Molecular biology--Deoxyribonucleic acid (DNA)

Molecular biology: definition

Molecular biology  is the study of molecular underpinnings of the process of replication, transcription, and translation of the genetic material.

·        This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

·        Much of the work in molecular biology is quantitative, and recently much work has been done at the interface of molecular biology and computer science in bioinformatics and computational biology.

·        Since the late 1950s and early 1960s, molecular biologists have learned to characterize, isolate, and manipulate the molecular components of cells and organisms include DNA, the repository of genetic information; RNA, a close relative of DNA; and proteins, the major structural and enzymatic type of molecule in cells.

Basic differences between eukaryotes and prokaryotes

Components involve in molecular biology

Deoxyribonucleic acid (DNA)

DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses.

DNA is a set of blueprints needed to construct other components of cells, such as proteins and RNA molecules.

Two long strands make the shape of a double helix.

two strands run in opposite directions to each other and are therefore anti-parallel.

Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of base, sugars and phosphate groups.

Sugar +Base = nucleoside

Phosphate+ sugar + Base = nucleotide

Bases

Types: - adenine and guanine (fused five- and six-membered heterocyclic compounds) – Purines

cytosine & thymine (six-membered rings)-Pyrimidines.

A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring

PAIRING: A =T and A=U G≡C

The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands.

One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.

Size:

The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Å (0.33 nm) long.

DNA replication

·        DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA.

·        In the process of "replication" each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand.

·        Two identical DNA molecules have been produced from a single double-stranded DNA molecule.

·        In a cell, DNA replication begins at specific locations in the genome, called "origins".

·        Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork.

·        In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

Step 1: Replication Fork Formation

Before DNA can be replicated, the double-stranded molecule must be “unzipped” into two single strands.

DNA has four bases called adenine (A), thymine (T), cytosine (C)and guanine (G) that form pairs between the two strands.

Adenine only pairs with thymine and cytosine only binds with guanine. In order to unwind DNA, these interactions between base pairs must be broken.

This is performed by an enzyme known as DNA helicase. DNA helicase disrupts the hydrogen bonding between base pairs to separate the strands into a Y shape known as the replication fork. This area will be the template for replication to begin.

DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies which side group is attached the DNA backbone.

The 5' end has a phosphate (P) group attached, while the 3' end has a hydroxyl (OH) group attached.

This directionality is important for replication as it only progresses in the 5' to 3' direction. However, the replication fork is bi-directional; one strand is oriented in the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two sides are therefore replicated with two different processes to accommodate the directional difference.

Replication Begins

Step 2: Primer Binding

The leading strand is the simplest to replicate. Once the DNA strands have been separated, a short piece of RNA called a primer binds to the 3' end of the strand. The primer always binds as the starting point for replication. Primers are generated by the enzyme DNA primase.

DNA Replication: Elongation

Step 3: Elongation

Enzymes known as DNA polymerases are responsible creating the new strand by a process called elongation. There are five different known types of DNA polymerases in bacteria and human cells.

In bacteria such as E. coli, polymerase III is the main replication enzyme, while polymerase I, II, IV and V are responsible for error checking and repair. DNA polymerase III binds to the strand at the site of the primer and begins adding new base pairs complementary to the strand during replication.

In eukaryotic cells, polymerases alpha, delta, and epsilon are the primary polymerases involved in DNA replication. Because replication proceeds in the 5' to 3' direction on the leading strand, the newly formed strand is continuous.

The lagging strand begins replication by binding with multiple primers. Each primer is only several bases apart. DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the strand between primers. This process of replication is discontinuous as the newly created fragments are disjointed.

Step 4: Termination

Once both the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with appropriate bases. Another exonuclease “proofreads” the newly formed DNA to check, remove and replace any errors. Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to 3′ direction.

The ends of the parent strands consist of repeated DNA sequences called telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby chromosomes from fusing.
A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA.

Once completed, the parent strand and its complementary DNA strand coils into the familiar helix shape. In the end, replication produces two DNA molecules, each with one strand from the parent molecule and one new strand.

Replication Enzymes

DNA replication would not occur without enzymes that catalyze various steps in the process. Enzymes that participate in the eukaryotic DNA replication process include:

• DNA helicase - unwinds and separates double stranded DNA as it moves along the DNA. It forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA.
• DNA primase - a type of RNA polymerase that generates RNA primers. Primers are short RNA molecules that act as templates for the starting point of DNA replication.
• DNA polymerases - synthesize new DNA molecules by adding nucleotides to leading and lagging DNA strands.
• Topoisomerase or DNA Gyrase - unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled.
• Exonucleases - group of enzymes that remove nucleotide bases from the end of a DNA chain.
• DNA ligase - joins DNA fragments together by forming phosphodiester bonds between nucleotides.

See you later, in another topic in Biochemistry!!!!!!!