enzymes Flashcards
what are enzymes important for
chemical reactions which are needed for necessary life processes
why can’t life processes be done without enzymes
- they happen very fast
- happen under high temperatures and pressures
- so would damage cell components
what are enzymes
biological catalysts and globular proteins
what do enzymes do
interact with substrate molecules causing them to react at much faster rates
what are anabolic reactions
- reactions needed for growth
give an example of anabolic reactions
- cellulose forms walls of plant cells
- long protein molecules form contractile filaments of muscles in animals
how are anabolic reactions catalyzed
by enzymes
catabolic reactions
breaking down molecules - energy is released
what is energy needed for
growth
how are catabolic reactions catalyzed
enzymes
give an example of a catabolic reaction
digestion
what is metabolism
- sun of all the different reactions and reaction pathways happening in a cell or an organism
how is metabolism controlled
enzymes
what affects enzyme action
temperature
pH
pressure
what is the Vmax
enzyme can only increase the rates of reaction up to a certain point = Vmax
for a reaction to occur what must happen
- they need to collide in the right orientation
how do we increase rate of reaction and what affect does this have
- at high temperatures and pressure
- speed of molecules increase
- numbers of successful collisions increase
=ror increased
what is enzyme specificity
- each enzyme catalyses one biochemical reaction of which there are thousands in any given cell
what is activation energy
the energy that needs to be supplied for most reactions to start
how do enzymes reduce activation energy
enzymes help the molecules collide successfully
what is the active site
an area within the tertiary structure of the enzyme that has a shape which is complementary to the shape of a specific substrate molecule
lock and key theory
the same way that only the right key will fit into a lock only a specific substrate will fit into the active site of the enzyme
how does an enzyme substrate complex form
when a substrate is bound to the enzymes active site
when a substrate reacts with an enzyme what is formed
enzyme product complex
what happens after an enzyme product complex is formed
products are released leaving the enzyme unchanged
how do the enzyme and substrate specifically react
substrate is held in such a way by the enzyme that the right atom groups are close enough to react
r groups within the active site of the enzyme will also interact with the substrate forming temporary bonds
these put a strain on the bonds within the substrate which helps the reaction along
what is the induced fit hypothesis
active site of the enzyme changes shape slightly as the substrate enters
why does the active side change shape slightly as sub rate enters
initial interaction between enzyme and substrate is weak
what do the weak interactions between enzyme and substrate cause
- changes in enzymes tertiary structure
- this strengthens the binding putting a strain on the substrate molecule
- this weakens a bond or bonds in the substrate
- lowers activation energy
intracellular enzymes
enzymes that act within cells
give an example of a reaction that requires intracellular enzymes
synthesis from polymers to monomers
example of a reaction which used intracellular enzymes
- making polysaccharides from glucose
what does the enzyme catalase do
ensures hydrogen peroxide is broken down to oxygen and water quickly to prevent accumulation
what is hydrogen peroxide
a toxic product of many metabolic pathways
where is catalase found
plant and animal tissues
what kind of enzyme is catalase
intracellular
what do nutrients supply
substrates that the organism needs to make products to keep cells up with the demand
what are nutrients needed for
growth
survival
what do nutrients come in the form of
proteins and polysaccharides which are large molecules
what is the issue with nutrients being large molecules
they can’t enter cells through the cell membrane and need to be broken down first
what are extracellular enzymes
enzymes which work outside of the cell that made them
how do enzymes help nutrients
they are released from cells and break down larger nutrient molecules into smaller ones in digestion
extracellular enzyme example
fungi
give an example of a single called organisms which needs extracellular enzymes
bacteria and yeast release enzymes to break down larger molecules such as proteins and the smaller molecules produced are then reabsorbed by the cells
give an example of when multicellular organisms need enzymes
- large molecules need to be digested so smaller molecules can be absorbed into the blood stream
give example of extracellular enzymes involved in digestion in humans
amylase
trypsin
where does the digestion of starch begin
mouth and continues to small intestine
what are starch molecules initially broken into and how ?
