26.4 Peptides and Proteins
3 min read•may 7, 2024
Amino acids are the building blocks of proteins, and their sequence determines a protein's structure and function. These molecules link together through peptide bonds, forming chains that can fold into complex shapes. Understanding amino acids is crucial for grasping protein chemistry.
Proteins have multiple levels of structure, from simple sequences to intricate 3D shapes. Secondary structures like alpha helices and beta sheets are stabilized by hydrogen bonds. Disulfide bridges and the also play key roles in maintaining protein stability and shape.
Amino Acids and Peptide Bonds
Peptide sequence construction
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- Amino acids represented by one-letter and three-letter abbreviations
- One-letter abbreviations use a single uppercase letter (G for , S for Serine)
- Three-letter abbreviations use three lowercase letters (Gly for Glycine, Ser for Serine)
- Peptide sequences written from to
- N-terminus has a free
- C-terminus has a free
- One-letter abbreviation peptide sequence example: AGCDE
- Corresponds to -Glycine---
- Three-letter abbreviation peptide sequence example: Ala-Gly-Cys-Asp-Glu
- Alanine-Glycine-Cysteine-Aspartic Acid-Glutamic Acid sequence
- The sequence of amino acids in a peptide or protein represents its
Peptide bond formation
- Peptide bonds form through between of one and amino group of another
- Carboxyl group loses a hydroxyl (-OH)
- Amino group loses a hydrogen (-H)
- Water molecule () released as byproduct
- Resulting covalent bond between carbon of carboxyl group and nitrogen of amino group called a
- Peptide bonds have partial double bond character due to resonance
- Formation of peptide bonds creates repeating structure called or
- Peptide backbone consists of alternating nitrogen-carbon-carbon (N-C-C) units
- Amino acid are individual amino acids within a peptide or protein connected by peptide bonds
- Side chains (R groups) of amino acid residues extend from peptide backbone
Disulfide Bridges
Disulfide bridges in proteins
- Disulfide bridges (disulfide bonds) are covalent bonds formed between sulfur atoms of two cysteine residues
- Cysteine (Cys or C) is an amino acid containing a (-SH) on its
- Formation of involves of two thiol groups resulting in covalent sulfur-sulfur bond (-S-S-)
- Oxidative coupling reaction requires an oxidizing agent
- Disulfide bridges can form within a single peptide or protein chain () or between two different chains ()
- Intramolecular disulfide bridges contribute to of a protein
- Intermolecular disulfide bridges can stabilize by linking multiple peptide or protein subunits
- Disulfide bridges play crucial role in stability and folding of proteins
- Help maintain proper three-dimensional conformation of a protein
- Can be reduced back to thiol groups using reducing agents ( or )
Protein Structure and Stability
Secondary structure
- Refers to local folding patterns of the protein backbone
- Two common types of :
- : a spiral-shaped structure stabilized by between backbone atoms
- : a pleated structure formed by hydrogen bonding between adjacent strands of the protein backbone
- Hydrogen bonding plays a crucial role in stabilizing elements
Factors influencing protein stability
- Hydrophobic effect: tendency of nonpolar amino acid side chains to cluster together in the protein core, minimizing contact with water
- Hydrogen bonding between amino acid side chains and the protein backbone contributes to overall stability
Key Terms to Review (46)
Alanine: Alanine is a non-essential amino acid that is commonly found in proteins. It plays a crucial role in various biochemical processes, including protein synthesis, energy production, and amino acid metabolism.
Alpha Helix: The alpha helix is a common secondary structure found in proteins, characterized by a right-handed spiral arrangement of the polypeptide backbone. This helical structure is stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amino hydrogen of another, creating a stable, coiled conformation that is crucial for protein folding and function.
Amino acid: Amino acids are organic compounds that serve as the building blocks of proteins, each containing an amino group (-NH2), a carboxyl group (-COOH), and a unique side chain (R group) attached to the central carbon atom. They play critical roles in various biological functions, including cellular structure, function, and regulation.
Amino Acid: Amino acids are organic compounds that serve as the fundamental building blocks of proteins. They consist of a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain that determines the specific properties of each amino acid.
Amino Acid Residue: An amino acid residue refers to the individual amino acid unit that is covalently bonded within a peptide or protein chain. It is the fundamental building block of these biomolecules, which play crucial roles in the structure and function of living organisms.
Amino Group: The amino group is a functional group consisting of a nitrogen atom bonded to two hydrogen atoms. It is a key structural feature of amino acids, which are the building blocks of proteins, and plays a crucial role in the chemistry and properties of these biomolecules.
