2.4* Flashcards
What is a active site?
Indented area on the surface of an enzyme molecule, with a shape that is complimentary tot he shape of a substrate molecule.
What is catalyst?
Chemical that speeds up the rate of a reaction and remains unchanged and reusable at the end of the reaction.
What is the meaning of extracellular?
Outside the cell.
What is the meaning of intracellular?
Inside the cell.
enzymes catalyse a wide range of intracellular as well as extracellular reactions
What is the meaning of metabolic/metabolism?
The chemical reactions that take place inside living cells or organisms.
What is the meaning of product?
A molecule produced from substrate molecules, by an enzyme catalysed reaction.
What is the meaning of substrate?
A molecule that is altered by an enzyme catalysed reaction?
Why are enzymes called biological catalysts?
Enzymes are called biological catalysts because they speed up metabolic reactions in living organisms. Their actions affect both structure and function within cells, tissues and organs.
Give examples of how enzymes effect both structure and function within cells?
Catalysts speed up chemical reactions and remain unchanged at the end of the reaction, able to be used again.
A small amount of catalysts can catalyse the conversion of a large number of substrate molecules into product molecules.
The number of reactions that an enzyme molecule can catalyse per second is known as its turnover number.
Why are enzymes better than chemical catalysts, regarding energy usage?
Whereas chemical catalysts usually need very high temperatures increased pressures and extremes of PH, enzymes speed up metabolic reactions by up to 10 to the power of 12 times at lower temperatures, often at neutral PH and at normal pressures. Hence, as biological catalysts, they re able to function in conditions that sustain life.
Why are enzymes better than chemical catalysts, concerning economy?
Enzymes are also more specific than chemicals catalysts. They do not produce unwanted by-products and rarely make mistakes. The cells in which they are made and/or act can also regulate their production and activity to fit the needs of the cell or organism at the time.
What may prevent an enzyme from functioning apart from heat and PH?
For enzymes to catalyse some reactions, they may need help from co-factors.
The instruction fro making enzymes are encoded in genes. If the gene has a mutation that alters the sequence of amino acids in a protien, then this may alter the enzyme tertiary structure and prevent it from functioning.
What causes a metabolic disorder?
If an enzyme that catalyses a metabolic reaction is deficient, then a metabolic disorder results.
What do enzymes catalyse that may cause the ‘Stone man syndrome’
Enzymes also catalyse the formation of the organisms structural component, such as collagen in bone, cartilage, blood-vessel walls, joints and connective tissue. Some genetic disorders cause malformations of connective tissue and can be very harmful, such as ‘stone man syndrome’.
Describe PKU.
Many metabolic disorders are caused by deficient or non-functioning enzymes, for example if the active site is misshapen. The genetic disorder phenylketonuria, PKU, results when the enzyme phenylalanine hydroxylase does not function and cannot convert the essential amino acid, phenylalanine, to another amino acid, tyrosine. As a result, sufferers cannot make melanin (which is made from tyrosine), and the accumulation of phenylaline in their blood impairs brain development leading to severe mental impairment.
How do we treat PKU?
Because this enzyme deficiency is so severe, all new born babies are screened for PKU, so that if the result is positive their diet can be adjusted to include only very small amounts of phenylalanine, to prevent the irreversible brain damage.
Describe the active site of an enzyme.
Enzymes are large molecules with a specific areas, an indentation or cleft on the surface of the molecule, called the active site. This consists of just a few - often about 6 to 10 - amino acids.
The active site is part of the enzyme molecule, not part of the substrate molecule.
Why is each type of enzyme specific in its function?
So, each type of an 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 crucial to make an enzymes shape complimentary to the shape of the substrate molecule?
The tertiary structure of the active site is crucial, as its shape is complimentary to the shape of the substrate molecule.
What be altered by changes in temperature and PH?
The shape of the enzymes active site, and hence its ability to catalyse a reactions, can be altered by changes in temperature and PH, as these affect the bonds that hold proteins in their tertiary structure.
