Enzyme Notes - Group 1 & 2 PDF

Group 1: Enzyme Structure and Function Group 1: Samantha, Charbelly, Liya ​ Syllabus Statements: ○​ "Enzymes are globular proteins that work as catalysts, speeding up chemical reactions." ○​ "The active site of an enzyme binds specifically to its substrate(s)."...

Group 1: Enzyme Structure and Function Group 1: Samantha, Charbelly, Liya ​ Syllabus Statements: ○​ "Enzymes are globular proteins that work as catalysts, speeding up chemical reactions." ○​ "The active site of an enzyme binds specifically to its substrate(s)." ○​ "The induced-fit model explains enzyme activity by showing how the enzyme and substrate undergo conformational changes upon binding." ○​ "Denaturation of proteins, including enzymes, is caused by factors such as heat and deviations in pH, leading to a loss of function." What are enzymes: Enzymes are proteins that boost the chemical processes in organisms that are alive. Enzymes can be found in living organisms as well as people because they are naturally produced by the body. Enzyme structure: Enzymes are structured of amino acids linked together in one or more polypeptide chains. They tend to form a globular shape during the tertiary structure to help them easily bind to substrates. Enzyme function: Enzymes work has helpers that make reactions happen faster and more efficiently. Each enzyme has a specific job and works on a particular substance( called a substrate). The active site is like a keyhole where the substrate fits in and the enzymes helps break it down or build something new. For example, enzymes help digest food and make energy. Diagram (induced-fit model): The induced fit model helps explain how substrates bind to the active site of an enzyme which causes a change in the shape of the enzyme to either enhance or inhibit its ability. The active site on an enzyme is where the substrate is bound to the enzyme as well as having the catalytic bonds that will be able to form or break bonds in the substrate. The substrate will go through changes once it has bonded to the enzyme. Enzymes have the ability known as substrate specificity which refers to how enzymes can act on one specific substrate to catalyze a reaction. The image above illustrates the substrate entering the active site of an enzyme to which it is bonded. The enzyme then slightly molds to the substrate for the ideal fit for catalysis. The catalytic elements of the enzyme’s active site react with the substrate forming products which are then released from the enzyme. Graph: Extremely high temperatures lead enzymes to lose their shape (denature) to the point where they stop working. Denaturation  -​ Denaturation occurs when external factors like heat or pH disrupt the enzyme’s structures -​ This process affects the active site as the enzyme is no longer in its natural form, preventing substrate binding and halting the reaction -​ Denaturated enzymes cannot regain their original structure under normal conditions Globular protein -​ Enzymes are mainly globular proteins -​ Globular proteins are proteins that have been folded into a rounded shape (tertiary structure) Group 2: Enzyme Activity and Catalysis Group 2: Marco, Karen, Ayesha ​ Syllabus Statements: ○​ "Enzymes lower the activation energy of biochemical reactions." -​ The bare minimum of energy needed to start a chemical reaction is known as activation energy. It stands for the energy barrier that molecules of the reactant must cross in order to transform into products. -​ Reactants stay in a stable condition and don't respond if there isn't enough activation energy. Because they offer a different, lower-activation-energy reaction route, enzymes facilitate the conversion of reactants into products. -​ They reduce the energy needed for reactants to come together and react. -​ The activation energy is the amount of energy required for reactant molecules to collide during a reaction in order to break bonds and create new ones. By lowering this activation energy, catalysts facilitate the reaction between reactants. This is accomplished by offering a different, lower-energy-demanding response route. ○​ "The rate of enzyme activity depends on the frequency of collisions between enzyme and substrate molecules." -​ The molecules of the substrate must come into contact with the active site of the enzyme for an enzyme-catalyzed reaction to take place. The development of the enzyme-substrate complex, which is necessary for catalysis, is made possible by these collisions. -​ The frequency and efficiency of these collisions determine the rate of enzyme activity. -​ A slower reaction rate results from the low chance of an enzyme-substrate collision at low substrate concentrations. -​ Up to a certain degree, the collision frequency grows with increasing substrate concentration, and the reaction rate climbs correspondingly. -​ The likelihood of collisions with substrate molecules increases as the concentration of the enzyme increases because there are more active sites accessible. -​ However, if all of the active sites are already occupied, the impact of adding more enzymes decreases at very high substrate concentrations.  ○​ "At high substrate concentrations, enzyme activity reaches a maximum as the enzymes become saturated." ○​ Enzyme activity essentially increases as the substrate reaction rises as well. This is specifically because of the recurring collisions between enzymes and substrate molecules. This will enable the reaction rate to reach its maximum capacity. The reason for that is that enzyme activity is now occupied and they can work at full capacity too. ○​ "Enzyme activity is affected by factors such as substrate concentration, temperature, and pH." ​ Graph: ○​ Plot enzyme activity vs. substrate concentration to demonstrate the saturation. -​ In order for substrates to perform a reaction, enzymes must bind to a certain number of active sites. Adding extra substrate speeds up the process since numerous active sites are free at low substrate concentrations. -​ The enzyme is operating at its maximum speed after all of its active sites are occupied. Since there are no more free active sites available for extra substrate molecules, adding more substrate won't speed up the process. ○​ Plot how temperature or pH affects enzyme activity. ​ - An enzyme's optimal pH or temperature is the precise setting at which it functions best, resulting in the maximum activity (reaction rate). The structure of the enzyme, particularly the active site, is now ideal for catalyzing the process. ○​ Key Terms: ​ Catalyst A catalyst is a substance that speeds up the rate of a chemical reaction without being consumed by the process. You lower the activation energy making it easier for the reactants to form a product. ​ Collision theory Collision theory is the process in which reacting particles must collide with one another. It can only happen when there is enough energy to overcome the activation energy barrier. Factors such as temperature and concentration play a major role in the frequency and collisions. ​ Molecular motion Molecular motion is the movement of a substance that alters from vibrational, translational, and rotational. As the increase of temperature rises causes more collisions of energy speeding up the reactions. ​ Substrate concentration  Substrate concentration is the molecule in which enzymes react. The rate at which when an enzyme is catalyzed increases the rate of substrate concentration. Beyond that point the enzyme becomes saturated therefore no additional substrate it won’t increase the rate of reaction. ​ Saturation Saturation occurs when all enzyme's active sites are used by the substrate molecules. The reaction rate will reach its maximum velocity to enable the enzyme to work at its fullest capacity. More subtle will increase the rate of reaction unless more of the enzymes are added too. Group 3: Enzyme Roles in Metabolism Group 3:, Zara, Mohamed, Sky, Luyanda ​ Syllabus Statements: ○​ "Metabolism is the web of all the enzyme-catalyzed reactions in a cell or organism." ○​ "Anabolism involves the synthesis of complex molecules from simpler molecules, requiring energy (e.g., condensation reactions)." ○​ "Catabolism involves the breakdown of complex molecules into simpler molecules, releasing energy (e.g., hydrolysis reactions)." ○​ "Enzymes play a critical role in both anabolic and catabolic pathways, such as glycolysis or photosynthesis." Diagram: Simple metabolic pathway showing products and enzymes: Illustrate condensation and hydrolysis reactions (e.g., protein synthesis or glycogen breakdown). Condensation The synthase enzymes catalyze the smaller molecules into bigger molecules. Then during the reaction water is released. These reactions create more complex molecules like proteins and nucleic acids from simpler building blocks. Hydrolysis Hydrolase enzymes catalyze the breakdown of the bigger molecules into smaller ones by adding water. This reaction breaks down starches or glycogen into smaller building blocks Graph: Key Terms: Metabolism: the chemical reactions in the body's cells that change fats (lipids) into energy. Anabolism: a