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Chapter

Cover Thrive in Biochemistry and Molecular Biology

Genome stability and gene expression  

This chapter assesses genome stability and gene expression. Genetic information is stored in DNA in the order of nitrogenous bases. Information in DNA must be accurately copied, ready to be passed to the next cell generation. DNA replication is the accurate and precise copying of DNA template by DNA polymerase. To access the information encoded in DNA, a relatively short-lived copy of the genetic information is made by transcription into RNA. The three-letter nucleotide code of messenger RNA is then translated into the amino acids of protein. Any errors in the bases of DNA must be corrected by specific DNA repair processes for the integrity of the genetic code to be maintained. DNA regions can be cut and rejoined differently to alter genome sequence by DNA recombination. The chapter then considers DNA exchange in bacteria.

Chapter

Cover Biochemistry and Molecular Biology

DNA synthesis, repair, and recombination  

This chapter considers DNA synthesis as semiconservative as it is catalysed by DNA polymerases, which require the four deoxyribonucleoside triphosphates, a template or parental strand to copy, and a primer. The chapter refers to the primer of prokaryotes which is synthesized by the primase enzyme and is a short RNA copy of part of the parental strand. Synthesis starts at a site of origin on the chromosome where strand separation occurs. The chapter notes that E. coli has a single site of origin while eukaryotic chromosomes have hundreds. The chapter clarifies how a helicase separates parental strands that produces supercoiling ahead of it, noting that supercoils are removed by topoisomerases. The problem of maintaining the 5′→3′ direction of synthesis of both strands is solved by continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand.

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 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 An Introduction to Molecular Ecology

Species, populations, and individuals  

This chapter discusses the importance of species. It looks into the possibility of solving the species problem using the concepts of biological species, morphological species, phylogenetic species, and the operational taxonomic unit. Speciation is the process resulting in the formation of new species and accounts for biological diversity which is then divided between anagenesis and cladogenesis. The chapter also explores the concept of hybrids, hybrid zones, environmental DNA, and ancient DNA techniques. It includes molecular markers which it states are delivering new insights into the nature of species and boundaries. Spatial differences are emphasized for studying speciation mechanisms alongside investigating the balance of local adaptation and gene flow.

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 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 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.

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 Molecular Biology

Chromosome structure and function  

This chapter examines the structure and function of chromosomes. Each chromosome contains many genes embedded within a single DNA molecule; between the genes lie stretches of intergenic DNA. Moreover, each organism contains a characteristic number of chromosomes in each cell. Diploid cells contain two sets of chromosomes in each cell while haploid cells contain just a single set of chromosomes. Chromosomes in all organisms are associated with proteins that help to condense and organize the DNA molecules inside the cell. The basic building block of chromatin is the nucleosome, which consists of around 146 bp of DNA, wrapped twice around the histone octamer in a left-handed manner. The chapter then looks at DNA methylation, the elements required for chromosome function, the centromere and the telomere, and chromosome architecture in the nucleus.

Chapter

Cover Top Drugs

Quinolones as antibacterial DNA gyrase inhibitors  

This chapter focuses on quinolone antibiotics which inhibit DNA gyrase: the poly-functional enzyme that mediates the processes involved in DNA replication and RNA transcription. Quinolone antibiotics thus prevent bacterial DNA synthesis, leaving a relaxed form of bacterial DNA that cannot yield the correctly folded chromosome. The chapter looks at the synthesis of norfloxacin, one of the second-generation quinolones. It also describes the synthesis of ciprofloxacin, mentioning the role of combinatorial chemistry in the solid phase approach to quinolones. Furthermore, the chapter considers the preparation of ofloxacin, which, unlike other quinolone antibiotics, possess an additional ring and a stereogenic centre that require attention during the synthesis.

