12: Biomolecules- Amino Acids, Peptides, and Proteins
- Page ID
- 500496
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)When you have completed Chapter 12, you should be able to
- fulfill all of the detailed objectives listed under each individual section.
- use the information provided by an amino acid analysis, an Edman degradation and a carboxypeptidase hydrolysis to determine the structure of an unknown polypeptide.
- outline the approach that you would use to synthesize a given peptide, providing appropriate mechanistic details if requested to do so.
- define, and use in context, the key terms introduced in this chapter.
Amino acids are important biochemicals, as they are the building blocks from which proteins and polypeptides are assembled. We begin this chapter with an examination of some of the fundamental chemistry of amino acids: their structures, stereochemistry and synthesis. We then discuss the nature of peptides and of the peptide bond, and present the complex issue of determining the order in which the various amino‑acid residues occur in a given peptide. Once a chemist knows the exact order the of the residues in a given peptide, the next challenge is to determine a method by which the same peptide can be prepared in the laboratory. Thus, two sections are devoted to the problem of protein synthesis. The final sections in the chapter deal with the classification, overall structure and denaturation of proteins.
- 12.0: Introduction
- This section introduces the significance of amino acids, peptides, and proteins in biochemistry. It explains their roles as the building blocks of proteins, highlighting their importance in biological functions, structures, and processes. Understanding these biomolecules is crucial for comprehending life at a molecular level, as they are involved in various physiological functions, including catalysis, signaling, and structural support.
- 12.1: Structures of Amino Acids
- This section covers the structures of amino acids, highlighting their core components: a central carbon atom, an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and a variable side chain (R group). The side chains define the unique characteristics and functions of each amino acid. The text also discusses the classification of amino acids into categories like nonpolar, polar, and charged based on the nature of their side chains.
- 12.2: Amino Acids and Isoelectric Points
- The section on amino acids explains their structure, emphasizing the basic amino group (–NH₂), acidic carboxyl group (–COOH), and unique side chains (R groups) that determine their properties. It discusses the importance of the Henderson-Hasselbalch equation in understanding amino acid ionization and calculating isoelectric points, where the amino acid carries no net charge. The isoelectric point is crucial for protein stability and solubility.
- 12.3: Synthesis of Amino Acids
- This section discusses the synthesis of amino acids, detailing both natural and synthetic methods. Naturally, amino acids are produced through metabolic pathways in organisms. Synthetic methods include various chemical reactions, which allow for the production of specific amino acids in the lab. The importance of these synthesis methods is highlighted in fields like biochemistry and pharmaceuticals, where amino acids serve as building blocks for proteins and other biomolecules.
- 12.4: Peptides and Proteins
- This section explores peptides and proteins, emphasizing their structure, function, and significance in biological processes. Peptides, short chains of amino acids, can form into proteins through various linkages. The diversity in protein structure leads to a wide range of functions, including enzymes, hormones, and structural components. The relationship between peptide bonds and protein folding is also highlighted, as well as how this folding affects protein functionality.
- 12.6: Automated Peptide Synthesis - Solid-Phase Technique
- The Merrifield solid-phase method is a revolutionary technique for automated peptide synthesis. This method involves attaching the first amino acid to a solid support and sequentially adding protected amino acids to build the peptide chain. The protective groups prevent undesired reactions, allowing for precise control over the synthesis process. Automated synthesizers streamline this process, making it efficient for producing peptides in bulk for research and pharmaceutical applications.
- 12.8: Protein Misfolding and Denaturation
- Misfolding of proteins, medical problems associated with the misfolding, and denaturation of proteins are described.
- 12.10: Regulation of Enzyme Activity
- Enzymes can be slowed down or even prevented from catalyzing reactions in many ways including preventing the substrate from entering the active site or preventing the enzyme from altering conformation to catalyze the reaction. The inhibitors that do this can do so either reversibly or irreversibly. The irreversible inhibitors are also called inactivators, and reversible inhibitors are generally grouped into two basic types: competitive and non-competitive.