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
Amino Acids, Peptides, and Proteins
Chapter
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
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
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
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.
