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Module 2- Foundations in Biology > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What are enzymes

A

Globular proteins which act as Biological catalysts which speed up metabolic reactions in living organisms by lowering activation energy, without being used up or changed themselves

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2
Q

Describe the properties of enzymes

A
  • Globular
  • Usually Soluble in water (a polar solvent)
  • Proteins
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3
Q

What is the term for how fast an enzyme works

A

Turnover rate

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4
Q

What is the term for how many reactions an enzyme molecule can catalyse

A

Turnover number

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5
Q

What is the benefit of enzymes

A

Chemical catalysts need very high temperatures, increased pressures or extremes of pH

Enzymes speed up metabolic reactions by up to 10*12 times at lower temperatures, and often at neutral pH and normal temperatures- biological catalysts- able to function in conditions that sustain life

More specific than chemical catalysts- no unwanted byproducts, rarely make mistakes- cells where made/acting can regulate production/ activity to fit needs of the cell/organism at that time

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6
Q

Describe the development/issues with enzyme stucture

A
  • instructions encoded in genes- if gene has mutation that alters sequence of amino acids in the protein, this may alter enzymes tertiary structure/active site and prevent it from functioning
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7
Q

What do enzymes need to catalyse some reactions

A

co-factors

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8
Q

What can result from enzyme malfunction

A
  • If an enzyme that catalyses a metabolic reaction is deficient, a metabolic disorder results
  • Enzymes also catalyse the formation of the organisms structural components- e..g. collagen in bone, cartilage, blood-vvessel walls, joints and connective tissue- some disorders can form malformations of connective tissue and can be very harmful- such as stone man syndrome
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9
Q

What is the active site of an enzyme

A

The specific area indented/ the cleft on the surface of the molecule

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10
Q

How many amino acids does an enzymes active site tend to contain

A

6-10

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11
Q

Describe the relation of tertiary structure to an enzymes active site

A
  • crucial- shape is complimentary to shape of substrate molecule
  • each type of enzyme highly specific in its function- can only catalyse a reaction involving the particular type of substrate molecule that fits into its active site
  • shape of the enzymes active site and hence its ability to catalyse a reaction can be altered by changes in temperature and pH, as these affect bonds that hold proteins in their tertiary structure
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12
Q

What are the 2 types of reactions enzymes catalyse

A
  • intracellular
  • extracellular
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13
Q

how many metabolic reactions can be going on at the same time in any cell, and what are some of these part of

A

up to 1000, metabollic pathways

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14
Q

describe metabolic pathways

A
  • each pathway in a living cell is one of a series of consecutive reactions- every step catalysed by a specific enzyme that produces a specific product
  • the various reactants and intermediates act as substrates for specific enzymes
  • the reactants, intermediates and products are called metabolites
  • respiration and photosynthesis examples of complex metabolic pathways with many enzymesinvolved
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15
Q

Describe catabolic and anabolic recations

A
  • catabolic- metabolites are broken down into smaller molecules- release energy
  • anabolic- energy used to synthesise larger molecules from smaller ones
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16
Q

What is an example of an intracellular enzyme

A

catalase

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17
Q

Where is catalase found and why

A

nearly all living organisms are exposed to oxygen, as it protects cells from damage by reactive oxygen by quickly breaking down hydrogen peroxide- a harmful by-product of of many metabolic reactions

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18
Q

What is the word equation of the reaction catalase catalyses

A

hydrogen peroxide –>water + oxygen

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19
Q

Describe the structure and features of catalase

A
  • 4 polypeptide chains
  • contains haem group with iron
  • fastest acting enzyme- highest turnover rate known- 6 million per second
  • in eukaryotic cells, found in small vescles called peroxisomes
  • when white blood cells ingest pathogens they use catalase to help kill the invading microbe
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20
Q

Describe the optimum conditions for catalase

A
  • optimum ph for humans is around ph7, but 4-11 for other species
  • humans temp is 45 degrees, but some thermophilic archaea it is 90 degrees
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21
Q

