Introduction
Amino acids are organic compounds that serve as the building blocks of proteins. They are composed of an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a side chain (R-group), all attached to a central carbon atom known as the α-carbon.
There are 20 standard amino acids that are commonly found in proteins. These amino acids differ from one another based on the specific chemical properties of their side chains, which can vary in size, shape, charge, and reactivity. The side chains give each amino acid its unique characteristics and determine its role and interactions within a protein.
The 20 standard amino acids are:
- Alanine (Ala, A)
- Arginine (Arg, R)
- Asparagine (Asn, N)
- Aspartic acid (Asp, D)
- Cysteine (Cys, C)
- Glutamine (Gln, Q)
- Glutamic acid (Glu, E)
- Glycine (Gly, G)
- Histidine (His, H)
- Isoleucine (Ile, I)
- Leucine (Leu, L)
- Lysine (Lys, K)
- Methionine (Met, M)
- Phenylalanine (Phe, F)
- Proline (Pro, P)
- Serine (Ser, S)
- Threonine (Thr, T)
- Tryptophan (Trp, W)
- Tyrosine (Tyr, Y)
- Valine (Val, V)
General Structure of Amino Acids
An amino acid has following the general structure-
- Amino Group: The amino group (-NH2) is a basic functional group composed of a nitrogen atom bonded to two hydrogen atoms. It is attached to the α-carbon of the amino acid. The amino group acts as a base and can accept a proton (H+) to become positively charged.
- Carboxyl Group: The carboxyl group (-COOH) is an acidic functional group composed of a carbon atom double-bonded to an oxygen atom and single-bonded to another oxygen atom, which is also bonded to a hydrogen atom. The carboxyl group is attached to the α-carbon of the amino acid. It acts as an acid and can donate a proton to become negatively charged.
- Hydrogen Atom: A single hydrogen atom (H) is attached to the α-carbon (Chiral Carbon). It does not significantly influence the chemical properties of the amino acid but is still part of its structure.
- R-Group (Side Chain): The R-group, also known as the side chain, is a variable group that differs for each amino acid. It is attached to the α-carbon and determines the unique chemical and physical properties of each amino acid. The R-group can be as simple as a single hydrogen atom (in the case of glycine) or as complex as a large aromatic ring or a chain of atoms. The nature of the R-group determines the amino acid’s polarity, charge, size, hydrophobicity, and reactivity, which influence its role within proteins.
Classifications of Amino Acids
The amino acids can be classified by R group. Such as –
1. Non-Polar, Aliphatic Amino Acids
The non-polar, aliphatic amino acids have non-polar side chains composed of carbon and hydrogen atoms. These amino acids do not possess charged or highly polar functional groups in their side chains. The non-polar, aliphatic amino acids include:
- Glycine (Gly, G): Glycine is the simplest amino acid, and its side chain consists of a single hydrogen atom. It is the only achiral amino acid since the α-carbon is not asymmetrically bound to any different groups.
- Alanine (Ala, A): Alanine has a methyl group (-CH3) as its side chain. It is a common amino acid found in proteins and plays a role in protein structure and function.
- Valine (Val, V): Valine has a branched side chain with three carbon atoms. It is a hydrophobic amino acid and is often found in the interior of proteins, contributing to their stability.
- Leucine (Leu, L): Leucine also has a branched side chain with three carbon atoms. It is commonly found in hydrophobic regions of proteins and is involved in protein folding and stability.
- Isoleucine (Ile, I): Isoleucine is another amino acid with a branched side chain. It differs from leucine in the position of a methyl group on the side chain. It is also hydrophobic and contributes to protein stability.
These non-polar, aliphatic amino acids are typically found in hydrophobic regions of proteins, where they contribute to protein structure, stability, and interactions with other molecules. Their non-polar nature allows them to interact with lipid membranes and form hydrophobic cores within proteins.
