Lecture 3 DA Flashcards
What are the benefits of genetic code redundancy (2)?
Offers some protection against mutation.
Can also mean mutation replaces an amino acid with a similar amino acid to minimise change.
Is proline an actual amino acid?
Is really a secondary amino acid, has a cyclic structure, better known imino acid.
When are proteins most stable?
At their lowest gibbs free energy.
Proteins are only marginally more stable in their native form vs another. Why?
Difference in energy between functional and non-functional protein forms is very small. So proteins are only marginally more stable.
What kind of interaction dominates the tertiary structure of proteins?
Weak interactions outnumber strong ones, so they determine folding.
Does the peptide bond have a neutral charge?
Carbonyl oxygen has a partial negative charge, while the amide nitrogen has a partial positive one. Results is a small dipole.
What is the smallest amino acid? What feature does this confer?
Glycine is the smallest amino acid. Allows the most flexibility.
In amino acid flexing, where does the flexibility occur? Is the peptide bond flexible?
Flexing occurs around the alpha carbons. The peptide bond is rigid.
What kind of backbone can proline form?
Cis-backbone.
What can proline’s unique structure and cis-backbone capability allow the formation of?
Can form turns and corners, present in beta sheet turns.
What are the flexibility angles called? What limits movement?
Phi and psi are the angles. Stearic hindrance limits movement, electron clouds, like charges etc.
How many amino acids present in a turn of an alpha helix?
3.6 amino acids.
How long is a turn of an alpha helix? How long per amino acid?
is 5.4A long, means 1.5A per amino acid.
An alpha helix turn takes 3.6 amino acids. Which amino acids interact with each other to form the helix?
The 1st and 4th amino acids interact.
Why do alpha helices form more readily vs other conformations?
It doesnt involve specific residues, is due to interactions between the amide and carbonyl.
There are left and right handed helices. Which is more stable? Which is found in nature?
Left handed is less stable, and usually isnt observed in proteins.
Which amino acid most readily forms a helix and why?
Alamine, it has the least free energy.
Which amino acids are the most difficult in forming alpha helices (2)?
Glycine and proline.
Does beta sheet formation require side chains?
No.
What conformation can a beta sheet have (3)?
Parallel or anti-parallel.
Multiple sheets stacked are called pleated beta sheets.
How many amino acids does a beta turn require? Which conformation is a beta turn found in? what amino acids does it usually involve (2)?
4 amino acids found. Found in the anti-parallel conformation. Usually involves glycine and proline.
A beta turn requires 4 amino acids. Which amino acids interact? What interaction is it?
1st and 4th amino acids have a H bond between them.
How many residues does a left handed alpha helix require?
3 per turn.
Which amino acid is found in left handed alpha helices, not normally found in right handed ones, and why?
Glycine, typically present on the inside as it needs to be tight and rigid.
