Dna

Question 0

What are the three types of topoisomerases and what do they do?

Answer 0

Type 1- relieves torsional stress caused by negative supercoiling
Type 2- introduces negative super coils
Type 3- introduces positive super coils, mostly in Archaea

Question 1

Archaea and bacteria have what kind of DNA ?

Answer 1

Circular

Question 2

What benefit does positive supercoiling have in hyper thermophilic Archaea?

Answer 2

It helps prevent denaturing of DNA in extreme environments

Question 3

What do type 1 topoisomerases do?

Answer 3

Enzyme attaches to DNA and causes a single strand break during replication

Question 4

What does type 2 topoisomerases do?

Answer 4

GyrB and GyrA
Creates negative supercoils, causes a double stranded break, costs ATP
Occurs after replication when packing up the DNA
Can also fix positive supercoiling

Question 5

How’s is eukaryotic DNA organized?

Answer 5

In chromatin where it is wrapped in histones
DNA + histones=nucleosome
Archaea DNA is similar

Question 6

What are the basic steps of DNA replication?

Answer 6

1. Binding of DNA-A, costs ATP
2. Formation of open complex
3. DNA-C is the loader that binds DNA-B
4. DNA-B unwinds helix
5. Primase (DNA-G) adds RNA primer
6. DNA polymerase 3 binds and creates new strand

Question 7

What is oriC?

Answer 7

Where DNA replication begins. DNA-A binds and melts DNA at the oriC

Question 8

What does opening the DNA during replication do?

Answer 8

Allows recruitment of helicase enzymes

Question 9

What are helicase s ?

Answer 9

DNA-G
Protein that opens up the 2 strands and two forks
One helicase per each fork
One helicase moves in each direction in front of polymerase
Recruits primase

Question 10

What is primase?

Answer 10

DNA g

Inserts RNA primer into genome so polymerase can start on the 3’ end

Question 11

What direction does replication go?

Answer 11

5’-3’

Polymerase can only attach to the 3’ OH

Question 12

What end does polymerase add to?

Answer 12

To the 3’

Question 13

What help repair lagging strand gaps?

Answer 13

RNase removes the primer
DNA polymerase 1 fills in gaps
Ligase seals nicks left in lagging strand

Question 14

What are catenanes?

Answer 14

2 circular daughter cells bound together after replication

Question 15

What happens at the Ter site?

Answer 15

It’s the termination site that causes polymerase and proteins to fall off

Question 16

What are the major characteristics of an eukaryotic genome?

Answer 16

Linear
Has multiple origins of replication
Only occurs during S- phase
Once replication begins it must finish or die

Question 17

What are the major characteristics of the prokaryotic genome?

Answer 17

No S-phase
Can have multiple strands of replication happening at the same time
Replication machinery stays stationary while chromosomes move around cell
Is bidirectional- 2 lagging strands and 2 leading strands

Question 18

What does DNA polymerase 3 do?

Answer 18

Proof reading

Removes mismatched base from 3’ end by exonuclease activity of enzyme

Question 19

How does mismatch repair work?

Answer 19

When a wrong base is put down, it results in a bulge
Mut S detects bulge and recruits Mut H to bind to base
Mut L binds Mut H and S together to fix bulge by methylating strand, marking it for destruction
Mut H nicks the DNA and exonucleases degrade bad strand

Question 20

How does base or nucleotide excision repair work?

Answer 20

Is when it’s bad nucleotide, not wrong base

Enzymes bind it, clean it up, then DNA polymerase comes back to fix it

Question 21

What is SOS repair?

Answer 21

When all else fails…DNA polymerase 3 finds damaged DNA, stalls and partially detaches to allow rec A to
Rec A- protein that binds and removes damaged sequences
Not always fixed correctly but allows replication to continue

Question 22

What is the holiday junction?

Answer 22

A 4 way intersection after the catanase starts to separate

Question 23

What is the shine dalgarno sequence?

Answer 23

The site where ribosomes clamp on to mRNA to initiate protein synthesis and proper alignment with the start codon

Question 24

What is transcription?

Answer 24

RNA synthesis under the direction of DNA. Has a complementary sequence to the template DNA

Question 25

What is the central dogma?

Answer 25

DNA replication, DNA transcription into RNA, RNA translation into proteins

Question 26

How does transcription begin?

Answer 26

An RNA polymerase binds at promoter to initiate transcription

Question 27

What are sigma factors?

Answer 27

A small protein within the RNA polymerase that guides the polymerase to the target DNA sequence

Question 28

What is transcription elongation?

Answer 28

Core polymerase adds to RNA to 3’ end, complementary to template strand.

Question 29

Describe transcription termination?

Answer 29

Polymerase slows at pause site, a GC rich sequence, and forms a stem loop.
Rho dependent termination- rho factor binds to mRNA breaks polymerase, mRNA off DNA
Rho independent termination- series of U residues downstream of pause site, very unstable, mRNA breaks off of DNA and the polymerase is released

Question 30

DNA replication steps

Answer 30

1. Genome w Ori C-
2. DNA A binds ATP- to the Ori c and starts opening, bids at a long string of A
3. Helicase ( DNA B)- protein that opens up the 2 strands and 2 forks, one helicase at each fork
4. Primase(DNA G)- inserts RNA primer ( about 10 bases of RNA) in genome so polymerase has the 3’ end to start
5. DNA polymerase 3- creates new strand