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Chapter

Cover Introduction to Protein Science

Introduction  

This introductory chapter provides an overview of proteins, which are a family of biological macromolecules that provide a variety of three-dimensional structures exquisitely shaped for their many different individual functions. They include structural proteins, enzymes, antibodies, regulatory proteins, sensors, transporters and pumps, and transducers. The common features of the chemical structures of proteins make possible a common synthetic mechanism: ribosomes assemble the great variety of proteins under the direction of different messenger RNA (mRNA) sequences. Both the DNA sequences of genes and the amino acid sequences of proteins are one-dimensional. The chapter asks: how then do proteins achieve their three-dimensional biologically active states? The three-dimensional structures of proteins are inherent in their amino acid sequences. It is the combination of a common synthetic machinery — the gene sequence dictating the amino acid sequence — with spontaneous folding to the native three-dimensional structure, that underlies the mechanism of molecular evolution.

Chapter

Cover Biochemistry and Molecular Biology

Manipulating DNA and genes  

This chapter looks at the technology of DNA manipulation. This has become the most powerful approach to many biological and medical problems. It shows how DNA manipulation permits the isolation of genes, the determination of their nucleotide sequences, the detection of abnormal genes, and the production of human and other proteins in unlimited amounts in hosts such as yeast and bacteria. DNA can be cut with precision at known sequences using a battery of restriction enzymes. The chapter describes DNA sequences which can be identified by hybridization with probes obtained by isolation or synthesis. Recombinant DNA molecules, in which different pieces of DNA are joined together, can be produced in a number of ways.

Chapter

Cover Concepts in Bioinformatics and Genomics

Phylogenetics  

This chapter introduces phylogenetics with a discussion of DNA, protein sequence information, and the construction of phylogenetic trees. It demonstrates how to use sequence information to categorize how species are related to each other. Phylogenetics is the utilization of sequence information to create evolutionary histories of species. Sequence information from recently extinct human subspecies Neanderthal and Denisovan has become available. Using phylogenetic software programs, the chapter shows at what point in time these human subspecies shared a common ancestor with us. Prior to our ability to identify DNA mutations directly, the field of paleontology was developed to study evolutionary histories (phylogeny). The chapter then explores how paleontology, together with sequence information, contributes to the study of evolutionary histories. Towards the end it delves into the analysis of sequence information.

Chapter

Cover Genetics

Genome Structure, Organization, and Variation  

This chapter covers the structure of the genome and the variation in genome organization found in different species, which are both the outcome of, and the ingredients for, natural selection. It discusses the structure of chromosomes, extrachromosomal DNA, changes in the genome, and integration of genomic findings with evolutionary and genetic principles. It also reviews the DNA sequence of an organism, which encodes the information that underpins and directs most of the biological processes taking place within that organism. The chapter points out that genomes of different species differ in their DNA sequences and in the organization of their genes and other genetic elements. It connects genomic information with well-defined evolutionary and genetic concepts, providing a framework to weave together the details of genetics, genomes, and evolution.

Chapter

Cover The Cell

Replication, Maintenance, and Rearrangements of Genomic DNA  

This chapter describes different DNA polymerase family members which play distinct roles in DNA replication and repair in both prokaryotic and eukaryotic cells. It covers DNA polymerases and various other proteins that act in a coordinated manner to synthesize both leading and lagging strands of DNA. It also shows how DNA polymerases increase the accuracy of replication by selecting the correct base for insertion and by proofreading newly synthesized DNA to eliminate mismatched bases. The chapter reviews DNA replication which starts at the origins of replication. This DNA replication contains binding sites for proteins that initiate the process. It reviews telomeric repeat sequences at the ends of chromosomes which are maintained by the action of a reverse transcriptase (telomerase) that carries its own template RNA.

Chapter

Cover Genomics

Genomics: Reading and Writing Genomes  

This chapter explores the incredible advances which have taken place—and are still taking place—in the technologies involved in DNA sequencing and in DNA manipulation. The invention of DNA sequencing technology enabled DNA to be read for the first time in the 1970s, using a process known as Sanger sequencing. The development of capillary sequencing then helped to speed up many genome sequencing projects, as it is faster and cheaper than the previous methods. Other developments include high-throughput short-read sequencing technologies and long-read sequencing technologies. Meanwhile, editing DNA sequences in cells using protocols such as CRISPR–Cas9 allows researchers to change the DNA sequences within cells, so they can test what specific DNA sequences do within cells and potentially change faulty sequences or improve outcomes. Writing entirely new genomes is now possible for simple cells, as it is now possible to join together long synthetic DNA sequences.