“Great Mr. Vickey Love Pure Islands”
memorization tricks
2. Polar, Uncharged Amino Acids
The polar, uncharged amino acids are a group of amino acids with side chains that are polar but do not carry a net charge at physiological pH. These amino acids are hydrophilic and often play important roles in protein function, including in protein-protein interactions and enzyme catalysis. The polar, uncharged amino acids include:
- Serine (Ser, S): Serine has a hydroxyl group (-OH) in its side chain. It is involved in various biological processes, such as phosphorylation reactions and protein folding.
- Threonine (Thr, T): Threonine has a hydroxyl group (-OH) in its side chain, similar to serine. It is essential for the synthesis of proteins and various other important molecules.
- Asparagine (Asn, N): Asparagine has an amide group (-CONH2) in its side chain. It is often involved in forming hydrogen bonds and is important for protein structure and stability.
- Glutamine (Gln, Q): Glutamine also has an amide group (-CONH2) in its side chain, similar to asparagine. It plays a role in protein synthesis, nitrogen transport, and nucleotide biosynthesis.
- Cysteine (Cys, C) – Cysteine has a sulfhydryl group (-SH) in its side chain. The distinguishing feature of cysteine is its ability to form disulfide bonds with other cysteine residues.
These polar, uncharged amino acids are often found on the surfaces of proteins, where they can interact with water molecules and participate in hydrogen bonding. They contribute to the overall hydrophilicity of proteins and play crucial roles in protein structure, function, and interactions.
Three Girls Are Sweet and Cute
memorization tricks
3. Aromatic R group Amino Acids
The aromatic R-group amino acids are a group of amino acids that have aromatic side chains. These side chains contain a ring structure that imparts unique chemical and physical properties to the amino acid. The aromatic R-group amino acids include:
- Phenylalanine (Phe, F): Phenylalanine has a phenyl group (-C6H5) as its side chain. It is hydrophobic and plays a crucial role in protein structure and stability.
- Tyrosine (Tyr, Y): Tyrosine has a hydroxyl group (-OH) attached to a phenyl group in its side chain. It is more polar than phenylalanine due to the presence of the hydroxyl group.
- Tryptophan (Trp, W): Tryptophan has an indole group (-C8H6N) as its side chain. It is the largest amino acid and has both aromatic and polar properties.
These aromatic R-group amino acids contribute to the unique properties of proteins. They are often found in the hydrophobic interior of proteins, where their aromatic rings participate in hydrophobic interactions. They can also be involved in protein-protein interactions, ligand binding, and signaling processes. The absorbance of ultraviolet (UV) light by the aromatic rings of these amino acids is often used in spectroscopic techniques to study protein structure and folding.
4. Positively Charged R Group Amino Acids
The positively charged R-group amino acids are a group of amino acids that have side chains with a positive charge at physiological pH. These amino acids contain basic functional groups that can accept a proton (H+) and become positively charged. The positively charged R-group amino acids include:
- Lysine (Lys, K): Lysine has an amino group (-NH2) in its side chain, which can accept a proton and become positively charged. It plays a crucial role in protein structure, enzymatic activity, and protein-DNA interactions.
- Arginine (Arg, R): Arginine has a guanidinium group (-C(NH2)3+) in its side chain, which can accept multiple protons and carry a net positive charge. It is involved in various biological processes, such as protein synthesis, signaling, and enzyme catalysis.
- Histidine (His, H): Histidine has an imidazole group (-C3H4N2) in its side chain, which can accept or donate a proton depending on the pH of the surrounding environment. It acts as a pH sensor and plays a crucial role in enzyme catalysis, protein structure, and signaling.
These positively charged R-group amino acids often participate in electrostatic interactions and are involved in protein-protein interactions, ligand binding, and enzyme-substrate interactions. They can form salt bridges with negatively charged amino acids or other negatively charged molecules, contributing to protein stability and function. Additionally, these amino acids are often found in active sites of enzymes and play important roles in catalytic processes.
