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Chapter

Cover The Cell

Protein Synthesis, Processing, and Regulation  

This chapter discusses proteins, which are the active players in most cell processes which implement the myriad tasks that are directed by the information encoded in genomic DNA. The chapter considers protein synthesis as the final stage of gene expression. It also describes the polypeptide chain that must fold into the appropriate three-dimensional conformation once synthesized and undergo various processing steps before being converted to its active form. The chapter shows how gene expression is controlled at the level of transcription and at the level of translation, which is an important element of gene regulation. It mentions how proteins once synthesized can be regulated in response to extracellular signals either by covalent modifications or by association with other molecules.

Chapter

Cover Developmental Biology

Differential Gene Expression  

Mechanisms of Cell Differentiation

This chapter reviews the evidence from molecular biology, cell biology, and somatic cell nuclear cloning that has shown that each cell of the body carries the same nuclear genome. It analyzes differential gene expression from genetically identical nuclei that creates different cell types and occurs at the levels of gene transcription, pre-mRNA processing, mRNA translation, and protein modification. It also shows how enhancer sequences regulate a gene's transcription in time and space. The chapter talks about DNA methylation, which can block transcription by preventing the binding of certain transcription factors or by recruiting histone methyltransferases or histone deacetylases to the chromatin. It covers Class A, B, C, D, and E transcription factors that function as homeotic regulators of floral organ identity.

Chapter

Cover Developmental Biology

Developmental Mechanisms of Evolutionary Change  

This chapter centers on evolution, which is the result of inherited changes in development and contributes to modifications of embryonic or larval development. It discusses the modularity of development that allows parts of the embryo to change without affecting other parts and is caused by the modularity of enhancers. It also considers the recruitment of existing genes and pathways for new functions as a fundamental mechanism for creating new phenotypes. The chapter details how new anatomical structures may result from duplicated genes whose regulation has diverged. It outlines the ways evolutionary change is affected through development at the level of gene expression: change in location (heterotopy), change in timing (heterochrony), change in amount (heterometry), and change in kind (heterotypy).

Chapter

Cover Thrive in Genetics

Control of Gene Expression  

This chapter studies the control of gene expression. The expression of most genes in prokaryotes and eukaryotes is regulated, i.e. genes are switched on and off according to a cell’s needs. This prevents cells’ resources being wasted. A low percentage of a cell’s genes, those that encode basic cellular functions, are expressed continually. In prokaryotes, changes in gene expression tend to be in response to environmental signals, while in eukaryotes, differential gene expression tends to be related to developmental stage. Gene expression can be regulated at various points between genotype and phenotype. In prokaryotes, most control mechanisms regulate the transcription of genes, while eukaryotes employ various translational as well as transcriptional control mechanisms.

Chapter

Cover Developmental Biology

The Genetics of Axis Specification in Drosophila  

This chapter considers drosophila cleavage as superficial as the nuclei divide thirteen times before being compartmentalized and reside in a syncytial blastoderm before cell formation. It details how the drosophila embryo undergoes a mid-blastula transition, wherein the cleavages become asynchronous and new mRNA is made. It also talks about gradients of morphogens which determine the specification of different cell types. The chapter looks at the gap gene proteins that activate and repress the pair-rule genes, which have modular enhancers that become activated in seven “stripes.” It analyzes how organs form at the intersection of dorsal-ventral and anterior-posterior regions of gene expression.

Chapter

Cover Biological Science

Reading the Genome  

Gene Expression and Protein Synthesis

This chapter provides an overview of gene expression and protein synthesis, which have two main phases: transcription and translation. It explains how cells utilize the information stored in their genome. Most genes encode proteins are synthesized via the expression of an intermediate RNA molecule called a messenger RNA (mRNA). However, some genes encode other types of RNA not destined to be translated into protein. Thus, gene expression is regulated mainly at the level of transcription, by DNA-binding proteins that bind regulatory sequences in gene promoters. The chapter details the process of RNA synthesis through transcription and protein synthesis through translation.

