Chap 4 - Enzymes Flashcards
Define activation energy
energy required to initiate a reaction.
what is an enzyme?
a biological catalysts that interacts with substrate molecules to facilitate chemical reactions
what type of protein make up enzymes?
globular proteins
Define active site
area of an enzyme with a shape complementary to a specific substrate, allowing the enzyme to bind a substrate with specificity
Define anabolic reaction
- metabolic reactions that construct molecules from smaller units
- require energy
Define catabolic reaction
- metabolic reactions that break molecules down into smaller units
- release energy
Define apoenzyme
protein that forms an active enzyme by combination with a cofactor
Define cofactor
non-protein component necessary for effective functioning of an enzyme (can be ions or organic molecules)
Define coenzyme
organic cofactor not permanently attached to the protein
Define competitive inhibitor
- inhibitor that competes with substrate to bind to active site on an enzyme
- prevents enzyme activity by binding to active site
Define digestion
process by which large biomolecules such as carbohydrates, lipids and proteins get hydrolysed into smaller constituent molecules
- allows absorbtion across cell membranes.
Define end-product inhibition, and why it is useful
- when product of a reaction inhibits the enzyme required for the reaction
- useful bc it makes sure that no excess products are made and resources are not wasted - negative feedback
Define enzyme inhibitor
- molecule prevents enzymes from carrying out their normal function of catalysis
- reduce the enzyme’s rate of reaction
Define holoenzyme
active form of an enzyme
Define inactive precursor enzyme
an enzyme that requires a biochemical change for it to become active
explain why enzymes may be produced as inactive precursors
- used to prevent some enzymes from causing damage within cells producing them/tissues when released
- used when an enzyme’s action needs to be controlled and only activated under certain conditions
Give an example of an inactive precursor enzyme
- trypsinogen and pepsinogen are inactive forms of trypsin and pepsin
- used to prevent proteases from digesting membrane proteins in vesicles storing them - would result in vesicles breaking down, prevent proteases from digesting other enzyme
Define initial rate of reaction
the instantaneous rate at the start of the reaction
- gradient of tangent to curve at t=0
Describe the importance of initial rate of reaction
- concentration of substrate is always changing - RoR constantly changes
- so only true RoR is initial
- (only moment where the two variables investigated are the only ones influencing rate)
Define irreversible inhibitor
- inhibitor that cannot easily dissociate from the enzyme, permanently disabling the enzyme
- effect cannot be reversed
what type of inhibitors are irreversible?
non-competitive
Define metabolism
sum of all of the different reactions and reaction pathways happening in a cell or an organism
Define non-competitive inhibitor
inhibitor that binds to an enzyme at an allosteric site
Define product
substances formed from a chemical reaction
Define substrate
- substance used, or acted on by another process or substance
Explain why enzymes are necessary for life.
- most important metabolic reactions are slow without catalysts - would need to happen at very high temp and pressures to be quick enough for important life processes
- these conditions would damage cell components and impossible to reach in living cells
- enzymes speed up metabolic reactions without need for harsh environmental conditions
define intracellular enzyme + example
enzymes that act within cells
- eg. catalase
define extracellular enzyme + example
enzymes that act outside of cells (released from cells to act outside them)
- eg. amylase, trypsin
State the substrates and products of enzymes catalase, amylase and trypsin.
- amylase ( starch ⟶ maltose)
- trypsin (proteins ⟶ peptides)
- catalase (hydrogen peroxide ⟶ water + oxygen)
Explain the role of extracellular enzymes in general.
- reactions in cells require constant supply of raw materials to make products required by organisms
- nutrients present in diet/environment are supply for raw materials
- nutrients often in form of polymers (proteins and polysaccharides) - can’t enter cells directly
- extracellular enzymes used to digest nutrients into smaller molecules so can be absorbed and used by cells
Summarise the digestion of starch as an example of the role of extracellular enzymes.
- starch polymers partially broken down into maltose (disaccharide) using amylase (released in saliva, produced by salivary glands and pancreas)
- maltose is broken into glucose (monosaccharide that can be absorbed by cells) using maltase (present in small intestine)
Summarise the digestion of proteins as an example of the role of extracellular enzymes.
- proteins are digested into smaller peptides using trypsin (produced in pancreas and released into small intestine)
- peptides are broken down further into amino acids by other proteases
- amino acids are absorbed by cell lining of digestive system and then absorbed into bloodstream
Define specificity
term that describes how each enzyme catalyses one biochemical reaction
Explain why an enzyme only catalyses one type of reaction.
- different enzymes have differently shaped active sites
- each specific active site shape complementary to a specific substrate
- each enzyme will only be able to catalyse a specific substrate and therefore only one type of reaction
State the sequence of events in an enzyme-controlled reaction.
