biology - enzymes

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what are enzymes?
biological catalysts
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what type of molecules are they?
globular proteins
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what is a catalyst?
substance that speeds up a reaction without changing the substances produced or being changed itself
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what type of reactions do enzymes catalyse?
biochemical/metabolic reactions
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what is metabolism?
sum of anabolic and catabolic processes in a cell
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what is an anabolic reaction?
building up reaction
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what is a catabolic reaction?
breaking down reaction
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are enzymes soluble? why?
are soluble as lots of hydrophilic sides on amino acids
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which part of the enzyme catalyses?
active site
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what is the active site?
small depression on surface of molecule with precise shape because of the way the large molecule is folded
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how much of the enzyme is the active site?
active site consists of only a few amino acids, the remainder amino acids maintain the precise shape of active site
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why is it important that the active site remains a precise shape?
if it denatures, won't catalyse/react as shape won't be right and substrate won't fit
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how do enzymes catalyse?
active site of enzyme binds to substrate
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what is the name of an enzyme bound to a substrate?
enzyme/subtrate complex
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what are the three factors which affect rate of reaction?
pH, temperature, concentration
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why are enzymes important?
most biochemical reactions happen way too slowly for humans to survive; essential for survival
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at what stage in protein synthesis are enzymes made?
as the mRNA transcribed from the DNA molecule is translated
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how many protein structures do enzymes have?
primary, secondary, tertiary, quaternary
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what does specificity mean?
characteristic of enzymes that means they will only catalyse a specific reaction or group of reactions, as result of precise active site shape
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why do temperature and pH affect the efficiency of an enzyme?
they affect the intramolecular bonds within the protein that are responsible for the shape of the molecule
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do most metabolic reactions happen as a single event?
no; they occur as a metabolic chain
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what is a metabolic pathway or metabolic chain?
series of linked reactions in the metabolism of a cell
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what are intracellular enzymes?
enzymes that catalyse reactions within the cell
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name an example of an intracellular enzyme and in which process they're used.
DNA ligase and DNA polymerase in DNA replication
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where also may intracellular enzymes work? name an example.
on a membrane; e.g. ATPase works across inner membrane of mitochondria to produce ATP
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what are extracellular enzymes?
enzymes that catalyse reactions outside the cell in which they were made
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name an example of an extracellular enzyme and in which process they're used.
pepsin in digestion in the stomach
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what enzyme is present in tears?
lysozyme
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where did the name 'enzyme' come from and when?
people suspected there were 'ferments' in yeast (single-celled fungus) that turned sugar to alcohol, name introduced in 1877, meaning 'in yeast'
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what was the name of the scientist who discovered the role of enzymes? what did he do to find this out?
eduard buchner; extracted a 'juice' from yeast cells that would breakdown various sugars outside a living cell
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what was the name of the scientist who discovered what enzymes were?
james b. sumner
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what year did james b. sumner conduct his reaction?
1926
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what did his experiment involve?
he extracted the first pure, crystalline enzyme (urease) from jack beans, found crystals were protein and concluded that enzymes were protein
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what is activation energy(Ea)?
input of energy before the enzymes begin to catalyse
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what happens to the Ea?
the enzyme lowers activation energy, creating transition state between enzyme and substrate (stable)
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how do enzymes lower the Ea?
enzymes form a complex with the substrate(s) of the reaction
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what is the 'lock-and-key' hypothesis?
model that explains enzyme action by an active site in the protein structure that has a very specific shape, the enzyme and substrate slot together to form a complex as a key fits in a lock
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how does the enzyme/substrate complex lower the Ea?
active site puts strain on the substrate, making it easier for bonds to make/break and reform, reacting substances brought closer together, making it easier for reformation of bonds between them
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what happens when reaction is complete?
products no longer in right shape to stay in active site so complex dissociates, products released, enzyme free for further reactions
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how has the 'lock-and-key' hypothesis been disproved?
