Topic 6, Lecture slides

Question 1

What is Camptothecin?

Answer 1

it is isolated from the happy tree, it stops topoisomerase 1
from working preventing DNA replication. it has anti cancer activity but many side effects.

Question 2

What is Topoisomerase 1

Answer 2

Its the enzyme responsible for DNA replication. it removes the supercoils that arise from DNA unwinding.
Induces a DNA break to relieve the supercoiling, then reseals it. Camptothecin stops the resealing and pervents topoisomearase from working.

Question 3

Define Conservative replication

Answer 3

<p>First replication, yeilds 1:1 old and new strand. 2nd replication yeilds 1:3 old and new strands </p>

Question 4

Define Dispersive Replication

Answer 4

Bits get replicatied and glued together,all DNA yeilds a mixture of old and new

Question 5

Define Semi Conservative

Answer 5

Produces new strands, but also produces mixture DNA with new and old strands glued together.

Question 6

Define the Meselson and Stahl experiment.

Answer 6

Used equilibrium density gradient centrifugation to distinguish between old and new DNA.
they band DNA with 15n and 14n new DNA is lighter than old DNA so when centrifuged will separate into old and new strands of DNA. They centrifuged the DNA 4 times.
1st with 15n whichs marks the dna with a heavy band.
2nd they let the dna replicate with addition of 14n, they spin again.
3rd spin they get new and old DNA split. The new is marked with 14n and the old is marked with 15n.
This proves that, all DNA molecules are a mixture of old and new DNA. and that new DNA is made from old DNA, and proves the Semi Conservative model.

Question 7

List the basic replication requirements

Answer 7

• DNA template
• Raw materials, building blocks
• Enzymes and other proteins that read the template and assemble the new strand.

Question 8

Template?

Answer 8

An original DNA strand to replicate from.

Question 9

Replication fork ?

Answer 9

replication goes in two directions, produces two new strands at the same time.

Question 10

Leading strand?

Answer 10

A strand in replication that replicates continuously.

Question 11

Lagging Strand?

Answer 11

A stand in replication that replicates discontinuously, or in sections.

Question 12

What are the fragments produced in the lagging strand called?

Answer 12

Okazaki Fragments

Question 13

list the 4 Mechanism of Replication in eukaryotes ?

Answer 13

• initiation
• Unwinding
• elongation
• Termination

Question 14

what is proof reading?

Answer 14

If a wrong nucleotide is found it will be cut out and replaced with the correct base. occurs during replication

Question 15

What is mis-match repair?

Answer 15

After replication is completed, if any mis matched nucleotides are found they are cut out and replaced (occurs after replication)

Question 16

Explain the role of DNA polymerase 1 ,111 ?

Answer 16

DNA polymerase 1 is the enzyme that adds nucleotides to a free 3’-OH group and removes RNA primers.
DNA polymerase 111 elongates a new nucleotide strande from the 3’-OH group provided by the primer

Question 17

DNA Ligase?

Answer 17

This enzyme will seal nicks in the DNA sugar phosphate backbone at the end of replication.

Question 18

DNA Primase?

Answer 18

Produces short RNA prmers with free 3’-OH ends.

Question 19

DNA helicase?

Answer 19

Unwinds DNA at replication fork

Question 20

Initiator Protein?

Answer 20

Binds to origin and separates Strands of DNA to initiate replication.

Question 21

DNA Gyrase?

Answer 21

Moves ahead of the replication fork, making and resealing breaks in the double helical DNA to release torque that builds up as a result of unwinding at the replication fork.

Question 22

Single-strand-binding proteins?

Answer 22

Attach to a single stranded DNA and prevent reannealing

Question 23

DNA Initiation

Answer 23

• Initiation starts at the origin of replication (oriC)
• Initiator proteins bind to oriC and cause unwinding of a short section of DNA.
• DNA helicase and other single-strand-binding proteins will subsequently bind.

Question 24

What do SSB Proteins do ?

Answer 24

Keep the strands separated.

Question 25

Bidirectional?

Answer 25

DNA replication occuring Anti-parallel to each other.

Question 26

Eukaryote Replication

Answer 26

Is more complex, contains many origins of replication that all have to fire at once and once only. is separated in two steps - origins are licensed by replication licensing factor. - replication is initiated. Telomeres play an important role due to linear DNA. nucleosomes form new and old histone proteins.

Question 27

Differences between circular and linear replication.

Answer 27

circular only has one origin of replication, and occurs completely around adding nucleotides to the free 3'-OH group. Linear has multiple origins of replication, happens bidirectional in a anti parallel order, consists of a leading strand and a lagging strand. needs primers to be synthesised, elongation of DNA strand and the removal of those primers.

Question 28

What happens to the telomeres during replication?

Answer 28

Telomeres are the ends of eukaryotic chromosome. they are replicated by an RNA- protein complex called telomerase. which adds nucleotides to the GC rich strand of telomere. The shortening of Telomeres may contribute to ageing. mice deficient in telomerease show premature ageing. Somatic cells can be made that have active telomerase, which will divide indefinitely. Werner Syndrome, autosomal recessive caused by a defect in WRN.

Question 29

Dyskeratosis?

Answer 29

The X-linked form causes a defect in dyskerin which processes the RNA component of telomerase Telomeres in the germ cells are shortened and each successive generation has shorter telomeres and more severe disease. ( anticipation) * cancer cells often express telomerase

Question 30

Transcription?

Answer 30

Is the synthesis of RNA molecules using DNA as a Template.

Question 31

The Primary and Secondary structure of Transcription.

Answer 31

``` Primary = linear Secondary= Folded ```

Question 32

Define mRNA, tRNA, rRNA.

Answer 32

``` mRNA= Messenger RNA, found in both nucleus and cytoplasm. carries the genetic code for protein. tRNA= Transfer RNA found in the cytoplasm. Helps incorporate amino acids into a polypeptide chain. rRNA= Ribosomal RNA, in the cytoplasm. Structural and functional components of the Ribosome. ```

Question 33

Template Strand

Answer 33

A single strand of DNA that codes for a single strand of RNA.

Question 34

Describe prokayotic transcription

Answer 34

Bacterial Transcription consists of 3 stages: 1. initiation. 2. elongation. 3. termination. * initiation is the main step for control, it involves a promoter recognition, formation of transcription bubble, creation of first complementary base pairings, escape of machinery from promoter. Its promoter consists of : - TATA box at -10 - -35 consensus sequence - sometimes a third upstream element * RNA polymerase is positioned at start site (+1)

Question 35

Termination in prokaryotes

Answer 35

Termination is either Rho dependent or Rho independent. inverted repeats repeats are transcribed and form a hairpin loop in Rho independent termination. In bacteria polycistronic mRNA can be formed multiple genes with one promoter and one terminator.

Question 36

Transcription in Eukaryote cells

Answer 36

No generic promoters found, depends on whether it is recognised by RNA ploymerase i,ii,iii many proteins take part in promoter binding and RNA polymerase cannot start transcription by itself. DNA structure has to be modified as well. Termination is NOT important. Transcription in Archea is NOT important.

Question 37

Transcription Initiation in Eukaryote cells

Answer 37

Transcription Initiation in eukaryote cells needs ; - general transcription factors ( forms the basal transcription apparatus ) - transcription activator proteins. - promoter sequences - enhancer sequences.