linda - prokaryotic genomes and genomics

Question 1

bacteria vs archaea

bacteria

Answer 1

• 0.5 to 10 Mb
• Mycoplasma, genitalium, E. Coli
• variabale genome sizes
• singular circular genome
• some possess multiple chromosomes

Question 2

bacteria vs archaea

Archaea

Answer 2

• smaller genomes 0.5 to 5 Mb
• more compact bc extreme environments
• single circular chromosome
• some have multiple chromosomes

Question 3

DNA packaging

Where is the genetic material located

Answer 3

Nucleoid, a region of the cytoplasm

Question 4

DNA packaging

Supercoiling

Answer 4

• process of twisting DNA beyond its relaxed state to reduce its overall size
• DNA gyrase introduces negative supercoiling, making DNA more compact
• Topoisomerase I which relaxes supercoils

Question 5

DNA packaging

Nucleoid-Associated Proteins (NAPs)

Answer 5

• organise and compact DNA.

Question 6

plasmids and their type

What are plasmids?

Answer 6

Small, circular DNA molecules that replicate independently of bacterial chromosomes.

Question 7

plasmids and their type

Are plasmids essential for bacterial survival?

Answer 7

No, they are not essential but can provide adaptive advantages

Question 8

plasmids and their type

How are plasmids transferred between bacteria?

Answer 8

Via horizontal gene transfer (HGT), particularly conjugation

Question 9

plasmids and their type

What is the size range of plasmids?

Answer 9

From 1 kb to over 200 kb.

Question 10

plasmids and their type

What is a low-copy-number plasmid?

Answer 10

A plasmid present in only one or a few copies per cell.

Question 11

plasmids and their type

What is a high-copy-number plasmid?

Answer 11

A plasmid present in dozens or hundreds of copies per cell.

Question 12

plasmids and their type

What is the function of F (fertility) plasmids?

Answer 12

They carry genes for bacterial conjugation.

Question 13

plasmids and their type

What do R (resistance) plasmids carry?

Answer 13

Antibiotic resistance genes.

Question 14

plasmids and their type

What do Col plasmids encode?

Answer 14

Bacteriocins – proteins that kill competing bacteria.

Question 15

Transposable Elements (TEs)

What are transposable elements (TEs)?

Answer 15

DNA sequences that can move within the genome (“jumping genes”).

Question 16

Transposable Elements (TEs)

How do TEs move?

Answer 16

Via transposition using a transposase enzyme.

Question 17

Transposable Elements (TEs)

Do TEs replicate independently?

Answer 17

No, they integrate into the genome or plasmids.

Question 18

Transposable Elements (TEs)

What are IS elements?

Answer 18

Insertion sequences – the simplest TEs (~700–2,500 bp) with only transposase and inverted repeats.

Question 19

Transposable Elements (TEs)

What are transposons (Tn elements)?

Answer 19

Larger, more complex TEs with additional genes (e.g., antibiotic resistance).

Question 20

Transposable Elements (TEs)

What are composite transposons?

Answer 20

Transposons flanked by IS elements; e.g., Tn10.

Question 21

Transposable Elements (TEs)

What are non-composite transposons?

Answer 21

Transposons flanked by inverted repeats (IR); e.g., Tn3.

Question 22

Transposable Elements (TEs)

What is conservative transposition?

Answer 22

“Cut and paste” – the transposon moves without replicating.

Question 23

Transposable Elements (TEs)

What is replicative transposition?

Answer 23

A copy of the transposon is inserted at a new site, increasing copy number.

Question 24

Genome Size and Variation

Why do genome sizes vary in prokaryotes?

Answer 24

Due to differences in ecological niche, lifestyle, and HGT.

Question 25

# Genome Size and Variation Why do intracellular parasites have small genomes?

Answer 25

They rely on the host for many functions.

Question 26

# Genome Size and Variation Why do free-living or soil bacteria have large genomes?

Answer 26

They need more genes to adapt to changing environments.

Question 27

# Genome Size and Variation What is genome streamlining?

Answer 27

Evolutionary reduction of non-essential genes for efficiency.

Question 28

# Genome Size and Variation What is gene redundancy?

Answer 28

The presence of multiple genes with the same function due to duplication.

Question 29

# Methods for Analyzing Bacterial Genomes What does PFGE stand for?

Answer 29

Pulsed-Field Gel Electrophoresis – separates large DNA fragments.

Question 30

# Methods for Analyzing Bacterial Genomes What is a major limitation of PFGE?

Answer 30

Low resolution; doesn’t provide exact DNA sequences

Question 31

# Methods for Analyzing Bacterial Genomes What is the advantage of whole-genome sequencing?

Answer 31

Most accurate method for genome size and gene content analysis.

Question 32

# Core vs Accessory Genome & Pangenome What is the core genome?

Answer 32

Genes shared by all strains; essential for basic functions.

Question 33

# Core vs Accessory Genome & Pangenome What is the accessory genome?

Answer 33

Genes present in some strains; often acquired via HGT.

Question 34

# Core vs Accessory Genome & Pangenome What is a pangenome?

Answer 34

The total gene set of all strains (core + accessory).

Question 35

# Core vs Accessory Genome & Pangenome What is the difference between open and closed pangenomes?

Answer 35

Open = high gene diversity (e.g., E. coli); Closed = limited diversity (e.g., B. anthracis).