on the same chromosome
correlated
what is the genetic crossover hypothesis?
traits that are usually linked are sometimes not inherited together because the chromosome pairs have wrapped around each other during meiosis
the probability of a radiation induced mutation is proportional to…
the density of ions produced by the radiation
chargaff’s rule =
DNA contains a 1:1 ratio of adenine:thymine and cytosine:guanine
what’s the difference between DNA and RNA sugar backbone?
DNA has a ribose sugar (with an OH) whilst RNA has a deoxyribose (with an H)
which position in the sugar is the base attached to?
1’
what holds DNA/RNA together
H bonds between bases.
van der waals forces
hydrophobic interactions
what is replication?
Making DNA from DNA
what is transcription?
making RNA from DNA
What is translation?
Making proteins from RNA
How many base pairs in human genome?
3x10^9
How many genes in human genome?
30,000
How many amino acids in average protein?
300
How many times shorter is a chromosome than the extended DNA?
10,000
DNA replication is catalysed by…
DNA polymerase
What is a primer?
A strand of DNA with a free 3’-OH group already bound to the template. DNA polymerase needs a primer to begin replication, but RNA polymerase does not.
In which direction does DNA elongation proceed?
5’ to 3’
codon =
a three base section of DNA/RNA representing one amino acid.
What is the initiation signal?
AUG
specific interactions =
strong bond which arises from a unique combination of physical forces between macromolecules. Typically involve geometric, steric, ionic and directional bonds
steric interaction =
short range quantum repulsion
limits to vDW theory (3)
cut-off distance is unknown as it depends on short range repulsive forces
other adhesive forces may be involved eg ionic, hydrogen, hydrophobic
there may be other repulsive forces eg thermal motion of soft surfaces can give rise to thermal fluctuation forces
what is a solvation force
a force which oscillates between attractive and repulsive over the size of a water molecule. For a hydrophobic surface this can be smoothly attractive
where is a solvation force attractive or repulsive
it is energetically unfavourable to be between layers of water molecules so the force is repulsive away from these regions.
roughly by how far are large molecules separated in a cell
a few layers of water molecules
primary structure =
the chain of amino acids
secondary structure =
how the amino acids are folded. Typically this is in an alpha-helix or beta pleated sheet
tertiary structure =
how the helix/pleated sheet folds in on itself
quaternary structure =
how multiple proteins assemble together
peptide bond =
a bond between the carboxyl group (COO) of one molecule and the amino group (NH) of another
three types of side chain which determine protein structure
non-polar side chains - these don’t want to be in touch with water so fall in on themselves
polar side chains - want to be in touch with water
electrically charged side chains - have an electric charge in water
what interactions determine secondary structure
H bonds
for alpha helix, the N-H hydrogen bonds to a backbone C=O
for beta sheet, the beta strands are connected laterally by hydrogen bonds
name two unusual interactions that hold tertiary structure together
disulphide bond
salt bridge
what is a disulphide bond?
a covalent bond between the sulphur atoms in two thiol groups.
How does a disulphide bond stabalise a protein (3)?
- Holds two parts of a protein together
- The disulfide bond may form the nucleus of a hydrophobic core of the folded protein, i.e., local hydrophobic residues may condense around the disulfide bond and onto each other through hydrophobic interactions.
- Related to 1 and 2, the disulfide bond links two segments of the protein chain, increases the effective local concentration of protein residues, and lowers the effective local concentration of water molecules. Since water molecules attack amide-amide hydrogen bonds and break up secondary structure, a disulfide bond stabilizes secondary structure in its vicinity. For example, researchers have identified several pairs of peptides that are unstructured in isolation, but adopt stable secondary and tertiary structure upon formation of a disulfide bond between them.
What is a salt bridge?
