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Molecular Diagnostics > Lecture 1: DNA Structure and Function > Flashcards

Lecture 1: DNA Structure and Function Flashcards

1
Q

Mononucleotides are composed of?

A

-nucleobase + sugar + phosphate

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2
Q

What is the bond between DNA and RNA (base + sugar)?

A
  • N-glycosidic bond
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3
Q

DNA and RNA structures:

__________ linkage (PO4 + sugar)

A
  • phosphodiester
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4
Q

What are the pyrimidine bases for DNA?

A

Cytosine and Thymine

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5
Q

What are the pyrimidine bases for RNA?

A

Cytosine and Uracil

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6
Q

Pyrimidine or Purine?

two ring structure-
one ring structure-

A

purine

pyrimidine

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7
Q

Ribose- _____ is on carbon #2

A

OH

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8
Q

Deoxyribose- _____ is on carbon #2.

A

H

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9
Q

H on both carbon #2 and #3

A

dideoxyribose

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10
Q

What reduces ribose to deoxyribose?

A

Ribonucleotide reductase

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11
Q

N-glycosidase linkage:
C-1 and N-___ pyrimidines;
C-1 and N-____ purines

A

1

9

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12
Q

Base + Sugar + phosphate(s) =

A

nucleotides

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13
Q

AMP or adenylate

A

Adenosine 5’-monophosphate

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14
Q

ADP

A

Adenosine 5’ diphosphate

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15
Q

ATP

A

Adenosine 5’ triphosphate

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16
Q

What are the functions of Nucleotides?

A

-Nucleic acid synthesis: DNA/RNA
* Energy currency of cell
* Second messengers in cellular communication
* Ingredients of co-enzymes
* Regulators of metabolic reactions

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17
Q

Purine Synthesis of AMP and GMP requires _______ ATP

A

7 or 8

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18
Q

Degradation of Purine Nucleotides:

Xanthine Oxidase
deficiency (1)

A

-Hypouricemia

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19
Q

Degradation of Purine Nucleotides:

HGPRTase, PRPP to
Purine (salvage pathway
enzymes) (2)

A

-Hyperuricemia
(Lesch-Nyhan)

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20
Q

Degradation of Purine Nucleotides:

Adenosine Deaminase
deficiency (3)

A

-Severe combined
immunodeficiency (SCID)

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21
Q

Degradation of purine produces…

A

uric acid

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22
Q

Diseases Associated with Purine Metabolism:

HGPRTase, PRPP deficiency (salvage pathway enzymes)

A

Hyperuricemia (Lesch-Nyhan Syndrome/Juvenile Gout)

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23
Q

Diseases Associated with Purine Metabolism:

  • Adenosine Deaminase deficiency.
    -Over expression- Hemolytic Anemia
  • SCID can also be caused by a variety of other enzyme defects.
A

Severe Combined Imunodeficiency Diseases SCID (missing body defense system T & B cells)

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24
Q

Diseases Associated with Purine Metabolism:

Level of uric acid in blood serum is below normal
* Xanthine Oxidase deficiency

A

Hypouricemia

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25
Q

-No expression of Adenosine Deaminase (bubble boy)
* Accumulation of dATP inhibits ribonucleotide reductase and depletes DNA precursors

A

Adenosine Deaminase deficiency

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26
Q
  • Do not require large Energy
  • EUK no significant salvage
A

Pyrimidine synthesis

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27
Q

Sources of carbon, and nitrogen atoms for pyrimidine synthesis?

A

N-1, C-4, C-5, and C-6 from aspartate

C-2 from CO2

N-3 from amide No of glutamine

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28
Q

Degradation of Pyrimidines:

  • Cytosine deaminated to uracil
  • uracil degraded to _________
A

b-alanine

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29
Q

Degradation of Pyrimidines

  • Thymidine degraded to _____________
    (aa deritive) ——-> urea
A

beta-aminoisobutyrate

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30
Q

Why do labs measure uric acid?

A

to determine increased purine degradation

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31
Q

What is required for thymidylate synthesis?

A
  • Folate and B12
    required - Involved in one carbon metabolism
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32
Q

thymidylate synthesis:

Involves

A

-thymidylate synthase
-B12

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33
Q

B12 is also known as…

A

Cobalamin

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34
Q

B9 is called?

A

Folic Acid

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35
Q

Folic acid works closely with vitamin ____ in making red blood cells and helps iron
function properly in the body.