Describe extracellular enzymes

A

secreted from cells where made and act outside of cell

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22
Q

Name and explain examples of extracellular enzymes

A
  • fungi (e.g. the bread mould mucor) release hydrolytic enzymes from hyphae- enzymes digest carbohydrates, proteins and lipids in bread and products of digestion- glucose, amino acids, glycerol and fatty acids are absorbed into the fungal hyphae for respiration and growth
  • digestive enzymes secreted from cells lining alimentary canal into gut lumen- intracellularly digest large molecules (e.g. proteins, lipids, carbohydrates and nucleic acids) found in food. Products then absorbed via epithelial cells of the gut wall into the bloodstream to be used for respiration, growth and tissue repair. E.g. amylase produced in salivary gland and pancreas to digest polysaccharide starch to disaccharide maltose in mouth and lumen of the small intestine. Trypsin made in pancreas, acts in lumen on small intestine to digest proteins into smaller peptides by hydrolyzing peptide ponds- optimum pH between 7.5-8.5
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23
Q

Name two models of enzyme action

A
  • lock and key hypothesis
  • induced-fit hypothesis
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24
Q

why do substrate molecules fit in their enzymes active site

A

the tertiary structure of the enzymes active site gives it an active site that is complementary to that of the substrate molecule- lock and key theory

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25
Q

describe 2 versions of the lock and key hypotheses (anabolic vs catabolic)

A
  • substrate molecules bind to specific and complimentary active site- temporary hydrogen bonds hold the 2 together forming an enzyme substrate complex- bonds in substrate molecule destabilised- enzyme-product complex, broken down into smaller product molecules that leave active site
  • sam other than bonds form between substrate molecules- enzyme product complex- larger product molecule leaves
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26
Q

how does the reaction between an enzyme and substrate strart

A
  • substrate molecules have kinetic energy- constatly moving randomly
  • if substrate molecule successfully collides with enzyme molecule, ES complex formed
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27
Q

what does the lck and key theory not exaplin

A

how the ES complex is stabilised

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28
Q

who proped the induced fit hypothesis

A

Daniel Koshland

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29
Q

what does the induced fit hypothesis suggest

A
  • the active site of an inzyme is not a rigid fixed structure- the presence of the substrate molecule in it induces a shape change- giving it a good fit
  • the active site still has a complementary shape to teh substrate molecule, but on binding, the subtle changes of shape to the side chains (R-groups) of the amino acids that make up the active site give a more precise conformation that exactly fits the substrate molecule
  • moulding allows substrate to bind more effectively to the active site
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30
Q

describe how an enzyme would break own a substance

A
  • substrate binds to active site
  • induced fit
  • form ES complex
  • bonds in substrate destabilize
  • EP complex formed
  • products leave site
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31
Q

what are exampes of bonds which hold binf the substrate to active site

A

Non-covalent fores- hydrogen bonds, ionic attractions, van der waals forces and hydrophilic interactions

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32
Q

what to chemical reactions need to activate/begin them

A

energy

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33
Q

what happens to start most chemical recations, what is the issue with this in te body and so what happens instead

A
  • most heated- increases kinetic energy- makes them react as moving faster randomly so more likely to successfully collide
  • in living cell, temperature cannot be raised too much or proteins would denature and lipids would melt.

Because enzymes have an active site specific only to the substrate molecules, they bring teh substrate molecules close enough together to react without need for execcisve heat- thus lower activation energy and speed up metabolic recations

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34
Q

Describe the effect of substrate concentration on rate of reaction

A
  • as substrate is added, ROR increased as more ES complexes can form
  • as a result, more product molecules are formed
  • substrate concentration is limiting factor because as it increases, ROR increases
  • Reaches point of saturation- adding more substrate molecules wont increase ROR
  • because all enzymes active sites are occupied with substrate molecules
  • if more substrate molecules are added, they cant successfully collide with and fit into an enzymes active site
35
Q

Graph of enzyme concentration

A
36
Q

what does enzyme concentration depend on in living cells

A
  • rate of enzyme synthesis and enzyme degradation
37
Q

Briefly describe rate of enzyme synthesis

A

Depending on cells needs, genes for synthesising particular enzymes can be switched on or off

38
Q

Describe and give advantages of enzyme degradation

A
  • protein component of living cells constantly being turned over
  • cells are continuously degrading old enzyme molecules to their component amino acids and synthesising new enzyme molecules from amino acids.
    Advantages:
  • elimination of abnormally shaped proteins that might otherwise accumulate and harm the cell
  • regulation of metabolism in the cell by eliminating superfluous (surplus to requirements) enzymes
    Enzyme degradation just as important as synthesis for metabolism
39
Q

