Protein Secondary Structure

Secondary structure refers to the regular _______ arrangement of local regions of the polypeptide backbone

repetitive

are alpha helixes usually left or right handed

right

where are h-bonds in an alpha helix

between the carbonyl oxygen and the n+4 residue of the amide hydrogen towards the c-terminus

what is the length of a hydrogen bond in an alpha helix

2.8 angstroms (0.28 nm)

how many amino acids per turn

3.6

Characteristics of the side chain in an alpha helix

points outward, doesnt participate in H-bonding

What amino acid cant be accommodated in the structure of an alpha helix. Why?

proline

It doesnt have an amide hydrogen to bond

The rigid ring restricts the conformation

To stabilize the helix, negatively charged amino acids are found on which terminus

N-terminus

To stabilize the helix, positively charged amino acids are found on which terminus

C-terminus

Where are the N and C termini located on the helix

on the surface

How is the charge at the termini neutralized

by interacting with water or charged ions

Many alpha helices are amphipathic. What does this mean?

they have a hydrophilic face and a hydrophobic face

When the protein is in an aqueous solution, the hydrophobic residues face _____?

inward

When the protein is in an aqueous solution, the hydrophilic residues face _____?

outward

When the protein is in lipid bilayers, the hydrophobic residues face _____?

outward

When the protein is in lipid bilayers, the hydrophilic residues face _____?

inward

In the ribbon model, a beta strand is depicted as an ____? What direction does in point towards?

arrow, C-terminus

Where are the side chains positioned related to the polypeptide backbone in a beta strand?

above and below

A peptide chain is almost fully _____ in a beta strand

extended

Beta strands arranged side by side become ______?

beta sheets

How are beta sheets held together?

H-bonds between backbone CO and NH groups on separate strands

What does it mean if a beta sheet is parallel? Is this stronger or weaker?

H-bond is not perpendicular. Weaker

What does it mean if a beta sheet is antiparallel? Is this stronger or weaker?

H-bond is perpendicular. Stronger

What configuration are the R groups in in a beta sheet?

trans. pointing outward and perpendicular to the H-bonding surface

Hydrophilic R groups in a beta sheet face what?

aqueous solvent

Hydrophobic R groups in a beta sheet face what?

the inside of the protein

B sheets can also be called what?

Beta pleated sheets

What are beta turns and loops?

Non-repeating regions that connect alpha helices and beta strands and cause directional changes

Beta turns connect two beta strands in an _______ beta sheet

antiparallel

How many types of beta turns? How many amino acids do they contain?

2 types. each contain 4 amino acids

Where is the H-bond in beta turns

between carbonyl oxygen of the first amino acid and amide hydrogen of the fourth amino acid

How many residues in length in a beta loop

6-20

Are the residues in a beta loop hydrophilic or hydrophobic? How much of the total protein length do they make up?

hydrophobic. 10%

Where are the residues in a beta loop? What are they doing?

On the protein surface. Interacting with other proteins