Protein Functions and Enzymes Overview

Protein Functions (Bindings)

• Proteins often bind other molecules reversibly, called ligands.
• Ligands bind to a complementary site on the protein. This complementary binding site is determined by size, shape, electrical charge, and chemical properties.
• Binding frequently triggers a conformational change in the protein. This change enhances the fit between the protein and ligand, leading to tighter binding.
• Within multi-subunit proteins, a change in one subunit can influence other subunits.

Two Types of Protein Interactions

• Enzymes: Proteins that act as catalysts, altering the chemical structure or composition of a molecule.
• Reversible ligand binding: For instance, the binding of oxygen to hemoglobin. The molecule's configuration doesn't change.

Enzymes – Lecture Overview

• Enzymes are a fundamental part of biochemical processes.
• They accelerate reactions within organisms.
• Their mechanisms and kinetics have been extensively studied.
• Different types of enzymes carry out specific functions.
• Enzymes can be inhibited.

Introduction to Enzymes

• Life depends on powerful and specific catalysts called enzymes.
• The human body has approximately 3,000 unique enzymes.
• Each type of enzyme accelerates a particular chemical reaction.
• Enzymes are crucial for brain function and muscle movement.
• Enzymes facilitate digestion by breaking down carbohydrates, proteins, and fats.
• Enzymes begin functioning at contact with the correct substrate.

Key Principles of Enzymes

• Enzymes are powerful biological catalysts.
• Enzymes display high specificity toward their substrates.
• Enzyme reactions occur within specialized pockets called active sites.
• Two concepts explain their catalytic acceleration and regulation mechanisms.

Brief History of Enzymes

• Eduard Buchner discovered cell-free yeast extracts could ferment sugar into alcohol. This proved the existence of catalyzing molecules.
• James Sumner isolated and crystallized the enzyme "urease," proving that enzymes are proteins (Nobel Prize in 1946).
• Other digestive enzymes were also found to be proteins.

Enzymes and Their Structure

• Enzymes are biological catalysts.
• With the exception of a few catalytic RNAs, enzymes are proteins.
• Their catalytic activity depends on their three-dimensional conformation.
• Denaturation or subunit dissociation loses catalytic activity.
• Breaking down into their constituent amino acids destroys the catalytic function.

Enzymes and Cofactors

• Some enzymes don't require additional components.
• Some enzymes need cofactors or coenzymes (metal ions or organic molecules).
• Coenzymes are bound tightly or covalently to the protein.
• This molecule combined with the enzyme protein is called a holoenzyme.
• The protein alone is called an apoenzyme or apoprotein.

Inorganic Ions as Cofactors

• Various inorganic ions act as cofactors for diverse enzymes.
• Examples include copper, iron, potassium, magnesium, manganese, molybdenum, nickel, and zinc.
• These ions facilitate a wide range of enzyme functions, including oxidation-reduction and catalysis.

Coenzymes as Transient Carriers

• Certain coenzymes function as transient carriers.
• They transport specific atoms or molecules during metabolic reactions.
• Examples include biotin, coenzyme A, flavin adenine dinucleotide, lipoate, NAD+, FAD, pyridoxal phosphate, and others.

Enzyme Classification

• Enzymes are categorized based on the reactions they catalyze.
• Groups include oxidoreductases, transferases, hydrolases, isomerases, lyases, and ligases.

How Enzymes Work

• Enzymes facilitate biochemical reactions that typically wouldn't occur or would proceed very slowly under typical bodily conditions.
• The location within the enzyme where a reaction takes place is called the active site.
• The molecule that binds to the active site of the enzyme is the substrate.
• The temporary complex formed between enzyme and substrate is the enzyme-substrate complex.
• The enzyme's purpose to speed up the rate of the reaction.
• The overall energy states of the reaction are not changed by the enzyme.

Substrate Binding Site/Active Site

• Enzymes have active sites complementary to their substrates.
• The lock-and-key model illustrates this initial fit.
• The induced fit model is an improved fit model, that better explains how the enzyme changes shape to accommodate the substrate with a more dynamic approach.
• The shape change aids in the reaction process.

Binding of a Substrate to an Enzyme

• The substrate's connection to the enzyme's active site is crucial.
• These sites have unique geometric shapes that adapt to the compound's molecular shape.

Understanding Catalysis

• Enzymes act as catalysts which speed up chemical reactions without being consumed during these processes.
• The catalyst does not affect the position of the reaction.
• Rate of chemical reaction is affected.

