Lecture #14: Bacterial Recombination

Question 1

HIV (Overview)

Answer 1

• Double-stranded RNA genome and it is a retrovirus that causes aids
• Enveloped virus with a genome and protein castle

Question 2

Retroviruses

Answer 2

• take up about 8% of the genome
• Most of the retroviruses are inactive
• Transposons take up about 44%

Question 3

Reverse transcriptase (functions)

Answer 3

3 different functions:
- RNA-dependent DNA polymerase,
- RNAse H activity (degrade original RNA strand)
- DNA-dependent DNA polymerase (allows it to form double-stranded DNA)
-used to try and reduce HIV infection: Major drug target in HIV therapy

Question 4

HIV timeline and t-cells

Answer 4

• This virus can go into a latent phase (long timeline)
• Major problem: loss of t-cells→ increased incidence and sensitivity to infectious disease and certain types of cancers

Question 5

Sars-CoV2

Answer 5

• Coronaviruses are a type of virus that can cause the common cold but have also been involved in multiple recent outbreaks.
  –>Single strand +RNA genome (sense strain)

Question 6

Covid Structure

Answer 6

• Has a membrane (envelope)
• Protein-bound capsid (nucleocapsid)
• Spike glycoprotein
• Membrane Protein
• Small envelope protein
• Nucleocapsid Protein
• RNA (within capsid)

Question 7

Covid Lifecycle (details)

Answer 7

• uses receptors on the surface, fuses with the cell (ACE2 receptor), and then release its genome.
• Because it is a sense genome, it can translate the genome directly
• In order for translation to be done, it will need the correct signals to do it (promoter region, etc.)
• no incorporation step, no latent phase

Question 8

Covid Lifecycle General

Answer 8

• Binding to ACE2 receptor
• Release of genome
• Translation–>proteolysis–>RNA replication–> Transcription and replication of genome
• Viral protein translation
• Viral assembly–>maturation–>release

Question 9

Sars-CoV2 Genome / Proteome

Answer 9

• Due to small genomes, it gets a limited amount of information (limited number of proteins)

Question 10

Bacterial genetics (overview)

Answer 10

• The genetics of bacteria (subtly different than those of eukaryotes)
• DNA organization

Question 11

E. Coli (general)

Answer 11

• Generic bacteria
• Discovered as a bacteria that could cause dysentery in infants
• Most E. Coli are not pathogenic
• They help to produce vitamin K in the human gut (digestive tract). Vitamin K is really important for blood clotting
• Credible tool for metabolism and genetics

Question 12

E.Coli Cell (structure)

Answer 12

• Plasmid (important for bacterial genetics)
• Nucleoid with DNA
• Cytoplasm containing ribosomes
• Capsule
• Cell wall
• etc.

Question 13

E.Coli chromosome

Answer 13

Approximately 4.6 million base-pairs, but it hase 4,288 protein coding genes

Question 14

Gene transfer and recombination in bacteria

Answer 14

• Bacteria don’t use sexual reproduction
• genetic recombination is how we make use of genetic material
• Use antibiotics to prevent growth

Question 15

Wild-type bacteria (with all genes being functional)

Answer 15

→ can grow on a minimal defined media. Make use of mutants that can’t grow on this media.

Question 16

Auxotrophs

Answer 16

→they need additional components to grow. Mutants have non-functional versions of some genes.

Question 17

Alleles

Answer 17

→are different functional versions of a given gene
- Versions of genes are alleles→ functional and non-functional

Question 18

Idea of clones

Answer 18

→bacteria grown from a single parent (close to genetically identical)

Question 19

3 ways genetic material can be transferred to bacteria, depending on the source and the mechanism. But, not all bacteria do every type.

Answer 19

• Transformation
• Transduction
• Conjugation

Question 20

Transformation

Answer 20

→ Environmental DNA (probably from dead bacteria in nature)
→ Griffons experiment→ transforming principle
→ About 1% of bacteria species can do this naturally. E.Coli isn’t one of them
→ this transformation mode will be used on plasmids. Often, these plasmids are R plasmids: which encode resistance genes to some antibiotics. (Ex. psc10-6.5kb- encodes resistance to tetracycline)
- these genes make a pump

Question 21

Transduction

Answer 21

• Transfer DNA between bacteria using bacteriophages
  → Phage invades cell
  → chop up the bacteria chromosome, split them up into the plus versions of themselves (A+ and B+)
  → Release A+ version to infect recipient cell and recombine to incorporate into new cell (A- becomes A+)
  → Recombinant Cell now exists

Question 22

Generalized and Specialized Transduction

Answer 22

• randomly translated into a virion
• a restricted set of bacterial genes are transferred to another bacterium.

Question 23

Conjugation

Answer 23

• Transfer of DNA between bacteria (donor and recipient) using specialized machinery. (mixture creating colonies)
• Changing the phenotype of the bacteria
• Spelling out the alleles
• Living bacteria making use of the others’ DNA