Enzymes Flashcards
What are enzymes
Globular proteins with a 3D shape so it will have a primary secondary and tertiary structure
They acts as biological catalysts for intra and extracellular reactions to determine structure n function. They affect metabolism of cells and whole organism
They have an active site which is complimentary to the shape of a specific substrate molecule
Why are enzymes 3D
Due to the interactions between the R groups of amino acids that make up the protein (ionic,H,covalent,Hphobic n Hphilic)
Why are enzymes so specific
They have an active site which is complimentary to the shape of a specific substrate molecule
This active site will have a specific sequence of amino acids causing it to have this specific shape. Changing the amino acid sequence and ape of active site likely to be changed
How do enzymes work
For reaction to work reaction molecules must have enough energy to cross potential energy barrier(AE)
All molecules have some KE but only some have enough for a reaction to occur.
The lower the potential energy barrier, the more reactant molecules have sufficient energy and faster the reaction
All catalysts function by forming transition state with reactants, of lower free energy than would be found in the uncatalysed reactions.
And the formation of enzyme substrate complexes lowers AE of metabolic reactions
What is metabolism
And what reactions are enzymes involved in
All chemical reactions inside a cell
Anabolic(building bigger molecules) and catabolic (breaking large molecules down)
Give eg of an exhume that catalyses intracellular reactions
Catalase:catalysed decomposition of hydrogen peroxide into H20 and O2
2 enzymes that catalyse extracellular reactions
Amylase:carbohydrate catalyses digestion of starch to maltose in saliva
Trypsin: pancreatic endopeptidase catalyses hydrolysis of peptide bonds in small intestine lumen
What do single celled organisms and fungi rely on to digest their food
Extracellular enzymes
Explain the induced fit model of enzyme action
Helps explain why enzymes are so specific and only bond to one specific substrate. The shape of the active site is not directly complimentary to the substrate and it’s flexible.so active site slightly changes shape to better fit a substrate molecule once it binds.
Conformational change (changes in 3D struct of enz when it binds toS)enables
ES complexes to form when substrate adsorbs
This puts strain on substrate bonds lowering the activation energy. Bonds in the EPC weaken and product desorbs
What’s the lock and key model theory
This is where the substrate fits into the enzyme in the same way a key fits into a lock-active site and substrate have a complimentary shape.
Active site has a rigid shape determined by the tertiary structure so it’s only complimentary to one substrate. Formation of the ES lowers activation energy
Limitation of the lock and key model
New evidence has shown enzyme substrate complex changed shape slightly to complete the fit and licking substrate even more tightly to enzyme
Unlike the lock and key model, the induced fit model emphasizes that the enzyme is not completely rigid, but can adjust its shape to better accommodate the substrate.
why does enzyme substrate lower activation energy
When bringing substrates tg it bends substrate molecules and bring em close tg in a way that facilitates bond-breaking, helping to reach the transition state. Reducing the repulsion between em
If enzymes catalysing a breakdown reaction fitting into active site the enzyme can induce strain on certain bonds within the substrate molecule, making them more susceptible to breaking and facilitating the reaction.
Factors affecting enzyme activity
Temp
Ph
Enzyme concentration
Substrate concentration
Limiting factors
How does temp affect enzyme activity
Upto the optimum temp, enzymes and substrates gain more KE so they move around more and faster
Greater chance of more successful collisions between enzymes active site and substrate molecules so higher ROR
What’s optimum and what happens to enzymes when they pass the optimum
Temperature at which rate of an enzyme controlled reaction is at its fastest.
When it’s above optimum, temperature increases, the extra KE begins to break bonds in tertiary structure of the enzyme.(H first)
Causes enzyme to change shape and active site changing shape so yes denatured. Active site no longer has complimentary shape to substrate so no esc formed and ror decreases.
What’s the temperature coefficient
Q10-R2(rate at higher temp)/R1(rate at lower temp
If a graph had a q10 value of 2 what would it mean and if it’s three too
Rate doubles when temp raises by 10
If it’s three it would treble
How does ph affect enzyme activity
All enzymes have different PHs. As environmental Ph moves away from optimum. The changing ratio of H+ and OH- interferes with hydrogen and ionic bonds that hold the enzymes tertiary structure in place . This resulting in active site changing shape so desaturation and it’s no longer complimentary to substrate so escs aren’t formed and rate of reaction decreases
How does enzyme concentration affect
Enzyme activity
The more enzyme molecule there are in a solution the more likely a substrate molecule is to collide with one as more active sites are available and form an enzyme substrate complex. So it inc ROR.
