Chapter 2.4-Enzymes Flashcards
What is a catalyst?
- chemical that speeds up the rate of of a reaction and remains unchanged and reusable at the end of the reaction
- small amount of catalyst can catalyse the conversion of a large number of substrate molecules into product molecules
What is a biological catalyst?
enzyme that speeds up metabolic reactions
What does metabolic/metabolism mean?
the chemical reactions that take place inside living cells or organisms
What is meant by the turnover number?
number of reactions that an enzyme molecule can catalyse per second
Why are enzymes so remarkable?
- enzymes speed up metabolic reactions by up to 10^12 times at lower temperature, neutral pH and at normal pressures
- more specific than chemical catalysts. Don’t produce unwanted by-products and rarely make mistakes
- cells are able to regulate their production and activity to fit the needs of the cell or organism at the time
What does intracellular mean?
inside the cell
What does extracellular mean?
outside the cell
What is a substrate?
molecule that is altered by an enzyme-catalysed reaction
What is a product?
molecule produced from substrate molecules, by an enzyme-catalysed reaction
What is a metabolic pathway which use intracellular enzymes?
series of consecutive reactions, every step catalysed by a specific enzyme that produces a specific product
What are metabolites?
the reactants, intermediates and products
What are catabolic pathways?
metabolites are broken down to smaller molecules and release energy
What are anabolic pathways?
energy is used to synthesise larger molecules from smaller ones
What are two examples of complex metabolic pathways
respiration and photosynthesis
How do extracellular enzymes work?
- enzymes are secreted from cells where they are made and act on their substrates, extracellularly.
- very important in digestion before uptake
What is an example of how extracellular enzymes work in Fungi?
-Fungi, such as the bread mould Mucor, release hydrolytic enzymes from their thread like hyphae. The enzymes digest carbohydrates, proteins and lipids in the bread, and the products of digestion-glucose, amino acids, glycerol and fatty acids, are absorbed into the fungal hyphae for use in respiration and growth
What is catalase and how is it an example of an intracellular enzyme?
- found in nearly all living organisms that are exposed to oxygen.
- very important enzyme within the cell as it breaks down the toxic hydrogen peroxide into water and oxygen
- 2H202—–02 +2H20
- Catalase consists of four polypeptide chains and contains a haem group with iron
- second fastest-acting enzyme, having the highest turnover number known, about 6 million per second
- found in small vesicles called peroxisomes in eukaryotic cells
- white blood cells use catalase when ingesting pathogens to help killl the invading microbe
What is the optimum pH for the catalase enzyme in humans?
around pH7
Whats the function of amylase enzyme and how is it an example of a extracellular enzyme?
- produced in the salivary glands, and acts in the mouth to digest the polysaccharide starch to the dissacharride maltose.
- also made in the pancreas and acts to catalyse the same reaction in the lumen of the small intestine
Whats the function of trypsin enzyme and how is it an example of an extracellular enzyme?
- made in the pancreas and acts in the lumen of the small intestine to digest proteins into smaller peptides by hydrolysing peptide bonds
- optimum pH is between 7.5 and 8.5
What is meant by an enzymes active site?
indented area on the surface of an enzyme molecule, with a shape that is complimentary to the shape of the substrate molecule
How does the tertiary structure of the active size on an enzyme molecule affect its function?
- the tertiary structure of the active site is crucial, as its shape is complimentary to the shape of the substrate molecule
- each type of enzyme is highly specific in its function, as it can only catalyse a reaction involving the particular type of substrate molecule that fits into its active site
What is a cofactor?
- substances that must be present to ensure an enzyme-catalysed reaction occurs at the appropriate rate
- they can be part of the enzyme structure or can form temporary associations with the enzyme
What is the name of a cofactor which is permanently bound to the enzyme structure?
prosthetic group
What is an example of an enzyme which has a prosthetic group attached and whats its function?