Chapter

Cover Thrive in Genetics

The Biochemical Basis of Heredity  

This chapter addresses the biochemical basis of heredity. Nucleotides, which polymerize to form long chains, are the building blocks of DNA and RNA. A DNA molecule consists of two chains of nucleotides coiled around each other to form a double helix, while an RNA molecule consists of a single chain. The DNA double helix is formed by complementary base pairing between nucleotides on opposite strands. During DNA replication, the two strands separate and each becomes a template for the synthesis of a new strand. The sequence of nucleotides encodes the genetic information. The chapter then looks at the types of DNA sequence as well as transposable elements.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Alignment  

Same but different

This chapter explores sequence alignment. Descent with modification creates hierarchies of similarities, such that close relatives will be more similar in many respects, including their genomes. As such, a systematic hierarchy based on descent allows prediction of similarity across many different characteristics. Therefore, taxonomic groups should be based on similarity by descent (homologies) not incidental similarities that evolved independently in different lineages (analogies). To use DNA sequences to trace evolutionary past and processes, we must first establish homology through sequence alignment, where sites all originally copied from the same ancestral sequences are compared across lineages to detect evolutionary changes. Indeed, sequence alignment is the process whereby homologies are distinguished from analogies.

Book

Cover Tools and Techniques in Biomolecular Science

Edited by Aysha Divan and Janice Royds

Tools and Techniques in Biomolecular Science looks at gene cloning to start with. It also looks at DNA mutagenesis, DNA sequencing, and measuring DNA. It also covers recombinant protein expression, protein purification, and antibodies as research tools. Next, it moves to look at measuring protein-protein interactions, structural analysis of proteins, and mass spectrometry. There are also chapters covering mass spectrometry, proteomic analysis, culturing mammalian cells, and flow. Finally, the text examines bioimaging, histopathology, mouse models in bioscience research, and mathematical models in biomolecular sciences.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Introduction  

The story in DNA

This introductory chapter provides an overview of the kind of information that can be gained from analysing DNA sequences. The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untangling family relationships. The chapter illustrates the information that can be gained from the analysis of DNA sequences by considering a single DNA sample and how it can shed light on the evolutionary history of individuals, families, social groups, populations, species, lineages, and kingdoms. The aim of this book is not to provide protocols for DNA sequencing or instructions for software packages used in the production and analysis of DNA sequences. Instead, it presents the background knowledge one needs to understand these techniques.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Replication  

Endless copies

This chapter examines DNA replication. The evolution of life depends on hereditary information being copied from one generation to the next. Thus, a basic grasp of DNA replication is essential for anyone wishing to understand evolution. Moreover, familiarity with the processes of DNA replication is the key to understanding many molecular techniques. DNA amplification (making millions of copies of a DNA sequence in the laboratory) relies upon the domestication of the DNA copying processes that occur in living cells. Understanding DNA replication is also central to appreciating the nature of biological information stored in DNA. DNA replication creates a nested hierarchy of differences between genomes that reveals the relationships between organisms and the processes of evolution.

Chapter

Cover Tools and Techniques in Biomolecular Science

DNA mutagenesis  

Sarah E. Deacon and Michael J. McPherson

This chapter takes a closer look at DNA mutagenesis, an essential tool in modern biology. DNA mutagenesis helps elucidate significant insights about the regulation of gene expression, the structure-function relationship of DNA, RNA, and proteins, as well as molecular interactions, among others. The chapter focuses on two major classes of in vitro mutagenesis: site-directed mutagenesis, in which specific nucleotides within a DNA sequence are targeted, and random mutagenesis, in which mutations are usually introduced either through inducing errors during DNA replication or by recombination of related DNA sequences. It describes different in vitro methods for introducing mutations into a known DNA sequence. Furthermore, it lays down the advantages and disadvantages of each method, allowing the reader to appreciate and select an appropriate method for DNA mutations for a particular project.

Chapter

Cover Biochemistry

Nucleic Acids  

This chapter analyses the nucleic acids DNA and RNA, which are polynucleotides that encode the genetic information used to construct and maintain living organisms. Double-stranded DNA is, in effect, the blueprint used to direct cell processes. The chapter highlights how cells convert DNA’s operating instructions into the nucleotide sequence of single-stranded RNA molecules. It outlines RNAs’ numerous functions, which include polypeptide synthesis, the regulation of gene expression, and protection from foreign nucleic acids introduced by viral infections. Investigations of nucleic acid structure and function, now almost 70 years old, have given humans a previously unimagined understanding of biological processes and a powerful tool used in such diverse fields as disease diagnosis and treatment and forensic investigations.

