Lecture #2 - Secondary structures

Question 1

Give brief descriptions of primary, secondary, tertiary and quaternary structures

Answer 1

1. Primary = each aa’ linked by peptide bonds 2. Secondary = Hydrogen bonded arrangement of the backbone 3. Tertiary = 3D structure (know where every atom is in space) 4. Quaternary = Multiple chains interact with each other (not all proteins have multiple chains)

Question 2

What is the phi angle? What is the psi angle? What is the omega angle?

Answer 2

Phi = Ca-N

Psi (trident) = C-Ca

Omega = C-N (peptide bond)

Question 3

What collision does Phi lead to? What collision does Psi lead to?

Answer 3

Phi = O-O Psi = NH-NH

Question 4

Which amino acid can adopt many phi and psi angles?

Answer 4

Glycine because it doesn’t have proper side chains

Question 5

Describe the Ramachandran plot in your head

Answer 5

Question 6

Omega is the angle of the peptide bonds - what is the angle of trans and cis? About 10% of the peptide bonds that precede _____ may be cis

Answer 6

Trans = 180 degrees

Cis = 0 degrees

Proline

Question 7

Chi - usually staggered or not? Why? Where do the values cluster?

Answer 7

Staggered (out og phase - H have more freedom so most proteins adopt staggered positions)

Values cluster near sterically free regions

Question 8

To do with the angles - is 180 and -180 the same?

When viewed from what terminus axis does the rotation clockwise increase the angle of rotation?

Answer 8

Yes

N

Question 9

The combination of all the angles for a protein leads to a description of its…..

Answer 9

Overall 3D structure

Question 10

Protein secondary structure is dominated by two _____ structures

Answer 10

Caconical (general)

Alpha helix and beta strand

Question 11

Alpha helix:

1. What adopts a spiral?
2. How to find the direction of the helix?
3. What two atoms and hydrogen bond and where are they found?
4. What is the distance between O and N? Why measure that?
5. How many residues per turn and how long vertically is a turn?
6. What are the phi and psi angles in a alpha helix?
7. Side chains point where?
8. Each time you move up a residue, how many Å have you moved up?
9. What residues are common helix breakers?
10. What are the dipoles they talk about?

Answer 11

Yeah

Question 12

Other than alpha, what other helix exists?

What is it?

Which two forms exist?

Which kind of peptide bond may occur?

How many residues per turn?

Variant is found where in humans?

Tell me about the glycines

Answer 12

-

Question 13

Beta structure

1. Hydrogen bonding between what?
2. B-sheet is how many strands at least?
3. Typically how many strands?
4. Each strand has up to how many aa’?
5. Average strand length is what?
6. What are the two types?

Answer 13

Question 14

More key properties about B-sheets:

1. What is an extended but pleated thing called?
2. Sheets - are they planar?
3. What’s the usal arrangment of a B strand?

Answer 14

-

Question 15

What resembles a polyproline helix?

Give the phi and psi angles for alpha helix (right handed), parallel beta sheet and antiparallel beta sheet. Also collagen.

Answer 15

Collagen

On plot, C - location of polyproline helix

Question 16

Turns:

1. Involve how many residues?
2. High content of what two aa’? Why?
3. What percentage of residues involved?
4. Hydrogen bond - common or not?
5. How many types of turns?
6. What are the most common?

Answer 16

-