- molecules in solution move & collide randomly
- when specific substrate collides with specific enzyme and it fits the active site, substrate binds to active site = enzyme-substrate complex
- substrate(s) react and product(s) are formed = enzyme-product complex
- product(s) released, leaving enzyme unchanged and able to catalyse more reactions
Describe the lock and key hypothesis of enzyme action.
- enzymatic action works the same way a specific key will fit into a specific lock
- the shape of the active site is exactly complementary to the shape of the substrate
- enzyme does not change shape
Describe the induced-fit hypothesis.
- enzyme changes shape slightly as substrate enters
- weak interactions between substrate and enzyme induce changes in enzyme’s tertiary structure - strengthen binding putting strain on substrate molecule
- weakens bonds in the substrate, lowering activation energy
Suggest how R-groups of amino acids are involved in catalysing reactions.
- R-groups interact with substrate, forming temporary bonds
- bonds put strain on bonds within substrate - helps lower the activation energy
Define rate of reaction
speed at which reactants are being turned into products
State what the presence of an enzyme does to the activation energy for a reaction and explain why this increases the rate of reaction.
- enzymes lower the activation energy
- lowers the minimum amount of energy required in particles in order for them to react
- higher proportion of particles are able to react - more reactions happen during a given time interval - higher rate
State 4 factors that affect the rate of an enzyme-controlled reaction.
- temperature
- pH
- substrate concentration
- enzyme concentration
Explain why increasing temp from below the optimum towards the optimum increases the rate of reaction.
- increasing temp increases kinetic energy of particles
- causes particles to move faster and collide more frequently
- results in more frequent successful collisions between substrate and enzyme –> increase in rate of reaction
Define temperature coefficient (Q10)
measure of how much the rate of a reaction increases with a 10˚C rise in temperature
State the usual Q10 value for enzyme controlled reactions.
for enzyme-controlled rxns = 2 (rate doubles with 10˚C increase)
rate of reaction at (t +10)˚C / rate of reaction at t˚C
Explain why increasing the temperature up from the optimum decreases the rate of reaction abruptly.
- at higher temp, bonds holding enzyme protein structure together vibrate more and eventually strain and break
- breaking of bonds result in change in the precise tertiary structure of the protein
- enzyme has changed shape - denatured
- active site has changed shape and is no longer complementary to substrate - substrate cant fit - enzyme is no longer a functional catalyst
Explain why a pH change away from optimum decreases the rate of reaction.
- hydrogen bonds and ionic bonds between amino R-groups hold protein in its precise 3D shape
- change in pH changes H+ concentration (more H+ - acidic - low pH) (less H+ - alkaline - high pH)
- active site is only in right shape at optimum pH so when it changes, structure and therefore active site is altered - reduces RoR
- f change is not too significant = enzyme can renature if pH is back to optimum
- if change is too significant = enzyme is irreversibly altered, active site no longer complementary - denatured
- happens because H+ intreact with polar and charged R-groups if more H+ less R-groups can interact with each other leading to ionic and hydrogen bonds breaking
Define Vmax
maximum initial rate of an enzyme-catalysed reaction
Explain how increasing the substrate concentration affects the initial rate of an enzyme-controlled reaction.
- as substrate concentration increases, rate of successful colisions between substrate and enzyme increases
- this increases the rate of formation of ES complexes = RoR increases
- rate stops increasing when all of the active sites are occupied
- at this point substrate is no longer limiting and increasing conc will not affect rate (Vmax)
Explain how increasing enzyme conc. affects the initial rate of an enzyme-controlled reaction.
- as enzyme concentration increases, more active sites are available and reaction rate increases
- leads to more frequent successful collisions between substrate and enzyme
- increases the rate of formation of ES complexes = rate increases
- rate stops increasing when substrate starts to run out and enzymes collide more often with each other than with substrate
- enzyme is no longer limiting and increasing conc will not affect rate (Vmax) because there will be nothing for enzymes to bind to
Describe and explain how to investigate any of the factors that affect the rate of enzyme-controlled reactions.
- use catalase from any living tissue and add it to hydrogen peroxide, measure gas produced (oxygen):
changing the ind. variables:
- substrate conc - increase hydrogen peroxide conc
- enzyme conc - eg crush up potatoes in solution and perform serial dilution of the solution
- temperature - heat the tissue/perform experiment in water bath where everything is at same temp
pH - add buffer solution to the reaction mixture
Explain how to calculate the rate of change from a graph showing a linear relationship.
