Elements of Protein Structure

Question 1

This is when amino acids are bonded together in a peptide or a protein

Answer 1

Amino acid residues

Question 2

How are amino acids numbered?

Answer 2

From the N (amino terminus) to C (carboxy terminus)

Question 3

Globular proteins are comprised of:

Answer 3

a-helix, B-structure, and turns

Question 4

What are the 4 levels of protein structure?

Answer 4

Primary, secondary, tertiary, quaternary

Question 5

This is the linear sequence of amino acids that make up the polypeptide

Answer 5

Primary structure

Question 6

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

Answer 6

Secondary structure

Question 7

This is the 3-dimensional structure of a complete protein chain

Answer 7

Tertiary structure

Question 8

This is the interchain packing and structure for a protein that contains multiple polypeptide chains (eg., haemoglobin)

Answer 8

Quaternary structure

Question 9

What is the bond angle between N and Ca?

Answer 9

phi bond angles

Question 10

What is the bond angle between Ca and C’?

Answer 10

psi bond angles

Question 11

What is the chain angle between C’ and N (peptide bond)? These bond angles can only be 180 degrees or 0.

Answer 11

Omega bond angles

Question 12

What is the specific bond angle of a polypeptide when it’s in its final structure?

Answer 12

180 degrees

Question 13

Why are there restrictions on phi and psi angles? Describe these restrictions.

Answer 13

Because of steric hindrance.

• Phi rotations can lead to O-O collision
  -Psi rotations can lead to NH-NH collision

Question 14

For a trans peptide bond, what is the bond angle?

Answer 14

180 degrees

Question 15

Where are the alpha carbon atoms found on trans peptide bond?

Answer 15

Opposite sides of the peptide bond.

Question 16

What is increased for cis peptide bonds?

Answer 16

Steric crowding because both alpha carbon atoms are on the same side of the peptide bond.

Question 17

Does the peptide bond angle rotate very much once formed? Why/why not?

Answer 17

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.

Question 18

What are the 2 main secondary structures?

Answer 18

a helix and B structures: B sheet and strand

Question 19

These are main chain spirals around the central axis. They participate in non-covalent interaction (hydrogen bonding).

Answer 19

alpha helix

Question 20

What stabilises the secondary structures?

Answer 20

Hydrogen bonds

Question 21

How do sidechains stabilise the alpha helix?

Answer 21

Hydrophilic side chains point out, hydrophobic sidechains fold towards the middle

Question 22

These are stretches of residue with a more extended structure than an a-helix.

Answer 22

B structure

Question 23

Each section of a B structure is called a…

Answer 23

B-strand

Question 24

What kind of bonding occurs between adjacent B-strands?

Answer 24

Hydrogen bonding

Question 25

What do adjacent B strand chains form?

Answer 25

Beta sheets

Question 26

What are the 2 types of hydrogen bonding interaction in a B-sheet?

Answer 26

Parallel and antiparallel

Question 27

Beta sheets are not planar they are:

Answer 27

pleated

Question 28

How are sidechains orientated in the B sheet?

Answer 28

Side chains either point above or below.

Question 29

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.

Answer 29

Turns

Question 30

This side chain is very flexible and has a lot of conformational freedom.

Answer 30

Glycine

Question 31

This is too rigid but has a built in turn because of the bonding between R-group and amino group.

Answer 31

Proline

Question 32

How many residues per turn in alpha helices?

Answer 32

3.6 residues per turn

Question 33

How many rises per turn in alpha helices?

Answer 33

5.4 rices

Question 34

Is the spiral of an alpha helix left or right handed?

Answer 34

Right handed

Question 35

What two residues are helix breaker and therefore would not be used to form helices?

Answer 35

Proline and glycine

Question 36

The dipole of the alpha helix is positive/negative in the N terminus?

Answer 36

Positive

Question 37

In an alpha helix, each amino acid side chain is separated by how much degrees? (in a helix wheel)

Answer 37

100 degrees

Question 38

Approximately how many strands are there in each beta sheet?

Answer 38

2-10 strans

Question 39

The average strand of a B strand is about how many amino acid residues?

Answer 39

6 amino acid residues, but the maximum would be around 15

Question 40

Which level of protein structure determines the overall shape of a protein?

Answer 40

Primary structure => because it contains the instructions for protein folding hence, protein shape

Question 41

This is the process of forming alpha helices and beta sheets early in the folding process.

Answer 41

Nucleation