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Biochemistry > [2] Class 6: Nucleotide Structure/ Metabolism > Flashcards

[2] Class 6: Nucleotide Structure/ Metabolism Flashcards

1
Q

DNA 5’ to 3’ gives:

A

Directionality

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2
Q

Which carbon of the ribose is deoxy in DNA:

A

2’

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3
Q

What type of bonds form between A-T and C-G

A

H bonds

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4
Q

DNA helix structure

A

R handed antiparallel 5’-3’

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5
Q

A-T how may h bonds?

A

2 h bonds

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6
Q

How many h bonds c-g

A

3 h bonds

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7
Q

Phosphodiester bond, where is it in dna?

A

Between 3’ carbon of ribose and 5’ methyl grp on other ribose (below)

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8
Q

Who observed nucleotides in DNA? Who received credit?

A

Rosalind franklin,

Watson and crick received the prize for it though

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9
Q

How many nucleotides in our genome?

A

3 billion

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10
Q

How is DNA condensed to fit in our cells?

A

DNA binding proteins (histones and non-histones) allows for dynamic state between condensation and rapid access for gene expression

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11
Q

Protein+Nuclear DNA=

A

Chromatin

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12
Q

Phosphate esters of nucleosides

Contain base, sugar and phosphate

A

Nucleotide

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13
Q

Base + sugar

A

Nucleoside

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14
Q

WHat type of bond is between the purine/pyramidine base and the ribose sugar?

A

Beta glycosidic linkage

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15
Q

Big ring:

Small ring:

A

Small name: purine

Big name: pyrimidine

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16
Q

Purine nucleotide base:

Nucleosides?

A

Adenine; guanine

Adenosine;guanosine

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17
Q

Pyramidine nucleotide base:

Nucleoside:

A

Cytosine, Uracil, thymine

Cytidine, uridine, thymidine

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18
Q

Difference in thymine and uracil?

A

2’ methyl on thymine,

H on uracil

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19
Q

What are the other purines?

A

Hypoxanthine, inosine, xanthine, xanthosine

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20
Q

How can you go from a nucleotide to a DEOXYnucleotide?

A

Ribonucleotide reductase

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21
Q

What stimulates and inhibits ribonucleotide reductase?

A

ATP stimulates ribonucleotide reductase,

dATP nucleotides inhibits ribonucleotide reductase

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22
Q

Bonds of the 3 phosphates in ATP:

A

Ester bond on the alpha phosphate and 2 anhydride bonds on beta and gamma phosphates

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23
Q

4 specific roles of nucleotides:

A

ATP, CoA, NAD+, FAD

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24
Q

DNA bonded together is a phosphodiester bond: another name for this is

A

A covalent bond

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25
Q

DNA measurements:

A 
Length between 1 full turn: 34å
10 basepairs /turn
Base pairs are separated by 3.4 å, 
36º turn w/ each rotation of a new base pair. 
20Å width of DNA
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26
Q

Why is DNA typically in B form: long and slender?

A

B/c it is typically hydrated in the cell

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27
Q

DNA is more stable w/ more o which base pair?

A

C-G b/c there are 3 H bonds

28
Q

Catalyzes the formation of a phosphodiester bridge:

A

DNA polymerase

29
Q

RNA of retrovirus is converted to DNA by what enzyme, and subsequent synthesis of DNA strand?

A

Reverse transcriptase

30
Q

What enzyme is responsible for cutting long chain RNA/DNA to short oligomers?

A

(Deoxy)ribonucleases

31
Q

CLeaves oligomers into nucleotides

A

Phosphodiesterase

32
Q

Cleaves nucleotides to nucleosides

A

Nucleotidase

33
Q

Cleaves Nucleoside to (deoxy)ribose and base

A

Nucleosidase

34
Q

What enzyme can be used to make Uric acid soluble?

