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Genetics > Genetic variation, genomes and mutation > Flashcards

Genetic variation, genomes and mutation Flashcards

Eukaryotic genomes, Human genome, Transposons, variation, single nucleotide polymorphisms, Indels, Replication slippage, evolution of sequencing, mutagens.

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Biology 101 flashcards
1
Q

How many base pairs is the human genome?

A

3,000,000,000

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2
Q

What form are prokaryotic and viral genomes?

A

Circular form.

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3
Q

What kind of genome, out of the previously mentioned ones is the most simple?

A

Viral genome.

Smallest known genome = MS2virus with 3569bp.
Most complex viral genome = Mimivirus with 1,181,000bp.

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4
Q

Therefore, across life, genomes vary in…

A

size.

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5
Q

How are eukaryotic genomes arranged?

A

As linear chromosomes.

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6
Q

Eukaryotes also have organellular genomes. Give an example.

A

Mitochondrial genome = 16500bp of circular DNA.

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7
Q

Human chromosome 22 is 51000bp.
List parts of this chromosome (9).

A
  • Centromere.
  • 2 telomeres (ends of linear chromosomes
    to protect the ends from deterioration and
    prevent them fusing with neighbouring
    chromosomes).
  • Origins of replication.
  • Heterochromatin.
  • Intergenic regions (sections of DNA within
    genes not coding for proteins/RNA).
  • Untranslated regions.
  • Promoters.
  • Introns.
  • Protein-coding regions.
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8
Q

What intergenic regions are in this chromosome?

A

Mostly repeated DNA sequences.

Pseudogenes (similar in sequence to functional genes but don’t produce a functional protein).

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9
Q

What percentage of the human genome is protein coding exons?

A

1.5%

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10
Q

What percentage of the human genome is introns?

A

24%

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11
Q

What percentage of the human genome is non-repetitive DNA (neither introns nor exons)?

A

26%

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12
Q

What percentage of the human genome is LINEs?

A

20%

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13
Q

What percentage of the human genome is SINEs?

A

13%

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14
Q

What percentage of the human genome is retrotransposons?

A

8%

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15
Q

What percentage of the human genome is DNA-only transposons?

A

3%

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16
Q

What percentage of the human genome is STRs?

A

3%

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17
Q

What percentage of the human genome is segment duplications?

A

6%

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18
Q

Approximately 50% of the human genome is unique sequences and the other 50% repeated sequences.
Name the parts of the human genome that are unique sequences and repeated sequences (and of these which are mobile genetic elements).

A

Unique sequences:
- protein coding exons
- introns
- non-repetitive DNA

Repeated mobile genetic elements:
- LINEs
- SINEs
- retrotransposons
- DNA-only transposons

Repeated sequences:
- STRs
- segment duplications

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19
Q

What are LINEs?

A

Long interspersed nuclear elements.
Transposable.

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20
Q

What are SINEs?

A

Short interspersed nuclear elements.
Transposable.

LINEs and SINEs do not transpose through DNA directly; instead, they transpose through an RNA intermediate using a process called retrotransposition.
Do not contain long terminal repeat sequences.

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21
Q

What are retrotransposons?

A

A type of genetic element that can move from one location to another within the genome

Transcription to RNA: The retrotransposon DNA sequence is transcribed into an RNA molecule.

Reverse Transcription to DNA: The RNA intermediate is reverse-transcribed back into DNA by an enzyme called reverse transcriptase, which many retrotransposons encode within their sequence.

Insertion into Genome: This new DNA copy is then inserted into a new location in the genome by an integrase or similar enzyme, effectively duplicating the retrotransposon.

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22
Q

What are STRs?

A

Short Tandem Repeats (STRs), also known as microsatellites, are repeating sequences of 2 to 6 base pairs of DNA that are found throughout the genome.

STRs are highly variable among individuals, making them valuable markers in various genetic studies.

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23
Q

What are transposons known as?

A

Jumping genes.

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24
Q

What did Barbara McClintock discover in 1940 whilst working on plant sciences in cold spring harbour laboratory that earned her the 1983 Nobel Prize in Physiology or Medicine?

A

Carried out genetic experiments in maize using microscopes and noticed if part of the chromosome is dethatched, it can replicate and insert itself into other parts of genome.