Chapter

Cover Biological Science

Reading the Genome  

Gene Expression and Protein Synthesis

This chapter provides an overview of gene expression and protein synthesis, which have two main phases: transcription and translation. It explains how cells utilize the information stored in their genome. Most genes encode proteins are synthesized via the expression of an intermediate RNA molecule called a messenger RNA (mRNA). However, some genes encode other types of RNA not destined to be translated into protein. Thus, gene expression is regulated mainly at the level of transcription, by DNA-binding proteins that bind regulatory sequences in gene promoters. The chapter details the process of RNA synthesis through transcription and protein synthesis through translation.

Chapter

Cover Biochemistry and Molecular Biology

Control of gene expression  

This chapter explains how gene expression can be regulated at each stage of protein synthesis, but the majority of regulation is of transcription. The chapter covers E. coli , wherein groups of genes called operons often occur and are transcribed together, forming polycistronic messengers. In the lac operon, comprising three genes, a repressor protein effects control by blocking an operator region at the initiation site of transcription. The chapter considers the repressor as an allosteric protein that detaches and allows transcription of genes required to form enzymes needed to utilize the sugar in the presence of lactose. Transcription factors (TFs) are the keys to eukaryotic gene-control.

Chapter

Cover Principles of Development

Cell differentiation and stem cells  

This chapter looks into cell differentiation and stem cells. It notes the link between gene expression and cell differentiation by addressing how referencing extracellular signals having have a key role in differentiation, as they by triggering intracellular signalling pathways that impact gene expression. Cell differentiation leads to distinguishable cell types, such as blood cells, nerve cells, and muscle cells. In addition, the chapter looks into the properties of mammalian embryonic stem cells. It mentions the degree of plasticity resulting after cell differentiation. The chapter then discusses how human stem cells cultured in vitro can also give rise to organoids that are used for drug testing and studying disease.

Chapter

Cover Molecular Biology of RNA

Stability and degradation of mRNA  

This chapter focuses on the stability and degradation of mRNA, highlighting other classes of RNA molecules that have regulated half-lives. It talks about regulating the stability of mRNA which provides another means of controlling gene expression. The chapter also clarifies that protein molecules can be synthesized if an mRNA is more stable. It also describes a classical way to demonstrate the stability of mRNA, which is to block transcription with the poison α-amanitin, a cyclic eight amino acid peptide found in the Amanita genus of mushrooms. The chapter covers the main issues connected with mRNA decay, which includes regulating the amount of protein produced and eliminating faulty mRNAs which could potentially produce toxic proteins. It presents special aspects of mRNA decay, such as the connection between extracellular stimuli and mRNA decay and the role of P-bodies as cytoplasmic zones of concentrated mRNA degradation.

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

The Inheritance of Single-gene Traits  

This chapter considers gene expression in its most general sense, which is a gene that produces a product, such as RNA or protein, that results in a change within a cell. It explains how the cellular activity influences the physical traits or the morphology of an organism, noting that the expression of genes provides the heritable component of the morphological diversity necessary for evolutionary change. It also discusses the physical traits or phenotypes that are used as tools to monitor inheritance, which are produced by the expression of genes. The chapter stresses that the inheritance patterns of individual genes are predictable and can be tracked by well-chosen phenotypes. It describes the predictable inheritance pattern of genes that arises from the behaviour of chromosomes during meiosis.

Chapter

Cover The Cell

Transcriptional Regulation and Epigenetics  

This chapter deals with the regulation of transcription, which is the primary level at which gene expression is controlled. It explains that the regulation of transcription is fundamental to all aspects of cell behavior, from the utilization of nutrients by bacteria to the complex behavior of neurons in the human brain. It also highlights the multifaceted mechanisms that determine patterns of gene expression in eukaryotes, including epigenetic control by modification of chromatin. The chapter describes the complex networks that regulate gene expression and determine the normal behavior of the many different cell types in the human body. It mentions abnormalities in transcriptional regulation that underlie many common diseases, including multiple types of cancer.

