Building blocks of proteins

Question 1

What is an alpha carbon?

Answer 1

Alpha carbon of amino acids is the one which has the side chain attached to it

Question 2

What are the non polar amino acids?

Answer 2

They are hydrophobic
Glycine, proline, cysteine, alanine, valine, leucine, isoleucine, methionine, tryptophan and phenylalanine

Question 3

Properties of glycine, proline and cysteine

Answer 3

Gly: R=H, non-chiral, flexible, almost in a group by itself
Pro: R-group bonds back to main chain N, imino acid, rigid, almost in a group by itself
Cys: not really non polar or polar

Question 4

What are the charged polar amino acids?

Answer 4

-ve charge : aspartic acid and glutamic acid
+ve charge : lysine, arginine and histidine
Found in surface of proteins or in active sites due to being charged

Question 5

What are the uncharged polar side chains?

Answer 5

Serine, threonine, tyrosine, asparagine and glutamine
Hydrophilic often found at surface of proteins

Question 6

What are the properties of non polar amino acids?

Answer 6

Only C or H at the end of their side chain
Hydrophobic

Question 7

What are the properties of polar amino acids?

Answer 7

Have -OH, -NH2 or -O in their side chain
Able to form bonds with other atoms
Hydrophilic

Question 8

What are the properties of +ve charged polar amino acids?

Answer 8

Have -OH, -NH2 or -O in their side chain
Able to form bonds with other atoms
Hydrophilic
+ charge at pH 7

Question 9

What are the properties of -ve charged polar amino acids?

Answer 9

Have -OH, -NH2 or -O in their side chain
Able to form bonds with other atoms
Hydrophilic
-ve charge at pH 7

Question 10

What is pKa and pI?

Answer 10

pKa value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised
pI is the pH at which the net charge on an amino acid is zero
pH<pKa = side chain protonated
pH>pKa = side chain deprotonated

Question 11

How do we know if something is ionisable?

Answer 11

Its polar
Has an H-atom that can participate in acid-base reactions
Donates and accepts electrons

Question 12

What is a post translational modification (PTM)?

Answer 12

When a chemical group is added to an amino acid residue after translation has occur. Added via covalent attachment

Question 13

What ways can amino acids be modified?

Answer 13

Phosphorylation, hydroxylation, carboxylation, metal binding, iodination, glycosylation

Question 14

What is phosphorylation?

Answer 14

An amino acid modification often used to control enzyme activity - like a chemical on/off switch

Question 15

What is hydroxylation?

Answer 15

An amino acid modification needed to prevent connective tissues diseases and scurvy, often proline and lysine involved

Question 16

What is carboxylation?

Answer 16

An amino acid modification needed for blood clotting, often glutamate involved

Question 17

What are peptide bonds?

Answer 17

A covalent bond, planar (flat), trans (prevents steric hinderince), dipole (ends have opposite charges), partial double bond character, formed via dehydration reaction between C-terminal of one AA and N-terminal of another

Question 18

What are peptides and polypeptides?

Answer 18

A short stretch of amino acids joined together by peptide bonds
A polypeptide is a very long chain of amino acids

Question 19

What is a protein?

Answer 19

A longer chain of amino acids joined together usually with a defined biological function

Question 20

What are amino acid residues?

Answer 20

Amino acids that are covalently joined in a peptide or protein that are no longer complete, individual, amino acids