Aspartic Acid: Aspartic acid is a non-essential amino acid that plays a crucial role in various metabolic processes within the body. As one of the 20 standard amino acids, it is a fundamental building block of proteins and peptides, and is integral to the structure and function of many biomolecules.
Backbone: In peptides and proteins, the backbone refers to the repeated sequence of atoms that forms the core structure to which the various side chains (R groups) of amino acids are attached. It consists primarily of a pattern of -N-C-C- (nitrogen-carbon-carbon) repeating units.
Beta Sheet: A beta sheet, also known as a beta-pleated sheet, is a secondary structure found in proteins where multiple parallel or anti-parallel polypeptide chains are held together by hydrogen bonds. This arrangement creates a sheet-like structure that is an important component of many protein structures.
C-terminus: The C-terminus, or carboxy-terminus, refers to the end of a polypeptide or protein chain where the carbon atom of the carboxyl (COOH) group is located. It is one of the defining structural features of peptides and proteins, and its properties play a crucial role in their function and behavior.
Carboxyl group: A carboxyl group is a functional group consisting of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group (-COOH). It is characteristic of carboxylic acids, giving these compounds their acidic properties.
Carboxyl Group: The carboxyl group is a functional group consisting of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group (-COOH). It is a key structural feature in various organic compounds, including carboxylic acids, amino acids, and proteins, and plays a crucial role in their chemical reactivity and properties.
Condensation Reaction: A condensation reaction is a type of chemical reaction where two molecules combine to form a single molecule, often with the elimination of a small molecule such as water or ammonia. This process is fundamental in the formation of many organic compounds, including polymers, peptides, and various condensation products.
Cysteine: Cysteine is a sulfur-containing amino acid that plays a crucial role in the structure and function of proteins. It is one of the 20 standard amino acids found in proteins and is known for its unique chemical properties that contribute to various aspects of biochemistry covered in this chapter.
Disulfide Bond: A disulfide bond is a covalent chemical bond formed between two sulfur atoms, typically found in the side chains of cysteine residues in proteins. These bonds play a crucial role in the stabilization of protein structure and function.
Disulfide Bridge: A disulfide bridge is a covalent bond formed between two sulfur atoms in the side chains of two cysteine amino acid residues within a protein structure. These bridges help stabilize the three-dimensional folding and conformation of proteins, contributing to their overall structural integrity and function.
Dithiothreitol: Dithiothreitol (DTT) is a reducing agent commonly used in biochemical applications to maintain proteins in their reduced state by preventing the formation of disulfide bonds. It is particularly relevant in the context of peptides and proteins, as well as amino acid analysis of peptides.
DTT: DTT, or dithiothreitol, is a reducing agent commonly used in the study of peptides and proteins. It functions by breaking disulfide bonds, which are important structural features in many proteins.
Glutamic Acid: Glutamic acid is a non-essential amino acid that plays a crucial role in various metabolic processes within the body. It is a key component in the formation of proteins and is involved in the synthesis of other important biomolecules.
Glycine: Glycine is the smallest and simplest of the 20 standard amino acids that are the building blocks of proteins. It plays a crucial role in various biochemical processes, including protein synthesis, metabolism, and neurotransmission.
Hydrogen Bonding: Hydrogen bonding is a special type of dipole-dipole interaction that occurs when a hydrogen atom covalently bonded to a highly electronegative element, such as nitrogen, oxygen, or fluorine, experiences an attractive force with another nearby highly electronegative element. This intermolecular force is stronger than a typical dipole-dipole interaction and has a significant impact on the physical and chemical properties of many organic compounds.
Hydrophobic Effect: The hydrophobic effect is the tendency of nonpolar or hydrophobic molecules and groups to self-associate in an aqueous environment in order to minimize their unfavorable interactions with water. This phenomenon drives the formation and stabilization of important biological structures like proteins and phospholipid membranes.
Intermolecular: Intermolecular refers to the interactions and forces that occur between molecules, as opposed to within a single molecule. These intermolecular forces play a crucial role in determining the physical and chemical properties of substances, particularly in the context of peptides and proteins.
Intramolecular: Intramolecular refers to processes or interactions that occur within a single molecule, as opposed to intermolecular which involves interactions between different molecules. This term is particularly relevant in the contexts of Claisen condensations and peptide/protein structures.
Intramolecular, intermolecular: Intramolecular reactions involve the chemical changes that occur within a single molecule, resulting in a rearrangement of its atoms to form a new product. In the context of organic chemistry and specifically carbonyl condensation reactions, these are reactions where two functional groups within the same molecule react with each other.
N-terminal amino acid: The N-terminal amino acid is the first amino acid in a peptide or protein chain, characterized by having a free amine group (-NH2) that is not involved in a peptide bond. It indicates the starting point of the peptide or protein synthesis.
