MCB Lecture 6-7 Protein Structure

Question 0

Which groups must form hydrogen bonds?

Answer 0

Polar groups must form hydrogen bonds

Question 1

Describe hydrogen bonding in proteins (h-bonds are between which atoms?)

Answer 1

Hydrogen bonding occurs between NH & C=O of two different residues

Question 2

Compare hydrogen bond length and with that of VDW interactions

Answer 2

H-bonds are shorter and allow the protein to pack more closely together than VDW interactions would allow.

Question 3

What are the three possibilities in terms of hydrogen bonding between different groups?

Answer 3

1. Backbone - Backbone
2. Backbone - Residue
3. Residue - Residue

Question 4

What is a feature of secondary structure of protein?

Answer 4

Regular dihedral angles of the residues

Question 5

Why have secondary structure in proteins?

Answer 5

Secondary structure allows close packing of the peptide, and increased stability

Question 6

What are the dihedral angles in Beta sheets?

Answer 6

Phi: -130
Psi: +130

Question 7

Between which two residues can beta sheets form?

Answer 7

Any two within a peptide

i and j

Question 8

Differentiate between beta sheets and beta strands

Answer 8

Individual beta strands make up a beta sheet

Question 9

How do hydrophobic faces of the beta sheet arise?

Answer 9

Side chains point directly up and directly down alternatively.
By having an alternating sequence of hydrophobic and hydrophilic side chains, all the hydrophobic ones will be on one side of the sheet.

Question 10

Differentiate between anti-parallel and parallel, as well as pure and mixed beta sheets

Answer 10

Anti parallel sheets: n termini are at different ends
Parallel: n termini are at the same end

Pure: sheet is made up of only parallel or anti parallel strands
Mixed: there are examples of parallel and anti parallel in the sheet

Question 11

What is a beta-barrel?

Answer 11

A beta barrel is a structure that forms when the beta sheets curve round to form a barrel.
Hydrophobic side chain project into the cavity of the barrel
Hydrophilic side chains project out into the solvent

Question 12

What are the dihedral angles in alpha helices?

Answer 12

Phi: -57
Pi: -47

Question 13

What are beta-sheet twists? What are the two types?

Answer 13

When the plane of the sheet is contorted.
This is really common

The two types are left handed and right handed twists

Question 14

Describe the handedness of alpha helices

Answer 14

Alpha helices are right handed.

Even when turned upside down, the handedness doesn’t change

Question 15

Between which two residues do alpha helices form

Answer 15

NHi and C=O i-4

There are three residues between the two that form hydrogen bonds

Question 16

Do all residues within a helix form bonds?

Answer 16

Yes, apart from four residues at either end

Question 17

How many residues per turn?

Answer 17

3.6

Question 18

Where do the side chains point?

Answer 18

All side chains point outwards

Question 19

Describe the dipoles in an alpha helix

Answer 19

The peptide dipoles add together, making one macro dipole

Question 20

What is an heptad repeat?

Answer 20

Repeat uni of seven residues in an alpha helix

Question 21

What does the heptad repeat give rise to?

Answer 21

‘a’ and ‘d’ are hydrophobic.

This gives rise to a hydrophobic stripe that curves around the alpha helix structure.

Question 22

One heptad repeat corresponds to how many turns in the alpha helix?

Answer 22

Roughly two turns

Question 23

What is a coiled coil?

Answer 23

A coiled coil is when two alpha helices coil around each other.
The two hydrophobic stripes interact.
This buries the hydrophobic side chains, sequestering them away from solvent

Question 24

How can beta sheets and alpha helices associate?

Answer 24

The hydrophobic stripe along an alpha chain interacts with the hydrophobic face of a beta sheet

Question 25

What are beta-turns?

Answer 25

Beta turns is a sequence of residues that changes the direction of the peptide

Question 26

Where are reverse turns normally found?

Answer 26

In beta sheets

Question 27

How many residues make up a beta-turn?

Answer 27

4

Question 28

Describe the structure of a beta turn

Answer 28

Four residues

The first and fourth residue interact with a hydrogen bond to increase the stability.

Question 29

Which amino acids is commonly found in position i+1? Why?

Answer 29

Proline. The phi bond of -60 is perfect for the turn required.

Question 30

What is the difference between the two types of beta turns?

Answer 30

The difference is the position of the carbonyl of the i+1 residue.

Question 31

How is entropy important in the formation of hydrophobic region?

Answer 31

It would seem intuitive that a folded structure of protein is more ordered and thus higher entropy than an unfolded protein.
This would be problematic though, because it would mean that the unfolded state is the naturally occurring one.
Obviously, this isn’t the case.

When a protein folds up, the hydrophobic side chains becomes buried in the core, away from water. This releases water molecules.
The water molecules are more disordered, and thus higher entropy.

Question 32

Formation of a hydrophobic core is driven by…

Answer 32

Entropy

Question 33

What are supersecondary structures?

Give three examples

Answer 33

Super secondary structures are interactions between beta sheets and alpha helices of one peptide.

aa hairpin
BB hairpin
BaB element

Question 34

What are the features of tertiary structures?

Answer 34

Tertiary structures, or domains, represent functional domains

Domains have specific functions, such as catalytic activity, lipid binding etc.

They must show some evidence of independent folding

Question 35

In general, how many residues are there in a domain?

Answer 35

40-700

Question 36

Protein domains are an example of … Structure

Answer 36

Tertiary

Question 37

What is quaternary structure?

Answer 37

Interaction of multiple peptides to form a molecule

Question 38

A single polypeptide can have multiple …

Answer 38

Domains

Question 39

In type II beta turns, … often takes position i+2.

Why?

Answer 39

Glycine often takes position i+2
Since glycine has no side chain, steric hindrance with the carbonyl of i+1 is reduced, since the two are close in type II Beta turns