Week 4

Question 1

What are bacteriophages and where are they found?

Answer 1

• Viruses that use bacteria as their host.

- Found everywhere there are bacteria.

Question 2

What structures make up a bacteriophage?

Answer 2

• head (capsid), collar, sheath, base plate, tail fibres and tail pins
• One type of nucleic acid as genome (usually dsDNA that is mainly linear)

Question 3

Where do bacteriophages reproduce?

Answer 3

• Only inside host cells as have no independent metabolism.

Question 4

What are the two types of bacteriophages?

Answer 4

• virulent phages

- temperate phages

Question 5

What type of infection does virulent phages cause?

Answer 5

• Lytic infections (lyse their host cells)

- T4

Question 6

What types of infection does a temperate phage cause?

Answer 6

• Lysogenic or lytic

Question 7

What is lysogenic infection?

Answer 7

• 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)

Question 8

What is transduction and when does it occur?

Answer 8

• 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.

Question 9

What are the two types of transduction?

Answer 9

• Generalised

- Specialised

Question 10

What is generalised transduction and when does it occur?

Answer 10

• Any part of bacterial genome can be transferred

- Occurs during lytic cycle of virulent phage (during viral assembly)

Question 11

What is specialised transduction and when does it occur?

Answer 11

• Only specific bacterial genome is transferred.
• Occurs when prophage is incorrectly excised.
• Carried out only by temperate phages that have established lysogeny.

Question 12

What are transposons?

Answer 12

• Jumping genes which exist in all organisms.

Question 13

Describe the structure of transposons.

Answer 13

• 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

Question 14

When does transposition occur and what is the outcome?

Answer 14

• 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).

Question 15

What are transposable elements and give 3 examples?

Answer 15

• 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

Question 16

What are composite transposors?

Answer 16

• Transposable elements which contain genes other than those used for transposition.

Question 17

Describe simple transposition.

Answer 17

• Cut and paste mechanism
• Transposase catalyse excision
• cleavage of new target and ligation into site

Question 18

Describe replicative transposition.

Answer 18

• 2 genes coding for enzymes (tranposase and resolvase)
• Original transposon remains at parental site in DNA
• copy inserted into target DNA

Question 19

What is horizontal gene transfer and what is the benefit?

Answer 19

• 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).

Question 20

What contributes to horizontal gene transfer?

Answer 20

• Plasmid: conjugation, transformation
• Phages: transduction
• Transposons: conjugation, transformation

Question 21

What is a genome?

Answer 21

• Complete set of DNA sequence of an organism

Question 22

What are the 3 main steps in genome analysis?

Answer 22

• Generate DNA sequence read
• Assemble
• Annotate

Question 23

What is a read?

Answer 23

• a length of readable ssDNA sequence that has been output by a sequencing machine.

Question 24

What does higher read mean?

Answer 24

• Greater depth/coverage (average number of times each nucleotide is sequenced in a genome- coverage of 100% mean genome sequence is complete).

Question 25

What 2 instruments can give reads?

Answer 25

• Sanger sequencing

- Next generation sequencing

Question 26

Who invented Sanger sequencing and how does it work?

Answer 26

• 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.

Question 27

What is bioinformatics?

Answer 27

• Analysis of genome data using computers (content, structure, arrangement, function)

Question 28

What are the 2 methods used in silico analysis?

Answer 28

• De novo: difficult and slow. Used when genome is unknown.

- Read-mapping/reference: easy and rapid. Used when genome is known.

Question 29

What is annotation and what is its functions?

Answer 29

• Process that locates genes in the genome map.
• Identifies each open reading frame (ORF) in genome.
• Position and function of each gene is identified.

Question 30

What is an open reading frame?

Answer 30

• 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.

Question 31

What is comparative genomics?

Answer 31

• To do with populations of bacteria
• Whole genomes compared
• Analysis through trace evolution, trace transmission and spread

Question 32

What is metagenomics?

Answer 32

• DNA from environmental samples.

- NGS allows all DNA to be sequenced.