N-terminus: The N-terminus, or amino-terminus, refers to the end of a polypeptide or protein chain that contains a free amino group. It is one of the two ends of a protein molecule and is an important structural feature that helps determine the overall folding and function of the protein.
Oxidation: Oxidation is a fundamental chemical process in which a substance loses electrons, resulting in an increase in its oxidation state. This term is central to understanding various reactions and transformations in organic chemistry, from the hydration of alkenes to the oxidation of alcohols and aldehydes.
Peptide Backbone: The peptide backbone, also known as the polypeptide backbone, is the structural framework of a protein molecule. It consists of a repeating sequence of nitrogen, carbon, and oxygen atoms that form the covalent bonds connecting the individual amino acid residues within a protein.
Peptide bond: A peptide bond is a covalent chemical bond formed between two amino acid molecules when the carboxyl group of one molecule reacts with the amino group of another molecule, releasing a molecule of water (a condensation reaction). This bond is integral in forming the primary structure of peptides and proteins.
Peptide Bond: A peptide bond is a covalent chemical bond formed between the carboxyl group of one amino acid and the amino group of another amino acid, resulting in the creation of a peptide chain. This bond is crucial in the formation and structure of proteins, which are essential macromolecules for life.
Polypeptide: A polypeptide is a long, linear chain of amino acids linked together by peptide bonds. It is the basic structural unit of proteins, which play crucial roles in the structure, function, and regulation of biological systems.
Primary structure: The primary structure of a protein is the specific sequence of amino acids in a polypeptide chain, determined by covalent peptide bonds. It dictates the protein's overall shape and function.
Primary Structure: The primary structure of a protein refers to the linear sequence of amino acids that make up the polypeptide chain. It is the most fundamental level of protein structure and forms the foundation for the higher-order structures that give proteins their unique functional properties.
Protein Backbone: The protein backbone, also known as the peptide backbone, is the fundamental structural framework of proteins. It consists of a continuous chain of amino acid residues linked together by peptide bonds, forming the primary structure of a protein molecule.
Quaternary structure: The quaternary structure of a protein describes the arrangement and interaction of multiple polypeptide chains (subunits) in a multi-subunit complex. It is the highest level of protein structure, determining the overall 3D arrangement of subunits that are individually folded into their tertiary structures.
Quaternary Structure: Quaternary structure refers to the three-dimensional arrangement of multiple polypeptide chains or subunits that come together to form a functional protein. It is the highest level of protein structure and is crucial for the proper functioning of many complex proteins.
R group: An R group is a side chain attached to a molecule that determines the molecule's chemical properties and reactivity. It can consist of a variety of atoms or groups of atoms, giving rise to diverse organic compounds.
R Group: The R group, also known as the side chain, is the variable part of an amino acid molecule that determines its unique chemical properties and biological functions. The R group is the key structural feature that distinguishes one amino acid from another and plays a crucial role in the formation of proteins and peptides.
Residues: In the context of peptides and proteins in organic chemistry, residues refer to the individual amino acids that are linked together by peptide bonds within a peptide or protein chain. Each residue retains its unique side chain which contributes to the overall structure and function of the molecule.
Secondary structure: In the context of protein structure, the secondary structure refers to the specific geometric shape or conformation that segments of a protein's polypeptide chain assume, primarily as a result of hydrogen bonding. These shapes include alpha-helices and beta-pleated sheets, which are fundamental to the protein's overall structure and function.
Secondary Structure: Secondary structure refers to the local three-dimensional structure of proteins, specifically the regular, recurring patterns formed by hydrogen bonding between the backbone atoms of the polypeptide chain. It is one of the key levels of protein structure that determines the overall shape and function of the protein molecule.
Side Chain: In the context of peptides and proteins, a side chain refers to the R-group or functional group attached to the alpha-carbon of an amino acid. The side chain is a crucial structural feature that contributes to the unique properties and functions of each amino acid within a protein.
Tertiary structure: The tertiary structure of a protein refers to the overall three-dimensional shape formed by the folding and coiling of its peptide chain, stabilized by various interactions among its amino acids. This structure is crucial for the protein's function and specificity.
Tertiary Structure: Tertiary structure refers to the three-dimensional folding and spatial arrangement of a protein molecule. It is the highest level of protein structure and is crucial for determining a protein's overall shape and function.
Thiol Group: A thiol group is a functional group consisting of a sulfur atom bonded to a hydrogen atom (SH). Thiols are organic compounds that play a crucial role in the structure and function of proteins, particularly in the context of peptides and proteins.