- pick two points on the line, calculate ∆y/∆x (gradient)
- suitable units will be units of dependent variable per unit independent
Explain how to estimate a rate of change at a particular point on a graph showing a non-linear relationship.
- draw a tangent to the point at which you are trying to find the gradient
- find ∆y/∆x of that straight line which will be the estimated gradient at the chosen point
Define cofactor and coenzyme.
- cofactor - non-protein component necessary for effective functioning of an enzyme (can be ions or organic molecules)
- coenzyme - organic cofactor not permanently attached to the protein
Describe the similarities and differences between cofactors, coenzymes and prosthetic groups.
- coenzymes and prosthetic groups are both cofactors
- coenzymes are organic cofactors that are not permanently attached to the protein
- prosthetic groups are cofactors that are permanently attached to the enzyme
- cofactors and prosthetic groups can be organic or inorganic (org molecules or ions)
Explain why the chloride ion necessary for the correct formation of the active site in amylase is a cofactor, not a coenzyme or prosthetic group.
- it is inorganic, coenzymes are organic
- it is not permanently attached, prosthetic groups are
Explain why zinc ion that forms an important part of the structure of carbonic anhydrase is a prosthetic group, not a cofactor or coenzyme.
- it is permanently attached - stating it is a cofactor is ambiguous - cofactors include both permanently and not permanently attached components
- it is inorganic, coenzymes are organic only
Give two examples of coenzymes synthesised from vitamins in our diet.
NAD (vitamin B3)
NADP (vitamin B3)
Describe 4 ways in which multi-step reaction pathways can be regulated by cells.
- competetive inhibition
- non-competetive inhibition
- end-product inhibition
- cofactors?
Explain how a competitive inhibitor affects the rate of an enzyme-controlled reaction.
- molecule/part of molecule with similar shape to substrate fits into the active site of the enzyme
- this blocks substrate from entering active site, preventing enzyme from catalysing
- enzyme cant carry out its function - inhibited
Substrate and inhibitor molecules will compete to bind to active sites - # of molecules binding to active site in given time reduced, rate of reaction slowed
State two examples of competetive inhibitors and describe their actions.
- statins are inhibitors of enzyme used in synthesis of cholesterol, reducing its production and blood conc
- aspirin irreversibly inhibits COX enzymes preventing synthesis of chemicals responsible for producing pain and fever
Explain how a non-competetive inhibitor affects the rate of an enzyme-controlled reaction.
- inhibitor binds to enzyme at allosteric site
- binding of inhibitor causes tertiary structure of enzyme to change, active site changes shape
- active site no longer has complementary shape to substrate so substrate is unable to bind to enzyme
- enzyme cannot carry out function - inhibited
- the inhibitor does not compete with the substrate for the active site
- # of available active sites is reduced permanently, less molecules bind to them in given time, rate of reaction reduced
State two examples of non-competetive inhibitors and describe their action.
- organophosphates (herbicides and insecticides) inhibit enzyme acetyl cholinesterase (responsible for nerve impulse transmission) - leads to muscle cramps, paralysis or death
- proton pump inhibitors (treat long-term indigestion) block enzyme system responsible for secreting H+ ions into stomach, reduces production of excess acid, preventing ulcers
Describe the effects of competitive inhibitors on an enzymes Vmax
- does not lower the Vmax of a reaction
- adding more substrate will result in more substrate than inhibitor
- original Vmax will be reached
Describe the effects of competitive inhibitors on an enzymes Vmax
- permanently lower the Vmax of a reaction
- adding more substrate will not overcome effect of them
Define end-product inhibition
when final product of a reaction inhibits the enzyme required for the next reaction
Describe end-product inhibition’s usefulness in controlling metabolic pathways.
makes sure that no excess products are made and resources are not wasted - negative feedback loop
Define inactive precursor enzyme
enzyme that requires biochemical change for it to become active
Explain why enzymes may be produced as inactive precursor enzymes
- used to prevent some enzymes from causing damage within cells producing them/tissues where released
- used when an enzyme’s action needs to be controlled and only activated under certain conditions
- used to prevent proteases from digesting membrane proteins in vesicles storing them which would result in vesicles breaking down, prevent proteases from digesting other enzymes
Describe 3 ways in which inactive precursor may be activated.
- adding a cofactor
- action of another enzyme
- change in conditions
Define zymogens and proenzymes
inactive enzymes that require a biochemical change (change in conditions/acted on by another enzyme) to become an active enzyme.
Give 2 examples of inactive precursor enzymes and describe how they are activated.
- pepsinogen becomes pepsin when exposed to stomach acid bc the low pH brings about the transformation
- trypsinogen becomes trypsin when cleaved into active form by enteropeptidase