What happens when enzyme concentrations plateaus off
Enzyme conc isn’t a limiting factor anymore Substrate amount is.There are active sites which are empty so rates cannnot increase any further.
Effect of substrate concentrations
The higher the substrate conc higher ROR. More substrate molecules increase collisions between substrates and enzymes so more active sites occupied and more enzyme substrate complexes formed.enzymes in excess atp and substrates acting limiting factor.
Sub conc dec over time so if no variable changed ROR dec too so initial ROR is highest ROR
What happens when substrate concentration plateaus off
All active sites are occupied no further increase in rate possible and it stays constant.sub conc no longer limiting factor.Another factors limiting like EC. Not enligh enzymes to act on inc no of substrate molecules as AS are all saturated.(vmax)
If we doubled the enzyme concentration what would happen
The maximum rate doubles (vmax) assuming there is sufficient substrate available
What’s vmax
Rate of reaction when enzyme is saturated with substrate - it’s the max ROR.
Relationship between ROR and conc of substrate depends on affinity of enzyme for its substrate.
Vmax reveals the number of substrate molecules being catalases per second
What are cofactors
Non protein facilitator molecules -increase rate of reaction by enabling enzyme activity
What are inorganic cofactors
Some cofactors could be inorganic molecules/iobs. They work by helping substrate and enzyme to bind tg. They don’t directly participate in reaction so aren’t used up in any way.Eg Cl2
For amylase
What are the organic cofactors
Co enzymes-participate in the reaction and are changed by it.Theyre just like a second substrate. They act as carriers moving chemical groups between different enzymes. Theyre continually recycled during. Eh vitamins are usually sources of coenzymes NAD from VB3
Prosthetic groups-non protein, tightly n permanently bound groups to enzymes which enables escs to form-bit directly involved in reaction . it will become a conjugate protein after.eg Zn2+- in carbonic anhydrase which breaks down co2 in rbc
Why do we need small quantities of vitamins in our diets
For a healthy metabolism so they can help release energy from food
What are enzyme inhibitors
Molecules that bind to enzymes and prevent enzyme action so can’t catalyse reactions.
What are the different inhibitors
Competitive inhibitors-have a similar shape to substrate molecules competing with them to bind to the active site but no reactions takes place. Instead they block active site so no substrate molecules can fit in it
How much it’s stopped by depends on conc of inhibitor and substrate.Jf theres high conc of inhibitor it w take up nearly all active sites n hardly any of substrate w get to enzyme . Higher conc of substrate then substrates chances of getting to active site before inhibitor increases.So increasing concentration of substrate will increase ROR
What do non competitive inhibitors do
Bind to the enzyme away from its active site.Theyre site they bind to the enzymes allosteric site. Causing changes in tertiary structure= active site to change shape so substrate molecules can no longer bind to it.
They don’t compete w substrate molecules to bind to active site cuz they’re a diff shape.Inc concentration of substrate won’t many a difference-enzyme activity still inhibited
What happens when more substrate molecules are added with a competitive inhibitor and a non competitive inhibitor
W competitive: same number of enzymes but when you add more substrates they outnumber the competitives so higher ROR reached. Effect of competitive inhibitor reached.
Non competitive : when adding more substrates, there are fewer active enzymes available n rate limited
So effect is not overcome
What are hyperthermophiles
And pyschrophiles
Hyperthermophiles have opt temp above 75c so grow at highest temp.Due to several adaptations that give proteins ability to retain structure and function in term of extreme temperatures.(more dialogue bonds,hydrophobic residues or ionic interactions
Pyschrophiles are capable of growth and reproductions in cold temperatures -20 to +10.less ke in cold condition for successful collisions and proteins lose flexibility .adaptations in proteins allow em to move n change shape at low temp w a flexible structure
Both require subtle changes in amino acid composition to stay functional in extreme conditions (changes in charge and hydrophobicity)
How can you measure the rate of reaction using hydrogen peroxide and catalase
Measure volume of gas produced in a given time
1)set up boiling tubes w same vol n conc of hydrogen peroxide,to keep ph constant add equal vol of buffer solution to each
2)set up trough of water and fill measuring cylinder w water n tip it upside down and put deliver tube in hole of cylinder
3) put each boiling tube in a water bath set to a different temperature (10,20,30,40) along w about tube w catalase. Wait 5 mins before moving to next step so enzyme gets upto temp
4) use pipe eye to add sane vol n conc of catalase to each BT. Attach bung quickly.
