Chapter 8 Part 3

Question 1

Genomes are dynamic which means they are constantly changing through:

Answer 1

1. Mutations
2. Horizontal Gene Transfer (HGT)

Question 2

Define Mutations

Answer 2

changes to existing (endogenous) genetic information

Question 3

Define HGT

Answer 3

acquisition of new (exogenous) genetic information

Question 4

List all the characteristics of Mutations

Answer 4

1. a change in DNA sequence
2. an uncorrected error
3. Mutations can be spontaneous
4. errors are made 1 out of a billion but still add up over time
5. Mutations can be increased/induced by mutagens
6. Mutations aren’t inherently good or bad

Question 5

What are mutagens? and give an example

Answer 5

agents that cause DNA damage
UV light

Question 6

How can mutations affect nucleotides?

Answer 6

• it can affect single, a few, or many nucleotides
• it can impact base substitutions
• small insertions and deletions (loosing track so adds or deletes a nucleotide)
• Rearrangements/duplications (chunk of DNA gets copied again or that chunk moves somewhere else)
  (a more complex mutation)

Question 7

How do mutations affect or not affect encoded proteins?

Answer 7

Synonymous mutation = no change to protein sequence (silent)
Non-synonymous mutation = changes protein sequence

Question 8

What are the 3 types of non-synonymous mutations?

Answer 8

1. missense
2. nonsense
3. frameshift

Question 9

Define missense

Answer 9

changes an amino acid to another amino acid
- single AA change

Question 10

define nonsense

Answer 10

changes an AA to a stop codon
- major mutation which makes it non-functional now

Question 11

define frameshift

Answer 11

shifts the reading frame so all subsequent codons are out of frame

Question 12

What is this mutation called?
Original: Met-Asp-Cys-Glu-Thr-Ala-Thr-Gly
Mutation: Met-Asp-Cys-Glu-Asp-Ser-Asp-Arg

Answer 12

Frameshift
Original: Thr-Ala-Thr-Gly
vs
Mutation: Asp-Ser-Asp-Arg

Question 13

Define Transposons

Answer 13

• Jumping genes
• more harmful than helpful
• small segments of DNA that move around within bacterial chromosomes
  -encodes a transposase gene
• can contain other genes as well like an antibiotic resistance gene

Question 14

What is an transposase?

Answer 14

a gene that facilitates the movement of the transposon
- cuts at inverted repeats to initiate recombination at a distal site

Question 15

What is the simplest version of a transposons?

Answer 15

an insertion sequence (IS)
composed of only inverted repeats and transposase gene

Question 16

How do bacteria transfer DNA to cells that are not their offspring?

Answer 16

Horizontal gene transfer

Question 17

What does a recombinant organism mean?

Answer 17

when traits are shared between unrelated bacteria

Question 18

What are the 3 ways of horizontal gene transfer?

Answer 18

1. Transformation
2. Conjugation
   3.Transduction

Question 19

Define Transformation

Answer 19

• the uptake of DNA from the environment (usually from cells that died
• Competency

Question 20

What is competency?

Answer 20

the ability to perform transformation

Question 21

How can transformation be done?

Answer 21

Natural or induced through electrical or through chemicals
natural - has apparatuses than can reach out and pull the DNA in to itself

Question 22

Define conjugation

Answer 22

• Direct transfer of DNA between two cells
  -involves a donor & recipient
• initiated by a sex pilus protruding from the donor cell

Question 23

Sex pili are encoded on ?

Answer 23

conjugative plasmid

Question 24

What do conjugative plasmids do?

Answer 24

mediate their own transfer from the donor cell to a recipient cell

Question 25

How does HGT occur?

Answer 25

when some of the recipient's DNA is transferred along with the conjugative plasmid

Question 26

Why would the donor want to share DNA?

Answer 26

the plasmids "want to"

Question 27

Why would the recipients want shared DNA?

Answer 27

for the anti-biotic resistant part

Question 28

Define Plasmids

Answer 28

- self-replicating circular pieces of DNA that are maintained within a cell - much smaller than bacterial chromosomes - does not encode essential genes (aka plasmids can be lost and the bacterial cell will still survive - often contains specialty genes (antibiotic resistance or virulence genes)

Question 29

what are virulence genes?

Answer 29

the ability to cause disease

Question 30

Define Fertility (F) Factor

Answer 30

- best studied conjugative plasmid found in e.coli - When a cell has a F factor (a plasmid) its an F+ cell

Question 31

What is the cell called after F factor is integrated into the bacterial chromosome?

Answer 31

HFR- high frequency recombination

Question 32

When does recombination happen?

Answer 32

between sites with similar sequence on the plasmid and chromosomes

Question 33

Recombination can also lead to what?

Answer 33

Excision meaning the F factor combines with the chromosomal DNA - donor donates a copy (doesn't lose anything)

Question 34

What is transduction?

Answer 34

DNA transfer mediated by a bacteriophage

Question 35

What is a bacteriophage?

Answer 35

a virus that infects bacteria

Question 36

Where do bacteriophage package their DNA ?

Answer 36

Capsid so they can infect other cells -but sometimes DNA from the bacterial chromosome gets packaged into the capsid instead so bacterial DNA is transferred from donor to recipient

Question 37

What is part of all 3 mechanisms?

Answer 37

Recombination

Question 38

Define recombinant

Answer 38

exchange of DNA between two DNA molecules - most efficient when regions are homologous (similar DNA sequences)

Question 39

Why is recombination important?

Answer 39

once DNA is required through HGT it must be maintained by the recipient cell or it will be lost - if the DNA is plasmid - will be maintained on its own - if the DNA is not a plasmid - has to integrate into the chromosome or it will be degraded by the cell

Question 40

What protein catalyzes the joining of the two strands (donor to recipient)?

Answer 40

RecA

Question 41

Recombinant is like

Answer 41

crossing over both strands