Exam 4 Biosynthesis of AA, Nucleotides, Related Molecules

Question 1

Amino Acid Synthesis Overview

Answer 1

• Source of N: Glu or Gln
• Comes from intermediates of: glycolysis, CAC, PPP
• bacteria can synthesize all 20 AA

Question 2

What are the seven precursors of amino acids, and what cycle are they from?

Answer 2

• Citric Acid Cycle: a-ketoglutarate, oxaloacetate
• Glycolysis: pryruvate, 3-phosphoglycerate, phosphoenolpyruvate
• Pentose Phosphate Pathway: ribose 55-phosphate, erythrose -phosphate

Question 3

What amino acids are derived from the precursor, a-Ketoglutarate?

Answer 3

Transamination of a-Ketoglutarate (add NH3)
-> Glutamate -> Glutamine, Proline, Arginine

Question 4

What amino acids derive from the precursor, 3-Phosphoglycerate (Glycolysis)?

Answer 4

3- Phosphoglycerate -> Serine -> Glycine, Cysteine

Question 5

What amino acids are derived from the precursors, Oxaloacetate and Pyruvate?

Answer 5

• Transamination of Oxaloacetate -> Aspartate -> Asparagine, Methionine, Lysine, Threonine
• Pyruvate -> Alanine, Valine, Leucine, Isoleucine

Question 6

What aromatic amino acids are derived from Phosphoenolpyruvate and Erythrose 44-Phosphate?

Answer 6

Phsophoenolyruvate -> Erythrose 4-Phosphate -> Phenylalanine (which can turn into Tyrosine), Tyrosine, Tryptophan
- In order to create double bonds: Rings must be synthesized, closed, then oxidized
- Common Intermediate: Chorismate

Question 7

What derives from the precursor, PPP Metabolite Ribose 5-Phosphate?

Answer 7

Histidine derives from PPP metabolite ribose 5-phosphate?
- PRPP: precursor (activated form of PPP), also starting material for nucleic acid

Question 8

PRPP 5-Phosphoribosyl-1-1-Pyrophosphate

Answer 8

Several pathways share PRPP as an intermediate
- PRPP is synthesized from ribose 55-phosphate of PPP via ribose phosphate pyrophosphokinase
- It is a highly regulated allosteric enzyme

Question 9

Regulation of Amino Acid Biosynthesis

Answer 9

Multilayered approach: more than one mechanism used
- Feedback inhibition of products
- Use of isozymes: allows E.Coli to produce the amino acids when needed (ex: isozyme A1 inhibited if Ile is high but not if Met/Thr is high -> only A1 is inhibited)

Question 10

What is Porphyrins? What is the precursor to Porphyrins?

Answer 10

Porphyrins make up the heme of hemoglobin, cytochromes, and myoglobin
- In higher animals: precursor is glycine reacting with succinyl-CoA
- In plants/bacteria: precursor is glutamate

This pathway makes two molecules of the intermediate, 5-aminolevulinate

Question 11

How is Heme synthesized?

Answer 11

Synthesis of Heme: 2 molecules of aminolevulinate condense to form porphobilinogen, 4 molecules of porphobilinogen form protoporphyrin, Fe ion is inserted into protoporphyrin with the enzyme Ferrochelatase.

Question 12

what are the defects that can happen in heme biosynthesis?

Answer 12

1) Mutations or misregulation of enzymes in the heme biosynthesis pathway: leads to porphyrias (due to precursors building up in RBCs, body fluids, liver)

2) Accumulation of the precursor, Uroporphyrinogen I
- Discolored urine (pink/purple), Teeth showing red under UV light, skin sensitive to UV light, craving for heme

Question 13

What is the source of bile pigments?

Answer 13

Heme (from degradation of erythrocytes) is degraded to bilirubin

2 Steps:
- Heme oxygenase linearizes heme to make biliverdin (green compound)
- Biliverdin reductase converts biliverdin to bilirubin
(Bilirubin: compound bound to serum albumin, travels in bloodstream & is major pigment of urine)

Question 14

What is jaundice caused by?

Answer 14

Bilirubin Accumulation

Jaundice: yellow pigmentation of skin, etc
- Comes from: impaired liver, blocked bile secretion, insufficient “glucouronyl bilirubin transferase” to process bilirubin (treated with IV to break it down)

Question 15

Biosynthesis of Nueclotides

Answer 15

• Can be synthesized “de novo” (from the beginning): from amino acids, ribose-5-phosphate, CO2, NH3
• Can be salvaged from RNA, DNA, and cofactor degradation

Question 16

What are promising antiparasite drugs?