Why might the same enzyme complex be known by different names?
Most enzymes catalyse a reaction in either direction depending on the cells needs. Hence ATPase can catalyse the formation of ATP or the hydrolysis of ATP. Sometimes an enzyme catalyses two reactions, because it is really a large enzyme complex and has more than one active site. So, the same enzyme complex may be known by different names.
How many metabolic reactions go on inside your body?
In any cell, and within its organelles, there may be up to 1000 metabolic reactions going on at the same time, each being catalysed by a different enzyme. Some of these reactions are part of a metabolic pathways.
What is each metabolic pathway in a living cell?
Each metabolic pathway in a living cell is one of a series of consecutive reactions, every step catalysed by a specific enzyme that produces a specific production.
Metabolic pathways:
What acts as substrates?
The various reactants and intermediates act as substrates for specific enzymes.
Metabolic pathways:
What are the reactants, intermediates and products known as?
The reactants, intermediates and products are known as metabolites.
Metabolic pathways:
Where is energy released?
In some metabolic pathways, described as catabolic, metabolites are broken down to smaller molecules and release energy.
Metabolic pathways:
When is energy used?
In other metabolic pathways, described as anabolic, energy is used to synthesise larger molecules from smaller ones.
Metabolic pathways:
Give some examples of complex metabolic pathways.
Respiration and photosynthesis are examples of complex metabolic pathways, with many enzymes involved.
(diagram of enzyme at the top of page 101)
Where is catalase found?
In nearly all living organisms.
Why is catalase important?
It is a very important enzyme, as it protects cells from damage by reactive oxygen by quickly breaking down hydrogen peroxide, a potentially harmful by-product of many metabolic reactions, to water and oxygen.
What does catalase consist of?
Four peptide chains and contains a haem group with iron.
What is unique about catalase?
It is the fastest-acting enzyme, having the highest turnover number known, of about 6 million per second.
Give two examples of where catalase is used.
In eukaryotic cells, catalase is found inside small vesicles called peroxisomes.
When white blood cells ingest pathogens they use catalase to help kill the invading microbe.
What the optimum conditions for catalase?
The optimum pH for human catalayse is around pH 7, but for other species it varies between pH 4 and 11. The optimum temperature also varies with species. For humans this is 45 degrees and for some thermophilic archaea it is 90 degrees.
Give an example of impacts of low catalase levels.
Some people lose hair pigment and go grey earlier in life than others. One reason may be that these people have lowered levels of catalase, and so more hydrogen peroxide bleaches their hair shafts from the inside.
Apart from animals digestive system give an example and explain an example of extracellular enzymes.
Some enzymes are secreted from the cells where they are made and act on heir substrates, extracellularly. 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 hypahe for use in respiration and growth.
Describe an example of how extracellular enzymes are used in our bodies.
In our digestive system many enzymes are secreted, from cells lining the alimentary canal, into the gut lumen. There they extracellularly digest the large molecules, such as proteins, lipids, carbohydrates and nucleic acids, found in food. The products of digestion are then absorbed, via epithelial cells of the gut wall, into the bloodstream in order to be used for respiration, growth and tissue repair.
Where is amylase produced and what is its purpose?
Amylase is produced in the salivary glands, and acts in the mouth to digest the polysaccharide starch to the disaccharide maltose. It is also made in the pancreas, and acts to catalyse the same reaction in the lumen of the small intestine.
Where is trypsin produced and what is its purpose?
Trypsin is made in the pancreas, and acts in the lumen of the small intestine to digest proteins into smaller peptides by hydrolysing peptide bonds. Its optimum pH is between 7.5 and 8.5.
Why are enzymes needed in the digestive system, what would happen without them?
If you had to wait for a meal to digest without any enzymes, it would take several years. Hence, without enzymes, the speed of chemical reactions inside living organisms could not sustain life . Humans produce about six times as much amylase as chimpanzees do. Chimpanzees eat some meat and a lot of fruit, but very few starchy vegetables.