- carbonic anhydrase contains a zinc ion permanently bound as a prosthetic group to its active site
- this enzyme is found in erythrocytes (red blood cells) and catalyses the interconversion of C02 and water to carbonic acid, which then breaks down to protons and hydrogen carbonate ions
- C02 + H20—–H2C03
- H2C03—–H+ + HCO3-
What is an enzyme-substrate complex?
complex formed by temporary binding of enzyme and substrate molecules during an enzyme-catalysed reaction
What are co-susbtrates?
cofactors which bind to the substrate to form the correct shape to bind to the active site of the enzyme
How else do cofactors work?
- change the charge distribution on the surface of the substrate molecule or on the surface of the enzymes active site
- make the temporary bonds in the enzyme-substrate complex easier to form
What are coenzymes?
- small organic non-protein molecules
- bind temporarily to active site (just before or with substrate)
- they are chemically changed during the reaction so they need to be recycled to their original state, sometimes by a different enzyme
What are some sources of coenzymes?
- vitamin B12 provides the coenzyme cobalamin coenzymes. If you are deficient in this coenzyme than you can get the disease pernicious anaemia
- Folic acid provides the coenzyme tetrahydrofolate. If you are deficient in this coenzyme than you can get the disease megablastic anaemia(large irregular shaped erythrocytes)
What is the lock and key hypothesis?
- the substrate molecules and enzyme molecules each have kinetic energy and are constantly moving randomly
- if a substrate molecule successfully collides with an enzyme molecule, then an enzyme-substrate complex (ES complex) forms as the substrate molecule fits into the complementary shaped active site on the enzyme molecule
- the substrate molecules are either broken down or built up into the product molecule, and these form an enzyme-product complex whilst still in the active site
- the product molecules leave the active site
- the enzyme molecule is now able to form another enzyme-substrate complex
- a small number of enzyme molecules can therefore covert a large number of substrate molecules into product molecules
What is the induced fit hypothesis?
- When the substrate molecule fits into the enzymes active site, the active site changes shape slightly to mould itself around the substrate molecule as it might not be the exact right shape.
- subtle changes of shape of the side chains (R-groups) of the amino acids that make up the active site give a more precise conformation that exactly fits the substrate molecule
- non-covalent forces such as hydrogen bonds, ionic attractions, van Der Waals forces and hydrophobic interactions, bind the substrate molecule to the enzymes active site.
- enzyme-prodcut complex forms when the substrate molecules are converted into product molecules.
- The product leaves and the enzyme molecule is ready to catalyse another reaction
What is the general equation of steps which outline how an enzyme catalyses a reaction?
Enzyme + substrate—Enzyme-substrate complex— Enzyme-product complex—- Enzyme +product
What is a enzyme-product complex?
enzyme moleucle with product molecules in its active site. The two are joined temporarily by non-covalent forces
What are enzyme-substrate complexes?
enzyme molecule with substrate molecules in its active site. The two are joined temporarily by non-covalent forces e.g. hydrogen bonds
How do enzymes affect activation energy?
they lower the activation energy and hence speed up metabolic reactions
How does increasing the temperature affect enzyme activity?
- both enzyme and substrate molecules will gain kinetic energy and move faster
- this will increase the rate (number per second) of successful collisions
- rate of formation of enzyme-substrate complexes increases, and the rate of reaction increases, increasing the number of enzyme-product complexes per second, up to a point
- at a particular temperature, called the optimum temperature, the rate of reaction is at its maximum.
How does increasing the temperature very high lead to enzymes denaturing?
- increased heat makes molecules vibrate more. this may break some of the weak bonds, such as hydrogen and ionic bonds, that hold the tertiary structure of the enzyme’s active site
- as the active site begins to change, the substrate molecules will not fit into it so well and the rate of reaction begins to decrease
- as more heat is applied, the shape of the enzyme’s active site completely and irreversibly changes so that it no longer is complimentary to the shape of the substrate molecule
- reaction cannot proceed at all because the enzyme has been denatured.
What is meant by the optimum temperature?
the temperature at which the enzyme works best. It is the temperature at which the enzyme has its maximum rate of reaction
What type of bacteria have enzymes which can function at cold temperatures?
psychrophilic bacteria which live in very cold conditions
What type of bacteria have enzymes which can function at very hot temperatures?
thermophilic bacteria in hot springs live at very high temperatures
What is the temperature co-efficient, Q10?
measure of the rate of change of a biological or chemical system as a consequence of increasing the temperature by 10 degrees
What’s the equation to work out the temperature co-efficient, Q10?