5. Negatively Charged R Group Amino Acids
The negatively charged R-group amino acids are a group of amino acids that have side chains with a negative charge at physiological pH. These amino acids contain acidic functional groups that can donate a proton (H+) and become negatively charged. The negatively charged R-group amino acids include:
- Aspartic Acid (Asp, D): Aspartic acid has a carboxyl group (-COOH) in its side chain, which can donate a proton and carry a negative charge. It is involved in protein structure, ligand binding, and enzyme catalysis.
- Glutamic Acid (Glu, E): Glutamic acid also has a carboxyl group (-COOH) in its side chain, similar to aspartic acid, and can donate a proton to become negatively charged. It plays a role in protein function, neurotransmission, and metabolic pathways.
These negatively charged R-group amino acids are often involved in electrostatic interactions with positively charged molecules or other negatively charged amino acids.
Amino acids can be classified by whether the amino acid needs to be obtained from the diet or if it can be synthesized by the body. Such as
- Essential amino acids
- Non-essential amino acids
Essential Amino Acids
Essential amino acids cannot be produced by the human body in sufficient amounts, so they must be obtained from dietary sources. There are nine essential amino acids:
- Histidine (His)
- Isoleucine (Ile)
- Leucine (Leu)
- Lysine (Lys)
- Methionine (Met)
- Phenylalanine (Phe)
- Threonine (Thr)
- Tryptophan (Trp)
- Valine (Val)
2. Non-essential Amino Acids
Non-essential amino acids can be synthesized by the human body through various metabolic pathways. Although they are termed “non-essential,” it does not mean they are less important. The body can produce these amino acids from other sources, such as the breakdown of proteins or through intermediates in metabolic pathways. There are 11 non-essential amino acids:
- Alanine (Ala)
- Arginine (Arg)
- Asparagine (Asn)
- Aspartic Acid (Asp)
- Cysteine (Cys)
- Glutamic Acid (Glu)
- Glutamine (Gln)
- Glycine (Gly)
- Proline (Pro)
- Serine (Ser)
- Tyrosine (Tyr)
It’s worth noting that the classification of amino acids as essential or non-essential can vary between species. For example, some non-essential amino acids for humans may be essential for certain animals.
Essential amino acids (PVT TIM HALL)
Non-essential amino acids (Get Valuable With PHIGS)
memorization tricks
Zwitterion
Zwitterion amino acids, also known as dipolar ions, are amino acids that exist in a neutral form with both a positive and a negative charge within the same molecule. The term “zwitterion” comes from the German word “zwitter,” meaning hermaphrodite or hybrid.
In the case of amino acids, zwitterions form due to the presence of both an amino group (-NH2) and a carboxyl group (-COOH) within the molecule. At physiological pH (around 7.4), the amino group accepts a proton (H+) and becomes positively charged (+NH3+), while the carboxyl group donates a proton and becomes negatively charged (-COO-). This results in the formation of a zwitterion with a net charge of zero.
The zwitterionic form of amino acids is the predominant form in biological systems, as the presence of both positive and negative charges allows for various interactions and stability within proteins and other biomolecules. These interactions contribute to protein folding, enzymatic activity, and the overall structure and function of proteins.
Examples of zwitterion amino acids include:
- Alanine (Ala)
- Glutamic Acid (Glu)
- Aspartic Acid (Asp)
- Lysine (Lys)
- Arginine (Arg)
It’s important to note that the zwitterionic form of amino acids can vary with changes in pH. At extreme pH values, the amino acid may exist predominantly in its charged or uncharged form, depending on the pKa values of its functional groups.
pKa of Amino Acids
The pKa of an amino acid refers to the negative logarithm (base 10) of the acid dissociation constant (Ka) for the ionizable groups present in the amino acid molecule. It is a measure of the acidity or basicity of the ionizable groups and indicates the propensity of these groups to lose or gain protons (H+ ions) in a solution.
