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Year 3: Genes and Gene Expression in Eukaryotic Cells > Genes and genomes > Flashcards

Genes and genomes Flashcards

1
Q

What is a genome?

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

What are some exceptions to the definition of a genome?

A
  • Viruses - Capture some of the hosts genome and use it for themselves
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3
Q

What are some of the things that should be noted about genome size?

A
  • Morphologically similar organsisms have very different genome sizes
  • Genome size doesn’t necessarily correlate with organism complexity
  • Genome size also doesn’t really correlate with organism size
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4
Q

Genomes are organised into chromosomes. Does chromosome number correlate to genome size?

A
  • No chromosome nuber doesn’t correlate with genome size
  • E.g. The fruit fly only has 8 chromosomes but has 165 million base pairs while the roundworm has 12 chromosomomes but only has 97 million base pairs
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5
Q

What are the 2 regions of a genome called?

A
  • Coding region
  • Non-coding region
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6
Q

What elements make up the coding and non-coding regions?

A
  • Coding region
    • Genes
  • Non-coding region
    • ​Introns
    • Gene control regions
    • Regions coding for functional RNA
    • Centromeres
    • Telomeres
    • Origins of replication
    • Mobile genetic elements?
    • Inserted viruses?
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7
Q

What are genes?

A
  • The basic unit of hereditary
  • A linear sequence of nucleotides along a segment of DNA that codes for the synthesis of RNA, which, when translated into protein, leads to the expression of hereditary character
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8
Q

Does Gene number correlate with genome size?

A
  • No gene number doesn’t correlate with genome size
  • E.g. The fruit fly has 13,000 genes and has a genome size of 165 million bp while the Arabidopsis plant has 25,000 genes and has a genome size of 157 million bp
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9
Q

Define the term “c value”

A
  • The c value is the total number of base pairs per haploid genome
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10
Q

Define the term “c value paradox”

A
  • The non-linear relationship between genome size, number of proteins synthesised and organism complexity
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11
Q

Briefly describe the structure of a typical human gene

A
  • Has 5-10 coding exons
  • Has introns inbetween each exon
  • ATG is the translation start site
  • Stop codon is translation stop site
  • Has 5’ and 3’ UTRs
  • Promoter upstream of 5’ UTR
  • Has 5’ and 3’ splicesites
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12
Q

Describe some characteristics of UTRs

A
  • Variable from protein to protein
  • They vary massively in size (can be 7 to several thousand base pairs)
  • They often contain elements that control the translation, degradtion and localisation of mRNA
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13
Q

What are some of the structures within UTRs that can control aspects of mRNA such as its tranlartion and localisation?

A
  • Stem-loop structures
  • Upstream initiation codons
  • Open reading frames
  • Internal ribsomome entry sites
  • cis-acting elements that are bound to RNA-binding proteins
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14
Q

Why are UTRs transcribed but not translated?

A
  • Because the 5’ UTR comes become ATG translation start site and 3’ UTR comes before Stop codon top site for translation
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15
Q

Are 5’ UTRs and 3’ UTRs the same size?

A
  • No, usually 3’ UTRs are 2-3x larger than 5’ UTRs
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16
Q

Are the no. of introns within a gene variable?

A
  • Numbers of introns per gene very variable (ranges from 0 to several hundred)
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17
Q

Are intron and exon sizes variable?

A
  • Both intron and exon sizes are very variable
  • 80% of exons < 200bp
  • 0.01% of introns are <20bp and 10% > 11,000bp
18
Q

Briefly describe the process of splicing

A
  1. 5’ splice site and 3’ splice site are recognised and bound to by SnRNPs (part of the spliceosome)
  2. The Spliceosome then cleaves the 5’ splice site and loops it around so it joins with the 3’ splice site
  3. This joining results in the formation of a lariat-like structure
  4. The spliceosome then cleaves the 3’ splice site causing the intron to be removed from the pre-mRNA
  5. RNA ligase is then used to join the 2 exons back together
19
Q

What is self-splicing?

A
  • Process that occurs when introns are able to splice themselves out of the pre-mRNA using RNA rather than protein (spliceosome)
20
Q

Explain the concept of alternative splicing

A
  • Because genes have multiple exons and not all exons are needed to produce mature mRNA, it means that one gene can produce multiple isoforms (proteins)
21
Q

What are some of the different ways that genes can be spliced?

A
  • Constituitive splicing - All introns spliced out and all exons ligased together
  • Exon skipping - One of the exons isn’t included in the mature mRNA
  • Mutually exclusive exons - Have one mRNA molecule could have exons 1, 2 and 4 while another could have exons 1, 3 and 4 but you can’t have both exons 2 and 3 in the same molecule
  • Alternative 5’ donor sites - 5’ ss is in a different place to normal so exon is sized differently compared to other exons
  • Alternative 3’ acceptor sites - 3’ ss is in a different place to normal so exon sized differently to others
22
Q

What is RNA editing?

A
  • Discreet changes made after the RNA has been transcribed usually at single nucleotide level
  • Can be insertion, deletion or deamination
23
Q

Give an example of a gene in humans that undergoes RNA editing?