A

B12

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36
Q

Folic acid is biochemically inactive, it is converted by ______________ to
tetrahydrofolic acid (THF) and methyltetrahydrofolate (MTHF)

A

dihydrofolate reductase

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37
Q

e folic acid congeners are transported by receptor-mediated endocytosis
across cells where they are needed to…

A

-maintain normal erythropoiesis,
* interconvert amino acids,
* methylate tRNA,
* generate and use formate,
* synthesize purine and thymidylate nucleic acids.

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38
Q

(commonly known as cyanocobalamin) is the most
chemically complex of all the vitamins.

A

Vitamin B12

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39
Q

Ture or false?

  • Cyanocobalamin cannot be made by plants or animals
A

Ture

  • Naturally found in foods including meat (especially liver and shellfish),
    eggs, and milk products.
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40
Q

What are the two forms of B12 that is used by the body?

A

-Methylcobalamin
-5-deoxyadenosyl cobalamin

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41
Q

B12 form:

serves as cofactor for conversion of the amino acid
homocysteine into methionine, and Methionine is required for DNA
methylation.

A

Methylcobalamin

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42
Q

B12 form:

serves as cofactor to convert l-methylmalonyl
CoA to succinyl CoA

A

5-deoxyadenosyl cobalamin

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43
Q

Two chemotherapeutic agents that inhibit thymidylate synthesis?

A

-DHFR
-Thymidylate synthase inhibitor

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44
Q

prevent one carbon
metabolism
Methotrexate
Aminopterin

A

DHFR inhibitor

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45
Q

5-fluorouracil (5-FU)- Pyrimidine Analog

A

Thymidylate synthase inhibitor

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46
Q

nucleobases linked by 3’ to 5’ _____________ bonds

A

phosphodiester

  • chain growth is always 5’ to 3’
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47
Q

Secondary Structure of DNA:

  • double stranded; anti-parallel; twists into helix
  • bases base paired through __________ bonding (WatsonCrick bond)
A

hydrogen

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48
Q

What bonds to A?

A

double bond by T

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49
Q

What bonds to C?

A

triple bond by G

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50
Q

What enzyme attaches nucleotides to 3’ OH end?

A

DNA polymerase III

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51
Q

DNA is __________ handed helical.

A

right

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52
Q

What is equivalent to “rungs of a ladder”

A

Nitrogenous
Base (A,T,G or C)

53
Q

What is equivalent to “legs of ladder”?

A

Phosphate & Sugar Backbone

54
Q

___’ to ____’ —> one strand is continuous (Leading strand), other strand is discontinuous (Lagging strand)

A

5, 3

55
Q

What are the 3 prokaryotic polymerases?

A
  • Pol I:(polA) replication and repair
  • Pol II: implicated in repair
  • Pol III: main processive replicative enzyme (de novo
    synthesis of DNA)
56
Q

Polymerase ____: replication and repair

A

Pol I:(polA)

57
Q

Polymerase ____: implicated in repair

A

Pol II

58
Q

Polymerase ____: main processive replicative enzyme (de novo synthesis of DNA)

A

Pol III

59
Q

Prokaryotic DNA Synthesis:
Sequence of Events…

A

Topoisomerase unwraps and separates strands
* Helicase breaks the base pairing
* SSB binds to ssDNA
* Primase lays RNA primer (gives 3’-OH)
* DNA pol III synthesizes DNA (high processivity)
* Pol I cuts out primers and re-synthesizes DNA
* Ligase reseals strand nicks after Pol I
* Gyrase (type II topoisomerase) rewraps and recoils

60
Q

______________ unwraps and separates strands

A

Topoisomerase

61
Q

___________ breaks the base pairing.

A

Helicase

62
Q

______ cuts out primers and re-synthesizes DNA

A

Pol I

63
Q

DNA ________ synthesizes DNA (high processivity)

A

pol III

64
Q

_______ reseals strand nicks after Pol I

A

Ligase

65
Q

______________ rewraps and recoils.

A

Gyrase (type II topoisomerase)

66
Q

Breaks hydrogen bonds linking the two strands of double helix.

A

Helicase

67
Q

Mitigates the supercoiling effect that occurs in advance of the replication fork.
topoisomerases bind to DNA and cut the phosphate backbone of either one or both the DNA strands. This intermediate break allows the DNA to be untangled or
unwound, and, at the end of these processes, the DNA backbone is resealed again.

A

Topoisomerase

68
Q

Acts as a retractor, preventing the single strands of the DNA double helix from rejoining.

