Biomolecules - Biosynthesis of Nucleic Acids

Nucleic acids are the genetic material of living organisms.
They are composed of chains of nucleotides, which are made up of a sugar molecule, a phosphate group, and a nitrogenous base.
The biosynthesis of nucleic acids involves two main processes: DNA replication and transcription.

DNA Replication

DNA replication is the process by which DNA makes an exact copy of itself.
It occurs during cell division and is essential for the transmission of genetic information.
The process involves several steps, including unwinding of the DNA double helix, separation of the DNA strands, and synthesis of new strands using existing strands as templates.

Steps in DNA Replication

Initiation: The replication begins at specific sites on the DNA molecule called replication origins.
Unwinding: The double helix is unwound by an enzyme called helicase, which breaks the hydrogen bonds between the base pairs.
Separation: The unwound DNA strands separate, forming a replication fork.
Synthesis: DNA polymerase adds new nucleotides to the exposed template strands, creating complementary strands.
- The new nucleotides are added in a 5’ to 3’ direction, using the existing strands as templates.
- The enzyme DNA ligase seals the gaps between the newly synthesized fragments, forming continuous strands.

Transcription

Transcription is the process by which genetic information in DNA is used to synthesize RNA.
It occurs in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells.
The process involves three main steps: initiation, elongation, and termination.

Steps in Transcription

Initiation: RNA polymerase binds to a specific site on the DNA called the promoter region.
Elongation: The RNA polymerase moves along the DNA template, synthesizing a single-stranded RNA molecule.
- The RNA molecule is complementary to the DNA template strand.
- The RNA polymerase adds nucleotides to the growing RNA chain in a 5’ to 3’ direction.
Termination: The RNA polymerase reaches a specific termination signal on the DNA template, causing it to detach and release the newly synthesized RNA molecule.

Nucleotides

Nucleotides are the building blocks of nucleic acids.
Each nucleotide consists of three components:
1. A five-carbon sugar molecule (ribose in RNA and deoxyribose in DNA)
2. A phosphate group
3. A nitrogenous base (adenine, guanine, cytosine, or thymine in DNA; adenine, guanine, cytosine, or uracil in RNA)

DNA Nucleotides

DNA nucleotides consist of deoxyribose sugar, a phosphate group, and one of the four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or thymine (T).
Adenine pairs with thymine, and guanine pairs with cytosine through hydrogen bonding, forming the complementary base pairs in DNA.

RNA Nucleotides

RNA nucleotides have ribose sugar, a phosphate group, and one of the four nitrogenous bases: adenine (A), guanine (G), cytosine (C), or uracil (U).
Adenine pairs with uracil, and guanine pairs with cytosine through hydrogen bonding, forming the complementary base pairs in RNA.

DNA Replication vs. Transcription

DNA replication and transcription are both essential processes for the maintenance and expression of genetic information.
However, they differ in their roles and outcomes:
- DNA replication creates an exact copy of the DNA molecule, preserving the genetic information.
- Transcription synthesizes RNA molecules from DNA templates, enabling the expression of genes.

Summary

The biosynthesis of nucleic acids involves DNA replication and transcription.
DNA replication creates an identical copy of the DNA molecule during cell division.
Transcription synthesizes RNA molecules from DNA templates, enabling gene expression.
Nucleotides are the building blocks of nucleic acids and consist of a sugar, phosphate group, and nitrogenous base.

References

Chemistry textbook for 12th Boards
Molecular Biology of the Cell, Alberts et al.

Slide 11

DNA replication and transcription are fundamental processes in genetics.
They play crucial roles in the growth and development of organisms.
Both processes involve the synthesis of nucleic acids, specifically DNA and RNA.
Understanding these processes is essential for studying genetic inheritance and gene expression.
Let’s explore the steps involved in DNA replication and transcription.

