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Biochemistry > DNA: Structure and function, replication > Flashcards

DNA: Structure and function, replication Flashcards

1
Q
  • Bond found between two nucleotides
  • Reaction to form the bond
A
  • Phosphodiester bond
  • Produced during condensation
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2
Q

Primary structure of DNA

A
  • Sequence of nucleotides
  • Order of mononucleotides
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3
Q

3’ end of the nucleotide

A

Free 3-OH group

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4
Q

5’ end of the nucleotide

A

Free 5-phosphate group

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5
Q

2 bound mononucleotides

A

Dinucleotide

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6
Q

3-10 bound mononucleotides

A

Oligonucleotide

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7
Q

11-100 bound mononucleotides

A

Polynucleotide

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8
Q

>100 bound mononucleotides

A

Nucleic acid (DNA/RNA)

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9
Q

Structure of RNA

A

Similar to DNA:

  • Ribose instead of deoxyribose
  • Uracil instead of Thymine
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10
Q

Secondary structure of DNA

A
  • 2 antiparallel strands
  • 3’ end of one meets 5’ end of the other
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11
Q

Chargaff-rule

A

Number of purine bases = Number of pyrimidine bases

in double-stranded DNA

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12
Q

Number of H-bonds between: Adenine-Thymine

A

2

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13
Q

Number of H-bonds between: Guanine-Cytosine

A

3

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14
Q

Denaturing of DNA

A
  • Heating
    • H-bonds broken
    • DNA becomes single-stranded
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15
Q

Renaturation of DNA

A
  • Cooling
    • Double-stranded structure rearranges
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16
Q

The melting point of DNA

A

When half of the total DNA becomes single-stranded

  • Dependent on:
    • Types of bases
    • More G-C pairs = higher melting point
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17
Q

The alpha-helix form of DNA is its…structure

A

Tertiary

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18
Q

Who discovered the tertiary structure of DNA?

A
  • Franklin & Wilkins
  • Watson and Krick
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19
Q

Is the DNA double helix left-handed or right-handed?

A

Right-handed

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20
Q

How many nucleotides in the tertiary DNA chain contribute to 1 turn of the helix?

A

10

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21
Q

On DNA, where do transcription factors bind?

A

In the major & minor groove

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22
Q

Minor groove on DNA

A

The distance between two DNA strands

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23
Q

Major groove of DNA

A

The distance between two turns of DNA

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24
Q

What are the varieties of DNA double helix?

A
  • A-DNA
  • B-DNA
  • Z-DNA
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25
Q

B-DNA structure

A

Based on the Watson-Wrick model

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26
Q

A-DNA

A
  • Decreased humidity
  • Increased salt concentration
  • Frequent turns in the strand
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27
Q

Quarternary structure of DNA

A
  • Superhelix
  • Found in prokaryotes
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28
Q

What are the three forms of DNA superhelix

A
  • Relaxed
  • Positive superhelix
  • Negative superhelix
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29
Q

Relaxed superhelix form

A

Double helix is loose

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30
Q

Positive superhelix form

A

Double helix is spirally twisted

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31
Q

Negative superhelix form

A

Double helix is twisted in the opposite direction

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32
Q

Out of the positive and negative superhelix forms of DNA, which is the most transcriptionally active?

A

Negative superhelix

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33
Q

Topoisomerases

A
  • Enzymes
  • Form the relaxed superhelix structure
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34
Q

How does Topoisomerase I form a relaxed superhelix

A
  • Splits and ligates one DNA strand
  • No energy is required
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35
Q

How does Topoisomerase II form a relaxed superhelix

A
  • Splits and ligates both DNA strands
  • Requires ATP
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36
Q

An alternative name for topoisomerase II

A

DNA gyrase

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37
Q

How many chromosomes do prokaryotes have?

A

1

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38
Q

DNA is organised into the form of…

A

Chromosomes

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39
Q

Prokaryotic chromosome structure

A
  • Double-stranded
  • Circular
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40
Q

Histone

A
  • Alkaline protein
  • High isoelectric point
  • Positive charge
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41
Q

Why is DNA is attracted to histones?