Energy in Biological Systems

• Free energy changes, often symbolized as G, are used to describe reactions in biological systems.
• A graph of energy versus reaction progress can be referred to as a reaction coordinate diagram.
• The initial and final states of the products are called ground states.
• The peak in energy is the transition state.
• The reactions are classified as endergonic or exergonic depending on whether energy is absorbed or released respectively.

Recap window – Chemical Energetic Reactions

• "Endergonic" and "exergonic" relate to energy changes in reactions.
• The terms endothermic and exothermic are solely energy changes related to heat.
• Reactions where energy is released may be called exergonic.
• Reactions where energy needs to be added to proceed are endergonic.

How Enzymes Work (Mechanism)

• For reactions to occur, there's an energy barrier.
• Enzymes help molecules overcome this barrier by decreasing the activation energy required.
• Enzyme-substrate complexes exist as intermediates in this process.
• Enzyme intermediates can lower the activation energy of the overall reaction.

Sucrose – Sugar Example

• The breakdown of sucrose (a sugar) with oxygen usually needs high energy.
• Enzymes speed up the reaction of sucrose reacting with oxygen.
• This reaction has a large negative G value, making sucrose chemically stable.
• The high activation energy is what keeps sucrose stable.

Catalytic Power and Specificity

• Enzymes significantly accelerate reactions.
• Enzymes readily distinguish between similar compounds.
• Urease is an example of an enzyme that hydrolyzes urea.

How can we explain it?

• Covalent Bonding: Chemical reactions often involve the rearrangement of covalent bonds amongst the enzymes' functional groups (amino acid side chains, metal ions, or coenzymes).
• Noncovalent Interactions: Weak noncovalent interactions between the enzyme and substrate are crucial for complex formation.

Binding Energy

• Binding energy in the enzyme-substrate complex stabilizes the interaction.
• Binding energy contributes to both catalytic specificity and efficiency.
• Weak interactions in the reaction's transition state are optimal.

Acid-Base Catalysis

• Acid-base catalysis involves proton transfer in biochemical reactions.
• Amino acid side chains in enzymes, such as those in the active site, can act as proton donors or acceptors.
• Such catalysis is vital for controlling the rate of many biological reactions.

Covalent Catalysis

• Covalent catalysis refers to the type of catalysis in which a transient covalent bond forms between the enzyme and substrate.
• Many reactions, or pathways, are aided by this method
• Covalent catalysis aids in the reaction. The activation energy and thereby the reaction is lower when using this method.

Metal Ion Catalysis

• Metals can participate in catalysis in several ways.
• Metals can help orient substrates.
• Metal ions can help stabilize reaction transition states.
• Metal-based enzymes often facilitate oxidation-reduction reactions.
• Almost one-third of known enzymes require metal ions.

Factors influencing Enzyme Activity

• Temperature and pH affect enzyme activity.
• The range of activity is usually narrow.

Enzyme Kinetics

• Enzyme kinetics study the rates of enzyme-catalyzed reactions.
• Enzyme kinetics describes the kinetics of enzymes.
• K_cat (turnover number) measures the rate of product formation for a fixed enzyme concentration.
• Km (Michaelis constant) measures the substrate concentration at half the maximal velocity.
• The maximum velocity (V_max) is the theoretical maximum rate of enzyme reaction.

Enzyme Inhibition

• Compounds that decrease or eliminate enzyme activity are called inhibitors.
• Inhibitors can decrease the rate of product formation or affect the enzyme's overall function.
• Two main categories of enzyme inhibition exist: reversible and irreversible.
• Many drugs and poisons employ enzyme inhibition.

Types of Enzyme Inhibitions

• Reversible Inhibition: These inhibitors bind to enzymes and dissociate.
• Various types of reversible inhibition exist, including competitive, uncompetitive, and mixed/noncompetitive inhibition.
• In this type of inhibition, the function of the enzyme may be repaired as the inhibitor is removed.
• Irreversible Inhibition: This type of inhibition permanently disrupts the enzyme.
• In these cases, the enzyme is unable to return to its original state or function.

Allosteric Regulation

• A ligand binds to a site other than the active site on the enzyme affecting its activity.
• This method activates or deactivates the enzyme function.
• The binding of effector molecules causes changes in the protein's conformation.
• Allosteric regulation is crucial in many cellular processes.

Irreversible Inhibition

• In this case, inhibitors bind to essential functional groups of enzymes, permanently disabling them.
• Mechanisms include covalent bonds, which often result in permanent inactivation.

Explore the critical roles of proteins and enzymes in biochemical processes. This quiz covers protein interactions, ligand binding, and the catalytic functions of enzymes. Test your understanding of how these molecular interactions influence biological reactions.