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GAG WK6 Flashcards

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1
Q

What are the two main forms of chromatin in the human genome?

A
  • euchromatin
  • heterochromatin
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2
Q

What are features of euchromatin

A

Less compact, accessible to transcription factors.

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3
Q

What are features of heterochromatin

A

More compact, less accessible to transcription factors.

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4
Q

What are the two types of heterochromatin?

A
  • facultative heterochromatin
  • constitutive heterochromatin
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5
Q

What is facultative heterochromatin

A

heterochromatin can change its structure to be less condensed

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6
Q

What is constitutive heterochromatin

A

heterochromatin that remains consistently condensed

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7
Q

What post-translational histone modifications define heterochromatin?

A
  • H3K9me3
  • H3K27me3
  • histone methylation
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8
Q

What is the effect of heterochromatin on chromatin structure and gene expression?

A

Heterochromatin tightly condenses chromatin, resulting in less gene expression

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9
Q

How many genes are in the human mitochondrial genome, and what do they code for?

A
  • 37 genes
  • 24 genes code for rRNA and tRNA
  • 13 genes code for energy production
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10
Q

What are satellite DNAs

A

tandem repeats

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11
Q

how are centromeric and telomeric repeats conserved?

A
  • centromeric = highly conserved
  • telomeric = poorly conserved
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12
Q

What are transposons

A

segments of DNA that can move around within the genome

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13
Q

What is the function of transposons?

A
  • they can insert themselves in genes and either
  • introduce new genetic variation
  • disrupt genetic variation
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14
Q

How do retrotransposons transpose, and what enzyme do they require?

A
  • use an RNA intermediate
  • need a reverse transcriptase
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15
Q

What are pseudogenes

A

non-functional copies of gene

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16
Q

How are pseudogenes formed?

A

A gene can be duplicated, and one copy may accumulate mutations preventing it from functioning properly and forming a pseudogene

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17
Q

What is the evolutionary significance of gene duplications that lead to pseudogenes?

A

they can mutate allowing for genetic diversity without affecting overall function (and the original gene is functional)

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18
Q

What are the two types of pseudogenes?

A
  • Unprocessed pseudogenes
  • Processed pseudogenes (retropseudogenes)
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19
Q

What are unprocessed pseudogenes

A
  • the result of recent gene duplication
  • they retain introns and other regulatory sequences of original gene
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20
Q

Where are unprocessed pseudogenes located

A

located near the original gene copy

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21
Q

How are unprocessed pseudogenes formed

A

Arise from unequal recombination events that lead to gene duplication

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22
Q

What are processed pseudogenes (retropseudogenes)

A
  • they are pseudogenes that have been inserted into the genome via reverse transcriptase
  • they don’t have introns
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23
Q

How are processed pseudogenes formed

A

formed from RNA through reverse transcription

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24
Q

What role do processed pseudogenes play in genetic diversity?

A
  • Can mediate exon shuffling by incorporating exons into new genes
  • Provide genetic backup for the original gene
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25
Q

How do processed pseudogenes facilitate evolution?

A
  • If retrotranscription extends past a weak polyadenylation signal, an exon can be incorporated into a new gene.
  • The second gene can mutate without affecting the original gene’s function
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26
Q

What does Metacentric mean

A

Centromere is in the middle

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27
Q

What does Submetacentric

A

Centromere is off-center.

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28
Q

What does Acrocentric

A

Centromere is near the end

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29
Q

What does Telocentric

A

Centromere is at the end.

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30
Q

What do the chromosome arms “p” and “q” represent?

A
  • p: Short arm of the chromosome.
  • q: Long arm of the chromosome
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31
Q

What is a banding system

A

each chromosome is further divided into bands and sub-bands for detailed identification

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32
Q

What does “proximal” refer to in chromosome nomenclature?

A

Proximal means closer to the centromere.

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33
Q

What does “distal” refer to in chromosome nomenclature?

A

Distal means further away from the centromere.

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34
Q

What is a deletion in chromosomal changes?

A

A segment of a chromosome is lost.

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35
Q

What is a duplication in chromosomal changes?

