What Are The Monomers Of Proteins Called

Proteins, the workhorses of our cells, are complex molecules built from smaller, repeating units. These fundamental building blocks are known as amino acids. Understanding amino acids, their structure, and how they link together is crucial to grasping the function and diversity of proteins.

The Foundation: Amino Acids

Amino acids are organic compounds that contain both an amino group (-NH2) and a carboxyl group (-COOH), hence the name "amino acid." These groups are attached to a central carbon atom, also called the alpha (α) carbon. The α-carbon is also bonded to a hydrogen atom and a side chain, denoted as "R". It is the R-group that distinguishes one amino acid from another and dictates its unique chemical properties.

General Structure

Let's break down the generic structure of an amino acid:

• Amino Group (-NH2): This group acts as a base, accepting protons (H+).
• Carboxyl Group (-COOH): This group acts as an acid, donating protons (H+).
• Alpha (α) Carbon: The central carbon atom to which the amino and carboxyl groups are attached.
• Hydrogen Atom (H): Also attached to the α-carbon.
• R-Group (Side Chain): The variable group that determines the identity and properties of each amino acid.

This seemingly simple structure gives rise to an enormous variety of functions.

The 20 Standard Amino Acids

While there are hundreds of amino acids found in nature, only 20 are commonly incorporated into proteins during translation. These are often referred to as the standard amino acids or proteinogenic amino acids. Each of these 20 has a unique R-group, contributing to differences in size, shape, charge, hydrophobicity (tendency to repel water), and reactivity. These differences ultimately determine the three-dimensional structure and function of the resulting protein.

Here's a brief overview of the 20 standard amino acids, categorized by their R-group properties:

1. Nonpolar, Aliphatic R Groups: These amino acids have hydrocarbon R-groups, making them hydrophobic.

• Glycine (Gly, G): The simplest amino acid, with a single hydrogen atom as its R-group. This allows for flexibility in protein structures.
• Alanine (Ala, A): Has a methyl group (-CH3) as its R-group.
• Valine (Val, V): Has an isopropyl group as its R-group.
• Leucine (Leu, L): Has an isobutyl group as its R-group.
• Isoleucine (Ile, I): Has a sec-butyl group as its R-group.
• Proline (Pro, P): A unique amino acid where the R-group cyclizes back to the amino group, forming a rigid ring. This restricts the flexibility of the peptide chain.

2. Aromatic R Groups: These amino acids have aromatic rings in their R-groups. They are relatively nonpolar and can participate in hydrophobic interactions. They also absorb UV light at 280 nm, a property used for protein quantification.

• Phenylalanine (Phe, F): Contains a phenyl group.
• Tyrosine (Tyr, Y): Contains a phenyl group with a hydroxyl group (-OH) attached. The hydroxyl group makes it slightly more polar than phenylalanine and allows it to form hydrogen bonds and be phosphorylated (addition of a phosphate group), an important regulatory mechanism.
• Tryptophan (Trp, W): Contains an indole ring system. It's the bulkiest of the aromatic amino acids.

3. Polar, Uncharged R Groups: These amino acids have R-groups that contain atoms (like oxygen or sulfur) that create a dipole moment, making them hydrophilic and capable of forming hydrogen bonds.

• Serine (Ser, S): Has a hydroxyl group (-OH) as its R-group.
• Threonine (Thr, T): Has a hydroxyl group (-OH) and a methyl group as its R-group.
• Cysteine (Cys, C): Has a sulfhydryl group (-SH) as its R-group. Two cysteine residues can form a disulfide bond (S-S) which can stabilize protein structures.
• Asparagine (Asn, N): Has an amide group (-CONH2) as its R-group.
• Glutamine (Gln, Q): Has a longer carbon chain than asparagine, but also has an amide group (-CONH2) as its R-group.

4. Positively Charged (Basic) R Groups: These amino acids have R-groups that are positively charged at physiological pH (around 7.4).

• Lysine (Lys, K): Has an amino group (-NH2) on its R-group.
• Arginine (Arg, R): Has a guanidino group on its R-group, which is positively charged over a wide pH range.
• Histidine (His, H): Has an imidazole ring in its R-group. Its pKa (the pH at which it is half protonated) is close to physiological pH, meaning it can be either protonated (positively charged) or deprotonated (neutral) depending on the local environment. This makes it important in enzyme catalysis.

5. Negatively Charged (Acidic) R Groups: These amino acids have R-groups that are negatively charged at physiological pH.

• Aspartate (Asp, D): Has a carboxyl group (-COOH) on its R-group.
• Glutamate (Glu, E): Has a longer carbon chain than aspartate, but also has a carboxyl group (-COOH) on its R-group.

Essential vs. Nonessential Amino Acids

From a nutritional standpoint, amino acids are classified as either essential or nonessential.

• Essential Amino Acids: These are the amino acids that the human body cannot synthesize on its own and must be obtained from the diet. The nine essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
• Nonessential Amino Acids: These are the amino acids that the body can synthesize from other molecules. They don't need to be directly obtained from the diet. The nonessential amino acids are: alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine. (Note: Arginine is sometimes considered conditionally essential, as it may be required in certain physiological states, such as growth or trauma.)

