BIO506T Quiz by Kainat Alvi and Arshia Ashfaq

BIOCHEMISTRY - II (BIO506T) · CURRENT FINAL TERM PAPER SPRING 2023 · SHORT QUESTIONS(3)

1. GLUT family occurring organs and 3 transporters.

Organs: Brain, Heart, Liver, Kidneys, Muscles, Adipose tissue, Pancreas, Intestines

GLUT Transporters: GLUT1, GLUT2, GLUT3, GLUT4

2. Example of stereospecific enzymes?/Stereospecific enzyme name

➢ Name: Fumarase (fumarate hydratase)

Stereospecific enzyme: An enzyme that selectively catalyzes a reaction with only one specific stereoisomer (mirror image) of a substrate, producing a product with defined stereochemistry.

The reversible hydration of fumarate to L-malate is catalyzed by fumarase (fumarate hydratase). • The transition state in this reaction is a carbanion. • This enzyme is highly stereospecific; it catalyzes hydration of the trans double bond of fumarate but not the cis double bond of maleate (the cis isomer of fumarate). • In the reverse direction (from L-malate to fumarate), fumarase is equally stereospecific: D-malate is not a substrate.

Q3. What happened when the electric current passes in the water?

When electric current passes through water:

Water molecules (H2O) break into ions.

H2O → H+ + OH- (ionization).

H+ ions combine with water molecules to form hydronium ions (H3O+)

H+ + H2O → H3O+

Hydronium ions (H3O+) move towards the cathode (negative electrode). Hydroxide ions (OH-) move towards the anode (positive electrode). At the electrodes, ions are neutralized:

o At the cathode: H3O+ + e- → H2O (water formation) o At the anode: OH- + e- → 1/2 O2 + H2O (oxygen gas and water formation)

This process is known as electrolysis of water.

Q4. Why pure water conduct electricity/Why electric current pass through water?

Pure Water ls Slightly lonized . Water molecules have a slight tendency to undergo reversible ionization to yield a hydrogen ion (a proton) and a hydroxide ion, giving the equilibrium reaction

H2O H+ + OH-

Hydrogen ions formed in water are immediately hydrated to hydronium ions (H3O+) . The ionization of water can be measured by its electrical conductivity. Pure water carries electrical current as H3O+ migrates toward the cathode and OHtoward the anode, allowing pure water to carry electrical current.

Water molecule break and produce ion? Hydrogen ion further react with other molecule?

Hydrogen ions formed in water are immediately hydrated to hydronium ions (H3O+) . The ionization of water can be measured by its electrical conductivity. Pure water carries electrical current as H3O+ migrates toward the cathode and OHtoward the anode, allowing pure water to carry electrical current.

5. Which kind of ions produced due to Ionization of water

Due to the ionization of water, the following ions are produced:

a. Hydrogen ions (H+) b. Hydroxide ions (OH-) These ions are produced in equal amounts, maintaining the electrical neutrality of the solution

Q6. Refsum disease ??

A disorder resulting from a genetic defect in phytanoyl-coA hydroxylase, leads to very high blood levels of phytanic acid and severe neurological problems, including blindness and deafness.

• phytanic acid accumulates in patients suffering from a peroxisome biogenesis disorder, which includes zellweger syndrome, neonatal adrenoleukodystrophy, and infantile refsum disease.
• formic acid and not CO2 is the primary reaction product of phytanic acid oxidation. the amount of formic acid was shown to be about 9-fold higher as compared to CO2

Q7. Effect of enzyme kinetics when the substrates Concentration increase than the enzyme concentration?

Substrate Concentration Affects the Rate of Enzyme-Catalyzed reactions

E + S ES EP E + P

A key factor affecting the rate of a reaction catalyzed by an enzyme is the concentration of substrate, [S]. However, studying the effects of substrate concentration is complicated because substrate is converted to product and because of reversibility of reactions, e.g. conversion of product back to substrate. One simplifying approach in kinetics experiments is to measure the initial rate (or initial velocity), designated V0, when [S] is much greater than the concentration of enzyme, [E]. • The velocity (v) of a reaction is the rate of product formation. Whereas V0 is the initial velocity and is measured as soon as the reactants and enzymes are mixed. At the start of a reaction, [S] is in large excess of [P]. Thus the initial velocity of the reaction will be dependent on substrate concentration. At that time, the concentration of product is very small and, therefore, the rate of the back reaction from P to S can be ignored. Increase in substrate concentration increases V0 i.e. initial velocity is increased Whenever a fixed Concentration of enzyme is mixed with an increased concentration of substrate.

Q8. Pentose phosphate pathway and write it’s other pathway??