Q10=rate of reaction at ( T+10) degrees/rate of reaction at T degrees
How does pH affect enzyme activity?
- hydrogen bonds and ionic bonds between amino acids hold the tertiary structure of an enzyme molecule, particularly the active site, in the correct shape so that the substrate molecule will fit into it
- excess hydrogen ions will interfere with these hydrogen bonds and ionic forces, and so the active site of the enzyme molecule will change shape. If the substrate molecule does not fit into the active site, then the rate of the reaction that the enzyme catalyses will be lowered.
- increased H+ ions will also alter the charges of the active site of an enzyme molecule, as more protons will cluster around negatively charged groups in the active site. This interferes with the binding of the substrate molecule to the active site.
What is the formula to work out pH?
log 1/[H+]
At extremes of pH what happens to the enzyme molecule?
-either low or high pH leads to the enzymes active site being permanently changed. When the enzyme is thus denatured, it cannot catalyse the reaction
What is a buffer?
something that resists changes in pH
What does concentration mean?
number of molecules per unit volume
How does increasing the substrate concentration effect the rate of enzyme-catalysed reactions?
- more enzyme-substrate(ES) complexes from
- more product molecules are formed
- substrate concentration is limiting the reaction, because, as it increases, the rate of reaction increases.
- substrate concentration becomes the limiting factor
When does substrate concentration not become the limiting factor?
- As the concentration of substrate is increased even further, the reaction will reach its maximum rate
- adding more substrate molecules to increase the substrate concentration will not increase the rate of reaction.
- This is because all the enzymes active sites are occupied with the substrate molecules
- if more substrate molecules are added, than they cannot successfully collide with and fit into an enzymes active site.
What is the limiting factor?
factor that limits the rate of reaction
How does increased enzyme concentration effect the rate of reaction?
- more active sites on the enzyme become available
- more successful collisions between the enzyme and substrate occur
- more enzyme-substrate(ES) complexes can form per units time, so the rate of reaction increases
- enzyme concentration is the limiting factor-as it increases, so does the rate of reaction
What happens when enzyme concentration isn’t the limiting factor anymore?
- if substrate concentration is fixed or limited, then all the substrate molecules will be occupying an active site.
- the reaction has reached its maximum rate
- no increase in the rate of reaction
- substrate concentration is now the limiting factor.
What are enzyme inhibitors?
a substance that reduces or stops a reaction
What are competitive inhibitors?
inhibition of an enzyme, where the inhibitor molecule has a similar shape to that of the substrate molecule and competes with the substrate for the enzymes active site. It blocks the active site and prevents the formation of enzyme-substrate complexes.
What would reduce the affect of competitive inhibitors?
increasing the concentration of substrate would reduce the effect of reversible competitive inhibition, as there would be more chance of an enzyme molecule colliding with a substrate molecule than with an inhibitor molecule
What is the name of the complex that forms when a competitive inhibitor binds to an enzyme?
enzyme-inhibitor complex
What is a non-competitive inhibitor?
inhibitor that attaches to a part of the enzyme molecule but not the active site. This changes the shape of the active site by disrupting the enzymes tertiary structure, which prevents enzyme-substrate complexes forming, as the enzymes active site is no longer complementary in shape to the substrate molecule.
What is the name of the region where non-competitive inhibitor bind to?
allosteric site
How does substrate concentration affect initial rate when there are competitive inhibitors present?
-increasing the concentration fo substrate increases the rate of reaction and reduces the effect of the competitive inhibitors
How does substrate concentration affect initial rate when there an non-competitive inhibitors present?
-adding more substrate might allow the reaction to attain a new, lower rate, but even very high concentrations of substrate will not allow the rate of reaction to return to its inhabited maximum.
What is end-product inhibition?
