Lecture #13: Transposable Elements and Viruses

Question 1

Genetics

Answer 1

The study of heredity and variation among organisms.

Question 2

Molecular genetics

Answer 2

The field of genetics that studies structure and function of genes at the molecular level.

Question 3

Transposable elements

Answer 3

DNA segment that can move from one location to another in the genome and increase in number.

Question 4

TE Overview (Pro v.s. Euk)

Answer 4

• Exist in all organisms
• sole purpose is to increase in number
• Powerful source for change in evolutionary timescales
  Pro: there are DNA transposons and simpler versions called insertion sequence
  Euk: DNA transposons and retrotransposons (bounded on either end by repeat DNA sequences)

Question 5

DNA Transposons (Class II transposons) are characterized by…

Answer 5

• Cut+ paste mechanism (1): TE leaves one location in DNA and moves to another.
  –>gene that codes for transposase (in cut+paste)
• Copy + paste mechanism (2): A copy of the TE leaves one location in DNA and moves to another (leaving the original behind).
• both result in duplication of the target site

Question 6

Genetic recombination

Answer 6

The process where DNA is cut (in the backbone) and ligated back together.

Question 7

Retrotransposon

Answer 7

• Copy +paste mechanism: making an RNA copy of the whole sequences
• Retrotransposon uses RNA to make a DNA copy
• The enzyme makes a double-stranded DNA copy of the retrotransposon from RNA
• Transposase encoded by the transposon (transposition) moves the copy to a new site on the DNA.

Question 8

Transposons and Humans

Answer 8

• Protein coding genes- 2% of the 3.2x10^9 base pairs in the human genome
• About 44% of the genome is transposable elements
• 0.2% of the genome is made up of active transposons

Question 9

Viruses

Answer 9

Biological particle that can infect living cells

Question 10

Why are viruses not defined as alive? (Why?)

Answer 10

• They cannot replicate independently
• They do not generate metabolic energy
  –> Viruses rely on cellular machinery to do these jobs
  –> Viruses possess proteins to help with viral genome replication, for manipulating host functions, and creating viral structure

Question 11

Viral Structure

Answer 11

• Nucleic acid core: contains viral genome
• Protein coat: a structural coat that protects the genome of the virus
• Spike protein: mechanism used to enter the cell

Question 12

Bacteriophage

Answer 12

Two types: Virulent and Temperate
- Bacteriophages can transfer bacterial DNA between cells, so they are an important mechanism influencing bacterial genetics.

Question 13

T-even Bacteriophage (Virulent)

Answer 13

*if something goes wrong, it will kill the cell
- a lysosome enzyme degrades host genome
- Phage injects DNA into a host cell, enzymes and proteins are produced for the phage lifecycle, and a phage-encoded enzyme breaks down the bacterial chromosome.
- viral genome is replicated
- Assemble virions
- release virions via cellular lysis

Question 14

Virulent Types use….

Answer 14

Generalized transduction:
- some virions incorporate a fragment of the host genome into the released virion which can be transferred to the next host.
- Randomized

Question 15

Lamda Bacteriophage (Temperate bacteriophage) (general overview)

Answer 15

• injects DNA into the host cell (Has a choice to go through the lytic cycle or the lysogenic cycle)
• Lysogenic cycle is through genetic recombination
  At some point, the bacteriophage in the lysogenic cycle shifts to the lytic cycle.
  -2 possible life-cycles: the phage genome can incorporate into the host genome in the lysogenic cycle.
• When the phage genome excises itself from the host genome to enter the lytic cycle, some host genome can be included. This leads to specialized transduction.

Question 16

Specialized Transduction

Answer 16

Phage genome inserts into specific locations of the host genome. It can include some fragments of portions of the host genome if inaccurately cut out, leading to the inclusion of host genome sequence in virion and potential transfer to a new host.
- can be predicted what type of the host genome is being included.

Question 17

Viruses Infecting Animals

Answer 17

A diverse group of viruses, categorized by:
→ nucleotide type used for the genome structure
→ species type tropism
→ Tissue tropism
→ may have originated from cellular DNA

Question 18

HIV (General)

Answer 18

A retrovirus that infects a specific group of T-cells in some mammals
- Causes diseases→ Aids (Acquired immune deficiency syndrome)

Question 19

HIV structure (General)

Answer 19

• Membrane-bound virus, including proteins in that membrane
• It has a lot of secondary structure

Question 20

HIV Life-cycle

Answer 20

• Viral particle enters cell
• Reverse transcriptase makes DNA copy of RNA genome
• DNA copy is incorporated into host DNA
• Viral DNA is transcribed into viral RNA, mRNAs, and then into proteins
• Viral RNAs and proteins assemble into particles that bud from the cell.