Structure and function of protein Flashcards
What is stereoisomer?
2 non-superimposable mirror images
What is naturally occuring proteins L or D?
L
What is special about proline?
- has a secondary amino group
2. Side chain forms a rigid ring structure (alpha helix breaker)
Amino acid that has nonpolar, aliphatic side chain
glycine
alanine
proline
methionine
Amino acid that has nonpolar, aliphatic, branched side chain
Valine
Leucine
Isoleucine
Amino acid with aromatic side chain
Phenylalanine
Tyrosine
Tryptophan
What is special about aromatic amino acid?
absorb UV light
Trp > Tyr > Phe
Sulfur containing amino acid?
Methionine, cysteine
What is special about cysteine
It has sulfhydryl group which can be oxidized to form disulfide bond (cystine)
Polar uncharged amino acid
asparagine glutamine serine threonine cysteine
What’s special about threonine and serine?
contain a hydroxyl group which can be phosphorylated or glycosylated
Negative (acidic) side chain amino acid
aspartate
glutamate
Positive (basic) side chain amino acid
arginine
lysine
histidine (dependent on pH pKa = 6)
Why is histidine a good buffer?
It has imidazole ring (pKa=6) which allow buffering of a possible drop in intracellular pH, which normally is 7.
Main blood buffer system
phosphate
Hb (contain histidine side chain)
Bicarbonate
How is biologically active amine formed?
amino group of alpha amino acid is retained, but carboxyl group is decarboxylated (removal as CO2)
Example of biologically active amine
GABA
Histamine
How is GABA formed from amino acid?
GABA is formed by decarboxylation of the alpha carboxyl group of glutamate
How is histamine formed from amino acid?
Histamine is formed by decarboxylation of alpha carboxyl group of histidine
How is serotonin formed from amino acid (2)
- Tryptophan is hydroxylased (add hydroxide)into 5’Hydroxy-tryptophan.
- Then, 5’hydroxy-tryptophan is decarboxylased into serotonin
Role of serotonin (3)
Pain perception
treat Affective disorder (mood disorder)
Regulation of sleep, temperature, BP
What is Prozac (fluoxetin)
selective serotonin re-uptake inhibitor (SSRI)
An antidepressant drug that blocks serotonin elimination from synaptic cleft»_space; prolonged effect of serotonin such as happiness and feeling of wellness
Types of catecholamines (3)
dopamine
norepinephrine
epinephrine
How are catecholamine formed from amino acid?
From tyrosine, it is hydroxylated to L-DOPA.
L-DOPA is then decarboxylated to dopamine.
What is produced when dopamine is hydroxylased?
norepinephrine
What is produced when norepinephrine is methylated?
Epinephrine
Role of dopamine
acting as neurotransmitter in brain and ANS
intermediate for synthesis of norepinephrine and epinephrine
Site of catecholamine synthesis
adrenal medulla
Does synthesis of tripeptide glutathione need ribosome, mRNA and tRNA?
NO
Is peptide bond charged?
No, EXCEPTION (Aspartate and glutamate)
Is peptide bond polar?
Yes
During denaturation, does peptide bond break?
NO
What is holoenzyme?
enzyme + coenzyme or cofactors
What is apoenzyme
enzymes without coenzyme
How do enzyme work? (3)
- It provides catalytic group that favor the formation of transition state.
- It provide an alternate reaction pathway that reduce the energy of activation
- DO NOT change the Gibbs energy of overall reaction
Where does fatty acid beta oxidation occur in the cell?
in mitochondria
Where does fatty acid synthesis de novo occur?
in cytoplasm
Where ketone body synthesis occur?
in mitochondria of liver cell only
Where gluconeogenesis occur?
cytoplasm of liver and kidney only
Effect of temperature on the velocity of enzyme
higher the temperature, higher the velocity.
Except when the temperature rises above 40, enzyme is denatured
Effect of pH on the velocity of enzyme
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
4 Ways of regulation of enzyme
- Concentration of substrates or products
- Modulation of enzyme concentration
- Covalent modification of enzyme
- Allosteric regulation (modulation of metabolic pathway)
How can we bring about synthesis of enzyme?
Induction of enzyme leads to synthesis of additional enzyme and can take hours to days
How happens if enzyme synthesis is repressed?
Repression of enzyme synthesis interferes transcription of enzyme
Allosteric enzymes show cooperative substrate binding and it does not follow Michaelis-Menten kinetics, then what is the shape of the kinetics curve?
sigmoid curve
What is the role of allosteric enzyme?
binding leads to a reversible conformational shift and can reduce or increase the activity of enzyme, changing the affinity for the substrate.
Two types of allosteric enzyme activity
- Feed-forward activation
2. Feedback down-regulation
What is feed-forward activation
The positive allosteric effector leads to a conformational shift of allosteric enzyme which leads to higher affinity to substrate.
What is feedback down-regulation?>
Negative allosteric effector leads to a conformational shift of allosteric enzyme, leading to lowering affinity.
What is the effect of feed-forward activator to the sigmoid curve and K0.5
Curve is moved to the left, resulting in a smaller K0.5.
What is the effect of feedback inhibitor to the sigmoid curve and K0.5?
Sigmoid curve is moved to the right, resulting in a larger K0.5.
