Chapter 4 - Enzymes Flashcards
metabolism definition?
the sum of all of the different chemical reactions and reaction pathways happening in a cell or an organism
in which 2 ways can reactions be sped up?
increasing temp - but can damage cells, denature proteins
2- catalyst
what is a catalyst?
a chemical that speeds up the rate of reaction and remains unchanged and reusable at the end of the reaction
what is a substrate?
any molecule that can have a reaction catalysed by an enzyme
what is an enzyme’s turnover rate?
the number of substrates an enzyme can catalyse in one minute
what is an active site?
the reactive part of an enzyme
what is complementary binding?
refers to when 2 molecules fit together to complete each other
what is activation energy?
the energy required to start a reaction
why will a reaction with a lower activation energy occur faster?
bc there will be more molecules with sufficient energy to react
enzymes catalyse reactions by lowering the ______ _____
activation energy required for the reaction to occur
how is the activation energy lowered?
when a substrate(s) binds to the active site, it is held in a specific orientation that facilitates its reaction
- bc it is held in such an efficient way that it makes all the chemical groups want to react
The active site can also ______ put pressure on the substrate, further lowering the ________ _____
physically, activation energy
enzyme mechanism- how do they work ?
- biological reactions take part in solution where enzymes and substrates are free to move around (cytoplasm)
- when a substrate collides with the correct enzyme, it binds with its active site forming an enzyme substrate complex
assumption of the lock and key model?
the enzymes active site is rigid and permanently complementary to the shape of its substrate, substrate fits perfectly into active site
- if substrate is wrong shape, no reaction will occur
what is the flaw of the lock and key hypothesis?
scientists discovered that the active sites are flexible in their shapes
induced fit model explanation?
- the enzyme’s active site is usually relaxed and not exactly complementary to the shape of the substrate, so they do not fit exactly together
- substrate INDUCES a conformational change in the shape of the enzyme
- the enzyme twists the substrate, making the bonds easier to break or pushes substrates closer together encouraging a link to be formed, AE is lowered
INDUCEd fit
substrate binding INDUCES active site to change shape
2 types of metabolic reactions that occur in the body are ?
(enzymes catalyse both)
- anabolic, catabolic
anabolic reactions definition
metabolic reactions that build molecules
catabolic reactions definition?
metabolic reactions that break down molecules
enzymes often work together to form more complex products, by …
using the products of one reaction as the substrate for a second
a series of enzymes can work together to form a ….
metabolic pathways e.g. Calvin Cycle
intracellular enzymes?
enzymes that work within cells
intracellular enzymes work within 2 types of intracellular enzymes:
- some are free moving within a cytoplasm
- some are fixed in place by binding with a membrane (mitochondria)
enzymes can affect both the _____ and ____ of bio moelcules
structure, function
e.g. can turn ADP -> ADP
Catalase?
- breaks down poisonous hydrogen peroxide into harmless carbon dioxide and water
extracellular enzymes?
enzymes that work outside of cells
digestion definition?
the breakdown of large insoluble molecules into smaller soluble molecules
what does protease do
breaks down proteins -> amino acids
what does lipase do?
lipids -> fatty acids, glycerol
what does carbohydrase do?
carbohydrates -> individual sugars like glucose
some extracellular enzymes can be excreted outside of the body?
to the external envir
- e.g. tears contain enzymes, mushrooms
amylase ?
- extra
- digestive enzyme secreted from salivary gland & pancreas
- breaks down starch -> maltose
Trypsin?
extra
- a protease that acts in the lumen of the small intestine
- HYDROLYSES PEPTIDE BONDS - breaks down proteins -> amino acids
what is the point of cofactors?
some enzymes can only work if they have a certain non-protein molecule attached to them
what is a cofactor?
substances that must be present to enable enzymes to catalyse reaction at the appropriate rate
cofactors work in 2 main ways:
- cofactors can affect the charges on either the substrate or the enzyme’s active site
- cofactors can pair with a substrate to form the correct shape to fit in an active site - these are called co- substrates
Contractors can bind to prosthetic groups permanently and are called ?
Prosthetic groups
Prosthetic groups definition?
Are inorganic cofactors that are permanently bound to an enzyme and form part of it’s structure
Organic non protein molecules are called?
