DNA Structure and Replication

Question 1

Chargaff’s rule

Answer 1

DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine

Question 2

Watson and Crick proved wrong

Answer 2

At first Watson and Crick thought the bases paired like for like; e.g. A pairs with A etc., but this doesn’t produce a molecule of uniform width * Pairing a purine with a pyrimidine resulted in a uniform width

Question 3

Chargaff’s second rule

Answer 3

The second rule holds that both Α% ≈ Τ% and G% ≈ C% are valid for each of the two DNA strands. This describes only a global feature of the base composition in a single DNA strand.

Question 4

When does Replication happen

Answer 4

S phase

Question 5

Semi-conservative model

Answer 5

each daughter molecule comprises one strand from the parent molecule and one newly made strand (Watson and Crick)

Question 6

Origins of replication

Answer 6

Replication begins at special sites called origins of replication, where the two strands separate, opening up a replication “bubble”. Replication proceeds from each origin until the entire molecule is copied

Question 7

Replication fork

Answer 7

At each end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating. More than a dozen enzymes and other proteins participate in DNA replication

Question 8

Helicases

Answer 8

enzymes that untwist and separate the double helix at the replication forks

Question 9

Single-stranded building protein

Answer 9

binds to and stabilizes single-stranded DNA until it can be used as a template

Question 10

Topoisomerase

Answer 10

corrects “overwinding” ahead of replication forks by breaking, swiveling and rejoining DNA strands

Question 11

Elongating the new strand

Answer 11

Elongation of new DNA at a replication fork is catalyzed by DNA polymerases
* Most DNA polymerases require a primer and a DNA template strand
* DNA polymerases add nucleotides only to the free 3’ end of a growing strand;
therefore, a new DNA strand can elongate only in the 5’ to 3’ direction
* The rate of elongation is about 500 nucleotides/sec in bacteria and 50 per/sec in a human cell

Question 12

Primer

Answer 12

A primer is a short nucleic acid sequence that provides a starting point for DNA synthesis. In living organisms, primers are short strands of RNA

Question 13

Nucleotide addition

Answer 13

Each added nucleotide is a nucleoside triphosphate
* dATP supplies adenine to DNA and is similar to the ATP of energy metabolism. The difference is in their sugars: dATP has deoxyribose while ATP has ribose
* As each monomer of dATP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate

Question 14

Antiparallel elongation:
the leading strand

Answer 14

Along one template strand, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork

Question 15

The lagging strand

Answer 15

• To elongate the other new strand (the lagging strand), DNA polymerase III must work in the direction away from the replication fork
• The lagging strand is synthesized as a series of segments called Okazaki fragments, which are subsequently joined together by DNA ligase
• DNA polymerase I replaces the RNA primers with DNA

Question 16

The DNA replication complex/fork

Answer 16

The proteins that participate in DNA replication form a large complex, a “DNA replication machine”
* The DNA replication machine is probably stationary during replication, with the DNA polymerase molecules “reeling in” parental DNA and “extruding” the newly made daughter DNA