Chapter

Cover Genetics

Transcription: Reading and Expressing Genes  

This chapter discusses the DNA sequence that comprises a gene which is expressed by the transcription of the gene into an RNA molecule. It details the regulation of transcription and describes cells with the same DNA sequence that have different appearances and functions because they transcribe different genes. It also considers transcript initiation as the key step through which gene expression can be controlled, noting that the transcription processes that are regulated by the cell are also those that have been subject to the most evolutionary variation. The chapter deals with gene expression, which is the process of transcribing a subset of the genes in a genome into RNA to mediate a biological function that differs across time and space. It looks at the processes of gene expression that provide the framework to highlight the many opportunities for control and evolutionary change.

Chapter

Cover Genetics

Evolution, Genomes, and Genetics  

This chapter introduces a recent study of the genomes of Charles Darwin’s finches, which identified genes that contribute to the differences in beak shape among the species. It links one of the most important and familiar examples of natural selection among Darwin’s finches with the underlying genetic and genomic basis for the differences observed among the birds. It also uses Darwin’s finches to discuss DNA, molecules, phenotypes, species, and evolution in a community of organisms. The chapter explores the current availability of genomic information from many species of bacteria, plants, and animals. It highlights how evolution has shaped DNA sequences, genes, and genomes throughout biology.

Chapter

Cover Foundations of Physical Chemistry: Worked Examples

Taking it further  

This chapter reviews examples that show the four base pairs involved in hydrogen bonding of stranded DNA, wherein the pairs thymine (T) and adenine (A), and cytosine (c) and guanine (G) are complementary. It addresses the question of whether there is any difference in the stability to heat of DNA sequences that contain a higher proportion of GC base pairs. It also shows the translation of RNA message into a protein and the DNA code contains four letters G, C, A, and T, wherein the DNA codes for proteins that are made up of chains of amino acids. The chapter explains how ethanol is removed from blood through the action of the enzyme alcohol dehydrogenase in the liver. It discusses the alcohol dehydrogenase that contains two zinc atoms one of which provides an active site for the reaction.

Chapter

Cover Evolution

The Tree of Life  

This chapter focuses on the aspect of evolution represented by a phylogenetic tree. It explains that phylogeny is the study of the history of cladogenetic events and explains how species or other taxa successfully arose from a common ancestor. The diversity of life has evolved over so long a time and this has involved hybridization and horizontal gene transfer. The chapter also notes how phylogenetic methods can be used to explain the history not only of species, but also of DNA sequences, gene families, tumors and other cell lineages, and cultural traits. It explains the notion of mosaic evolution wherein different characters commonly evolve at different rates.

Chapter

Cover Biochemistry

Genetic Information  

This chapter describes all living organisms as information-processing systems. Their ultimate source of information is encoded in the nucleotide base sequence of DNA. As biochemists have searched ever more deeply into the mysteries of genetic information storage and transmission, how DNA is replicated, and gene expression is controlled, they have transformed all of the life sciences. The chapter cites the knowledge and technologies that were acquired during this pursuit and that have provided an understanding of the intricacies of living processes that is still unfolding. It also reviews the instructions required to produce a certain type of organization that must be stably stored to safeguard their accuracy and availability for use. Information must also be converted into a form that can be utilized.

Chapter

Cover Introduction to Bioinformatics

Introduction  

This introductory chapter presents the major components of bioinformatics: DNA and protein sequences and structures, genomes and proteomes, databases and information retrieval, the World Wide Web, and computer programming. Before the advent of modern technologies and the internet, biological observations were fundamentally anecdotal and fragmentary. In recent generations, the data have become not only much more quantitative, but also more precise and comprehensive. Biological databases have recently supplemented the archives of nucleic acid sequences, amino acid sequences of proteins, and structures of proteins and protein–nucleic acid complexes. Given the data streams, analysis has become ever more challenging. Not only has bioinformatics developed powerful tools, but its methods are becoming more deeply integrated into the biomedical enterprise.

Chapter

Cover Introduction to Bioinformatics

The panorama of life  

This chapter discusses the basic sizes, contents, and organizing principles of simple and complex genomes. A single gene coding for a particular protein corresponds to a sequence of nucleotides. In cells, genes may appear on either strand of DNA. Bacterial protein-coding genes are continuous regions of DNA, while in eukaryotes, the nucleotide sequences that encode amino acid sequences of proteins are organized in a more complex manner. The chapter then looks at proteomics and transcriptomics. It considers how the genomes of prokaryotes and eukaryotes differ systematically, before exploring the variety of transcribed RNA molecules encoded in the human genome. The chapter then highlights the power of DNA sequences in studying human history, including inference of human migration patterns, and as records of plant and animal domestication. It also assesses the power of comparative genomics to identify features responsible for differences between species.