Lec. 3: DNA Structure and Replication

Question 1

What is a locus?

Answer 1

precise location of a gene on a chromosome

Question 2

What is the basic unit of chromatin? What compacts chromosomes to make chromatin? What is a basic unit consistent of?

Answer 2

Histone proteins compact chromosomes to make chromatin
basic unit of chromatin is a nucleosome
-consists of 147 base pairs and a histone octamer (2 molecules each of H2A, H2B, H3, and H4)

Question 3

What connects individual nucleosomes in a chromatin?

Answer 3

Linker DNA which is bound by H1 histone

Question 4

What does the remodeling of nucleosomes allow for?

Answer 4

Allows for differential access to DNA by proteins for gene expression, replication, repair. Allows genes to be turned on or off

Question 5

What are the purines? What are the pyrimidines?

Answer 5

Purines = A and G
Pyrimidines = C and T

Question 6

What kind of bone links:
The sugar backbone to the base?
Adjacent nucleotides?
Two strands of DNA via base pairs?

Answer 6

Glycosidic bond links the base to the sugar
Phosphodiester bond links the sugars together
Hydrogen bonds link nucleotide bases together (A-T = 2 H bonds, G-C = 3 H bonds)

Question 7

What is a sense strand?

Answer 7

The strand that has the sequence the SAME as the mRNA strand. The other strand is complementary and is antisense

Question 8

Where does DNA replication initiate? What unwinds the DNA?

Answer 8

Initiator proteins bind to the origin of replication and recruit other proteins for DNA replication
-first unwound by helicases

Question 9

What are the two ‘semi’ of DNA replication?

Answer 9

Is semi-conservative
-each DNA strand acts as a template
Is semi-discontinuous
-Leading and lagging strand differences

Question 10

What is the direction that DNA is always synthesized?

Answer 10

5’ -> 3’

Question 11

What protein joins Okazaki fragments together?

Answer 11

DNA ligase

Question 12

Which DNA polymerase synthesizes the leading strand? Which for the lagging strand?

Answer 12

Leading strand = polymerase epsilon

Lagging strand = polymerase delta

Question 13

Which DNA polymerase is associated with primases?

Answer 13

Pol. alpha has primases that synthesize small RNA primers

Question 14

Which DNA polymerases are involved in DNA repair? Which are involved in replication of mitochondrial DNA

Answer 14

Pol beta, eta, zeta, delta, epsilon are all involved in DNA repair
Pol gamma is involved in replication of mitochondrial DNA

Question 15

What is the first polymerase to begin the leading strand, and what polymerase takes over? What happens on the lagging strand? What removes the RNA after priming?

Answer 15

• Primase on pol. alpha synthesizes primers, then pol. alpha adds nucleotides, pol. epsilon takes over afterwards
• pol delta carries other synthesis on the lagging strand at the same time
• RNase H activity removes RNA primers, then pol. delta and epsilon replace, DNA ligase seals the strand

Question 16

What binds ssDNA and prevents base pairing?

Answer 16

RPA (ssDNA binding protein)

Question 17

What is PCNA?

Answer 17

The sliding clamp that is required for DNA pol delta and epsilon activity

Question 18

What is the function of DNA topoisomerase?

Answer 18

Relaxes DNA by breaking and rejoining phosphodiester bonds

Question 19

What protects the ends of chromosomes from degredation, and what enzyme extends these?

Answer 19

Telomeres protect the ends of chromosomes

telomerase uses an internal RNA template to extend telomeres

Question 20

What is the importance of telomerase in cancers?

Answer 20

Telomerase is present in embryonic stem cells and germ cells, but normal somatic cells lack this enzyme. Cancer cells utilize telomerase to allow for repeated replication

Question 21

Approximate rate of DNA replication error?

Answer 21

very low; 10^(-10)