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Basic introduction of DNA structure, Study notes of Molecular biology

This document provides an overview of DNA structure, including the types of bonds involved, different forms of DNA, and the key enzymes that participate in the process of DNA replication.

Typology: Study notes

2024/2025

Available from 05/14/2025

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Structure of DNA and RNA
DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) are fundamental nucleic
acids that serve as the genetic material in all known living organisms and many
viruses. They are both long-chain polymers composed of repeating units called
nucleotides. Each nucleotide is made up of three components: a nitrogenous base, a
five-carbon sugar (pentose), and a phosphate group.
Pentose Sugars
The main structural difference between DNA and RNA lies in their sugar
components:
DNA contains deoxyribose, a five-carbon sugar in which the 2′ carbon atom
lacks a hydroxyl (-OH) group. Instead, it has a hydrogen atom, which
contributes to the overall stability and resistance to hydrolysis, making DNA a
better long-term storage molecule for genetic information.
RNA contains ribose, which has a hydroxyl (-OH) group at the 2′ carbon. This
hydroxyl group makes RNA chemically more reactive and less stable than
DNA. However, it also allows RNA to adopt a variety of structural
conformations and perform multiple roles in the cell, such as acting as a
messenger (mRNA), a structural and catalytic component (rRNA), or an
adaptor molecule (tRNA).
The presence or absence of the hydroxyl group significantly influences the biological
function and stability of the molecules. Due to the lack of OH group at 2’ Carbon the
DNA’s gains chemical stability which makes it suitable for preserving genetic
information, while RNA’s flexibility and reactivity make it ideal for short-term
processes like protein synthesis, gene regulation, and catalysis (in the case of
ribozymes).
Other Key Differences to Structure:
Lifespan: DNA molecules are long-lived, often persisting for the entire
lifespan of a cell or organism. In contrast, RNA molecules are generally short-
lived and are rapidly degraded after their function is fulfilled.
Function: DNA’s primary role is to store and transmit genetic information.
RNA performs various roles including carrying genetic messages (mRNA),
forming core structural and enzymatic components of ribosomes (rRNA), and
aiding in protein synthesis (tRNA), among others.
Base Composition: DNA contains the bases adenine (A), guanine (G),
cytosine (C), and thymine (T), while RNA contains uracil (U) in place of
thymine.
Phosphodiester Bond
Nucleotides are linked together to form long chains (polynucleotides)
through/phosphodiester bonds. The bond is formed between the 3' carbon atom of
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Structure of DNA and RNA

DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) are fundamental nucleic acids that serve as the genetic material in all known living organisms and many viruses. They are both long-chain polymers composed of repeating units called nucleotides. Each nucleotide is made up of three components: a nitrogenous base, a five-carbon sugar (pentose), and a phosphate group.

Pentose Sugars

The main structural difference between DNA and RNA lies in their sugar components:  DNA contains deoxyribose, a five-carbon sugar in which the 2′ carbon atom lacks a hydroxyl (-OH) group. Instead, it has a hydrogen atom, which contributes to the overall stability and resistance to hydrolysis, making DNA a better long-term storage molecule for genetic information.  RNA contains ribose, which has a hydroxyl (-OH) group at the 2′ carbon. This hydroxyl group makes RNA chemically more reactive and less stable than DNA. However, it also allows RNA to adopt a variety of structural conformations and perform multiple roles in the cell, such as acting as a messenger (mRNA), a structural and catalytic component (rRNA), or an adaptor molecule (tRNA). The presence or absence of the hydroxyl group significantly influences the biological function and stability of the molecules. Due to the lack of OH group at 2’ Carbon the DNA’s gains chemical stability which makes it suitable for preserving genetic information, while RNA’s flexibility and reactivity make it ideal for short-term processes like protein synthesis, gene regulation, and catalysis (in the case of ribozymes). Other Key Differences to Structure:Lifespan : DNA molecules are long-lived, often persisting for the entire lifespan of a cell or organism. In contrast, RNA molecules are generally short- lived and are rapidly degraded after their function is fulfilled.  Function : DNA’s primary role is to store and transmit genetic information. RNA performs various roles including carrying genetic messages (mRNA), forming core structural and enzymatic components of ribosomes (rRNA), and aiding in protein synthesis (tRNA), among others.  Base Composition : DNA contains the bases adenine (A), guanine (G), cytosine (C), and thymine (T), while RNA contains uracil (U) in place of thymine.

Phosphodiester Bond

Nucleotides are linked together to form long chains (polynucleotides) through phosphodiester bonds. The bond is formed between the 3' carbon atom of

one sugar molecule and the 5' carbon atom of the next sugar molecule, with a phosphate group bridging them. The phosphodiester bonds create the sugar- phosphate backbone of the DNA and RNA strands, which is negatively charged due to the phosphate groups. phosphate group ensures stability and integrity. The bond formation through condensation reaction, the reaction releases water molecule and creates a continuous sugar phosphate bond.

