Prokaryotes

Question 1

Prokaryotes are cells with co-_ _ on their main chromosomes

Answer 1

co-transcriptional translation

Question 2

What is the plate count anomaly?

Answer 2

Easily isolated organisms appear on a culture plate however only contribute to <1% of all microbial species

Question 3

Prokaryotic chromosomes can be structured in…

Answer 3

circular
linear
circular/linear
megaplasmids

Question 4

Prokaryotes exhibit a _ gene density

Answer 4

uniform

Question 5

What are the shaping factors of prokaryotic genomes?

Answer 5

1. Homologous recombination
2. introns and inteins
3. Insertion Sequence (IS) elements
4. Genomic Islands

Question 6

How does homologous recombination generate diversity within prokaryotic genomes? What causes rates of recombination to drop?

Answer 6

generates novelty by recombining existing alleles w/in a species

rate drops exponentially as sequences diverge

Question 7

What are Insertion Sequence Elements? What are the characteristics of their sequences?

Answer 7

small DNA fragments capable of transposition

up to 2.5 kb in length
1 or 2 ORFs encoding a transposase (mobility facilitation)

Question 8

Non-replicative IS elements…

Answer 8

insert into a new site regardless of cell cycle stage

Question 9

Replicative IS elements…

Answer 9

insert into a new site during DNA replication

Question 10

What mediates the recognition of IS sequences?

Answer 10

Inverted repeats recognized by transposase

Question 11

IS elements are often found on _ and mediate recombination with _ DNA

Answer 11

plasmids

chromosomal DNA

Question 12

Genomic islands are evidence of _ and are often _ that have lost their excision ability

Answer 12

horizontal gene transfer

ICEs

Question 13

Genomic islands are often enriched in…

Answer 13

mobile elements
tRNA genes
repetitive sequences
virulence factors

Question 14

What are the mechanisms of horizontal gene transfer?

Answer 14

1. Transformation - uptake from lysed cells
2. Transduction - phage transfer
3. Conjugation - exchange of a sex plasmid

Question 15

ICEs stand for _ that are mobile elements residing in the _

Answer 15

integrative & conjugative elements

host chromosome

Question 16

ICEs are capable of _ & _ via the Type _SS and _ replication

Answer 16

excising & conjugation
IV
rolling circle replication

Question 17

ICE integration occurs often at _ genes and recombines at _-sites

Answer 17

tRNA

att-sites

Question 18

What are the two methods of HGT detection?

Answer 18

1. Compositional anomalies

2. Phylogenetic incongruence

Question 19

If the donor DNA is significantly different in characteristics such as _ & _ then it may be ID’ed. What deteriorates these signals?

Answer 19

G/C content
codon usage

ameriolation

Question 20

Ameriolation is _ pressures that assimilate the donor gene into the recipient. What effect does this have on HGT detection?

Answer 20

selective/mutational

HGT sequence anomalies only provide a signal for ~100k years

Question 21

What is phylogenetic incongruence?

Answer 21

If the topology of gene/protein alignment is incongruent then it may be of a HGT origin

Question 22

What are some factors influencing the frequency of HGT?

Answer 22

1. physical proximity
2. mechanism
3. metabolic compatibility
4. gene expression systems

Question 23

The pan-genome represents the _ collection of genes shared amongst a species

Answer 23

full

Question 24

The core genome represents the _ collection of genes shared amongst a species

Answer 24

stable/essential

Question 25

The variable genome represents the _ collection of genes in a species

Answer 25

unique/individually found