What Monomers Are Proteins Made Of

Proteins, the workhorses of our cells, are complex molecules built from smaller, repeating units. Understanding the fundamental building blocks of proteins is crucial to comprehending their diverse functions and intricate structures.

The Monomeric Units of Proteins: Amino Acids

The monomers that make up proteins are called amino acids. These organic molecules serve as the fundamental building blocks, linking together in a specific sequence to form polypeptide chains, which then fold into functional proteins. There are 20 standard amino acids commonly found in proteins, each with a unique chemical structure and properties.

General Structure of Amino Acids

All 20 standard amino acids share a common core structure, consisting of:

• A central carbon atom, known as the alpha (α) carbon.
• An amino group (-NH2) bonded to the α-carbon.
• A carboxyl group (-COOH) bonded to the α-carbon.
• A hydrogen atom (-H) bonded to the α-carbon.
• A side chain (R-group) bonded to the α-carbon.

The key difference between the 20 standard amino acids lies in their side chain (R-group). This unique R-group determines the specific chemical properties of each amino acid, influencing its interactions with other amino acids and molecules within the protein structure.

Classification of Amino Acids Based on Side Chain Properties

Amino acids are often classified based on the properties of their side chains, which dictate their behavior in aqueous solutions and their interactions within a protein structure. The main categories include:

1. Nonpolar, Aliphatic Amino Acids: These amino acids have hydrophobic side chains composed primarily of carbon and hydrogen atoms. They tend to cluster together in the interior of proteins, away from the aqueous environment. Examples include:

   • Alanine (Ala, A)
   • Valine (Val, V)
   • Leucine (Leu, L)
   • Isoleucine (Ile, I)
   • Proline (Pro, P) - Proline is unique because its side chain forms a cyclic structure, connecting to the α-carbon and the amino group, creating a rigid structure that influences protein folding.
   • Glycine (Gly, G) - Although technically aliphatic, Glycine's side chain is simply a hydrogen atom, making it the smallest amino acid. It can fit into tight spaces within a protein structure where other amino acids would be too bulky.

2. Aromatic Amino Acids: These amino acids contain an aromatic ring in their side chain. They are relatively nonpolar and can participate in hydrophobic interactions. They also absorb ultraviolet light, which is useful for protein detection and quantification. Examples include:

   • Phenylalanine (Phe, F)
   • Tyrosine (Tyr, Y)
   • Tryptophan (Trp, W)

3. Polar, Uncharged Amino Acids: These amino acids have polar side chains that can form hydrogen bonds with water and other polar molecules. They are typically found on the surface of proteins, interacting with the aqueous environment. Examples include:

   • Serine (Ser, S)
   • Threonine (Thr, T)
   • Cysteine (Cys, C) - Cysteine contains a sulfhydryl group (-SH) which can form disulfide bonds with other cysteine residues, contributing to protein stability.
   • Asparagine (Asn, N)
   • Glutamine (Gln, Q)

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

   • Lysine (Lys, K)
   • Arginine (Arg, R)
   • Histidine (His, H) - Histidine's side chain has a pKa close to physiological pH, allowing it to act as a proton donor or acceptor, playing a role in enzymatic catalysis.

5. Negatively Charged (Acidic) Amino Acids: These amino acids have negatively charged side chains at physiological pH. They are also hydrophilic and typically found on the surface of proteins. Examples include:

   • Aspartic acid (Asp, D)
   • Glutamic acid (Glu, E)

Essential and Non-Essential Amino Acids

From a nutritional perspective, amino acids are classified as either essential or non-essential.

• Essential amino acids cannot be synthesized by the human body and must be obtained from the diet. These include: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
• Non-essential amino acids can be synthesized by the body and do not need to be obtained from the diet. These include: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine. (Note: Arginine is considered conditionally essential, meaning that it is essential under certain conditions such as growth or stress.)

Polymerization of Amino Acids: Peptide Bond Formation

Amino acids are linked together to form polypeptide chains through peptide bonds. This process occurs through a dehydration reaction, where the carboxyl group of one amino acid reacts with the amino group of another amino acid, releasing a molecule of water (H2O) and forming a covalent bond between the carbon atom of the first amino acid and the nitrogen atom of the second amino acid.

The Peptide Bond

The peptide bond (–CO–NH–) is a planar, rigid bond that exhibits partial double-bond character due to resonance. This limits rotation around the bond and influences the conformation of the polypeptide chain. The peptide bond also has a dipole moment, contributing to the overall polarity of the protein.

Polypeptide Chains

Multiple amino acids linked together by peptide bonds form a polypeptide chain. The polypeptide chain has a defined directionality, with an N-terminus (amino terminus) at one end, containing a free amino group, and a C-terminus (carboxyl terminus) at the other end, containing a free carboxyl group. The sequence of amino acids in the polypeptide chain is called the primary structure of the protein.

From Polypeptide to Protein

While the terms are often used interchangeably, there's a subtle difference between a polypeptide and a protein. A polypeptide is simply a chain of amino acids. A protein, however, is a functional molecule that consists of one or more polypeptide chains folded into a specific three-dimensional structure. This structure is crucial for the protein's function.

Levels of Protein Structure

The three-dimensional structure of a protein is hierarchical, with four levels of organization:

1. Primary Structure: The linear sequence of amino acids in the polypeptide chain. This sequence is determined by the genetic code and dictates the higher levels of protein structure.