Nucleosides and Nucleotides

Nucleic acids like DNA and RNA are composed of smaller molecular units called nucleotides, which themselves are derived from nucleosides.

  1. Nucleoside Formation : A nucleoside is formed when a nitrogenous base (either a purine— adenine or guanine—or a pyrimidine— cytosine, thymine, or uracil) is covalently attached to a five-carbon sugar (either ribose in RNA or deoxyribose in DNA). This attachment occurs at the 1′-carbon of the sugar. 2 .Nucleotide Formation: When one or more phosphate groups are attached to the 5′-carbon of the sugar in a nucleoside, the structure becomes a nucleotide. Nucleotides are thus composed of three components: a nitrogenous base, a sugar, and a phosphate group. Depending on the number of phosphate groups, they can be called: •Nucleoside monophosphate (NMP) •Nucleoside diphosphate (NDP) •Nucleoside triphosphate (NTP) — e.g., ATP (adenosine triphosphate)

Glycosidic Bond

The nitrogenous base in nucleotides is attached to the 1' carbon atom of the pentose sugar through a glycosidic bond (specifically, a β-N-glycosidic bond). It Ensures the proper orientation of nitrogenous bases and facilitate complimentary base pairing and helical structure. In Purine the bond is between 1’ carbon of sugar and the N9 atom of the base. In Pyrimidine the bond is between 1’ carbon of sugar and N1 atom of base

narrow, while the minor groove is broad and shallow. RNA-DNA hybrids and double-stranded RNA often adopt an A-like structure. It plays specific role in certain protein-DNA interactions and crystallographic studies.  Z-DNA: This is a less common left-handed helix with about 12 base pairs per turn. The sugar-phosphate backbone has a zigzag appearance (hence the name "Z"). Z-DNA can form in regions with alternating purine and pyrimidine sequences. Its biological role may involve transcription regulation or recombination, cellular stress response, gene expression, believed to act as a transient structure during transcription and super calling, influencing genome stability. Diameter of around 18Å.

Structure of RNA

RNA is typically single-stranded , although it can fold upon itself to form complex secondary and tertiary structures through intramolecular base pairing (A-U and G-C). These structures are essential for the diverse functions of different types of RNA, such as messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). RNA does not typically form a long, stable double helix like DNA, although short regions of double-stranded RNA can occur.

Enzymes Involved in DNA Replication in E. coli

DNA replication in E. coli is a complex process involving numerous enzymes and proteins working in a coordinated manner at the replication fork. DNA application is a semiconservative process with a daughter having one parental strand, and one newly synthesised strand. The replication begins at the origin of replication, which is normally called OriC and the proceeds bidirectionally Key enzymes include:  DNA Helicase (DnaB): Unwinds the double-stranded DNA at the origin of replication (oriC), creating two replication forks. It breaks the hydrogen bonds between the complementary bases using ATP hydrolysis. DnaC +ATP Loads DnaB with help of ATP hydrolysis.  Single strand binding proteins: stabilises, single tan DNA exposed to helicase, prevents reannealing of SSDNA. Protects the DNA from nuclear which can degrade it and. Facilitates the binding of other replication enzyme to DNA template.  DNA Primase (DnaG): Synthesizes short RNA primers (about 10- nucleotides long) that provide a free 3'-OH group for DNA polymerase to initiate DNA synthesis.  DNA Polymerase III Holoenzyme: The primary enzyme responsible for synthesizing new DNA strands. It is a complex enzyme with high processivity (ability to add many nucleotides without dissociating from the template) and proofreading activity (3' to 5' exonuclease activity to remove incorrectly incorporated nucleotides).  Sliding clamps: enhances processivity of DNA polymerase III. It forms ring shaped structure that and circles the DNA and anchor’s DNA polymerase III to template strand, allows continuous and rapid synthesis of DNA without the polymerase dissociating from the template.  Clamp loader complex: It load sliding clamps onto DNA template. Includes gamma complex which open and closes the beta clamp around the DNA. Essential for initiating replication on both the leading and lagging strands.

DnaA protein: initiates replication by binding to specific sequence within OriC, causing local unwinding of the DNA. It facilitates the loading of helicase(DnaB) on the DNA.  DNA Polymerase I: Possesses 5' to 3' exonuclease activity to remove RNA primers and fill the resulting gaps with DNA. It also has 5' to 3' polymerase and 3' to 5' exonuclease (proofreading) activities.  DNA Ligase: Catalyzes the formation of phosphodiester bonds to join the Okazaki fragments on the lagging strand and to seal nicks in the DNA. it requires energy in NAD+ & ATP form.  Topoisomerases (DNA Gyrase): Relieve the torsional stress ahead of the replication fork caused by DNA unwinding. DNA gyrase is a type II topoisomerase specific to bacteria that introduces negative supercoils.  Single-Stranded Binding Proteins (SSB): These proteins attach to the single-stranded DNA exposed by helicase, preventing the strands from re- annealing or forming secondary structures. They also protect the single- stranded DNA from degradation by nucleases and help maintain it in an extended form, making it accessible for other replication enzymes.