A
  • Histone: positive charge
  • DNA: Negative charge
  • Strong ionic interaction
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42
Q

The composition of histone octamers

A

Pairs of core histones:

  • H2A
  • H2B
  • H3
  • H4
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43
Q

Histone H1

A

Fixes and strengthens DNA binding on the histone octamer

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44
Q

Structure of a nucleosome

A

Regularly repeating unit:

Histone octamer + DNA + histone H1

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45
Q

The effect of histone modifications

A
  • Histones can be modified covalently
  • Nucleosome therefore changes
  • Transcription is altered
46
Q

Which modifications of histones are possible?

A
  • Acetylation
  • Methylation
  • Phosphorylation
47
Q

What is the acetylation histone modification?

A

Binding of acetyl groups

48
Q

What is the methylation histone modification?

A

Binding of methyl groups

49
Q

What is the phosphorylation histone modification?

A

Binding of phosphate groups

50
Q

The makeup of chromosomes

A

Nucleosomes → Chromatine → Chromatids → Chromosome

51
Q

What is a gene?

A
  • A unit of heredity
  • The region of DNA coding:
    • A protein
    • An RNA molecule
52
Q

Amino acids are coded by…

A

Nucleotide/base triplets

1 amino acid → Base triplets of DNA = 1 code

53
Q

The reading frame in the genetic code system is

A
  • Universal (for each organism)
  • Confluent (commaless)
  • Non-overlapping sequence
54
Q

A triplet code can make a genetic code for how many different combinations?

A

64 (43 = 64)

55
Q

Steps of the central dogma

A
  • DNA code from base triplets
  • Transcription
  • tRNA transports amino acids → ribosomes
  • Translation
56
Q

Transcription

A
  • mRNA synthesis
  • mRNA base triplets = Codon
57
Q

Base triplets of tRNA

A

Anticodon

58
Q

Translation

A

Protein synthesis in the ribosome

59
Q

DNA replication

A

Reduplication of DNA

  • Forwarding genetic information during cell division
60
Q

What is the structure of DNA during replication?

A

The double helix is split into two single strands

Acts as a template

61
Q

Describe the semi-conservative theory of DNA replication

A
  • Produced double helix is composed of:
    • 1 parental strand
    • 1 newly synthesised strand
62
Q

The three phases of DNA replication

A
  1. Initiation
  2. Elongation
  3. Termination
63
Q

Where does DNA replication of prokaryotes initiate?

A

The replication origo

64
Q

Replication origo is composed of…

A

Consensus sequences

65
Q

DNA-A during prokaryote DNA synthesis

A
  • Proteins recognise replication origo
  • DNA-A binds to DNA-A binding sites
66
Q

DNA-B and DNA-C during prokaryote DNA synthesis

A
  • Bind to a DNA-A protein
  • Helicase activity
    • H-bonds split
    • Double helix opens
    • ‘Replication bubble’ forms
67
Q

Replication of prokaryotes: Initiation phase (Phase 1)

A
  • Single strand proteins (SSB-proteins) separate the two strands
68
Q

Which group of the DNA is needed for synthesis in prokaryotes

A

3’-OH-group

69
Q

Primer

A
  • Short RNA sequence
  • Has a free 3’-OH-group
70
Q

Synthesis of primers is by…

A

Primosomes

71
Q

Primosome

A
  • Protein complex
  • Contains Primase
  • Contains synthesising primer
72
Q

Replication of prokaryotes: Elongation phase (Phase 2)

A
  • Continuous & discontinuous synthesis
  • The building of nucleotides in new strands
73
Q

In prokaryotes, where does continuous synthesis occur?

A

The leading strand

74
Q

In prokaryotes, where does discontinuous synthesis occur?

A

The lagging strand

75
Q

A primer + DNA is known as…

A

Okazaki-fragment

76
Q

In prokaryotes, synthesis of the new DNA strand is responsible by…

A

DNA polymerase III

77
Q

DNA polymerase synthesises in which direction?

A

From the 5’ → 3’

78
Q

The building blocks for new DNA strands

A

dNTP

(Deoxyribonucleoside triphosphate)

79
Q

How is dNTP made into nucleotides

A

dNTP → dNMP + 2Pin

80
Q

Replication of prokaryotes: Termination phase (Phase 3)

A
  • DNA polymerase III dissociates
  • Primers hydrolysed
  • DNA polymerase I moves between DNA fragments
  • Ligation of new DNA
81
Q

During prokaryote termination which enzyme will hydrolyse and cut out primers?

