26.1 Structures of Amino Acids
3 min read•may 7, 2024
Amino acids are the building blocks of proteins, each with a unique structure and properties. They consist of an , a , and a attached to a central carbon atom. These structural features determine their classification and behavior in biological systems.
At physiological pH, amino acids exist as zwitterions, with both positive and negative charges. This property, along with their classification as essential or nonessential, plays a crucial role in their function within the body. Understanding structure and properties is key to grasping protein behavior and function.
Amino Acid Structure and Classification
Structural features of amino acids
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- General structure consists of an amino group () and a () attached to the -carbon along with a hydrogen atom and a side chain () specific to each (, )
- Side chain properties determine the classification of amino acids into nonpolar aliphatic (Glycine, Alanine, ), aromatic (, ), polar uncharged (, ), positively charged (, ), and negatively charged (, )
- Presence of four different groups attached to the -carbon makes all amino acids except glycine chiral with naturally occurring amino acids being L-stereoisomers (L-Alanine, L-Serine)
- Contain both acidic (carboxyl group) and basic (amino group) functional groups allowing them to act as acids or bases depending on the pH of the solution (Lysine, Glutamic acid)
- of amino acids plays a crucial role in their biological function and interactions with other molecules
Amino acids as zwitterions
- Exist predominantly as zwitterions at physiological pH (around 7.4) with a proton transferred from the carboxyl group to the amino group resulting in a molecule with both positive and negative charges and a net charge of zero (Glycine, Lysine)
- Exhibit behavior by acting as both acids (donating a proton from the carboxyl group) and bases (accepting a proton at the amino group) in solution (Aspartic acid, Arginine)
- represents the pH at which an amino acid has a net charge of zero due to equal numbers of positive and negative charges (, )
Essential vs nonessential amino acids
- cannot be synthesized by the human body and must be obtained through diet including Histidine, , Leucine, Lysine, , Phenylalanine, Threonine, , and Valine with deficiency leading to health issues such as impaired growth and development
- Nonessential amino acids can be synthesized by the human body from other compounds and include Alanine, Arginine, , Aspartic acid, , Glutamic acid, , Glycine, , Serine, and Tyrosine but still play important roles in various biological functions
- Serve as building blocks of proteins essential for cellular functions, involved in the synthesis of neurotransmitters (Serotonin, Dopamine), hormones (Insulin, Glucagon), and other biologically active compounds, and play a role in energy metabolism and nitrogen balance (Urea cycle, Glucose-Alanine cycle)
Amino Acid Interactions and Properties
- Amino acids can form peptide bonds to create longer chains called polypeptides, which are the building blocks of proteins
- Cysteine residues can form disulfide bonds, which contribute to protein stability and tertiary structure
- between amino acid side chains plays a crucial role in protein folding and maintaining protein structure
- The of amino acid side chains influences protein folding and interactions with the surrounding environment
Key Terms to Review (60)
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 Carbon: The alpha carbon is the carbon atom directly attached to a functional group, such as a carbonyl group in aldehydes and ketones, or to the carboxyl group in amino acids. It is a crucial structural feature that influences the reactivity and properties of these organic compounds.
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 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.
Amphiprotic: An amphiprotic substance is one that can both donate and accept a proton (H+ ion) in a chemical reaction. In the context of amino acids, this property is crucial for their ability to act as buffers in biological systems.
Anti stereochemistry: Anti stereochemistry describes the spatial arrangement in a chemical reaction where two substituents are positioned on opposite sides of a double bond or ring structure after the reaction. It is particularly relevant in the halogenation of alkenes, resulting in products where the added atoms are located across from each other.
Arginine: Arginine is a semi-essential amino acid that plays a crucial role in the body's metabolism and various physiological processes. It is involved in the structure and function of proteins and serves as a precursor for important biomolecules, making it an essential component in the context of amino acid structures and peptide sequencing.
Asparagine: Asparagine is a non-essential amino acid that is commonly found in proteins. It plays a crucial role in the structure and function of proteins, as well as in various metabolic processes within the body.
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.
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.
Chirality: Chirality is a fundamental concept in organic chemistry that describes the three-dimensional arrangement of atoms in a molecule. It refers to the property of a molecule that is non-superimposable on its mirror image, resulting in the existence of two distinct forms known as enantiomers. Chirality is a crucial factor in understanding the behavior and properties of various organic compounds, including their interactions with living systems.