evidence from X-ray crystallography, chemical analysis of active sites suggests that active site isn't rigid shape
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what is the induced-fit hypothesis?
active site still has distinctive shape and arrangement, but its flexible. once substrate enters active site, shape modified around it to form active complex, once products left the enzyme reverts to its inactive, relaxed form until another reaction
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how much does urease affect the catabolic breakdown of urea?
rate of reaction increased by factor of 10¹⁴ (one hundred trillion)
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how much do enzymes generally catalyse reaction rates?
increase reaction rates by factors from 10⁸ to 10²⁶; why only tiny amounts of enzyme needed
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what is the initial rate of reaction?
fastest change in the rate (at initial stage)
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why is it important to use a high substrate concentration in rate of reaction practicals (unless substrate concentration under investigation)?
gives maximum reaction rate for an enzyme under particular conditions
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what is important to remember about enzymes?
don't change or contribute to end products that form, or affect the equilibrium of the reaction, ONLY catalyse
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what is the molecular activity (turnover number)?
number of substrate molecules transformed per minute by a single enzyme molecule
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what is the number of hydrogen peroxide molecules catalysed by catalase (extracted from liver cells) per minute?
6 x 10⁶ in one minute
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what is hydrogen peroxide?
toxic byproduct of metabolism, after catalysed water and oxygen are products
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what inorganic catalysts catalyse?
many metals, e.g. platinum frequently catalyses many different reactions, often only in extreme temperatures and pressure
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how far can substrate concentration speed up a reaction?
only to certain extent; until the enzyme is saturated with substrate molecules (all active sites occupied by substrate molecules) and then only enzyme concentration can catalyse
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how does temperature affect rate of reaction?
increases/decreases number of successful collisions of molecules; increases kinetic energy of molecules
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what is temperature coefficient(Q¹⁰)?
measure of the effect of temperature on the rate of a reaction?
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what is the Q¹⁰ formula?
rate of reaction at (x + 10)°C ➗ rate of reaction at x
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what is the Q¹⁰ for any reaction between 0⁰C and 40⁰C?
2; it doubles
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at what temperature do enzymes stop catalysing completely, in most cases?
60⁰C
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at what temperature do enzymes begin to denature?
over 40⁰C
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what are some exceptions to enzymes denaturing at high temperatures?
thermophilic bacteria; live in hot springs at temperatures of up to 85⁰C , made up of temperature-resistant proteins that contain a high density of h bonds and disulfide bonds which hold them together at high temperatures
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what is sub-optimum temperature?
before optimum temperature
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how does pH affect the rate of reaction?
different enzymes have different optimum pH, changes in pH affect the interactions between R groups (e.g. h bonds and ionic bonds that hold 3d protein structure together)
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is the optimum pH of an enzyme always the same as its surroundings? why?
no; one way in which cells control the effects of their intracellular enzymes, increasing or decreasing their activity by minute changes in the pH
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what is the full name of RuBisCo?
ribulose biphosphate carboxylase/oxygenase
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why is RuBisCo important?
catalyses fixing of carbon dioxide from the air into the biochemistry of sugar formation in the process of photosynthesis
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how is RuBisCo inefficient? (1)
catalyses 0.3% of reactions (3 out of 1000 expected), plants overcome this by producing lots of this enzyme (half of protein in photosynthetic plant cell is this enzyme)
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how is RuBisCo inefficient? (2)
can bind to carbon dioxide but also oxygen (photorespiration), affinity for carbon dioxide 80 times greater than for oxygen, only 25% of RuBisCo binds to oxygen
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how do scientists believe RuBisCo evolved?
in an atmosphere containing very little oxygen and much more carbon dioxide than it does today; oxygen binding was not a disadvantage at the time and so not selected against in evolution
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what are enzyme inhibitors?
substances that slow down enzymes or stop them from working
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what are the two main types of inhibition?
reversible inhibition and irreversible inhibition
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what is reversible inhibition?