Chapter

Cover The Cell

RNA Synthesis and Processing  

This chapter discusses the initial level at which gene expression is regulated in both prokaryotic and eukaryotic cells, which is the first step in expression of a gene and transcription of DNA into RNA. It highlights different types of RNA that play distinct roles in cells, such as messenger RNAs (mRNAs) that serve as templates for protein synthesis. It also considers other noncoding RNAs function in gene regulation, mRNA splicing, rRNA processing, and protein sorting in eukaryotes. The chapter examines the roles of noncoding RNAs as regulators of gene expression in eukaryotic cells. It describes mRNA processing and the roles of snRNAs and patterns of alternative splicing, including RNA editing.

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 Genetic Analysis

Mutant phenotypes and gene activity  

This chapter discusses what mutant phenotypes and DNA sequences can tell us about molecular function. It looks specifically at pleiotropy—a mutation in a gene that influences more than a single phenotype. Conditional mutations and temperature-shift experiments have been used to analyse mutant phenotypes and associated gene activity. The chapter notes biological noise as the stochastic variation in the level of gene expression occurring under natural conditions. It also looks at mosaic organisms, which have wild-type and mutant cells; such organisms can be used to focus on gene activity at a cellular level. While small changes in the level of gene expression can be easily determined, the same cannot be said of their impact on changes to phenotype.

Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Gene  

Making an organism

This chapter focuses on genes, which, on their own, are inert. It is only when they are transcribed (copied into RNA) that they can influence an organism's development, morphology, and behaviour. The expression of genes requires the co-ordinated interaction of a great many sequences, not only the gene itself but the regulatory sequences that control its expression and the genes that make the biochemical equipment needed for transcription and translation. Typically, for molecular phylogenetics, we are interested in the genotype (the information in the genome) rather than the phenotype (the form and function of the individual that develops from that genome). However, it is important to understand the role of a sequence in the formation of phenotype in order to appreciate the different patterns of evolution we see in different parts of the genome.

Chapter

Cover An Introduction to Molecular Ecology

Genomics  

This chapter looks at genomics as the methodologies and processes used to sequence, assemble, and study the structure and function of genomes. It looks at comparative genomics. Specifically, it considers the genomes of red algae, lions, tigers, and snow leopards, aiming to reveal complex hybrid origins of root knot nematodes (RKN). Next, the chapter explores gene architecture and gene expression. The chapter also looks at the link between population genomics and population genetics. In addition, it explores the concept of genome sequencing, comparative biology, evolutionary genomics, phylogenomics, proteomics, metabolomics, epigenomics, transcriptomic approaches, and conservation biology. The chapter recognizes the technological advances improving genome editing by referencing CRISPR.

Book

Cover Molecular Biology of Cancer
Molecular Biology of Cancer starts with an introduction. It then looks at the cancer genome. Other chapters consider the regulation of gene expression, growth factor signaling, and oncogenes. The cell cycle is also considered, as are tumor suppressor genes. The text moves on to look at apoptosis, cancer stem cells and the regulation of self-renewal and differentiation pathways. There are also chapters on metastasis, angiogenesis, reprogrammed metabolism and diet, tumor immunology and immunotherapy, and inflammation and infection. Finally, the text considers strategies and tools for research and for drug development.

Chapter

Cover Molecular Biology of Cancer

Regulation of gene expression  

This chapter analyzes the molecular components involved in gene expression, including transcription factors, chromatin modifications and chromatin-binding proteins, non-coding RNAs (ncRNAs), and telomeres, and how they can contribute to the processes underpinning cancer. It emphasizes that gene expression may be modulated in various ways: through the regulation of transcription, chromatin structure, and post-transcriptional mechanisms. The chapter also describes the structure of a gene within the context of chromatin in order to elucidate how gene and chromatin structure affects gene expression. Next, the chapter displays the roles of ncRNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) that play a role in gene regulation, including post-transcriptional gene expression. It also assesses the effect of telomere position and length on gene expression.