What is a cofactor?
A substance that has to be present to ensure to ensure that an enzyme-catalysed reaction takes place at the appropriate rate. Some cofactors (prosthetic groups) are part of the enzymes structure, and others (mineral ion co-factors and organic co-enzymes)form temporary associations with the enzyme.
What is a enzyme-substrate complex?
Complex formed by temporary binding of enzyme and substrate molecules during an enzyme-catalysed reaction.
What do some enzymes need to have attached to them?
Some enzymes, particularly those involved in catalysing oxidation-reduction reaction, can only work if another small non-protien molecule is attached to them. These small molecules are called cofactors.
What is a cofactor permanently bound, by covalent bonds, to an enzyme molecule called?
A prosthetic group.
How does which enzyme catalyse the interconversion of carbon dioxide and water yo carbonic acid?
The enzyme 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 carbon dioxide and water to carbonic acid, which then breaks down to protons and hydrocarbonate ions.
Describe the enzyme controlled reaction of carbon dioxide and water to carbonic acid.
CO2 + H2O H2CO3 H+ + HCO3-
As with most enzyme-catalysed reactions, this reaction may proceed in either direction, depending on the concentration of substrate or product molecules.
When is the enzyme controlled reaction of carbon dioxide and water to carbonic acid important?
The reaction is vitally important, as it enables carbon dioxide to be carried in the blood from respiring tissues to the lungs.
Give examples of molecules with a haem group or a prosthetic group.
The enzyme catalyse contains a haem group with iron. Other proteins, besides enzymes, have prosthetic groups. For example haemoglobin also has a haem group.
Why is zinc important to humans?
Zinc is important to humans. As well as being needed to make carbonic anhydrase, Zinc is necessary for the polypeptide hormone, insulin, to function correctly. People whose diets do not contain much meat may be deficient in zinc.
How are scientists tackling zinc deficiency?
Some genetically modified crop plants such as plantain (a type of banana), use a lot in East Africa, are nutritionally enhanced to contain more zinc. This is useful, as meat is still too expensive for many people in these countries to obtain enough of it, but plantain is their staple diet.
How may cofactors work with enzymes without permanently binding to them?
Whereas the zinc associated with carbonic anhydrase is present in compound that is permanently bound to the enzymes active sit, some enzymes work better in the presence of ions that are not permanently bound to them. These ions are also called cofactors.
How may the presence of certain ions increase the rate of the enzyme catalysed reaction.
During an enzyme-catalysed reaction, the enzyme and substrate molecules temporarily bind together to form an enzyme-substrate complex. The presence of certain ions that may temporarily bind to either the substrate or the enzyme molecule may ease the formation of such enzyme-substrate complexes and therefore increase the rate of the enzyme-catalysed reaction.
What can cofactors act as apart from to ensure that the reaction happens at the appropriate rate?
Some co-factors act as co-substrates - they and the substrate together form the correct shape to bind to the active site of the enzyme.
Some of the co-factors change the charge distribution on the surface of the substrate molecule or on the surface of the enzyme’s active site, and make the temporary bonds in the enzyme-substrate complex easier to form.
Give an example of enzyme that needs the presence of chloride ions.
The enzyme amylase digests starch to maltose, and will only function if chloride ions are present.
Describe what cofactors can be made up of and how each type bond to the enzyme.
Coenzymes are a type of cofactor. they are organic but not made of protien. They bind temporarily to the enzymes active site.
Metallic ions may also be cofactors of certain enzymes. Some stay bound to the enzyme permanently, forming prosthetic groups.
Some metallic ions temporarily attach to the enzyme or to the substrate in order to aid the formation of enzyme-substrate complexes.
Describe the role of the co-enzyme in the reaction, and how it is affected by the reaction.
