Lecture 1: General Properties of Amino Acids (BCM 251)

General Properties of Amino Acids

-amino and -carboxyl groups -

The -amino group gives amino acids basic properties, while the -carboxyl group provides acidic properties. Together, they allow amino acids to exist as zwitterions, having both positive and negative charges at physiological pH.

-amino group properties -

The -amino group contributes to the basic character of amino acids, facilitating proton acceptance, which affects the overall charge and reactivity of the amino acids.

Absolute configuration -

Refers to the specific spatial arrangement of atoms or groups in a molecule around a chiral center, which can be defined using R/S or D/L notation.

Absolute configuration in stereochemistry -

Refers to the spatial arrangement of atoms around a chiral center.

Absolute configuration of D-alanine -

Determined using the Cahn-Ingold-Prelog priority rules and represented in a 3D stereochemical drawing.

Achiral object -

An object that can be superimposed on its mirror image by rotation; it has symmetry.

Additional enantiomers of isoleucine -

The two other enantiomers that can be synthesized are L-allo-isoleucine and D-allo-isoleucine.

Additional enantiomers of threonine -

The two other enantiomers that can be synthesized are L-allo-threonine and D-allo-threonine.

Amines from Glutamic Acid -

Glutamic acid is decarboxylated to produce Gamma-Aminobutyric Acid (GABA), which serves as a neurotransmitter.

Amines from Histidine -

Histidine is decarboxylated to form Histamine. Histamine plays a crucial role in the local immune response.

Amines from Tryptophan -

Tryptophan is decarboxylated to form Tryptamine, which functions as a neurotransmitter.

Amines from Tyrosine -

Tyrosine is decarboxylated to produce Tyramine. Tyramine has a role in the blood-brain barrier.

Amino acid residue -

Each amino acid in a protein chain is referred to as an amino acid residue.

Amino Acids -

Understanding the structure of amino acids is crucial in biochemistry because it helps explain how proteins are formed, how they function, the role of enzymes, and the significance of protein folding and stability in biological systems.

Amino acids and benzaldehyde -

The reaction with benzaldehyde leads to Schiff's base formation, which is an intermediate in all transamination reactions important for the biosynthesis of amino acids.

Amino acids and mineral acids -

When an amino acid (R-CHNH2-COOH) reacts with HCl, it forms R-CHNH3+-COOHCl, illustrating how amino acids can interact with acids.

Amino acids to be configured in Exercise 3 -

D-Alanine, L-Alanine, L-Alanine, and D-Ornithine.

Amino acids with two pairs of enantiomers -

Isoleucine and threonine are the amino acids that have two pairs of enantiomers due to the presence of two chiral centers.

Amino Group Interaction with Alkali -

The functional group responsible for the ability of amino acids to interact with alkali is the amino group (-NH2), which can accept protons in alkaline conditions.

Amino Group Interaction with Sanger's Reagent -

The functional group that enables amino acids to interact with Sanger's reagent is the free amino group (-NH2). Sanger's reagent specifically reacts with the amino group.

Asymmetric carbon -

The chiral center that allows for the formation of two distinct spatial arrangements of the attached groups.

Basic formula of an amino acid -

The basic formula that represents the structure of an amino acid is R-CH(NH2)-COOH, where R represents the specific R-group of that amino acid.

Basic structure of an amino acid -

The basic amino acid structure is R-CH(NH2)-COOH, where R represents the side chain that varies between different amino acids.

Bond joining amino acid residues -

Amino acid residues are joined to their neighbors by covalent bonds known as peptide bonds.

Building blocks of proteins -

Amino acids are the fundamental building blocks of proteins.

Cadaverine formation -

Cadaverine formation from Lysine occurs spontaneously in dead bodies, whereas the other decarboxylation reactions are catalyzed by specific enzymes.

Cadaverine Formation -

The formation of Cadaverine differs from other amino acid decarboxylation reactions.

Chemical properties of amino acids -

The presence of both an alpha-amino group and an alpha-carboxyl group in all amino acids contributes to their overall chemical properties, such as their ability to act as buffers, participate in acid-base reactions, and form peptide bonds.

Chiral and Achiral Objects -

Chiral objects are those that cannot be superimposed on their mirror images, while achiral objects can be superimposed through rotation without changing their appearance.

Chiral Center in Amino Acids -

A chiral center in amino acids refers to a carbon atom that has four different substituents attached to it, leading to the existence of two stereoisomers (D and L forms). This carbon atom is crucial for determining the chirality of the amino acid.

Chiral center of amino acids -

The 19th carbon of all amino acids, except glycine, is connected to four different substituents, making it a chiral center that renders a pair of enantiomers: L- and D- stereoisomers.

Chiral centers -

Carbon atoms in a molecule that are attached to four different groups, leading to the existence of stereoisomers.

Chiral centers in a molecule -

Yes, a molecule can have several chiral centers, which increases the complexity and number of possible stereoisomers it can produce.

