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Biochemistry II > Nucleotides > Flashcards

Nucleotides Flashcards

1
Q

What is the difference between DNA and RNA structure?

A

The difference between DNA and RNA is the sugar component and one of the bases.

Sugar: In the deoxy- it means that it has an -H- in place of -OH that would be found on the 2’-carbon atom of ribose.

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2
Q

What type of bond is seen between complementary bases?

A

Hydrogen bonds hold complementary bases together

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3
Q

What type of bonds hold sugar backbone together?

A

Phosphodiester bonds are seen between sugars in the backbone.

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4
Q

What are the names of the purine bases?

A

adenine and guanine

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5
Q

What are the names of the pyrimidine bases?

A

thymine, uracil, and cytosine

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6
Q

What is the definition of a nucleotide?

A

A nucleotide is a single monomer unit within the DNA or RNA polymer. A single nucleotide includes one of the four bases, a phosphate, and a sugar.

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7
Q

What is the central dogma?

A

only viruses have the machinery to go from RNA to DNA.

Proteins cannot be reversed back to nucleotides, but RNA can be converted back to DNA.

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8
Q

What is the basic DNA structure?

A

sugars are bond together by phosphodiester bonds to form the phosphate back bone. 5’-3’ direction

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9
Q

How do the complementary bases interact?

A

C-G

A-T

They interact via hydrogen bonds

C-G has 3 hydrogen bonds

A-T has 2 hydrogen bonds.

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10
Q

What creates the major and minor groove of the DNA double helix?

A

The strand backbones are closer together on one side of the helix than on the other. The major groove occures where the backbones are far apart and the minor groove occurs where they are close together.

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11
Q

How far apart are adjacent bases in the helix?

A

3.4 angstroms

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12
Q

What is meant by the dynamic situation of condensed DNA?

A

This is just the idea that condensed DNA should allow rapid localized access to DNA for gene expression.

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13
Q

What is chromatin?

A

Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus or euk cells

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14
Q

What does chromatin consist of?

A

Chromatin is composed of nuclear DNA, histones, and other chromosomal proteins.

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15
Q

what is a nucleic acid?

A

polynucleotide = made up of multiple nucleotides

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16
Q

What does a nucleotide consist of?

A

Nucleotides consist of a base, sugar, and phosphate.

or

Nucleoside + phosphoric acid

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17
Q

What is a nucleoside?

A

a base and sugar

or

its a nucleotide minus the phosphoric acid

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18
Q

What are the sugars?

A

ribose and deoxyribose

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19
Q

What is the difference between a nucleotide and a nucleoside?

A

Nucleoside is a nucleotide without the phosphoric acid.

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20
Q

Name this molecule.

A

Nucleoside

(notice it does not have a phosphate ester attached)

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21
Q

Name this molecule.

A

Nucleotide

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22
Q

Name this molecule.

A

deoxynucleotide

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23
Q

What type of bond is seen between the sugar and base?

A

There is a beta- glycosidic linkage between the sugar and base.

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24
Q

what are nucleic acids and what is meant by purine/pyrimidine classification?

A

The nucleic acids are basically substitutions on one of two types of heterocyclic rings. (big name=small ring)

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25
Q

What is the name of this structure?

A

Purine

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26
Q

What is the name of this structure?

A

pyrimidine

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27
Q

What is the name of this structure?

A

adenine

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28
Q

What is the name of this structure?

A

adenosine

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29
Q

What is the name of this structure?

A

adenosine 5’-phosphate (AMP= adenosine monophosphate)

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30
Q

Name this structure

A

Thymidine 5’-phosphate (TMP)

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31
Q

Name this structure

A

Thymine

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32
Q

Name this structure.

A

guanine

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33
Q

Name this structure

A

cytosine

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34
Q

Name this structure.

A

adenine

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35
Q

Name this structure

A

uracil

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36
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of adenine?

A
  1. base= adenine; abbreviation=Ade
  2. nucleoside=adenosine ; abbreviation=A
  3. Nucleotide= Adenosine monophosphate; AMP
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37
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of guanine?

A
  1. base=guanine; Gua
  2. nucleoside=guanosine; G
  3. nucleotide= GMP
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38
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of hypoxanthine?

A
  1. Base= hypoxanthine; Hyp
  2. nucloeside = inosine; I
  3. nucleotide = IMP
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39
Q

Is hypoxanthine a purine or pyrimidine?