5) record how much o2 produced in the first minute of reaction using a stopwatch
6) repeat exp three times and find mean volume of O2 produced
7)calculate mean rate of reaction at each temperature by volf of oxygen produced / time taken.units cm3s-1
Weird equation for action of catalase
Hydrogen peroxide-oxygen and water
Controlled variants for this catalase reaction
Enzyme vol n conc
Substrate vol n conc
Ph
Hazards n safety for catalase
HP is irritant. Wear goggles n avoid skin
Take care in handling hot water baths n wash hands after dealing w source of catalase
Gore to find the effect of enzyme concentration on ROR using amylase
1) put drops of iodine into each well of spitting tile
2) make a serial solution of amylase to make several concentrations
3)add same vol n conc of starch to first booing tube at same time n start timer
4) use dropping pure to put drop of mixture into one of the wells containing iodine solution at regular intervals
5) time how long it takes for colour to turn blue black
6) repeat 2 more times and calculate mean time taken
7) repeat experiment for each amylase conc
Controlled variables for amylase practical
Temperate
Ph
Enzyme vol
Substrate conc n vol
How to do a dilution for catalase w a dilution factor of two so it halves
Start with 2% catalase solution and add 4cm3 to first boiling tube
Using syringe add 2cm3 of solution in first tube to next tube making it 1% catalase solution
Repeat to make 0.50,0.25,0.13
What is a stem cell
Undifferentiated cells that can divide indefinitely and turn into other specific cell types. All multicellular organism have some form of stem cell
What’s the four types of stem cell
Totipotent-can develop into any cell type including placenta umbilical cord dev fetus and embryo and their formed shortly after fertilisation of egg so versatile af. After 4 days they specialise slightly into PP
Pluripotent-can develop into any cell type w out placenta n embryo. Not as versatile as T
Eg embryonic stem cells and induced pluripotent stem cells(lab)are PP cells
Multipotent- can only develop into few different types of cell. Cells of. Certain class n category
Unipoyent- can only develop into one type of cell
characteristics of a stem cell
1)self renew(mitosis)
2)differentiate into a specialised cell type
Where are stem cells from embryonic cells derived from
Zygotes which turn into blastocyts which then turn into embryos
Why is there high demand for stem cells when it comes to RBC
We need to make a lot of em often as they only last 120 days
What’s differentiation
Stem cells divide to become new cells which become specialised this is differentiation. Eg in animals adult stem cells are used to replace damaged cells. Adult stem cells divide n differentiate into bone barrow to replace worn out blood cells (erythrocytes n neutrophils)
How does stem cells differ between kids n humans
Stem cells are found in early embryos and in the first few days of an embryos life any of its cells can develop into a type of human cell.
In adults stem cells are only found in few places like bone marrow but they’re not as flexible as they can only clop into a limited range of cells
Embryonic stem cells can divide indefinitely whilst adult can’t so getting adult ones r harder
Adult cells alr specialised so potential to repair damaged tissue is very limited
Where are stem cells found in plants
Meristems of plants (where growth takes place most) in the roots n stem stemcells of vascular cambium divide and differentiate to become xylem vessels n phloem sieve tubes
What type of stem cells is a meristematic one
Totipotent that develops into various types of plant cell
Uses of stem cells in medicine
They could treat neurological diseases like Alzheimer’s-brain cells are destroyed as a reult of the build up of abnormal proteins : drugs only alleviate these symptoms n they’re tryna regrow healthy nerve cells.
Parkinson’s- ppls suffer from tremor that they can’t control.loads to loss of a. Type of nerve cell in brain that releases dopamine for control movement . Transplanted stem cells may help degenerate the dopamine producing cells
Treat heart disease- muscle tissue is damaged as a result of heart attack body can’t replace these cells so ppl tryna use stem cells to make replacement heart cells
How does ppl t1 diabetes use stem cells
Ppl w insulin dependent diabetes they’re body destroys the cells that produce this insulin from pancreas , so stem cells to replicate this insulin is used n injected
What else are stem cells used for
Drug trials-new drugs can be tested in cultures of stem cells before animals n humans
Researching developmental biology-study of changes that occur as multicellular organism grow n develop from a single cell as a fertilised egg.Dtem cells are umpirtant for this ad they divide indefinitely and differentiate into any cell within an organism.