Coenzymes are small organic non-protien molecules that bind temporarily to the active site of enzyme molecules, either just before or at the same time that the substrate binds. The coenzymes are chemically changed during this reaction, and they need to be recycled to their original state, sometimes by a different enzyme.
Where are many coenzymes derived from?
Many co-enzymes are derived from water-soluble vitamins. If these vitamins are deficient in the diet of humans, then certain diseases may result.
What coenzyme is derived from, and which human deficiency disease is caused from a lack of B12.
Cobalamin coenzymes. Pernicious anaemia (progressive and fatal anaemia)
What coenzyme is derived from, and which human deficiency disease is caused from a lack of Folic acid?
Tetrahydrofolate . Megablastic anaemia (large, irregularly shaped erythrocytes)
What coenzyme is derived from, and which human deficiency disease is caused from a lack of Nicotinamide B3?
NAD, NADP.
Pellagra (diarrhoea, dermatits and dementia)
What coenzyme is derived from, and which human deficiency disease is caused from a lack of Pantothenate, B6?
Coenzyme A
Elevated blood-plasma triglyceride levels.
What coenzyme is derived from, and which human deficiency disease is caused from a lack of Thaimine, B1?
Thaimine pyrophosphate
Beriberi (mental confusion, irregular heartbeat, muscular weakness, paralysis and heart failure)
What are NAD and NADP both?
Hydrogen acceptors, they are both derivatives of nucleotides.
What is a enzyme-product complex?
Enzyme molecule with product molecule(s) in its active site. The two are joined temporarily by non-covalent forces.
What is a enzyme-substrate complex?
Enzyme molecule with substrate molecule(s) in its active site. The two are joined temporarily by non-covalent forces.
Why does the substrate molecule fit in the specific indented area on the surface of the enzyme?
The tertiary structure of the enzymes active site gives it a shape that is complimentary to that of the substrate molecule - rather like the way in which only one specific key will fit into a lock.
In the lock and key hypothesis explain how smaller product ,molecules are formed.
Substrate molecules fits into the enzyme’s active site. Temporary hydrogen bonds hold the two together forming an enzyme-substrate complex (ES complex). The substrate molecule is broken into smaller product molecules that leave the active site.
In the lock and Key hypothesis describe how a larger product molecule is formed.
Substrate molecules fit into the active site, forming an enzyme-substrate complex (ES complex). Bonds form between substrate molecules forming an enzyme-product complex.
The lock and key hypothesis;
What do enzymes forming a larger and smaller molecule have in common?
In each case at the end of the reaction, the enzyme is able to form an ES complex with another substrate molecule and catalyse another reaction.
How is a ES complex formed?
If a substrate molecule successfully collides with an enzyme, them an enzyme-substrate complex (ES complex) forms as the substrate molecule fits onto the complementary-shaped active site on the enzyme molecule.
Why do the substrate and enzyme molecules collide?
The substrate and enzyme molecules have kinetic energy and are constantly moving randomly.
When is the enzyme-product complex formed?
The substrate molecules are either broken down or built up into the product molecule(s) and these form an enzyme-product complex whilst still in the active site.
What happens when the product is formed?
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 convert a large number of substrate molecules into product molecules.
What did the scientist Emil Fischer discover?
A scientist, Emil Fischer, discovered in 1894 that glycolytic (sugar-splitting) enzymes could distinguish between sugar molecules that have the same molecular formula but slight differences in he geometry of how the atoms are arranged within the molecules (think of a left hand and a right hand glove). This led him to form his lock-and-key hypothesis, which explains enzyme specificity.
What have scientists inly known about since the 1930’s?
Although scientists have known about enzymes since the late 19th century, it was only in the 1930’s that it was established that enzymes are proteins.
What was the first enzyme to have its amino acid sequence worked out?
The first enzyme to have its amino acid sequence worked out was bovine pancreatic ribonuclease, in 1963.
What has been discovered about enzymes since 1965?
