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Genetics > GENE 4: Comparing the genome > Flashcards

GENE 4: Comparing the genome Flashcards

1
Q

Name two genome browsers

A

UCSC and Ensembl

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2
Q

How do you define genomic position for UCSC and Emsembl

A

Genomic position is defined as: chr:start-end
e.g. chr3:36993332-37050918
this defines the region between the 36993332th and the 37050918th nucleotide on chromosome 3

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3
Q

Except for displaying linear sequence of DNA what can genome browsers show?

A

Annotated genes
Transcript isoforms
CpG rich islands

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4
Q

What is the purpose of UCSC and Emsembl?

A

To calculate the similarity of genomic sequences between species

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5
Q

Similar sequences in the genome between species are known as?

A

Orthologs

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6
Q

What does ‘Cons 100 Verts’ determine?

A

It is the 100 vertebrates basewise conservation by phyloP and its a track that shows a histogram denoting the degree of conservation across different species

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7
Q

What does alignment mean?

A

A match between two sequences: these can be exact matches or have a few mismatches or gaps

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8
Q

What is BLAST used for?

A

Computational analysis of sequences alignments. It can determine whether there will be off-target effects of a homology-based molecular tool (e.g. PCR primers or CRISPR gRNAs)

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9
Q

Give two names of tools used for alignment analysis

A

BLAST and CLUSTAL omega

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10
Q

What is CLUSTAL omega used for? What do results show?

A

alignment of multiple genomic sequences that are input. If all input sequences have an identical base, it is denoted by an asterisk(*), if there are gaps they are denoted by a dash (-)

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11
Q

What are the features of optimal alignment?

A
  • Most bases matching
  • fewest gaps
  • smallest gaps
  • fewest mismatches
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12
Q

What was found when comparing the DNA of mice, humans, fruit fly and yeast using CLUSTAL?

A

Some regions are identical across the four genomes

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13
Q

Why were conserved regions not seen within introns in yeast?

A

Yeast genome do not have introns

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14
Q

What do conserved sequences between species suggest?

A

That there must be a reason they have remained unchanged in the millions of years of evolution and genetic variation. Sequences which are highly conserved include protein-coding sequences and regulatory regions, such as enhancers.

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15
Q

Why are phylogenetic trees generated?

A

To examine the relationships between the species and estimate their branch-points in evolution

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16
Q

What tool can be used to upload an alignment file to determine the phylogenetic relationship between species?

A

EBI simple phylogeny

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17
Q

What does EBI simple phylogeny data show?

A

Distances between the species represents the differences between them. Thus, looking at the tree we can see that Human and Mouse are related closely and that the Fruit fly sequence diverged from mammalian.

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18
Q

What do mechanisms of genetic change mostly involve?

A

Base substitutions and structural rearrangements that are mostly deleterious resulting in an organism less-suited to its environment.

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19
Q

Name the different types of genetic mutations

A 
deletion
duplication
translocation
insertion
inversion 
substitution
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20
Q

What is the most common mechanism of genomic change?

A

Recombination which occurs during prophase I

21
Q

Give 3 reasons why recombination is a successful way of introducing genetic diversity

A
  • Parental chromosomes came from organisms able to survive to reproductive age thus incorporating changes between them is unlikely to be deleterious
  • By occurring in germ cells, the changes can be passed to future generations
  • No risk of random mutation
22
Q

Why does recombination not occur in cells in prophase for mitosis?

A

Differences in chromosome shape

23
Q

Explain why recombination is able to occur during prophase I, name the proteins holding the chromosomes together

A

Meiotic chromosomes form denser structures and line up as bivalents allowing all 4 copies of a gene to align. The maternal and paternal chromosomes are held together by the cohesion complex following replication. The maternal and paternal chromosomes are held to each other at branch points, known as chiasmata, wherein recombination can occur.

24
Q

What happens with the chromosomes for people with down syndrome?

A

Chromosome 21 does not segregate properly resulting in a zygote with an extra chromosome 21

25
Q

What happens in Charcot-Marie-Tooth disease?