In the context of amino acids, there are two main ionizable groups: the carboxyl group (-COOH) and the amino group (-NH2). The pKa values of these groups represent the pH at which half of the molecules of that group are in the protonated (charged) form, and the other half are in the deprotonated (uncharged) form.
For the carboxyl group, the pKa value represents the equilibrium between the protonated form (-COOH) and the deprotonated form (-COO-). A lower pKa value indicates a stronger acid, meaning it is more likely to lose a proton and become negatively charged.
For the amino group, the pKa value represents the equilibrium between the protonated form (-NH3+) and the deprotonated form (-NH2). A higher pKa value indicates a weaker base, meaning it is less likely to accept a proton and become positively charged.
The specific pKa values of the carboxyl and amino groups in amino acids can vary slightly depending on the specific amino acid and environmental conditions.
Understanding the pKa values of amino acids is important in determining their behavior in different pH environments, protein folding, enzymatic activity, and other biochemical processes. It helps in understanding the ionization state of amino acids and their ability to participate in acid-base reactions.
Here are the approximate pKa values for the ionizable groups in amino acids:
- Carboxyl group (-COOH):
- pKa ≈ 2.2 to 2.4
- Amino group (-NH2):
- pKa ≈ 9.4 to 10.6
These pKa values are general estimates and can vary slightly depending on the specific amino acid and environmental conditions. It’s important to note that different amino acids may have slightly different pKa values for their ionizable groups due to variations in their side chains.
Additionally, it’s worth mentioning that certain amino acids have additional ionizable side chains with their own pKa values. For example, the side chain of histidine (His) is known to have a pKa value around 6.0, which is close to physiological pH, making histidine an important contributor to acid-base reactions in proteins.
Keep in mind that these pKa values are useful for understanding the behavior of amino acids and their ionization states under different pH conditions, which is crucial in various biological processes, including protein structure, enzymatic reactions, and ion channel activity.
Isoelectric Point of Amino Acids
The isoelectric point (pI) of an amino acid is the pH at which the amino acid exists as a neutral zwitterion, meaning it has an equal number of positive and negative charges. At the isoelectric point, the net charge of the amino acid is zero.
The pI of an amino acid is influenced by the presence of its ionizable groups, primarily the carboxyl group (-COOH) and the amino group (-NH2). These groups can either accept or donate protons depending on the pH of the surrounding environment.
To determine the pI of an amino acid, you need to know the pKa values of its ionizable groups. The pKa is the pH at which half of the molecules of a particular group are deprotonated (charged) and half are protonated (uncharged). The pI can be calculated by averaging the pKa values of the two ionizable groups (carboxyl and amino) that contribute to the overall charge of the amino acid.
Here are the approximate pI values for some common amino acids:
- Alanine: pI ≈ 6.0
- Glutamic Acid: pI ≈ 3.2
- Aspartic Acid: pI ≈ 2.8
- Lysine: pI ≈ 9.7
- Arginine: pI ≈ 10.8
It’s important to note that the pI can vary slightly depending on the specific environment and the neighboring amino acids in a protein sequence. Additionally, amino acids with additional ionizable side chains (such as cysteine with its thiol group) will have more complex pI values.
Understanding the pI of amino acids is crucial in various biological processes, such as protein purification and characterization, as it helps determine the optimal conditions for the separation and manipulation of amino acids and proteins.
The isoelectric point (pI) of an amino acid can be estimated using the Henderson-Hasselbalch equation. The Henderson-Hasselbalch equation is commonly used to calculate the pH of a solution containing a weak acid and its conjugate base.
For amino acids, the equation is modified to consider the two ionizable groups, the carboxyl group (-COOH) and the amino group (-NH2). The pI is the pH at which the net charge of the amino acid is zero, meaning it exists as a neutral zwitterion.
The Henderson-Hasselbalch equation for estimating the pI of an amino acid is as follows:
pI = (pKa1 + pKa2) / 2
where pKa1 is the pKa of the carboxyl group and pKa2 is the pKa of the amino group.