Describe what happens as you increase enzyme concentration

A
  • as it increases, more active sites become available so more successful collisions between enzyme and substrate occur
  • more ES complexes can form per unit time- ROR increases
  • enzyme concentration is limiting factor- as it increases, so does ROR
  • if substrate concentration fixed or limited, all substrate molecules will be occupying/occupied an active site- reaction at maximum rate for fixed substrate concentration
  • if enzyme concentration is increased further, there will be no increase in ROR as active sites of extra will not be occupied
  • enzyme concentration no longer limiting factor- as it increases, ROR doesn’t
  • substrate concentration now limiting factor- lack of substrate molecules preventing ROR increasing
40
Q

Enzyme concentration graph

A

Same as substrate one (when substrate limited, if not, straight line)- change words

41
Q

Which part of any enzyme catalysed reaction is the fastest and why

A
  • the initial rate is the fastest
  • at the start, when enzyme and substrate molecules are first mixed and moving randomly, there is a great chance of a substrate molecule successfully colliding with and enzymes active site
  • as the reaction proceeds, substrate molecules are used up as they are converted into product molecules- so the concentration of substrate drops
  • as a result, te frequency of successful collisions between enzyme and substrate molecules decreases because some enzymes may collide with product molecules, and so the ROR slows down
  • thus, the initial ROR is fastest
42
Q

What is Q10

A

temperature coefficient- calculate by didviding ROR at (T+10)oC by the ROR at ToC- should be around 2 unless above optimum temperature as denaturing

43
Q

Describe what happens to molecule movement as temperature increases

A
  • All molecules have kinetic energy and can continuously move around randomly
  • If a substance is heated, the extra energy in the form of heat causes the molecules to move faster
  • This increases rate of collisions between molecules
    • It also increases the force with which they collide, as they are moving faster
44
Q

Describe the effect of temperature on ROR

A
  • both enzyme and substrate molecules will gain kinetic energy and move faster
  • Increases rate of successful collisions
  • rate of formation of ES complexes increases- ROR increases- increasing rate of EP complexed formed up to point
    • Optimum temperature- ROR is at maximum
45
Q

Describe the other effect on enzymes raising temperature has

A
  • as well as making molecules faster, will make them vibrate
  • My break some of weak hydrogen and ionic bonds that hold tertiary structure of active site
  • As AS begins to change, the substrate molecules wont fit into it so well and ROR begins to decrease
  • AS more heat is applied, the shape of AS is changed completely- no longer complementary to substrate molecule
      • reaction cant proceed- enzyme is denatured
46
Q

Which part of an enzyme does increased temperature not affect, what does this mean

A
  • doesnt break peptide bonds between amino acids
  • Enzymes primary structure not altered
  • Hydrophobic core region contains non polar side chains- hydrogen bonds can form to polar side chains on the outside of the molecule- these break
47
Q

Describe optimum temperature and whether it varies- describe

A
  • temperature at which enzyme works best- has maximum ROR
  • different for different enzymes as adapted to living in different conditions- e.g. psychrophillic bacteria in cold, thermophilic bacteria in hotsprings
48
Q

What is the equation and units for ROR

A

1/time taken to reach end point, S-1

49
Q

Describe pH

A

Indicates whetehr a substance is acidic (0-6), neutarl (7) or alkaline (8-14)

50
Q

Describe how 2 different types of acid dissociate

A

Hydrochloric- H plus and Cl-

Organic acids are proton donors- e.g lactic acid into H plus and lactate

51
Q

What is a buffer, describe how they work in the body

A
  • something that resists change in pH
  • certain chemicals in blood which help resist changes in pH so blood pH remains in fairly narrow range of close to 7.4
  • These chemicals can donate or accept hydrogen ions
  • Some proteins such as haemoglobin can also donate or accept protons so act as buffers
52
Q

Describe how changes in pH affect enzymes

A
  • Hydrogen ions have positive charge so are attracted to negatively charged ions/parts of molecules
  • Hydrogen and ionic bonds hold together tertiary structure of enzymes- including active site so substrate will fit
  • If placed in aciding solution, there will be more H+ ions- bonds will break as OH- will from bonds wit H+ ions closer
  • Same if alkaline- more OH- ions- H+ ions will form bonds with
  • If bonds broken, active site will change shape
  • If substrate moleule doesn’t fit well onto AS, ROR that enzyme catalyses will be lowered
  • Increasing concentration of hydrogen ions will also alter charges on active site of enzyme molecules as more protons will cluster around negatively charged groups (e.g. amino acid R groups) in active site. Interferres with the binding of the substrate molecule to the active site.
53
Q