A

Hypoxanthine is a purine

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40
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of xanthine?

A
  1. base=xanthine; Xan
  2. nucleoside = xanthosine (X)
  3. nucleotide = XMP
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41
Q

Is xanthine a purine or a pyrimidine?

A

xanthin is a purine

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42
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of cytosine?

A
  1. base=cytosine; cyt
  2. nucleoside=cytidine; C
  3. nucleotide = CMP
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43
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of uracil?

A
  1. base=uracil; Ura
  2. Nucleoside=cytidine (C)
  3. nucleotide = UMP
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44
Q

What is the abbreviation for the 1)base 2)nucleoside 3) nucleotide of thymine?

A
  1. base=thymine; Thy
  2. nucleoside= thymidine; T
  3. nucleotide= TMP
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45
Q

What does the enzyme ribonucleotide reductase facilitate?

A

Ribonucleotide reductase facilitates the formation of deoxyribonucleotides from ribonucleotides by reduction of the 2’ carbon with the addition of 2 hydrogen atoms (this is why it requires NADPH).

with further processing another phosphate is added making the dNTP’s

46
Q

How does the presence of ATP or dATP effect the activity rate of ribonucleotide reductase?

A

The main purpose of ribnucleotide reductase is to maintain balanced quanitites of dNTPs. So where there is increased dNTP then it will act as a negative feedback loop and inhibit the RNR. When there is an increase in ATP then it will stimulate RNR.

47
Q

What are the 3 components of the ATP structure and what type of bonds hold them together?

A
  1. adenine (base)
    • N- glycosidic bond
  2. ribose(sugar)
    • phosphoric acid ester bond
  3. phosphate groups (alpha, beta, gamma)
    • phosphoric acid anhydride bonds
48
Q

According to Gibb’s free energy would phosphate molecules rather be plucked off one by one, or would they go off in pairs or triplets?

A

They would rather leave in pairs according to this slide attached.

When Gibb’s free energy is negative it means it is more spontaneous. So separating the diphosphate is the least spontaneous while removing diphosphate from ATP is more spontaneous than removing one phosphate.

49
Q

What is the universal currency of free energy in biological systems?

A

ATP

50
Q

NADH and NADPH is a carrier molecule. What group does this molecule carry?

A

NADPH and NADH carry electrons. NAD+ structure is attached.

Has an adenosine nucleotide within the structure.

51
Q

FADH2 is a carrier molecule. What group does this molecule carry?

A

FADH2 carries electrons. The attachment shows FADHto FADH2 mechanism.

Has adenosine nucleotide within the structure.

52
Q

Coenzyme A is a carrier molecule. What group does this molecule carry?

A

Coenzyme A carries an Acyl group.

has adenosine nucleotide within structure.

53
Q

what is the measurement of one helical turn in the DNA strand?

A

34 angstroms

54
Q

How many base pairs are there per turn?

A

There are 10 base pairs per turn and this measures 34 angstroms.

55
Q

What type of interaction is there between the base pairs above and below each other?

A

Base pairs are perpendicular to the direction of helix and they are nearly stacked on top of each other. There are van der waals interactions between base pairs making DNA very stable.

56
Q

What type of turn does DNA exhibit? right or left handed turns?

A

A, B, and C forms of DNA are right-handed turn helix

While Z DNA is left-hand turn DNA

57
Q

What is the most common form of DNA found in the human body?

A

B DNA

58
Q

What is the difference between A and B form DNA?

A

B form DNA is the most commonly seen DNA in the body.

A form DNA is thicker and has shorter distance between base pairs because the base pairs are slightly tilted and not flat like bases in B DNA. Also, A DNA sugar C-3’ lies out of the plane causing sugar puckering. A form DNA is seen in RNA-DNA duplexes and RNA-RNA duplexes.

59
Q

What enyzme is responsible for catalyzing the formation of a phosphodiester bridge?

A

DNA polymerase.

60
Q

In what direction are nucleotides added to the newly replicated DNA strand?

A

from 5’ to 3’

61
Q

What must be present on the DNA template strand before DNA polymerase can begin?

A

There must be a primer with a 3’-OH must be present on the template strand before DNA polymerase can begin.

62
Q

Which phosphate of the dNTP attaches to the primer and where?

