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Chapter

Cover Biochemistry and Molecular Biology

The structure of proteins  

This chapter focuses on proteins, which are made up of one or more polypeptide chains constructed from 20 species of amino acids. The length and sequence of each polypeptide is specified by its gene. The chapter describes 20 different amino acids which are of differing sizes and degrees of hydrophobicity, hydrophilicity, and electrical charge. These present the possibility of a vast variety of different proteins. The primary structure is the linear amino acid sequence, while the secondary structure involves folding of the polypeptide backbone. The chapter explains that the main secondary structure motifs are the α helix and the β-pleated sheet, which are stabilized by hydrogen bonding. The tertiary structure involves the further folding of the secondary structure motifs into the three-dimensional form of the protein.

Chapter

Cover Molecular Biology of RNA

Translation of messenger RNA  

This chapter covers the process of mRNA translation. Itbegins by reviewing the structure and function of the essential machinery of translation, namely the ribosome and transfer RNA. The chapter outlines the three phases of translation: initiation, elongation, and termination. It also discusses several ways in which mRNA translation can be regulated. The chapter details how ribosomes catalyse the synthesis of polypeptide chains that form when amino acids are covalently linked through peptide bonds. The chapter explains that ribosomes are made up of large and small subunits that contain ribosomal RNA (rRNA) and a multitude of ribosomal proteins. The chapter then looks at the different components of the ribosomal subunits that are distinguished according to the rate at which they sediment, as measured in Svedberg units.

Chapter

Cover Biochemistry

Amino Acids, Peptides, and Proteins  

This chapter discusses proteins as molecular tools. These perform an astonishing variety of functions. In addition to serving as structural materials in all living organisms, proteins are involved in diverse functions as catalysis, metabolic regulation, transport, and defence. Proteins are composed of one or more polypeptides, unbranched polymers of 20 different amino acids. The chapter looks at the genomes of organisms which specify the amino acid sequences of thousands or tens of thousands of proteins. It describes proteins as a diverse group of macromolecules that are directly related to the combinatorial possibilities of the 20 amino acid monomers. Amino acids can be theoretically linked to form protein molecules in any imaginable size or sequence.

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 Genetics

The Central Dogma of Molecular Biology  

This chapter explains that the Central Dogma of molecular biology is that DNA provides the template to make RNA, which provides the template to make a polypeptide that contributes to phenotypes. It illustrates the structure of DNA and the Central Dogma, highlighting features of the DNA molecule that have an impact on its function. It points out modifications to the traditional view of the Central Dogma and introduces the basic structure of a gene. The chapter describes information content that flows from DNA to RNA to polypeptide, which is inherent in the structures of the molecules and encodes the amino acid sequence of the polypeptide. It also shows that, according to genome analysis, a surprising number of RNA molecules do not serve as templates for making polypeptides but are functional themselves.

Chapter

Cover Inorganic Chemistry in Biology

Structures and functions  

This chapter reviews the spectroscopic properties of metalloproteins that are vital for their monitoring and for their illuminating of the details of the metal site. The chapter mentions properties that are directly related to the function of the metalloprotein, which are distributed between those that originate from polypeptide from those arising from the metal ion. It also analyses the artificial division of metalloprotein that act synergistically, which results in a unique entity. The chapter talks about protein, which imposes a rigid and often unusual arrangement of ligands around the metal ion. It explains how protein provides a pathway for the protected or guided entry of substrates to the metal site.

Chapter

Cover Biological Science

Proteins and Proteomes  

This chapter focuses on the structure, features, and function of proteins. It cites amino acids as the building blocks of proteins. Proteins carry a range of functions, such as the agents of biochemical reactions of cellular metabolism or hormones transmitting signals from one cell to another. The chapter then details the four levels of protein structure that are dependent on polypeptide chains. Enzymes function as biological catalysts that make a chemical reaction more likely to occur and speed up the overall rate. The chapter acknowledges how modern protein technology methods allow the rapid identification of proteins and the growth of proteomics as a field of study.

Chapter

Cover Thrive in Genetics

From Genotype to Phenotype II: RNA to Protein  

This chapter explores translation, which is the mechanism by which amino acids are assembled into proteins according to information encoded in messenger RNA (mRNA). It takes place on ribosomes, which attach near the 5′ end of mRNA and move towards its 3′ end, positioning and linking amino acids according to the codons they encounter. Translation involves a number of RNA–RNA interactions: between mRNA and ribosomal RNA (rRNA), which holds the mRNA for translation; mRNA codon and transfer RNA (tRNA) anticodon; and tRNA and the rRNA of ribosomes. Translation in both prokaryotes and eukaryotes involves three main stages: initiation, elongation, and termination. The chapter then considers the post-translational modification of polypeptides.

Chapter

Cover Biological Science

Proteins and Proteomes  

This chapter focuses on the structure, features, and function of proteins. It cites amino acids as the building blocks of proteins. Proteins carry a range of functions, such as the agents of biochemical reactions of cellular metabolism or hormones transmitting signals from one cell to another. The chapter then details the four levels of protein structure that are dependent on polypeptide chains. Enzymes function as biological catalysts that make a chemical reaction more likely to occur and speed up the overall rate. The chapter acknowledges how modern protein technology methods allow the rapid identification of proteins and the growth of proteomics as a field of study.

Chapter

Cover Foundations of Chemical Biology

The structures of proteins  

This chapter analyses the properties of a protein that are determined by its shape and its chemical functionality, noting that proteins form well-defined three-dimensional structures. It reviews the role of some proteins as structural materials, which can be understood in terms of their molecular architecture. It also elaborates how proteins adopt compact globular structures. The text uses an illustration of an enzyme called triose phosphate isomerase. The chapter discusses the overall structure of a protein that is related to the order of the monomer units in the chain and the conformation that each monomer residue adopts. It outlines the appreciation of the three-dimensional structures of proteins that is achieved by considering the stereochemical preferences of a short stretch of a polypeptide chain.