A

A segment of a chromosome is copied and inserted.

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36
Q

What is an inversion in chromosomal changes?

A

A segment of a chromosome is reversed end to end.

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37
Q

What is a translocation in chromosomal changes?

A

A segment of one chromosome is transferred to another chromosome.

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38
Q

What are the effects of chromosomal changes?

A
  • looping in meiosis
  • haploinsufficiency
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39
Q

What is looping in meiosis

A
  • chromosomes can loop
  • leads to unequal segregation of genetic material
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40
Q

What is the cause of looping in meiosis

A

deletions and duplication chromosomal changes

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41
Q

What is haploinsufficiency?

A

A condition where only one functional copy of a gene is present (due to deletion), and this single copy is not sufficient to maintain normal function

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42
Q

How can deletions occur due to incorrect double-strand break (DSB) repair?

A

Errors in repairing double-strand breaks in DNA can cause deletions

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43
Q

Name 2 ways tandem repeats lead to chromosomal changes?

A
  • unequal crossover
  • repeat expansion
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44
Q

Explain how unequal crossover can lead to chromosomal changes

A

Tandem repeats can cause unequal crossover, resulting in reciprocal deletions or duplications.

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45
Q

Explain how repeat expansion can lead to chromosomal changes

A

Replication fork slippage can expand these repeats, potentially leading to genetic diseases.

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46
Q

What is Non-Allelic Homologous Recombination (NAHR)?

A

when homologous regions that are not alleles recombine, leading to the loss or duplication of genetic material between repeats.

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47
Q

What are Low Copy Number Repeats (LCRs)

A

homologous regions in the genome.

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48
Q

how do Low Copy Number Repeats relate to NAHR?

A

NAHR between LCRs can cause variations in gene copy numbers and contribute to deletions.

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49
Q

What is a tandem duplication?

A

duplicated DNA segment located next to the original segment

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50
Q

What is a displaced duplication?

A

A duplicated DNA segment on the same chromosome but not adjacent to the original segment.

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51
Q

What is a reverse duplication?

A

A duplicated DNA segment that is inverted (flipped) compared to the original segment

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52
Q

What is a displaced reverse duplication?

A

An inverted duplicated DNA segment located at a distance from the original segment.

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53
Q

What are the effects of duplications on chromosomes?

A
  • unstable pairing
  • intra-chromosomal recombination recombination
  • copy number variations
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54
Q

Explain unstable pairing as an effect of duplication

A

Duplicated segments can align in various ways during meiosis, causing different pairing outcomes

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55
Q

Explain intra-chromosomal recombination as an effect of duplication

A

May lead to excision (removal) of the duplicated segment.

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56
Q

Explain the copy number variations as an effect of duplication

A

Can cause differences in gene copy numbers, potentially leading to gene imbalances.

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57
Q

What is an inversion in chromosomal changes?

A

An inversion is when a segment of DNA is reversed in orientation.

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58
Q

What are the two types of inversions?

A
  • Paracentric inversion: Does not include the centromere.
  • Pericentric inversion: Includes the centromere.
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59
Q

What are the effects of inversions on DNA?

A
  • No DNA loss
  • Gene disruption
  • altered gene expression
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60
Q

Explain the no loss of DNA as an effect of inversion

A

Inversions do not involve DNA loss but can have phenotypic effects

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61
Q

Explain the gene disruption as an effect of inversion

A

Inversion points may disrupt or fuse genes.

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62
Q

Explain altered gene expression as an effect of inversion

A

Genes within the inversion may be affected due to changes in position relative to regulatory elements

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63
Q

Provide an example of a phenotypic effect caused by an inversion.

A

In haemophilia A, about 50% of cases are caused by a large inversion disrupting the F8 gene, essential for blood clotting.

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64
Q

What is the effect of inversions during meiosis?

A

Inversions can suppress recombinants, hindering proper recombination and affecting genetic diversity.

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65
Q

What is a translocation in chromosomal changes?

A

A translocation is the rearrangement of chromosome segments.

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66
Q

What are the three types of translocations?

