26: Biomolecules- Amino Acids, Peptides, and Proteins
- Page ID
- 448843
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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 26, 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.
- 26.0: Why This Chapter?
- 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.
- 26.1: 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.
- 26.2: Amino Acids, the Henderson-Hasselbalch Equation, 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.
- 26.3: 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.
- 26.4: 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.
- 26.5: Amino Acid Analysis of Peptides
- This section discusses methods for analyzing amino acids in peptides, focusing on techniques like chromatography and mass spectrometry. It highlights the importance of these methods in determining peptide composition and structure, which are crucial for understanding biological functions. The analysis aids in identifying the sequence of amino acids and can reveal modifications that influence peptide behavior.
- 26.6: Peptide Sequencing- The Edman Degradation
- The Edman degradation is a method for sequencing amino acids in a peptide. It involves selectively removing one residue at a time from the amino end of the peptide, which is then identified through chromatography. This technique is valuable for determining the primary structure of peptides and proteins. The process is effective for shorter peptides and allows for the sequential analysis of amino acids, contributing significantly to protein characterization and understanding their biological func
- 26.7: Peptide Synthesis
- Peptide synthesis involves the stepwise formation of peptide bonds between amino acids, typically using solid-phase peptide synthesis. which allows for the rapid assembly of peptides by attaching amino acids to a solid resin, enabling easy purification. Protective groups are employed to prevent unwanted reactions during the synthesis process. This technique is crucial for producing peptides for research and therapeutic applications, the study of protein function and the development of drugs.
- 26.8: Automated Peptide Synthesis- The Merrifield Solid-Phase Method
- 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.
- 26.9: Protein Structure
- Protein structure is categorized into four levels: primary (amino acid sequence), secondary (local folding into alpha helices and beta sheets), tertiary (3D folding due to interactions among side chains), and quaternary (assembly of multiple polypeptide chains). Each level is crucial for the protein's overall function and stability. Proper folding and structural integrity are essential for biological activity, and misfolding can lead to diseases.
- 26.10: Enzymes and Coenzymes
- Enzymes are biological catalysts that speed up chemical reactions in cells, functioning by lowering activation energy. They are often proteins, though some RNA molecules (ribozymes) can act as enzymes. Coenzymes are non-protein organic molecules that assist enzymes, often derived from vitamins. Together, they play crucial roles in metabolic pathways and cellular processes, ensuring efficiency and specificity in biochemical reactions.
- 26.11: How do Enzymes Work? Citrate Synthase
- Citrate synthase is an enzyme crucial for the citric acid cycle, catalyzing the condensation of acetyl-CoA and oxaloacetate to form citrate. Its function involves binding substrates, stabilizing transition states, and undergoing conformational changes to facilitate the reaction. This mechanism highlights how enzymes lower activation energy and increase reaction rates, demonstrating the importance of enzyme structure and substrate interaction in metabolic processes.
- 26.12: Chemistry Matters - The Protein Data Bank
- The Protein Data Bank (PDB) is a crucial repository for three-dimensional structural data of biological macromolecules, primarily proteins and nucleic acids. It facilitates research by providing scientists with access to information on molecular structures, aiding in drug design and understanding biological processes. The PDB plays a vital role in structural biology, allowing researchers to visualize and analyze the structures of proteins, enzymes, and other biomolecules.
- 26.14: Summary
- Proteins and peptides are large biomolecules made of α-amino acid residues linked together by amide, or peptide, bonds. Twenty amino acids are commonly found in proteins, and all except glycine have stereochemistry similar to that of L sugars. In neutral solution, amino acids exist as dipolar zwitterions.