A

DNA polymerase I

82
Q

During prokaryote termination which enzyme ligates new DNA?

A

DNA ligase

83
Q

The function of DNA ligase

A
  • DNA ligase: ATP → AMP + 2Pin
  • AMP binds to the activated enzyme
  • 5’-end and 3’-end of two fragments
    • → Phosphodiester bond
  • AMP dissociated from enzyme
84
Q

Function of topoisomerases

A
  • Strands become tense during replication
  • Topoisomerase cuts DNA strand
  • DNA rotates to remove coils
  • Topoisomerase rejoins the DNA strands
85
Q

DNA gyrase is a type of…

A

Topoisomerase

86
Q

How does DNA polymerase act as a dimer?

A

Simultaneous replication of two DNA strands

87
Q

Where are proteins needed for replication organised?

A

Replisome

88
Q

The three main differences between eukaryote and prokaryote DNA replication

A
  • Eukaryotes
    • Numerous replication origos
    • Distinct DNA polymerase names
    • Telomeric sequences
89
Q

List the DNA polymerases of Eukaryotes

A
  • DNA polymerase α
  • DNA polymerase β
  • DNA polymerase γ
  • DNA polymerase δ
90
Q

The responsibility of DNA polymerase α

A

Synthesis of new DNA strand

Acts as the equivalent of DNA Polymerase III in prokaryotes

91
Q

The responsibility of DNA polymerase β

A
  • Repair DNA during replication
  • Removes the primer
  • Filling of gaps

Acts as the equivalent of DNA Polymerase I & II in prokaryotes

92
Q

The responsibility of DNA polymerase γ

A

Replication of mitochondrial DNA

93
Q

The responsibility of DNA polymerase δ

A
  • Synthesis of new DNA strand
  • Requires PCNA protein for operation
94
Q

Telomeric sequences are used to solve which problem?

A
  • Lagging strand:
    • Last primer of the 5’-end cannot be replaced by nucleotides
    • Chromosome would be shortened
95
Q

Telomere

A
  • Extra sequence attached to 3’ end of chromosome
  • Telomerase synthesis the telomeric sequences
96
Q

The process of DNA repair

A
  • UV-specific endonuclease
    • Cuts damaged strand
  • Damaged/mismatching bases removed and replaced
    • DNA polymerase I & II (Prok.)
    • DNA polymerase β (Euk.)
  • DNA ligase links fragments
97
Q

Mutation

A

Heritable change of DNA base sequences

98
Q

Types of mutation

A
  • Spontaneous mutation
  • Induced mutation
  • Gametic mutation
  • Somatic mutation
  • Chromosome mutation
  • Gene mutation
99
Q

Causes of induced mutation

A

Caused by physical conditions

100
Q

Gametic mutation

A
  • Mutation in ovum/sperm
  • Forwarded onto descendants
101
Q

Somatic mutation

A
  • In somatic cells
  • Causes tumours
102
Q

Gene mutation

A
  • Mostly point mutation
  • Only a single nucleotide is changed
103
Q

Forms of point mutation

A
  • Substitution mutation
  • ‘Frameshift’ mutation:
    • Insertion
    • Deletion
104
Q

Substitution mutation

A

A non-complimentary nucleotide is built into the chain rather than a complimentary nucleotide

105
Q

Varieties of substitution mutation

A
  • Missense mutation
  • Nonsense mutation
  • Silent/samesense mutation
106
Q

Missense mutation

A

Mutated base sequence → Different amino acid produced

107
Q

Nonsense mutation

A

Mutated base → Stop code produced → Translation halts → Produced protein is shorter

108
Q

Silent/samesense mutation

A

Mutated base → Same amino acid is produced

109
Q

Insertion

A

Extra nucleotides introduced into the DNA

110
Q

Deletion

A

Nucleotides missing from the DNA

111
Q

Thymine dimer formation

A
  • UV radiation → covalent bonds between pyrimidine bases
  • Replication and transcription affected
  • Mutagenic process → Melanoma
112
Q

Sickle-cell anaemia

A
  • Missense substitution mutation
  • β-globin gene affected
  • Change from Glutamine → Valine production
  • Change is haemoglobin solubility

Biochemistry (21 decks)

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