Unit 4 - DNA Replication + Gel Electrophoresis + PCR

Question 1

What does it mean when dna replication is semi conservative

Answer 1

when making new dna strands, only 1/2 of the strand is synthesized with new bases,

• the other half is used from past dna –> semi conservative

Question 2

New nucleotides can only be added on which side of the dna strand?

Why?

Answer 2

3’ –> 5’

3’ carbon has a OH group,

Phosphodiester bonds are connected through this OH group

5C’ CH2 - Oh - phosphate - Oh connected through Carbon

–> cannot be added without oxygen
–> only between 2 hydroxyl groups

• phosphodiester bond adds new sugar back bone, this allows for new bases to be added

Question 3

Dna replication process involves what?

Answer 3

1. Origin of Replication
2. Replication Bubble
   2a. Unwinidng of DNA seperating the strand leading into 2 replication forks
3. New DNA is synthesied
4. Bye rna primers and hellow dna
5. reconnected and sealed

Question 4

Helicase function and apart of what role in dna replication?

Answer 4

Function: unwinds dna by breaking Hydrogen bonds between the two base pairs

Role: Unwinding the DNA

Question 5

Single Stranded DNA function and apart of what role in dna replication?

Answer 5

Function: Keeps the 2 parent strands apart to prevent them from reforming hydrogen bonds and connecting again

Role: Unwinding the DNA

Question 6

Topoisomerase function and apart of what role in dna replication?

Answer 6

Function: Releases the tension of the unwinded dna, preventing it from stressing to the point of the dna breaking

Role: Unwinding the DNA:

Question 7

DNA primase function and apart of what role in dna replication?

Answer 7

Function: To make a starter complimentary strand of RNA to start the rest of the dna synthesis and a starting spot for DNA poly III

Role: DNA Synthesis

Question 8

DNA Poly III function and apart of what role in DNA replication?

Answer 8

Function: synthesizes a new dna strand with complementary bases from the DNA primer
- starts at the primer and ends at either the origin of replication or at the replication fork

Role: DNA Synthesis

Question 9

DNA Poly I function and apart of what role in dna replication?

Answer 9

Function: Removes the RNA segments which were added by the DNA primase and replaces it with DNA

Role: DNA Synthesis

Question 10

DNA Ligase function and apart of what role in dna replication?

Answer 10

Function: Connects the OKazaki Fragments from the lagging strand and the two leading and lagging strand

Role: DNA Synthesis

Question 11

What is the Poly III proofreading function?

Answer 11

Poly III –> when a wrong base was added and matched by one it was not suppose to by mistake
- this is extremely rare but when there is it goes back and deletes all of the base pairs,
- removes the past couple of base pairs and sets them free in the cytoplasm and repairs them.

Role: Apart of DNA Synthesis

Question 12

What is the leading strand?

Answer 12

The part of the replication where the replication fork and the 5’ –> 3’ directionality match up.
- allowing for poly III to keep on synthesizing DNA as the replication fork opens

Question 13

What is the Lagging strand? What does this strand have that the leading strand doesnt?

Answer 13

The part of replication where the replication fork and the 5’ –> 3’ directionality DO NOT match up.
- forces a dna primase to be added at replication fork, once it keeps going to add more and travels right it forces there to be a new primase and poly iii to work from there till replication of orgin or prior rna primase.

CREATES OKAZAKI FRAGMENTS

Question 14

What is PCR?

Answer 14

A way for scientists to analyaze a specific dna sequence.
- can be put into different experiments to see if there is something wrong with them or if it can cause a certain gene expression

Question 15

What are the 3 parts of PCR?

Answer 15

1. Dentruation
2. Annealing
3. Extension

Question 16

What is Denaturation?

What is the temperature?

Answer 16

seperates the double stranded dna through making the enviornment unfit for the hydrogen bonds.

Increased to HOT 95 C

Question 17

What is added artifically to the PCR?

Answer 17

• heat is altered and changed
• DNA primers - which are dna not rna, poly III, nucleotide bases, and the dna sequence

Question 18

What is Annealing?

Temp?

Answer 18

DNA primers can form hydrogen bonds with dna sequence

Temperature is cooled down to 55 C

Question 19

What is Extension?

Temp?

Answer 19

Temp allows for the hydrogen bonds between bases to form

Poly III taq which can withstand hella heat start adding bases after the prior nucleotides.

Temperature got warmer 75 C

Question 20

Dideoxy ribose lacks what?

• this prevents?

Answer 20

a OH group on the third carbon.

phosphodiester bonds to be added, no nucleoside, not base can be added
–> sequence is terminated

Question 21

What is Gel Electrophoresis?

Answer 21

A process in which a part of dna is added in a gel, and it can be seperated through size and charge

Question 22

Are larger dna will be closer to the positive side of the gel (bottom) or closer to top

Answer 22

Closer to top
- more dense –> needs more energy to go to the + side

Question 23

Is smaller DNA will be closer to the positive side of the gel (bottom) or closer to top

Answer 23

• Closer the the bottom
• Less dense and it will be more pulled to the bottom

Question 24

What is Sanger DNA Sequencing?

Answer 24

• Mixes a small quantity of dideoxy nucleoities with Dna + DNA polly iii and primers
• mix of DNA fragments from the whole dna sequence
• through gel entrophines it is put in order from smallest to largest
• order puts which sequence was first – find out base sequence of dna