Slide 12

Steps in DNA Replication

Initiation:
- DNA replication starts at specific sites called replication origins.
- Enzymes like helicase unwind the double helix structure.
- Accessory proteins stabilize the unwound DNA strands.
Unwinding:
- Helicase breaks the hydrogen bonds between the base pairs, separating the DNA strands.
- Topoisomerases help relieve the tension caused by unwinding.
Separation:
- The unwound DNA strands form a Y-shaped structure called the replication fork.
- Replication proceeds bidirectionally from each replication fork.
Synthesis:
- DNA polymerase adds complementary nucleotides to the exposed template strands.
- New DNA strands are synthesized in the 5’ to 3’ direction.
- Leading and lagging strands are synthesized differently.
Termination:
- The replication process ends at specific termination sites.
- DNA ligase joins the Okazaki fragments on the lagging strand.

Slide 13

Steps in Transcription

Initiation:
- RNA synthesis starts at a specific DNA region called the promoter.
- RNA polymerase recognizes and binds to the promoter.
- Transcription factors assist in the binding process.
Elongation:
- RNA polymerase synthesizes an RNA molecule.
- It moves along the DNA template, adding complementary nucleotides.
- The growing RNA chain is antiparallel to the DNA template strand.
Termination:
- Transcription terminates at specific sites called terminator sequences.
- The RNA molecule is released, and the RNA polymerase detaches from the DNA template.

Slide 14

DNA replication and transcription share some similarities, such as using nucleotides and involving the synthesis of nucleic acids.
However, they differ in several aspects, including their purposes and locations.
DNA replication occurs during cell division and ensures DNA duplication for inheritance.
Transcription takes place in the nucleus (eukaryotes) or cytoplasm (prokaryotes) and produces RNA for protein synthesis.

Slide 15

Differences between DNA Replication and Transcription

	DNA Replication	Transcription
Purpose	Duplication of DNA for cell division and inheritance	Synthesis of RNA for protein production
Enzymes involved	DNA polymerase, helicase, topoisomerase, ligase, etc.	RNA polymerase
Template	Double-stranded DNA	Single-stranded DNA
End product	Two identical DNA molecules	RNA molecule
Location	Nucleus (eukaryotes); cytoplasm (prokaryotes)	Nucleus (eukaryotes); cytoplasm (prokaryotes)

Slide 16

Nucleotides in DNA and RNA

Nucleotides are the building blocks of nucleic acids.
They consist of three components: a sugar molecule, a phosphate group, and a nitrogenous base.
In DNA, the sugar is deoxyribose, while in RNA, it is ribose.

Examples:

DNA nucleotides: deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP), deoxythymidine triphosphate (dTTP)
RNA nucleotides: adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), uridine triphosphate (UTP)

Slide 17

Base Pairing in DNA

In DNA, adenine (A) forms hydrogen bonds with thymine (T), and guanine (G) forms bonds with cytosine (C).
These base pairs bind the two complementary strands of DNA together.

Example: A double-stranded DNA sequence could be:

5' - ATGCCGA - 3'
3' - TACGGCT - 5'

Here, A binds with T and G binds with C.

Slide 18

Base Pairing in RNA

In RNA, adenine (A) forms hydrogen bonds with uracil (U), and guanine (G) forms bonds with cytosine (C).
RNA base pairing rules are similar to DNA, except that uracil replaces thymine in RNA.

Example: RNA sequence complementary to the previous DNA sequence would be:

5' - UACGGCU - 3'

Here, A binds with U, G binds with C, and T is replaced by U.

Slide 19

Importance of DNA Replication and Transcription

DNA replication ensures accurate transmission of genetic information from one generation to the next.
Transcription allows the expression of specific genes and the production of functional proteins.
Both processes are critical for the growth, development, and survival of organisms.

Examples: DNA replication during cell division and transcription in protein synthesis.

Slide 20

Summary

DNA replication and transcription are essential processes in genetics.
DNA replication creates an identical copy of the DNA molecule during cell division.
Transcription synthesizes RNA molecules from DNA templates for gene expression.
Nucleotides are the building blocks of nucleic acids and consist of a sugar, phosphate group, and nitrogenous base.

References: Chemistry textbook for 12th Boards, Molecular Biology of the Cell, Alberts et al. 21.

