Concepts and Techniques in Genomics and Proteomics

N Saraswathy, P Ramalingam

• Publisher: Woodhead Publishing
• Year: 2011
• Print ISBN: 9781907568107
• eBook ISBN: 9781908818058
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

Concepts and techniques in genomics and proteomics covers the important concepts of high-throughput modern techniques used in the genomics and proteomics field. Each technique is explained with its underlying concepts, and simple line diagrams and flow charts are included to aid understanding and memory. A summary of key points precedes each chapter within the book, followed by detailed description in the subsections. Each subsection concludes with suggested relevant original references. - Provides definitions for key concepts - Case studies are included to illustrate ideas - Important points to remember are noted

1

Introduction to genes and genomes

Abstract:

The cell is the basic structural and functional unit of all living organisms. Information governing cellular activity is stored in the nucleus of the cells. In all organisms, except in few viruses, the hereditary material is the deoxyribonucleic acid (DNA). In this chapter, a brief introduction to the building blocks of DNA and its structures is given. Many experiments that prove that DNA is the genetic material are discussed. Structures of prokaryotic and eukaryotic genes and genomes are also dealt with.

Key words

chromosome

DNA

gene

gene expression

genome

nucleosome

operon

ORF

replication

transcription

translation

All living forms are the lineal descendants of those which lived long before.

Charles Darwin

Key concepts

•. All living organisms possess genetic material which is inherited from their parents.

•. DNA is the genetic material in most organisms except in a few viruses.

•. The entire genetic content present in a cell of an organism is known as the genome.

•. The genome consists of coding and non-coding sequences of DNA.

•. Prokaryotes have comparatively smaller genomes and are haploid. Genes of prokaryotes are organized into operons.

•. Eukaryotes have large and complex genomes which are mostly diploid and sometimes polyploids. Genes of eukaryotes comprise exons and introns.

•. Genetic information, which is stored in the nucleus, is used for synthesizing RNA, which, in turn, codes for a protein which executes cellular functions. This series of events is known as gene expression.

1.1 Introduction

Life on Earth originated about 3.5 billion years ago. Although many theories had been put forward to explain the origin of life on Earth, scientifically conclusive evidence came from the experiment by Miller and Urey. They found they could obtain several organic compounds resembling biological molecules from inorganic compounds by simulating the atmospheric conditions that prevailed on the primordial Earth. Primitive anaerobic self-living organisms were derived from early biomolecules, which are called coacervates. Today, there are about 1.75 million well-documented organisms in the world and it is estimated that about 30 million species are yet to be explored.

Stanley Lloyd Miller (1930–2007)

Miller, an American chemist, earned his PhD in Chemistry from the University of Chicago. He was a student of Harold Urey. He proposed a biogenesis theory and proved that biological molecules can be created from inorganic precursors through his famous Miller-Urey experiment. In fact, in 2008, it was proved that 22 amino acids could be produced using his experiment.

Harold Clayton Urey (1893–1981)

Urey, an American physical chemist, received the Nobel Prize in 1934, for his work on isotopes in deuterium (heavy water); he also played a significant role in the development of the atom bomb. Along with his student, Stanley Miller, he proposed the formation of organic molecules from inorganic compounds.

1.2 The cell

The cell is the basic structural and functional unit of life. In the seventeenth century, Robert Hooke discovered cells when he was observing cork, which he described as having a honeycomb-like structure. The information for life and heredity is stored in the cells of living organisms. Based on the structure of the nucleus, living organisms are grouped into two broad categories, the prokaryotes and the eukaryotes. In prokaryotes, the genetic material is not contained in a true nucleus, as opposed to eukaryotes, in which the genetic material is stored in a separate well-organized membrane bound organelle, called the nucleus (Figure 1.1).

Figure 1.1 Prokaryotic cell (A) has simple internal structures and the genetic material is not contained inside nucleolar membrane. Eukaryotic cell (B) has complex internal structures and their genetic material is contained within defined nucleolar membrane.

Robert Hooke (1635–1703)

A natural philosopher and an architect, Hooke described the law of elasticity, over which he had a dispute with Christian Huygens for a long time. Finally, he demonstrated the balance-controlled watch before the members of the Royal Society. He served in the capacity of curator of the experiment for 40 years in the Royal Society. In 1665, he published a book entitled Micrographia, in which he used the term ‘cell’ for the first time.

1.3 Mendel’s contributions

All living organisms possess well-defined cellular architecture which is controlled by the genes that they have inherited from their parents. The branch of science dealing with heredity and variation is known as genetics. The history of genes and genetics dates back to Gregor Mendel’s work on pea plants in the nineteenth century. Before Mendel’s work, pangenesis and blending inheritance theories were the accepted theories in the biological world to explain inheritance in living organisms, but Mendel’s work explained the inheritance based on scientific experiments. He is honoured with title ‘Father of Genetics’. He observed that different traits such as height, colour of the flower, etc., are controlled by particulate matters present in the cell, which he termed factors. The factor controlling each trait is particulate in nature and the factors interact with each other when they are passed on to the progenies but they do not contaminate each other. In 1905, Mendel’s work was rediscovered by Hugo de Vries, Carl Correns and Erich von Tschermak. Subsequently, Mendel’s laws of inheritance were explained.

Gregor Johann Mendel (1822–84)

Mendel was a priest and a scientist. He devised a systematic experimental set up to study inheritance. His scientific achievements were recognized only after his death. Besides pea plants, he also worked on honeybees but he could not prove inheritance in honeybees as controlled mating was not possible.

1.4 The chromosomal theory of inheritance

Scientists were looking for the physical material of inheritance and they discovered that it is located in the chromosomes; this is an important step in exploring the nature of genes and its chemical make-up. Chromosomes are physical entities that can be seen and which carry the genetic material in the cell. Chromosomes are well-organized structures made of DNA and protein; since they can be stained intensely with dyes, they are called chromosomes. Cell division in somatic cells undergoes mitotic division, during which chromosomes duplicate and are equally distributed among daughter cells. Another type of cell division is meiosis, which occurs in germ line cells, in which the number of chromosomes in daughter cells is reduced to half.

After fertilization, the actual chromosome number of that species is restored. Careful study of movement of chromosomes during meiosis showed that chromosomes are t...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• List of figures
• List of tables
• Preface
• Acknowledgements
• List of abbreviations
• About the authors
• Chapter 1: Introduction to genes and genomes
• Chapter 2: The human genome project
• Chapter 3: Genomes of model organisms
• Chapter 4: High capacity vectors
• Chapter 5: DNA sequencing methods
• Chapter 6: Genome mapping
• Chapter 7: Genome sequencing methods
• Chapter 8: Genome sequence assembly and annotation
• Chapter 9: Functional genomics
• Chapter 10: Introduction to proteomics
• Chapter 11: Two-dimensional gel electrophoresis of proteins
• Chapter 12: Mass spectrometry for proteomics
• Chapter 13: Protein Identification by Peptide Mass Fingerprinting (PMF)
• Chapter 14: Protein sequencing techniques
• Chapter 15: Phosphoproteomics
• Chapter 16: Glycoproteomics
• Conclusion
• Glossary
• Index