A

The innermost phosphate (alpha?) attacks the 3’-OH of the primer nucleotide via nucleophilic attack.

The two other phophates are detached by pyrophosphatase.

63
Q

What does pyrophosphatase do?

A

Pyrophosphatase is an enzyme that extra phosphates as pyrophosphate after the formation of the phosphodiester bond.

64
Q

Are bases hydrophobic or hydrophilic?

A

Bases of DNA are hydrophobic and are therefore on the interior of the helix. The hydrophobic effect helps form the DNA double helix.

65
Q

What is the significance of this table?

A

Chargaff was the first to observe that the A:T and G:C ratios were nearly the same in all species but the A:G ratio varied considerably. This is because the bases are complementary and pair up during formation.

66
Q

What does reverse transcriptase do?

A

In retroviruses, reverse transcriptase converts RNA to DNA. It catalyzes the synthesis of DNA on an RNA template and later digests that RNA so that it can synthesize a second DNA strand.

67
Q

What does ribonuclease do?

A

Ribonuclease catalyzes the degradation of RNA into short chain oligomers.

68
Q

What is deoxyribonuclease (also called DNase)?

A

An enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone to form short chain oligomers.

69
Q

What is a phosphodiesterase?

A

Phosphodiesterase is an enzyme that catalyzes the hydrolysis and degradation of phosphodiester bonds of the DNA/RNA back bone.

RNA/ DNA oligomers —> dNMPs or NMPs

70
Q

What is a nucleotidase?

A

A nucleotidase is an enzyme that catalyzes the hydrolysis of a nucleotide into a nucleoside and a phosphate.

dNMPs and NMPs —> nucleosides and deoxynucleosides

71
Q

What is a nucleosidase?

A

A nucleosidase is an enzyme that catalyzes the reaction to separate the base (purine/pyrimidine) from the ribose or deoxyribose.

72
Q

What is purine nucleoside phosphorylase (PNP)?

A

Purine nucleoside phosphorylase converts inosine to hypoxanthine by removal of a ribose.

73
Q

What is the sequence of intermediates in the adenine monophosphate catabolism?

A

AMP –nucleotidase—> adenosine –adenosine deaminase–> inosine –PNP—->hypoxanthine –xanthine oxidase–>xanthine –xanthine oxidase—>uric acid

74
Q

What is the sequence of intermediates in the inosine monophosphate catabolism?

A

IMP —-> Inosine –PNP–> hypoxanthine —xanthine oxidase–> xanthine –xanthine oxidase–> uric acid

75
Q

What is the sequence of intermediates in the guanosine monophosphate catabolism?

A

GMP–nucleotidase–> Guanosine –PNP—> Guanine –guanine deaminase—> xanthine —xanthine oxidase—> uric acid

76
Q

What does a deficiency in adenosine deaminase enzyme result in?

A

Severe combined immunodeficiency disorder (SCID), which is a result of the inability to convert deoxyadenosine to deoxyinosine. This causes a buildup of deoxyadenosine which is toxic to lymphocytes.

77
Q

What does excessive amounts of adenosine deaminase result in?

A

Excessive amounts of adenosine deaminase depletes adenine nucleotide pool and triggers premature destruction of RBCs and leads to anemia.

78
Q

What is allopurinol?

A

Allopurinol is a medication used to treat excess uric acid in the blood/gout. Allopurinol inhibits the activity of xanthine oxidase and as a result holds up catabolism of purines and decreases the concentration of purine catabolism - uric acid.

79
Q

What is Gout and what are the causes?

A

Gout is a condition in which there is a build up of uric acid in the blood and uric crystals build up in joints. This may be caused by excess purines in a person’s diet, inability of kidneys to get rid of uric acid or because the body just creates too much uric acid. Gout is treated with xanthine oxidase inhibitor such as allupurinol.

80
Q

What is Gout treated with?

A

Gout is treated with xanthine oxidase inhibitor such as allopurinol.

81
Q

What is urate oxidase?

A

Urate oxidase is an enzyme that converts uric acid to allantoin (soluble). This is significant because the human body has the gene to create urate oxidase yet does not express it suggesting that our uric acid levels are not typically too high or else the protein would express itself again.

Urate oxidase is a protein drug that can be taken to treat acute hyperuricemia.