Chiral centers in amino acids -

Carbon atoms bonded to four different substituents, dictating the stereochemistry and biological function of the amino acids.

Chiral molecule -

A molecule that is attached to four different chemical groups or radicals, making it asymmetrical.

Chiral object -

An object that cannot be superimposed on its mirror image by any rotation, lacking symmetry.

Chirality in Amino Acids -

Chirality refers to the property of a molecule to exist in two non-superimposable mirror image forms. In amino acids, this arises due to the presence of asymmetric carbon atoms. All amino acids except glycine exhibit chirality.

Chirality of amino acids -

Understanding chirality is significant in biology because many biological processes are sensitive to the specific three-dimensional shapes of molecules.

Citrulline classification -

Citrulline is classified as an L-amino acid.

Common chemical properties of amino acids -

They all contain one amino group (-NH2) and one carboxyl group (-COOH).

Common functional groups in amino acids -

All amino acids share two common functional groups: an alpha-amino group (NH2) and an alpha-carboxyl group (COOH).

Completing absolute configuration of amino acids -

Involves identifying and attaching the appropriate radicals to the central carbon atom in accordance with the priority rules.

D,L system in stereochemistry -

Refers to the designation of amino acids based on their ability to rotate polarized light: 'D' for dextrorotatory and 'L' for levorotatory.

Decarboxylation -

A chemical reaction that removes a carboxyl group from the amino acid, often resulting in the formation of amines.

Decarboxylation -

Decarboxylation in amino acids is a process where amino acids lose a carboxyl group (-COOH), leading to the formation of the corresponding amines. This reaction is a natural pathway in the biosynthesis of various important biological molecules.

Decarboxylation of Lysine -

Lysine decarboxylates to form Cadaverine, which is a toxin produced spontaneously in dead bodies and does not follow enzymatic control.

Definition of a peptide bond -

A peptide bond is a covalent bond formed between the amino group of one amino acid and the carboxyl group of another, resulting in the release of a molecule of water.

Dextrorotatory -

An enantiomer that rotates light to the right.

DNB-amino acid reaction -

The DNB-amino acid reaction is used to detect the concentration of amino acids in solutions. It specifically frees the N-terminal amino acid in a polypeptide, making it vital for protein sequencing.

Elements in amino acids -

Amino acids are built of the following elements: carbon, hydrogen, oxygen, nitrogen, and sulfur.

Enantiomer definition -

An enantiomer is one of two molecules that are mirror images of each other and cannot be superimposed on one another.

Enantiomer of L-isoleucine -

The enantiomer of L-isoleucine is D-isoleucine.

Enantiomer of L-threonine -

The enantiomer of L-threonine is D-threonine.

Enantiomers -

Enantiomers are pairs of chiral objects that are non-superimposable mirror images of each other. They typically exhibit different optical activities.

Enantiomers -

Pairs of stereoisomers that are non-superimposable mirror images of each other.

Equation of DNB-amino acid reaction -

The equation represents the reaction where AA-NH2 (the N-terminal amino acid) reacts with Sanger's reagent, resulting in the formation of a derivative that is measurable for quantification.

Esterification -

Esterification in amino acids occurs when the amino acid reacts with alcohols, resulting in the formation of esters. This reaction typically involves the -carboxyl group of the amino acid.

Example of Achiral Object -

An example of an achiral object is a plain coffee mug without any text or asymmetry. It can be rotated and placed over its mirror image without any difference.

Exceptions to the general rule of chirality for amino acids -

Glycine, isoleucine, and threonine.

Formation of Zwitterion -

At normal pH cellular levels, a zwitterion is formed when one proton is transferred from the carboxyl group (-COOH) to the amino group (-NH2) of the same molecule.

Functional Groups in Amino Acids -

The two functional groups present in amino acids attached to the same carbon atom are the -amino group (-NH2) and the -carboxyl group (-COOH).

Fundamental structural roles of proteins -

Proteins serve as the fundamental structural molecules of all cells and tissues in living organisms.

GABA in neurotransmission -

GABA (Gamma-Aminobutyric Acid) is derived from Glutamic acid and functions as an inhibitory neurotransmitter in the brain, helping to regulate neuronal excitability.

General structure of amino acids -

Consists of a carbon center with four substituents: an alpha-amino group (NH2), an alpha-carboxyl group (COOH), a hydrogen atom (H), and a side radical (R).

General structure of an amino acid -

The general structure of amino acids consists of a central carbon atom known as the alpha-carbon, four substituents: an amino group (NH or NH2), a carboxyl group (COOH), a hydrogen atom (H), and a distinctive R-group or side chain that determines the identity and chemical properties of each amino acid.

Geometric Representation of Chiral Objects -

Chiral objects can be represented using models where one form is a mirror image of another. For example, the right-handed and left-handed forms of a coffee mug illustrate chirality: one cannot be superimposed onto the other despite being mirror images.

