Topic 5-L1 - Microbial Genomes

Question 1

All cells store their genetic information as

Answer 1

DNA

Question 2

information flow & the central dogma of life

Answer 2

• DNA is copied (DNA replication) as the first step in cell division
• Genetic info of DNA is copied to RNA in
  transcription o Open reading frames from messenger RNA (mRNA) are converted to proteins via translation
• Other RNAs (non-coding RNAs, such as
  ribosomal RNA – rRNA) are not converted to
  protein, but serve their cellular function as RNAs

Question 3

DNA is a polymer comprised of strings of

Answer 3

nucleotide monomers

Question 4

Nucleotides comprised of 4 different

Answer 4

• nucleobases (or nitrogenous bases) attached to a deoxyribose (5 carbon sugar) which carries a phosphate at the 5’ carbon. Nucleosides lack a phosphate group.

Question 5

Nucleotides connected via. All linear

Answer 5

phosphodiester bonds between 5’-phosphate groups and 3’hydroxyl (OH) groups

• DNA has 5’ end & 3’ end

Question 6

Two complementary DNA strands run

Answer 6

anti-parallel to form a helix via interaction of their nucleobases

– genomic DNA is double stranded

Question 7

C/T are

Answer 7

pyrimidines (6 membered rings)

Question 8

A/G are

Answer 8

purines (fused 5/6 membered rings).

Question 9

A/T base pair, forming a

Answer 9

weaker interaction with 2 hydrogen bonds

Question 10

C/G base pair, forming a

Answer 10

stronger interaction with 3 hydrogen bonds

Question 11

Base pairing is the key to DNA’s function: it enables identical copies to be

Answer 11

made and genetic information to be converted to RNA/protein.

Question 12

Differences between DNA and RNA

Answer 12

• RNA contains a 2’-hydroxyl group (OH) on its sugar (ribose) that is absent in DNA.
• RNA less stable then DNA (2’-OH can attack the sugar phosphate backbone - hydrolysis of the phosphodiester bond.)
• urical
• RNA single stranded

Question 13

Structure of prokaryotic chromosomes

Answer 13

usually circular, but within cell not a simple “relaxed circle” - there is extensive supercoiling & additional structuring layered on top. Many proteins involved in structuring the chromosome

• makes DNA compact enough to fit in cell
• nucleoid

Question 14

Nucleoid –

Answer 14

region of cell containing the chromosome (not membrane bound, but synonymous to the concept of the nucleus)

Question 15

Bacteria and archaea almost always have

Answer 15

one, circular chromosome

Question 16

Vibrio Cholerae is an example of a bacterium with

Answer 16

two (circular) chromosomes – one is ~3 Mbp (million bp), other ~1Mbp

Question 17

Streptomyces (those antibiotic producers) have

Answer 17

linear chromosomes!

Question 18

Eukaryotes have

Answer 18

multiple linear chromosomes

Question 19

Saccharomyces cerevisiae, has

Answer 19

12 chromosomes that vary in size

Question 20

Eukaryotes, including microbes, generally have

Answer 20

larger and less compact genomes (fewer genes per kbp of DNA) than prokaryotes

Question 21

eukaryotic microbes

Answer 21

smaller/more compact genomes than higher eukaryotes.

Question 22

karyotic microbes have more compact genomes than higher eukaryotes, in part because they have

Answer 22

fewer introns (non- coding gene segments removed during splicing) per gene

Question 23

Genes are segments of genetic material that encode a functional

Answer 23

protein or RNA product

Question 24

A typical microbial genome is comprised of:

Answer 24

~85-90% protein-coding genes

~1-2% RNA coding genes (tRNA, rRNA, other functional RNAs)

~10% non-coding DNA (E.g., regulatory sequences, junk DNA)

Question 25

Genes can run in

Answer 25

either direction (be encoded by either DNA strand) and can overlap

Question 26

Genes often organized into functionally-related

Answer 26

clusters – function of surrounding genes can offer insight into a gene’s function

Question 27

Genes of a related function can also be

Answer 27

scattered around chromosome

Not always together

Question 28

Endosymbionts

Answer 28

(can only live within the cells of another organism)

Question 29

parasites

Answer 29

(require another organism) can have very small genomes – rely on host for many functions

Question 30

Mycoplasma (parasite - canlive freely) has a 0.5 Mb genome ~500
genes –

Answer 30

smallest genome capable of independent life?

Question 31

Free-living bacteria/archaea have

Answer 31

larger genomes. (E.g. E. coli ~4.5 Mb )

Question 32

Some bacteria with complex life cycles
(lots of regulation, different needs for
different stages) have genomes as

Answer 32

large as ~15 Mb

Question 33

In prokaryotic genomes, as genome size increases, so does

Answer 33

of genes

Question 34

Genes that encode specialized functions for adapting to different
environments or operating in different lifestyles

Answer 34

increase in larger genomes.

Question 35

Core genome –

Answer 35

Genes present in all members. Usually conserved genes important for biology of that lineage

Question 36

Pan genome –

Answer 36

All genes present in any member. Includes rare genes that encode highly specialized functions.

Question 37

Genomes of closely-related lineages often exhibit significant

Answer 37

synteny

Question 38

synteny –

Answer 38

homologous genes arranged in the same order in their genomes

Question 39

Unique genes of a particular genome are often found in blocks of genes

Answer 39

large blocks = genomic island

small blocks = genomic islet

Question 40

Genomic island and islets often represent

Answer 40

horizontally acquired genes.

In many cases, the genes have a related function that confers that lineage with unique properties.

Question 41

Diagram of SalmonellaPathogenicity Island-1 (SPI-1):

Answer 41

Encodes many genes required for a type III secretion system, which enables Salmonella to enter host cells. Also encodes iron acquisition genes (iron is hard to acquire inside cells).

Question 42

Bacteriophages (or phages)

Answer 42

are viruses that infect bacteria (archaea are also infected by similar viruses)

Question 43

Some bacteriophage, known as temperate phage, can integrate into
bacterial genomes, where they become a part of the genome called a __________. Can be stable or transient.

Answer 43

Some bacteriophage, known as temperate phage, can integrate into
bacterial genomes, where they become a part of the genome called a
prophage. Can be stable or transient.

Question 44

Prophage content can vary from

Answer 44

strain to strain.

Question 45

Prophage can carry cargo genes that have

Answer 45

nothing to do with phage biology - can provide the bacterial host with useful new genes.

Question 46

important bacterial toxins are encoded by

Answer 46

prophage

Question 47

In this specific map:

Answer 47

• Genes on one strand in blue
• Genes on other strand in red
• Green shows bacteriophage genes (prophage)
• Specialized biosynthetic genes in yellow (a feature of special interest for this particular paper)
• Grey genes are thought to be horizontally-acquired
• Squiggly line is % GC content - Inner rings show tRNA and rRNA genes

Question 48

In addition to their genomes, many Bacteria and Archaea contain

Answer 48

plasmids

Question 49

Plasmids are typically

Answer 49

circular DNA molecules are replicated in the cytoplasm – encode “non-essential” accessory genes – genes important under certain conditions such as antibiotic resistance genes