A
  • reciprocal translocation
  • non-reciprocal translocation
  • robertsonian translocation
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67
Q

What is reciprocal translocation

A

Segments from two different chromosomes exchange places.

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68
Q

What is non-reciprocal translocation

A

A segment from one chromosome is transferred to another without reciprocal exchange.

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69
Q

What is Robertsonian translocation:

A

Fusion of two acrocentric chromosomes at their centromeres, forming a single chromosome

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70
Q

What is the basic nature of DNA replication?

A

DNA replication is semi-conservative, producing two DNA molecules, each with one parental and one newly synthesised strand.

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71
Q

How many origins of replication do eukaryotic genomes have

A

30,000 to 50,000 origins of replication

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72
Q

What is the function of origins of replication

A

where DNA replication begins.

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73
Q

How does DNA replication proceed from each origin?

A

DNA replication is a bi-directional process

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74
Q

What is the difference between the leading and lagging strands during DNA replication?

A
  • Leading strand: Synthesised continuously.
  • Lagging strand: Synthesised discontinuously in short segments called Okazaki fragments.
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75
Q

What is required to initiate DNA synthesis?

A

DNA polymerase requires a primer, which is synthesised by primase and extended by DNA polymerase alpha.

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76
Q

What causes the end replication problem?

A
  • DNA synthesis is in the 5’ to 3’ direction.
  • RNA primer at the end of the lagging strand leaves a terminal gap because no upstream template is available for extension
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77
Q

What are telomeres

A

repetitive DNA sequences at the ends of eukaryotic chromosomes

78
Q

What are the effects of the single-stranded overhang at telomeres?

A
  • Lagging telomere loss
  • Leading telomere shortening
79
Q

Explain lagging telomere loss

A

Slight sequence loss with each replication due to primer remova

80
Q

Explain leading telomere shortening

A

Significant loss (100-200 nucleotides) due to the lack of a template.

81
Q

What is the solution to the end replication problem?

A

Telomerase, a reverse transcriptase, extends telomeres by adding back lost sequences

82
Q

How does telomerase function?

A
  • Telomerase uses its RNA template to synthesise telomeric DNA repeats
  • This helps maintain chromosome length during cell division
83
Q

Why is genetic variation important?

A

Genetic variation is the foundation of evolution, providing raw material for natural selection

84
Q

What is a mutation?

A

a structural change in a gene’s DNA sequence.

85
Q

What are the two main types of point mutations?

A
  • transitions
  • transversions
86
Q

What are Transitions point mutations

A

Change between two purines (A↔︎G) or two pyrimidines (C↔︎T).

87
Q

What are transversion point mutations

A

Change between a purine and pyrimidine (A↔︎C or G↔︎C).

88
Q

What is an insertion mutation?

A

The addition of one or more nucleotides in a DNA sequence.

89
Q

What is a deletion mutation?

A

The removal of one or more nucleotides in a DNA sequence

90
Q

What are two primary sources of mutations?

A
  • Errors during DNA replication.
  • External factors like mutagens
91
Q

How do organisms limit harmful genetic variation?

A

Through DNA repair mechanisms that repair and prevent harmful changes.

92
Q

Name the types of DNA repair

A
  • direct repair
  • base excision repair
  • nucleotide excision repair
  • mismatch repair
  • double-strand break repair
93
Q

What is direct repair

A

Reversal of specific DNA damage (e.g., photoreactivation).

94
Q

What is base excision repair

A

Repairs lesions caused by oxidative damage.

95
Q

What is nucleotide excision repair

A

Repairs lesions caused by UV radiation.

96
Q

What is mismatch repair

A

Corrects replication errors.

97
Q

What is double-strand break repair

A

Fixes breaks using homologous recombination or non-homologous end joining.

98
Q

What is replication fork slippage, and what does it cause?

A

Replication fork slippage occurs in DNA repeat regions when DNA polymerase slips, causing misalignments that lead to insertions or deletions of repeats

99
Q

What can replication fork slippage lead to?

A

It can cause frameshift mutations

100
Q

What are nucleotide repeat expansion diseases?

A

Diseases caused by DNA repeat expansion in a gene, often due to replication fork slippage.

