Molecular Biology: DNA and RNA Basics

Overview

• Nucleic acids structure and function, genome diversity and organisation were the topics of the lecture.
• The course text for the lecture wa s Molecular Biology of the Gene 6th Ed, by Watson et al.

Overview Textbook

• Chapter 6: Explores the structure of DNA at an atomic level, including the chemistry of bases and backbone, base pairing interactions, and forces holding the two strands together. It also explores RNA's structure, highlighting its unique properties.
• Chapter 7: Discusses chromosomes, chromatin, and the nucleosome structure. DNA is packaged with specialized proteins as chromatin, allowing long DNA molecules to fit within the cell during cell division. It introduces the histones and other components of chromatin, along with enzymes that modify chromatin.

Objectives - Lecture 1

• Describe the 3 main components of nucleic acids.
• Describe the main functions of DNA and RNA.
• Demonstrate how the structures of DNA and RNA account for their functions.
• Illustrate the basic monomeric structure of DNA and RNA.
• Describe the conformations of DNA.
• Explain how DNA molecules, which are extraordinarily long, are packaged within the nucleus.

Why Study Nucleic Acids?

• DNA is the blueprint for an organism's individuality.
• An organism's life, growth, and unique features depend on its DNA.

Significance

• Life depends on cells' ability to store, retrieve, and translate genetic instructions to build and maintain an organism.
• Hereditary information is passed on from a cell to its daughter cells during cell division and from one generation to the next through reproductive cells.

Relevance

• These genetic instructions are stored in every living cell as genes.
• Genes determine the characteristics of a species and its individuals.

Structure and Function of DNA & RNA

• This section focuses on the structure and function of DNA and RNA.

Discovery of DNA Structure

• DNA structure discovery shows good examples of scientific principles.
• Successful discoveries are often made through steps, including mistaken assumptions, collaborative efforts, and the value of sharing knowledge.

Watson and Crick

• James Watson and Francis Crick are key figures in DNA structure discovery.

Franklin and Wilkins

• Rosalind Franklin and Maurice Wilkins' contributions to DNA structure determination were significant and contributed significantly towards the development of understanding the chemical basis of base pairing in DNA and the analysis by Erwin Chargaff.

DNA Helix

• Franklin's X-ray diffraction pattern of DNA showed a helical structure.
• The pattern also showed the recurring bases.

Components of Nucleic Acids

• DNA is the hereditary material of humans.
• RNA transcribes DNA's instructions and translates them into protein construction.
• DNA and RNA are polymers made of polynucleotides.
• The monomers of DNA are deoxyribonucleotides and for RNA, ribonucleotides.

Components of Nucleic Acids (cont.)

• 5-carbon sugars (pentose) are important components of nucleic acids.
• β-D-ribose is a key component of RNA.
• β-D-2-deoxyribose is a key component of DNA.
• Nitrogen bases are crucial for nucleic acid structure and function.
• Purines (adenine and guanine) are double-ringed nitrogenous bases.
• Pyrimidines (cytosine, thymine, and uracil) are single-ringed nitrogenous bases.

Nucleotide

• A nucleoside is one of the four nitrogenous bases covalently attached to the C1' position of a sugar.
• Nucleosides differ from nucleotides in their lack of phosphate groups.
• Adenine, guanosine, uridine, thymidine, and cytidine are examples of nucleosides.

Nucleoside Functions

• Nucleoside 5' triphosphates are essential sources of chemical energy for metabolism.
• ATP is the main energy currency of the cell.
• CTP is important for phospholipid biosynthesis.
• GTP powers protein synthesis.
• UTP fuels carbohydrate biosynthesis.
• Examples of nucleoside functions in medical treatments, include: AZT and acyclovir.

Nucleoside Functions (cont.)

• Adenosine plays diverse roles including acting as a local hormone, affecting blood vessels, smooth muscle contraction, neurotransmitter release and influencing nutrient delivery during muscle exertion. It is involved in various physiological processes, such as regulating heart rate to sleep regulation.

Nucleotide

• A nucleotide consists of a 5-carbon sugar, a purine or pyrimidine base, and a phosphate group.
• Deoxyribose is the sugar for DNA; ribose is the sugar for RNA.

Nucleotide Pentose Ring

• This section presents a visual diagram of a nucleotide's pentose ring, highlighting the phosphate, a purine or pyrimidine base, and the sugar's location.

Nucleotide (cont.)

• The terms ATP, GTP, CTP, and UTP refer to nucleoside triphosphates that contain ribose.
• dNTPs (deoxyribonucleoside triphosphates)contain deoxyribose.
• A nucleoside triphosphate (NTP) is a molecule with a nucleoside attached to three phosphate groups. This is a type of nucleotide.

Adenosine Triphosphate (ATP)

• A visual depiction of adenosine triphosphate(ATP) is presented that includes the chemical structure, highlighting the phosphate anhydride linkage and the different chemical parts of ATP.

Nucleotide Functions

• Nucleotides are the building blocks of nucleic acids.
• Nucleotides act as key components in metabolic pathways.
• Examples include UDP-glucose in glycogen synthesis and CDP-ethanolamine/choline in lipid synthesis.
• Nucleotides such as ATP and ADP, GTP and GDP function as energy currency.
• Nucleotides like cAMP and various G proteins act as regulatory molecules.

Nomenclature

• This table provides the nomenclature (names) of RNA and DNA nucleosides and nucleotides.

Base Composition of Nucleic Acids

• This section examines the base composition of DNA and RNA, showing that the base pairings (A-T and G-C) are relatively constant within a species but can vary widely among different species.

Base Composition of DNA

• Erwin Chargaff's analysis demonstrated that the four bases in DNA do not always occur in equal proportions and that the ratio of bases varies between species.
• In all species observed there was always an equivalent amount of pyrimidines and purines.

Chargaff's Rules (1952)

• Four bases in DNA don't always occur in equal amounts, and this amount varies per species.
• There's an equivalent amount of A and T and also G and C, as well as an equivalent amount of purines and pyrimidines.

Base Composition (cont.)

• Base composition of DNA varies considerably among different organisms.
• G+C proportions are relatively stable among related species, from 25% to 75% in various bacterial species, while the range is between 39%- 46% for mammals.
• These rules do not apply perfectly to RNA.

Base Pairs Rules

• Adenine pairs with thymine( or uracil if it's RNA ).
• Cytosine pairs with guanine.
• Hydrogen bonds form between the paired bases.

Nucleotide/Nucleotide Comparison

• Nucleosides are sugar + base
• Nucleotides are sugar + base + phosphate.
• Nucleotide analogues are used in antiviral and anti-cancer drugs.
• Nucleosides and nucleotides have similar names, but nucleotides include phosphate groups as part of the name (e.g., 5'-uridine monophosphate).

Summary

• A nucleic acid's three primary components are a 5-carbon sugar (pentose), a purine/pyrimidine nitrogenous base, and a phosphate group.
• The monomer for DNA is a deoxyribonucleotide, and for RNA, a ribonucleotide.
• DNA and RNA are polynucleotides.

This quiz covers fundamental concepts in molecular biology related to DNA and RNA. Topics include nucleotide components, functions of nucleic acids, and the significance of DNA structure and basic pairing rules. Test your understanding of the roles of nucleotides and the distinctions between DNA and RNA.