Protein Structure and Folding

Question 1

How man amino acids are there in the human body?

Answer 1

20

Question 2

How can you differentiate AA?

Answer 2

Properties: charge, ability of H bonding, acidic/basic, neutral, hydrophobic, hydrophilic, aliphatic, aromatic. Non-polar = side chain: alkyl. Polar = side chain: neutral, acidic, basic

Question 3

What is the structure of an AA?

Answer 3

Central C, a H, a carboxyl group COOH, an amino group NH2, an R group

Question 4

What is an AA residue?

Answer 4

what remains of AA after it has been joined by peptide bond

Question 5

Describe a protein in a primary structure

Answer 5

linear chain of AA joined by petide bond (condensation reaction) between –> amino + carboxyl

Question 6

What is the bond present in a primary structure?

Answer 6

Peptide/covalent

Question 7

What are the bonds in a secondary structure?

Answer 7

helices, H bonds between N-H and C=O

Question 8

Describe a tertiary structure and the bond present

Answer 8

3-D, folding into globular shape. Hydrophobic on inside. Covalent, ionic, H bonds, van der waals, hydrophobic. Disulphide: bonds of 2 sulphides, 2 cys residues

Question 9

What bonds are in a quaternary structure?

Answer 9

multi-subunit protein. Covalent, ionic, H bonds, van der waals, hydrophobic. Disulphide: bonds of 2 sulphides

Question 10

How does pH affect a protein in terms of pK?

Answer 10

If the pH of the solution < the pK value then the group will be protonated. If the pH of the solution > the pK value then the group will be deprotonated

Question 11

What are amyloid fibres?

Answer 11

Misfolded, insoluble form of a normal soluble protein. Highly ordered, high degree of β-sheet

Question 12

What is a peptide bond?

Answer 12

Type of covalent bond, joins AA, between N-C terminus via condensation reaction. Planar, trans conformation, C-N bond has partial double bond characteristics = unable to rotate

Question 13

What is pI?

Answer 13

pI = isoelectric point = pH at which there is no overall net charge of the protein. pH < pI is protonated, pH > pI is deprotonated

Question 14

What is a base?

Answer 14

Proton acceptor, NH2 amino group

Question 15

What is an acid?

Answer 15

Proton donor, carboxyl group COOH

Question 16

what is pKa?

Answer 16

tells you the strength of the acid = how likely the groups are to loose/gain protons

pH at which the weak acid or base exists in 50% ionised and 50% unionised form

Question 17

if an AA has a high pKa what does that indicate?

Answer 17

its a basic AA

Question 18

what is a zwitter ion?

Answer 18

AA usually present in this state. Molecule or ion having separate positively and negatively charged groups

Question 19

what happens when pKa is equal to pH?

Answer 19

there will be equal amounts of protonated and deprotonated forms

Question 20

what is the henderson-hasselbach equation?

Answer 20

pH = pKa+log(base/acid)