Enzymes and metabolism C1.1

• What is a catalyst?

  A catalyst is a substance that speeds up the rate of a chemical reaction without being consumed or permanently changed in the process.
• How do catalysts increase the rate of reaction?

  Catalysts lower the activation energy required for a reaction to occur, making the reaction happen faster, increasing the rate of reaction. The rate of reaction is the amount of product produced per unit time.
• What is an inorganic catalyst?

  An example of an inorganic catalyst is platinum- used to covert unburned hydrocarbons in exhaust gases to carbon dioxide and water in combustion engines.
• What do enzymes do?

  Enzymes are globular proteins composed of one or more polypeptides, biological catalysts- made by living cells to speed up biochemical reactions. They convert substrates into products. Enzymes allow essential biochemical reactions to occur efficiently under the mild conditions like body temperature and physiological ph:

  Digestion: Enzymes like amylase break down starch into simple sugars.

  Respiration: Enzymes help break down glucose to release energy in the form of ATP.

  DNA Replication: Enzymes like DNA polymerase assist in copying genetic material before cell division.
• What is metabolism?


  Metabolism is the complex network of interdependent and interacting chemical reactions that occurs in living organisms, to maintain life. These reactions provide energy for vital processes and synthesize or break down molecules.
• How are enzymes different to non-biological catalysts?

  Enzymes are different to non-biological catalysts in the sense that they are specific to one reaction or one specific group of reaction. This is due to the unique 3D shape of the enzyme's active site, which matches only one particular substrate.

  Lock and Key Model - The substrate fits into the enzyme's active site like a key in a lock.

  Induced Fit Model - The active site undergoes slight changes to fit the substrate more precisely, enhancing binding and catalysis.

  Because of enzymes specificity, organisms must make large numbers of different enzymes- a single prokaryote will make hundreds of different enzymes.

  Its specificity allows organisms to control metabolism, through driving a specific reaction to occur. Through creating more or less of a specific enzyme, an organism may control the reactions.
• What is catabolism?


  In catabolism, larger molecules are broken down into smaller ones- releasing energy. They are also hydrolysis reactions, so water is required.
• What are some examples of catabolism?

  Digestion of food (in the mouth, stomach and small intestine) is catabolic

  Cell respiration, in which glucose or lipids are oxidised to carbon dioxide and water, releasing energy, which is catabolic.

  Decomposition of complex carbon compounds is catabolic too.

  Glycogenolysis - deconstruction of glycogen to glucose in the body is catabolic.
• What is anabolism?


  In anabolism, macromolecules are produced from monomers, using energy from ATP. They are also condensation reactions, because water is a by-product.
• What are some examples of anabolism?

  Photosynthesis is an example of anabolism, because molecules ae combined to produce larger molecules, using energy from light.

  Protein synthesis (translation) through ribosomes is anabolic too.

  DNA synthesis (replication) is also anabolic.

  Synthesis of complex carbohydrates (starch, cellulose, glycogen) is anabolic.
• What are globular proteins and what are their functions?

  Globular proteins are a type of protein with a compact, spherical shape, formed by the folding of polypeptide chains. They have several key properties:

  Soluble in Water - Their hydrophilic (water-attracting) amino acid residues are on the outer surface, making them soluble in aqueous environments.

  Functional Proteins - Unlike fibrous proteins (which provide structural support), globular proteins are often involved in biological functions, such as enzymes, hormones, and transport proteins.

  Specific 3D Shape - Their structure is stabilized by hydrogen bonds and ionic bonds, giving them a precise shape necessary for their function.
• What is the active site?

  The active site is a region of polar amino acids on the surface of the enzyme, matching certian groupings (catalytic groups) on the substrate molecule, enabling the enzyme-substrate complex to form. Often the amino acids that form the active site are not next to one another in the polypeptides that make up the enzyme, brought together by polypeptide folding. As the enzyme-substrate complex forms, a slight change in shape is induced in the enzyme and substrate molecules (as per the induced-fit model) which raises the substrate molecule to the transition state in which it can react. The active site contains properties necessary for catalysis- binding to the substrate, holding onto it during the chemical reaction, and lowering the energy of the transition state.
• What is the lock-and-key model?

  Lock and Key Model - The substrate fits into the active site perfectly, like a key in a lock.
• What is the induced fit model?

  The Induced Fit Model is a refined explanation of enzyme-substrate interaction, improving upon the older Lock and Key Model. It suggests that:

  The enzyme's active site is flexible rather than a rigid shape.

  When the substrate binds, the active site undergoes a slight conformational change to fit the substrate more closely.

  This enhances binding and puts stress on the substrate's bonds, making the reaction occur more easily.

  Once the reaction is complete and the product is released, the enzyme returns to its original shape, ready for the next reaction.
• What is the enzymatic process of catalysis?

  1- Substrate binds to the active site (induced-fit binding), attracted due to structural and chemical specificity, forming an enzyme-substrate complex.

  2- While substrates are bound in the active site, bonds in the substrate are stressed or weakened, causing it to change into different chemical substances (the products)

  3- The products separate from the active site, leaving it vacant for substrates to bind again
• What is collision theory?

  Collision theory states that for a reaction to take place, reactant molecules must collide with sufficient energy and proper orientation.
• How are immobilised enzymes used in industry?

  Immobilised enzymes may be utilised industrially in cell-free preparations- for example in the preparation of lactose free milk. Enzymes are attactched to an insoluble material with the substrate moving over it, converting the lactose into galactose or glucose. This method is convenient as the enzymes can be reused.
• How does enzyme and substrate movement occur in the presence of immobilised enzymes?