A

Single-strand binding
proteins

69
Q

Synthesizes RNA primers used in DNA daughter strands formation. Certain DNA polymerases also act as part of the DNA repair machinery

A

RNA primase

70
Q

Synthesizes DNA daughter strands. Certain DNA polymerases also act as part of the DNA repair machinery

A

DNA polymerase

71
Q

Links newly synthesized DNA fragments (Okazaki fragments)

A

DNA ligase

72
Q

Eukaryotic DNA Synthesis:

  • Replication in _____ phase of cell cycle
  • Unwrap DNA from histone proteins
A

S

73
Q
  • Larger genome, __________ origins of replication on each eukaryotic chromosome
  • Humans can have up to 100,000 origins of replication across the
    genome
A

multiple

74
Q

There are ____ known DNA polymerases in eukaryotes.

A

14

75
Q

What polymerases are known to have major roles during replication and have been well studied?

A

pol α, pol β, pol γ, pol δ, and pol ε

76
Q

Polymerase alpha…

A

Activities: polymerase, primase, 3’ –> 5’ exonuclease

Role: primer synthesis repair

77
Q

Polymerase beta…

A

activities: polymerase

role: repair

78
Q

Polymerase gamma…

A

activities: polymerase, 3’ —> 5’ exonuclease

role: mitochondrial DNA replication

79
Q

Polymerase delta…

A

activities: polymerase, 3’ –> 5’ exonuclease

role: lagging-strand synthesis , repair

80
Q

Polymerase epsilon…

A

activities: polymerase,
3’ —> 5’ exonuclease
5’ —>3’ exonuclease

role: leading-strand synthesis, gap filling on lagging strand

81
Q

group of enzymes that remove nucleotide bases from the end of a DNA chain.

A

Exonucleases

82
Q

__________ inhibit DNA gyrase

A

Quinolines

Ex: Norfloxacin, Ciprofloxin, Novobiocin

83
Q

Inhibitors of DNA Synthesis?

A

-Quinolines
-Methotrexate and Aminopterin, Trimethiprin
-Chemotherapeutic Agents

84
Q

Inhibitors of DNA Synthesis that are chemotherapeutic agents?

Chain terminator

What inhibits thymidylaye synthase

And?

A
  • Methotrexate
  • AZT-DNA chain terminator (no 3” OH)
  • 5’Fluorouricil-inhibits thymidylate synthesis
85
Q
  • inhibit dihydrofolate reductase
    (inhibits DNA synthesis via thymidylate synthesis)
A

Methotrexate and Aminopterin, Trimethiprin

86
Q

What do Nucleoside analogs do?

A

inhibiting viral replication and stopping cancer cell proliferation.

87
Q

3 examples of nucleoside analogs?

A

-AZT
-5FU
-Uracil

88
Q

When does replication occur in prokaryotes?

A

-cellular size
-environmental factors

89
Q

When does replication occur in eukaryotes?

A

stage of cell cycle
* M
* G1
* S
* G2

90
Q

Polynucleotide and Chromatin:

tertiary Structure in prokaryotes?

A

-circular DNA supercoiled into compact rings

91
Q

Polynucleotide and Chromatin:

tertiary structure in eukaryotes?

A
  • wrapped around histone proteins- supercoiling
  • packed into solenoid
  • condensed into chromatin
  • wrapped on scaffolding proteins
92
Q

Chromosomal Organization:

DNA double helix of about 2.0 nm thick is wrapped around a core of 4 pairs of histone molecules to form ___________.

A

nucleosomes

93
Q

Chromosomal Organization:

Linker DNA (C) connects between nucleosomes.
Nucleosomes attach
together by peripheral ________ and condense
forming a fiber of about 30 nm thick.

A

histone (HI)

94
Q

Chromosomal Organization:

The nucleosomal fibers form loops radiating from scaffolding nonhistone protein to form the DNA protein complex of
________________
during cell division.

A

chromatin fibers

95
Q

Chromosomal Organization:

As a result of DNA replication, each chromosome becomes two sister____________ attaching
at centromere and of about 1400 nm in thickness in metaphase.

A

chromatids

96
Q

Each Homologous set is made up of 2 _____________.

A

Homologues

97
Q

Chromosomes are most condensed (thickened) and highly coiled in ___________, which makes them most suitable for visual analysis.

A

metaphase

98
Q

The analysis of ___________
chromosomes is one of the main tools of classical cytogenetics and cancer studies.

