Biochemistry > DNA: Structure and function, replication > Flashcards

DNA: Structure and function, replication Flashcards

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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
B-DNA structure
Based on the Watson-Wrick model
26
A-DNA
* Decreased humidity * Increased salt concentration * Frequent turns in the strand
27
Quarternary structure of DNA
* Superhelix * Found in prokaryotes
28
What are the three forms of DNA superhelix
* Relaxed * Positive superhelix * Negative superhelix
29
Relaxed superhelix form
Double helix is loose
30
Positive superhelix form
Double helix is _spirally twisted_
31
Negative superhelix form
Double helix is _twisted in the opposite direction_
32
Out of the positive and negative superhelix forms of DNA, which is the most transcriptionally active?
Negative superhelix
33
Topoisomerases
* Enzymes * Form the _relaxed_ superhelix structure
34
How does Topoisomerase I form a relaxed superhelix
* Splits and ligates one DNA strand * No energy is required
35
How does Topoisomerase II form a relaxed superhelix
* Splits and ligates both DNA strands * Requires ATP
36
An alternative name for topoisomerase II
DNA gyrase
37
How many chromosomes do prokaryotes have?
1
38
DNA is organised into the form of...
Chromosomes
39
Prokaryotic chromosome structure
* Double-stranded * Circular
40
Histone
* Alkaline protein * High isoelectric point * Positive charge
41
Why is DNA is attracted to histones?
* Histone: positive charge * DNA: Negative charge * Strong _ionic_ interaction
42
The composition of histone octamers
Pairs of _core histones_: * H2A * H2B * H3 * H4
43
Histone H1
Fixes and strengthens DNA binding on the histone octamer
44
Structure of a nucleosome
Regularly repeating unit: Histone octamer + DNA + histone H1
45
The effect of histone modifications
* Histones can be modified covalently * Nucleosome therefore changes * Transcription is altered
46
Which modifications of histones are possible?
* Acetylation * Methylation * Phosphorylation
47
What is the _acetylation_ histone modification?
Binding of acetyl groups
48
What is the methylation histone modification?
Binding of methyl groups
49
What is the _phosphorylation_ histone modification?
Binding of phosphate groups
50
The makeup of chromosomes
Nucleosomes → Chromatine → Chromatids → Chromosome
51
What is a gene?
* A unit of heredity * The region of DNA coding: * A protein * An RNA molecule
52
Amino acids are coded by...
Nucleotide/base triplets _1 amino acid → Base triplets of DNA = 1 code_
53
The reading frame in the genetic code system is
* Universal (for each organism) * Confluent (commaless) * Non-overlapping sequence
54
A triplet code can make a genetic code for how many different combinations?
64 (43 = 64)
55
Steps of the central dogma
* DNA code from base triplets * Transcription * tRNA transports amino acids → ribosomes * Translation
56
Transcription
* mRNA synthesis * mRNA base triplets = Codon
57
Base triplets of _tRNA_
Anticodon
58
Translation
Protein synthesis in the ribosome
59
DNA replication
Reduplication of DNA * Forwarding genetic information during cell division
60
What is the structure of DNA during replication?
The double helix is split into _two single strands_ Acts as a template
61
Describe the semi-conservative theory of DNA replication
* Produced double helix is composed of: * 1 parental strand * 1 newly synthesised strand
62
The three phases of DNA replication
1. Initiation 2. Elongation 3. Termination
63
Where does DNA replication of prokaryotes initiate?
The replication origo
64
Replication origo is composed of...
Consensus sequences
65
DNA-A during prokaryote DNA synthesis
* Proteins recognise replication origo * DNA-A binds to DNA-A binding sites
66
DNA-B and DNA-C during prokaryote DNA synthesis
* Bind to a DNA-A protein * _Helicase activity_ * H-bonds split * Double helix opens * _'Replication bubble'_ forms
67
Replication of prokaryotes: Initiation phase (Phase 1)
* Single strand proteins (SSB-proteins) separate the two strands
68
Which group of the DNA is needed for synthesis in prokaryotes
3'-OH-group
69
Primer
* Short RNA sequence * Has a free 3'-OH-group
70
Synthesis of primers is by...
