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Biochemistry > Biochemistry Final > Flashcards

Biochemistry Final Flashcards

1
Q

Describe the structure of Purines

A

consist of a six-membered and a five-membered nitrogen-containing ring, fused together

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2
Q

Describe the structure of Pyrimidines

A

a six-membered nitrogen-containing ring

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3
Q

Draw a purine ring

A
  1. Draw a six-membered aromatic ring.
  2. Starting at top left carbon, number counter-clockwise.
  3. Links a 3-atom segment between atoms 4 and 5. From top to bottom, number these 7-9.
  4. Draw a double bond between atoms 7 and 8.
  5. Atoms 1, 3, 7 and 9 are Nitrogen.
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4
Q

Draw a pyrimidine ring

A
  1. Draw a six-membered aromatic ring
  2. Starting at bottom carbon, number counter-clockwise.
  3. Atoms 1 and 3 are Nitrogen.
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5
Q

Give the common and structural names for four (4) biologically important purines

A
  1. Adenine 6-amino purine
  2. Guanine 2-amino-6-oxy purine
  3. Hypoxanthine 6-oxy purine
  4. Xanthine 2,6-dioxy purine
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6
Q

Give the common and structural names for four (4) biologically important pyrimidines

A
  1. Uracil 2,4-dioxy pyrimidine
  2. Thymine 2,4-dioxy-5-methyl pyrimidine
  3. Cytosine 2-oxy-4-amino pyrimidine
  4. Orotic acid (Orotate) 2,4-dioxy-6-carboxy pyrimidine
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7
Q

Describe the structure of a nucleoside

A

A nitrogenous base + Sugar.

Purines:
Carbon 1 of Ribose or 2-deoxyribose adds to Nitrogen 9.

Pyrimidines:
Carbon 1 of Ribose or 2-deoxyribose adds to Nitrogen 1

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8
Q

How are nucleosides named?

A
  1. Purine nucleosides end in -osine
  2. Pyrimidine nucleosides end in -idine
  3. Atoms of sugar retain their numbering, but are made prime (e.g. 5’) to indicate they are attached to higher priority structure.
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9
Q

Describe the structure of a nucleotide

A

Nucleoside (Nitrogenous base + Sugar) + 1 or More Phosphate (PO4-)

  1. Phosphate generally ester linkaged to 5’-carbon of sugar, and by convention no designation in name needed.
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10
Q

Describe the structure of a polynucleotide

A
  1. Nucleotides are linked by phosphodiester bonds (phosphate participating in TWO ester bonds)
  2. The phosphate on the 5’-carbon (the flag pentose carbon) of Nucleotide 1 links to 3’-carbon (bottom left pentose carbon) of Nucleotide 2.
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11
Q

What are the end products of purine catabolism?

A

uric acid

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12
Q

What are the end products of pyrimidine catabolism?

A

beta-amino acids, ammonia and carbon dioxide

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13
Q

List (5) steps of purine catabolism

A

[GMP starts at step 1; AMP first converted to IMP by deamination [removal of NH2 on carbon-6]

  1. Nucleotide hydrolyzed to Nucleoside by nucleotidase [removes Phosphate with water]
  2. Phosphorolysis (cleavage by addition of phosphate) of Nucleoside yields base and Ribose 1-P.
  3. GMP catabolism yields the base guanine. AMP catabolism yields the base hypoxanthine
  4. Conversion to Xanthine: (a) Guanine deaminated (b) Hypoxanthine oxidized.
  5. Xanthine oxidized to Uric acid and excreted.
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14
Q

List the steps of pyrimidine catabolism

A
  1. Hydrolysis of nucleotide followed by phosphorylation to yield free base

OR

  1. Ring reduced and opened by NADPH
  2. Atoms 2 and 3 released as carbon dioxide and ammonia, respectively.
  3. The remaining chain is a beta-amino acid.
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15
Q

List the source of each of the 9 atoms in the purine ring in de novo synthesis

A
  1. Nitrogen from Aspartate
  2. Tetrahydrofolate
  3. Nitrogen from Glutamine
    4,5,7. Three carbon chain from Glycine
  4. C=O from CO2
  5. Tetrahydrofolate
  6. Nitrogen from Glutamine
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16
Q

What is the first product in purine de novo synthesis?

A

Inosine Monophosphate (IMP) [Base: Hypoxanthine]

17
Q

What is the committed step of purine de novo synthesis?

A

The replacement of the 1’-pyrophosphate group of PRPP (5-phosphoribosyl-1-pyrophosphate) with nitorgen from Glutamine.

18
Q

How is IMP converted to GMP?

A

Requires ATP:

  1. Hypoxanthine base of IMP first oxidized (NAD) to form XMP.
  2. 2-oxy group converted to 2-amino using glutamine.
19
Q

How is IMP converted to AMP?

A

Requires GTP:

1. 6-oxy group of IMP converted to 6-amino using aspartate to form AMP.

20
Q

What is the first product in pyrimidine de novo synthesis?

A

Orotic acid (orotate)

21
Q

List the source of each of the 6 atoms in the pyrimidine ring in de novo synthesis

A
  1. Atom 2 (carbon) and 3 (nitrogen) supplied by Glutamine and bicarbonate as Carbamoyl Phosphate.
  2. Atoms 1, 4, 5 and 6 supplied by Aspartate.
22
Q

What is the committed step in pyrimidine de novo synthesis?

A

Synthesis of Carbamoyl Phosphate using Carbamoyl Phosphate Synthetase II.

23
Q

How is Orotic acid converted to the other pyrimidine nucleotides (UMP, CMP, TMP)

A
  1. Orotic acid converted to OMP with PRPP
  2. OMP decarboxylated to form UMP
  3. UMP converted to UTP
  4. UTP aminated with glutamine and ATP to form CTP.
  5. TMP not synthesized in this pathway.
24
Q

Purine salvage pathways involve what products and reactants?

A

The addition of a base to 1’-carbon of PRPP catalyzed by Phosphoribosyltransferase (PRT)

  1. HG-PRT most important, acting on bases guanine and hypoxanthine.
  2. A-PRT less important, acting on adenosine, which is catabolized through inosine/hypoxanthine.
25
Q

Pyrimidine salvage pathways involve what products and reactants?

A
  1. Nucleoside phosphorylase forms a nucleoside by combining ribose 1-phosphate and a base.
  2. Nucleoside kinase converts nucleoside to nucleotide.
  3. These enzymes exist for uridine and deoxythymidine.
26
Q

How is the majority of TMP synthesized?

A
  1. UDP conveted to dUDP
  2. dUDP converted to dUMP
  3. dUMP converted to TMP
27
Q

How is Purine biosynthesis regulated?

A

Synthesis of PRPP inhibited by purine monophosphates (IMP, AMP, GMP)

28
Q

How is pyrimidine biosynthesis regulated?

A

Aspartate transcarbamoylase balances purine and pyrimidine pools:

  1. Activated by ATP
  2. Inhibited by CTP (feedback inhibition)
29
Q

What are the seven (7) activities required for DNA replication?

A 
1. DNA polymerase
2 .DNA helicase
3 .Topoisomerase
4. Single strand binding protein
5. DNA primase
6. Nuclease
7. DNA ligase

Biochemistry (7 decks)

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