101
Q

Provide an example of a nucleotide repeat expansion disease.

A

Huntington’s disease

102
Q

What is endogenous DNA damage?

A

Damage caused by internal agents within cells

103
Q

What are the primary endogenous agents that damage DNA?

A
  • water
  • methylation
  • reactive oxygen species
104
Q

How does water damage DNA

A

Causes hydrolytic damage, leading to DNA breaks.

105
Q

What types of damage are caused by oxidative stress?

A
  • Strand breakage: Causes single or double-strand breaks in DNA.
  • Base attacks: Damages purine bases.
106
Q

What happens when guanine is oxidised?

A

Oxidised guanine can pair incorrectly with adenine via Hoogsteen base pairing, leading to mismatches and potential mutations.

107
Q

What is the primary role of DNA polymerase during replication?

A

DNA polymerase synthesises the new strand of DNA, selects the correct nucleotide, and improves fidelity through proofreading using exonuclease activity

108
Q

How does DNA polymerase proofread DNA?

A

It uses exonuclease activity to remove incorrectly placed nucleotides and replace them with the correct ones.

109
Q

What happens if DNA polymerase fails to correct a mismatch?

A

Post-replication mismatch repair (MMR) pathways correct misincorporated nucleotides.

110
Q

What are base tautomers?

A

alternative structural forms of DNA bases

111
Q

Compare the normal and rare forms of tautomers

A
  • Normal forms: Stable and pair normally.
  • Rare forms: Less stable and can cause spontaneous mutations by incorrect pairing.
112
Q

What is an example of tautomerisation at GC base pairs?

A

Guanine can shift to its enol form, leading it to mispair with thymine instead of cytosine

113
Q

What is an example of tautomerisation at AT base pairs?

A

Adenine can shift to its imino form, leading it to mispair with cytosine instead of thymine

114
Q

Why can’t DNA polymerase synthesise DNA in the 3’ to 5’ direction?

A
  • no high-energy bond to drive the reaction
  • Proofreading would be impossible, as removing an incorrect nucleotide would leave no way to continue synthesis
115
Q

Why is 5’ to 3’ synthesis energetically favourable?

A

High-energy phosphate bonds in dNTPs provide the energy needed for forming bonds during synthesis.

116
Q

What is depurination?

A

Loss of a purine base (adenine or guanine) from DNA due to glycosidic bond cleavage.

117
Q

What is depyrimidination?

A

Loss of a pyrimidine base (cytosine or thymine) from DNA due to glycosidic bond cleavage.

118
Q

What is deamination, and what does cytosine deamination produce?

A

Deamination converts cytosine to uracil, which is found in RNA but not DNA.

119
Q

How does the base excision repair pathway handle cytosine deamination?

A

It removes uracil to prevent mutations

120
Q

What happens during methylated cytosine deamination?

A

Methylated cytosine is converted to thymine, resulting in a C to T mutation, corrected by the mismatch repair pathway.

121
Q

What is the role of methyltransferases in methylation?

A

Methyltransferases add methyl groups to cytosines using S-adenosylmethionine as the methyl donor.

122
Q

What is an example of non-enzymatic methylation?

A

Formation of 3-methyladenine, which distorts DNA and impairs replication and transcription.

123
Q

What are mutagens?

A

Agents that cause induced mutations by altering DNA.

124
Q

What are the 2 types of mutagens

A
  • chemical mutagens
  • physical mutagens (ex: UV light)
125
Q

What are base analogues?

A

Base analogues resemble normal DNA bases but are prone to tautomeric shifts, causing incorrect base pairing.

126
Q

Give an example of a base analogue

A

5-bromouracil (5-Br-dU) substitutes for thymine but can pair incorrectly.

127
Q

What do deaminating agents do to DNA?

A

Remove amino groups from bases, altering their pairing properties.

128
Q

What is an example of a deaminating agent, and what does it produce?

A
  • nitrous acid
  • Deamination of adenine produces hypoxanthine, which pairs with cytosine, causing T to C transitions.
129
Q

What do alkylating agents do

A
  • Add alkyl groups to DNA bases, altering base pairing and causing point mutations
130
Q

Give an example of alkylating agents

A

Ethyl methane sulfonate (EMS).