Chirality centers: A chirality center in organic chemistry is an atom, typically carbon, that has four different groups attached to it, leading to non-superimposable mirror image forms of the molecule. These centers are crucial for determining the 3D spatial orientation of molecules, affecting their chemical behavior and interactions.
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.
D-amino acid: A D-amino acid is a type of amino acid that has the opposite stereochemical configuration compared to the naturally occurring L-amino acids found in proteins. The 'D' prefix indicates that the amino acid's α-carbon is in the D-configuration, meaning the side chain is on the opposite side of the molecule compared to the L-form.
Deprotonation: Deprotonation is the process of removing a proton (H+) from a molecule or ion, resulting in the formation of a negatively charged species. This chemical reaction is central to various organic chemistry topics, as it allows for the generation of reactive intermediates and the manipulation of molecular structures.
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.
Electrophoresis: Electrophoresis is a technique used to separate and analyze charged molecules, such as proteins, nucleic acids, or amino acids, based on their differential migration in an electric field. It is a fundamental tool in biochemistry, molecular biology, and analytical chemistry.
Essential amino acid: Essential amino acids are the amino acids that the human body cannot synthesize on its own and must be obtained through diet. They are crucial for protein synthesis and other metabolic processes.
Essential Amino Acids: Essential amino acids are a group of amino acids that the human body cannot synthesize on its own and must be obtained through the diet. These amino acids are crucial for various physiological processes, including protein synthesis, tissue repair, and energy production.
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.
Glutamine: Glutamine is a non-essential amino acid that plays a crucial role in various metabolic processes within the body. It is the most abundant free amino acid in the human body and is essential for maintaining proper physiological function, particularly in the context of amino acid structures.
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.
Histidine: Histidine is a semi-essential amino acid that plays a crucial role in various biological processes, including protein synthesis, enzyme function, and pH regulation. It is particularly notable for its involvement in aromatic heterocyclic compounds and its unique properties as an amino acid.
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.
Hydrolases: Hydrolases are a class of enzymes that catalyze the cleavage of chemical bonds through the addition of water. They play a crucial role in the digestion and processing of biomolecules, such as amino acids, peptides, and proteins.
Hydrophobicity: Hydrophobicity is a physical property of molecules or surfaces that repel water, or do not interact favorably with water molecules. It is a key concept in understanding the structures and interactions of amino acids, which are the building blocks of proteins.
Isoelectric Point: The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. This is a crucial concept in understanding the behavior of organic acids, organic bases, and amino acids.
Isoelectric point (pI): The isoelectric point (pI) is the pH at which an amino acid or a peptide has no net electric charge. At this pH, the molecule does not move in an electric field during electrophoresis.
Isoleucine: Isoleucine is an essential amino acid that is critical for protein synthesis, energy production, and the regulation of blood sugar levels in the body. It is one of the three branched-chain amino acids, along with leucine and valine, and plays a vital role in various metabolic processes.
Isomerases: Isomerases are enzymes that catalyze the rearrangement of atoms within a molecule, resulting in the conversion of one isomer into another. They play a crucial role in metabolic pathways by facilitating structural changes in biomolecules without adding or removing atoms.
L-amino acid: L-amino acids are a class of amino acids that have the same absolute configuration as the naturally occurring amino acids found in proteins. They are characterized by the presence of a carboxyl group (-COOH) and an amino group (-NH2) attached to the same carbon atom, known as the α-carbon.
Leucine: Leucine is a branched-chain amino acid that is essential for human nutrition. It is one of the three branched-chain amino acids, along with isoleucine and valine, and plays a crucial role in protein synthesis, muscle growth, and energy production within the body.
Lyases: Lyases are a class of enzymes that catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure. They play critical roles in the metabolism of amino acids and other biomolecules.
Lysine: Lysine is an essential amino acid that plays a crucial role in protein synthesis and various metabolic processes within the body. As one of the 20 standard amino acids, lysine is a building block for proteins and is essential for proper growth and development.
Methionine: Methionine is an essential amino acid that plays a crucial role in protein synthesis and various metabolic processes within the human body. As one of the 20 standard amino acids, it is a fundamental building block for proteins and is involved in the translation of genetic information into functional proteins.