Coenzymes
Coenzymes definition?
Are organic molecules that temporarily bind to the active site of enzyme either right before or at the same time as the enzyme-substrate complex forms
UNLIKE enzymes, coenzymes are
CHANGED by the reaction they help catalayse
Energy profile diagram - between substrates and products is
TRANSITION STATE
The rate of reaction is
The speed at which a reaction occurs
What affects ROR?
- Conc of enzymes and substrates
- temp, PH
What are optimal conditions?
Conditions that maximise an enzymes ROR
As substrates are used up, enzymes
Take LONGER TO COLLIDE with the next one
The effect of temp on rate?
When temp ⬆️ of a solution, KE of enzyme & sub molecules increases, so chance of sucessful collisions increases, rate of ESC formation increases
- optimum - IROR is highest as max KE, max chance of SC & enzyme hasn’t started to denatrue yet
- denatured - more and more denature (NOT ALL AT ONCE OTHERWISE WOULD BE STRAIGHT LINE DOWN)
What is the temperature coefficient?
The temp coefficient for a specific reaction is the effect of a 10°C rise in temp on the rate of reactiob
The effect of PH on rate?
- Acids and alkalis can affect the shape of proteins
- the H plus and OH minus ions can change the way chemical groups react with each other so can affect shape of protein, denatures
Enzymes can be activated by _____ and deactivated by ______
Cofactors - activation
Inhibitiors- deactivation
Inhibitors definition?
molecules that prevent enzymes from carrying out their normal function of catalysis (or slow them down)
Competitive inhibitors?
- fits into the active site of an enzyme instead of a substrate- so it competes with the substrate
- these inhibitors form a physical barrier that prevent the formation of an enzyme substrate complexes
Non competitive inhibitors?
- bind to a separate part of an enzyme called its allosteric site
- binding to a non-competitive inhibitor causes a conformational change in the enzyme.
- this alters the shape of the enzyme’s active site so that it is not complementary with its substrate, substrate cannot bind, ESCs can’t form
End product inhibition?
- enzymes can work together to complete metabollic processes
- most of the time, a cell will only want a certain amount if a mol being produced.
- in some cases, one of the products acts as an inhibitor to another enzyme in the pathway
If the inhibitor is non competitive and the last product ij the pathway it is called?
End product inhibition
How is end product inhibition an example of negative feedback loop?
- If conc of final product is high the more inhibition can occur
- greater inhibition will lead to a decrease in the amount of end product being produced
- if conc of end product decreases, inhibition does too
what type of protein are enzymes?
gloubular
what is the V max ?
max IROR or rate of the enzyme catalysed reactions
Enzymes lower the ?
activation energy
when enzyme denatures?
the active site changes first and is no longer complementary to the substrate
what is end product inhibition?
enzyme inhibition that occurs when the product of a reaction acts an as inhibitor to the enzyme that produces it
the difference between cofactors and coenzymes?
if the cofactor is an organic molecule it is called a coenzyme
prosthetic groups are a ______ feature of the protein
permenant
precursor enzymes?
- many enzymes are produces in an inactive form, known as inactive precursor enzymes, particularly damaging enzymes or enzymes whose action needs to be controlled
what are enzymes ?
- globular proteins that are biological catalysts
ANABOLIC + CATABOLIC REACTIONS =
METABOLIC REACTIONS
what can we measure to calc the enzyme’s ROR?
- the build up of products
- reduction of reactants
- change in colour
- change in PH
the gradient at 0 sec gives IROR which is max ROR in these condition:
- enzyme conc
- sub conc
- temp
- PH
factors affecting rate of enzyme catalysed reactions - enzyme conc?
- as E conc increases, ROR increases
- when E conc is 2x, no.of active sites is 2x so chance of successful collisions is also 2x
factors affecting rate of enzyme catalysed reactions - sub conc?
more subs, IROR increases = more subs that can bind to the active site of enzymes
- (enzyme conc is fixed)
- at point of velocity max, a plateau is reached as all of the active sites are being used up at once, so IROR can’t increase
How does temp acc denature an enzyme?
