- Created by: 11APhillips
- Created on: 30-12-19 15:31
Double stranded: Humans
SIngle stranded: Parvovirus
Double stranded: E. Coli
Single stranded: M13 bacteriophage
Double stranded: bluetongue virus
Single stranded: retrovirus
- They have an envelope protein, a reverse transcriptase, and a capsid with RNA
- The smallest free living genome is pelagibacter ubique, at 1389 genes
- The smallest genome is nasuia deltocephalinicola, at 112 kb.
- Polyomavirus and phi X174 have overlapping genes to pack maximal information into minimal space.
- Most bacteria have a single chromosome and plasmids.
- Some have additional replicons (megaplasmids or minichromosomes)
- Sometimes, the plasmid DNA count is higher than the chromosomal DNA count.
- Bacterial chromosomes have a single origin of replication, but genes closer to the origin of replication have higher copy numbers.
- Resultantly, essential genes are kept near the origin of replication
- Genes are oriented in the direction of replication to prevent collisions between enzymes
The minimal genome
- The minimal genome is the theoretical minimal set of genes required to sustain cellular life.
- Genes are divided into essential genes and genes that, while not necessary, give an advantage.
- An M. Genitalium genome was produced in vitro and introduced into a host cell, marking the genome with tet resistance and lacz.
- The host cell will eject either the orignal or synthetic genome as it doesn't want to have 2, but due to the markers, the original will be ejected.
- The lacZ makes the desired colonies appear blue.
- They called it synthia, and the current iteration has fewer than 500 genes.
The human genome
- Has 3200 megabases of DNA
- The Tetroadon has a similar chromosome number to humans, but the genes are all on different chromosomes
- Only 1.5% of the genome is translated, and we don't know how much of the genome is transcribed.
- 95% of human genes have multiple transcripts, which is known as differential splicing.
- DNA contains thymine and not uracil because cytosine can be deaminated to uracil, and the body wouldn't be able to detect it if there was uracil there already.
- RNA keeps uracil as it costs much less to produce in energy terms than thymine does.
- 10* of cytosine in DNA is methylated, but only those 5' of guanidine residues (5' CpG 3')
- They are rare in the vertebrate genome.
- There are 2 types of methylation:
- Maintenance methylation - Methyl groups added to new DNA opposite methyl groups on the parent strand.
- De novo methylation - Methyl groups added to the chromosome, repressing gene activity by binding to methyl CpG-binding proteins, which then recruit histone deacetylases.
- Unmethylated CpG regions are called CpG islands.
- CpG islands disappear in inactive genes because the inactivation is caused by methylation, which sets up the C to be deaminated to T. Can't happen if CpG isn't methylated.
Genes can be present in different structures...
1. Repeated gene clusters
- E.G. The rRNA 5.8S 18S and 28S genes - The cluster is repeated many times identically.
- It is done for gene products needed in high amount, and can be compared to increased copy number in prokaryotes.
2. Multigene families
- e.g. Beta globin, which has different varients of the same protein expressed throughout an organisms life time: Embryonic/fetal/adult
- One of the genes in this example is a pseudogene
- A mutation in a gene sequence causes it to be non-functional.
- Mutations continue to accumulate.
- Processed pseudogenes are from retroviral RNA that was converted to DNA and then reincorporated back into the genome, forming a gene with no introns or promoters.
4. Gene fragments - incomplete sections of genes
Interspersed repeated intergenic DNA
- Repeat units found throught the DNA, seperated by inter-repeat regions.
- Short ones (SINES), have a frequency of 1.5 million in a genome.
- Long ones (LINES), have a frequency of 900,000.
- Long terminal ones (LTRs), have a frequency of 300,000.
- They are formed by transposable elements that accidentally leave a copy behind when they are transposed to a different part of the genome.
- They move through the use of an RNA intermediate.
- A fourth type (f = 300,000) does not use an RNA intermediate: the DNA transposon.
Tandemly repeated extragenic DNA
- They can form in microsatellites, minisatellites, or satellites (size order).
- Microsatellites are caused by replication slippage, where the two strands become misaligned by the DNA polymerase and extra repeats are added or deleted.
- The length of these repeats is unique to an individual; DNA fingerprinting.
- In DNA fingerprinting, the allele frequency must be considered.
- If a match is of a high frequency allele, the match is much less significant than if it was a low frequency allele.
- If a suspects two alleles are different, the probability must be multiplied by 2.
- The prosecutor's fallacy confuses the probability that a person will have a matching fingerprint with the probability that they are guilty.
- Transcription of genes involves 5' capping and polyA tailing.
- Introns are transcribed but not translated.
- An example of a gene that undergoes differential splicing is the human slo gene, which produced 500 different transcripts.
- All introns are preceded by a 5' splice site and succeeded by a 3' splice site, which itself is preceded by a polypyrimidine tract.
1. A cut made at the 5' end branches and bonds with an A in the middle of the intron through hydroxyl attack.
2. A bond forms between the 5' and 3' splice site.
3. The intron is debranched and degraded.
- Small nuclear RNAs (SnRNA) play an important role as part of the spliceosome complex.
- Different types of introns, such as the GU-AG introns, work in different places.
- Two hypotheses exist for the fate of introns:
- Early hypothesis - introns are ancient and are being lost
- Late hypothesis - introns are recent and are accumulating (more evidence for this).
- Introns can actually contain genes, which are translated before splicing.
- Twintrons are introns within introns, and are spliced separatley, with the internal intron going first.
- Examples of introns in genes:
- Insulin - has 2 introns that take up 70% of the gene.
- Dystrophin - Has 78 introns that take up 98% of the gene.
Small nucleolar RNAs
- E.G. snoRNA
- It is used to modify rRNAs, such as through methylation.
- It can also do pan-editing, which is where an extra nucleotide is added through the snoRNA acting as a guide RNA.
- aka miRNA
- These are bits of RNA that bind to the untranslated region between the stop codon and the polyA tail.
- It stops translation, suppressing gene expression through causing the removal of the polyA tail.
1. miRNA made as a long molecule.
2. It folds up into stem loops.
3. An enzyme called Drosha cuts it into miRNA precursor.
4. These are cut by a dicer, which produces the miRNA
Short interfering RNA
- aka siRNA
1. Double stranded viral RNA is cut by dicer nuclease.
2. The siRNA fragments that result, once they have been made into a single strand, attach to the viral mRNA
3. This causes incorporation into the RISC complex.
4. Argonaute cuts the mRNA opposite to where the siRNA has bound.
- This is called RNA interference (RNAi).
- The double stranded RNA can actuallty be made by transcribing the gene in both directions, therefore artificially triggering RNAi.
- It is about 20bp long, and is important for research as you can use it to knockdown a gene to see its function,