131
Q

What are intercalating agents

A

Molecules that insert between DNA bases, disrupting spacing and leading to insertion mutations.

132
Q

Give an example of intercalating agents

A

Ethidium bromide.

133
Q

How does UV radiation damage DNA?

A
  • Causes pyrimidine dimers
  • Leads to replication machinery skipping or deleting bases.
134
Q

What effect does heat have on DNA?

A
  • accelerates hydrolysis of glycosidic bonds, causing loss of bases and forming AP sites.
  • AP sites can lead to replication errors
135
Q

What is the effect of ionising radiation on DNA?

A

Causes severe DNA damage, including double-strand breaks, depending on type and intensity

136
Q

Why is DNA repair important?

A
  • To correct spontaneous damage (e.g., base loss, deamination, alkylation)
  • protect against environmental and metabolic damage, maintaining genome stability.
137
Q

What does S-Adenosylmethionine (SAM) do to DNA?

A

Acts as a weak alkylating agent, causing methylation

138
Q

What are common sources of DNA damage?

A
  • Endogenous damage: oxidative stress, hydrolysis, methylation.
  • Environmental sources: UV light, chemicals.
  • Replication errors during DNA synthesis.
139
Q

What are the disease features of DNA repair defects?

A
  • Cancer susceptibility: Increased mutation rates.
  • Progeria: Accelerated ageing due to telomere defects.
  • Neurological features: Neurodegeneration and neuronal death.
  • Immunodeficiency: Impaired immunoglobulin and T-cell receptor production.
140
Q

Why do eukaryotic genomes require robust DNA repair mechanisms?

A

To address both internal DNA damage (oxidative stress, hydrolysis, methylation) and external exposures (UV light, chemicals)

141
Q

What type of damage does Base Excision Repair (BER) address?

A

Corrects modified bases and AP sites caused by depurination and depyrimidination.

142
Q

What are the steps in BER?

A
  • Recognition
  • Cleavage
  • Backbone Cut:
  • Gap Filling:
  • Sealing:
143
Q

What happens during the recognition step of BER

A

DNA glycosylase identifies the damaged base.

144
Q

What happens during the cleavage step of BER

A

Glycosylase cleaves the N-glycosidic bond, creating an AP site.

145
Q

What happens during the backbone cut step of BER

A

Endonucleases/phosphodiesterases cut at the AP site

146
Q

What happens during the gap filling step of BER

A

DNA polymerase inserts the correct nucleotide.

147
Q

What happens during the sealing step in BER

A

DNA ligase seals the DNA strand.

148
Q

What type of damage does Nucleotide Excision Repair (NER) address?

A

Repairs bulky lesions that distort the DNA helix

149
Q

What are the steps in NER?

A
  • Detection
  • unwinding
  • excision
  • synthesis
  • sealing
150
Q

What happens during the detection during NER

A

Proteins identify DNA helix distortion.

151
Q

What happens during the uwinding step of NER

A

Helicases unwind DNA around the lesion.

152
Q

What happens during the excision step of NER

A

Nucleases remove a 24-32 nucleotide segment.

153
Q

What happens during the synthesis step of NER

A

DNA polymerase fills in the missing nucleotides

154
Q

What happens during the sealing step of NER

A

DNA ligase restores the DNA strand.

155
Q

What type of errors does Mismatch Repair (MMR) correct?

A

Corrects mismatches, small insertions, and deletions during DNA replication

156
Q

What are the steps in MMR?

A
  • Recognition
  • Incision
  • Excision
  • Synthesis
  • Sealing:
157
Q

What happens during recognition step of MMR

A

Proteins identify the mismatch or small insertion/deletion

158
Q

What happens during the incision step of MMR

A

PMS2 nuclease cuts near the mismatch site.

159
Q

What happens during the excision step of MMR

A

Exo1 exonuclease removes the incorrect bases.

160
Q

What happens during the synthesis step of MMR

A

DNA polymerase inserts the correct bases.