doesn't permanently affect the functioning of the enzyme and can be removed from the enzyme; often used to control reaction rates within a cell
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what are the two forms of reversible inhibition?
competitive inhibition and non-competitive inhibition
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what is competitive inhibition?
inhibitor molecule similar in shape to substrate molecule and competes with substrate for binding at the active site, forming an enzyme/inhibitor complex
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how can the inhibition be reduced?
if inhibitor amount fixed, percentage of inhibition can be reduced by increasing the substrate concentration (more substrate molecules, less likely that inhibitor will bind to active site)
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what is non-competitive inhibition?
inhibitor may form a complex with either the enzyme or with the enzyme/substrate complex, inhibitor not competing for active site as it joins to the molecule elsewhere
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how is this theory confirmed?
only the concentration of inhibitor affects the level of inhibition in non-competitive inhibition, substrate concentration makes no difference
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what does the inhibitor do?
presence of inhibitor on enzyme or enzyme/substrate complex deforms or changes the active site shape so that it can no longer catalyse a reaction
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what is irreversible inhibition?
inhibitor combines with the enzyme by permanent covalent bonding to one of the groups vital for catalysts to occur; changes shape and structure of molecule permanently (permanently inactivated)
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how fast does irreversible inhibition happen?
occurs more slowly than reversible, but much more devastating and never used within cell to control metabolism
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what are some examples of materials that exert irreversible inhibition on enzyme systems? (3)
arsenic, cyanide, mercury (all poisonous)
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how do some nerve gases work in warfare?
combine and inactivate enzymes, such as; acetyl cholinesterase (which breaks down chemicals used to transfer impulses from the nervous system to muscles of the body)
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what does inhibiting acetyl cholinesterase do?
function of this enzyme is to destroy the neurotransmitter called acetylcholine at the junctions between neurones and muscle cells, doing this as soon as impulse passed from nerve to a muscle, when inhibited, impulse continues
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what then happens in humans?
muscles go into prolonged spasms (breathing and swallowing becomes impossible) causing death
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how do enzymes manage their reactions in a controlled way? (4)
membrane compartments keep reactions apart, variations in pH change reaction rate, amount of substrate available, regulatory enzymes
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what are regulatory enzymes?
enzymes that have site separate to active site where another molecule can bind to have either an activating or inhibitory (non-competition) effect
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where are regulatory enzymes found?
widely found in complex metabolic pathways (e.g. photosynthesis, respiration)
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what is end-product inhibition?
control system in many metabolic pathways in which the regulatory enzyme at the beginning of the pathway is inhibited by one of the end products of the reaction
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name an example of end-product inhibition in the pathways of cellular respiration.
phosphofructokinase (PFK) involved in production of ATP in process of glycolysis in cellular respiration, PFK controls rate of respiration by end-product inhibition
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how does PFK control the rate of respiration?
PFK inhibited by ATP, which binds non-competitively and changes active site shape; if ATP concentration goes up, PFK is inhibited and cellular respiration slows down
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what happens if ATP concentration rises or falls?
if ATP falls, ATP molecules detach from PFK and enzyme is active again so rates of cellular respiration (ATP production) increase
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what is oxidoreductase?
transfer of electrons in redox reactions, occurs during anaerobic respiration
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what is it catalysed by?
alcohol dehydrogenase
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what is transferase?
transfer of functional group from one molecule to another
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what is it catalysed by?
glutamic acid transminase
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what is hydrolase?
hydrolysis of bonds, occurs in digestion
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what is it catalysed by?
maltase
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what is lyase?
split bonds, other than hydrolysis or oxidation, occurs in immune system
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what is it catalysed by?
histidine decarboxylase
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what is isomerase?
isomerization of molecules, occurs in respiration
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what is it catalysed by?
phosphoglucomutase
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what is ligase?
joining of two molecules by formation of covalent bonds, occurs in protein synthesis
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what is it catalysed by?
aminoacyl tRNA synthetase
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