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25
Q

What are the two categories of transposon? What are they based on?

A

Cut and paste transposition and replicative transposition.

How they move around.

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26
Q

Describe the mechanism of replicative transposition.

A
  1. transposon transcribed to mRNA
  2. reverse transcribed to dsDNA copy
  3. copy inserted into target DNA
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27
Q

What is variation?

A

Individuals are not genetically identical.

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28
Q

What is an allele?

A

Broadly used term to describe alternative forms of a heritable trait.

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29
Q

Genes and genomes are altered by several different mechanisms.
List 6.

A

Mutation within a gene.
Mutation in regulatory DNA.

Gene duplication and divergence.
Exon shuffling.
Transposition.
Horizontal transfer.

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30
Q

What are single nucleotide polymorphisms (SNPs)?

A

Variations at a single nucleotide position in the DNA sequence among individuals of a species.

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31
Q

What is human genomic variation?
How is this determined?

A

How many single nucleotide differences there are between any two humans.

Reference and other genome sequence are compared.

32
Q

In 2001, the first human genome sequence was published.

In 2007, James Watson’s genome was sequenced.
How many differences relative to the human genome project reference was there in his genome?

A

3.3 million nucleotide differences.

~ 0.1% of genome was different to James
Watson’s

33
Q

How many SNPs are there in humans?

A

~ 10 million

~ 1% SNP rate vs chimpanzee

34
Q

What are indels?

A

Insertions/deletions.

35
Q

How many indel polymorphisms are identified in the human genome?

A

~ 4 x 10^5

30% of these are tandem repeat expansion polymorphisms (copy of number of back to back repeats increases).

36
Q

30% of these are tandem repeat expansion polymorphisms (copy of number of back to back repeats increases).

What can occur when this goes wrong?

A

Huntington’s disease.

37
Q

How can indels be analysed?

A

PCR and gel electrophoresis.

38
Q

Why are STRs used in genetic profiling (forensic and maternity testing)?

A

They are multi-allelic (multiple variants exist at locus).

39
Q

What results in a strand having an extra nucleotide?

A

Newly synthesised strand loops out so one nucleotide is added on the new strand.

39
Q

What generates STRs?

A

Replication slippage.

40
Q

What results in a strand missing a nucleotide?

A

Template strand loops out so one nucleotide is omitted on the new strand.

41
Q

Why does most genetic variation have no phenotypic effect?

A

It may fall in and intergenic region or a non-coding region of a gene (introns/promoter).

42
Q

If variation occurs in a UTR, what might this affect?

A

Gene expression (due to having affect on regulatory elements and mRNA stability).

43
Q

Variation may have various effects if it occurs in the region of a gene coding for…

A

proteins.

44
Q

How can base substitutions affect coding regions of a gene?

A

Silent/synonymous (change does not alter the amino acid sequence of the resulting protein).

Missense/non-synonymous.

45
Q

In a missense base substitution, what does non-conservative refer to?

A

If the amino acid is acid and changes to basic and visa versa.

Specifically when the substituted amino acid has different biochemical properties (like size, charge, or hydrophobicity) to the original.

46
Q

What is a mutation called between purines (or between pyrimidines)?

A

transitions

47
Q

What is a mutation called from purine to pyrimidine or visa versa?

A

transversions

48
Q

Sickle cell anemia involves a base pair change from A to T in the human beta haemoglobin gene. What is this disorder?

A

A single nucleotide polymorphism with a phenotypic effect.

49
Q

What is the effect of inserting 1 base/deleting 1 base/deleting 2 bases to a wildtype coding region of the genome?

A

Frameshift.

50
Q

Why would deletion of 3 bases together not cause a frameshift?

A

The rest of the protein would still be the same.

51
Q

What are these examples of?

Cystic fibrosis is due to deletion of CTT in human CFTR (cystic fibrosis transmembrane regulator) gene.
CF mucus in the lungs affects oxygen carrying capacity of individual.

Oculocutaneous albinism due to insertion of 1 base pair T-A.

A

Indels with phenotypic effects.

52
Q

What are Mendelian/Monogenic diseases?

A

Genetic disorders caused by single gene mutation.

There are more than 3000 in humans and most are rare.

53
Q

Many common human diseases are influenced by genetic factors as well as…

A

environmental conditions.