biochemical process in metabolism where simple molecules combine to generate complex molecules Catabolism: the set of metabolic processes that break down large molecules Condensation: a chemical reaction during which monomers (small molecules) join to form polymers (large molecules or macromolecules), releasing a water molecule. Hydrolysis: any chemical reaction in which a molecule of water breaks one or more chemical bonds. In this unit: it refers to the opposite of condensation reaction. Group 4: Protein Structure and Environmental Factors Group 4: Ivy, Khushi, Luan ​ Syllabus Statements: ○​ "Proteins are made up of amino acids linked by peptide bonds, forming primary, secondary, tertiary, and quaternary structures." ○​ "The shape of a protein is critical to its function and is determined by the interactions between amino acids." ○​ "Environmental factors such as temperature and pH can denature proteins, disrupting their structure and function." ○​ "Enzymes function optimally at specific pH and temperature conditions." Protein Structure and Environmental Factors ​ Amino acids are the building blocks (monomers) of protein. There are 20 types of amino acids. Amino acids are indirectly encoded by our genes through the process of gene expression. ​ Proteins is a polymer that is made of monomers called amino acids. These amino acids join together through a peptide bond that occurs through a condensation reaction. ​ A peptide bond is a covalent bond that is formed between the amine group of one amino acid and the carboxyl group of another amino acid. ​ Multiple amino acids joined together through the peptide bonds are called a peptide chain. This is the Primary structure of a protein. ​ The function of its protein is dependent on its shape, structure and its ability to interact with other molecules. If the protein does not have the correct shape or structure it will not be able to function. ​ The structure and shape of a protein is determined by its amino acid sequence. ​ Factors that can cause denaturation include temperature, ph, acid, high salt concentration, alcohol, etc. ​ Extreme changes in ph can cause denaturation. High temperatures can break weak hydrogen bonds causing denaturation. Low temperatures can also affect the structure of the protein ​ The optimum ph for most enzymes is 7 which is a neutral ph. The optimum temperature for most enzymes is 37 degrees celsius (96.9 degrees Fahrenheit). Key Terms and Definitions: ​ Denaturation - The process of unfolding or breaking of a protein. It is a loss or disruption of the secondary and tertiary structure.  ​ Optimum pH - it is the ph at which an enzyme or a protein can function best. ​ Optimum temperature - the temperature at which an enzyme or any process is highly effective. ​ Enzyme stability - Proteins Structure: 1.Primary Structure: The Primary protein structure is represented by a linear sequence of amino acids that are joined together by peptide bonds, each of them are linked that form a long chain of amino acids. Significance: This specific sequence of amino acids is what determines the higher levels of protein structure and its function. 2.Secondary Structure: In this structure, the polypeptide chains start to fold into regular structures like alpha helices and beta sheets. These structures are formed by hydrogen bonds between the backbone atoms in the polypeptide chain. Alpha Helices: Its a right-handed coil structure stabilized by hydrogen bonds. Beta sheets: It's a sheet-like structure where they stand side by side being connected by the hydrogen bonds. Significance: The secondary structure is responsible for contributing the overall shape and stability of the protein. 3.Tertiary Structure: The third structure is a third-dimensional folding of a single polyptide chain that is driven by interactions between the side chains( that are the R groups) of the amino acids. Types of interactions: ​ Hydrophobic Interactions: Nonpolar side chains that are clustered together away from water. ​ Ionic Bonds: Are Positive and Negative side chains in Between. ​ Hydrogen Bonds: Between polar side chains. ​ Disulfide Bridges: Are covalent bonds that are between sulfur atoms in cysteine residues. Significance: The third structure's function is to create a unique shape that is necessary for the protein's biological activity. 4.Quaternary Structure: This fourth structure arises when two or more polypeptide chains(subunits) come together to form a functional protein complex. Signifcance: The arrangement of these subunits affects the protein its stability and function.