DNA Structure

DNA (deoxyribonucleic acid) is a polynucleotide.

Each nucleotide is made of 3 subunits:

• Phosphate

• Deoxyribose (pentose)

• Nitrogenous base

4 Possible Nitrogenous Bases

2 are Purines: (double rings)

Adenine (A)

Guanine (G)

2 are Pyrimidines: (single ring)

Cytosine (C)

Thymine (T) only in DNA

Sugar-Phosphate Backbone

A polynucleotide strand has a backbone made up of alternating phosphate and sugar molecules.

• The phosphate group end is called 5’ end (pronounced 5 prime).

• The sugar group end is called 3’ end (3 prime).

Sugar-Phosphate Backbone: Dehydration Synthesis

The –OH group from phosphate and –H group from sugar leaves as a water molecule.

3’ oxygen joins together with 5’ phosphate to form the sugar-phosphate backbone.

Sugar-Phosphate Backbone: Directionality

Double Stranded DNA

DNA is made up of 2 polynucleotides.

The two polynucleotides run antiparallel.

Antiparallel: Opposite direction

One strand runs from 5’ 3’

Another strand runs from 3’ 5”

Complementary Base Pairing

A purine must be paired with a pyrimidine.

(Two rings + One rings)

Adenine – Thymine

2 Hydrogen Bonds

Guanine – Cytosine

3 Hydrogen Bonds

Chargaff’s Rule

The number of A and T are the same in a DNA molecule.

#A=#T

The number of G and C are the same in a DNA molecule.

#G=#C

This is due to complementary base pairing.

Hydrogen Bonds

The two strands of polynucleotides are connected by the hydrogen bonds between each complementary base pair.

Double Helix

The two strands are intertwined into helical shape.

Summary: DNA structure

• Sugar-Phosphate Backbone

• Antiparallel

• Complementary Base Pairing

• Double Helix

DNA Replication

DNA Replication

DNA replication is the process of producing two identical replicas of DNA molecule from one original DNA molecule.

During cell division, two replicas of DNA must be made to ensure each daughter cell obtain one copy.

DNA replication is semi-conservativeHalf of each molecule is made of the parent strand, and half daughter strand.

Origin of replication

The replication of DNA molecule must begin at a special site, origin of replication.

There are many origin of replication on each strand.

At the origin, the DNA strands separated, forming a replication “bubble” with one replication fork at each end. An enzyme called helicase separates the strands.

Helicase

Helicase “unzips” the DNA double helix by breaking hydrogen bonds between the complementary base pairs.

DNA polymerase

After the two strands are separated, DNA polymerase reads the bases on the template strand and attach complementary base to form new strand.

DNA polymerase can only attach the 5’ phosphate of one nucleotide to the 3’ hydroxyl (OH) group of the previous nucleotide.

The new strand will grow in the 5’ 3’ direction.

Daughter strand grows in 5’ 3’ direction

Template strand is being read in 3’ 5’ direction

Remember that DNA molecule is antiparallel? This poses a problem.Since helicase will unzip the double helix away from origin of replication, one of the strand has the “wrong “ configuration.

DNA polymerase adds nucleotides only to the 3’ end, but can only do that to one strand, the leading strand. The leading strand can be read continuously (the same direction as the opening of replication fork).

The other strand is called lagging strand, and is being read in the opposite direction as the opening of replication fork. The short sequence of nucleotides are called Okazaki fragments. (discontinuous)

Ligase

An enzyme which connects the short Okazaki fragments together to form a complete daughter strand of polynucleotide.

RNA primase

DNA polymerase cannot initiate the synthesis of a new DNA strand. A short sequence of nucleotides must be built where DNA polymerase can attach to and start the process. The sequence of nucleotide is called primer, and it is made of RNA. Primers are made by RNA primase. Only 1 primer is needed for leading strand. Multiple primers are needed for the lagging strand, one for each Okazaki fragment.

DNA polymerase can make error while replicating a new strand. Error in DNA strand can leading to mutation (change in DNA sequence). DNA polymerase has proof reading ability which allows it o double check its DNA sequence after its completed. If errors are found, it will be fixed.

Exposure to chemical, UV radiation, viruses can cause higher chance of mutation.