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Miller OnRamps Biology > 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

3’ end of the nucleotide

A

Free 3-OH group

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3
Q

5’ end of the nucleotide

A

Free 5-phosphate group

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4
Q

2 bound mononucleotides

A

Dinucleotide

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5
Q

3-10 bound mononucleotides

A

Oligonucleotide

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6
Q

11-100 bound mononucleotides

A

Polynucleotide

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7
Q

>100 bound mononucleotides

A

Nucleic acid (DNA/RNA)

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8
Q

Structure of RNA

A

Similar to DNA:

  • Ribose instead of deoxyribose
  • Uracil instead of Thymine
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9
Q

Secondary structure of DNA

A
  • 2 antiparallel strands
  • 3’ end of one meets 5’ end of the other
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10
Q

Chargaff-rule

A

Number of purine bases = Number of pyrimidine bases

in double-stranded DNA

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11
Q

Number of H-bonds between: Adenine-Thymine

A

2

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12
Q

Number of H-bonds between: Guanine-Cytosine

A

3

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13
Q

Denaturing of DNA

A
  • Heating
    • H-bonds broken
    • DNA becomes single-stranded
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14
Q

Renaturation of DNA

A
  • Cooling
    • Double-stranded structure rearranges
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15
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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16
Q

The alpha-helix form of DNA is its…structure

A

Tertiary

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17
Q

Who discovered the tertiary structure of DNA?

A
  • Franklin & Wilkins
  • Watson and Krick
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18
Q

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

A

Right-handed

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19
Q

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

A

10

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20
Q

On DNA, where do transcription factors bind?

A

In the major & minor groove

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21
Q

Minor groove on DNA

A

The distance between two DNA strands

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22
Q

Major groove of DNA

A

The distance between two turns of DNA

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23
Q

What are the varieties of DNA double helix?

A
  • A-DNA
  • B-DNA
  • Z-DNA
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24
Q

