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Genes, Genomes and Biomedical Implications > Intro to Genes and Genomes Dynamics > Flashcards

Intro to Genes and Genomes Dynamics Flashcards

1
Q

Why is the structure not sufficient to define function?

A

99.9% of our ~25000 genes are identical

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2
Q

Why is NGS more common than PCR for the purpose of genome sequencing?

A

it is much more fast-paced and uses pre-defined adapters

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3
Q

What is coronavirus?

A

the largest RNA virus that forms enveloped and spherical particles of around 100-160nm in diameter

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4
Q

Describe the coronavirus genome

A

positive sense, ssRNA genome of ~30kB

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5
Q

What is the distribution of the ORFs in the coronavirus genome?

A

ORF1a is expressed in much higher levels but both are required to make a replicate

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6
Q

What does polyadenylation do?

A

stabilise the 5’ end of RNA (capping with poly-A tail)

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7
Q

What does spike protein do?

A

interact with ACE2 to enter into the host and replicate and propagate the genome

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8
Q

What is an ORF?

A

a span of DNA or RNA between the start and stop codons

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9
Q

How many frames are used to check if the RNA sequence contains a stop codon?

A

3

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10
Q

What would happen if there was a stop codon present in RNA?

A

the polymerase would be terminated

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11
Q

What would mutations in one locus of DNA likely affect?

A

the reading frames of another gene if both genes were being encoded by the same locus

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12
Q

What do most naturally arising S antibodies and MAbs do?

A

target the receptor binding domain (RBD)

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13
Q

What are the MAb fab and Fc domains responsible for?

A
  • fab = antigenic recognition
  • Fc = immune effector functions
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14
Q

What percentage of the human genome encodes for proteins?

A

less than 5%

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15
Q

What are possible functions of intergenic regions?

A
  • encoding of regulatory RNA (miRNA)
  • long-range elements that control the folding and topology of DNA organisation
  • gene regulation
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16
Q

Why are promoters generally more obvious than enhancers?

A

due to their larger consensus sequences

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17
Q

How can enhancers work to regulate genes from far away?

A

by chromosomal loops and structures within the DNA

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18
Q

How is the gene regulatory machinery stabilised?

A

by chromosomal loops

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19
Q

What percentage of genes undergo alternative splicing in the brain?

A

30%

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20
Q

What are the introns removed during splicing used for?

A

to make pre-miRNA

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21
Q

What are dicer proteins used for?

A

recruiting the pre-miRNA; they cleave the pre-miRNA to retain the targeting miRNA

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22
Q

What happens to the targeting miRNA?

A

it can associate with other proteins to form the activated RISC that grabs the target mRNA and degrades it

23
Q

What is the RISC?

A

RNA-induced silencing complex

24
Q

When are RNA and DNA complimentary?

A

during transcription (bubble) and reverse transcription (RNA-dependent DNA polymerase e.g. telomerase)

25
Q

What is RNA interference?

A

a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by dsRNA, through translational or transcriptional repression

26
Q

What are miRNAs?

A

genome-encoded short RNAs that regulate gene expression by translational repression and/or degradation of cognate mRNAs

27
Q

How do miRNAs regulate gene expression?

A

by suppressing the availability of mRNA by degradation or physically stopping the ribosome from proceeding to full translation

28
Q

Why doesn’t miRNA act at the DNA level?

A

due to compartmentalisation

29
Q

What are the key differences between miRNA and siRNA?

A
  • siRNA is derived from the introduction of exogenous dsRNA to the cells while miRNA is generated from the expression of the endogenous non-coding RNA
  • siRNA is present in lower animals and plants but not mammals and miRNA is present in all plants and animals
  • siRNA is highly specific with only one mRNA target while miRNA can inhibit translation of multiple mRNA targets due to its lower specificity when pairing
  • siRNA primarily provides viral defence and genome stability while miRNA functions as an endogenous gene expression regulator
30
Q

How can special complimentary RNA oligos be re-engineered?

A

in the form of siRNA or shRNA to introduce them into cells to target and degrade target genes of interests

31
Q

What are oligos?

A

short, single- or double-stranded synthetic RNA sequences that can serve as the starting point for many molecular biology and synthetic biology applications

32
Q

What are RGENs?

A

programmable genome engineering tools adapted from CRISPR/Cas system

33
Q

What does Cas9 form?

A

a sequence-specific endonuclease that targets a sequence that is 23bp in length, ending with two guanines (GG) i.e. can essentially cleave any region of the genome

34
Q

What can CRISPR do?

A

effectively knockout/delete the gene of interest and replace it with a specific mutant of interest

35
Q

What can CRISPR be used for?

A

narrowing down not just what the gene does, but potentially how the gene and the protein encoded would execute their functions at the biochemical and molecular levels

36
Q

What is a syntenic group?

A

a set of loci in two different species which is located on the same chromosome in each (not necessarily in the same order)

37
Q

Give examples of rearrangements to the genome during evolution

A
  • chromosome translocations
  • meiosis
38
Q

What can meiosis do?

A

separate 2 loci resulting in the loss of synteny between them

39
Q

What may conserved chromosomal domains be important for?

A

chromosomal function

40
Q

What predicts evolutionary relationships?

A

similarities in genetic loci and their order

41
Q

What do speculative positive selection pressures do?

A
  • minimise random mutations of genes
  • increase gene duplications
  • increase chromosomal rearrangement
42
Q

What are selection pressures?

A

external agents which affect an organism’s ability to survive in a given environment

43
Q

What do negative and positive selective pressures do respectively?

A
  • negative = decrease the occurrence of a trait
  • positive = increase the proportion of a trait
44
Q

What is the centromere?

A

part of the chromosome important for mitosis and meiosis; the region where the cell’s spindle fibres attach

45
Q

What is heterochromatin and what does it consist of?

A

a highly condensed form of DNA and mostly consists of repetitive DNA sequences and non-coding RNA transcripts

46
Q

What is euchromatin and what does it consist of?

A

the opposite of heterochromatin and is made up of repeating units called nucleosomes which each contain a segment of DNA wound around eight histone proteins

47
Q

What are very active in the pufferfish (Fugu) genome?

A

transposable elements

48
Q

What are SINEs and LINEs?

A

short (SINE) and long (LINE) interspersed retro-transposable elements that invade new genomic sites using RNA intermediates

49
Q

Where are SINEs and LINEs found?

A

almost all eukaryotes (although not in S. cerevisiae)

50
Q

When does equal crossover between homologous chromosomes occur?

A

when sister chromatids crossover during meiosis

51
Q

What is unequal crossover?

A

a type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis

52
Q

What is slipped strand mispairing/replication slippage and what does it involve?

A

a mutation process which occurs during DNA replication that involves denaturation and displacement of the DNA strands resulting in mispairing of the complimentary bases

53
Q

What is GC content?

A

the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C)

54
Q

What are CpG islands?

A

short interspersed non-methylated DNA regions with a high concentration of phosphate-linked CG pairs

Genes, Genomes and Biomedical Implications (15 decks)

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