Biomolecules (Proteins And Enzymes)

Proteins

Proteins are macromolecules that are essential for life. They are polymers made up of monomers called amino acids, linked together by peptide bonds.

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Amino Acids

Amino acids are organic molecules that contain both an amino group ($-NH_2$) and a carboxyl group ($-COOH$). The general structure of an amino acid is:

The central carbon atom is called the alpha-carbon ($C_\alpha$). It is attached to:

• A hydrogen atom (H)
• An amino group ($-NH_2$)
• A carboxyl group ($-COOH$)
• A side chain or R-group, which is unique for each amino acid.

There are 20 different types of amino acids that are commonly found in proteins. The R-group determines the chemical properties of the amino acid, such as its polarity, charge, and size.

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Classification Of Amino Acids

Amino acids can be classified based on the properties of their R-groups:

1. Based on the Number of Amino and Carboxyl Groups:

• Neutral Amino Acids: Have an equal number of amino and carboxyl groups (e.g., glycine, alanine).
• Acidic Amino Acids: Have more carboxyl groups than amino groups (e.g., aspartic acid, glutamic acid).
• Basic Amino Acids: Have more amino groups than carboxyl groups (e.g., lysine, arginine, histidine).

2. Based on the Nutritional Requirement:

• Essential Amino Acids: These cannot be synthesized by the human body and must be obtained from the diet (e.g., valine, leucine, isoleucine, lysine, methionine, phenylalanine, tryptophan, threonine, histidine).
• Non-essential Amino Acids: These can be synthesized by the human body (e.g., glycine, alanine, aspartic acid, glutamic acid).

3. Based on the Polarity of the R-group:

• Nonpolar Amino Acids: Have nonpolar R-groups, which are hydrophobic (e.g., alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline).
• Polar Amino Acids: Have polar R-groups, which are hydrophilic. These can be further divided into:
  • Uncharged Polar Amino Acids: The R-groups contain electronegative atoms but do not carry a net charge (e.g., serine, threonine, cysteine, tyrosine, asparagine, glutamine).
  • Charged Polar Amino Acids: The R-groups carry a net charge at physiological pH.
    • Acidic (Negatively Charged): Aspartic acid, Glutamic acid.
    • Basic (Positively Charged): Lysine, Arginine, Histidine.

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Structure Of Proteins

The sequence of amino acids in a protein is called its primary structure. This sequence determines the higher-order structures of the protein, which are crucial for its function.

Primary Structure:

The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.

A peptide bond is formed by the dehydration reaction between the carboxyl group of one amino acid and the amino group of another:

$R_1-COOH + H_2N-R_2 \rightarrow R_1-CO-NH-R_2 + H_2O$

Secondary Structure:

The regular, repeating arrangements of the polypeptide chain backbone, stabilized by hydrogen bonds between the peptide groups.

• Alpha-helix ($\alpha$-helix): A coiled structure where the polypeptide chain is twisted into a helix. The hydrogen bonds form between the oxygen of a carbonyl group and the hydrogen of an amino group four amino acids further down the chain.
• Beta-pleated sheet ($\beta$-pleated sheet): A structure where polypeptide chains are arranged side-by-side and held together by hydrogen bonds between adjacent chains.

Tertiary Structure:

The three-dimensional folding of a single polypeptide chain, including $\alpha$-helices and $\beta$-sheets, into a compact, globular or fibrous shape. This structure is stabilized by various interactions between R-groups:

• Hydrogen bonds
• Ionic bonds (salt bridges)
• Hydrophobic interactions
• Disulfide bonds (covalent bonds between the sulfur atoms of two cysteine residues)

The tertiary structure is responsible for the protein's overall function.

Quaternary Structure:

The arrangement of multiple polypeptide chains (subunits) to form a functional protein complex. Not all proteins have a quaternary structure. If they do, the subunits are held together by the same types of interactions as in tertiary structure.

Example: Hemoglobin, which consists of four polypeptide subunits.

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Denaturation Of Proteins

Denaturation is the process by which a protein loses its native three-dimensional structure (secondary, tertiary, and quaternary structures) while its primary structure remains intact. This loss of structure often leads to a loss of biological activity.