• The oxidative pentose phosphate pathway
• Phosphogluconate pathway
• Hexose monophosphate pathway

The pentose phosphate pathway (PPP) is a metabolic pathway that generates:

1. NADPH (reducing power)
2. Pentoses (5-carbon sugars)
3. Ribose-5-phosphate (precursor for nucleotide synthesis)

This pathway is a parallel route to glycolysis and occurs in the cytosol of cells. It's divided into two stages:

1. Oxidative phase: Glucose-6-phosphate is converted to ribulose-5-phosphate, producing NADPH.
2. Non-oxidative phase: Ribulose-5-phosphate is converted to ribose-5-phosphate, generating pentoses.

9. First order with respect to substrate concentration

When [S] is much less, then the velocity of the reaction is approximately proportional to the substrate concentration. The rate of reaction is then said to be first order with respect to substrate.

10.

Competitive Inhibitor and non competitive inhibitor difference

• Competitive inhibitors resemble the substrate and compete for binding to the active site of the enzyme.
• Noncompetitive inhibitors do not bind at the active site. They bind either free enzyme at a site other than active site or the ES complex.

11.

Competitive Inhibition and non competitive inhibition difference

❖ Competitive Inhibition :

This type of inhibition occurs when the inhibitor binds reversibly to the same site that the substrate would normally occupy i.e. active site and, therefore, competes with the substrate for that site. Competitive inhibitors bind to the enzyme’s active site. Reversible inhibitors bind to enzymes through non covalent bonds. Dilution of the enzyme inhibitor complex results in dissociation of the reversibly bound inhibitor, and recovery of enzyme activity

❖ Noncompetitive Inhibition:

Inhibitors bind enzymes at sites distinct from the substrate-binding site and generally bear little or no structural resemblance to the substrate. Noncompetitive inhibition cannot be overcome by increasing the concentration of substrate.

12. Hyperchromicity of DNA.

Concomitant with this denaturation of the DNA molecule is an increase in the optical absorbance of the purine and pyrimidine bases—a phenomenon referred to as hyperchromicity of denaturation.

The absorbance of double-stranded DNA (dsDNA) at 260 nm is less than that of either singlestranded DNA (ssDNA) or the free bases. This is called “hyperchromism.”

13.

Three function of catalyst/ Write three uses of Catalysts?

• The function of a catalyst is to increase the rate of a reaction.
• Catalysts do not affect reaction equilibria .
• Catalysts enhance reaction rates by lowering activation energies.

14.

First step in the synthesis of aceteoacetate formation/acetoacetate formed in which process give the name of enzyme?

•• The first step in the formation of acetoacetate, occurring in the liver, is the enzymatic condensation of two molecules of acetyl-CoA, catalyzed by thiolase; this is simply the reversal of the last step of oxidation of fatty acids. • The acetoacetyl-CoA then condenses with acetyl-CoA to form Beta-hydroxyBetamethylglutaryl-CoA (HMG-CoA), which is cleaved to free acetoacetate and acetyl-CoA. • The acetoacetate is reversibly reduced by D-Beta-hydroxybutyrate dehydrogenase, a mitochondrial enzyme, to D-Beta-hydroxybutyrate. • This enzyme is specific for the D stereoisomer; it does not act on L Beta-hydroxyacyl-CoAs and is not to be confused with L-Beta-hydroxyacyl-CoA dehydrogenase of the Beta-oxidation pathway.

15.

ydroxyacyl-CoAf Fatty acids for cell?

Cells can obtain fatty acid fuels from three sources:

a. Fats consumed in the diet b. fats stored in cells as lipid droplets c. fats synthesized in one organ for export to another

Some species use all three sources under various circumstances, others use one or two. Vertebrates, obtain fats in the diet, mobilize fats stored in specialized tissue (adipose tissue, consisting of cells called adipocytes), and, in the liver, convert excess dietary carbohydrates to fats for export to other tissues.

16.

What is the function of Cofactor of pyruvate dehydrogenase enzyme?

The Coenzymes and prosthetic groups of pyruvate dehydrogenase

Cofactor · Location · Function

Thiamine pyrophosphate Bound to E1 Decarboxylates pyruvate

Lipoic acid Covalently linked to a Lys on E2 (lipoamide) Accepts hydroxyethyl carbanion from TPP CoenzymeA Substrate for E2 Accepts acetyl group from lipoamide FAD (flavin) Bound to E3 reduced by lipoamide NADH Substrate for E3 Reduced by FADH2

17.

Function of Coenzyme A as a Cofactor

o Cofactor: CoenzymeA o Location: Substrate for E2 o Function: Accepts acetyl group from lipoamide

18.

Omega carbon and why its name so

The carbon atom closest to the carboxyl group is the alpha carbon, the next carbon is the beta carbon and so on. the (omega) carbon—the carbon most distant from the carboxyl group.

19.

What is omega oxidation and why its name is Omega Oxidation?

Omega oxidation (ω-oxidation) is a process of fatty acid metabolism in some species of animals. • The carbon atom closest to the carboxyl group is the alpha carbon, the next carbon is the beta carbon and so on. • It is an alternative pathway to beta oxidation that, instead of involving the β carbon, involves the oxidation of the ω carbon (the carbon most distant from the carboxyl group of the fatty acid). • In