into maltose
by enzyme amylase
where is amylase produced
salivary glands and pancreas
what from does amylase take in digestion
saliva - salivary glands
pancreatic juice - small intestine
after starch is broken down into maltose what is it then broken down into and how
glucose
by enzyme maltase
where is maltase produced
small intestine
what enzyme catalyses the digestion of proteins
trypsin
what are proteins broken down into
smaller peptides
where is trypsin produced and released
produced pancreas
released with pancreatic juice in small intestine
what happens to the amino acids produced by the action of proteases
absorbed into bloodstream by cells lining in digestive system
what kind of enzyme is trypsin
a protease
what is a protease
an enzyme which catalyses the digestion of proteins into smaller peptides
what it’s important about the structure of enzymes for a reaction to occur
- it needs to be the right shape so it’s complementary to the substrate
what affects enzyme activity
temperature
ph
vmax
substrate concentration
enzyme concentration
what happens when we increase the temperature of a enzyme reaction
- increases kinetic energy of particles
- particles move faster
- collide more
- more successful collisions
- increased rate of reaction
what is temperature coefficient
how much the rate of reaction increases with a 10 degree rise in temperature
what happens to enzyme controlled reactions at very high temperatures
- bonds holding the protein together vibrate more
- vibrations increase
- until bonds strain and break
- tertiary structure changes
DENATURED
what happens when the enzyme has denatured
- active site changes shape
- no longer complementary to substrate
- substrate can’t fit into active sites
- enzyme can’t function as a catalyst
what is optimum temperature
- temperature at which the enzyme has the highest rate of activity
what is generally the optimum temperature for enzyme reactions in humans
40 degrees
what are the optimum temperature for thermophilic organisms (bacteria found in hot springs) generally
70 degrees
what is the general optimum temp for psychrophilic organisms (live in cold)
below 5 degrees
what happens once enzymes have denatured above optimum temperature
decrease in rate of reaction is fast
after an enzyme has denatured what doesn’t apply
temperature coefficient
what happens if an enzyme controlled reaction is below optimum temperature
enzymes don’t denature they are just less active and rate of reaction slows down
give an example of extremely cold environments
deep oceans
high altitudes
polar regions
how are enzymes working in the cold structured
- more flexible particularly at active site
- less stable
- smaller temperature changes will denature them
what are thermophiles
organisms adapted to living in very hot environments
give examples of very hot environments
hot springs
deep sea vents
explain the structures of enzymes adapted to hot environments
- more stable
- more bonds (H and sulfur bridges ) in tertiary structure
- more resistant to change as temp rises
give an example of how enzymes show they are affected by temperature
- tyrosinase produces melanin - pigment responsible for dark coloured fur
- siamese cats produce a form of this that is denatured and inactive at normal body temperature so they are usually white/cream
- at tail ears and limbs at a lower temperature the mutated tyrosinase denatures
- causing discoloration (black) as melanin is produced
what hold proteins and enzymes in their precise shape
hydrogen bonds
ionic bonds
between amino acid R groups
how do the bonds holding proteins and enzymes together form
from interactions between polar and charged R groups present on amino acids forming primary structures
what does a change in pH refer to
change in hydrogen ion concentration
at a low pH how many hydrogen ions are present
lots
at a low pH how many hydrogen ions are present
lots
at a higher pH how many hydrogen ions are present
fewer
what is the optimum pH
where the active site will only be at the right shape at a certain hydrogen ion concentration
what happens when the pH changes from optimum
- the structure of the enzyme changes and active site alters
what is renaturation
when pH returns to optimum the protein will resume its normal shape and will catalyse the reaction again
what happens if the pH significantly changes ?