A

metaphase

-Metaphase chromosomes make the classical picture of
chromosomes (karyotype).

99
Q

____________ makes up chromosomes. changes to
its structure can prevent or allow certain regions of the genetic code to be read and
expressed.

A

Chromatin

100
Q

______________ is the genetically active type of
chromatin involved in transcribing RNA to produce
proteins.

A

Euchromatin

101
Q

What is the predominant type of chromatin found in
cells during interphase?

A

euchromatin (it is more
diffused)

102
Q

______________ is genetically inactive type of chromatin.

A

Heterochromatin

103
Q

Heterochromatin tends to be most concentrated along…

A

chromosomes at certain regions of the structures, such as the centromeres and
telomeres.

104
Q

Heterochromatin or Euchromatin?

-more condensed
-silenced genes (methylated)
-gene poor (high AT content)
-stains darker

A

Heterochromatin

105
Q

Heterochromatin or Euchromatin?

-less condensed
-gene expressing
-gene rich (higher GC content)
-stains lighter

A

Euchromatin

106
Q

The chromosome region that attaches to a spindle fiber at metaphase
of mitosis or meiosis and moves to the spindle pole at anaphase

A

centromere

107
Q

The position of the centromere is constant for a particular chromosome, but variable between ____________.

A

chromosomes

108
Q

What are the centromere types?

A

metacentric, acrocentric, submetacentric, or telocentric

Telocentric< Afrocentric < submetacentric< metacentric

Based on P arm size

109
Q

A repetitive nucleotide sequences, present in the buffer zone, serves as termination signal

A

telomeres

110
Q

In humans the sequence is TTAGGG (called “cap” sequence) repeated several thousand times.

A

telomere

111
Q

Telomeres erosion does not affect cell function but protects against…

A

lose of functionally important genetic material.

112
Q

functions to add more nucleotides to the telomeres, regenerating these protective “cap” DNA sequences to avoid vital region of DNA from damage.

A

Telomerase

113
Q

Over expression of _______________ may could help cancer cells to grow faster and live longer, potentially leading to more dangerous strains of cancer.

A

telomerase

114
Q

Loss /reduced telomerase activity may cause…

A

premature cell aging and death.

115
Q

Short chromosome arms are designated _________.

Long chromosome arms are designated _________.

A

p (petit)

q (next letter of alphabet)

116
Q

How are chromosome regions (bands) numbered?

A

numbered consecutively from centromere
outward to telomere.

117
Q

To designate a specific region of the chromosome …

A

-Chromosome number written first
-Location on the short or long arm
-Region of the arm (specific band) (exp. 18p22.31)

118
Q

What is this? t(9;22)(q34;q11.2)

A

band 34 on long arm of chromosome 9 has exchanged places with band
11.2 on long arm of chromosome 22.

119
Q

Stages in cell cycle?

A
  • G0
  • G1 Check point
  • S
  • G2 Checkpoint
  • M
    -metaphase= check point
120
Q

What are the phases in M?

A
  • prophase,
  • Metaphase Checkpoint
  • anaphase,
  • telophase
  • cytokinesis
121
Q

quiescent/senescent:

Gap 0, G0, function?

A

A resting phase where the cell has left the cycle and has stopped dividing.

122
Q

Interphase:

Gap 1, G1 functions?

A

Cells increase in size in Gap 1. The G1 checkpoint control mechanism ensures that everything is ready for DNA synthesis.

123
Q

Interphase:

Synthesis, S, function?

A

DNA replication occurs during this phase

124
Q

Interphase:

Gap 2, G2, function?

A

During the gap between DNA synthesis and mitosis, the cell will continue to grow. The G2 checkpoint control mechanism ensures that everything is ready to enter the M (mitosis) phase and divide.

125
Q

Cell division:

Mitosis, M, function?

A

Cell growth stops at this stage and cellular energy is focused on the orderly division into two daughter cells. A checkpoint in the middle of mitosis (Metaphase Checkpoint) ensures that the cell is ready to complete cell division.

126
Q

Major Proteins that Control Cell Cycle?

A

-control proteins
-complexes Cdk-cyclin
*Chemical reactions of phosphorylation/dephosphoryation are the foundation of protein activation

127
Q

Control proteins?

A

-Cyclin-dependent protein kinases (Cdks)
-Cyclins

128
Q

Complexes: Cdk-cyclin:

ability of Cdk to “P” target is dependent on the _______ that it forms a complex with

A

cyclin

Molecular Diagnostics (12 decks)

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