Protein Structure and Function

Question 1

Describe the basic structure of amino acids

Answer 1

Tetrahedral centre alpha carbon
Carboxyl, amine, R, Hydrogen

Question 2

What isomers does every amino acid have (Except glycine)

Answer 2

D and L - Handedness - Asymmetric/chiral
(Based on COO- or NH3+)

Question 3

How to distinguish between D and L forms of amino acids

Answer 3

D-form the groups read CORN in the anticlockwise direction (carboxyl, R group, amine)

L-form reads CORN in a clockwise direction

Question 4

Where are L-form aas found

Answer 4

All aas incorporated into proteins by living organisms are in the L-form

Question 5

Where are D-form amino acids found

Answer 5

Cell walls in bacteria, used in some therapeutics

Question 6

What do the amino and carboxyl terminals give the polypeptide

Answer 6

Structural orientation and polarity

Question 7

What is a peptide residue

Answer 7

Each repeating unit of the polypeptide chain is termed a residue

Question 8

What makes up each residue in a polypeptide chain

Answer 8

Alpha carbon, C’=O and NH3 group

Question 9

How is the variable side chain R arranged in a polypeptide

Answer 9

Trans conformation (but 0.1% peptide bonds have a less energetically favourable cis arrangement)

Question 10

Describe the secondary structure of a protein

Answer 10

E.g. beta sheet formed from the folding of the polypeptide chain. Beta sheet made up of beta strands. The bonds stabilise the overall sheet.

Question 11

What two arrangements can Beta pleated sheets be in and which orientation is more stable

Answer 11

Antiparallel, parallel
Hydrogen bonds
Antiparallel is more stable

Question 12

Describe four features of the alpha helix in the secondary structure

Answer 12

Right handed helix
Stabilised by H-bonds
H-bonds are 4 residues apart, between residue 1 and 5
3.6 residues/turn or 0.54 nm /turn

Question 13

How do the proteins gain their properties for structure and function

Answer 13

Arrangement of side chain (in alpha helix and beta sheet, they protrude outwards)

Question 14

How is the tertiary structure formed

Answer 14

Combining secondary structures
E.g. seven helices of the transmembrane domain of the CXCR4 chemokine receptor

Question 15

How is the quaternary structure formed

Answer 15

Two or more folded polypeptides combine to form the mature protein, same bonds stabilise the structure
Haemoglobin - 2 Hbalpha and 2Hbbeta polypeptides

Question 16

What do some proteins require for their function or folding and name some examples

Answer 16

Some proteins require cofactors for their function or folding.

Heme - Haemoglobin - Hb and Fe
Nicotinamide adenine diphosphate (NAD) Reduction/oxidation
Flavin adenine dinucleotide (FAD) Reduction/oxdiation

Organic cofactors - Coenzymes

Question 17

Describe water soluble proteins

Answer 17

Globular in shape
Hydrophilic residues mostly on the external surface
Hydrophobic residues usually buried inside the protein

Some may assemble into filaments (E.g. actin) or tubes (e.g. tubulin) or coiled-coils (cortexillin)

Question 18

How are residues organised in membrane proteins

Answer 18

Membrane spanning regions have externally located hydrophobic residues that interact with the membrane lipids. They may have hydrophilic central channels

Question 19

List some non-polar/hydrophobic amino acids

Answer 19

Alanine
Valine
Phenylalanine
Proline
Isoleucine
Leucine
Methionine

Question 20

List some polar aliphatic amino acids

Answer 20

Serine
Threonine
Glutamine
Asparagine
Cysteine

Question 21

List some polar aromatic amino acids

Answer 21

Tyrosine
Histidine
Tryptophan

Question 22

How are glycine and histidine different to the other amino acids classified

Answer 22

Glycine is sometimes nonpolar or in a separate group
Histidine is sometimes a charged basic amino acid.

Question 23

What is the key difference between polar and charged amino acids

Answer 23

Polar amino acids contain oxygen atoms as part of carbonyl groups/nitrogens as secondary amine groups rather than carboxyl/amine groups (in charged amino acids)

Question 24

If an amino acid has neither an amine/carboxyl group or a secondary amine/carbonyl group then what does it have and what is it classified as

Answer 24

Hydrocarbon
Non-polar hydrophobic

Question 25

Describe the properties and features of a peptide bond

Answer 25

Delocalised electrons of the N-CO make the bond ridged, with the O and H atoms on opposite sides lying in the same plane.

The peptide bond is thus a planar structure with the rotational freedom within a polypeptide is found around alpha carbon NOT the peptide bond.

