ABI Bioinformatics Guide 2024
  • INTRODUCTION
    • How to use the guide
  • MOLECULAR BIOLOGY
    • The Cell
      • Cells and Their Organelles
      • Cell Specialisation
      • Quiz 1
    • Biological Molecules
      • Carbohydrates
      • Lipids
      • Nucleic Acids (DNA and RNA)
      • Quiz 2
      • Proteins
      • Catalysis of Biological Reactions
      • Quiz 3
    • Information Flow in the Cell
      • DNA Replication
      • Gene Expression: Transcription
      • Gene Expression: RNA Processing
      • Quiz 4
      • Chromatin and Chromosomes
      • Regulation of Gene Expression
      • Quiz 5
      • The Genetic Code
      • Gene Expression: Translation
    • Cell Cycle and Cell Division
      • Quiz 6
    • Mutations and Variations
      • Point mutations
      • Genotype-Phenotype Interactions
      • Quiz 7
  • PROGRAMMING
    • Python for Genomics
    • R programming (optional)
  • STATISTICS: THEORY
    • Introduction to Probability
      • Conditional Probability
      • Independent Events
    • Random Variables
      • Independent, Dependent and Controlled Variables
    • Data distribution PMF, PDF, CDF
    • Mean, Variance of a Random Variable
    • Some Common Distributions
    • Exploratory Statistics: Mean, Median, Quantiles, Variance/SD
    • Data Visualization
    • Confidence Intervals
    • Comparison tests, p-value, z-score
    • Multiple test correction: Bonferroni, FDR
    • Regression & Correlation
    • Dimentionality Reduction
      • PCA (Principal Component Analysis)
      • t-SNE (t-Distributed Stochastic Neighbor Embedding)
      • UMAP (Uniform Manifold Approximation and Projection)
    • QUIZ
  • STATISTICS & PROGRAMMING
  • BIOINFORMATICS ALGORITHMS
    • Introduction
    • DNA strings and sequencing file formats
    • Read alignment: exact matching
    • Indexing before alignment
    • Read alignment: approximate matching
    • Global and local alignment
  • NGS DATA ANALYSIS & FUNCTIONAL GENOMICS
    • Experimental Techniques
      • Polymerase Chain Reaction
      • Sanger (first generation) Sequencing Technologies
      • Next (second) Generation Sequencing technologies
      • The third generation of sequencing technologies
    • The Linux Command-line
      • Connecting to the Server
      • The Linux Command-Line For Beginners
      • The Bash Terminal
    • File formats, alignment, and genomic features
      • FASTA & FASTQ file formats
      • Basic Unix Commands for Genomics
      • Sequences and Genomic Features Part 1
      • Sequences and Genomic Features Part 2: SAMtools
      • Sequences and Genomic Features Part 3: BEDtools
    • Genetic variations & variant calling
      • Genomic Variations
      • Alignment and variant detection: Practical
      • Integrative Genomics Viewer
      • Variant Calling with GATK
    • RNA Sequencing & Gene expression
      • Gene expression and how we measure it
      • Gene expression quantification and normalization
      • Explorative analysis of gene expression
      • Differential expression analysis with DESeq2
      • Functional enrichment analysis
    • Single-cell Sequencing and Data Analysis
      • scRNA-seq Data Analysis Workflow
      • scRNA-seq Data Visualization Methods
  • FINAL REMARKS
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  • Introduction
  • Nucleic acids are made of nucleotides
  • DNA and RNA structure
  • Summary

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  1. MOLECULAR BIOLOGY
  2. Biological Molecules

Nucleic Acids (DNA and RNA)

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Last updated 11 months ago

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Introduction

Nucleic acids are polymers utilised by cells as information molecules. The genetic information is stored in the form of deoxyribonucleic acid (DNA) providing instructions for the synthesis of proteins needed to build and maintain functioning cells, tissues, and organisms. Notably, some viruses employ ribonucleic acid (RNA) for storing genetic information. Within cells, RNA serves to carry the instructions from the DNA to the protein-synthesising machines, known as ribosomes.

The choice of nucleic acids as information molecules is determined by their ability to drive their self-replication. The replication of DNA before cell division enables each cell to have its copy of the genetic material.

Nucleic acids are made of nucleotides

Nucleic acids are often referred to as polynucleotides since they consist of monomers called nucleotides.

Each nucleotide comprises three components: a five-carbon sugar, a phosphate group and a nitrogenous base. In RNA, the sugar is ribose, while DNA incorporates deoxyribose. The nitrogenous bases are attributed to one of two families: purines and pyrimidines. Purines, distinguished by their larger size and two fused rings, include adenine (A) and guanine (G). Pyrimidines contain one ring and include cytosine (C), thymine (T) and uracil (U). Thymine is exclusive to DNA, while uracil is only found in RNA.

DNA and RNA structure

In a polynucleotide, nucleotides are joined by phosphodiester linkages formed through condensation reactions. This bonding creates the sugar-phosphate backbone, characterized by an alternating pattern of sugars and phosphates. The two ends of a polynucleotide molecule feature distinct chemical groups. The end with a phosphate group is termed the 5' end, while the end with a hydroxyl group is called the 3' end.

A DNA molecule is comprised of two polynucleotide strands that intertwine, forming a double helix. The strands are referred to as antiparallel as they run in opposite 5' to 3' directions. The nitrogenous bases are positioned inwardly towards the double helix from the sugar-phosphate backbone. Thus, the nitrogenous bases of the two strands face each other forming complementary base pairs. In DNA, adenine (A) always pairs with thymine (T), while guanine (G) pairs with cytosine (C). The complementary bases are held together by hydrogen bonds. There are two hydrogen bonds between A and T, and three hydrogen bonds between G and C.

The majority of RNA molecules are single-stranded. However, the complementary base-pairing between regions of the same RNA molecule can make it fold into a complex three-dimensional shape. A striking example is the 3D L-shape of transfer RNA (tRNA) molecules that serve to carry amino acids to the ribosome.

Summary

The videos below provide the summary of the topic and some additional details:

DNA is the template for the synthesis of RNA which is decoded by a ribosome to make a protein Image source: OpenStax - https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Preface, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=30131214
The structure of DNA enables a replication mechanism in which two identical copies of the parental molecule are produced Image source: Genomics Education Programme - Semi conservative replication of DNA, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=50542923
Nucleotides make up nucleic acids (a) Each nucleotide contains a pentose sugar, a phosphate and a nitrogenous base (b) Nitrogenous bases (c) Fice-carbon sugars of DNA and RNA Image source: OpenStax College - Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013., CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=30131164
DNA structure Image source: Zephyris - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=15027555
Left: the regions of complementarity in tRNA Right: tRNA 3D shape Image source: Kyle Schneider (SchneiderKD) (Transfered by BQmUB2010090/Original uploaded by SchneiderKD) - Schneider KD (Original uploaded on en.wikipedia), Public Domain, https://commons.wikimedia.org/w/index.php?curid=12309266