BIOMOL Midterms 1 PDF

0762 BIOMOLECULES 1 Bachelor of Science in Medical Biology Midterm Transes | AY 2024-2025 LEC 1: Enzymes INTRODUCTION...

0762 BIOMOLECULES 1 Bachelor of Science in Medical Biology Midterm Transes | AY 2024-2025 LEC 1: Enzymes INTRODUCTION ➔ MACROMOLECULES CONSTRUCTION - Enzymes PRINCIPLES facilitate biosynthesis, enabling the construction of larger biomolecules from smaller precursor molecules. This is essential for growth, repair, and maintaining cell structure. ➔ CHEMICAL ENERGY USAGE - Enzymes are involved in metabolic pathways which conserve and transform chemical energy. CLASSIFICATION CHARACTERISTICS ACCORDING TO COMPONENT ACTIVE SITE - Typically a pocket or groove found on an enzyme’s surface, uniquely shaped to accommodate its substrate. Formed by the enzyme's three-dimensional structure which consists of various amino acid residues that interact with the substrate, this facilitates conversion of substrates into products through lowering the activation energy. SUBSTRATES - Specific molecules which enzymes act upon. The binding of this to the active site leads to an enzyme-substrate complex. Nature: Most enzymes are globular proteins, with a few COENZYMES - Specific type of organic cofactor derived from RNA-based enzymes. vitamins that help transfer chemical groups between Function: Each reaction in the cell requires a specific molecules during enzymatic reactions. enzyme, thus, thousands of different enzymes exist within human cells. Denaturation: Enzymes can denature due to changes in temperature or pH, which can significantly impact their activity. IMPORTANCE ➔ DIGESTION - Enzymes break down complex food molecules into smaller, absorbable components. This enzymatic process allows nutrients to be absorbed efficiently by the body. Lehninger's Principles of Biochemistry JRPD - DGTT 0762 BIOMOLECULES 2 Bachelor of Science in Medical Biology Midterm Transes | AY 2024-2025 ACCORDING TO LOCATION MECHANISM OF ENZYME ACTION ATTACHMENT COFACTORS - Non-protein molecules or ions that assist enzymes in catalyzing reactions. They can be either organic or ➔ LOCK AND KEY MODEL - A model of enzyme action that inorganic and are essential for the enzyme's activity. suggests the active site has a fixed, rigid shape, allowing only specific substrates to bind, much like a key fits into a specific lock. ➔ INDUCED FIT MODEL - A model proposing that the active site is flexible, adjusting its shape to accommodate the substrate upon binding, allowing for a more precise CONJUGATED ENZYMES - Composed of an apoenzyme– the fit and enhancing the enzyme’s catalytic activity. protein part, and a cofactor. The apoenzyme alone cannot catalyze reactions, however, when combined with its cofactor, it forms a functional holoenzyme that is biochemically active. SPECIFICITY ACCORDING TO REACTION 1. ABSOLUTE SPECIFICITY - Catalyzes only one specific substrate. Most restrictive of all specificity. 2. GROUP SPECIFICITY - Acts on similar substrates with specific functional groups. 3. LINKAGE SPECIFICITY - Acts on particular types of chemical bonds regardless of molecular structure. Most general of all enzyme specificity. 4. STEREOCHEMICAL SPECIFICITY - Distinguishes between stereoisomers. Chirality is inherent in active site as amino acids are chiral compounds. INHIBITION AND REGULATION INHIBITORS A. COMPETITIVE INHIBITION - An inhibitor resembles and competes with the substrate for binding at the active site. This process is reversible by increasing substrate concentration. Lehninger's Principles of Biochemistry JRPD - DGTT 0762 BIOMOLECULES 3 Bachelor of Science in Medical Biology Midterm Transes | AY 2024-2025 B. NONCOMPETITIVE INHIBITION - An inhibitor binds to an allosteric site, altering the enzyme’s tertiary structure and active site, disabling substrate binding. This type of inhibition is reversible but depends on reducing inhibitor concentration. PROTEASES PROTEOLYTIC ENZYMES - Enzymes that catalyze the breaking of peptide bonds in proteins. To prevent them from damaging the tissues that produce them, they are typically produced in an inactive form. ZYMOGENS - The inactive precursors of proteolytic enzymes. They are activated only when needed, ensuring that these enzymes are “turned on” at the right time and place. C. IRREVERSIBLE INHIBITION - An inhibitor permanently deactivates an enzyme through binding with its active site using strong covalent bonds. Addition of excess substrate doesn’t reverse this process. COVALENT MODIFICATION COVALENT MODIFICATIONS - Represent the third mechanism of enzyme activity regulation, involving the alteration of enzyme activity through covalent changes to the enzyme's structure. This process typically entails the addition REGULATORS or removal of a functional group from the enzyme. The most common type of covalent modification is the addition or ALLOSTERIC ENZYMES - Exhibit a quaternary structure, removal of a phosphate group, which is frequently derived consisting of two or more protein chains. These enzymes from an ATP molecule. possess multiple binding sites, including