What are embryonic stem cells
Inside a blastocyst cells can be cultured into an embryonic stem cell. They’re undifferentiated but they have unique ability to divide indefinitely into almost any type of cell in body
Limits of ES cells n why animal cells are better
There aren’t enough of them from ivf n Donors as there’s a huge demand.
So we need to use animal cells but this can cause uproar saying chimeras are created they’re not used for transplants in humans as it can cause diseases but they’re sooo useful for research and animal ones you could get so many of them
What are embryonic stem cells used for
Cloned to form any type of tissue in body. Including specific tissues for transplants with no rejection from immune system
Can study disease. Cells cloned from someone w a disease will carry faulty genes that cause it and scientists can study this n try out new drugs on cell
Allows us to study earliest stages of human development so we can prevent birth defects miscarriages etc
Ethics towards es cells
Removal of embryonic stem cells results in destruction of the embryos
Many ppl believe life begins at conception and destruction of embryos is murder bsc. Lack of consensus to when embryo has rights
This argument stops treatment of many incurable diseases. Umbilical cord stem cells may help treatment can overcome the problem but they only multipotent not pluripotent limiting use.
Adult can be used to but can’t divide as much and can have mutations.
What are induced pluripotent cells
What’s gene therapy
Ce therapy
Cell reprogramming
Cells that can be reprogrammed from skin or blood cells to become any type of cell in body
Technique to test n prevent disease by correcting mutation
Cell therapy-treatment that uses stem cells to repair damaged cells in body
Process of having identity of cell and returning it to a more primitive state of gene expression .
Evaluate between human stem cells n plants stem cells
They both have specific regions where stem cells are found so bone marrow and skin and meristems for plants at roots n shoots
Both undergo process of mitosis n differentiation
Neither have totipotent stem cells and they have been specialised slightly so they can be one type of cell
Animals are multi potent and meristems are Pluripotent
Plant stem cells facilitate growth of cell animal helps replace cell
Meristematic becomes transport vessels however bone marrow stem cells continue towards the blood cells which are transported
How are metabolic poisons enzyme inhibitors enzyme inhibitors
Metabolic poisons-cyanide is a non competitive irreversible INH of an enzyme that catalyses respiration reactions.cells that can’t respire die
Ethylene glycol- metabolises ethanol dehyrogenase to oxalic acid as ethylene glycol is similar in shape to ethanol which acts a competitive inhibitor of above reactions . Mixing large amounts of ethanol w ethylene glycol slow ROR
How do medicinal drugs act as inhibitors
Antibiotics like penicillin inhibits transpeptase which catalyse formation of protein in bacterial cell walls. It weakens cell walls as its structurally similar to one of substrates used in wall building and as P is different from substrate it prevents bacterium from regulating its osmotic pressure.cell bursts and bacterium killed
Antiviral drugs can -eg reverse transcriptase INH which treat HIV as they inhibit enzyme reverse transcriptase which catalyses replication of viral dna preventing virus from replicating.
What is a metabolic pathway and what ar they regulated by
A series of connected metabolic reactions
Product of first reaction is used in second etc and each reactions catalysed by diff enzyme but many enezume are inhibited by product they catalyse which is product inhibition
End product inhibition- final product in metabolic pathway that inhibits enzyme that acts earlier on in pathway .its reversible so level of product drops level of inhibition falls to and enzyme function again n more esc formed
Function of end product inhibition again and give an example
Regulated metabolic pathways and controls amount of end product that’s made
Phosphofrucyokinase involved in metabolic pathway that breaks down glucose to make atp. ATP inhibits Mr p over here so high level of atp prevents more atp being made
How are enzymes synthesized to be inactive precursor molecules
Part of precursor molecules inhibits action as an enzyme. So only work when activated which is done Once it’s removed via chemical reaction then enzyme becomes active
This is good as it prevents enzyme from damaging cells
What are the different inhibitors enzyme could be
Drugs
Metabolic poison
Control mechanism in end product inhibition
Inactive precursor molecules
2 examples of enzymes that catalyse extracellular reactions
Trupsin :pancreatic endopeptidase catalyses hydrolysis of appetite bonds in small intestine lumen
Amylase carbohydrate catalyses digestion of starch to maltose in saliva /small intestine lumen
How does end product inhibition work
The final product of a metabolic pathway binds to an allosteric site on the first enzyme in the pathway.
This binding inhibits the enzyme’s activity, shutting down the pathway.
When the concentration of the end product decreases, the inhibition of the enzyme is reduced.
The metabolic pathway can then proceed again.
