Protein Structure, Function, and Enzyme Activity

Protein Structure

Levels of Protein Structure

Proteins are complex biological macromolecules composed of amino acids. Their structure is organized into four hierarchical levels, each contributing to the protein's overall shape and function.

• Primary Structure: The linear sequence of amino acids in a polypeptide chain. Example: Gly-Ser-Asp-Cys.

• Secondary Structure: Local folding patterns such as alpha helices and beta sheets, stabilized by hydrogen bonds along the peptide backbone.

• Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, formed by interactions among side chains (R groups) of amino acids.

• Quaternary Structure: The assembly of multiple polypeptide chains (subunits) into a larger functional protein complex.

Key Point: Each level of structure is essential for the protein's stability and biological activity.

Example: Hemoglobin is a quaternary protein composed of four polypeptide subunits.

Protein Functions

Major Biological Roles of Proteins

Proteins perform a wide variety of functions in living organisms, reflecting their diverse structures.

• Cellular Transport: Proteins such as channels and co-transporters facilitate movement of molecules across cell membranes.

• Immune Defense: Immunoglobulins (antibodies) and T cell receptors are crucial for recognizing and neutralizing pathogens.

• Storage: Proteins like ferritin and calmodulin store essential ions and molecules.

• Hormones: Protein hormones such as renin and leptin regulate physiological processes.

• Gene Regulation: Transcription factors control the expression of genes.

• Osmotic Proteins: Serum albumin helps maintain osmotic balance in blood.

• Structural Proteins: Collagen provides strength and support to tissues.

• Fuel: Some proteins can be metabolized for energy.

• Enzymes: Proteins that catalyze biochemical reactions; approximately 75,000 different enzymes exist in humans.

Key Point: The function of a protein is determined by its structure and the specific sequence of amino acids.

Enzymes: Biological Catalysts

Definition and Role

Enzymes are specialized proteins that act as catalysts, speeding up chemical reactions without being consumed in the process.

• Catalyst: A substance that increases the rate of a chemical reaction.

• Enzyme: A protein catalyst that is highly specific for its substrate.

Example: Amylase catalyzes the breakdown of starch into sugars.

Enzyme Function: Basics

Substrate and Active Site

Enzymes function by binding to specific molecules called substrates at a region known as the active site.

• Substrate: The molecule upon which an enzyme acts.

• Active Site: The region of the enzyme where the substrate binds and the reaction occurs.

General Reaction:

• $E + S \rightarrow E\text{-}S \text{ Complex} \rightarrow E + P$

Example: The enzyme sucrase binds sucrose (substrate), breaks it into glucose and fructose (products).

Enzyme-Substrate Interaction

Mechanism of Action

Enzymes and substrates form a temporary enzyme-substrate complex, facilitating the conversion of substrates into products.

• Specificity: Enzymes are highly specific, typically catalyzing only one type of reaction.

• Induced Fit Model: The enzyme changes shape slightly to accommodate the substrate, enhancing catalysis.

Example: The binding of glucose and fructose to sucrase stresses the bond, leading to its cleavage.

Enzyme Kinetics

Reaction Rates and Parameters

Enzyme kinetics studies the rates of enzyme-catalyzed reactions and how they are affected by various factors.

• Vmax: The maximum rate of reaction when the enzyme is saturated with substrate.

• Km: The substrate concentration at which the reaction rate is half of Vmax; indicates enzyme affinity for substrate.

Key Equation:

• $v = \frac{V_{max}[S]}{K_m + [S]}$

Example: A low Km means high affinity; the enzyme reaches half-maximal velocity at a low substrate concentration.

Enzyme Regulation and Inhibition

Types of Inhibitors

Enzyme activity can be regulated by molecules called inhibitors, which decrease or block enzyme function.

• Competitive Inhibitors: Bind to the active site, competing with the substrate. Can be overcome by increasing substrate concentration.

• Noncompetitive Inhibitors: Bind to a site other than the active site, altering enzyme structure and reducing activity regardless of substrate concentration.

Effect on Kinetics:

Type of Inhibition	Effect on Vmax	Effect on Km
Competitive	No change	Increases
Noncompetitive	Decreases	No change

Example: Many drugs act as enzyme inhibitors to treat diseases.

Environmental Effects on Enzyme Activity

Temperature and pH Sensitivity

Enzyme activity is highly sensitive to environmental conditions such as temperature and pH.

• Temperature: Each enzyme has an optimum temperature for activity. High temperatures can denature proteins, causing loss of function.

• pH: Each enzyme has an optimum pH. Deviations can alter enzyme structure and reduce activity.

Example: Human enzymes typically have optimum activity at 37°C and neutral pH, but some, like pepsin, function best at acidic pH.

Protein Misfolding and Disease

Prions and Protein Misfolding

Misfolded proteins can lead to serious diseases. Prions are infectious proteins that cause other proteins to misfold, resulting in neurodegenerative disorders.

• Prion Diseases: Include mad cow disease (Bovine Spongiform Encephalopathy), scrapie, chronic wasting disease, Creutzfeldt-Jakob disease, and fatal familial insomnia.

• Mechanism: Misfolded prions aggregate into plaques, disrupting normal brain function.

Example: The normal prion protein (PrP) is harmless, but its misfolded form is infectious and pathogenic.

Additional info: Protein misfolding can also contribute to other diseases such as Alzheimer's and Parkinson's.