- enzyme is irreversibly altered and active site is no longer complementary to the substrate
what is denaturation ?
substrates can no longer bind to the active sites
rate of reaction is reduced
what do hydrogen ions interact with
polar and charged r groups
how to hydrogen ion interactions change when you change the concentration of hydrogen ions
- the degree of the interaction is changed between polar and charged r groups and hydrogen ions
how does the concentration of hydrogen ions changing affect r groups
it affects the interaction of r groups with each other
the lower the pH and the more hydrogen ions present, the what ?
- the less R groups are able to interact with each other
- this leads to bonds breaking and the shape of the enzyme changing
where is salivas site of action
mouth/throat
what is the pH of saliva
neutral - 7/8
what enzymes is in saliva
amylase
what is the function of saliva
break starch into maltose
where is gastric juice produced
stomach
gastric juice pH
1-2
what enzymes are in gastric juice
pepsin
what is the function of gastric juice
turns proteins into polypeptides
where is pancreatic juice found
small intestine/ duodenum
pH of pancreatic juice
8
enzymes in pancreatic juice
trypsin
lipase
amylase
maltase
function of pancreatic juice
proteins to polypeptides
triglycerides into glycerol and fatty acids
starch into maltose
maltose into glucose
what do we mean by changing the concentration of the substrate
the number of substrate molecules, atoms, ions in a particular area/volume increases
what happens when we increase substrate concentration
- higher collision rate with active site of enzymes
- formation of more enzyme substrate complex
- rate of reaction increases
what happens when the concentration of an enzyme increases
- number of available active sites increases in a particular area
- formation of enzyme substrate complexes at a faster rate
what is a Vmax
the point where all of the enzyme active sites are used up by substrate particles and no more enzyme substrate complexes can be formed until products are released
how do you increase rate of reaction when Vmax is reached
add more enzyme
increase the temperature
when more enzyme is added so the rate of reaction can rise towards a higher Vmax what becomes the limiting factor
concentration of substrate - when we increase this the reaction rate will rise until the new Vmax is reached
describe a how we can conduct an experiment to determine the effect of temperature on enzymes
- place liver tissue into hydrogen peroxide solution
- measure volume of oxygen released every 5 seconds
- repeat, but boil the liver tissue 5 minutes before placing in a solution
what is a serial dilution
a repeated stepwise dilution of a stock solution of known concentration
what factor is serial dilutions usually done by
factor of 10 to produce a range of concentrations
even if the concentration of the initial solution is unknown, how are serial dilutions useful
relative concentrations
give an example as to when serial dilutions are useful
to investigate the effect of changing the concentration of an enzyme or a substrate in a reaction
how may a stock solution be set up
add 1ml of stock solution to 9ml if distilled water gives 10ml of dilute solution in which there is 1ml of stock out of 10ml = 10 fold dilution
repeat this a number of times to give a serial dilution
why is it important that reactions do not happens too fast
to prevent the build up of excess products
what are the different steps in reaction pathways controlled by
different enzymes
what does controlling enzyme activity at crucial points of metabolic pathways do
regulates the rate and quantity of product formation
how can enzymes be activated
with cofactors
how can enzymes be inactivated
with inhibitors
what is a competitive inhibitor
a molecule that has a similar shape to the substrate of an enzyme and can fit into the active site of the enzyme
this blocks the substrate from entering the active site preventing the enzyme from catalysing the reaction
enzyme can’t carry out function so is inhibited
how are substrate and inhibitor molecules said to compete with each other
to bind to active sites of enzymes
how do competitive inhibitors reduce the rate of reaction-
- it reduces the number of substrate molecules binding to the active sites in a given time
what does the degree of inhibition with competitive inhibitors depend on ?
the relative concentrations of the substrate inhibitor and enzyme
how long do competitive inhibitors bind to active sites for
only temporarily
is the effect of competitive inhibitors reversible
yes
what are the exceptions of reversible competitive inhibitors
aspirin
do competitive inhibitors effect Vmax
no, it only reduces the rate of reaction for a given concentration of substrate
what happens to competitive inhibition when substrate concentration increases enough ?
