Describe what the two types of metabolic action are
o Anabolic: Build complex molecules, are biosynthetic (e.g. photosynthesis)
o Catabolic: Break down complex molecules, are degradative (e.g. cellular respiration)
Define what a catalyst and an enzyme is
- Catalyst: a substance that speeds up a reaction without being used up itself
- Enzyme: a biological catalyst that speeds up biochemical processes but they remain unchanged at the end of the process
Describe enzyme structure
- Enzymes are globular proteins so have very specific 3-D shape
- Active site- cleft or indentation found on the surface of the enzyme made up from only a few amino acids within the enzyme structure
- The remaining amino acids are involved in maintaining the tertiary structure and thus tertiary structure of the active site
- If the active site of an enzyme changes (e.g. due to temperature or Ph.) the enzyme will not work
What are intracellular reactions?
- Enzymes have an essential role in both the structure and function of cells, the synthesis of polymers from monomers uses enzymes.
- Enzymes that act within cells are called intracellular enzymes
- For example, Hydrogen Peroxide is a toxic product of many metabolic pathways and the enzyme catalase ensures HO is broken down to oxygen and water quickly to prevent its accumulation
What are extracellular reactions
- All the reactions happening within cells need substrates (raw materials) to make products needed by the organism
- Nutrients needed as substrates are often polymers so need to be broken down before entering the cell to get through the cell surface membrane
- Enzymes are released from cells to break these nutrients down into monomers in the process of digestion.
- These enzymes are extracellular enzymes as they work outside the cell that made them and in some organisms, they work outside the body (e.g. fungi)
- Single-celled organises (e.g. yeast and bacteria) release enzymes into their immediate environment to digest the large molecules they want to ingest
- Many multicellular enzymes eat food to gain nutrients, although in the digestive system these are broken down into smaller molecules to be absorbed into the bloodstream
Name two examples of extracellular enzymes
• Digestion of starch: Two steps with two different enzymes
1. Starch polymers partially broken down into maltose (disaccharide) by amylase. Amylase is produced by the salivary glands and the pancreas and is released in saliva into the mouth and in pancreatic juice into the small intestine
2. Maltose is then broken down into glucose (monosaccharide) by maltose which is present in the small intestine.
• Digestion of proteins:
o Trypsin is a protease, a type of enzyme that catalyses the digestion of proteins into peptides which can be broken down further into amino acids.
o Trypsin is produced in the pancreas and released with the pancreatic juice into the small intestine.
Describe what lock and key hypothesis is
- An area within the tertiary structure of an enzyme is complimentary to the shape of a specific substrate molecule (active site)
- In the same way, a specific key fit into the right specific lock
- When the substrate is bound to the active site an enzyme-substrate complex is formed. The substrate/s react and the product/s are released, leaving the enzyme unchanged and able to take part in later reactions.
- The R-groups within the active site of the enzyme will also interact with the substrate, forming temporary bonds. These put strains on the bonds within the substrate, which also helps the reaction along.
Describe induced fit hypothesis
- Most recently, evidence from research suggests the active site of the enzyme changes slightly as the substrate enters.
- The initial interaction between the enzyme and substrate is relatively weak, but these weak interactions rapidly induce changes in the enzyme’s tertiary structure.
- This strengthens the binding, putting strain on the substrate molecule.
- This can weaken a bond or bonds in the substrate therefore lowering the activation energy for the reaction
What is activation energy
- Chemical reactions require energy to kick start them. This is Ea.
- The activation energy increases the KE of the molecule so they are more likely to collide successfully and react
- Heating reactants isn’t possible in a living cell because the proteins would denature and lipids would melt.
- Enzymes work by lowering the activation energy
How does temperature affect enzyme activity?
• Increasing the temperature of a reaction environment increases the KE of particles.
• In enzyme-controlled reactions an increase in temperature will result in more frequent collisions between the substrate and enzyme which would lead to an increase in the rate of reaction.
• The temperature coefficient (Q10) of a reaction is a measure of how much the rate of reaction increases with a 10 degree increase in temp. For enzyme-controlled reactions this is usually 2 (doubles with 10-degree increase)
• As enzymes are proteins, temperature can affect their structure.
o At higher temperatures, the bonds holding the protein together vibrate more and as temperature increases the vibrations increase until the bonds strain and break
o The breaking of these bonds leads to a change in the precise tertiary structure meaning the specific shape of the active site is adjusted
o The enzyme is denatured
How does pH affect enzyme activity?
- Hydrogen bonds and ionic bonds between amino-acid R groups hold proteins in their precise tertiary structure.
- These bonds result from interactions between the polar and charged R-groups present on the amino acids forming the primary structure.
- A change in pH refers to a change in the hydrogen ion conc.
- The active site will only be right at the correct H ion conc (optimum pH)
- When the pH changes from the optimum it alters the shape of the active site so it is no longer complementary to the substrate.
- However, if the pH returns to optimum the active site will resume it’s normal shape and catalyse the reaction again (renaturation)
- When the pH changes more significantly the active site will permanently alter (denaturation)
- The more H ions present (low pH), the less R groups can interact with each other. This leads to bonds breaking and the shape of the enzyme changing. The reverse is true when fewer H ions (high pH) are present.
How does substrate and enzyme conc affect enzyme activity?
- When the conc of a substrate is increased the number of substrate molecules, atoms or ions in a particular area or volume increases.
