Elements of Protein Structure Flashcards
This is when amino acids are bonded together in a peptide or a protein
Amino acid residues
How are amino acids numbered?
From the N (amino terminus) to C (carboxy terminus)
Globular proteins are comprised of:
a-helix, B-structure, and turns
What are the 4 levels of protein structure?
Primary, secondary, tertiary, quaternary
This is the linear sequence of amino acids that make up the polypeptide
Primary structure
This is the 3-dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues. Includes a-helices and B-sheets
Secondary structure
This is the 3-dimensional structure of a complete protein chain
Tertiary structure
This is the interchain packing and structure for a protein that contains multiple polypeptide chains (eg., haemoglobin)
Quaternary structure
What is the bond angle between N and Ca?
phi bond angles
What is the bond angle between Ca and C’?
psi bond angles
What is the chain angle between C’ and N (peptide bond)? These bond angles can only be 180 degrees or 0.
Omega bond angles
What is the specific bond angle of a polypeptide when it’s in its final structure?
180 degrees
Why are there restrictions on phi and psi angles? Describe these restrictions.
Because of steric hindrance.
- Phi rotations can lead to O-O collision
-Psi rotations can lead to NH-NH collision
For a trans peptide bond, what is the bond angle?
180 degrees
Where are the alpha carbon atoms found on trans peptide bond?
Opposite sides of the peptide bond.
What is increased for cis peptide bonds?
Steric crowding because both alpha carbon atoms are on the same side of the peptide bond.
Does the peptide bond angle rotate very much once formed? Why/why not?
Because the peptide bond is a double bond. There will always be limited rotation when it comes to double bonds because there’s that sp1 structure that covers the whole molecule.
What are the 2 main secondary structures?
a helix and B structures: B sheet and strand
These are main chain spirals around the central axis. They participate in non-covalent interaction (hydrogen bonding).
alpha helix
What stabilises the secondary structures?
Hydrogen bonds
How do sidechains stabilise the alpha helix?
Hydrophilic side chains point out, hydrophobic sidechains fold towards the middle
These are stretches of residue with a more extended structure than an a-helix.
B structure
Each section of a B structure is called a…
B-strand
What kind of bonding occurs between adjacent B-strands?
Hydrogen bonding
What do adjacent B strand chains form?
Beta sheets
What are the 2 types of hydrogen bonding interaction in a B-sheet?
Parallel and antiparallel
Beta sheets are not planar they are:
pleated
How are sidechains orientated in the B sheet?
Side chains either point above or below.
These are needed to form globular proteins. Often short, hairpin like and involves 3/4 residues. Has a high Gly/Pro content and often have H-bond across width.
Turns
This side chain is very flexible and has a lot of conformational freedom.
Glycine
This is too rigid but has a built in turn because of the bonding between R-group and amino group.
Proline
How many residues per turn in alpha helices?
3.6 residues per turn
How many rises per turn in alpha helices?
5.4 rices
Is the spiral of an alpha helix left or right handed?
Right handed
What two residues are helix breaker and therefore would not be used to form helices?
Proline and glycine
The dipole of the alpha helix is positive/negative in the N terminus?
Positive
In an alpha helix, each amino acid side chain is separated by how much degrees? (in a helix wheel)
100 degrees
Approximately how many strands are there in each beta sheet?
2-10 strans
The average strand of a B strand is about how many amino acid residues?
6 amino acid residues, but the maximum would be around 15
Which level of protein structure determines the overall shape of a protein?
Primary structure => because it contains the instructions for protein folding hence, protein shape
This is the process of forming alpha helices and beta sheets early in the folding process.
Nucleation