Chapter

Cover Making the Transition to University Chemistry

Amines and Amino Acids  

This chapter describes the mechanisms of amines and amino acids. It also notes the two common naming systems of amines, which are known to be one class of organic compounds with nitrogen atoms. Amines are classified in terms of their general formulas, alkyl group, and hydrogen atoms attached to the nitrogen atom. The Gabriel synthesis is a method of successfully making a primary amine. Amino acids have two function groups: an amino group and a carboxylic acid group. Amino acids also polymerize to construct polypeptides. The chapter discusses the effects of pH and zwitterions as well.

Chapter

Cover Exploring proteins: a student’s guide to experimental skills and methods

Conceptual toolkit: the molecular principles for understanding proteins  

This chapter discusses the principles for understanding the structures and functions of proteins. It begins by reviewing the properties of amino acids, which represent the building blocks of proteins. The chapter looks at the structure of proteins on four levels. The primary structure refers to the sequence of amino acids in the polypeptide chain, i.e. the covalent structure of the protein. The secondary structure refers to the local folding of the polypeptide chain, such that segments of the chain may form helices, strands of sheet, or turns. Meanwhile, the tertiary structure refers to the long-range folding of the polypeptide chain so that portions of the chain that are remote in terms of sequence are brought close together in space. The quaternary structure refers to the association of the individual polypeptide chains in a multi-subunit protein. The chapter then considers the forces contributing to the structures and interactions of proteins.

Chapter

Cover Chemistry for the Biosciences

Biological macromolecules: the infrastructure of life  

This chapter studies some of the key biological macromolecules that make life happen: amino acids and proteins, nucleic acids, carbohydrates, and lipids. Amino acids join together to form polymers named polypeptides. The structure of proteins is built up over four levels of hierarchy: primary, secondary, tertiary, and quaternary. Protein structure is stabilized by both non-covalent interactions (including hydrogen bonds and hydrophobic interactions) and covalent bonding, including disulfide bonds. The chapter also describes the two key natural nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are polymers of nucleotides. The chapter then considers the three main classes of carbohydrate (sugar)—monosaccharides, disaccharides, and polysaccharides. It also looks at the three most important types of lipid: steroids, triacylglycerols, and the glycerophospholipids.

Chapter

Cover Genetics

Translation: From Nucleic Acids to Amino Acids  

This chapter reviews RNA transcripts made from the DNA sequence of a gene which are translated into the amino acid sequence of polypeptides. It explains that the process of translation is highly similar in all living organisms and arose only once with relatively small modifications during evolution. It also highlights genome-based analysis of transcription that has led to the realization that the genomes of nearly all organisms are pervasively transcribed. The chapter reviews the Central Dogma that originally did not include non-coding RNA but posits that the functional molecules in the cell are polypeptides and that a gene encodes the capacity to make a polypeptide. It details the process of translating information from the string of nucleotides in nucleic acids into the string of amino acids in polypeptides.

Chapter

Cover Chemistry of the First-row Transition Metals

Bio-transition metal chemistry  

This chapter examines the functions of metals in biology which are generally classified into two major groups: metalloproteins and metalloenzymes. Metalloproteins are sub-divided into transport and storage functions, while metalloenzymes are non-protein systems that are involved in photo-redox activity. It also discusses proteins that consist of one or more polypeptide chains, which are comprised of amino acids that are usually connected by a peptide bond. The chapter refers to metalloproteins that incorporate one or more metal atoms as a normal part of the tertiary structure of the protein. It also describes metalloenzymes, which are applied to systems that require the participation of metal ions at the active site to function.

Chapter

Cover Molecular Biology

Translation  

This chapter focuses on translation, the process by which a polypeptide chain is synthesized according to the instructions in an mRNA template molecule; it is the final step in the flow of genetic information from DNA to protein. tRNAs are bifunctional molecules that decipher the genetic information through Watson–Crick pairing interactions with the mRNA, bringing the activated amino acid along for peptide bond formation. The chapter then considers aminoacyl-tRNA synthetases and the structure of the ribosome. Aminoacyl-tRNA synthetases are responsible for the first event in decoding as they determine which of the 40 or so tRNAs in the cell get attached to which amino acids. Meanwhile, the ribosome is the macromolecular ribonucleoprotein machine that coordinates the process of translation through events in two distinct subunits, one primarily responsible for decoding and the other for making peptide bonds. Translation can be divided into multiple stages: initiation, elongation, termination, and ribosome recycling.

Chapter

Cover Protein Science

Protein Structure  

This chapter discusses the basic chemistry of proteins and illustrates some of the salient features of their three-dimensional structures. The principles of construction and design of proteins start with amino acids and builds up to complete structures. Amino acids form peptide bonds, to create a polymer chain. Each amino acid within a polypeptide chain contains a sidechain. The sequences of sidechains—dictated primarily by the DNA sequences of the genes—determine the three-dimensional structures and, thereby, the functions of proteins. In addition to the polypeptide chain, many proteins may contain atomic ions, have small organic molecules, or undergo covalent post-translational modifications. The chapter then looks at protein folding and denaturation. Most proteins form native states, folding into a compact three-dimensional structure dictated by the amino-acid sequence. In contrast, the denatured state arises when conditions of temperature or solvent break up the native state. Finally, the chapter considers protein structures, protein families, and protein interactions.