  The enzyme is fixed (e.g., attached to a surface), so only the substrate moves and must collide with the active site. This allows for better control and reusability of enzymes For example: in the preparation of lactose free milk. Enzymes are attactched to an insoluble material with the substrate moving over it, converting the lactose into galactose or glucose..
• How does enzyme and substrate movement occur in the cytoplasm?

  Both enzymes and substrates move freely due to Brownian motion, leading to random collisions. For example: Glycolysis in the cytoplasm.
• How does enzyme and substrate movement occur in the presence of large substrates?

  The enzyme moves to the substrate, or the substrate may undergo conformational changes to fit into the active site. The reaction takes longer due to the size and complexity of the substrate. For example: DNA polymerase binding to a DNA strand.
• What is the formation of an enzyme-substrate complex dependent on?

  The molecular motion of both enzyme and substrate, causing random collisions between molecules. All metabolic reactions occur in aqueous solution, which enables the molecule's continual motion.

  The correct alignment and angle between substrate and enzyme affects the success of the collision

  The speed of movement, which is affected by the molecules size. Substrates are usually smaller than enzymes, so their movement is faster.
• What is denaturation?


  Denaturation is the structural alteration of an enzyme (or protein) that results in the loss of its biological function. This happens when the enzyme's tertiary (3D) structure is disrupted, destroying the active site shape so it can no longer bind to its substrate effectively.
• What are some factors that commonly cause enzymatic denaturation?

  High temperatures, pH changes, heavy metal ions, organic solvents, high salt concentration
• How does temperature affect enzymes?

  As temperature increases, so does the rate of reaction- due to more kinetic energy.

  Enzyme and substrate molecules move faster, increasing the chances of frequent collisions with the active site and the enzyme. Therefore the enzymatic activity also increases.

  However, when enzymes are heated above optimum, the chances of bonds breaking within the molecule increases, due to increased vibration between them. The structure changes irreversibly, and the enzyme is denatured. Some enzymes are specialised to withstand extreme temperatures- a thermophile can withstand extremely high temperatures before its enzymes denature.
• How does a change in pH affect enzymes?

  Enzymes have optimum pH at different ranges to one another, dependent on when their activity is highest.

  pH is actually a measure of hydrogen ions in solution, and the higher the concentration of hydrogen ions, the lower the ph.

  When the pH is not optimum for the enzyme, the hydrogen ions (or lack of them) will interfere with the bonds between the enzyme and the charge of amino acids in the active site, denaturing them. However, this denaturation is often reversable if the pH returns back to normal, and was never too extreme.
• How does a change in substrate concentration affect enzymes?

  Increasing substrate concentration increases the rate of reaction, because the chances of molecular (successful) collisions between active site of the enzyme and substrate have increased.

  At the optimum concentration of substrate molecules, all active sites are full and working at maximum efficiency.

  Any increase in concentration beyond the optimum will have no added effect as there are no extra active sites to be used - a greater and greater proportion of substrate-active site collisions are blocked.
• What is absolute specificity?

  Absolute Specificity - Enzymes that catalyse only one specific reaction for one particular substrate. Example: Urease only breaks down urea.
• What is group specificity?

  Group Specificity - Enzymes that act on a group of related molecules with similar structures. Example: Hexokinase breaks down different six-carbon sugars like glucose and fructose.
• What is linkage specificity?

  Linkage Specificity - Enzymes that target a specific type of bond rather than a specific substrate. Example: Proteases break down peptide bonds in proteins, regardless of the specific amino acids involved.
• What is stereochemical specificity?

  Stereochemical Specificity - Enzymes that distinguish between different stereoisomers (mirror-image molecules). Example: Lactase only breaks down lactose, which contains the beta-glycosidic bond, but not similar sugars like maltose.
• What is the rate of reaction?

  The speed at which substrates are converted to products, with units of change in the amount of chemical/time. This may be found through:

  Allow the reaction to occur for a fixed amount of time, then measure the amount of substrate used up, or product formed

  Begin with a known amount of substrate, then allow the reaction to occur until all of the substrate has been converted to products. Measure the time that this took.

  In both, the quantity of product/substrate is divided by time.
• How would you investigate catalase activity?

  Enzyme: Catalase

  Reaction: Hydrogen peroxide → Water + Oxygen

  Method: Place catalase (e.g., potato extract) in a test tube with hydrogen peroxide. Collect the oxygen gas produced using a gas syringe or an inverted water-filled measuring cylinder. Measure the volume of oxygen over time to determine the rate.
• How would you investigate amylase activity?

  Enzyme: Amylase

  Reaction: Starch → Maltose

  Method: Mix starch solution with amylase and take samples at intervals. Add iodine solution to detect starch presence (blue-black indicates starch, yellow/brown means starch has broken down). The faster the colour disappears, the higher the enzyme activity.
• How would you investigate protease activity

  Enzyme: Pepsin (protease)

  Reaction: Protein → Amino acids

  Method: Place protein (e.g., egg white) in a test tube with pepsin and buffer solution. Use a pH probe to measure changes in acidity (as amino acids lower the pH). A faster decrease in pH indicates a higher enzyme activity.
• What is activation energy?

  Activation energy is the minimum amount of energy required for a chemical reaction to occur (to reach the transition state)
• How do enzymes lower activation energy?

  In any reaction, energy is required to reach a transition state before completing a reaction. The transition state is an intermediate state before being converted into products (bonds need to be broken or weakened). Activation energy is used to transfer a molecule into its transition state. An enzyme lowers the activation energy by the substrate binding to the active site. This binding lowers the overall energy level of the transition state, meaning less energy is needed for the reaction to occur. After the products have been formed, energy is released. The net amount of energy produced is not changed, but the activation energy is still reduced, so the rate of reaction is far greater.