Primosomes
71
Primosome
* Protein complex * Contains _Primase_ * Contains _synthesising primer_
72
Replication of prokaryotes: Elongation phase (Phase 2)
* Continuous & discontinuous synthesis * The building of nucleotides in new strands
73
In prokaryotes, where does continuous synthesis occur?
The leading strand
74
In prokaryotes, where does discontinuous synthesis occur?
The lagging strand
75
A primer + DNA is known as...
_Okazaki-fragment_
76
In prokaryotes, synthesis of the new DNA strand is responsible by...
DNA polymerase III
77
DNA polymerase synthesises in which direction?
From the 5' → 3'
78
The building blocks for new DNA strands
dNTP | (Deoxyribonucleoside triphosphate)
79
How is dNTP made into nucleotides
dNTP → _dNMP_ + 2Pin
80
Replication of prokaryotes: Termination phase (Phase 3)
* DNA polymerase III dissociates * Primers hydrolysed * DNA polymerase I moves between DNA fragments * Ligation of new DNA
81
During prokaryote termination which enzyme will hydrolyse and cut out primers?
DNA polymerase I
82
During prokaryote termination which enzyme ligates new DNA?
DNA ligase
83
The function of DNA ligase
* 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
Function of topoisomerases
* Strands become tense during replication * Topoisomerase cuts DNA strand * DNA rotates to remove coils * Topoisomerase rejoins the DNA strands
85
DNA gyrase is a type of...
Topoisomerase
86
How does DNA polymerase act as a dimer?
Simultaneous replication of two DNA strands
87
Where are proteins needed for replication organised?
Replisome
88
The three main differences between eukaryote and prokaryote DNA replication
* Eukaryotes * Numerous replication origos * Distinct DNA polymerase names * Telomeric sequences
89
List the DNA polymerases of Eukaryotes
* DNA polymerase α * DNA polymerase β * DNA polymerase γ * DNA polymerase δ
90
The responsibility of DNA polymerase α
Synthesis of new DNA strand ## Footnote *Acts as the equivalent of DNA Polymerase III in prokaryotes*
91
The responsibility of DNA polymerase β
* Repair DNA during replication * Removes the primer * Filling of gaps ## Footnote *Acts as the equivalent of DNA Polymerase I & II in prokaryotes*
92
The responsibility of DNA polymerase γ
Replication of mitochondrial DNA
93
The responsibility of DNA polymerase δ
* Synthesis of new DNA strand * Requires _PCNA_ protein for operation
94
Telomeric sequences are used to solve which problem?
* Lagging strand: * Last primer of the 5'-end cannot be replaced by nucleotides * Chromosome would be shortened
95
Telomere
* Extra sequence attached to 3' end of chromosome * _Telomerase_ synthesis the telomeric sequences
96
The process of DNA repair
* 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
Mutation
Heritable change of DNA base sequences
98
Types of mutation
* Spontaneous mutation * Induced mutation * Gametic mutation * Somatic mutation * Chromosome mutation * Gene mutation
99
Causes of induced mutation
Caused by physical conditions
100
Gametic mutation
* Mutation in ovum/sperm * Forwarded onto descendants
101
Somatic mutation
* In somatic cells * Causes tumours
102
Gene mutation
* Mostly _point mutation_ * Only a single nucleotide is changed
103
Forms of point mutation
* _Substitution_ mutation * 'Frameshift' mutation: * _Insertion_ * _Deletion_
104
Substitution mutation
A _non-complimentary_ nucleotide is built into the chain rather than a complimentary nucleotide
105
Varieties of substitution mutation
* Missense mutation * Nonsense mutation * Silent/samesense mutation
106
Missense mutation
Mutated base sequence → Different amino acid produced
107
Nonsense mutation
Mutated base → Stop code produced → Translation halts → Produced protein is shorter
108
Silent/samesense mutation
Mutated base → Same amino acid is produced
109
Insertion
Extra nucleotides introduced into the DNA
110
Deletion
Nucleotides missing from the DNA
111
Thymine dimer formation
* UV radiation → covalent bonds between _pyrimidine bases_ * Replication and transcription affected * Mutagenic process → Melanoma
112
Sickle-cell anaemia
* Missense substitution mutation * _β-globin_ gene affected * Change from _Glutamine_ → _Valine_ production * Change is haemoglobin solubility
Biochemistry
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