(03) Prokaryotic Genetics

Question 1

T or F: bacteria only encode a single RNA polymerase

Answer 1

True

Question 2

What is an operator?

- location relative to promoter.

Answer 2

Operator:
- Binds Proteins in involved in gene expression

• Located near the promoter

Question 3

Why can transcription be paired with translation in bacteria?

Answer 3

1. No Introns

2. No Nucleus

Question 4

What is an operon?

- what bacterial type contains the lac operon?

Answer 4

• Cluster of Genes involved in a related function that is transcribed on a single mRNA (aka polycistronic)

Gram (-) bacillus Escherichia Coli

Question 5

What 3 genes make up the lac operon?

• what is its function?
• Does gene transcription take place in unison or individually?

Answer 5

1. Lac Z –> ß-galactosidase
2. Lac Y –> Lactose Permease
3. Lac A –> Lactose Transacetylase

• Allows Gram (-) Bacillus Escherichia Coli to use lactose
• Transcrption takes place together but RNA translation takes place individually

**Note: if this was not the case, then they would be translated together then cleaved apart

Question 6

What are the reasons for an operon rather than genes located on different parts of the chromosome?

Answer 6

1. Operons help to ward off loss of function
   - if genes were in different part of the genome they could more easily be lost by evolutionary divergence
2. Use of a single promoter and operator provides co-regulation of genes in the operon. ALLOWS FOR COORDINATED EXPRESSION

Question 7

What are the 3 types of gene regulation?

• which type is most rare?
• why?

Answer 7

1. Constitutive
   - no regulation, genes always expressed
   * *Most rare because of ATP expenditure
2. Positive Regulation
   - Activator Protein promotes RNA polymerase binding to promoters
3. Negative Regulation
   - Repressor protein binds operator sequence and prevents transcription until it is removed

Question 8

Is positive or negative regulation more common?

- why?

Answer 8

Negative regulation

• From an evolutionary standpoint loss of promoter leads to complete loss of the gene while loss of repressor, then the gene is still functional

Question 9

What is a regulon?

Answer 9

Independently transcribed genes or multiple operons are controlled by the same regulator protein = Regulon

Question 10

Steps of 2 component signaling?

Answer 10

1. Extracellular Molecule Binds Receptor in membrane = SENSOR that has an intracellular TRANSDUCER
2. SENSOR then TRANSDUCER get phosphorylated
3. TRANSDUCER works on operator

***Important in Quorum Sensing

Question 11

What processes use 2 component signaling?

Answer 11

1. Changing Temperature
2. Osmolarity
3. Extracellular Iron availability

Question 12

What is quorum sensing?

- what virulence factor relies on this hardcore?

Answer 12

• Bacteria Communication via releasing and measuring signaling molecules
• More signaling molecules released as population grows until CONCENTRATION THRESHOLD is reached
• All cells now begin expressing new gens

**Particularly important in biofilm formation

Question 13

What are the signaling molecules in quarum sensing?

Answer 13

• Non-peptides

- Usually cyclic structures like lactones or quinolones

Question 14

What challenges are posed to bacteria as a result of them being haploid?
- How are these challenges overcome?

Answer 14

1. Mutations readily lead to LOSS of FUNCTION
   - Overcome by SHEER NUMBERS, loss of millions of bacteria doesn’t matter much
2. Phenotypic Diversity could be limited because of only a single pair of alleles
   - Phase Variation
   - Antigenic Variation

Question 15

What is phase variation?

- what is the consequence of phase variation?

Answer 15

a. Gene can be inverted into the ON position
- aka Aligned with its promoter

b. Gene could be inverted into OFF position
- aka Gene FLIPPED so that PROMOTER IS NOT LONGER ALIGNED WITH GENE

**Results in an on and off switch for the gene

Question 16

Antigenic Variation

• what is the overall result
• what bacteria is known to use this?
• what is the clinical presentation for antigenic variation?

**SEE SCHEME for STEPS

Answer 16

Bacteria:
- Neisseria Gonorrheae

Overall Result:
- Large array of Surface Components

• Recurring infection because they are constantly changing their pilus

Question 17

Requirements for Antigenic Variation?

Answer 17

• Large numbers of bacteria
• Lots of growth

**Because you need functional mutant to expand and take over

Question 18

What are 4 ways that bacteria can actually acquire new genes?

Answer 18

1. Transposition
2. Conjugation
3. Transduction
4. Transformation

Question 19

What is transposition?

- 4 basic elements?

Answer 19

• Genetic elements hop or put an additional copy of themselves into their genome
• *All happens in one cell, does not jump from one to the next

1. Insertion sequences
2. Transposase
3. Repressor
4. Beneficial host gene (ANTIBIOTIC RESISTANCE GENE)

Question 20

What are the functions of the 4 basic transposon elements?

Answer 20

1. Insertion Sequences
   - Inverted DNA repeats
2. Transposase
   - Recombinase that allows insertion of sequence
3. Repressor
   - Regulates frequency of Transmission
4. Beneficial Host Gene
   - Antibiotic Resistence Gene
   - other virulence factor gene

Question 21

How can transposons be detrimental to cell health?