Nonessential amino acid: Nonessential amino acids are amino acids that the human body can synthesize on its own and do not need to be obtained directly through diet. They play various roles in metabolic processes, but their dietary intake is not critical for healthy individuals.
Nonpolar Amino Acids: Nonpolar amino acids are a class of amino acids that have hydrophobic, uncharged side chains. They do not contain any charged functional groups and are often referred to as 'hydrophobic' or 'nonpolar' amino acids. These amino acids play a crucial role in the structure and function of proteins.
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.
Phenylalanine: Phenylalanine is an essential 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 also a precursor for the synthesis of other important compounds in the body.
PKa: pKa, or the acid dissociation constant, is a measure of the strength of an acid in a solution. It represents the pH at which a particular acid is 50% dissociated into its conjugate base. This value is crucial in understanding the behavior and properties of acids, bases, and their reactions in organic chemistry.
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.
Proline: Proline is a unique amino acid that has a distinctive cyclic structure, setting it apart from the other 19 standard amino acids. Its distinct properties and role in protein structure make it an important consideration in the study of amino acids, their synthesis, and peptide sequencing.
Protonation: Protonation is the process of adding a proton (H+) to a molecule or atom, resulting in the formation of a positively charged species. This fundamental chemical reaction is central to various organic chemistry topics, as it can significantly influence the reactivity and stability of molecules.
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.
Serine: Serine is a non-essential amino acid that plays a crucial role in various biological processes, including protein synthesis, cell signaling, and metabolism. It is a key component in the understanding of chirality, amino acid structures, peptide analysis, and phospholipid composition.
Side chain: In the context of amino acids, a side chain is a unique chemical group attached to the central carbon atom that differentiates one amino acid from another. The properties of these side chains determine the overall behavior and function of the amino acid in proteins.
Stereochemistry: Stereochemistry is the study of the three-dimensional arrangement of atoms in molecules and how this arrangement affects the chemical and physical properties of the substance. It examines the spatial orientation of atoms and their relationship to one another, which is crucial in understanding many organic chemistry concepts.
Threonine: Threonine is an essential amino acid that plays a crucial role in protein synthesis and various metabolic processes within the body. It is one of the 20 standard amino acids found in proteins and is particularly important in the context of understanding the structures of amino acids and analyzing peptides through amino acid analysis.
Titration: Titration is an analytical technique used to determine the concentration of an unknown solution by adding a measured volume of a standard solution of known concentration until the reaction is complete, as indicated by a change in color or pH. It is a fundamental tool in organic chemistry for analyzing the properties of amino acids.
Transferases: Transferases are enzymes that catalyze the transfer of functional groups, such as a methyl or phosphate group, from one molecule (the donor) to another (the acceptor). They play a crucial role in various biochemical pathways, including those involved in the metabolism of amino acids.
Tryptophan: Tryptophan is an essential amino acid that plays a crucial role in various biological processes, including the synthesis of proteins, the production of the neurotransmitter serotonin, and the regulation of the sleep-wake cycle. This versatile compound is particularly relevant in the context of polycyclic aromatic compounds, amino acid structures, and peptide sequencing.
Turnover number: In the context of enzymes, including those related to amino acids, peptides, and proteins in organic chemistry, the turnover number is the maximum number of substrate molecules an enzyme molecule can convert to product per unit time. It serves as a measure of the catalytic efficiency of an enzyme.
Tyrosine: Tyrosine is a non-essential amino acid that plays a crucial role in the structure and function of proteins. It is one of the twenty standard amino acids found in proteins and is involved in various metabolic processes within the body.
Valine: Valine is a branched-chain amino acid that is essential for human health. It plays a crucial role in the structure and function of proteins, as well as in various metabolic processes within the body.
Vitamin: Vitamins are organic compounds that are essential in small amounts for the proper functioning and health of living organisms, including humans. They cannot be synthesized in sufficient quantities by an organism, and therefore must be obtained from the diet.
Zwitterion: A zwitterion is a neutral molecule that contains both a positive and a negative charge within the same structure. This unique characteristic allows zwitterions to play a crucial role in the structures and properties of amino acids, which are the building blocks of proteins.