Glycine and Chirality -

Glycine is considered achiral because it does not have a chiral carbon atom. Its two hydrogen atoms attached to the alpha carbon make it superimposable on its mirror image.

Histamine in immune responses -

Histamine promotes vasodilation, increases vascular permeability, and recruits immune cells to areas of inflammation, enhancing local immune responses.

Importance of Functional Groups -

Functional groups are crucial as they determine how amino acids interact with various reagents, solvents, and other molecules, influencing biochemical reactions and properties.

Importance of studying chiral molecules in drug design -

Studying chiral molecules is important in drug design because enantiomers can have dramatically different biological effects.

Influence of Carboxyl Group -

The presence of the carboxyl group in amino acids influences their properties by enabling salt formation, allowing esterification reactions with alcohols, facilitating reactions with amines to form amides, and undergoing decarboxylation to form corresponding amines.

Interaction with Alcohols -

The hydroxyl (-OH) groups or any polar functional groups present in the structure of some amino acids facilitate their interaction with alcohols.

L- and D-isomers in amino acids -

Two forms of chiral amino acids, with the majority of proteinogenic amino acids existing as L-stereoisomers.

L-stereo-isomers in amino acids -

Defined by the orientation of functional groups around chiral centers in molecules such as L-glyceraldehyde.

Levorotatory -

An enantiomer that rotates light to the left.

Limitation of Sanger's Reagent -

One limitation of Sanger's reagent is that it blocks the carboxyl groups of amino acids, preventing further reactions with them.

Maximum stereoisomers formula -

The maximum number of stereoisomers for a molecule is given by the formula 2^n, where n is the number of chiral centers.

Measuring Amino Acid Concentrations -

The Sanger reaction allows for the measurement of amino acid concentrations in solutions by assessing the color intensity resulting from the reaction products.

Natural form of isoleucine -

The natural form of isoleucine is L-isoleucine.

Natural form of threonine -

The natural form of threonine is L-threonine.

Natural products containing D-amino acids -

D-amino acids may be found in several natural products synthesized by non-ribosomal polypeptide synthetases (NRPS) and in the cell walls of bacteria.

Neurotransmitters from amino acids -

Neurotransmitters derived from amino acids, such as Glutamate (excitatory) and GABA (inhibitory), are crucial for proper communication between neurons, regulating mood, anxiety, and overall brain function.

Ninhydrin -

A reagent used in biochemical assays to detect amino acids, producing a colored product known as Ruhemann's purple.

Ninhydrin reaction -

The Ninhydrin reaction is a sensitive chemical reaction used for detecting amino acids. Upon oxidative decarboxylation of amino acids, Ninhydrin reacts with the liberated ammonia (NH3) to produce a blue-colored Rhumanns complex.

Nomenclature system for stereochemical configuration -

Proposed by Emil Fischer in 1891.

Optical activity determination -

The optical activity of a molecule is determined by the presence of chiral centers, which allow the molecule to rotate plane-polarized light.

Optical isomers -

Another name for stereoisomers that differ in their 3D configuration, affecting their optical activity.

Optical isomers of isoleucine -

There are 4 optical isomers of isoleucine.

Optical isomers of threonine -

There are 4 optical isomers of threonine.

Optical Properties of Amino Acids -

Optical properties of amino acids refer to their ability to rotate plane-polarized light.

Optical stereoisomers from one chiral center -

One chiral center results in two optical stereoisomers, which are mirror images (enantiomers) of each other.

Optical stereoisomers in amino acids -

All amino acids except glycine have optical stereoisomers because they contain one or two chiral carbon atoms.

Pathways Affected by Functional Groups -

The functional groups in amino acids influence several pathways, including: 1. Salt formation - affects amino acid solubility and transport. 2. Esterification - involved in lipid and carbohydrate metabolism. 3. Formation of amides - relevant in protein synthesis and enzyme formation. 4. Decarboxylation - critical in the synthesis of neurotransmitters and signaling molecules.

Peptide bonding -

Peptide bonding occurs when the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water (dehydration synthesis) and forming a covalent bond called a peptide bond.

Percentage of total body weight from proteins -

Proteins constitute nearly 17% of total body weight.

Polypeptides -

Polypeptides are long linear chains of amino acids that make up proteins and determine their structure, properties, and functions.

Primary Use of Sanger Reaction -

The primary use of the Sanger reaction is in protein sequencing to identify the amino acid sequence of proteins.

Properties of Amino Acids -

The individual properties of amino acids are determined by their side chains (R groups), which can contain different functional groups such as aliphatic chains, aromatic rings, hydroxyl groups, and additional amino or carboxyl groups.

Properties of amino acids -

The presence of the -COOH (carboxyl) group in amino acids provides these compounds with acidic properties and influences their reactivity and interactions.

Proteinogenic amino acids -

Those that are incorporated into proteins during translation, and all proteinogenic amino acids are L-stereoisomers.