Answer 21

• It could enter in a bad spot in the genome (e.g. before lacZ)
• Must insert before a gene

**Cause problems when they bind to genes or operons

Question 22

What two ways do transposons increase cell diversity?

Answer 22

1. Introduction of an antibiotic resistance gene or another gene
2. Creation of mutants lacking non-essential wild-type functions

**all others will die

Question 23

Plasmids

• what are they?
• How big are they?
• Gene types?

Answer 23

Plasmids - Extrachromosomal (episomal) circular DNAs found in MOST bacteria

2-500 kilobase pairs

Targets for antibiotic genes for transposons

Question 24

T or F: smaller plasmids can replicated independently of the genome

Answer 24

True

Question 25

Why are plasmids maintained in the genome if they don't contain genes needed for cell survival?

Answer 25

- They many have transposons in them that contain Antibiotic Resistance Genes

Question 26

While transposons in themselves are retained to the cell from which they orginated, how could they travel to another cell?

Answer 26

- Could go to another cell via a Plasmid during Conjugation

Question 27

Conjugation - how does it occur - how is genetic diversity conferred as a result?

Answer 27

How: - High Frequency Transfer (Hfr) or F+ cells transfer F factor plasmid from one cell to another that is F- via a sex pilus Genetic Diversity: - Results from the fact that genomic DNA can enter off of chromosomes that are Hfr that allow some of their own genetic material to enter the second cell. - Cell2 can either put Hfr into genome or make a T or R factor plasmid

Question 28

What are PAIs (pathogenicity-associated islands)? | - what leads to their formation?

Answer 28

- Large regions of a chromosome that encode various virulence factors, toxins, and iron acquisition components. - Hfr are believed to be the major source of PAIs

Question 29

What are two factors that help us to know that PAIs are from an external source?

Answer 29

1. NON-pathogenic strains of the same bacterium lack PAIs | 2. Also lack G+C

Question 30

What is the difference between an F factor and an R factor?

Answer 30

F Factor: - plasmid that does not contain resistance genes R Factor: - plasmid that has acquired antibiotic resistance genes LIKELY FROM A TRANSPOSON

Question 31

Given that F factor is needed for formation of the sex pilus, how can R factor spread?

Answer 31

1. R Factor may be conjugative (can form the pilus) OR 2. It may be dependent on F factor for conjugation

Question 32

What is the major thing that confers antibiotic resistance of bacteria, and why is this?

Answer 32

- R Factor why? - It can spread through intERspecies conjugation and sometimes even across genera **Bacteria with several different R factors may confer multidrug antibiotic resistance

Question 33

What are viruses called that prey on bacteria? - what are the two types? - how do they differ?

Answer 33

- Phage 1. Lytic - Phage infects --> Replicates --> released from cell (usually by lysis) 2. Lysogenic (temperate) - Phage genomes integrate at specific sites in the bacterial chromosome (aka lysogen) - Lysogen remains in the cell until the cell undergoes stress (radiation etc.) - Stress induces Lytic Replication

Question 34

What is transduction? | - what processes can cause transduction?

Answer 34

- Transfer of genes from bacteria 1 (host) to bacteria 2 via a phage - Phages moves from one cell to the next causes this

Question 35

Generalized Transduction - who carries it out - how - what are the consequences

Answer 35

(transfer of genes horizontally among bacteria via phage) - ONLY carried out by LYTIC phage How: 1. Lytic phage cleaves bacterial chromosome into small fragments 2. Fragments may be similar size as virus (phage) genome and packages into Phage Particles 3. Phage particles containing Bacteria 1 DNA will be inserted into Bacteria 2 Consequences: - Any bacterial gene can be transduced to a recipient cell (resistance genes may be passed along)

Question 36

Specialized Transduction - who carries it out - how - what are the consequences

Answer 36

- Carried out by Temperate (lysogenic) phages How: - lysogen (viral genome) is inserted into the host genome - when stress occurs ABERRANT EXCISION causes some of the viral DNA to be left behind and BACTERIAL DNA is included instead - New phage is stable and will continue to carry bacterial DNA with it Consequences: **Original lysogen only inserts at certain parts of the genome, therefore only a few specific bacterial genes can be transduced by any particular phage

Question 37

Of the two types of transduction, which is most important to generating genetic diversity?

Answer 37

Specialized transduciton

Question 38

What is transformation? - what is its role in nature - what are cells called that can carry out transformation? Example?

Answer 38

- Uptake of Naked DNA from one cell to another - Insignificant role in creating genetic diversity in nature - Cells that can carry out transformation = Competent - e.g. Streptococcus Pneumoniae

Question 39

Overall, what is the most common way that bacteria exchange information?

Answer 39

Conjugation

Question 40

What is the paradigm case of transduction? | - what type?

Answer 40

Cholera Toxin (specialized transduction)

Question 41

What is the rate of both generalized and specialized transduction?

Answer 41

1/1000 - 1/10,000

Question 42

What is the rate of antigenic variation?

Answer 42

1/1000