Forming the Protein: Peptide Bond Formation

Amino acids don't exist in isolation within a protein. They are linked together by peptide bonds to form polypeptide chains. A peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another, with the release of a water molecule (H2O). This is a dehydration reaction or condensation reaction.

The Process

1. The carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another amino acid.
2. A molecule of water (H2O) is removed.
3. A covalent bond (the peptide bond) is formed between the carbon atom of the carboxyl group and the nitrogen atom of the amino group.

The resulting dipeptide (two amino acids linked together) has a free amino group on one end (the N-terminus) and a free carboxyl group on the other end (the C-terminus). Additional amino acids can be added to either end, but in biological systems, they are almost always added to the C-terminus.

Polypeptides and Proteins

As more amino acids are joined together by peptide bonds, a polypeptide chain is formed. A polypeptide is simply a chain of amino acids linked by peptide bonds. The terms polypeptide and protein are often used interchangeably, but there is a subtle distinction. A polypeptide refers specifically to the amino acid chain, while a protein refers to the functional biological molecule, which may consist of one or more polypeptide chains folded into a specific three-dimensional structure and potentially associated with other molecules like cofactors or prosthetic groups.

The Importance of Amino Acid Sequence

The sequence of amino acids in a polypeptide chain is called its primary structure. This sequence is genetically encoded in DNA and determines the protein's higher-order structure and, ultimately, its function. Even a single amino acid change in a protein can have significant consequences.

Genetic Basis

The sequence of amino acids in a protein is determined by the sequence of codons in messenger RNA (mRNA). Each codon (a sequence of three nucleotides) specifies a particular amino acid. The genetic code is nearly universal, meaning that the same codons specify the same amino acids in almost all organisms.

Mutations

Mutations in DNA can lead to changes in the amino acid sequence of a protein. These changes can have a variety of effects, ranging from no effect at all to complete loss of function. For example, sickle cell anemia is caused by a single amino acid substitution in the hemoglobin protein.

Protein Structure: Beyond the Primary Sequence

The primary structure (amino acid sequence) is just the beginning. Proteins fold into complex three-dimensional structures that are essential for their function. There are four levels of protein structure:

1. Primary Structure: The linear sequence of amino acids.
2. Secondary Structure: Localized folding patterns, such as alpha-helices and beta-sheets, stabilized by hydrogen bonds between the backbone atoms of the amino acids.
3. Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions between the R-groups of the amino acids. These interactions can include hydrogen bonds, hydrophobic interactions, ionic bonds, and disulfide bonds.
4. Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein.

Factors Influencing Protein Folding

Protein folding is a complex process influenced by a variety of factors, including:

• Amino Acid Sequence: The primary determinant of protein structure.
• Chaperone Proteins: Assist in the folding process and prevent misfolding or aggregation.
• pH: Can affect the charges of amino acid R-groups and influence interactions.
• Temperature: High temperatures can denature proteins, causing them to unfold.
• Salt Concentration: Can affect ionic interactions.

Functions of Proteins

The diversity of amino acid side chains and the resulting three-dimensional structures allow proteins to perform a vast array of functions in living organisms. Here are some key examples:

• Enzymes: Catalyze biochemical reactions.
• Structural Proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
• Transport Proteins: Carry molecules across cell membranes or through the bloodstream (e.g., hemoglobin, albumin).
• Hormones: Chemical messengers that regulate various physiological processes (e.g., insulin, growth hormone).
• Antibodies: Part of the immune system, recognizing and neutralizing foreign invaders.
• Contractile Proteins: Enable movement (e.g., actin, myosin).
• Storage Proteins: Store nutrients (e.g., ferritin, casein).
• Receptor Proteins: Bind to signaling molecules and initiate cellular responses.

Beyond the 20: Non-Standard Amino Acids

While the 20 standard amino acids are the primary building blocks of proteins, other amino acids can be found in proteins, often formed by post-translational modifications. These non-standard amino acids expand the functional repertoire of proteins.

Examples

• Hydroxyproline and Hydroxylysine: Formed by hydroxylation of proline and lysine, respectively. Important for collagen stability.
• Pyrolysine and Selenocysteine: Genetically encoded, but incorporated by special mechanisms.
• Phosphorylated Serine, Threonine, and Tyrosine: Phosphorylation is a common regulatory modification.

Clinical Significance

Understanding amino acids and protein structure is crucial in medicine. Many diseases are caused by mutations in genes encoding proteins, leading to misfolded or non-functional proteins. Furthermore, dietary deficiencies in essential amino acids can have serious health consequences.

Examples

• Phenylketonuria (PKU): A genetic disorder caused by a deficiency in the enzyme phenylalanine hydroxylase, which converts phenylalanine to tyrosine.
• Maple Syrup Urine Disease (MSUD): A genetic disorder caused by a deficiency in the enzyme branched-chain alpha-keto acid dehydrogenase, which is involved in the metabolism of branched-chain amino acids (leucine, isoleucine, and valine).
• Nutritional Deficiencies: Lack of essential amino acids can lead to growth retardation, immune dysfunction, and other health problems.

Conclusion

Amino acids, the monomers of proteins, are fundamental to life. Their diverse structures and properties dictate the structure and function of the proteins they form. From catalyzing biochemical reactions to providing structural support, proteins play essential roles in every aspect of biology. A thorough understanding of amino acids is therefore crucial for understanding the molecular basis of life and disease.