Lecture 2: Basic Features of Bacterial Genomes

Question 1

What is bioremediation?

Answer 1

Bacterial breakdown of hydrocarbons

Question 2

Describe 7 differences between bacterial and eukaryotic genomes

Answer 2

1) Bacteria have circular DNA, euks have linear
2) bacteria have no introns, euks do
3) bacteria have plasmids, euks don’t
4) bacteria have phage, euks don’t
5) bacteria have operons, euks don’t
6) bacteria are haploid, euks are diploid
7) bacteria don’t reply on histones for DNA organisation as rely on supercoiling, euks do

Question 3

What are operons?

Answer 3

genes linked together with a single promoter and can move around together

Question 4

what is the difference between gram positive and negative bacteria?

Answer 4

positive are able to be stained as have thick peptidoglycan layer that dye binds to, negative aren’t

Question 5

what did cyanobacteria give rise to?

Answer 5

chloroplasts

Question 6

what did proteobacteria give rise to?

Answer 6

mitochondria

Question 7

describe the genome of clostridium difficile

Answer 7

semi-conservative replication, bidirectional replication forks. not continuous as DNA polymerases can only move in the 5 to 3 prime direction so one jumps in okazaki fragments

Question 8

what is strand bias/strandedness?

Answer 8

most genes are coded on the leading strand

Question 9

What is different about RNA polymerases in bacteria?

Answer 9

They allow replication and transcription to occur at the same time

Question 10

What is the G+C content

Answer 10

the proportion of G and C in the whole genome

Question 11

Give an example of a low, medium and high G+C content bacteria

Answer 11

endosymbiotic proteobacteria, E.coli, soil dwelling bacteria

Question 12

There is a rough correlation between G+C content and genome size, true or false?

Answer 12

True

Question 13

What are the two views of why G+C content correlates with genome size?

Answer 13

Selectionist: G+C content reflects adaptation
Mutationist: no adaptive value, just mutations
selectionist favoured

Question 14

bacteria in hosts might have fewer genes, why?

Answer 14

have weaker selection, are cared for so need fewer genes

Question 15

what is the most frequent mutation? how frequent is it?

Answer 15

C to T, 100x more frequent

Question 16

What happens if you leave DNA to mutate?

Answer 16

accumulates T and A and G and C declines

Question 17

What is the GC skew?

Answer 17

on a leading strand there is more G and T, on the lagging strand there is more A and C

Question 18

Explain why the GC skew occurs

Answer 18

one strand has continuous, the other has discontinuous replication. the discontinuous strand is left more vulnerable to mutation

Question 19

give the three main causes of intra-species genomic variation

Answer 19

differences in gene order (synteny), gene content and sequence diversity between orthologous genes

Question 20

What is synteny?

Answer 20

The order of genes on a chromosome

Question 21

What can cause loss of synteny

Answer 21

genome rearrangements eg inversions, insertion sequences causing rearrangements, selfish DNA elements, translocations, deletions

Question 22

What is the pan genome?

Answer 22

Describes the full set of genes in a clade

Question 23

what is the accessory genome?

Answer 23

genes present only in some strains of a species

Question 24

what is the core genome?

Answer 24

genes present in all strains of a species

Question 25

Give examples of things coded in the core genome

Answer 25

transcription, translation, cell envelope, replication

Question 26

give examples of things coded in the accessory genome

Answer 26

pathogenicity, antibiotic resistance

Question 27

what is different about the GC content of accessory genes?

Answer 27

tend to be lower

Question 28

What are ORFans?

Answer 28

genes present only in one strain

Question 29

what three factors determine genome size and structure?

Answer 29

gene acquisition, duplications, deletions

Question 30

what parts of the body does Staphylococcus Aureus colonise mostly?

Answer 30

skin and nose

Question 31

what is the open pan genome?

Answer 31

total gene set of all strains increases with number of sequences strains

Question 32

what is the difference between short read and long read whole genome sequencing?

Answer 32

short read is high throughput, maps for phylogenetics, long read is expensive, complete gene content, gene annotation