Causes of Denaturation:

• Heat: Increased temperature disrupts the weak bonds holding the protein structure together.
• pH changes (Acids and Bases): Alterations in pH can disrupt ionic bonds and hydrogen bonds by changing the ionization state of amino acid side chains.
• Mechanical agitation: Vigorous shaking can unfold protein molecules.
• Chemical agents:
  • Urea and Guanidine hydrochloride: Disrupt hydrogen bonds and hydrophobic interactions.
  • Detergents: Disrupt hydrophobic interactions.
  • Heavy metal ions (e.g., lead, mercury): Can bind to sulfhydryl groups, disrupting disulfide bonds and other interactions.

Consequences of Denaturation:

• Loss of biological activity (e.g., enzymes become inactive).
• Changes in physical properties like solubility and viscosity.
• The protein becomes more susceptible to hydrolysis by proteases.

Denaturation is usually irreversible, although in some cases, a protein can refold into its active conformation if the denaturing agent is removed (renaturation).

Enzymes

Enzymes are biological catalysts, which are primarily proteins (though some RNA molecules, called ribozymes, also have catalytic activity). They speed up biochemical reactions in living organisms without being consumed in the process.

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Mechanism Of Enzyme Action

Enzymes work by binding to specific reactant molecules called substrates at a region on the enzyme called the active site. This binding forms an enzyme-substrate complex (ES complex).

The enzyme then facilitates the conversion of the substrate into products. Once the reaction is complete, the products are released from the active site, and the enzyme is free to bind to another substrate molecule.

Key Concepts in Enzyme Action:

1. Specificity: Enzymes are highly specific for their substrates. This is due to the unique three-dimensional shape and chemical properties of the active site, which are complementary to the substrate. This is often described by two models:
   • Lock and Key Model: Proposed by Emil Fischer, this model suggests that the active site of the enzyme has a rigid shape that is precisely complementary to the shape of the substrate, like a lock and key.
   • Induced Fit Model: Proposed by Daniel Koshland, this model suggests that the active site is flexible and undergoes a conformational change upon binding with the substrate. The enzyme 'molds' itself around the substrate to achieve an optimal fit.
2. Lowering Activation Energy: Enzymes lower the activation energy ($E_a$) of a reaction. Activation energy is the minimum amount of energy required for a reaction to occur. By lowering $E_a$, enzymes make it easier for the reaction to proceed, thus increasing the reaction rate.
   The reaction proceeds via the formation of an enzyme-substrate complex:

   $E + S \rightleftharpoons ES \rightarrow E + P$

   Where:
   • $E$ = Enzyme
   • $S$ = Substrate
   • $ES$ = Enzyme-substrate complex
   • $P$ = Product
3. Active Site: The active site is a small region within the enzyme molecule where the substrate binds and the catalytic activity occurs. It is composed of specific amino acid residues that participate in substrate binding and catalysis. These residues can be involved in:
   • Binding the substrate through non-covalent interactions (hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic interactions).
   • Lowering the activation energy by stabilizing the transition state of the reaction.
   • Facilitating the chemical transformation of the substrate into products.
4. Factors Affecting Enzyme Activity: The rate of an enzyme-catalyzed reaction can be influenced by several factors:
   • Temperature: Enzyme activity generally increases with temperature up to an optimal point, after which it rapidly decreases due to denaturation.
   • pH: Each enzyme has an optimal pH at which it exhibits maximum activity. Deviations from the optimal pH can alter the ionization of amino acid residues in the active site and affect substrate binding and catalysis, leading to a decrease in activity.
   • Substrate Concentration: As substrate concentration increases, the reaction rate increases until the enzyme becomes saturated with substrate (all active sites are occupied). Beyond this point, further increases in substrate concentration do not increase the reaction rate.
   • Enzyme Concentration: The reaction rate is directly proportional to the enzyme concentration, assuming sufficient substrate is available.
   • Inhibitors and Activators: Certain molecules can inhibit (decrease) or activate (increase) enzyme activity.