9.1 Amino Acids and Peptide Bonds
2 min read•july 25, 2024
Amino acids are the building blocks of proteins, each with a unique structure and properties. Their central α-carbon connects to an , , hydrogen, and a distinctive , determining their behavior in different environments and roles in protein formation.
Peptide bonds link amino acids, creating the backbone of proteins. These bonds have special properties that influence protein structure and function. The sequence and interactions of amino acids determine the complex 3D structures of proteins, from α-helices to quaternary assemblies.
Amino Acid Structure and Properties
Structure of amino acids
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- General structure includes central α-carbon bonded to amino group (), carboxyl group (), hydrogen atom, and unique side chain (R group) determines properties
- Chirality manifests as L-form predominates in proteins due to evolutionary selection
- Zwitterionic nature allows behavior changes at different pH levels affecting overall charge
- Acid-base properties depend on values of amino and carboxyl groups influencing protonation state
- Solubility varies based on side chain polarity affecting interactions with water ( vs )
Classification of amino acids
- (hydrophobic) amino acids repel water, cluster inside proteins
- Aliphatic with straight or branched hydrocarbon chains (glycine, alanine, valine, leucine, isoleucine)
- Aromatic containing ring structures (phenylalanine, tryptophan)
- (hydrophilic) amino acids interact with water, often on protein surfaces
- Uncharged form hydrogen bonds (serine, threonine, asparagine, glutamine, tyrosine)
- contribute to electrostatic interactions (aspartic acid, glutamic acid - negative; lysine, arginine, histidine - positive)
- Special cases exhibit unique properties
- Proline has cyclic structure restricting protein backbone flexibility
- Cysteine forms disulfide bonds crucial for protein stability
Peptide Bonds and Protein Structure
Formation of peptide bonds
- Chemical reaction occurs through condensation between carboxyl and amino groups releasing water molecule
- properties include planar structure due to resonance, partial double bond character restricting rotation, and trans configuration predominance for steric reasons
- Dipole moment of peptide bonds creates local charge distribution affecting interactions
- Hydrogen bonding capability influences formation (α-helices, β-sheets)
Amino acids in protein structure
- defined by amino acid sequence determines overall protein properties
- Secondary structure forms through hydrogen bonding patterns
- : spiral shape stabilized by hydrogen bonds every 4 residues
- : extended strands connected by hydrogen bonds between chains
- results from folding driven by side chain interactions
- Hydrophobic core formation minimizes exposure to water
- Salt bridges between charged residues stabilize folding
- Disulfide bonds between cysteines provide covalent cross-links
- arises from subunit interactions in multi-chain proteins (hemoglobin)
- Functional implications emerge from 3D structure
- Active sites in enzymes shaped by specific amino acid arrangements
- Binding site specificity determined by complementary shapes and charges
- Structural proteins provide mechanical strength (collagen in connective tissue, keratin in hair and nails)
Key Terms to Review (24)
Amide bond: An amide bond is a type of chemical linkage that forms between a carboxylic acid and an amine, resulting in the release of a water molecule. This bond is crucial in the structure of proteins as it connects amino acids together, creating long chains known as peptides or proteins, which are fundamental to biological processes and structures.
Amino group: An amino group is a functional group composed of a nitrogen atom bonded to two hydrogen atoms, represented as -NH2. This group is a key component of amino acids, the building blocks of proteins, and plays a crucial role in the formation of peptide bonds, linking amino acids together to form proteins.
Carboxyl Group: A carboxyl group is a functional group characterized by the presence of a carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group (-COOH). This group is crucial in organic chemistry as it contributes to the acidity of molecules and is a key component of amino acids, which are the building blocks of proteins. The carboxyl group's ability to donate a proton makes it an important player in biochemical reactions and metabolic pathways.
Charged: In the context of bioengineering, 'charged' refers to the electrical state of molecules or atoms, where they possess an unequal number of protons and electrons, resulting in a net electric charge. This charge can significantly influence molecular interactions, stability, and functionality, especially in biological systems where ionic interactions are critical for protein structure and activity.
Chromatography: Chromatography is a powerful analytical technique used to separate and analyze components within a mixture based on their differing affinities for a stationary phase and a mobile phase. This separation technique is crucial in various fields, allowing for the analysis of complex biological samples, the characterization of enzymes, the study of amino acids, and the understanding of glycobiology in cellular interactions.
Codon: A codon is a sequence of three nucleotides in messenger RNA (mRNA) that specifies a particular amino acid or a stop signal during protein synthesis. Each codon corresponds to a specific amino acid, forming the genetic code that dictates how proteins are assembled from amino acids, connecting to the formation of peptide bonds between those amino acids.
Dehydration synthesis: Dehydration synthesis is a chemical reaction in which two molecules are joined together by the removal of a water molecule. This process is fundamental in the formation of larger biomolecules, such as carbohydrates, proteins, and lipids, by linking smaller units together while releasing water as a byproduct.
