Protein Structure and function

Question 1

What are the functions of proteins?

Answer 1

Carrier functions - transporting oxygen
Metabolic functions - enzymes producing and using energy
Form parts of cellular machinery - microtubules, nucleosomes
Sensing molecules - receptors and their ligand

Question 2

Structure of an amino acid

Answer 2

Tetrahedral with an alpha carbon in the centre
Variable side chain
Each bond allows rotational freedom

Question 3

What happens to an amino acid when you change the pH?

Answer 3

Low pH - NH3+ so acts as a base, which accepts H+
Neutral pH - COO- NH3+ so forms a zwitterion at intermediate pH
High pH - COO- so acts an acid, which donates H+

Question 4

When an amino acid acts as an acid or a base what does it ensure?

Answer 4

Dynamic equilibrium

Question 5

Explain what are dextro and levo isomers

Answer 5

Mirror images
Asymmetrical/ chiral
Dextro isomers has the amine group on the left and carboxyl group on the right(NROC) and it’s residues are used to comprise cell walls of bacteria and is also often used in therapeutics
Levo isomers have the groups the opposite way round(CORN) and all amino acids incorporated into proteins by living organisms are in this form

Question 6

What causes the variable side chain to be classed as polar or non-polar?

Answer 6

Polar is when the side chain is the hydrophilic region of the cell (these can be subdivided into polar acidic, polar basic and polar neutral) whereas the non polar is when the side chain is in the hydrophobic parts of the cell (these can be broken down into aliphatic or aromatic)

Question 7

What is the polypeptide backbone?

Answer 7

A repeating sequence of atoms along the core of the polypeptide chain

Question 8

What are essential amino acids?

Answer 8

These are amino acids that our body cannot produce so have to be consumed through out diet

Question 9

Describe the primary structure of a protein

Answer 9

Linear arrangement of amino acids
Unbranched chain by covalent amine bonds (peptide bonds)
(Occasional disulfide bonds form covalently linking side chains together)
Repeated amine, alpha carbon, carbonyl or each amino acid residue form the backbone of the protein
This allows various side chains to project from these

Question 10

What is residue?

Answer 10

Repeating units in a polypeptide chain
Consist of an alpha carbon, amine group, carboxyl group
Variable side chain is usually arranged in trans formation

Question 11

What percentage of peptide residues are in CIS conformation and why so less?

Answer 11

Less than 0.1%

Due to being less energetically favourable

Question 12

Describe the secondary structure of a protein

Answer 12

Stable spatial arrangement of polypeptide chains which is held in place by hydrogen bonds
May contain more than one form of secondary structure

Question 12

Alpha helices

Answer 12

Backbone forms spiral structure
Amino and carboxyl groups bonded
Stable arrangement of hydrogen bonds holds the backbone in straight coiled cord with side chains branching out
Hydrophilic/hydrophobic determined by side chains

Question 13

How many residues per turn does an alpha helix have?

Answer 13

3.6

Question 14

Beta sheets

Answer 14

Laterally packed beta strands
Beta strands are short (5 to 8 residues)
Hydrogen bonding occurs between backbone atoms in separate but adjacent B strands
Forms pleats
Anti parallel - hydrogen bonds stronger
Direction of beta sheets determined by the orientation of the peptide bond

Question 16

What are more stable parallel or antiparallel beta sheets?

Answer 16

Antiparallel beta sheets as there are loops connecting beta sheets and are longer in parallel compared to antiparallel

Question 17

Beta turn

Answer 17

Composed of 4 residues forming a U shape
Located on surface of protein forming bends that reverse the direction of polypeptide backbone
Help large protein structures to bend into compact structures

Question 18

What 2 proteins are commonly used in beta turns?

Answer 18

Glycine as it lacks in large side chains

Proline as it is built in bend

Question 19

Describe the tertiary structure of a protein

Answer 19

Overall conformation of polypeptide chains (3D structure)
Primarily stabilised by hydrophobic interactions between non polar chains, hydrogen bonds between polar side chains and disulfide bridges (between side chains of cysteine residues). This is a covalent bond so restricts , movement of side chain and stabilises protein
Combination of secondary structures

Question 20

Describe the quaternary structure of a protein

Answer 20

2 or more polypeptide chains combine to form the mature protein (haemoglobin have 2 alpha and beta polypeptide chains)

Question 21

What are cofactors?

Answer 21

Some proteins require these to function correctly and these are sometimes called cofactors

Question 22

What structure is required for normal function?

Answer 22

Water soluble proteins are globular in shape
Hydrophilic residues are mostly on the external surface
Hydrophobic residues are usually buried inside the protein
Membrane spamming regions like on receptors have externally located hydrophobic residues which interact with the membrane lipids