- This increased number of substrate particles leads to a higher collision rate with the active site of enzymes and the formation of more enzyme-substrate complexes.
- The rate of reaction therefore increases
- This is also true when the conc of enzyme increases as it will increase the number of available active sites in a particular area or volume leading to the formation of enzyme-substrate complexes at a faster rate
- The rate of reaction increases to its maximum (Vmax). At this point, all the active sites are occupied by substrate particles, so no more enzyme-substrate complexes can be formed
- If the enzyme conc is increased then the reaction rate can rise to a higher Vmax. However, this is also limited as the rate will increase until the new Vmax is reached.
Describe a practical investigation into the effects of different factors on enzyme activity
- Catalase is an enzyme present in plant and animal tissue, making it a good choice for investigations because its readily available. It catalyses the breakdown of HO into H2O and O2.
- The volume of oxygen gas collected in a set length of time can be used as a measure of rate of reaction.
- You can use the equipment in the diagram to determine the effect of temp on enzymes.
- Liver tissue was put into HO solution and the vol of O2 released every 5 seconds was measured.
- In the second experiment the liver was boiled for 5 minutes before being placed in the HO solution
Describe how you would do a serial dilution
- A serial dilution is a repeated, stepwise dilution of a stock solution of known conc.
- It’s usually done by factors of 10, to produce a range of concentrations.
- Can be used for the effect of different concentrations of an enzyme or substrate in a reaction, and in determining the numbers of microorganisms in a culture.
What are competitive enzyme inhibitors?
• Inhibitors in similar shape to substrate- competes to occupy active site
• Inhibitor molecules block the active site and prevent the substrate from entering, this slows the rate of reaction.
• The extent of the effect depends on the relative concentration of the enzyme, substrate and inhibitor.
• Doesn’t affect the Vmax of the enzyme it inhibits.
• Statins are competitive inhibitors of an enzyme used in the synthesis of cholesterol.
o These are regularly prescribed to help people reduce the blood cholesterol concentration as high blood cholesterol can lead to heart disease
• Most competitive inhibitors work reversibly.
• However, some are irreversible (e.g. aspirin)
o Aspirin irreversibly inhibits the active site of COX enzymes, preventing the synthesis of prostaglandins and thromboxane, the chemicals responsible for producing pain and fever.
What are non-competitive enzyme inhibitors
• Bind to the enzyme at an allosteric site ( away from active site) causing the tertiary structure of the enzyme molecule to change shape so substrate can no longer bind to the complementary shape of the active site
• Increasing the conc of the enzyme or substrate wont overcome the effect of the non-competitive inhibitor but increasing the conc of the inhibitor will the decrease the rate of reaction further as more active sites become inhibited
• Many non-competitive inhibitors act irreversibly.
o Organophosphates used as insecticides and herbicides irreversibly inhibit the enzyme acetyl cholinesterase, an enzyme necessary for nerve impulse transmission. This can lead to muscle cramps, paralysis and even death if ignored.
o Proton pump inhibitors (PPIs) are used to treat long term indigestion. They irreversibly block an enzyme responsible for secreting hydrogen ions into the stomach. This makes PPIs very effective in reducing the production of excess acid which, if left untreated, can lead to formation of stomach ulcers.
• They often stop enzyme-controlled reactions and their effects are not reduced by increasing the substrate concentration.
What is end product inhibition
• Term used for enzyme inhibition that occurs when the product of a reaction acts as an inhibitor to the enzyme that produces it.
• This acts as negative feedback control mechanism for the reaction so excess products are not made and resources aren’t wasted (an example of non-competitive inhibition)
• Respiration is a metabolic pathway resulting in the production of ATP.
o Glucose is broken down in a set of steps.
o The first step: addition of two phosphate groups to the glucose. The addition of the second phosphate group, which results in the initial breakdown of the glucose molecule, is catalysed by phosphofructokinase (PFK)
o PFK is competitively inhibited by ATP. ATP therefore regulates its own production.
o When levels of ATP are high, more ATP binds to the allosteric site on PFK and less glucose is broken down and ATP is not produced at same rate (vice versa).
What are cofactors?
- Cofactors are molecules that increase the rate of reaction or are required for enzyme.
- They aren’t proteins, they just help proteins (enzymes) but can help non-enzyme proteins too
- Inorganic cofactors are obtained via diet (e.g. amylase catalyses the breakdown of start and contains a chloride ion that is necessary for the formation of a correctly shaped active site
- Cofactors, by definition, are non-protein helper components that may transfer atoms or groups from one reaction to another in a multistep pathway or may actually form part of an active site. These are usually inorganic minerals.
What are coenzymes?
- If the cofactor is an organic molecule then its classed as a coenzyme
- For example vitamin B3 is used to synthesise NAD (nicotinamide adenine dinucleotide), a coenzyme responsible for the transfer of hydrogen atoms between molecules involved in respiration
- Another example is vitamin B5, which is used to make coenzyme A. Coenzyme A is essential in the breakdown of fatty acids and carbohydrates in respiration.
What are prosthetic groups?
- Are cofactors that are tightly bound and form a permanent feature of the protein.
- Instead of, like other cofactors, being loosely or temporarily bound to the enzyme protein in-order-to activate them.
- For example, zinc ions form an important part of the structure of carbonic anhydrase, an enzyme necessary for the metabolism of carbon dioxide.