A combindation of hydrogen bonding and electrostatic interactions. They form between electrically charged amino acids eg a COO- and NH3+
Afinsen’s dogma =
the native structure of a protein is determined only by the amino acid sequence
3 consequences of Afinsen’s dogma
- Uniqueness - each sequence only has one structure
- stability - small environmnetal changes won’t change the configuration
- kinetic accessability - freen energy path must be fairly smooth ie no random deep dips that a protein could get stuck in
levinthal’s paradox =
there is an astronomically large set of possible protein configurations yet proteins fold on a milisecond scale
name the five main contributors to the total free energy
- conformational entropy due to loss of degrees of freedom
- intramolecular hudrogen bonds and hydrogen bonds between protein and water
- van der waals bonds and other hydrophobic bonds
- coulomb energy of electrostatic bonds ie salt bridges
- valence bond energy and energy from disulphide bridges
what holds an alpha helix together?
hydrogen bond between backbone N-H and C=O
what holds a beta sheet together?
backbone hydrogen bonds between strands
RNA world hypothesis =
- Originally there was some pre-RNA biopolymer that could self-replicate.
- This was replaced by RNA
- This was replaced by RNA and protein systems which required the existence of ribosomes (which are formed of RNA)
- New enzymes evolved which can replicate DNA and make RNA copies of it
Evidence of RNA world hypothesis (4)
- RNA can store, replicate and transmit genetic information, just like DNA.
- Some viruses use RNA instead of DNA
- Ribozymes are catalysts made from RNA
- There is evidence for basing building blocks having come from meteorites ie these molecules must be widespread
Issues with RNA world hypothesis
- cytosine only has relatively short lifetime - not long enough for accumulation
- RNA is arguably too complex to have arisen prebiotically
- catalytit repetoire is too small
- need large RNA molecules to perform catalysis
How are phylogenetic trees calibrated and why is calibrdation required?
Using the fossil record
The numer of divergences in the DNA between two cells is proportional to the time since they diverged, however, the constant of proportionality is different for different proteins.
In which groups do amino acids tend to be substituted?
- Hydrophilic, acidic
- Hydrophilic, basic
- Polar, uncharged
- Hydrophobic
Name 4 ways in which genes can be altered
- Intragenic mutation
- Gene duplication
- DNA segment shuffling
- Horizontal transfer
Intragenic mutation =
where a mutation occurs within a length of DNA
Gene duplication =
where a mistake is made during cell division where not all genes are duplicated. The cell does not divide and so contains extra genes which can mutate, and if the mutation is not helpful, the cell can carry on as normal as it still has a good copy of the DNA.
DNA segment shuffling
where two genes switch some DNA
horizontal transfer =
where DNA is transferred between two organisms
Homology =
simliarity due to shared ancestry between a parit of structures of genes
Two types of homology
- Orthology - likely to have same function. Dervie from last common anestor
- Parology - likely to have different function. Derive from gene duplication in same gene
which level of structure is most conserved?
Tertiary
Why do we want to understand protein folding?
- Cheaper to be able to predict structure than use conventional crystallography etc
- Helps understand dieses caused by misfolded proteins eg Parkinsons, Alzheimers, mad cow disease
- Helps to engineer proteins that could carry out novel functions
transition state ensemble =
the set of conformations of highest free energy along the path of lowest free energy between the native folded and unfolded macrostates. The TSE limits the rate of folding.
How do small proteins fold?
In a 2 step process with a low energy barrier. This means they fold quickly.
Name 3 ways of probing folding of small proteins
- Using NMR allows you to see when a region of the protein becomes shielded from the solvant.
- Using simulations of the molecular dynamics
- By engineering them - mutate a single protein then measure its equilibrium state and kinetics
Why is it easier to find the transition state during unfolding of small proteins?
- The transition state is formed early in the unfolding process so is within the timescale of molecular dynamics simulation
- The initial state is the native state which is well defined
Number of qays to go from i-1 to i coiled states in binomial model
nCi = n!/(i!(n-1)!)
Number of qays to go from i-1 to i coiled states in zipper model
n-i+1
Persistance length of DNA?
150bp
Error rate of replication
1/10^9
Three factors that effect replication error rate?
- Intrinsic error rate ~1/10^7
- Proofreading by DNA polymerase
- Post replication mismatch repair mechanisms - compare DNA to original
Find the probability distribution of a freely jointed chain model
Derive the mean squared length of a worm like chain model