161
Q

What happens during the sealing step of MMR

A

DNA ligase seals the gap

162
Q

What causes single-stranded DNA breaks

A

Caused by replication errors or oxidative damage.

163
Q

How are single-stranded DNA breaks repaired

A
  • Simple damage: DNA ligase seals the break.
  • Complex damage: PARP detects the break and recruits repair machinery.
164
Q

What is Non-Homologous End Joining (NHEJ)

A

Directly ligates two free DNA ends without a template.

165
Q

what are its pros and cons of NHEJ

A
  • Pro: Functions even without a homologous DNA template.
  • Con: Error-prone, may introduce small insertions or deletions.
166
Q

How does Homologous Recombination (HR) repair double-stranded breaks?

A
  1. Broken ends are prepared for recombination.
  2. Single-stranded DNA invades homologous DNA to find a complementary sequence.
  3. DNA polymerase extends the strand using homologous DNA as a template.
  4. Recombination structures are resolved, and DNA ligase seals gaps.
167
Q

what is a locus

A

position of a gene

168
Q

what is an allele

A

version of a gene

169
Q

what does amorph mean

A

mutation leads to a loss of gene function

170
Q

what does hypomorph mean

A

mutation that leads to reduced gene function

171
Q

What does hypermorph mean

A

increased gene function

172
Q

What does neomorph mean

A

new gene function

173
Q

What does antimorph

A

dominant allele inhibits the function of wild-type gene

174
Q

What is anticipation in telomerase-related disorders?

A

Disease worsens or appears earlier in successive generations due to progressive telomere shortening.

175
Q

What are null mutations,

A

Null mutations result in a complete loss of gene function

176
Q

How do null mutations occur

A
  • nonsense mutations
  • splicing mutations
  • partial deletions
  • missense mutations
177
Q

What is a gain-of-function mutation?

A

A mutation that causes a gene to be abnormally activated, leading to altered function or expression.

178
Q

What is the effect of gain of function mutation

A

May result in proteins that are:
- Continuously active.
- Expressed in inappropriate cell types or at incorrect times.
- Responsive to inappropriate signals.

179
Q

Provide an example of a gain-of-function mutation in disease

A
  • Chronic Myeloid Leukemia (CML)
  • The fusion protein is constitutively active, promoting uncontrolled cell growth and leading to leukemia.
180
Q

What is pathogenic load

A

Most mutations are not harmful.

181
Q

Why are nonsense and frameshift mutations easier to identify as harmful?

A

They drastically alter protein structure, making their effects more predictable compared to other mutation types

182
Q

How are missense mutations evaluated for pathogenicity?

A
  • Assessed based on evolutionary conservation of the affected amino acid.
  • Highly conserved residues are more likely to have harmful mutations
183
Q

Why are noncoding RNA mutations challenging to assess for pathogenicity?

A

Noncoding RNAs are poorly conserved.

184
Q

What is the redundancy of the genetic code

A

The genetic code’s redundancy allows for mutations that do not change the resulting amino acid.

185
Q

What are conservative mutations

A

Replace an amino acid with one of similar properties.

186
Q

How do conservative mutations effect vary

A
  • Protein Position: Mutations in active sites are more disruptive.
  • Amino Acid Properties: For example, proline disrupts alpha helices, affecting protein structure.
187
Q

What is nonsense-mediated decay (NMD)

A

NMD detects and degrades mRNA with premature stop codons to prevent harmful truncated protein production

188
Q

what is the purpose of NMD?

A

Prevents dominant negative effects by eliminating defective transcripts

189
Q

What are splice site mutations

A

Mutations in critical splicing sequences disrupt normal splicing.

190
Q

what are the consequences of splice site mutations

A
  • Exon Skipping: Exons are omitted, altering protein structure.
  • Intron Retention: Introns are retained, usually creating nonfunctional proteins.
191
Q

What are cryptic splice sites

A

Mutations that create new, non-standard splice sites

192
Q

how do cryptic splice sites affect splicing?

A
  • Produce truncated or extended exons.
  • May result in frameshifts or altered protein function.

Human Genomics & Genetics (7 decks)

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