an active site for the substrate and a regulatory site for a regulator molecule. The Phosphate Addition: Phosphorylation is catalyzed by a active and regulatory binding sites are distinct in both shape Kinase enzyme and location. Binding of a regulator molecule to its regulatory Phosphate Removal: Dephosphorylation is catalyzed by site causes changes in three-dimensional structure. a Phosphatase enzyme. Positive Regulator: Up-regulates enzyme activity by enhancing the active site, making it more capable of accepting substrates. Negative Regulator: Non-competitive inhibitor that down-regulates enzyme activity by compromising the active site, thereby reducing its ability to accept substrates. QUESTIONS FEEDBACK CONTROL ❖ Why is an enzyme active site important to the function of FEEDBACK CONTROL - A regulatory process where the the enzyme? activation or inhibition of an earlier reaction step in a ❖ Why is the enzyme regulatory binding site important for sequence is influenced by the product of that sequence. This controlling the activity of the enzyme? mechanism is one of the ways allosteric enzymes are ❖ Why are coenzymes important to the function of some regulated. In most biochemical processes, reactions occur in enzymes? multiple steps, with each step catalyzed by a different enzyme, where the product of one step serves as the HEALTHCARE APPLICATIONS substrate for the subsequent enzyme. PRESCRIPTION DRUG INHIBITOR 1. ACE INHIBITORS - Lower blood pressure by inhibiting the Angiotensin-Converting Enzyme. 2. SULFA DRUGS - Antibiotics that function as competitive inhibitors of bacterial enzymes responsible for converting PABA to folic acid. Folic acid deficiency hinders bacterial growth, ultimately leading to bacterial death. Lehninger's Principles of Biochemistry JRPD - DGTT 0762 BIOMOLECULES 4 Bachelor of Science in Medical Biology Midterm Transes | AY 2024-2025 3. PENICILLINS - β-lactam antibiotics that inhibit the transpeptidase enzyme, which is crucial for strengthening the bacterial cell wall by forming peptide cross-links between polysaccharide strands. When transpeptidase is inhibited by penicillin, the bacterial cell wall weakens, ultimately leading to bacterial death. DIAGNOSIS AND TREATMENT 1. LACTATE DEHYDROGENASE - Typically found within cells and not in high levels in the bloodstream. However, elevated levels of LDH in the blood can indicate a myocardial infarction or heart attack. 2. TISSUE PLASMINOGEN ACTIVATOR - A medication D. ENZYME CONCENTRATION - Enzyme concentration that activates the enzyme plasminogen, helping to directly affects enzyme activity, with increased dissolve blood clots. It is commonly used for treating concentrations generally leading to higher reaction rates myocardial infarction. until a saturation point is reached, beyond which additional enzymes cannot further enhance the rate. 3. BLOOD UREA NITROGEN - The enzyme urease converts urea into ammonia, which can be easily measured and serves as an indicator of urea levels. BUN tests are commonly used to assess kidney function, as elevated urea levels in the blood can indicate potential kidney malfunction. QUESTIONS ❖ What is the function of an enzyme in a chemical reaction? FACTORS AFFECTING ENZYME ACTION ❖ What happens to the enzymes when the body temperature rises from 37°C to 42°C? A. TEMPERATURE - Increased temperature generally ❖ If an enzyme has broken down and is non-functional, increases reaction rates up to an optimal point, usually what would happen to the chemical reaction normally around 37°C for human enzymes. Beyond this point, facilitated by the enzyme? Explain. enzymes may denature. ADDITIONAL ENZYME VARIANTS ➔ ALDOLASE - An enzyme which plays a crucial role in converting glucose into energy and is predominantly found in high levels in muscle tissue throughout the body. When muscle damage occurs, aldolase levels in the blood tend to rise. Consequently, an aldolase blood test may be ordered to diagnose and monitor specific conditions related to skeletal muscle. In addition, it specifically catalyzes the reversible reaction converting fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. B. POWER OF HYDROGEN - Each enzyme has an optimal pH range for stability and efficiency. pH regulation is essential for effective enzyme function in biological systems. ➔ ISOENZYMES - Catalyze the same reaction in different tissues throughout the body. Specifically, the LDH1 isoenzyme is predominantly found in heart muscle, while the LDH5 form is more prevalent in skeletal muscle and C. SUBSTRATE CONCENTRATION - Enzyme activity the liver. Because isoenzymes are specific to certain increases with substrate concentration until reaching a tissues, they can be used as markers to identify damaged saturation point where all active sites are occupied, or diseased organs or tissues. resulting in a maximum reaction rate (Vmax). The Michaelis-Menten constant (Km) indicates the substrate concentration needed to achieve half of Vmax, reflecting the enzyme's affinity for the substrate. Lehninger's Principles of Biochemistry JRPD - DGTT