Question 26

What is the significance of having rotational freedom of bonds in a polypeptide chain

Answer 26

Huge variation in conformation, allowing for the formation of structural arrangements such as alpha helices and beta sheets.

Question 27

What is energy minimisation in regards to polypeptides

Answer 27

The minimisation of the molecule’s specific energetic state (the free energy) determines the most favourable arrangement of the atoms

The change in free energy upon folding is called (Change in triangle)G

If (tri)G is negative then the molecule will spontaneously fold

Question 28

What environmental factors affect the free energy of conformation

Answer 28

Aqueous or lipid (membrane)
Other proteins or molecules including salts and their ionic state
Changes in the environment can induce further conformational change e.g. cofactors, binding a ligand

Question 29

How do non-covalent and covalent bonds determine structural stability

Answer 29

Weak non-covalent bonds have 1/20 strength of covalent bonds
But the overall contribution of non-covalent bonds is significant because non-covalent bonds are far larger in number.

Question 30

List the non-covalent bonds/forces

Answer 30

Electrostatic attraction
Hydrogen bonds
VdW attractions - dipole
Hydrophobic interactions

Question 31

Describe electrostatic attraction

Answer 31

Positive - Negative charge
Falls off exponentially as distance increases, affected by electrostatic environment (aqueous environment)

Question 32

Describe hydrogen bonds

Answer 32

Bonds between hydrogen atoms
Transient bonds similar in some respects to covalent bonds

Question 33

Describe VdW attractions - Dipole

Answer 33

Weak forces between two atoms determined by fluctuating charge
Attraction at close distance balanced by repulsion due to how close they are
VdW induced by how close molecules are

Question 34

Describe hydrophobic interactions

Answer 34

(Water is a polar molecule) hydrophobic interactions minimise disruption of water network - ie the fourth weak force

Question 35

Describe featuers of disulphide bonds

Answer 35

Disulphide bonds formb etween the side chains of two cysteine residues

The bonds form in an oxidative reaction
The SH groups from each cysteine cross link
This usually occurs in distant parts of the primary sequence but adjacent in the three-dimensional structure
Can form on the same (intra-chain) or different (inter-chain) polypeptide chains e.g. insulin left

Question 36

What happens if a protein is mis-folded

Answer 36

Almost always the function is lost or reduced

Mis-folded proteins often self-associate and form aggregates
E.g.
Huntingtin Htt
Amyloid-beta AB (Alzheimer’s)
Prion protein Creutzfeldt-Jakob disease
Alpha-synuclein - Parkinson’s
Serm amyloid - AA Amyloidosis
Islet amyloid polypeptide (Type 2 diabetes)

Question 37

What is aggregation

Answer 37

When proteins accumulate and clump up together as a result of misfolding

Question 38

Give reasons for protein misfolding

Answer 38

1. Somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding
2. Errors in transcription or translation leading to the production of modified proteins unable to properly fold
3. Failure of the folding machinery
4. Mistakes of the post-translational modifications or in trafficking of proteins
5. Structural modification produced by environmental changes
6. Induction protein mis-folding by seeding and cross-seeding by other proteins

Question 39

Describe the role of protein misfolding in Alzheimer’s disease

Answer 39

Proteolytic cleavage of amyloid precursor protein (APP) is observed

APP has multiple functions but is involved in G-protein signalling

Cleavage of APP results in a @40 residue peptide beta amyloid

In the intact molecule this anchors the protein in the membrane APP accumulates and mis-folds to form beta sheets.

Question 40

Describe the beta amyloid peptide

Answer 40

In Alzheimer’s the beta amyloid peptide accumulates.

Mis-folding of the protein results in a planar arrangement and polymerisation

This forms fibrils of mis-folded protein

Beta amyloid fibres are formed from stacked beta sheets in which the side chains interdigitate

Question 41

Describe the role of mis-folding in cystic fibrosis

Answer 41

A deletion of phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regular (CFTR) occurs

(tri)F508del leads to mis-folding of the protein whilst it is still in the ER

This is recognised by the cellular machinery that identifies and processes misfolded proteins

This results in ubiquitination, trafficking to the proteasome and degradation

Question 42

What are prions

Answer 42

Mis-folded proteins that interact with other normal proteins

Question 43

Describe prion action

Answer 43

Mis-folding of the normal protein and polymerisation is induced

Oligomers form fibrils of mis-folded protein

Reliant upon the concept of energy minimisation - More stable aggregated structure