Microbial Genomics

Question 1

Growth?

Answer 1

Definition
• Increase in cell-mass
• Increase in cell-number

Bacteria multiply through binary fission
• The gene pool needs to “double” before the fission

The gene pool is a DNA-molecule
• Most genes in the chromosome
• Some genes are encoded on plasmids
In prokaryotes the replication starts in one place
• The replication start is called ”origin of replication”, ori

Question 2

Gene-expression?

Answer 2

Constitutive gene expression
• Genes that encode factors that always need to be present are often constitutively expressed

Most genes are regulated
• Most genes encode factors that only need to be present at specific situations, e.g. at a
specific growth phase or for causing a certain type of infection etc.

Question 3

Genes?

Answer 3

Promotor
• Is recognized by the RNA-polymerase

Gene
• Piece of DNA that encodes a protein

Terminator
• “Informs” when the gene terminates

Question 4

The operon concept?

Answer 4

An operon consists of a set of structural genes that are regulated together, depending on the cell
metabolic requirements

• These structural genes code for a group of enzymes or proteins that are responsible for a
specific task or metabolic process, and their regulation is achieved via one or more common
regulatory mechanisms

Question 5

Pol and Sigmafactor?

Answer 5

RNA-polymerase
• The enzyme synthesizing RNA
Sigma-factor
• Required for the polymerase to
recognize the promotor

Question 6

mRNA:s?

Answer 6

Ribosome-binding site, RBS
• Also called: Shine-Dalgarno sequence, SD
• The region recognized by the ribosomes

Start codon
• Translation start

Stop codon
• Translation stop

Question 7

Regulation?

Answer 7

The amount of protein that are synthesized is regulated
• On the transcriptional level
o Varying the amount of mRNA made
• On the translational level
o Varying how much mRNA that are translated
The activity of proteins can also be regulated!

Question 8

DNA-binding proteins?

Answer 8

In order for transcription to occur the RNA-polymerase
must bind to specific promoter-sites
• This is generally controlled by regulatory proteins
that help (activating gene transcription) or prevent
(inhibiting gene transcription) the RNA-polymerase
from binding the DNA

The interaction between proteins and nucleic acids
• Specific: regulatory proteins bind a specific site
• Unspecific: regulatory proteins bind anywhere

Question 9

Enzyme repression and induction?

Answer 9

Enzyme repression
• The final product (corepressor) of a biosynthetic
pathway represses the enzymes of the process
• Often anabolic enzymes (e.g. arginine-operon)

Enzyme induction
• An enzyme (inducers) is made only when its substrate is present
• Often catabolic enzymes (e.g. the lactose-operon)
The enzymes bind to specific DNA-binding proteins, which in turn affect gene transcription

Question 10

The lac operon (enzyme induction)?

Answer 10

Glucose is the favorite carbon and energy
source for Escherichia coli
If a bacterial culture is grown in a medium containing both
glucose and lactose it will exclusively feed on the former till it
is exhausted before “switching”
• The bacterial growth curve will thus show two distinct phases

Question 11

Positive control - Activation?

Answer 11

The synthesis is under positive control
• The transcription requires the binding of a DNA-binding protein called activator protein
• E.g. maltose-catabolism

The role of activator proteins
• Help RNA-polymerase to recognize the promoter and begin transcription
• In such regulation RNA-polymerase bind weakly to nucleotide sequence

Question 12

Gene transfer in Bacteria?

Answer 12

Vertical gene transfer
• Organisms replicate their genome and
provide copies to descendants

Horizontal gene transfer
• A donor cell contributes parts of genome to a recipient cell
o Bacterial conjugation
o Transformation
o Transduction

Question 13

Conjugation?

Answer 13

1. Donor cell (F+
   ) attaches to recipient cell (F-
   ) with its pilus.
2. The pilus draws the cells together and the cells contact one another
3. Transfer of one strand from donor- to recipient cell
4. Simultaneously replication of the complementary strand
5. Cells separate

Question 14

Transformation?

Answer 14

A recipient cell takes up DNA from the environment (such as DNA from a dead organism)
Was identified in 1928 by Frederick Griffith
• Tried to develop a vaccine for Streptococcus pnuemoniae

Question 15

Transduction?

Answer 15

DNA from a donor cell is transferred to another via a replicating virus (bacteriophage)

1. Phage injects its DNA
2. Phage enzymes degrade host DNA
3. Cell synthesizes new phages that incorporate phage DNA and mistakenly some host DNA
4. Transducing phage injects donor DNA
5. Donor DNA is incorporated into recipient´s chromosome by recombination