5.3.1 DNA in Prokaryotes and Eukaryotes

Question 1

History of DNA

Answer 1

James Watson (1928 -) and Francis Crick (1916 - 2004) realized that both strands of DNA individually contained all the information **necessary to make a new copy of the entire molecule, and that the aperiodic order of bases might provide a “genetic code”.

For this discovery, Watson and Crick shared the Nobel Prize in 1962 for their discovery, along with Maurice Wilkins (1916 - 2004), who had continued research to provide a large body of crystallographic data supporting the model.

Working in the same lab, Rosalind Franklin (1920 - 1958) had earlier produced the first clear crystallographic evidence for a helical structure. She had a major contribution in the discovery of structure of DNA but did not get the Nobel prize as she died in 1958 from cancer due to X-Ray radiation exposure.

Question 2

Watson-Crick DNA Model

Answer 2

Deoxyribonucleic acid (DNA) is a double-stranded, helical molecule consisting of two sugar-phosphate backbones on the outside, held together by hydrogen bonds between pairs of nitrogenous bases on the inside. The individual “building blocks” are called nucleotides, which include a nitrogenous base, and a phosphate group and pentose group which alternate in a chain to form the sugar-phosphate backbone.

The four nitrogenous bases are adenine (A), cytosine (C), guanine (G) and thymine (T). The pairing of bases in DNA always occurs between A + T (two hydrogen bonds) or C + G (three hydrogen bonds).

Question 3

Purines

Answer 3

Purines refer to adenine and guanine with two rings.

Question 4

Pyrimidines

Answer 4

Pyrimidines refers to cytosine, uracil and thymine with one ring.

Question 5

DNA

Answer 5

• Stores genetic information that controls the cell
• Main chemical making up chromatin.
• Responsible for transmitting inherited information from one cell to another during division.
• DNA contains thymine as one of its nitrogenous bases.

Question 6

RNA

Answer 6

• Nucleic acid with small amount in nucleus and large in cytoplasm.
• Has uracil instead of thymine.
• Includes mRNA (carrying and transporting), rRNA (brings mRNA and tRNA together), and tRNA (translated mRNA message onto proteins).
• RNA uses uracil instead of thymine (adenine translates into uracil, not thymine).

Question 7

Double Helix

Validation of the Model

Answer 7

X-ray crystallography suggests that a helix measuring 3.4nm for every turn, which fitted a model with 10 base pairs making up one twist of the helix.

Question 8

Pairing of Nitrogenous Bases

Validation of the Model

Answer 8

Chargaff’s rule states that DNA has a 1:1 ratio of pyrimidine and purine bases, meaning that the amounts of guanine were equal to cytosine and adenine to thymine.

Question 9

Hydrogen Bonds

Validation of the Model

Answer 9

Chemically, when A bonds to T, a double hydrogen bond forms, and with C and G, a triple hydrogen bond.

Question 10

Antiparallel Backbones

Validation of the Model

Answer 10

DNA crystal images looked the same when turned upside down or backwards.

Question 11

Self-Replication

Validation of the Model

Answer 11

Two complementary strands “unzip” by breaking the hydrogen bonds between the base pairs, allowing it to act as a template for the production of a complementary strand.

Question 12

DNA in Prokaryotes

Answer 12

In prokaryotes, DNA is found in free-floating chromosomes within the cytoplasm, not bound by any proteins. Prokaryotes also have small, extra-chromosomal DNA segments called plasmids.

Question 13

DNA in Eukaryotes

Answer 13

In eukaryotes, DNA is found in chromosomes within the nucleus, wound tightly around proteins called histones. The DNA then forms supercoils which pack together to form a chromosome.

Question 14

DNA Replication

Answer 14

1. DNA replication starts with a double-stranded DNA helix molecule.
2. The enzyme, helicase, attaches to and unwinds the double-stranded DNA helix. Helicase also facilitates the breaking of hydrogen bonds between the nitrogenous bases.
3. Each of the two now separated DNA single strands act as templates for free (available) nucleotides from the nucleoplasm (inside nuclear membrane) to join via complementary base pairing. The enzyme, DNA polymerase, moves along the DNA strands during this process to catalyse the reaction, allowing complementary base pairing to occur.
4. The enzyme, DNA ligase, secures each of the new DNA strands formed with free nucleotides (monomers) with complementary base pairing.
5. Each DNA double strands return to their chemical stable state by winding up spontaneously to form a two double-stranded DNA helix.

Question 15

Topoisomerase

DNA Enzymes

Answer 15

relaxes DNA from its supercoiled state, always working ahead of the replication fork (e.g. gyrase)

Question 16

Helicase

DNA Enzymes

Answer 16

follows topoisomerase and unwinds the double helix by breaking hydrogen bonds between bases, causing the two strands to separate and creating a replication fork

Question 17

Primase

DNA Enzymes

Answer 17

connects RNA primer to a strand to initiate DNA replication and synthesises a short complementary RNA molecule, which binds to DNA, serving as the starting point for DNA synthesis by polymerase

Question 18

DNA Polymerase I

DNA Enzymes

Answer 18

mainly functions in ‘editing’ — recognises and repairs base pairing errors (exonuclease)— while also having a function in replication by removing primers ahead of the main polymerising enzyme

Question 19

DNA Polymerase II

DNA Enzymes

Answer 19

editing function but no exonuclease activity

Question 20

DNA Polymerase III

DNA Enzymes

Answer 20

synthesises new DNA strands, using existing strands as a template, and joins the phosphate group of each nucleotide to the next one by creating phosphodiester bonds between each molecule to make the sugar-phosphate backbone

Question 21

Ligase

DNA Enzymes

Answer 21

connects and seals the two strands of the DNA molecule and also connects Okazaki fragments