A

An incurable neurological disease caused by duplication of the PMP22 gene on chromosome 17

26
Q

How does duplication of the PMP22 gene on chromosome 17 occur? (Charcot-Marie-Tooth disease)

A

Misdirected recombination due to 2 similar repetitive regions flanking a gene

27
Q

Name 4 types of repetitive regions which could be responsible for misalignment of chromosomes prior to recombination

A

LINEs
SINEs
LTRs
STRs

28
Q

What could misalignment of chromosomes prior to homologous recombination lead to?

A

Duplication of a gene in one gamete and the deletion of the gene in the other

29
Q

The globin genes are an example of a _______

A

gene family

30
Q

How did the globin gene family arise?

A

If the single ancestral globin gene was duplicated during recombination, the resulting offspring would have two copies of the gene. Transposition to different chromosomes occurred. The two gene copies could then accumulate separate sequence changes, causing them to become two slightly different versions of the gene a-globin and b-globin. These families develop if possessing multiple specialised versions of a given protein confers a selective advantage.

31
Q

What are pseudogenes within gene families assumed to be?

A

Evolutionary dead-ends as the regions have mutated to become non-functional

32
Q

Why would pseudogenes still be conserved?

A

If they have mutated again to form advantageous regulatory structures such as non-coding RNA or transcription factor binding sites

33
Q

Give an example of how genes can be passed between species

A

Viral genes being incorporated into host genomes if they are beneficial. Retrotransposons are highly repetitive DNA that are transcribed into mRNA and then reverse transcribed into the DNA.

34
Q

What are retrotransposons?

A

Highly repetitive DNA that are transcribed into mRNA and then reverse transcribed into the DNA.

35
Q

Give two theories about the relationship between retrotransposons and retroviruses

A

1) an endogenous retrovirus that was thought to have been a virus that infected humans then lost its pathogenic effect. It then mutated and transposed around the genome until beneficial regulatory effects were realised.
2) Transposable elements became retroviruses after developing a means to leave the host cell.

36
Q

How do bacteria, viruses and cancer cells develop resistance to drugs

A
  • variation in population
  • beneficial mutations
  • positively selected for
  • due to environmental selection pressure
37
Q

How many base pairs in human genome?

A

3 billion

38
Q

What do conserved identical sequences across species indicate? why?

A

That specific sequence is essential for survival, the lack of alternative sequences suggests a strong selection pressure to retain this exact sequence.

39
Q

How do you compare genomes?

A

The varying positions of the same gene in different genomes can be found and compared/studied

40
Q

What is the driving force for evolution of complex organisms by chromosome rearrangement/recombination?

A
  • gene gets duplicated} generating offspring with 2 copies of the same gene on 1 chromosome
  • over time, the 2 copies diverge and accumulate different sequence changes to form two similar but distinct genes
  • further chromosome rearrangement may result in the two genes being located on different chromosomes where they may duplicate and diverge further
41
Q

What % of the human genome do retrotransposons make up?

A

8%

42
Q

What are single nucleotide polymorphisms?

A

single positions of the genome which can have different nucleotides

43
Q

what is dsSNP?

A

A catalogue of human genetic variation, containing genetic variation across geographical locations known as the 1000 genome project

44
Q

List 4 areas how genomic comparison has been a useful tool in medicine

A
  • diagnosing cancer
  • AIDS treatment
  • Genetic disease risk management
  • disease outbreak monitoring
45
Q

Explain how genomic comparison is used for diagnosing cancer

A

Cell-free DNA in the bloodstream can be compared to DNA within normal cells to screen for cancer-causing mutations to enable early detection

46
Q

Explain how genomic comparison is used for AIDS treatment

A

ARV drugs can be tailored to the specific genomic sequence of the virus

47
Q

Explain how genomic comparison is used for genetic disease risk management

A

Increased risk of heart-disease, stroke, cancer or diabetes can be known and symptoms can be managed before the disease becomes serious

48
Q

Explain how genomic comparison is used for disease outbreak monitoring

A

Pathogen genomes can be sequenced and compared in order to identify the origin of an outbreak in order to help prevent one occurring in the future.

Genetics (10 decks)

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