Describe the range of pH enzymes work in, and whether changes can be restored

A
  • narrow range
  • small changes wither side of optimum pH slow ROR as shape of active site is altered
  • However, if normal optimum pH is restores, H bonds can reform and the active sites shape is restored
  • At extremes of pH, the enzymes active site may be permanently changed- when enzyme is thus denatured, ot cant catalyse the reaction
54
Q

Do acidic solutions have more or less H+ ions and why

A

More- pH is 1/[H+]

55
Q

WHat does [] mean on a graph/formula

A

Concentration

56
Q

Temperature-ROR enzymes graph

A
57
Q

pH-ROR enzymes graph

A
58
Q

What is enzymes that work intracellularly’s optimum pH

A

Close to 7

59
Q

Describe an example of variations in optimum oH

A

Digestive system:

  • amylase in mouth- 6.8
  • pepsin in stomach- 1-2
  • trypsin and enterokinase- 7.8 (neurtralised from stomach by bile)
60
Q

What are inhibitors

A

Substances that reduce the activity of enzymes

61
Q

What are the 2 types of inhibitors

A
  • Competitive
  • Non-competitive
62
Q

How do competitive inhibitors work

A
  • Fits into the AS of an enzyme so a substrate molecule cant enter
  • compete directly with substrate molecule for a position on an enzymes AS, forming an enzyme inhibitor complex
  • On the AS, the inhibitor molecule is not changed by the enzyme as a normal substrate molecule would be
    • Most is reversible, but if it combines irreversibly it is called an inactivator
63
Q

Describe how competitive inhibitors alter ROR

A
  • The amount of inhibition depends on the relative concentration of substrate and inhibitor molecules
  • More inhibitor molecules mean more inhibitors collide with active sites so the effect of inhibition is greater
  • Increasing the substrate concentration effectively ‘dilutes’ the effect of the inhibitor- if enough substrate is added, the inhibitor is unlikely to collide with the enzyme
  • presence of inhibitor reduces prevents the substrate molecule from joining to the AS- reduces the rate of formation of ES complexes and of product molecule formation
  • A competitive inhibitor reduces the number of free active sites available for the substrate molecules to bind to and form ES complexes
  • As collision between enzyme and substrate or inhibitor molecules are random, increasing the concentration of substrate would reduce the effect of reversible competitive inhibition, as there would be more chance of an enzyme molecule colliding with a substrate molecule than an inhibitor one
64
Q

Describe how non-competitive inhibitors work

A
  • don’t compete wit substrate molecules for a place in the enzymes AS
  • They attach to an allosteric site on the enzyme- not the AS
  • This disrupts the enzymes tertiary structure and changes its shape
    • This distortion changes the shape of the AS so that it is no longer complementary to the shape of the substrate molecule, and the substrate molecules can no longer bind to the enzymes AS- ES complexes cant form
    • Some bind reversibly to the allosteric site, others irreversibly
65
Q

Describe how non-competitive inhibitors affect ROR

A
  • The maximum ROR is reduced
  • Adding more substrate might allow the reaction to attain its new, lower rate, but even very high concentrations of substrate wont allow the ROR to return to its uninhibited maximum
  • The more inhibitor molecules the greater degree of inhibition, because more enzyme molecules are distorted and either can’t form ES complexes or can’t complete the catalytic reaction involving ES complexes
66
Q

Graph comparting effect of non and competitive inhibition on ROR

A
67
Q

Describe end-product inhibition

A
  • One way enzyme-catalysed reactions may be regulated
  • After the enzyme-catalysed reaction has reached completion, product molecules may stay tightly bound to the enzyme
  • In this way, the enzyme cant form more of the product than the cell needs
    • example of negative feedback
68
Q

