Amino Acids + Protein Stucture + Folding

Question 1

What bond is between amino acids?

Answer 1

Peptide bonds

Question 2

Features of peptide bonds

Answer 2

• Planar
• Rigid
• Trans conformation
• Bonds on either side of peptide bond are free to rotate

Question 3

Describe the molecular structure of an amino acid

Answer 3

Carboxyl- group
Amine group
R group - classified by R group

Question 4

Polar vs non-polar classification of amino acids

Answer 4

• Polar: uneven distribution of electrons
• Non-polar: even distribution of electrons

Question 5

What is the isoelectric point? pl

Answer 5

The pH at which there is no overall net charge

Question 6

Describe the structure + formation of disulphide bonds

Answer 6

• R group of cysteine is -SH (sulfhydryl group)
• two -SH groups are oxidised > cystine which contains a disulphide bond

Question 7

Cysteine vs cystine

Answer 7

Cysteine is an amino acid
Cystine is a dimer of cysteine

Question 8

What is the range of physiological pH?

Answer 8

7.35-7.45

Question 9

Outline the behaviours of acidic amino acids?

What 2 amino acids have acidic side chains?

Answer 9

• proton donors
• at physiological pH, the side chains have negative charg > negative carboxyl group (—COO-)
• Aspartate
• Glutamate

Question 10

Outline the behaviours of basic amino acids?

What 3 amino acids have basic side chains?

Answer 10

• proton acceptors
• strong: at physiological pH, side chains are fully ionised + positively charged
• weak: at physiological pH, side chains are uncharged
• arginine - strong
• lysine - strong
• histidine - weak

Question 11

What is determined by the amino acid sequence of a protein?

Answer 11

• folding
• physical characteristics

Question 12

How can amino acids be classified based on their chemical properties?

Answer 12

• hydrophobic vs hydrophilic
• polar vs non polar
• acidic vs basic vs neutral

Question 13

How can amino acids be classified based on their physical properties?

Answer 13

Aromatic
Aliphatic

Question 14

Compare PKA values between acidic and basic amino acids

Answer 14

• Basic: - positively charged R groups
  - higher pKa
• Acidic: - negatively charged R groups
  - lower pKa

Question 15

Relationship between pK and pH values of amino acids

Answer 15

• R group is protonated: solution pH > amino acid pK
• R group is deprotonated: solution pH < amino acid pK

Question 16

Relationship between pI and pH of proteins

Answer 16

• Protonated: pH < pI
• Deprotonated: pH > pI

Question 17

What are conjugated proteins?

Answer 17

Proteins covalently bonded to other chemical components

e.g. haemoglobin

Question 18

How are B sheets stabilised?

Answer 18

Hydrogen bonds

Question 19

List the types of intermolecular forces present in the types of protein structure levels

Answer 19

• Primary: peptide bonds
• Secondary - hydrogen bonds
• Tertiary + Quaternary - non covalent forces

Question 20

What are the N and C terminals of proteins

Answer 20

N - free amino acid terminal
C - free carboxyl terminal

Question 21

5 biochemical roles of proteins and examples

Answer 21

• catalysts e.g. enzymes
• transporters e.g. haemoglobin
• structural support e.g.collagen
• immune protection e.g. immunoglobins
• receptors e.g. for hormones, neurotransmitters…

Question 22

What interactions stabilise tertiary structure?

Answer 22

Disulphide bonds
Hydrophobic interactions
Hydrogen bonds
Ionic interactions

Question 23

Describe the role + structure of fibrous proteins
Examples

Answer 23

• Role: support, shape + protection
• Structure: single repeating secondary structure > forms long strands or sheets

e.g. collagen, keratin

Question 24

Describe the role + structure of globular proteins
Examples

Answer 24

• Role: catalysts, regulation + transport
• Structure: several types of secondary structure

e.g. myoglobin, haemoglobin

Question 25

How are amino acids classified?

Answer 25

According to to the chemical properties of their R groups