It’s important to note that this equation provides an estimate, and the actual pI can be influenced by factors such as the specific environment and neighboring amino acids.
For example,
let’s calculate the pI of alanine, which has a pKa1 of approximately 2.35 and a pKa2 of approximately 9.87:
pI = (2.35 + 9.87) / 2 ≈ 6.11
Therefore, the estimated pI of alanine is approximately 6.11
let’s calculate the pI of glycine, which has a pKa1 of approximately 2.34 and a pKa2 of approximately 9.60:
pI = (2.34 + 9.60) / 2
pI = 11.94 / 2
pI ≈ 5.97
Therefore, the estimated pI of glycine is approximately 5.97.
Remember that this equation gives an approximation and the actual pI can differ slightly. Experimental methods, such as electrophoresis, are often used to determine the precise pI values of amino acids.
Important Facts About Amino Acids
- Alanine, glycine, and valine are Neutral Amino Acids as these contain one amino and one carboxyl group each.
- Lysine and arginine are Basic Amino Acids because they carry two amino groups and one carboxylic group.
- Glutamic acid (glutamate) and aspartic acid (aspartate) contain one amino and two carboxyl groups each and are classified as Acidic Amino Acids.
- Protein amino acids are laevorotatory and a-type except glycine.
- Most amino acids are laevo-rotatory while glycine is optically inactive.
- Two amino acids viz. arginine and histidine are semi-indispensable amino acids as they can be synthesized by human beings but very slowly.
- Cysteine, cystine, and methionine are sulfur-containing amino acids.
Functions of Amino Acids
Amino acids play numerous vital roles in biological systems. Here are ten functions of amino acids:
- Protein synthesis: Amino acids serve as the building blocks for protein synthesis. They are joined together in specific sequences to form polypeptide chains, which then fold into functional proteins.
- Enzyme catalysis: Many enzymes are composed of amino acids and rely on their specific arrangement and chemical properties to catalyze biochemical reactions in cells.
- Signal transduction: Certain amino acids, such as serine, threonine, and tyrosine, can undergo phosphorylation and dephosphorylation, playing a crucial role in signal transduction pathways and cellular communication.
- Metabolism and energy production: Amino acids participate in metabolic pathways, including the breakdown of nutrients for energy production. Some amino acids can be converted into intermediates that enter the citric acid cycle or glycolysis.
- Neurotransmitter synthesis: Amino acids such as glutamate, glycine, and GABA (gamma-aminobutyric acid) serve as neurotransmitters in the central nervous system, facilitating communication between nerve cells.
- Precursors for other molecules: Amino acids can serve as precursors for the synthesis of various molecules, including hormones, nucleotides, and other important biomolecules.
- Immune function: Certain amino acids, such as glutamine, arginine, and cysteine, play essential roles in immune system function, including supporting immune cell proliferation and function.
- pH regulation: Amino acids can act as buffers, helping to maintain the pH balance within cells and body fluids. They can accept or donate protons to regulate acidity or alkalinity.
- Structural components: Amino acids contribute to the structural integrity of cells and tissues. Collagen, for example, is rich in the amino acids glycine, proline, and hydroxyproline, providing strength and support to connective tissues.
- Transport and storage of molecules: Amino acids are involved in the transport and storage of various molecules in the body. For instance, certain amino acids transport ions across cell membranes, while others facilitate the transport of metals or other nutrients.
- Formation of amines: On losing the carboxyl groups as carbon dioxide, amino acids form biologically active amines such as histamine. Histamine is required for the functioning of muscles, blood capillaries and gastric juices.
- Formation of other biomolecules: tyrosine is converted into the hormones thyroxine and adrenaline, as well as the skin pigment melanin, glycine is involved in the formation of heme and tryptophan in the formation of the vitamin nicotinamide as well as the plant hormone indole-3-acetic acid.
