Exam 2 Lecture 15

Question 1

Silent change in DNA?

Answer 1

A base change that doesn’t result in a change of AA

Question 2

Missense change?

Answer 2

Single base change that results in a different AA being encoded, can make a protein non-functional or change the function

Question 3

Nonsense Change?

Answer 3

Base pair change that encodes a new stop codon in the middle of the protein

Question 4

Translational frameshifts?

Answer 4

Insertion or deletions that make everything downstream change by one or two base pairs and can change the protein code bigtime!!!

Question 5

How do big changes happen?

Answer 5

Insertion Sequences (IS), Transposons, genomic Island insertions like secretion systems and metabolic cassettes, addition of independent replicating elements, and integration of viral genes or genomes

Question 6

What is an IS element?

Answer 6

They are typically 700-1500 bp long that encode a protein Tnp that can move DNA elements. Transposase

Question 7

What are Transposons like Tn5?

Answer 7

Longer sequences than ISs often with several genes in them flanked by IS elements. When they move they either be good such as add antibiotic resistance or be bad and disrupt regular gene function (knock out mutation)

Question 8

Three main types of HGT (horizontal gene transfer)?

Answer 8

1. Transformation
2. Conjugation
3. Transduction

Question 9

What was the first description of HGT?

Answer 9

The Griffiths experiment and Streptococcus pneumoniae

Heat killed S cells with capsid and live R cells with out capsid killed rat.

Capsid genes transferred from dead cells to live cells in a process known as transformation

Question 10

Steps of Transformation?

Answer 10

1. dsDNA bind to exterior of competent cell by DNA binding proteins

2 DNA is transported using ATP by DNA competence channal while transforming it into ssDNA

3. Rec A mediates recombination of DNA into host DNA using homologous sequences of 20-30 bps

Question 11

In transformation is the donor living or dead?

Answer 11

Often dead

Question 12

Can you get big insertions in transformation?

Answer 12

Yes if the genes are flanked by homologous sequences.

Question 13

Name some bacteria that transformation occurs in?

Answer 13

Bacteria- Bacillus, Pseudomonas, Hemophilus, and Neisseria

Question 14

Name some archaea that transformation occurs in?

Answer 14

Methanococcus and Thermococcus

Question 15

Does conjugation happen from live or dead cells?

Answer 15

Live

Question 16

During conjugation does the donor lose DNA?

Answer 16

No

Question 17

What is a plasmid?

Answer 17

Extrachromosomal dsDNA that replicates independently from the chromosome

Can have a host range and can be incompatible with each other if in the same host

Question 18

Plasmid shape and size?

Answer 18

Usually circular, vary in size from 3-200+ kbs

Question 19

Do Plasmids carry essential genes?

Answer 19

No, but can encode for important functions that can give a significant selective advantage

Question 20

Plasmid size and copy number (number of copies of the plasmid that the cell carries) relationship?

Answer 20

small size = high copy number

large size = low copy number

low copy number means low initiation of replication

Question 21

First Plasmid identified?

Answer 21

F (fertility) plasmid in E coli

99kb with several IS/Tn elements and transfer and replication and inc functions

(no antibiotic resistance in F plasmid)

Question 22

How do conjugative plasmids get transferred?

Answer 22

With conjugative pili

Question 23

What is a conjugative pili?

Answer 23

A thin protein filament that is polymerized as it is extended from donor cell that makes contact with recipient cell

Question 24

Steps of Conjugation?

Answer 24

1. Pilusis extended from T4SS makes contact and contracts closing distance between two cells

2 Relaxase unwind DNA at OriT and second relaxase is recruited to bubble

3.One strand is nicked at OriT and a relaxase attaches to 5’ end and is passed through T4SS to recipient cell while the other relaxase stay in donor cell continuing to unwind DNA

4 RNA poly III synthesises new strand in donor cell and recipient cell once transfer is complete

Now both are donor

Question 25

What type of secretion systems does conjugation use?

Answer 25

Type IV

Question 26

Does conjugation use energy?

Answer 26

Yes ATP, very energy intensive

Question 27

Where are transfer genes carried?

Answer 27

On the plasmid

Question 28

Which end of the DNA is transferred first in conjugation?

Answer 28

the 5’ end

Question 29

What is the downside of having a pilus?

Answer 29

Viruses can attack it and it opens the cell up for infection.