B-DNA structure

A

Based on the Watson-Wrick model

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25
A-DNA
* Decreased humidity * Increased salt concentration * Frequent turns in the strand
26
Quarternary structure of DNA
* Superhelix * Found in prokaryotes
27
What are the three forms of DNA superhelix
* Relaxed * Positive superhelix * Negative superhelix
28
Relaxed superhelix form
Double helix is loose
29
Positive superhelix form
Double helix is _spirally twisted_
30
Negative superhelix form
Double helix is _twisted in the opposite direction_
31
Out of the positive and negative superhelix forms of DNA, which is the most transcriptionally active?
Negative superhelix
32
Topoisomerases
* Enzymes * Form the _relaxed_ superhelix structure
33
How does Topoisomerase I form a relaxed superhelix
* Splits and ligates one DNA strand * No energy is required
34
How does Topoisomerase II form a relaxed superhelix
* Splits and ligates both DNA strands * Requires ATP
35
An alternative name for topoisomerase II
DNA gyrase
36
How many chromosomes do prokaryotes have?
1
37
DNA is organised into the form of...
Chromosomes
38
Prokaryotic chromosome structure
* Double-stranded * Circular
39
Histone
* Alkaline protein * High isoelectric point * Positive charge
40
Why is DNA is attracted to histones?
* Histone: positive charge * DNA: Negative charge * Strong _ionic_ interaction
41
The composition of histone octamers
Pairs of _core histones_: * H2A * H2B * H3 * H4
42
Histone H1
Fixes and strengthens DNA binding on the histone octamer
43
Structure of a nucleosome
Regularly repeating unit: Histone octamer + DNA + histone H1
44
The effect of histone modifications
* Histones can be modified covalently * Nucleosome therefore changes * Transcription is altered
45
Which modifications of histones are possible?
* Acetylation * Methylation * Phosphorylation
46
What is the _acetylation_ histone modification?
Binding of acetyl groups
47
What is the methylation histone modification?
Binding of methyl groups
48
What is the _phosphorylation_ histone modification?
Binding of phosphate groups
49
The makeup of chromosomes
Nucleosomes → Chromatine → Chromatids → Chromosome
50
What is a gene?
* A unit of heredity * The region of DNA coding: * A protein * An RNA molecule
51
Amino acids are coded by...
Nucleotide/base triplets _1 amino acid → Base triplets of DNA = 1 code_
52
The reading frame in the genetic code system is
* Universal (for each organism) * Confluent (commaless) * Non-overlapping sequence
53
A triplet code can make a genetic code for how many different combinations?
64 (43 = 64)
54
Steps of the central dogma
* DNA code from base triplets * Transcription * tRNA transports amino acids → ribosomes * Translation
55
Transcription
* mRNA synthesis * mRNA base triplets = Codon
56
Base triplets of _tRNA_
Anticodon
57
Translation
Protein synthesis in the ribosome
58
DNA replication
Reduplication of DNA * Forwarding genetic information during cell division
59
What is the structure of DNA during replication?
The double helix is split into _two single strands_ Acts as a template
60
Describe the semi-conservative theory of DNA replication
* Produced double helix is composed of: * 1 parental strand * 1 newly synthesised strand
61
The three phases of DNA replication
1. Initiation 2. Elongation 3. Termination
62
Where does DNA replication of prokaryotes initiate?
The replication origo
63
Replication origo is composed of...
Consensus sequences
64
DNA-A during prokaryote DNA synthesis
* Proteins recognise replication origo * DNA-A binds to DNA-A binding sites
65
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
66
Replication of prokaryotes: Initiation phase (Phase 1)
* Single strand proteins (SSB-proteins) separate the two strands
67
Which group of the DNA is needed for synthesis in prokaryotes
3'-OH-group
68
Primer
* Short RNA sequence * Has a free 3'-OH-group
69
Synthesis of primers is by...
Primosomes
70
Primosome
* Protein complex * Contains _Primase_ * Contains _synthesising primer_
71
Replication of prokaryotes: Elongation phase (Phase 2)
* Continuous & discontinuous synthesis * The building of nucleotides in new strands
72
In prokaryotes, where does continuous synthesis occur?
The leading strand
73
In prokaryotes, where does discontinuous synthesis occur?
The lagging strand
74
A primer + DNA is known as...
_Okazaki-fragment_
75
In prokaryotes, synthesis of the new DNA strand is responsible by...
DNA polymerase III
76
DNA polymerase synthesises in which direction?
From the 5' → 3'
77
The building blocks for new DNA strands
dNTP | (Deoxyribonucleoside triphosphate)
78
How is dNTP made into nucleotides
dNTP → _dNMP_ + 2Pin
79
Replication of prokaryotes: Termination phase (Phase 3)
* DNA polymerase III dissociates * Primers hydrolysed * DNA polymerase I moves between DNA fragments * Ligation of new DNA
80
During prokaryote termination which enzyme will hydrolyse and cut out primers?
DNA polymerase I
81
During prokaryote termination which enzyme ligates new DNA?
DNA ligase
82
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
83
Function of topoisomerases
* Strands become tense during replication * Topoisomerase cuts DNA strand * DNA rotates to remove coils * Topoisomerase rejoins the DNA strands
84
DNA gyrase is a type of...
Topoisomerase
85
How does DNA polymerase act as a dimer?
Simultaneous replication of two DNA strands
86
Where are proteins needed for replication organised?
Replisome
87
The three main differences between eukaryote and prokaryote DNA replication
* Eukaryotes * Numerous replication origos * Distinct DNA polymerase names * Telomeric sequences
88
List the DNA polymerases of Eukaryotes
* DNA polymerase α * DNA polymerase β * DNA polymerase γ * DNA polymerase δ
89
The responsibility of DNA polymerase α
Synthesis of new DNA strand ## Footnote *Acts as the equivalent of DNA Polymerase III in prokaryotes*
90
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*
91
The responsibility of DNA polymerase γ
Replication of mitochondrial DNA
92
The responsibility of DNA polymerase δ
* Synthesis of new DNA strand * Requires _PCNA_ protein for operation
93
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
94
Telomere
* Extra sequence attached to 3' end of chromosome * _Telomerase_ synthesis the telomeric sequences
95
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
96
Mutation
Heritable change of DNA base sequences
97
Types of mutation
* Spontaneous mutation * Induced mutation * Gametic mutation * Somatic mutation * Chromosome mutation * Gene mutation
98
Causes of induced mutation
Caused by physical conditions
99
Gametic mutation
* Mutation in ovum/sperm * Forwarded onto descendants
100
Somatic mutation
* In somatic cells * Causes tumours
101
Gene mutation
* Mostly _point mutation_ * Only a single nucleotide is changed
102
Forms of point mutation
* _Substitution_ mutation * 'Frameshift' mutation: * _Insertion_ * _Deletion_
103
Substitution mutation
A _non-complimentary_ nucleotide is built into the chain rather than a complimentary nucleotide
104
Varieties of substitution mutation
* Missense mutation * Nonsense mutation * Silent/samesense mutation
105
Missense mutation
Mutated base sequence → Different amino acid produced
106
Nonsense mutation
Mutated base → Stop code produced → Translation halts → Produced protein is shorter
107
Silent/samesense mutation
Mutated base → Same amino acid is produced
108
Insertion
Extra nucleotides introduced into the DNA
109
Deletion
Nucleotides missing from the DNA
110
Thymine dimer formation
* UV radiation → covalent bonds between _pyrimidine bases_ * Replication and transcription affected * Mutagenic process → Melanoma
111
Sickle-cell anaemia
* Missense substitution mutation * _β-globin_ gene affected * Change from _Glutamine_ → _Valine_ production * Change is haemoglobin solubility

Miller OnRamps Biology (8 decks)

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