2. Secondary Structure: Localized folding patterns within the polypeptide chain, stabilized by hydrogen bonds between the backbone atoms (amino and carboxyl groups). The most common secondary structures are:

   • α-helix: A coiled structure stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of an amino acid four residues down the chain.
   • β-sheet: A sheet-like structure formed by hydrogen bonds between adjacent strands of the polypeptide chain. β-sheets can be parallel (strands running in the same direction) or antiparallel (strands running in opposite directions).
   • Turns and loops: Regions of the polypeptide chain that connect α-helices and β-sheets, often containing proline or glycine residues, which allow for flexibility and changes in direction.

3. Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the side chains (R-groups) of the amino acids. These interactions include:

   • Hydrophobic interactions: Nonpolar side chains cluster together in the interior of the protein, away from water.
   • Hydrogen bonds: Polar side chains form hydrogen bonds with each other or with water molecules.
   • Ionic bonds: Oppositely charged side chains form ionic bonds (salt bridges).
   • Disulfide bonds: Cysteine residues can form covalent disulfide bonds between their sulfhydryl groups, stabilizing the protein structure.
   • Van der Waals forces: Weak, short-range attractive forces between atoms.

4. Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein. Not all proteins have quaternary structure; it only applies to proteins composed of two or more polypeptide chains. Subunits are held together by the same types of interactions that stabilize tertiary structure. Hemoglobin, for example, is a protein with quaternary structure, composed of four subunits (two α-globin and two β-globin chains).

The Importance of Amino Acid Sequence

The sequence of amino acids in a protein is critical for its function. A single amino acid change can have significant consequences, altering the protein's folding, stability, and interactions with other molecules. This is evident in genetic diseases like sickle cell anemia, where a single amino acid substitution in the hemoglobin protein (glutamic acid to valine) leads to abnormal hemoglobin aggregation and distorted red blood cell shape.

Protein Folding

The process of protein folding is complex and influenced by various factors, including:

• Amino acid sequence: The primary sequence dictates the possible interactions between amino acid side chains, guiding the protein towards its native conformation.
• Chaperone proteins: These proteins assist in protein folding by preventing aggregation and promoting proper folding pathways.
• Environmental conditions: Temperature, pH, and the presence of ions can affect protein folding and stability.

Misfolded proteins can lead to aggregation and the formation of amyloid fibrils, which are associated with neurodegenerative diseases such as Alzheimer's and Parkinson's disease.

Functions of Proteins

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

• Enzymes: Catalyze biochemical reactions, accelerating the rate of reactions in cells.
• Structural proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
• Transport proteins: Carry molecules across cell membranes or throughout the body (e.g., hemoglobin, albumin).
• Motor proteins: Mediate movement (e.g., myosin, kinesin).
• Antibodies: Recognize and bind to foreign substances (antigens), protecting the body from infection.
• Hormones: Act as chemical messengers, coordinating various physiological processes (e.g., insulin, growth hormone).
• Receptor proteins: Bind to signaling molecules and initiate cellular responses.
• Storage proteins: Store nutrients or other essential molecules (e.g., ferritin, casein).
• Regulatory proteins: Control gene expression and other cellular processes (e.g., transcription factors).

Protein Degradation

Proteins are not static molecules; they are constantly being synthesized and degraded. Protein degradation is essential for removing damaged or misfolded proteins and for regulating cellular processes. The major pathways for protein degradation in cells are:

• Ubiquitin-proteasome system (UPS): Proteins are tagged with ubiquitin molecules, which target them for degradation by the proteasome, a large protein complex that breaks down proteins into smaller peptides.
• Autophagy: A process in which cells engulf and digest their own components, including proteins, within lysosomes.

Conclusion

Amino acids, the monomeric units of proteins, are fundamental to life. Their unique structures and properties dictate the diverse functions and intricate structures of proteins. Understanding the chemistry of amino acids and their polymerization into polypeptide chains is crucial for comprehending the complexities of protein structure, function, and their role in biological processes. From catalyzing biochemical reactions to providing structural support and mediating movement, proteins are essential for life as we know it, and their building blocks, the amino acids, are at the heart of it all.

Frequently Asked Questions (FAQ)

1. What are the 20 standard amino acids?

The 20 standard amino acids are: Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, and Valine.

2. What is the difference between essential and non-essential amino acids?

Essential amino acids cannot be synthesized by the body and must be obtained from the diet. Non-essential amino acids can be synthesized by the body.

3. What is a peptide bond?

A peptide bond is a covalent bond that links amino acids together in a polypeptide chain. It is formed through a dehydration reaction between the carboxyl group of one amino acid and the amino group of another amino acid.

4. What are the levels of protein structure?

The four levels of protein structure are: primary, secondary, tertiary, and quaternary.

5. Why is protein folding important?

Proper protein folding is essential for protein function. Misfolded proteins can lead to aggregation and disease.

6. What are some of the functions of proteins?

Proteins perform a vast array of functions in living organisms, including catalysis, structural support, transport, movement, immune defense, hormonal regulation, and gene expression control.

7. What happens to proteins when they are no longer needed?

Proteins are degraded by the ubiquitin-proteasome system (UPS) or autophagy.

8. Can a single amino acid change affect a protein's function?

Yes, a single amino acid change can have significant consequences, altering the protein's folding, stability, and interactions with other molecules.

9. What role do chaperone proteins play in protein folding?

Chaperone proteins assist in protein folding by preventing aggregation and promoting proper folding pathways.

10. How are amino acids classified?

Amino acids are classified based on the properties of their side chains, including nonpolar, aromatic, polar uncharged, positively charged (basic), and negatively charged (acidic).