DNA Replication: Initiation

DNA replication begins at specific sites called replication origins.
Replication origins contain specific nucleotide sequences recognized by initiator proteins.
Initiator proteins bind to replication origins and recruit other proteins to initiate replication.
Examples of initiator proteins include DnaA in bacteria and ORC (origin recognition complex) in eukaryotes.
The binding of initiator proteins marks the starting point for DNA replication.

DNA Replication: Unwinding

Helicase enzymes unwind the double helix structure of DNA.
Helicases bind to the origin of replication and move along the DNA, separating the two strands.
As helicase moves, it disrupts the hydrogen bonds between the complementary base pairs.
Unwinding of the DNA double helix generates tension and creates localized DNA regions called replication bubbles.
Topoisomerases help relieve the supercoiling tension generated during DNA unwinding.

DNA Replication: Separation

The unwound DNA strands form a Y-shaped structure called a replication fork.
Replication forks move bidirectionally from the origin of replication.
Each replication fork has a leading strand and a lagging strand.
The leading strand is synthesized continuously in the 5’ to 3’ direction following the replication fork.
The lagging strand is synthesized discontinuously as short fragments called Okazaki fragments.

DNA Replication: Synthesis - Leading Strand

Leading strand synthesis occurs continuously and is synthesized as a single, uninterrupted strand.
The leading strand is synthesized in the 5’ to 3’ direction.
DNA polymerase adds nucleotides to the growing leading strand using the template strand as a guide.
Primase synthesizes a short RNA primer that is complementary to the leading strand template in order to start DNA synthesis.
DNA polymerase then extends from the primer, continuously adding nucleotides to the growing leading strand.

DNA Replication: Synthesis - Lagging Strand

Lagging strand synthesis occurs discontinuously as a series of Okazaki fragments.
Okazaki fragments are short DNA fragments synthesized in the 5’ to 3’ direction but in the opposite direction of overall DNA replication.
Primase synthesizes RNA primers on the lagging strand template at regular intervals.
DNA polymerase then extends from each primer and synthesizes a short fragment of DNA, which is an Okazaki fragment.
The process is repeated multiple times to complete the synthesis of the lagging strand.

DNA Replication: Synthesis - Leading and Lagging Strand

On the leading strand, DNA synthesis occurs smoothly and continuously.
On the lagging strand, DNA synthesis occurs discontinuously, as Okazaki fragments are synthesized in the opposite direction.
The individual Okazaki fragments are later joined together by DNA ligase.
This process ensures that both strands of the original DNA molecule are replicated.

DNA Replication: Termination

DNA replication terminates when the replication forks meet at specific termination sites.
Termination sites contain specific nucleotide sequences that signal the end of replication.
Replication forks converge, and DNA synthesis is halted by various terminators.
Replication proteins dissociate from the DNA molecule, completing the replication process.
The newly synthesized DNA molecules are now ready to be utilized for cellular processes.

Transcription: Initiation

Transcription begins at specific DNA regions called promoters.
Promoters have specific sequences that are recognized by RNA polymerase.
RNA polymerase binds to the promoter region and recruits other proteins to form a transcription initiation complex.
Transcription factors help in the binding of RNA polymerase to the promoter.
The promoter sequence determines the initiation site and the direction of transcription.

Transcription: Elongation

During transcription elongation, RNA polymerase moves along the DNA template, synthesizing an RNA molecule.
RNA polymerase unwinds the DNA helix ahead of its active site and rewinds it behind.
The DNA strand not used as a template is called the non-template (coding) strand.
RNA polymerase adds complementary ribonucleotides to the growing RNA chain in the 5’ to 3’ direction.
The growing RNA molecule is antiparallel to the non-template strand.

Transcription: Termination

Transcription terminates at specific DNA sequences called terminators.
Termination signals cause RNA polymerase and the newly synthesized RNA molecule to detach from the DNA template.
There are two types of termination: intrinsic termination and Rho-dependent termination.
Intrinsic termination occurs when specific terminator sequences cause the RNA to fold into a hairpin structure followed by a string of uracil residues.
Rho-dependent termination involves the binding of a protein called Rho to the mRNA molecule, leading to transcription termination.

References:

Chemistry textbook for 12th Boards
Molecular Biology of the Cell, Alberts et al.