The Monomers That Make Up Proteins Are Called ________.

Amino acids are the fundamental building blocks of proteins, the workhorses of the cell, essential for virtually every biological process. Understanding the structure and properties of amino acids is crucial to comprehending the complexity and function of proteins. This article explores the world of amino acids, covering their basic structure, classification, properties, and the critical roles they play in the formation and function of proteins.

The Foundation: What Are Amino Acids?

Amino acids are organic molecules that serve as the monomers, or building blocks, of proteins. Each amino acid contains a central carbon atom (the alpha-carbon) bonded to four different groups:

• An amino group (-NH2)
• A carboxyl group (-COOH)
• A hydrogen atom (-H)
• A variable side chain (also called an R-group)

It is the R-group that distinguishes each of the 20 common amino acids from one another, imparting unique chemical properties and influencing the overall structure and function of the protein.

Diving Deeper: The Structure of Amino Acids

Let's break down each component of an amino acid in more detail:

The Alpha-Carbon: The Central Hub

The alpha-carbon is the central atom of the amino acid, acting as the point of attachment for the amino group, carboxyl group, hydrogen atom, and the R-group. The tetrahedral arrangement of these groups around the alpha-carbon is crucial for the spatial arrangement and reactivity of the amino acid.

The Amino Group: The Base

The amino group (-NH2) is a basic functional group that can accept a proton (H+). At physiological pH (around 7.4), the amino group is typically protonated, carrying a positive charge (-NH3+). This positive charge is important for ionic interactions within proteins and with other molecules.

The Carboxyl Group: The Acid

The carboxyl group (-COOH) is an acidic functional group that can donate a proton (H+). At physiological pH, the carboxyl group is typically deprotonated, carrying a negative charge (-COO-). This negative charge, like the positive charge on the amino group, is crucial for ionic interactions within proteins.

The Hydrogen Atom: Simple but Essential

The hydrogen atom (-H) is the simplest component of the amino acid, but it plays a role in the overall shape and stability of the molecule.

The R-Group: The Key to Diversity

The R-group, or side chain, is the most variable part of an amino acid and is what gives each amino acid its unique properties. R-groups can vary in size, shape, charge, hydrogen-bonding capacity, and chemical reactivity. These variations determine how the amino acid will interact with other molecules and how it will contribute to the overall structure and function of a protein.

Classifying Amino Acids: Understanding Their Properties

Amino acids are classified based on the properties of their R-groups. This classification helps predict how an amino acid will behave in different environments and how it will contribute to the structure and function of a protein. The main categories are:

• Nonpolar, Aliphatic R-groups: These amino acids have hydrophobic (water-repelling) side chains composed of carbon and hydrogen. They tend to cluster together within the interior of proteins, away from the aqueous environment. Examples include:

  • Alanine (Ala, A): A simple methyl group as its side chain.
  • Valine (Val, V): Has an isopropyl group.
  • Leucine (Leu, L): Possesses an isobutyl group.
  • Isoleucine (Ile, I): Has a sec-butyl group.
  • Proline (Pro, P): Unique in that its side chain is bonded to both the alpha-carbon and the nitrogen atom, creating a cyclic structure. This restricts its conformational flexibility and often introduces kinks in protein structure.
  • Glycine (Gly, G): Although technically aliphatic, Glycine's R-group is simply a hydrogen atom. This makes it the smallest amino acid and allows it to fit into tight spaces within proteins.
  • Methionine (Met, M): Contains a sulfur atom in its side chain.

• Aromatic R-groups: These amino acids have aromatic rings in their side chains. They are relatively nonpolar and can participate in hydrophobic interactions. They also absorb ultraviolet light at 280 nm, which is a useful property for quantifying protein concentrations. Examples include:

  • Phenylalanine (Phe, F): Contains a benzyl group.
  • Tyrosine (Tyr, Y): Has a phenol group.
  • Tryptophan (Trp, W): Contains an indole ring.

• Polar, Uncharged R-groups: These amino acids have polar side chains that can form hydrogen bonds with water and other polar molecules. They are generally found on the surface of proteins, interacting with the aqueous environment. Examples include:

  • Serine (Ser, S): Contains a hydroxyl group (-OH).
  • Threonine (Thr, T): Also has a hydroxyl group (-OH).
  • Cysteine (Cys, C): Contains a sulfhydryl group (-SH), which can form disulfide bonds with other cysteine residues, stabilizing protein structure.
  • Asparagine (Asn, N): Has an amide group.
  • Glutamine (Gln, Q): Also has an amide group.

• Positively Charged (Basic) R-groups: These amino acids have side chains that are positively charged at physiological pH. They are hydrophilic and often found on the surface of proteins, interacting with negatively charged molecules. Examples include:

  • Lysine (Lys, K): Has an amino group at the end of its side chain.
  • Arginine (Arg, R): Contains a guanidinium group.
  • Histidine (His, H): Has an imidazole ring. Its pKa is close to physiological pH, so it can be either protonated (positively charged) or deprotonated (neutral) depending on the environment. This makes it important in enzyme active sites where proton transfer is required.

• Negatively Charged (Acidic) R-groups: These amino acids have side chains that are negatively charged at physiological pH. They are hydrophilic and often found on the surface of proteins, interacting with positively charged molecules. Examples include:

  • Aspartate (Asp, D): Contains a carboxyl group.
  • Glutamate (Glu, E): Also contains a carboxyl group.

The Peptide Bond: Linking Amino Acids Together

Amino acids 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 process is called dehydration synthesis or condensation reaction.

The formation of a peptide bond creates a repeating backbone structure in the polypeptide chain, consisting of the alpha-carbon, carbonyl carbon, and nitrogen atoms. The R-groups of the amino acids project out from this backbone, determining the unique properties of the polypeptide.