A
  • Apolipoprotein B gene
  • In the liver, apolipoprotein B gene doesn’t undergo RNA editing so you end up with the apolipoprotein B 100
  • Howver, in the intestine, RNA editing changes a CAA codon to a UAA (a stop codon) resulting in early termination
  • This means in the the intestine you get apolipoprotein B 48
24
Q

Briefly explain the mechanism of RNA editing

A
  • RNA editing carried out by a editosome complex
  • Within the complex there’s a guide RNA (gRNA) which determines which bases within the RNA are changed
  • At the point where the guide RNA has a different sequence to the mRNA, the sequence of the mRNA is editied to match that of the guide RNA
25
Q

What are the 2 types of DNA editing? Give an example for each type

A
  • Recombination e.g. Mammalian immune system where re-sorting of DNA in immune cells allows for generation of multiple types of antibodies
  • Programmed DNA elimination
    • Chromosome diminution - chromosomes break and regions of chromosomes are lost
    • Chromosome elimination - whole chromosomes are lost
26
Q

What processes are associated with DNA elimination?

A
  • Differentiation of somatic cells
  • Sex determination
27
Q

What is a multigene family?

A
  • When you have multiple copies of the same gene within a chromosome where the copies can either have slight differences between each other or can differ greatly to each other
28
Q

How can multigene families vary between each other?

A
  • The number of family members
  • How closely related the copies are
  • Genomic locations (copies can be located far away or close to each other, sometimes in clusters can be more than 1 cluster in the genome)
29
Q

Describe how the expression pattern may vary between genes in a multigene family?

A
  • Copies can be expressed in the same pattern but may show different expression instead e.g. tissue specific/stress induced
30
Q

Apart from active genes what other type of gene may a multigene family contain?

A
  • Psuedogene
31
Q

Why aren’t pseudogenes expressed?

A
  • Because although they contain coding information they lack the appropriate controlling elements
32
Q

As well as the programmed variation within a genome there’s also variation due to mutation. What are the 2 major classes of mutation that can occur ewithin a genome?

A
  • Chromosomal instability - Gains or losses of whole chromsomes as well as inversions, deletions, duplications and translocations of large chromosomal segements
  • Nucleotide level instability - mutations of single or small groups of nucleotides - not morphologically visible
33
Q

How can natural variation be measured and what can these measurements be used for?

A
  • Can be measured using single nucleotide polymorphism (SNP) analysis
  • These can be used as signposts for disease susceptibility and drug reaction
  • Also used in forensics
34
Q

Bacteria have operons which represent the most extreme type of gene clustering. Do eukaryotes have operons?

A
  • Eukaryotes don’t usually have operons with the exception of slime molds
  • However, they still do have co-translation of genes by other mechanisms with many of them being able to operate over long distances and on different chromosomes
35
Q

Why do bacteria have operons?

A
  • By having genes that are co-regulated and part of the same biological pathwya it allows bacteria to adapt to their environment very quickly
36
Q

What are some of the different gene clusters present in eukaryotes?

A
  • rDNA genes - Code for 18s and 28s RNA of the ribosome
  • Globin gene family - Higher vertebrates have a single myoglobin gene and clusters of

α and β globin genes.

* In humans all functional genes in both clusters are transcribed in the same direction and expressed developmentally in a serial fashion * **Immunoglobin genes** - 3 loci - Heavy gene locus (chr 14); kappa locus, light chain IGK, chr 2, and the Lambda locus, light chain IGL, chr 22 * **Histone genes** - H1, H2a, H2b, H3, H4 arranged mainly in 2 clusters * **tRNA genes** - 22 mitochondrial tRNA genes, 497 cytoplasmic and 324 pseudogenes - multiple clusters on multiple chromosomes
37
Q

Why must gene expression be set up and maintained accurately?

A
  • Because cell identity is determined by the gene expression profile of the cell
38
Q

What are the different levels at which gene expression can be controlled?

A
  • Modification of DNA - e.g. methylation or histone modification
  • Transcriptional control
  • Posttranscriptional control of mRNA - e.g. mRNA may be sequestered and transcribed at a later point
  • Translational control
  • Posttranslational modification of protein - e.g. Acetylation
39
Q

As well as the nuclear genome eukaryotes also have mitochondrial genomes. State some characteristics of the mitochondrail genome

A
  • Codes for 13 proteins mainly involved in processes related to mitochondrial function
  • Genome is circular
  • Don’t have chromatin structure
  • Inheritance is maternal only
  • Only 3% is non-coding
  • Gemes transcribed in a polycistronic manner - genes code for multiple polypeptides (like bacterial genes)
  • Tend to be multiple genomes inside a single mitochondrian
40
Q

Chloroplasts are similar to mitochondria in that they also have their own genomes. State some characteristics of the chloroplast genome

A
  • Codes for 100 proteins also mainly for processes related to chloroplast function.
  • Genome is also circular
  • Multiple genomes inside a single chloroplast (15-20)
  • Doesn’t have chromatin structure
  • Genes are transcribed in operons like bacterial genes
  • 43% non coding
  • Contain 2 inverted repeats that mirror each other
41
Q

How can knowledge of the genome help medically?

A
  • Can help with diagnosis
    • ​Can identify different mutations in any gene associated with disease (simple or complex)
  • Can help with treatment
    • Can tell you whether particular drug is appropriate to treat a particular disease
    • Can tell you if doseage is appropriate for patient
42
Q

What techniques can be used for genome analysis?

A
  • DNA sequencing - hi throughput next gen sequencing
  • Linkage studies
  • Analysis of polymorphsisms - SNP analysis to give HAPMAP
  • Genetic studies - Marker analysis/co-segregation traits
  • Microarrays
  • RNA-seq
  • Proteomics

Year 3: Genes and Gene Expression in Eukaryotic Cells (4 decks)

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