Chapter

Cover Molecular Biology

Cellular responses to DNA damage  

This chapter discusses cellular responses to DNA damage. The preservation of genetic information from one generation to the next requires the DNA sequence of the cell's genome to be maintained without alteration. Yet the integrity of the DNA sequence is under constant threat of damage as a result of errors in normal cellular processes such as DNA replication and transcription, and from reactive metabolites and environmental agents. Such DNA damage can result in changes in base sequence or even in chromosome structure. The effects of DNA damage are greatly reduced by specialized processes of DNA repair. This chapter looks at post-replication mismatch repair, repair of DNA damage by direct reversal, repair of DNA damage by base excision repair, nucleotide excision repair of bulky lesions, and translesion DNA synthesis. It also considers the DNA damage response in bacteria and in eukaryotes, and DNA damage and cell death in mammalian cells.

Chapter

Cover Thrive in Genetics

Working with Genes: Analysing and Manipulating DNA  

This chapter explores the process of analysing and manipulating deoxyribonucleic acid (DNA). A wide range of molecular biology techniques enables DNA to be manipulated and analysed, yielding information about the nature and function of genes. The terms recombinant DNA technology, DNA cloning, and gene cloning all refer to the same process, namely the transfer of a DNA fragment from one organism to a self-replicating genetic element that replicates the fragment in a foreign host cell. Multiple copies of a DNA sequence can be produced by cloning or by using the polymerase chain reaction. Genes are isolated from DNA libraries and gel electrophoresis separates different-sized DNA fragments. Meanwhile, the nucleotide sequence of a segment of DNA is determined by Frederick Sanger’s dideoxy method or next generation sequencing methods. Finally, forward and reverse genetics are different analytical approaches to linking phenotype and genotype.

Chapter

Cover Molecular Biology

Repair of DNA double-strand breaks and homologous recombination  

This chapter examines the repair of DNA double-strand breaks and homologous recombination. DNA double-strand breaks are particularly dangerous lesions—failure to repair them can lead to chromosome fragmentation and cell death. There are two major strategies for double-strand break repair: non-homologous end joining (NHEJ) and homology-directed repair. NHEJ rejoins the ends across a double-strand break in the absence of a DNA template. It is often mutagenic because of nucleolytic processing of the ends prior to joining. Meanwhile, homology-directed DNA synthesis can repair double-strand breaks by synthesizing new DNA across the break. The chapter then explains homologous recombination, which is the reciprocal exchange of large segments of DNA between homologous duplexes. Homologous recombination occurs during meiosis to generate gametes and occurs between the bacterial chromosome and exogenous DNA that enter the cell by conjugation or transformation, or in viruses.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

DNA  

The immortal germline

This chapter traces the history of the discovery of the genomic information system, illustrating the important principles of heredity. Life relies upon the continuity of genetic information coded in DNA and copied from generation to generation. The DNA found in every living cell contains the genetic information needed to construct the organism, as well as providing biologists with a wealth of information about evolutionary past and processes. While Charles Darwin clearly illustrated the role of heredity in the process of evolution by descent with modification, he did not know how information about an organism's form or behaviour was transmitted to its offspring. The material basis of heredity was not uncovered until Rosalind Franklin's images of the DNA helix allowed James Watson and Francis Crick to uncover how complementary base pairing provided a means to copy information endlessly down the generations. The chapter then considers the process of DNA extraction.

Book

Cover Molecular Biology

Nancy L Craig, Rachel Green, Carol Greider, Gisela Storz, Cynthia Wolberger, and Orna Cohen-Fix

Molecular Biology focuses on the key principles of the discipline to provide a robust conceptual framework. It emphasizes the commonalities between the three kingdoms but also discusses differences between them that offer insights into molecular processes and underpin biological diversity. It begins by covering the flow of biological information, biological molecules and the chemical basis of life. It looks at chromosome structure and function, the cell cycle, DNA replication, and chromosome segregation. It then considers transcription, regulation of transcription, and RNA processing. It also examines the regulation of translation, regulatory RNAs, protein modification and targeting, and cellular responses to DNA damage. Finally, it looks at the repair of DNA double-strand breaks and homologous recombination, mobile DNA, genomics and genetic variation, and tools and techniques in molecular biology.