Structure and function of protein

Question 1

What is stereoisomer?

Answer 1

2 non-superimposable mirror images

Question 2

What is naturally occuring proteins L or D?

Answer 2

L

Question 3

What is special about proline?

Answer 3

1. has a secondary amino group

2. Side chain forms a rigid ring structure (alpha helix breaker)

Question 4

Amino acid that has nonpolar, aliphatic side chain

Answer 4

glycine
alanine
proline
methionine

Question 5

Amino acid that has nonpolar, aliphatic, branched side chain

Answer 5

Valine
Leucine
Isoleucine

Question 6

Amino acid with aromatic side chain

Answer 6

Phenylalanine
Tyrosine
Tryptophan

Question 7

What is special about aromatic amino acid?

Answer 7

absorb UV light

Trp > Tyr > Phe

Question 8

Sulfur containing amino acid?

Answer 8

Methionine, cysteine

Question 9

What is special about cysteine

Answer 9

It has sulfhydryl group which can be oxidized to form disulfide bond (cystine)

Question 10

Polar uncharged amino acid

Answer 10

asparagine 
glutamine
serine
threonine
cysteine

Question 11

What’s special about threonine and serine?

Answer 11

contain a hydroxyl group which can be phosphorylated or glycosylated

Question 12

Negative (acidic) side chain amino acid

Answer 12

aspartate

glutamate

Question 13

Positive (basic) side chain amino acid

Answer 13

arginine
lysine
histidine (dependent on pH pKa = 6)

Question 14

Why is histidine a good buffer?

Answer 14

It has imidazole ring (pKa=6) which allow buffering of a possible drop in intracellular pH, which normally is 7.

Question 15

Main blood buffer system

Answer 15

phosphate
Hb (contain histidine side chain)
Bicarbonate

Question 16

How is biologically active amine formed?

Answer 16

amino group of alpha amino acid is retained, but carboxyl group is decarboxylated (removal as CO2)

Question 17

Example of biologically active amine

Answer 17

GABA

Histamine

Question 18

How is GABA formed from amino acid?

Answer 18

GABA is formed by decarboxylation of the alpha carboxyl group of glutamate

Question 19

How is histamine formed from amino acid?

Answer 19

Histamine is formed by decarboxylation of alpha carboxyl group of histidine

Question 20

How is serotonin formed from amino acid (2)

Answer 20

1. Tryptophan is hydroxylased (add hydroxide)into 5’Hydroxy-tryptophan.
2. Then, 5’hydroxy-tryptophan is decarboxylased into serotonin

Question 21

Role of serotonin (3)

Answer 21

Pain perception
treat Affective disorder (mood disorder)
Regulation of sleep, temperature, BP

Question 22

What is Prozac (fluoxetin)

Answer 22

selective serotonin re-uptake inhibitor (SSRI)
An antidepressant drug that blocks serotonin elimination from synaptic cleft&raquo_space; prolonged effect of serotonin such as happiness and feeling of wellness

Question 23

Types of catecholamines (3)

Answer 23

dopamine
norepinephrine
epinephrine

Question 24

How are catecholamine formed from amino acid?

Answer 24

From tyrosine, it is hydroxylated to L-DOPA.

L-DOPA is then decarboxylated to dopamine.

Question 25

What is produced when dopamine is hydroxylased?

Answer 25

norepinephrine

Question 26

What is produced when norepinephrine is methylated?

Answer 26

Epinephrine

Question 27

Role of dopamine

Answer 27

acting as neurotransmitter in brain and ANS | intermediate for synthesis of norepinephrine and epinephrine

Question 28

Site of catecholamine synthesis

Answer 28

adrenal medulla

Question 29

Does synthesis of tripeptide glutathione need ribosome, mRNA and tRNA?

Answer 29

NO

Question 30

Is peptide bond charged?

Answer 30

No, EXCEPTION (Aspartate and glutamate)

Question 31

Is peptide bond polar?

Answer 31

Yes

Question 32

During denaturation, does peptide bond break?

Answer 32

NO

Question 33

What is holoenzyme?

Answer 33

enzyme + coenzyme or cofactors

Question 34

What is apoenzyme

Answer 34

enzymes without coenzyme

Question 35

How do enzyme work? (3)

Answer 35

1. It provides catalytic group that favor the formation of transition state. 2. It provide an alternate reaction pathway that reduce the energy of activation 3. DO NOT change the Gibbs energy of overall reaction

Question 36

Where does fatty acid beta oxidation occur in the cell?

Answer 36

in mitochondria

Question 37

Where does fatty acid synthesis de novo occur?

Answer 37

in cytoplasm

Question 38

Where ketone body synthesis occur?

Answer 38

in mitochondria of liver cell only

Question 39

Where gluconeogenesis occur?

Answer 39

cytoplasm of liver and kidney only

Question 40

Effect of temperature on the velocity of enzyme

Answer 40

higher the temperature, higher the velocity. | Except when the temperature rises above 40, enzyme is denatured

Question 41

Effect of pH on the velocity of enzyme

Answer 41

Different enzyme can have different optimal pH EX) Pepsin cleave protein at acidic condition Trypsin cleave protein in duodenum at pH 5-6 Alkaline phosphtase cleave phosphate group from nucleotides and protein at 9-10

Question 42

4 Ways of regulation of enzyme

Answer 42

1. Concentration of substrates or products 2. Modulation of enzyme concentration 3. Covalent modification of enzyme 4. Allosteric regulation (modulation of metabolic pathway)

Question 43

How can we bring about synthesis of enzyme?

Answer 43

Induction of enzyme leads to synthesis of additional enzyme and can take hours to days

Question 44

How happens if enzyme synthesis is repressed?

Answer 44

Repression of enzyme synthesis interferes transcription of enzyme

Question 45

Allosteric enzymes show cooperative substrate binding and it does not follow Michaelis-Menten kinetics, then what is the shape of the kinetics curve?

Answer 45

sigmoid curve

Question 46

What is the role of allosteric enzyme?

Answer 46

binding leads to a reversible conformational shift and can reduce or increase the activity of enzyme, changing the affinity for the substrate.

Question 47

Two types of allosteric enzyme activity

Answer 47

1. Feed-forward activation | 2. Feedback down-regulation

Question 48

What is feed-forward activation

Answer 48

The positive allosteric effector leads to a conformational shift of allosteric enzyme which leads to higher affinity to substrate.

Question 49

What is feedback down-regulation?>

Answer 49

Negative allosteric effector leads to a conformational shift of allosteric enzyme, leading to lowering affinity.

Question 50

What is the effect of feed-forward activator to the sigmoid curve and K0.5

Answer 50

Curve is moved to the left, resulting in a smaller K0.5.

Question 51

What is the effect of feedback inhibitor to the sigmoid curve and K0.5?

Answer 51

Sigmoid curve is moved to the right, resulting in a larger K0.5.