Week 2: Protein Structure, Chromosomes & Chromatin, DNA & Histone Modification Flashcards
Why do proteins have such a diverse array of specialized functions?
Because they have a diverse set of building blocks - amino acids
Amino acids structure + linkage
- joined by covalent bonds
- each free amino acid has: a central carbon (C(alpha)), an amino group (-NH3+), and carboxolate group (-COO-), and a side chain
~20 diff types of side chains!
How do amino acids exist?
besides glycine
as 2 distinc steroisomers that differ in arragement about the alpha carbon
* the L- and D- aa: contain identicall types of atoms and chemical bonds, but are mirror images of each other
Peptide bonds are…
+ how they form
…the covalent linkages that form polypeptides (polymer of aa)
* form between carboxylate group of 1 aa and amino group of another
* precipitates 1H2O
Amino acid residues are
the amino acids that have been incorporated
Peptide backbone
and structure
repeating series of atoms from which the aa side chains protrude
* one end has an exposed amino group (N-terminus) while the other has an exposed carboxyl group (C-terminus)
ribosome synthesizes beginning at N-term
Importance of the deolocalization of the e- in atoms of the peptide bond unit
- causes these atoms to all lie in a plane (resonance)
- prevents free rotation of one of the bonds that form the overall peptide bond unit, locking the atoms into a planar configurations
- each aa unit has only 2 covalent bonds about which free rotation can occur: The N-alpha carbon bond, and the C-alpha carbon bond
A ramachandran plot provides a graphical depiction of the allowable combos of N-alpha carbon and C-alpha carbon angles
What is protein folding driven by?
non-covalent interactions between atoms in the polypeptide chain
What are the four levels of organization of protein folding
Primary structure: sequence of amino acids
Secondary structure: short regions of the polypeptide chain can form regular, repeating regions of structure stabilized by hydrogen bonds (alpha helices and beta sheets)
Tertiary structure: when a protein folds and the regular repeating element come together to form a defined shape
Quaternary structure: complexes formed by the association of several folded polypeptides
Alpha helices formation and structure
What are amphipathic alpha helices?
In an alpha helix, the backbone curves in a right-handed helical pattern
* hydrogen bonds form between the carbonyl oxygen of one residue and the amide nitrogen of residues further along the chain
* structure is a cylinder with side groups outside, backbone inside
* amphipathic alpha helices: hydrophobic side chains on one face, polar side chains on other
Beta sheet formation and structure
parallel vs antiparallel beta sheet?
Beta sheets form when 2+ segments of the backbone (beta strands) H-bond throug their carbonyl and amide groups
* sheet-like structure that is slightly twisted
* can form between 2+ non-contiguous segments of a polypeptide
* parallel beta sheet: strands oriented in same direction (N to C term)
* antiparallel beta sheet: strands oriented in opposite directions
* (mixed sheets can also occur)
Importance of tertiary structure function
why is it energetically favorable?
In the tertiary structure, the hydrophobic groups in the polypeptide chain interact inside the protein (primarily van der waals), while polar groups are on the proteins surface (because of the polar, aqueous environment of the cell)
It is energetically more favorable because:
* bury hydrogen-bonded polar atoms in hydrophobic interior
* very few empty spaces/gaps interior
* *folded *form of polypeptide
* - when hydrophobic side chains are outside, H2O molecules have more limited orientation options (less entropy) vs when hydrophobic side chains are inside, whole system has more entropy as the H2O molecules have more options
What is possible/not possible to predict about protein structure based on sequence?
Process of protein folding is so complex that is impossible to precisely predict tertiary structure from aa sequence, but is possible to predict whether 2 proteins will have a similar structure based on their aa sequence… if they have a sequence identity of just 25% they will be fairly similar
Can also predict secondary elements pretty well
Can use already-known protein aa sequences and structure to help predict the structure of another aa sequence: if any proteins have at least 25% of aa in common, likely to adapt the same fold… often, but not always, means that the proteins perform a similar function
What do chaperones do?
They help the protein folding process go smoothly
(Proteins can be denatured by things that change solutions conditions such as heat, chemicals, etc)
Definition of protein fold
Protein fold = the arrangement of secondary structure elements that characterizes a particular protein
Proteins may not have identical structures, but can still have identical folds
Even though there is lots of diversity in types of proteins folds that are known, the number of protein folds found in nature is limited… why?
Most arbitrary amino acid sequences would fail to fall into a stable structure
What types of changes are tolerated in aa sequence of proteins vs not tolerated?
Changes in the aa sequence that do not alter overall fold.properties may be tolerated, but changes that are more deleterious are not tolerated
As a protein collects further mutations, may evolve a new function
Divergent evolution
proteins with new characteristic, and eventually separate functions evolve from a single ancestral protein
Convergent evolution
whe nature solves the same problem twice: 2 proteins that carry out a similar function, but have evolved independently
Domain
a compact region of protein structure, usually made up of a contiguous segment of the poplypeptide chain, that is capable of folding on its own
Most proteins are built up in a modular fashion from several domains fused together.
A given DNA sequence can be characterized by what?
A distinct array of hydrogen bond donors and acceptors, as well as by methyl groups that are exposed in the grooves
Why is there less variability in the chemical surface exposed in the minor groove?
What does this imply for protein binding?
The pattern of H-bond donors and acceptors is the same for A-T and T-A base pairs and C-G and G-C base pairs
This means that most DNA binding proteins that recognize a particular sequene do so primarily through major groove contacts
ex: H-bond donor paired with H-bond acceptors while a hydrophobic side chain might be in van-der-waals contact with the methyl group of thymine
What can increase chances that side chains on a given protein will approach functional groups on the DNA?
If the shape of the protein is complementary to that of the DNA
What usually binds in the major groove
(protein structure)
In the major groove, usually alpha helices and 2-stranded beta sheets bind because their shape fits
What usually binds in the minor groove?
(protein structure)
The minor groove is usually too narrow to fit either alpha helices or beta sheets, but can happen with an energetic penalty that comes from distorting DNA
What two amino acids are generally involved in protein interactions with DNA?
arginine and lysine (positively charged)
Also the hydroxyl groups on serines or tyrosines (partial positive charge) can form favorable electrostatic interactions with phosphate groups
Results of German’s isolation of histones and separation by gel eletrophoresis?
How did we know that DNA + histones = nucleosomes?
- electron microscopy shows “beads on a string”
- Nuclease digestion of DNA in nuclei: useful in saying both expressed and unexpressed genes found in nucleosomes
* isolate nuclei, add micrococcal nuclease (breaks phosphodiester bonds)
* then stop enzyme, remove all proteins, look at size of DNA
* do as a function of time
