Lecture 2- Amino Acids

Question 1

What is the configuration of the amino acids?

Answer 1

All L stereoisomers (S) based on the chirality of the alpha-carbon (only glycine is not chiral)

Question 2

How are atoms numbered in amino acids?

Answer 2

Greek lettering begins at C2 (alpha carbon). C1 is the carboxylic acid carbon.

Beta, gamma, delta carbons after that in the side chain (i.e. glutamate)

Question 3

Which amino acids have aromatic rings in their R groups? Why is this important?

Answer 3

Phenylalanine (F), Tryptophan (W), Tyrosine (Y)

You can measure the amount of protein in something by knowing what relative abundance of tryptophan there is since it absorbs light at 280 nm.

Question 4

Why is proline imporant?

Answer 4

Lacks a free amino group, the nitrogen is part of the R group. This affects protein structure.

Question 5

Which amino acids are the sites of protein phosphorylation?

Answer 5

Serine, Threonine, and Tyrosine. They have polar hydroxyl groups which can switch out H for a phosphate. All uncharged, polar groups

Question 6

What amino acids are used in O-linked glycosylation?

Answer 6

Serine and Threonine only (not tyrosine)

Question 7

What amino acid is used in N-linked glycosylation?

Answer 7

Asparagine (not glutamate)

Question 8

What amino acids are uncharged at neutral pH, but only mostly?

Answer 8

Cysteine and Tyrosine - they have ionizable side chains

Cysteine has a pKa of 8.3 (sulfur holds negative charge well)

Tyrosine has a pKa of 10.1 (oxygen negative charge stabilized by aromatic ring)

Question 9

Which amino acids are negatively charged at neutral pH?

Answer 9

Aspartic acid (D), Glutamic acid (E)

Question 10

Which amino acids are positively charged at neutral pH?

Answer 10

Histidine (H), Lysine (K), Arginine (R)

Question 11

Which amino acids are most relevant to medicine and why?

Answer 11

Asp, Glu, Arg, His, Lys, Cys, Tyr are weak organic acids / bases, depend on pH and are thus relevant to medicine.

Question 12

What is Ka?

Answer 12

Equilibrium constant for weak acid

[H+][A-]/[HA]

Question 13

What is pKa or pH?

Answer 13

-log([Ka]) or -log([H+])

Question 14

What is the Henderson-Hasselbalch equation?

Answer 14

pH = pKa + log ([A-]/[HA])

Question 15

When is buffering most effective?

Answer 15

Near the pKa of a weak acid, when the ratio of conjugate base over weak acid is between 10 and 0.1 (pH is in range of pKa +/- 1). This occurs at 50% dissociation

Question 16

What is a zwitterion? What are the pKa’s of the groups?

Answer 16

Amino acid harboring both positive and negative charge (positive amino and negative carboxylic acid), typical at physiological pH of 7.2-7.4

pKa - carboxyl - 2.2-2.8
pKa - amino - 8.5-9.5

Question 17

How does pKa of weak acids depend on enviroment?

Answer 17

May be very different within a protein due to presence of adjacent polar / nonpolar residues which will raise or lower the pKa

Question 18

What is the most common catalytic residue in the active site of enzymes and why?

Answer 18

Histidine imidazole group -> close enough to neutral pH (pKa = 6.0) for enzymes to utilize its acid/base chemistry, and for it to act as an effective protein buffer in biological fluids.

Question 19

What is pI and how is it calculated?

Answer 19

Isoelectric point - where amino acids have a net charge of zero. For AA without ionizable side chains, take the average of the two pKa’s.

For amino acids with an ionizable side chain, take the pKa’s around the species with no net charge and average them

Question 20

How does pI affect an amino acid’s interactions with water?

Answer 20

Least soluble -> no longer charged

Will not migrate in electric field

Question 21

Why is [H+] used in lab tests rather than pH?

Answer 21

pH is a log 10 scale, so small movements in pH can mean large changes in free proton concentration which are clinically important

Question 22

What is Kwashiorkor?

Answer 22

Disease marked by calorie-rich diet deficient in essential amino acids. It is characterized by edema (fluid retention) especially in the gut due to insufficient protein in the blood, upsetting osmolar balance.

Common when children are weaned too early “disease of the displaced child”

Question 23

What is Marasmus?

Answer 23

Literally means “decay” syndrome that indicates the diet is several deficient in all energy sources, no accompanied by edema.