82
Q

What is the product of purine catabolism and how does it leave the body?

A

Uric acid is the end product of purine catabolism and leaves the body as uric acid.

83
Q

Other than allopurinol what is another way to treat Gout?

A

Gout can also be treated with colchicine which decreases movement of granulocytes to the affected area. This is relevant because in this condition phagocytic cells engulf urate crystals and release factors that initiate an acute inflammatory response.

84
Q

What does the enzyme xanthine oxidase consist of?

A
  • 2 FADs
  • 2 Mo atoms
  • 8 Fe atoms
85
Q

What are the products of pyrimidine catabolism?

A

ketogenic

malonyl CoA

glucogenic

methylmalonyl CoA

succinyl CoA

86
Q

What is the product of purine catabolism?

A

xanthine —> uric acid (which can be converted to soluble allantoin by urate oxidase)

87
Q

Name this base.

A

adenine (Ade)

88
Q

Name this base

A

Guanine (Gua)

89
Q

Name this base.

A

hypoxanthine (hyp)

90
Q

Name this base.

A

xanthine (Xan)

91
Q

Name this base.

A

cytosine (Cyt)

92
Q

Name this base.

A

Uracil (Ura)

93
Q

Name this base.

A

(Thy) Thymine

94
Q

Name this structure.

A

Orotate

95
Q

What are the sources of the ring atoms in a purine base?

A
  1. CO2
  2. Gln - glutamine
  3. Gly - glycine
  4. Asp- aspartate
  5. N10-formyl THF - folate
96
Q

What are the sources of ring atoms in pyrimidines?

A
  1. HCO3-
  2. Gln - glutamine
  3. Asp aspartate
  4. N5
  5. N10-methylene THF - folate
97
Q

What is the committed step in purine synthesis ?

A

Formation of phosphoribosyl amine

98
Q

What are the two salvage enzymes in purine biosynthesis?

A
  1. hypoxanthine guanine phosphoribosyl transferase
  2. adenine phosphoribosyl transferase
99
Q

What is the comitted step in purine biosynthesis?

A

The committed step is the displacement of pyrophosphate by ammonia, converting PRPP to 5-phosphoribosyl-1-amine, and is catalyzed by glutamine phosphoribosyl amidotransferase.

100
Q

From what constituent is the ribose ring in purines contributed by?

A

PRPP

101
Q

What creates the 5 member ring in purine synthesis between PRA and IMP?

A
  1. (C-C-N) glycine
  2. 1 carbon (thf)
  3. 1 nitrogen (glutamine)
102
Q

What completes the 6 member ring that forms IMP?

A
  1. CO2 (1 carbon)
  2. aspartate (N)
  3. THF (1 carbon)
103
Q

What is the significance of Methotrexate?

A

Methotrexate is used as a chemotherapy treatment because it binds with higher affinity and inhibits dihydrofolate reductase, leading to ineffective folate and disrupts DNA replication

104
Q

Where in the purine synthesis is the forward reaction regulated?

A
  • Synthesis of PRPP and PRA are inhibited by purines (GMP,AMP,IMP)
  • synthesis of IMP is inhibited by methotrexate from lack of folate
  • synthesis of AMP and GMP from IMP is inhibited by AMP and GMP
  • AMP synthesis is stimulated by GTP
  • GMP synthesis is stimulated by ATP
105
Q

What is the action of nucleoside monophosphate kinases and nucleoside diphosphates?

A

nucleoside monophosphate kinase: transfers terminal phosphate group from triphosphate molecule (usually ATP) to a monophosphate molecule.

Nucleoside diphosphate kinase: transfers phosphates between two different diphosphate molecules

106
Q

What is the committed step in pyrimidine synthesis?

A

The committed step is carbamoyl phosphate + aspartate = carbamoyl aspartate

107
Q

What molecule donates hydrogen for the reduction of ribonucleoside diphosphate to doexyribonucleoside diphosphate?

A

Thioredoxin or glutaredoxin

108
Q

What are two major control points in the pyrimidine synthesis pathway?

A
  • Carbamoyl phosphate synthetase is inhibited by UMP and purines and stimulated by PRPP
  • Aspartate transcarbamoylase is feedback inhibited by CTP
109
Q

What is the limiting factor in DNA synthesis?

A

dTTP

110
Q
A

Biochemistry II (1 decks)

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