Proteins

Question 1

What are proteins?

Answer 1

Fundamental functioning molecules of the cell

Question 2

Which functions do proteins provide the cell?

Answer 2

• Carriers e.g. trafficking O2
• Metabolic e.g. enzymes
• Cellular machinery e.g. spliceosomes
• Structural scaffolding e.g. microtubules
• Sensory molecules e.g. receptors

Question 3

How are proteins formed?

Answer 3

Synthesised by the ribosome during translation from amino acids

Question 4

Which isomer form of amino acid do humans amino acids take?

Answer 4

L- Amino acids (read CORN clockwise)

Question 5

Where are D form amino acids found?

Answer 5

In peptidoglycan bacterial cell walls

Question 6

Why are amino acids referred to as ɒ amino acids?

Answer 6

The central C is bonded to the acidic carboxyl group

Question 7

What is a zwitterion?

Answer 7

The structure amino acids take at an intermediate pH with a net neutral charge

Question 8

What determines the form an amino acid takes?

Answer 8

pH

Question 9

Which form does the amino acid take at low pH (acidic)?

Answer 9

positive NH3+ charge

Question 10

In alkaline conditions what does the amino acid look like?

Answer 10

negative COO- charge

Question 11

How many amino acids are there in total?

Answer 11

There are 20

Question 12

How many essential amino acids are there ?

Answer 12

9 essential amino acids obtained from the diet only

Question 13

What is a residue?

Answer 13

a repeating peptide unit

Question 14

Describe the structure of a peptide bond

Answer 14

Flat planar structure
Fixed arrangement
Rotational freedom of bonds
- enables movement of rest of the chain

Question 15

How many levels of protein folding are there?

Answer 15

4 levels of folding

Question 16

What are the folding structures of a protein?

Answer 16

Primary structure
- amino acids joined by strong covalent bonds

Secondary structure
- H bonding between ɒ helices or Β pleated sheets

Tertiary structure
- Β continuous folding due to intramolecular H bonds stabilised by
covalent disulphide bonds
- globular or fibrous structure formed

Quartenary structure
- dependent on weak ionic bonds

Question 17

What enables bond rotation within proteins?

Answer 17

The other bonds around the ɒ carbon allow bond rotation as the peptide bond is ridged

Question 18

In terms of energetic state, how are proteins arranged?

Answer 18

Polypeptides adopt a structure based on energy minimalisation
- each molecular structure has a specific energetic state

Question 19

Are parallel or anti parallel Β pleated sheets stronger & why?

Answer 19

Anti parallel are stronger

- parallel Β sheets require longer Β turns which are destabilising

Question 20

Which weak interactions occur within polypeptides to give them their structure

Answer 20

• Ionic Bonds: between -ve and +ve side chains
• Hydrogen Bonds: betwen polar side chains (H+ and ℷ
  atoms)
• VDW Forces: caused by Hydrophobic residues
• Disulphide bridges: sulfhydryl side chains of Cysteine

Question 21

What experimental techniques can be used to identify protein structures?

Answer 21

Xray crystallography

NMR

Question 22

What shape do water soluble proteins take?

Answer 22

Globular shape

Question 23

Where are hydrophilic proteins located?

Answer 23

Externally on the surface

Question 24

When many polypeptides assemble together, what are the 2 bigger protein structures they form called?

Answer 24

Filaments (actin)

Tubes (tubulin)

Question 25

Where are hydrophobic residues located?

Answer 25

Usually buried inside the protein

Question 26

How do membrane proteins differ from regular protein

molecules?

Answer 26

Their hydrophobic residues externally located

hydrophilic residues internally located

Question 27

Which non-covalent bonds help stabilise a proteins folded structure?

Answer 27

Several non-covalent bonds which stabilise a protein;
- hydrogen bonds
- van der Waals forces
- ionic interactions
These are weak bonds compared to covalent bonds
but are collectively strong.

Hydrogen bonds form where a H is shared between an N and an O.
VDW forces are dipole-dipole interactions and are weak but as they are often numerous, they are significant in stabilising a folded structure.

Question 28

The folded form of a polypeptide chain has a lower Gibbs free energy than the unfolded form.

What role does entropy (of the polypeptide and the surrounding water) play in the folding process?

Answer 28

Gibbs free energy is higher in the non-folded form than in the folded form of the polypeptide.
Therefore the folded form is preferred.
Folding is associated with a loss of entropy (gain in structure) of the polypeptide, whereas the surrounding water molecules gain entropy. Thus during
folding (the favourable) entropy gain of the solvent, partially offsets the disfavoured entropy loss
of the polypeptide.

Question 29

Explain what is meant by the term ‘folding pathway’ and why they are the subject of very intense research activity?

Answer 29

A ‘folding pathway’ is a series of steps an unfolded protein takes to produce the final folded form.

The final shape is not a result of random conformational interconversions but exactly how proteins fold is still a mystery. If this pathway could be determined, the 3D shape a protein could form could be determined by analysis of the amino acid sequence
– i. e. without
having to study the 3D structure which requires a lot of work and money.

A series of steps occur in the folding process but a method has not been found to find out what these are