Dipeptide: A dipeptide is a molecule formed by the covalent bonding of two amino acids through a peptide bond. This process involves the removal of a water molecule, known as a condensation reaction, resulting in a structure that retains characteristics of both amino acids while forming a unique compound. Dipeptides serve as important building blocks in the synthesis of proteins and play crucial roles in various biological processes.
Hydrolysis: Hydrolysis is a chemical process where water molecules are used to break down a compound, resulting in the formation of smaller molecules. This reaction is essential in various biological systems, facilitating nutrient absorption and metabolic pathways, and it plays a key role in the breakdown of macromolecules like proteins and polysaccharides.
Hydrophilic: Hydrophilic refers to the property of a molecule that has a strong affinity for water, allowing it to interact favorably with water molecules. This property is crucial in biological systems, as it influences how substances dissolve in water and how they interact with various biomolecules. Hydrophilic substances often contain polar or charged groups, which help them form hydrogen bonds with water, making them soluble in aqueous environments.
Hydrophobic: Hydrophobic describes substances that do not interact well with water, often repelling it due to a lack of polar or charged groups. These substances tend to be nonpolar, which means they do not form hydrogen bonds with water molecules, resulting in a tendency to cluster together to minimize contact with water. This characteristic is crucial in many biological processes, such as protein folding and membrane formation.
Mass spectrometry: Mass spectrometry is an analytical technique used to measure the mass-to-charge ratio of ions. It allows for the identification and quantification of molecules, including amino acids and carbohydrates, by generating charged particles and analyzing their behavior in an electric or magnetic field. This method is crucial for understanding complex biological molecules and their interactions, making it essential in studies involving peptides and cellular recognition processes.
Nonpolar: Nonpolar refers to a type of molecule or functional group that does not have a significant charge difference across its structure, meaning there is an equal distribution of electron density. This property affects how nonpolar substances interact with other molecules, particularly in terms of solubility and reactivity. In the context of biological molecules, nonpolar characteristics are crucial in determining the structure and function of proteins, as well as how amino acids contribute to peptide bonds.
Peptide bond: A peptide bond is a covalent chemical bond that links two amino acids together, forming a peptide or protein. This bond is formed through a dehydration synthesis reaction, where the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water. Peptide bonds are fundamental in determining the structure and function of proteins, as they create chains that can fold into specific three-dimensional shapes.
Polar: In chemistry, 'polar' refers to molecules that have a significant difference in electronegativity between their atoms, leading to an uneven distribution of electron density. This results in the formation of positive and negative regions within the molecule, giving it distinct electrical properties. Polar molecules often interact more strongly with other polar substances, which is critical in biological systems, particularly in the structure and function of proteins formed by amino acids and linked by peptide bonds.
Polypeptide Chain: A polypeptide chain is a linear sequence of amino acids linked together by peptide bonds, forming the primary structure of proteins. These chains can vary in length and composition, leading to the immense diversity of proteins found in living organisms. The specific sequence of amino acids in a polypeptide chain determines how the protein will fold and function.
Primary structure: Primary structure refers to the unique sequence of amino acids that make up a protein. This specific arrangement is crucial because it dictates how the protein will fold into its three-dimensional shape, ultimately determining its function within biological systems.
Quaternary Structure: Quaternary structure refers to the highest level of protein organization, where multiple polypeptide chains (subunits) come together to form a functional protein complex. This level of structure is crucial for the functionality of many proteins, as it influences their stability, activity, and regulation within biological systems.
Secondary structure: Secondary structure refers to the local folded structures that form within a protein due to hydrogen bonding between the backbone atoms. This aspect of protein structure primarily includes alpha helices and beta sheets, which contribute significantly to the overall shape and stability of proteins, impacting their function and interactions with other molecules.
Side chain: A side chain, also known as a R group, is the specific part of an amino acid that varies among different amino acids and defines their unique characteristics. The side chain can determine the polarity, charge, and overall reactivity of the amino acid, influencing protein structure and function significantly. Understanding side chains is crucial for grasping how proteins fold and interact, impacting everything from enzyme activity to structural integrity.
Tertiary structure: Tertiary structure refers to the overall three-dimensional shape of a protein, formed by the folding and interactions of its secondary structures. This level of organization is crucial for a protein's functionality, as it determines how the protein interacts with other molecules and carries out its biological roles.
Zwitterion: A zwitterion is a molecule that carries both a positive and a negative charge, resulting in an overall neutral charge. This unique structure is commonly found in amino acids, where the amino group is positively charged and the carboxyl group is negatively charged, allowing for various biochemical interactions and stability in biological systems.
α-helix: An α-helix is a common structural motif in proteins, characterized by a right-handed coil where the amino acid residues are arranged in a helical pattern. This structure is stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of another, four residues down the chain, contributing to the overall stability and functionality of proteins.
β-sheet: A β-sheet is a common structural motif in proteins characterized by parallel or antiparallel strands of amino acids linked together by hydrogen bonds. This secondary structure contributes to the overall stability and functionality of proteins, playing a crucial role in their three-dimensional shape.