A

URate oxidase makes it into allantoin

35
Q

Allopurinol inhibits

A

Xanthine oxidase

36
Q

Structure of xanthine oxidase

A

2 FADs
2 Mo atoms
8 Fe atoms

37
Q

Colchicine helps w/ gout by:

A

Decreasing movement of granulocytes to affected area

38
Q

Norma serum uric acid 4-8.6 mg/dL

What is the increased risk of gout measurement?

A

> 9 mg/dL

39
Q

Which bases are converted to Glucogenic and ketogenic metabolites

A

Pyrimidines

40
Q

5 components that form purines:

5 components of pyrimidines:

A

CO2, Gln, Asp, N10-formyl-THF

HCO3, Gln, Asp, N5, N10-methylene THF

41
Q

What is the committed step in purine synthesis?

A

The formation of phosphoribosyl amine (PRA)

42
Q

Do you commonly see inosinate in DNA or RNA?

A

No it is converted to guanosine monophosphate and AMP

43
Q

2 salvage enzymes in purine:

A

HGPT and APT

44
Q

Central constituent of nucleotide metabolism

Synthesized from ribose phosphate and ATP.

A

Phosphoribosyl pyrophosphate

PRPP

45
Q

Which ring is synthesized attached to ribose phosphate?

A

Purine ring

46
Q

When purines are synthesized onto a ribose sugar…what initially contributes to the ribose sugar?

A

PRPP

47
Q

What is the committed step in purine synthesis ?

A

Formation of PRA

48
Q

PRPP + glutamine =

A

PRA

49
Q

Purine synthesis key step and is inactivated w/ methotrexate:

A

THF closes the base ring

50
Q

Methotrexate targets what enzyme that results in inhibiton of DNA replication

A

Dihydrofolate reductase

It is an analog of folate substrate

51
Q

TCA intermediates made in purine synthesis:

A

Fumarate and adenylsuccinate

52
Q

Synthesis of purine nucleotides is controlled by ______________________ at several sites to balance the productions of purine

A

feedback regulation

53
Q

If PRPP is made then inhibited what other 2 molecule would it become?

A

Histidine and pyrimidine nucleotides

54
Q

AMP and GMP synthesis is stimulated by:

Synthesis of PRPP, PRA, and GMP and AMP from IMP is

A

feedback inhibited

55
Q

Pyramiding is synthesized from:

A

carbamoyl phosphate

56
Q

Synthesized from carbamoyl phosphate and aspartate by aspartate-transcarbamoylase

A

Pyrimidine ring

57
Q

What is the first and committed step of pyramiding synthesis:

A

Formation of carbomoyl aspartate and carbamoyl phosphate

58
Q

What happens before the rxn w/ PRPP in pyramiding synthesis?

It is catalyzed by orate phosphoribosyl transferase

A

The ring forms

59
Q

Human hereditary disorder involving the synthesis of pyrimidine nucleotides

A

Orotic aciduria

Tx: oral uridine

60
Q

Formed from the ribonucleotides by the reduction of the ribonucleoside diphosphates

A

Deoxyribonucleotides

61
Q

Ribonucleotide diphosphate to deoxyribonucleotide by ribonucleotide reductase…what is the H donor for the reduction?

A

Thioredoxin or glutaredoxin

62
Q

2 major control points of pyrimidine biosynthesis:

A
  1. Carbamoyl phosphate synthetase is hibited by UMP and purines BUT stimulated by PRPP
  2. Asp transcarbamoylase is feedback inhibited by CTP
63
Q

DNA is synthesized from dATP,dCTP,dGTP, and dTTP. The [ ] of which is limiting factor?

A

dTTP

64
Q

Salvage pathway

A

Base by self needs to be put back on sugar…this is cheaper then remaking the base

65
Q

Purine salvage enzymes (2):

A

Adenine phosphoribosyl-transferase (APRT)

Hypoxanthine guanine phosphoribosyl transferase (HGPRT)

66
Q

Pyrimidine nucleotide salvage enzymes (2):

A

Uridine phosphoprylase

Thymidine phosphoprylase

Biochemistry (13 decks)

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