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genes and gene expression > lecture 1: genes & genomes > Flashcards

lecture 1: genes & genomes Flashcards

1
Q

what is a genome?

A
  • A genome is an organism’s complete set of DNA.
  • Each genome contains all the information needed to build & maintain that organism
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2
Q

genome size

A
  • morphologically similar organisms have very different genome sizes
  • genome size doesn’t correlate with organismal complexity or size of the organism
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3
Q

how are genomes organised?

A
  • organised into chromosomes
  • BUT chromosome number doesn’t necessarily correspond to genome size
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4
Q

what are the non-coding elements that make up genomes?

A
  • gene control regions
  • introns
  • regions coding for functional RNA
  • centromeres
  • telomeres
  • origins of replication
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5
Q

what are the coding regions of a genome?

A
  • genes
  • abot 98% of the genome is non-coding
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6
Q

definiton of genes

A

a basic, physical unit of heredit; a linear sequence of nucleotides along a segment of DNA that provides the coded instructions for synthesis of RNA which when translated into protein, leads to expression of hereditary character.

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7
Q

what is the c value?

A

the total number of base pairs per haploid genome

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8
Q

what is the c value paradox?

A

related to the non-linear relationship between genome size, number of protein synthesised and organismal complexity

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9
Q

what is the structure of a typical human gene?

A
  • ATG is the translation start site
  • STOP is translation stop site
  • UTRs (untranslated regions) are transcribed but not translated
  • coding regions (exons) are separated by introns; transcribed but not translated
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10
Q

what are UTRs?

A

an untranslated region on either side of a coding sequence on a strand of mRNA
- variable from protein to protein

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11
Q

the size of UTRs

A

wide variation (from 7 to several thousand)

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12
Q

what do these UTRs contain?

A
  • elements that control the translation, degradation and localisaiton of the mRNA
  • e.g:
    stem loop structures, upstream initiation codons & open reading frames, internal ribosome entry sites & various cis-acting elements that are bound by RNA binding proteins
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13
Q

introns and exons

A
  • number of introns per gene vary (average is 7-8)
  • sizes of them vary
  • some organisms have no introns
  • recognised by specific sequences at 5’ and 3’ junctions that allows them to be recognised and targeted for removal by splicing
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14
Q

what is splicing?

A
  • occurs at the end of the transcription process as part of the pre-mRNA processing
  • coding regions of mRNA (exons) are kept and non-coding (introns) are removed
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15
Q

what is alternative splicing?

A

a cellular process in which exons from the same gene are joined in different combinations leading to different but related mRNA transcripts

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16
Q

RNA editing

A
  • discreet changes made after the RNA has been transcribed usually at single nucleotide level.
  • can be insertion, deletion or deamination
17
Q

intron retention

A

occurs where a complete and unspliced intron remains in mature DNA
-VERY RARE

18
Q

where was RNA editing first found?

A

in trypanosomes but also in humans
- e.g. the apolipoprotein B gene

19
Q

genes in lower eukaryotes

A

often (but not always) only have 1 copy of a gene

20
Q

multigene families

A
  • quite often in mammals, several copies of a gene in a genome
21
Q

on what terms of multigene families do they vary?

A
  • the number of family members (2-hundreds)
  • how closely related the copies are (very close- distantly related)
  • genomic locations (different regions of the genome, located close to each other sometimes in clusters, can be more than 1 cluster in the genome)
22
Q

pseudogenes

A
  • as well as active copies, gene genomes can also contain pseudogenes
  • contain coding information but are not expressed to the lack of appropiate controlling elements
23
Q

chromosomal instability (CIN)

A

gains or losses of whole chromosomes as well as inversions, deletions, duplications & translocations of large chromosomal segments

24
Q

nucleotide level instability

A

mutations of single or small goups of nucleotides; not visible morphologically; trinucleotide repeate diseases.

25
Q

what are SNPs

A
  • single nucleotide polymorphism
  • natural variation
  • can be used as signposts for disease susceptibility & drug reaction
26
Q

what is an operon?

A

a unit made up of linked genes which is thought to regulate other genes responsible for protein synthesis

27
Q

bacteria & operons

A

bacteria contain the ‘lac operon’ which represents the most extreme type of clustering

28
Q

do eukaryotes have operons?

A

with the exception of slime molds, eukaryotic operons are very RARE but they still have co-translation of genes by other mechanisms many of which can operate over long distances and on different chromosomes.

29
Q

gene expression

A

cell identity is largely determined by gene expression profile of the cell.
Therefore, robust mechanisms must be in place to ensure that this is set up and maintained accurately.

30
Q

process of gene expression

A

modification of DNA > Transcription > Post-transcription > Translation > Post-translation

31
Q

mitochondrial genes

A
  • mitochondrial have their own genomes
  • codes for 35 proteins related to mitochondrial functions
  • genome is circular
  • multiple genes inside a single mitochondrion
  • no chromatin structure
  • only 3% is non-coding
  • inheritance is maternal only
    -genes are transcribes more like bacterial genes in poly-cistronic manner
  • plays a role in aging
32
Q

chloroplast genome

A
  • have their own genomes
  • codes for 100 proteins also mainly for processes related to chloroplast function
  • genome is circular
  • multiple genes (15-20) inside single chloroplast
  • no chromatin structure
  • genes are transcribed in operons like bacterial genes
  • usually chloroplast genome contains two inverted repeates that mirror images of one another in terms of gene complement
  • 43% non coding
33
Q

genome knowlege and diagnosis:

A
  • simple disease (only 1 locus involved)
  • complex disease (byproduct of multiple loci)
  • different mutations in any of these genes
34
Q

genome knowledge and treatment:

A
  • is drug used appropriate for cause of that patients problems (different causes of condition/polymorphisms)
  • is dosage used appropriate for individual
35
Q

techniques for genome analysis

A
  • DNA sequencing: hi throughput next gen sequencing
  • linkage studies
  • analysis of polymorphisms : SNP analysis to give HAPMAP
  • genetic studies: marker analysis/ co-segregation traits
  • microarrays
  • RNAseq
  • proteomics changes in protein/modifications

genes and gene expression (14 decks)

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