Week 4 Flashcards
What are bacteriophages and where are they found?
- Viruses that use bacteria as their host.
- Found everywhere there are bacteria.
What structures make up a bacteriophage?
- head (capsid), collar, sheath, base plate, tail fibres and tail pins
- One type of nucleic acid as genome (usually dsDNA that is mainly linear)
Where do bacteriophages reproduce?
- Only inside host cells as have no independent metabolism.
What are the two types of bacteriophages?
- virulent phages
- temperate phages
What type of infection does virulent phages cause?
- Lytic infections (lyse their host cells)
- T4
What types of infection does a temperate phage cause?
- Lysogenic or lytic
What is lysogenic infection?
- When phage genome integrates into host genome (aka prophage)
- Phage genome replicates with host DNA (in all bacterial offspring)
- Phage can excise itself from host DNA and revert to lytic growth (when conditions are right)
What is transduction and when does it occur?
- Accidental transfer of bacterial DNA by bacteriophages.
- Can occur during excision or lytic cycle when bacterial DNA is lysed, damaged & accidentally packaged into phages’ head.
What are the two types of transduction?
- Generalised
- Specialised
What is generalised transduction and when does it occur?
- Any part of bacterial genome can be transferred
- Occurs during lytic cycle of virulent phage (during viral assembly)
What is specialised transduction and when does it occur?
- Only specific bacterial genome is transferred.
- Occurs when prophage is incorrectly excised.
- Carried out only by temperate phages that have established lysogeny.
What are transposons?
- Jumping genes which exist in all organisms.
Describe the structure of transposons.
- All contain inverted repeats (IR)
- During transposition, target site is duplicated at either end to produce direct repeats (DR).
- Target site may not be specific
When does transposition occur and what is the outcome?
- Rarely happens, must be tightly regulated
- Consequences (insertion mutation) are severe and at a high rate result in many lethal mutations.
- Can be cut out and inserted elsewhere (cut and paste) or copied then inserted elsewhere (replicative transposition).
What are transposable elements and give 3 examples?
- Segments of DNA that move about the genome during transposition (can integrate into diff sites in chromosome)
- simplest one is insertion sequences (IS element)/simple transposons, replicative transposons, composite transposons
What are composite transposors?
- Transposable elements which contain genes other than those used for transposition.
Describe simple transposition.
- Cut and paste mechanism
- Transposase catalyse excision
- cleavage of new target and ligation into site
Describe replicative transposition.
- 2 genes coding for enzymes (tranposase and resolvase)
- Original transposon remains at parental site in DNA
- copy inserted into target DNA
What is horizontal gene transfer and what is the benefit?
- Transfer of genes from one mature independent organism to another.
- Not active process
- Increase ability of organism to fit to its environment (phenotypic diversity in bacteria).
What contributes to horizontal gene transfer?
- Plasmid: conjugation, transformation
- Phages: transduction
- Transposons: conjugation, transformation
What is a genome?
- Complete set of DNA sequence of an organism
What are the 3 main steps in genome analysis?
- Generate DNA sequence read
- Assemble
- Annotate
What is a read?
- a length of readable ssDNA sequence that has been output by a sequencing machine.
What does higher read mean?
- Greater depth/coverage (average number of times each nucleotide is sequenced in a genome- coverage of 100% mean genome sequence is complete).
What 2 instruments can give reads?
- Sanger sequencing
- Next generation sequencing
Who invented Sanger sequencing and how does it work?
- Fred Sanger
- Like DNA sequencing but also uses ddNTP (dideoxynucleotides) to give different size fragments. This is because the lack of OH group at 3’ end stops synthesis.
What is bioinformatics?
- Analysis of genome data using computers (content, structure, arrangement, function)
What are the 2 methods used in silico analysis?
- De novo: difficult and slow. Used when genome is unknown.
- Read-mapping/reference: easy and rapid. Used when genome is known.
What is annotation and what is its functions?
- Process that locates genes in the genome map.
- Identifies each open reading frame (ORF) in genome.
- Position and function of each gene is identified.
What is an open reading frame?
- a reading frame >100 codons uninterrupted by a stop codon
- has an apparent ribosomal binding site at 5’ end and terminator sequence at 3’ end.
What is comparative genomics?
- To do with populations of bacteria
- Whole genomes compared
- Analysis through trace evolution, trace transmission and spread
What is metagenomics?
- DNA from environmental samples.
- NGS allows all DNA to be sequenced.