- shape of active site changes
- due to increased internal vibrations which cause hydrogen bonds within protein to break
Q little 10 - the temp co-efficient
“for a 10 degrees C rise in temp, the ROR doubles”
when Q little 10 does not equal 2:
- q10 only works when molecules are free to move in solution
- if mols rn’t free to move, Q10 doesn’t work & doesn’t =2
- E.g. LDRs of photosynthesis
what is PH?
a measure of hydrogen ion conc
why do enzymes only have a narrow PH range?
- active site will only be in right shape a certain H ion conc- this is optimum PH
- when PH changes, excess or reduction in H ions disrupts 3D shape of the protein, denatured
but what if PH changes back?
- if returns to optimum, protein will resume its normal shape and catalyse reactions again - renaturation
- when PH conc changes more sig, structure is irreversibly altered - no renaturation
enzyme e.g. & their optimum PHs?
- pepsin - a protease that works in stomach - PH2
- salivary amylase - 7 - in mouth
- arginase - enzyme that works in liver cells - 9.5
what is the point of enzyme inhibition?
it’s important that the rate of an enzyme catalysed reaction in a cell is controlled/ doesn’t go too fast
how does a competitive inhibitor work?
- competitive inhibitor competes with the substrate for the enzyme’s active site
- ESC can’t form if the enzyme is bound to inhibitor
- slows ROR
why is Vmax still achieved with competitive inhibitor:?:
- eventually the substrate molecule ratio increases, the sub conc becomes so sig comp to competitive inhibitotr conc (fixed), that the comp inhibitor has very little/ no effect on the IROR
examples of competitive inhibitiors - statins?
inhibit one of the enzymes responsible for production of cholesterol and therefore lowering cholesterol
examples of competitive inhibitiors - aspirin?
inhibits the production of molecules that cause pain
examples of competitive inhibitiors - ethylene glycol poisoning/ anti freeze?
- ethanol is used as the inhibitor
- ethylene glycol is broken down into oxalic acid by an enzyme in the liver (ethanol hydrogenase).
- Oxalic acid causes blood acidosis, kidney damage… ethanol slows down reaction,
- and so liver can detoxify the molecules
examples of competitive inhibitiors - why can ethanol be used?
- similar shape to ethylene glycol
- some short term side effects
(super vet, icicle)
examples of competitive inhibitiors - peniclillin?
antibiotic that prevents the formation of bacterial cell walls
irreversible inhibitors are often very?
toxic, as they can destroy the enzyme they bind to
why can V max not be achieved with non comp inhibition?
as substarte conc increases, the ratio of inhibitor to enzyme molecules doesn’t change
- so there’s always the same no. of enzyme molecules being inhibited no matter the substrate conc
examples of non competitive inhibitors - digoxin?
a drug that reduces heat rate and increases force of muscle contraction- extracted from foxgloves
example of non competitive inhibitors (farming) ?
organophosphate pesticides
examples of non competitive inhibitors
proton pump inhibitors - treat indigestion
difference between serial dilutions and dilution series table?
serial dilution - don’t start from stock solution, instead start from previous solution (like compound interest), decrease in conc by a factor of 10 each time
dilution series - always starts from stock solution, a set volume is made up
Bio: cofactors description?
Usually inorganic small often ions
- bind temporarily to enzyme
Bio: cofactors EXAMPLE*
CHLORIDE IONS ACT AS COFACTORS FOR SALIVARY AMYLASE
Bio: Coenzymes description ?
Organic, larger, more complex, often derived from vitamins
Bind temporarily to enzyme
Bio: examples of coenzymes *
Vitamin B 3
- Vitamins act as coenzymes
Bio: prosthetic groups description?
Form a permanent part of the enzymes structure
Bio: prosthetic groups examples?
- Haem group in Haemoglobin (Haemoglobin isn’t an enzyme tho)
- Zn 2 plus allow carbonic anhydrase to form carbonic acid from H2O in erythocytes (RBCs)
Bio: Inactive precursor molecules?
Pepsinogen
- some enzymes secreted as INACTIVE precursor molecules, especially digestive enzymes that coild harm cells that secrete them
- these enzymes are activated by other enzymes or a change in PH outside the cell
- E.g. pepsinogen is an inactive protease released into the stomach. Low PH in stomach activates Pepsinogen turning it into Pepsin
