L2 - Protein folding and function

Question 1

What is the primary structure of a protein?

Answer 1

The linear amino acid sequence of the polypeptide chain

Question 2

What is the secondary structure of a protein?

Answer 2

The local spatial arrangement of the polypeptide backbone - determined by hydrogen bonds between the backbone but NOT R-groups

Question 3

What is the tertiary structure of a protein?

Answer 3

The 3D arrangement of all atoms in a polypeptide

Question 4

What is the quaternary structure of a protein?

Answer 4

The 3D arrangement of protein subunits in multimeric proteins

Question 5

Describe four features of alpha-helices

Answer 5

3.6aa/turn
0.54nm pitch (vertical distance per complete turn)
Right-handed helix
R-groups sit on the outside

Question 6

Describe thfeatures of beta-sheets

Answer 6

Fully extended conformation
0.35nm between adjacent AAs
R-groups alternate between opposite side of the chain
Alternate side-chains also point in opposite directions

Question 7

Which bonds can rotate in a polypeptide and how does this affect its conformation?

Answer 7

The peptide bond cannot rotate but the C-C bond in the backbone between peptide bonds can. The angle of these bonds determines the conformation of the backbone. Bulky R-groups can stop certain conformations occuring.

Question 8

Between which atoms do the hydrogen bonds in an alpha-helix form?

Answer 8

Between the backbone -C=O group of one residue and the -NH group of the residue FOUR amino acids away

Question 9

Which two residues are strong helix formers?

Answer 9

The small hydrophobic residues such as alanine and leucine

Question 10

Which two residues are strong helix breakers?

Answer 10

Proline - because rotation around the N-C(alpha) bond is impossible
Glycine - because the tiny R-group supports other conformations (it’s very flexible)

Question 11

What are the two main types of beta-sheet?

Answer 11

Parallel and anti-parallel

Question 12

Describe fibrous proteins. What roles do they tend to have?

Answer 12

Long strands or sheets
Little or no tertiary structure
Single type of repeating secondary structure
Usually insoluble
Often have a structural role
E.g. Collagen

Question 13

Describe globular proteins. What roles do they tend to have?

Answer 13

Compact shape
Complex tertiary structure
Several types of secondary structure
Usually soluble
Many different roles

Question 14

Describe the repeating structure of collagen alpha-chains

Answer 14

Glycine every 3 residues

Question 15

When describing a tertiary structure, what is a motif?

Answer 15

A folding pattern containing one or more elements of secondary structure e.g. Beta-alpha-beta loop.

Question 16

When describing a tertiary structrue, what is a domain?

Answer 16

Part of a polypeptide chain that folds into a distinct shape. It often has a specific functional role e.g. The calciu binding domains of tropo in C.

Question 17

Describe the difference in amino acid distribution between soluble proteins such as myoglobin and membrane proteins such as porins

Answer 17

Soluble proteins: fold so hydrophobic amino acids are in the centre and Hydrophillic are on the outside
Membrane proteins: fold so that there is often a water-filled hydrophilic channel through their centre and a largely hydrophobic exterior

Question 18

Describe the quaternary structure of haemoglobin

Answer 18

Adult Haemoglobin contains two alpha-subunits and two beta-subunits, held together by non-covalent interactions

Question 19

What type of bonds are involved in primary protein structure?

Answer 19

Covalent peptide bonds

Question 20

What forces are involved in secondary protein structure?

Answer 20

Hydrogen bonds between the polypeptide backbone

Question 21

What forces are involved in tertiary and quaternary protein structure?

Answer 21

Hydrophobic interactions
Ionic interactions
Hydrogen bonds
Van Der Waals forces
Covalent (di-sulphide bonds)

Question 22

Why do proteins which are secreted tend to have Disulphide bonds?

Answer 22

Disulphide bonds are very strong (214kJ/mol) therefore do not tend to break once formed. Proteins that are secreted (e.g. Into the gut), tend to enter a hostile environment and therefore need a more rigidly held protein structure to stop the protein from denaturing quickly.

Question 23

List the forces involved in maintaing protein structure from strongest to weakest

Answer 23

Covalent/di-sulphide - 214kJ/mol
Ionic/ hydrogen bonds - 10-30kJ/mol
Hydrophobic effect - approx. 10kJ/mol
Van Der Waals - 4kJ/mol

Question 24

Define denaturation

Answer 24

The process in which proteins or nucleic acids lose the quaternary, tertiary, secondary structure which is present in their native state.

Question 25

What can cause protein Denaturation?

Answer 25

1. Heat - increased vibration energy
2. PH - alters ionisation state of AAs, changes ionic and hydrogen bonds
3. Detergents/ organic solvents - disrupt hydrophobic interactions

Question 26

How do proteins fold?

Answer 26

The information needed for folding is contained in the polypeptide sequence. Folding occurs in a step-wise manner and may proceed through localised folding.
Some proteins need chaperone proteins to assist in folding.

Question 27

Describe a disease which is caused by protein misfolding and discuss its mechanism

Answer 27

Transmissible spongiform encephalopathies (BSE/ Kuru/ CJD) are caused by an altered conformation of normal human protein. This altered conformation converts exiting native conformations of the same proteins into a disease state. These abnormal forms then aggregate, forming relatively insoluble amyloid fibrils.

Question 28

Define amyloidoses

Answer 28

Diseases that result form errors in normal folding which cause a build-up of misfolded proteins (amyloids).

Question 29

Describe the strcuture of amyloid fibres

Answer 29

1. Contain misfolded, insoluble form of a normally soluble protein
2. Highly ordered with a high degree of beta-sheet
3. Core beta-sheet forms before the rest of the protein
4. Inter-chain assembly stabilised by hydrophobic interactions between aromatic amino acids

Question 30

What condition or reagent could disrupt a Disulphide bond?

Answer 30

Reducing agents e.g. Mercado ethanol, dithiothreitol (or heat)

Question 31

What condition or reagent could disrupt a hydrogen bond?

Answer 31

PH extremes (or heat)

Question 32

What condition or reagent could disrupt a hydrophobic interaction?

Answer 32

Detergents/ organic solvents/ urea (or heat)

Question 33

What condition or reagent could disrupt a ionic interaction?

Answer 33

Changes in pH or ionic strength (or heat)

Question 34

Why are peptide bonds important for the secondary structure of proteins?

Answer 34

They contain carbonyl and amino groups which are able to hydrogen bond. These groups are a major determinant of the secondary structure of proteins e.g. Alpha-helices and beta-sheets.

Question 35

What is the pitch of an alpha-helix?

Answer 35

0.54nm

Question 36

How many amino acids per turn of an alpha-helix?

Answer 36

3.6 amino acids