-end product of a reaction is able to influence or inhibit the action of the enzyme of the enzyme that actually makes it
Describe the steps in a metabolic pathway involving enzymes and end-product inhibition
- the product of one enzyme-catalysed reaction becomes the substrate for the next enzyme-catalysed reaction in the metabolic pathway
- cells do not need to accumulate too much of the end product, sot he product of the last enzyme-catalysed reaction in the metabolic pathway may attach to a part of the first enzyme in the pathway, but not at its active site.
- this binding changes the shape of enzyme 1’s active site, preventing the pathway from running. This is non-competitive inhibition, but it is reversible.
- when the concentration of this product falls within the cell, these molecules will detach from enzyme 1 and allow its active site to resume its normal shape: the metabolic pathway can run again.
Why are enzyme inhibitors important?
regulation of metabolism
How do toxins(poisons) exert their effect?
they inhibit or inactivate enzymes
How does cyanide inhibit enzymes and act as a metabolic poison?
- potassium cyanide (KCN) is highly toxic because it inhibits aerobic respiration.
- inhibits catalase which is an enzyme that converts hydrogen peroxide to water and oxygen
- when KCN is ingested, it is hydrolysed to produce hydrogen cyanide (HCN), a very toxic gas that can readily dissociate into H+ and CN- ions.
- these CN- ions can bind irreversibly to enzymes found in the mitochondria which is the site of respiration (inhibits aerobic respiration)
How does snake venom inhibit enzymes and act as a metabolic poison?
- the venom of a green mamba snake contains a chemical that inhibits the enzyme acetylcholinesterase
- this enzyme is important as it breaks down acetycholine which is a neurotransmitter found at synapses
- without this enzyme, muscles are able to relax and this can lead to paralysis, as movement depends on muscles being able to contract and relax alternatively
How does aspirin act as a medicinal drug by carrying out enzyme inhibition?
- inhibits the enzymes Cox 1/2. These enzymes convert salicylic acid into prostaglandins which increase sensitivity to pain and increases swelling.
- inhibiting Cox1/2 stops the formation of prostaglandins so their is less feeling of pain and less swelling
How does ATPase act as a medicinal drug by carrying out enzyme inhibition?
- extracts from purple foxglove leaves
- treats heart failure and atrial arrhythmia (abnormal beat rate of the atria)
- chemical involved is digitalin
- digitalin inhibits the sodium potassium pump in the cell membranes of heart-muscle cells, and allow more calcium ions to enter the cells. Calcium ions increase muscle contraction, and this strengthens the heartbeat
How do ACE inhibitors act as medicinal drugs by carrying out enzyme inhibition?
- inhibit the angiotensin converting enzyme (ACE), which increases your blood pressure
- they are used to treat hypertension (increased blood pressure), heart failure, and also reduces the risk of second heart attack for a person who has suffered a myocardial infarction
How do protease inhibitors work?
- prevent the replication of virus particles within the hosts cell, by inhibiting protease enzymes so that the viral coats cannot be made.
- competitive inhibition
How do nucleoside reverse transcriptase inhibitors work?
- used to treat HIV
- prevent viruses from making DNA to insert into the host genome
Describe how an enzyme breaks down a substrate?
- substrate / protein , shape is (nearly) complementary to active site
- substrate / protein , enters / fits into , active site (on enzyme) ;
- induced fit / description of induced fit ;
- (forms) enzyme-substrate complex / ESC
- destabilising / straining / AW , of bonds (in substrate) ; then (forms) enzyme-product complex ;
- product(s) / amino acids , leave (active site)
Why are the lock-and-key and induced fit explanations called models?
- simple representation of the process/structure
- showing people how it works
Why do scientists now accept the induced-fit model rather than the lock-and-key model?
- supported by more evidence/new research
- it has now be found that the enzyme shape changes during the reaction
Why is it undesirable to lose unique enzymes when species become extinct?
- enzyme could have potential/future application e.g. medical use
- scientific research
Explain why different enzymes are involved in each stage of the digestion process (metabolic pathway)?
- enzymes are specific
- the carbohydrate molecules are different shapes
- active site and substrate are complimentary
- substrate will fit (enzyme-substrate complex)
- lock and key (induced fit model)