In 1965 , the first 3D structure of an enzyme, hen egg-white lysozyme, was worked out using X-ray diffraction. Since then, the structures of many enzymes have been elucidated. In the 1990s, scientists discovered that some types of RNA have catalytic properties in cells.
What does the lock and key hypothesis not explain?
Although the lock and key hypothesis explains enzyme specificity, it does not explain how the transition state - namely the ES complex - is stabilised.
Who modified the lock and key hypothesis and when?
In 1958 Daniel Koshland modified the lock and key hypothesis by suggesting that the active site of the enzyme is not a rigid fixed structure, but that the presence of the substrate molecule in it induces a shape change giving it a good fit.
What did Daniel Koshland suggest?
When the substrate molecules fit into the enzyme’s active site, the active site changes shape slightly to mould itself around the substrate molecule. Think of putting on a glove - it will only accept a hand shaped object, but when you insert your hand the glove moulds around and fits your hand perfectly.
In the induced fit hypothesis what changes to induce the fit of the substrate?
The active site still has a shape complimentary to the shape of the substrate molecule. But, on binding, the 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. This moulding enables the substrate to bind more effectively to the active site.
What binds the substrate molecule to the enzyme and what does this form?
An enzyme-substrate complex is formed, and non-covalent forces such as hydrogen bonds, ionic attractions, van der Waals forces and hydrophobic interactions, bind the substrate molecule to the enzyme’s active site.
When is an enzyme-product complex formed?
When substrate molecules have been converted to the product molecules and these are still in the active site, they form an enzyme-product complex.
Why does the product detach from the active site of an enzyme?
AS the product ,molecules have a slightly different shape from the substrate molecule, they detach form the active site.
What happens the the product molecule has detached from the active site of an enzyme?
The enzyme molecule is now free to catalyse another reaction with another substrate molecule of the same type.
What equation outlines how an enzyme catalyses a reaction?
Enzyme + substrate -> Enzyme - substrate complex -> Enzyme product complex -> Enzyme + product.
E + S -> ESC -> EPC -> E + P
Chemical reactions need energy to activate or begin them. How can this activation energy be provided outside of the body?
Many chemicals can be heated to provide this activation energy and make them react together. This increases the kinetic of the molecules so that they move about more, in a random fashion, and are more likely to successfully collide and then react together.
Chemical reactions need energy to activate or begin them. How can this activation energy be provided inside of the body?
In a living cell, the temperature cannot be raised too much or the proteins within it would denature and lipids would melt. Because enzymes have an active site specific to only the substrate molecules, they bring the substrate molecules close enough together to react, without the need for excessive heat. Therefore they lower the activation energy and hence speed up metabolic reactions.
How does the enzyme maltase change the activation energy required to hydrolyse maltose to glucose?
Adding the enzyme maltase reduces the amount of activation energy required for the reaction to take place. (graph on page 107)
What does the word digestion mean and what word should it be used with in an explanation?
Digestion means to break down. Large molecules in food, such as proteins and starch, are digested by being broken down by hydrolysis to smaller molecules, such as amino acids and glucose, Therefore the words ‘digestion’ and ‘hydrolysis’ may be used synonymously.
How can you investigate enzyme specificity?
Yeast, Saccharomyces Cerevisiae, is a single celled fungus. It is a facultative anaerobe, which means it can respire with or without oxygen. If oxygen is absent then it can respire anaerobically.
When yeast respires anaerobically it produces ethanol and carbon dioxide. The carbon dioxide produced during a unit time, such as 10 minutes, can be collected and its volume measured.
Yeast may respire different sugars. Enzymes are specific and each type will catalyse a specific sugar. You can investigate whether yeast can metabolise the monosaccharide sugars glucose, fructose and galactose.
What is Q10?
Temperature coefficient, calculated by divided the rate of reaction at (T + 10) degrees, by the rate of reaction at T degrees.
What makes molecules collide with one another?
All molecules have kinetic energy and can continuously move around randomly. In doing so, molecules will collide with none another.
