Amino Acid Structure and Function Lecture 5 Ford

Question 1

What does an amino acid look like at physiological pH? Why?

Answer 1

It is in a zwitterion form (neutral form) because at physiological pH, the amino group is protonated because we are below its pKa value, but the carbonyl group is deprotonated because we are above its pKa value

Question 2

What form of amino acids is the physiologically relevant form?

Answer 2

L form amino acids

Question 3

What are the hydrophobic AA?

Answer 3

G, A, P, V, L, I, M, W, F

Question 4

What are the polar AA?

Answer 4

S, T, Y, N, Q, C

Question 5

What are the positively charged AA?

Answer 5

K, R, H

Question 6

What are the negatively charged AA?

Answer 6

D, E

Question 7

What makes cysteine an odd but extremely important AA?

Answer 7

It can form disulfide bridges with other cysteine residues to form cystine; these are important in protein folding and function

Question 8

What are the tiny AA?

Answer 8

A, C, G, S

Question 9

What are the small AA?

Answer 9

P, D, T, N

Question 10

What are the medium AA?

Answer 10

V, E, H, Q

Question 11

What are the large AA?

Answer 11

I, K, L, R, M

Question 12

What are the very large AA?

Answer 12

Y, F, W

Question 13

What are the essential AA?

Answer 13

F, V, W, T, I, M, H, R, K, L

Mnemonic: PVT TIM HALL

Question 14

What are the non-essential AA?

Answer 14

A, N, D, C, Q, E, G, P, S

Question 15

Which essential AA do we have to consume because they are difficult to produce enough of on our own?

Answer 15

R and M

Question 16

Where do you find the 21st AA (selenocysteine) and the 22nd AA (pyrrolysine)?

Answer 16

21st in all 3 domains of life and are important for health; 22nd in only some prokaryotes (methanogens) and these are present in the intestinal microbiome

Question 17

What can nonproteinogenic AA be used for?

Answer 17

Can be used in non-ribosomal protein synthesis (NRPS), in the production of antibiotics via NRPS, can be found in bacterial cell walls, neurotransmitters, toxins/antimicrobials, and are found in metabolism intermediates

Question 18

Primary Structure

Answer 18

Chain of AA

Question 19

Secondary Structure

Answer 19

Local folding of the polypeptide chain

Question 20

Tertiary Structure

Answer 20

Folding of the secondary structure

Question 21

Quaternary Structure

Answer 21

Interaction of multiple peptides

Question 22

Where do you find the peptide bond in proteins?

Answer 22

Between the carbonyl carbon of one AA and the amino nitrogen of the next AA

Question 23

What modifications can be made during primary structure of a protein?

Answer 23

Enzymatic cleavage of signal sequences, chemical modifications of side chains (phosphorylation, glycosylation, methylation)

Question 24

What is the pka of the ionizing side chain of Arginine?

Answer 24

12.5

Question 25

What is the pka of the ionizing side chain of Aspartic acid

Answer 25

4.1

Question 26

What is the pka of the ionizing side chain of cysteine?

Answer 26

8.3

Question 27

What is the pka of the ionizing side chain of histidine?

Answer 27

6.0

Question 28

What is the pka of the ionizing side chain of lysine?

Answer 28

10.0

Question 29

What is the pka of the ionizing side chain of tyrosine?

Answer 29

10.1

Question 30

What are the health benefits of selenocysteine?

Answer 30

• reduce oxidative stress with vitamin E
• growth of cerebellar neurons
• moderate inflammatory responses

Question 31

What results from a selenium deficiency?

Answer 31

Keshan (cardiomyopathy) 
Statin intolerance (rhabdo)

Question 32

What results from too much selenium?

Answer 32

Hair and nail brittleness, garlic breath, GI neurons lesions, and other bad things