L10: DNA Organization and Replication

Question 1

Can you discern among the polynucleotides, DNA and RNA, based on their sugar, nitrogenous bases, and their organization?

Answer 1

DNA nucleotides are built with deoxyribose sugar. DNA nucleotides possess one of four Nitrogenous bases: two purines (A, G) and two pyrimidines (C, T). DNA tends to be
organized as a double-stranded anti-parallel helix.

RNA nucleotides are built with ribose sugar. RNA nucleotides possess one of four Nitrogenous bases: two purines (A, G) and two pyrimidines (C, U). RNA tends to be single-stranded; but sometimes folds onto itself.

Question 2

What is the general difference between a purine and a pyrimidine?

Answer 2

purines are nitrogenous based with 2 ring structure (A,G)

pyrimidine are nitrogenous based with 1 ring structure (C,T,U)

Question 3

What are the purines and pyrimidines used to make DNA and RNA?

Answer 3

Purines:
- adenine (A)
- guanine (G)

Pyrimidines:
- Cytosine (C, in DNA & RNA)
- Thymine (T, in DNA)
- Uracil (U, in RNA)

Question 4

DNA is organized as double-stranded anti-parallel helix. What does this mean?

Answer 4

One strand 3´➟5´; the other is 5´➟3´. Both twisted into a helical (spiral) orientation.

Question 5

In discovering this model of DNA organization, what role did Chargaff, Franklin, and Watson and Crick play?

Answer 5

Erwin Chargaff discovered complementarity of base pairs: a [purine] = [pyrimidine].

Rosalind Franklin discovered the helical shape of DNA using X-ray diffraction.

However, it was Watson and Crick who finally deduced the model of DNA during 1950s (DID NOT DISCOVER DNA JUST FIGURED THE MODEL)

Question 6

What is a base-pair? What aspect of base-pairs make two strands of DNA in a helix parallel?

Answer 6

a base pair is a purine (2) and pyrimidines (1) connected through a hydrogen bond

2:1 ration keeps the strand even

Question 7

What does ‘anti’ in antiparallel mean?

Answer 7

opposite way

Question 8

What are Chargaff’s rules?

Answer 8

Chargaff’s rules: A H-bonds with T; C with G

Question 9

Can you use Chargaff’s rules to replicate a sequence of DNA? (I hope so!)

Answer 9

Original DNA: TAC-ATA-AAA-GGC-CCG-ATC
Synthesized DNA: ATG-TAT-TTT-CCG-GGC-TAG

Question 10

Why do cells replicate their DNA?

Answer 10

to multiply

Question 11

What roles do the following proteins/enzymes serve in DNA replication: helicase, topoisomerase, single-strand bonding protein, primase, DNA pol III, DNA pol I, and DNA ligase. You should draw/label a replication fork including each of these proteins/enzymes.

Question 12

I organized my lesson based on six problems/solutions. You should be able to recall the context and specifics of this organization. You must invest considerable time in this endeavor.

Question 13

Which direction does DNA pol III move on template DNA strands? Which direction does DNA pol III move on new DNA strands? Which direction does DNA pol III move on leading strands? Which direction does DNA pol III move on lagging strands?

Answer 13

3’ - 5’

Question 14

What is a replication bubble? What is a replication fork? How many replication forks are found per replication bubble?

Question 15

How do prokaryotic and eukaryotic cells differ in the organization of dsDNA within chromosomes, origins, and replication bubbles?

Answer 15

Eukaryotes have more enzymes (e.g., 11 DNA polymerases).
Eukaryotes have several pieces of linear dsDNA (one for each
chromosome).
Each has multiple origins; hence, multiple replication bubbles.
Linear nature of eukaryotic dsDNA results in an additional, monumental problem: THE END REPLICATION PROBLEM…

Question 16

How does replication differ for leading and lagging strands?

Question 17

The end replication problem (ERP) was a problem associated with the linear dsDNA/chromosomes in eukaryotes. What happens to the length of dsDNA/chromosome arms as a consequence of ERP?

Answer 17

There is no enzyme to fill in these gaps however exonuclease can trim (✂) ssDNA template strands (but doing so erodes DNA). Length of DNA gets shorter and shorter as it replicates.

Question 18

Which enzyme is used to ‘fix’ ERP? When does this enzyme quit working in most of your cells?

Answer 18

Telomerase repeatedly adds sacrificial DNA sequences (e.g.,
TTAGGG), called telomeres, at end of each chromosome.

Telomerase activity shuts down in most cell lines after birth.

May help explain senescence. Only have so much sacrificial DNA added to your chromosome that cant be made again and so the human body eventually dies when using up material.

Question 19

What are telomeres and what role do they serve in ‘fixing’ ERP?

Answer 19

Telomeres is a work around the end replication problem. Telomerase adds sacrificial DNA sequences, called telomeres, but you’re only born with a certain amount of telomere as it doesn’t produce anymore after birth.

Question 20

What happens to your telomeres as you age? What happens when your telomeres erode away entirely?

Answer 20

Telomere is used up as you age. When it erodes away entirely your body starts to trim into your DNA that’ll lead to senescence.

Question 21

Many cancers have cells that do not experience ERP. What property do such cells have and why?

Answer 21

Many cancer cell lines have increased telomerase activity making them potentially immortal.

Increased telomeres makes cancer cells able to escape the end replication problem.