Answer 16

Compounds that inhibit salvage pathways

Many parasites can’t do “de novo” and rely on salvage -> compounds that inhibit those pathways can get rid of parasites

Question 17

How does De Novo biosynthesis of nucleotides work?

Answer 17

The same in all organisms: bases are synthesized while attached to ribose
- Glu: provides most amino groups
- Gly: precursor for purines
- Asp: precursor for pyrimidines

Continuous synthesis b/c nucleotide pools are kept low -> synthesis can limit transcription and replication rates (pathway for nucleotides is slow and more regulated)

Question 18

Precursors involved in the origin of ring atoms in purines

Answer 18

• CO2
• Aspartate
• Glycine
• Formate
• Amide N of glutamine

Question 19

How does DeNovo biosynthesis of purines work? (starts with PRPP)

Answer 19

• Synthesis begins with reaction of PRPP with Glutamine
• 3 carbons are added from Glycine, and this allows Purine ring to build up
• First intermediate with full purine ring: Inosinate (IMP)
• Adenine and Guanine are synthesized as AMP and GMP

Question 20

Synthesis of AMP and GMP from IMP

Answer 20

• ATP is used to phosphorylate GMP precursor
• GTP is used to phosphorylate AMP precursor
  The cell is balancing out the availability of precursors through this process of synthesis

Question 21

How does De Novo synthesis of Pyrimidine Nucleotides work?

Answer 21

Starts differently from Purine synthesis: Pyrimidine ring (in the form of orotate) is formed first, then attached to ribose 5-phosphate

• Aspartate and Carbamoyl phosphate provide atoms needed for the ring structure
• First possible pyrimidine: Urindylate
• UMP phosphorylated to UTP
• Amination of UTP converts UTP to CTP

Question 22

What is the precursor to Deoxyribonucleotides?

Answer 22

Ribonucleotides are the precursor
- 2’C-OH bond is reduced to 2’-H bond, catalyzed by ribonucleotide reductase (no activation of carbon)
- Mechanism: 2 H atoms are donated by NADPH (e- donor) and carried by Thioredoxin or Glutaredoxin

Question 23

How are free radicals involved in the ribonucleotide reductase mechanism?

Answer 23

Most enzymes have 2 catalytic/regulatory subunits and 2 radical-generating subunits (has Fe3+ and dithiol groups)
- 3’-ribonucleotide radical forms
- 2’-OH protonated to eliminate H2O and form radical-stabilized carbonation
- Electrons are transferred to 2’-C

Question 24

How does Folic Acid deficiency lead to reduced Thymidylate synthesis?

Answer 24

Folate is crucial cofactor for Thymidylate -> deficiency leads to reduced synthesis
- Reduced thymidylate synthesis causes Uracil to be incorporated into DNA (Uracil not meant to be in DNA)
- Repair mechanisms remove the Uracil by: creating strand breaks that affect structure and function of DNA

Question 25

How does Catabolism of Purines work?

Answer 25

1) Dephosphorylation (via 5’-nucleotidase)
2) Deamination and hydrolysis of ribose -> production of Xanthine
3) Hypoxanthine and Xanthine oxidized into uric acid by Xanthine oxidase

Question 26

What leads to Gout?

Answer 26

Gout is caused by excess uric acid
- Symptoms: painful joins due to deposits of sodium urate crystals
- Mostly affects males, can involve genetic under-excretion of urate and/or fructose overconsumption
- Treatment: using Allopurinol (xanthine oxidase inhibitor) or avoiding purine-rich foods/fructose

Question 27

How does catabolism of Pyrimidines work?

Answer 27

• Lead to NH4+ and Urea
• Produce intermediates of CAC (ex: thymine degraded to succinyl-CoA)

Question 28

How are purine and pyrimidine bases salvaged?

Answer 28

By Salvage Pathways
- brain is dependent on salvage pathways

Question 29

What leads to Lesch-Nyhan syndrome?

Answer 29

Lack of hypoxanthine-guanine phosphoribosyltransferase (HPRT) -> HPRT is important for recycling/salvaging purines
- Symptoms: Neurological Impairment and Finger/Toe-biting behavior