Amino Acids And Primary Structure 6

Question 1

4 levels of protein structure

Answer 1

• primary structure: sequence of amino acid residues
• secondary: localized conformation of the polypeptide backbone
• tertiary: 3-d structure of an entire polypeptide, including side chains
• quaternary: spatial arrangement of polypeptide chasing in a protein with multiple subunits

Question 2

Amino acids

Answer 2

• all proteins are linear polymers of a-amino acids (residues in proteins)
• amino and carboxyl groups are ionized at physiological pH
• 20 common amino acid, each have different side chain
• 2 main amino acids categories:
  
  • non-polar (hydrophobic)
  • polar (neutral or charged)

Question 3

Amino acid stereochemistry

Answer 3

• most amino acids have a chiral atom
• amino acids in proteins are in the L confirmation
• for multiple chiral centres, the R,S system must be used (most are S)

Question 4

Hydrophobic amino acids

Answer 4

Alanine (Ala, A)
Valine (Val, V)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M)
Proline (Pro, P)

Question 5

Polar amino acids

Answer 5

Serine (Ser, S)
Threonine (Thr, T)
Tyrosine (Tyr, Y)
Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Histidine (His, H)
Glycine (Gly, G)

Question 6

Charged Amino acids

Answer 6

Aspartate (Asp, D)
Glutamate (Glu, E)
Lysine (Lys, K)
Arginine (Arg, R)

Question 7

Hydrophobic amino acids (aliphatic)

Answer 7

• Ala, Val, Leu and Ile all have aliphatic side chain (only organic compounds which carbon atoms form open chains) and are hydrophobic
• diversity of these side chains contributes to optimal packing in the protein interior
• relatively innocuous Ala is often chosen as a replacement to determine amino acid function using site-directed mutagenesis

Question 8

Hydrophobic (others)

Answer 8

• Met is one of 2 aa that contain soulful, but it is inert
  
  • could be oxidized to S=O or O=S=O
• Trp is the largest aa and has UV absorbable 280nm can be used to measure protein concentration
• Phe is just Ala with a phenyl group
• Pro is unique (only imino acid: side chain connected to NH group) which creates a kink into the polypeptide chains
  
  • unable to form hydrogen bonds

Question 9

Polar amino acids

Answer 9

• Gly is the simplest aa: side chain only H atom
• Asn and Gln are the corresponding uncharged amides of the acidic amino acids Asp and Glu; which can be H bond donors or acceptors
• His has an imidazole side chain, which can be positively charged with neutral pH
• Ser, Thr, and Tyr have a hydroxyl group that often acts as a nucleophile in biochemical rxns
  
  • OH groups can also be covalently attached to other groups (reversible phosphorylation in enzyme regulation/signalling)
• Tyr is a derivative of Phe and both are precursors of aa neurotransmitters

Question 10

Cys residues can form disulphide bonds

Answer 10

• Cys has a sulfhydrl group (SH) that can be oxidized to form a disulphide bond (S-S) with another Cys-provides covalent cross linking either within or between polypeptide chains
• can link 2 strands/chains
• insulin

Question 11

Cellular oxidation and reduction

Answer 11

• Cys is usually in its SH form in an intracellular (reducing) environment, and usually S-S outside the cell
• Glutathione is the biological reducing agent
• in vitro, reducing agents maintain sulfhydryl (reduced) form
• amino acids play many other roles (signalling, metabolism)

Question 12

Charged amino acids

Answer 12

• Asp and Glu have negatively charged carboxyl side chains at pH 7 (referred to as Acidic aas)
  
  • often bind metals
  • protons can move around
• Lys and Arg have positively charged side chains at pH 7 (referred to as basic aas)
• His and Cys may also have charged side chains under some conditions

Question 13

Peptide bonds

Answer 13

• partial double bond character
• rigid and planar
• trans configuration (more favourable)
• uncharged but polar