Peptides

Question 1

What is a property structure of amino acids ?

Answer 1

• amphoteric
• charge variability = changes with pH

Question 2

what is the isoelectric point ?

Answer 2

• the pH at which an amino acid has no net charge because it exists in its “zwitterion” form
• pH 6.5–7.5

Question 3

properties of non-polar, neutral amino acids ?

Answer 3

• no charge on side chains
• no H bonding = no electronegative atoms
• not soluble in water

Question 4

properties of polar neutral amino acids ?

Answer 4

• soluble in water, can form H bonds

Question 5

properties of charged amino acids ?

Answer 5

• either positive or negative charge
• can form H and ionic bonds
• soluble in water

Question 6

chirality of amino acids ?

Answer 6

• all amino acids except glycine have chiral α-carbon
• Only L amino acids are found in proteins.
• Most L amino acids have an absolute
  configuration of S

Question 7

what is the human protein atlas ?

Answer 7

• map showing all the known proteins in the body and how they are distributed in tissues and organs

Question 8

how do acidic side chains affect the (pI) isoelectric point of an amino acid?

Answer 8

• lower the pI compared to average pka due to side chain adding extra -ve charge

Question 9

how do basic side chains affect the pI point of an amino acid ?

Answer 9

• higher than the average of pKa for amine and acid groups as the side chain introduces extra +ve charge

Question 10

what are 3 methods for separating amino acids ?

Answer 10

• pI separation by electrophoresis ( Nonpolar travel faster)
• Chromatography
• Ion exchange chromatography

Question 11

How are peptides synthesized from α-halo acids?

Answer 11

• carboxylic acid to α-halo acids = Br2,PBr, H2O
• react with excess NH3
• halogen replaced by NH3+

Question 12

How are peptides synthesized via Strecker synthesis ?

Answer 12

• aldheyde converted to imine (C=N) using NH3
• imine reacts with cyanide ion to form aminonitrile
• hydrolysis of aminonitrile to form amino acid (CN hydrolysed to COOH using HCl)

Question 13

What is the peptide bond?

Answer 13

• covalent bond formed between the carboxyl group (–COOH) of one amino acid and the amine group (–NH₂) of another

Question 14

Why is the peptide bond resonance-stabilized?

Answer 14

• delocalization of electrons between the carbonyl oxygen (C=O) and the amide nitrogen (–NH)
• lone pair of electrons on the nitrogen

Question 15

How are electrons distributed in the peptide bond ?

Answer 15

• unequally
• greater electron density on the carbonyl oxygen
• higher electronegativity than N

Question 16

what is the primary structure of a protein ?

Answer 16

• sequence of amino acids in polypeptide chain

Question 17

What is the secondary structure of a protein ?

Answer 17

• localized folding patterns within the polypeptide chain
• stabilized by H bonds
• α-helix and β-pleated sheets

Question 18

What is the α-helix (𝛼-helix), and how is it structured?

Answer 18

• right-handed spiral structure
• each C=O forms a H bond with the NH of the amino acid four residues earlier

Question 19

What is the β-pleated sheet (𝛃-sheet) ?

Answer 19

• 2 or more lengths of the polypeptide chain lie parallel to each other
• R groups of the amino acids point above and below the sheets
• NH and C=O parts of the peptide bond point towards each other
• H-bonds between these sections

Question 20

Ramachandran Plot

Answer 20

• way to visualise dihedral angles ψ against φ of amino acid residues in protein structure
• recognised that many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms

Question 21

What is the tertiary structure of a protein?

Answer 21

• final 3D shape, which is determined by the interactions between the R-groups

Question 22

What are the four main types of interactions that stabilize the tertiary structure of proteins?

Answer 22

• Ionic bonds
• Hydrophobic interactions
• Hydrogen bonds
• Disulphide bridges (covalent)

Question 23

What is the quaternary structure of a protein?

Answer 23

• two or more polypeptide chains interact
• Forces between these chains, SAME AS TERTIARY structure

Question 24

What are the two categories of proteins based on quaternary structure, and examples?

Answer 24

• Fibrous proteins: long linear structures providing support and strength (e.g., collagen).
• Globular proteins: compact, spherical shapes and often have functional roles, such as enzymes or transport (e.g., hemoglobin).

Question 25

What is protein denaturation ?

Answer 25

• loss of structure + activity due to disruption to interactions
• denaturation can be reversible or irreversible