A polypeptide chain has two distinct ends:

• The amino-terminus (N-terminus): The end with a free amino group.
• The carboxyl-terminus (C-terminus): The end with a free carboxyl group.

The sequence of amino acids in a polypeptide chain, starting from the N-terminus and ending at the C-terminus, is called the primary structure of the protein.

From Polypeptide to Protein: Folding and Function

A polypeptide chain is not yet a functional protein. It must fold into a specific three-dimensional structure to perform its biological role. This folding process is driven by interactions between the amino acid R-groups, including:

• Hydrophobic interactions: Nonpolar R-groups cluster together in the interior of the protein, away from water.
• Hydrogen bonds: Polar R-groups form hydrogen bonds with each other and with water.
• Ionic bonds: Oppositely charged R-groups form ionic bonds.
• Disulfide bonds: Cysteine residues can form covalent disulfide bonds, which can stabilize the protein structure.

The three-dimensional structure of a protein is described in terms of:

• Secondary structure: Localized, repeating patterns of folding, such as alpha-helices and beta-sheets, stabilized by hydrogen bonds between backbone atoms.
• Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions between R-groups.
• Quaternary structure: The arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein.

The specific three-dimensional structure of a protein is critical for its function. The shape of the protein determines which molecules it can bind to and how it can interact with other proteins and cellular components.

Essential Amino Acids: What You Need to Know

Humans can synthesize some amino acids, but others, known as essential amino acids, must be obtained from the diet. These are:

• Histidine (His, H)
• Isoleucine (Ile, I)
• Leucine (Leu, L)
• Lysine (Lys, K)
• Methionine (Met, M)
• Phenylalanine (Phe, F)
• Threonine (Thr, T)
• Tryptophan (Trp, W)
• Valine (Val, V)

In addition, arginine (Arg, R) is considered conditionally essential, meaning that it is essential under certain conditions, such as during growth or illness.

A balanced diet containing sufficient protein sources is necessary to ensure adequate intake of all essential amino acids.

The Diverse Roles of Proteins: Function Follows Form

Proteins perform a vast array of functions in living organisms, including:

• Enzymes: Catalyze biochemical reactions.
• Structural proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
• Transport proteins: Carry molecules within the body (e.g., hemoglobin, albumin).
• Motor proteins: Facilitate movement (e.g., myosin, kinesin).
• Antibodies: Defend against foreign invaders (e.g., immunoglobulins).
• Hormones: Regulate physiological processes (e.g., insulin, growth hormone).
• Receptors: Receive and respond to signals from the environment (e.g., hormone receptors, neurotransmitter receptors).
• Storage proteins: Store nutrients (e.g., ferritin, casein).

The specific function of a protein is determined by its unique amino acid sequence and three-dimensional structure. Understanding the relationship between protein structure and function is a central goal of modern biology.

Genetic Code and Amino Acids: The Blueprint of Life

The sequence of amino acids in a protein is determined by the genetic code, which is encoded in DNA. DNA is transcribed into messenger RNA (mRNA), which then serves as a template for protein synthesis (translation) on ribosomes.

Each three-nucleotide sequence (codon) in mRNA corresponds to a specific amino acid. There are 64 possible codons, but only 20 amino acids. This means that some amino acids are encoded by multiple codons (degeneracy). There are also codons that signal the start and stop of protein synthesis.

The genetic code is nearly universal, meaning that it is the same in almost all organisms, from bacteria to humans. This is strong evidence for the common ancestry of all life on Earth.

Amino Acid Metabolism: Beyond Protein Synthesis

Amino acids are not only used for protein synthesis but also play important roles in other metabolic pathways:

• Energy production: Amino acids can be broken down to provide energy through gluconeogenesis or ketogenesis.
• Biosynthesis of other molecules: Amino acids are precursors for the synthesis of other important molecules, such as neurotransmitters, hormones, and nucleotides.
• Nitrogen disposal: Excess nitrogen from amino acid breakdown is converted to urea and excreted in the urine.

Disruptions in amino acid metabolism can lead to various metabolic disorders, such as phenylketonuria (PKU) and maple syrup urine disease (MSUD).

Common Questions About Amino Acids

• What is a zwitterion?

  A zwitterion is a molecule that contains both a positive and a negative charge. Amino acids are zwitterions at physiological pH because the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).

• What is the isoelectric point (pI)?

  The isoelectric point (pI) is the pH at which a molecule has no net electrical charge. For amino acids, the pI is the average of the pKa values of the amino and carboxyl groups. At the pI, an amino acid is least soluble in water and will not migrate in an electric field.

• What are unnatural amino acids?

  Unnatural amino acids are amino acids that are not among the 20 common amino acids found in proteins. They can be synthesized chemically and incorporated into proteins using modified translation systems. Unnatural amino acids can be used to introduce new functionalities into proteins, such as fluorescent probes or reactive groups.

• What is protein engineering?

  Protein engineering is the process of designing and modifying proteins to have desired properties, such as increased stability, altered activity, or new binding specificities. Protein engineering can be accomplished through various techniques, including site-directed mutagenesis, directed evolution, and computational design.

Conclusion: The Indispensable Monomers of Life

Amino acids are the fundamental building blocks of proteins, the molecular machines that drive virtually all biological processes. Understanding the structure, properties, and classification of amino acids is essential for comprehending the complexity and function of proteins. From their role in protein folding and stability to their involvement in metabolism and signaling, amino acids are indispensable for life as we know it. Further exploration into the world of amino acids will undoubtedly continue to unlock new insights into the intricate workings of living systems and pave the way for advances in medicine, biotechnology, and beyond.