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.
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
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
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
5
Q
What are the 2 regions of a genome called?
A
- Coding region
- Non-coding region
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?
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
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
9
Q
Define the term “c value”
A
- The c value is the total number of base pairs per haploid genome
10
Q
Define the term “c value paradox”
A
- The non-linear relationship between genome size, number of proteins synthesised and organism complexity
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
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
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
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
15
Q
Are 5’ UTRs and 3’ UTRs the same size?
A
- No, usually 3’ UTRs are 2-3x larger than 5’ UTRs
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)
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
- 5’ splice site and 3’ splice site are recognised and bound to by SnRNPs (part of the spliceosome)
- The Spliceosome then cleaves the 5’ splice site and loops it around so it joins with the 3’ splice site
- This joining results in the formation of a lariat-like structure
- The spliceosome then cleaves the 3’ splice site causing the intron to be removed from the pre-mRNA
- 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
What are the 2 types of DNA editing? Give an example for each type
* **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
What processes are associated with DNA elimination?
* Differentiation of somatic cells
* Sex determination
27
What is a multigene family?
* 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
How can multigene families vary between each other?
* **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
Describe how the expression pattern may vary between genes in a multigene family?
* Copies can be expressed in the same pattern but may show different expression instead e.g. tissue specific/stress induced
30
Apart from active genes what other type of gene may a multigene family contain?
* Psuedogene
31
Why aren't pseudogenes expressed?
* Because although they contain coding information they lack the appropriate controlling elements
32
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?
* **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
How can natural variation be measured and what can these measurements be used for?
* 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
Bacteria have operons which represent the most extreme type of gene clustering. Do eukaryotes have operons?
* 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
Why do bacteria have operons?
* 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
What are some of the different gene clusters present in eukaryotes?
* **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
Why must gene expression be set up and maintained accurately?
* Because cell identity is determined by the gene expression profile of the cell
38
What are the different levels at which gene expression can be controlled?
* **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
As well as the nuclear genome eukaryotes also have mitochondrial genomes. State some characteristics of the mitochondrail genome
* 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
Chloroplasts are similar to mitochondria in that they also have their own genomes. State some characteristics of the chloroplast genome
* 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
How can knowledge of the genome help medically?
* **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
What techniques can be used for genome analysis?
* **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**
