Biochem 200 Midterm 1: Topic 3 Protein Secondary Structure

Are loops disordered?

No, they have their own unique structure same for every duplicate copy. They are not flexible and are highly specific (don't change).

What occasion can Proline be found in?

At the end or beginning of the α-helix

What is a β-sheet?

They are sheets formed by multiple β-strands arranged side by side

How are β-sheet bonded?

The H bonds between strands in the peptide (amine Hydrogen bonds with COO- oxygen)

How are R-groups in β-sheets arranged? Are bulky groups allowed?

R-groups are outside and alternating above and below sheets. Bulky groups are allowed.

How are primary structures stabilized?

peptide bonds

How are secondary structures stabilized?

Hydrogen bonds between groups in the peptide backbone

(carbonyl oxygen of one peptide and the amino hydrogen of another)

How are α-helix stabilized?

Hydrogen bonds between peptide backbone groups in the same helices

How are quaternary structures stabilized?

Hydrophobic interactions

Salt Bridges (ion pairs)

Hydrogen Bond

What are the four major levels of protein structure? What is it made out of?

Primary = aa sequence
Secondary = alpha helix, beta sheets, irregular
Tertiary = globular, fibrous, domains
Quaternary = multiple tertiary (3) polypeptides

How do the properties of peptide bonds limit the possible conformations a polypeptide can adopt?

Folding conformations are limited due to steric hinderance (same charges too close)

What are regular secondary structures?

Alpha helices & Beta sheets

What determines the structure of the secondary structure? Does the R-group contribute?

H-bonding of the alpha groups in the backbone determine it's structure. R-group does not determine structure

What is a irregular secondary structure?

loops (hairpin, longer loops)

What are 5 special features of an α-helix?

1. Right handed twist (N terminus bottom C on top)

2. R-groups point down (to N-term)

3. Less bulky R-groups (proline, tyrosine)

4. No Gly, Pro, Tyr, Ser in backbone

5. NH bonded to COO- in specific pattern

Why isn't glycine found in α-helix?

Glycine: lacks a β (R-group) carbon

How do the carbonyl oxygens bond with the NH groups?

C1 bonds to N5

C2 bonds to N6

Are the first 4 -NH groups or the last 4 -CO groups involved with bonding to form the α-helix?

No, they are tails

In α-helix, which direction does R-groups point towards?

Point downwardss towards N terminus unless N terminus is facing up.

What is the major groove in 2 helical strands good for fitting? What about minor?

Major groove good for α-helix minor good for β-sheet

How are the β-strands joined? What is it made out of?

By loops made out of amino acids

Difference between parallel and anti-parallel β-sheet

Parallel: Strands run in same direction (tilted)

Anti: Strands run in opposite direction (more stable and straight)

How are the loops (irregular structures) different in parallel and anti-parallel β-sheets?

Parallel: Loop longer, on top or bottom of sheet

Anti: Loop smaller outside of sheet

What is the difference between what you should state if asked regular secondary structure or secondary structure?

Regular: State everything but loops (i.e. sheets or helices, parallel or anti)

No regular: include loops

Does the peptide back bone change in regular secondary structures if the amino acids change?

Referring to alpha & beta: peptide backbone stays the same

How are β-sheets stabilized?

Hydrogen bonds between peptide backbone groups in the neighboring strands

How are tertiary structures stabilized?

Hydrophobic Effect (MAIN)/ hydrophobic interactions

Salt bridges

Hydrogen bonds

Disulfide bonds