there will be much more substrate than inhibitor and original Vmax can still be reached
give examples of competitive inhibitors
- statins
- aspirin
what do statins do
reduce blood cholesterol
what can high blood cholesterol cause
heart disease
what does aspirin inhibit
active site of COX enzymes, preventing the synthesis of prostaglandins and thromboxane which are chemicals responsible for pain and fever
how does non competitive inhibiton work
- inhibitor binds to an enzyme at an allosteric site of an enzyme
what is the allosteric site
a different part of an enzyme, not the active site
what does the inhibitor binding to the allosteric site cause
- tertiary structure of enzyme to change
- active site shape also changes
- active site is no longer complementary to substrate so it can’t bind to the enzyme
enzyme inhibited
why is it called a non competitive inhibitor
the inhibitor doesn’t compete with the subtrate
will increasing the concentration of an enzyme/substrate overcome the effect of a non competitive inhibitor
no,
what happens if you increase the concentration of the non competitive inhibitor
decrease of reaction rate, as more active sites become unavailable
what are irreversible inhibitors
inhibitors which can’t be removed from the part of the enzyme they are attached to
they are often very toxic
give examples of irreversible inhibitors
- organophosphates = used as insectisides and herbicides
what enzyme does organophosphates inhibit
acetyl cholinesterase is necessary for nerve impulse transmission which can cause cramps, paralysis and death
what do proton pump inhibitors do
- treat long term indigestion
- irreversibley block an enzyme system responsible for secreting hydrogen ions into the stomach
- reduces production of excess acid
what is end product inhibition
- enzyme inhibition that occurs when the product of a reaction acts as an inhibitor to the enzyme that produces it = negative feedback loop
give an example of end product inhibition in respiration
- when ATP levels are high more ATP binds to allosteric site on the phosphofructokinase preventing the addition of the second phosphate group to glucose
- glucose isn’t broken down and ATP isn’t produced at the same rate
- when ATP is used up, less binds to PFK and enzyme catalyses addition of a second phosphate group to glucose so respiration continues
what is a cofactor
a non protein ‘helper’ component to help proteins carry out their function
what do cofactors do
may transfer atoms or groups from one reaction to another in a multi step pathway or they could form part of the active site of the enzyme
what is a coenzyme
an organic cofactor
how are inorganic cofactors obtained via the diet
as minerals, e.g
calcium
chloride
zinc
why does amylase need chloride
to make sure it has a correctly formed active site
how are many coenzymes derived
vitamins
what are vitamins
a class of organic molecule found in the diet
give an example as to how vitamins help enzymes
vitamin B5, helps to make coenzyme A which breaks down fatty acids and carbohydrates in respiration
what are prosthetic groups
cofactors which are needed by some enzymes to carry out their catalytic function
how are prosthetic groups bound to the enzyme
tightly bound, they form a permanent feature of the protein
give an example of a prosthetic group
zinc ions form an important part of the structure of carbonic anhydrase an enzyme needed for metabolism of CO2
what are precursor enzymes
enzymes which are produced in an inactive form
why are some enzymes precursor enzymes
if they cause damage within the cells producing them
enzymes whose actions need to be controlled under certain conditions
what do precursor enzymes need to do to become activated
change shape
how can precursor enzymes change shape
- by addition of a cofactor
what is an apoenzyme
a precursor enzyme before a prosthetic group is added
what is a holoenzyme
a precursor enzyme once the cofactor is added and enzyme is activated
how can changes in an enzymes tertiary structure be brought about to change shape of a precursor enzyme
by action of another enzyme
give an example as to when 1 enzyme changes the tertiary structure of another enzyme
protease cleaves certain bonds in the molecule and changes some conditions, e.g temperature or pH, activating a precursor enzyme
what are zymogens/proenzymes
a precursor enzyme which is metabolised into an enzyme
TET enzymes
increases rate of transcription
how do TET enzymes affect metabolism at cellular and whole organism level
- changes protein production inside cells
- some proteins are affected to secrete other cells
- increased proteins synthesis requires more energy
- increases rate of respiration