54
Q

Give 3 methods that illustrate the evolution of sequencing.

A

First generation
Second/next generation
Third generation

55
Q

Describe first generation sequencing.

A
  • Short read sequencing.
  • Sanger sequencing, Maxam and Gilbert,
    Sanger chain termination.
  • Infer nucleotide identity using dNTPs, then
    visualise with electrophoresis.
  • 50-1000bp fragments.
  • Relatively slow and expensive (single
    sequence ~ £4).
56
Q

Describe next/second generation sequencing.

A
  • Short read sequencing.
  • 454, Solexa, Ion Torrent Illumina.
  • High throughput from the parallelization
    of sequencing reactions.
  • High accuracy.
  • 50-500bp fragments.
  • Faster and more affordable.
57
Q

Describe third generation sequencing.

A
  • Long read sequencing.
  • PacBio, Oxford Nanopore.
  • Sequence native DNA in real time with
    single-molecule resolution.
  • Traditionally lower accuracy than next
    generation sequencing.
  • Tens of kb (kilo base) fragments.
58
Q

How does Oxford Nanopore sequencing work?

A

DNA is passed through a small flow cell with nanopore proteins attached on a strip.
Signal decoded to find sequence because each base gives a different kind of signal.

Finds out entire genomes in short time.

59
Q

Errors occur during DNA replication but cells have many mechanisms to prevent and correct…

A

Mutations.

60
Q

List 4 of these mechanisms.

A

Proofreading DNA polymerase(s).
Post-replication mismatch repair.
DNA repair by homologous recombination.
Cell cycle checkpoints.

61
Q

Uncorrected errors are passed on as mutations to…

A

daughter cells.

62
Q

Germline cells produce gametes so mutations can be passed to…

A

offspring.

63
Q

Somatic cell mutations are a common cause of…

A

Cancers.

64
Q

What do somatic cell mutations affect in an individual?

A

A small proportion of tissue.

65
Q

What can mutagens do?

A

Cause mutations as a result of DNA damage.

66
Q

UV radiation damage from the sun can lead to point mutations.
What are point mutations?

A

Change in single nucleotide base pair in DNA sequence.

67
Q

Give 6 examples of chemical mutagens.

A

Intercalating agents
Base analogues
Base modifying agents
Hydroxylating agents
Deaminating agents
Alkylating agents

68
Q

What are intercalating agents?

A

Planar molecules that insert between base pairs e.g. proflavin and acridine orange cause frameshift mutations.

69
Q

What are base analogues?

A

Similar molecular structure to bases and incorporated into DNA in place of normal base but might form different base pairings.
e.g. 5-bromouracil is an analogue of thymine but can also base pair with guanine.

70
Q

What are base modifying agents?

A

Covalently alter a base causing it to mis pair (base substitution).

71
Q

What do hydroxylating agents do?

A

Add hydroxyl (-OH) groups.

72
Q

What do deaminating agents do?

A

Remove amino (-NH2) groups.
For example when NH2 is removed from cytosine it is converted to uracil so G is changed to an A.

73
Q

What do alkylating agents do?

A

Add alkyl groups (-CH3 or -CH3CH2).
For example ENU/EMS converts guanine to O-6-Ethyl guanine which can pair with thymine so a C is replaced with an A.
MMS acts similarly but adds a methyl group.

Also ethylation of thymine causes it to pair with guanine changing an A to a C.

ENU = ethyl nitrosourea
EMS = ethyl methanesulphonate
MMS = methyl methanesulphonate

74
Q

Mutant E.coli cell requires histidine to proliferate.
Caused mutation in His gene to become inactive because a mature stop codon in the mRNA means the enzyme required to make histidine is eliminated.

Explain how to measure mutation rates in the lab.

A

Inoculate and culture mutant E.coli in a medium containing histidine to allow them to multiply.

As cells divide, random mutations arise spontaneously.

Spread a sample of cells on a Petri dish containing a medium lacking histidine.

Rare colony of cells that contains new mutation enables proliferation in absence of histidine.

The new mutation restores production of enzyme required to make histidine.

Count the mutant colonies on each plate, which represent cells where the mutation occurred.
Calculate the mutation rate using the following formula:
Mutation rate = (number of mutants) / (total cell population × number of generations).

Genetics (10 decks)

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