Describe how enzymes controll metabollic sequences

A
  • Many metabolic processes e.g. photosynthesis/respiration involve a series of enzyme-catalysed reactions
  • The product of one enzyme-catalysed reaction becomes the substrate of the next in the metabolic pathway
  • Cells don’t need to accumulate too much of the end-product, so the product of the last enzyme catalysed reaction may attach to a part of the first enzyme in the pathway, but not its active site
  • This changes the AS of enzyme 1 preventing the pathway from running (non-competitive inhibition), but is reversible
  • When the concentration of product molecules within the cell falls, those molecules will dettatch from enzyme 1 and allow its AS to return to its normal shape- the metabolic pathway can run again
  • Multi-enzyme complexes increase the efficiency of metabolic reactions without increasing substrate concentration, as they keep the enzyme and substrate molecules in the same vicinity and reduce diffusion time
    • Many metabolic reactions are carried out in particular regions or organelles in cells, and this also increases the efficiency of metabolism. Some of the enzymes within organelles are bound into organelle membranes
69
Q

Name example of metabollic enzyme inhibitors

A

Poisons- cyanide, snake venom

Medicinal- Aspirin, ATPase, ACE inhibitors, Protease inhibitors, Nucleoside reverse transcriptase inhibitors

70
Q

Describe cyanide

A
  • Potassium cyanide
  • When ingested, KCN is hydrolysed to produce hydrogen cyanide- gas that can readily dissociate to form H+ and CN- ions
  • CN- ions bind irreversibly to cytochrome oxidase enzymes found in mitochondria- non-competitively inhibits- stops final stage of respiration (combining H and O to form H2O)- no ATP creation
  • Aerobic respiration stops
  • Any reaction requiring ATP stop- body eventually has no energy supply causing total cell failure
    • Causes death even though all reactants for respiration still present
71
Q

Describe snake venom

A
  • contains chemical that inhibits the enzyme acetycholinesterase - enzyme important at neuromuscular synapses to break down neurotransmitter acetylcholine
  • If inhibited, the acetylcholine stays attached to receptors on the muscle membrane and keeps the muscle contracted
  • Competitive inhibitor
  • in skeletal muscles it stops nerve impulses from being transmitted and hence stops muscle contraction- muscles rely on contracting and relaxing alternately
  • Eventually leads to flaccid paralysis/ suffocation if in breathing muscles
72
Q

Describe aspirin

A
  • Contains salicylic acid- binds to enzymes that catalyse the formation of prostaglandins
  • Therefor prevents the formation of prostaglandins (cell signalling molecules) that increase swelling and make nerves more sensitive to pain
  • Also thins blood- can take to reduce risk of blood clots forming in blood vessels- reduces risk of heart attacks
73
Q

Describe protease inhibitors

A
  • Competitively inhibit HIV protease enzymes
  • Normally virus uses these to cut viral RNA into smaller pieces so as to implant genes into the host cells DNA and hence replicate
  • Inhibitors bind specifically with the HIV protease enzymes active site preventing longer RNA strands from binding
  • As a result, RNA cant be cut into pieces so it cant be implanted in host cells DNA- no replication
  • Host cell can be infected by HIV but it can’t be hijacked into making more HIV copies as a result of DNA implantation by the virus
74
Q

Describe ACE inhibitors

A
  • Medical drugs that inhibit the angiotensin-converting enzyme (ACE), which normally operates in a metabolic pathway that ultimately increases blood pressure

They are used to:

  • lower blood pressure in patients with hypertension who cant take beta-blockers
  • treat heart failure- a low dose is given at first, and the patients blood pressure is checked incase it falls too low
  • rminimiseisk of a 2nd heart attack or stroke in patients who have suffered a myocardial infraction
75
Q

Describe ATPase inhibitors

A
  • extracts from purple foxglove leaves have been used for centuries to treat heart failure and arterial arrythmia
  • The chemicals are now identified as cardiac glycosides, AKA digitalis, digitoxin, digitalin, or digoxin
  • they inhibit the sodium potassium pump in the cell membranes of heart-muscle cells, and allow more calcium ions to enter the cells
  • calcium ions increase muscle contraction, and this strengthens the heartbeat
76
Q

Describe nucleoside reverse transcriptase inhibitors

A
  • many of the antiviral drugs (e.g. zidovudine and abacavir) used to treat patients who are HIV positive are nucleoside reverse transcriptase inhibitors
  • They inhibit enzymes involved in making DNA using the viral RNA as a template
77
Q

Describe cofactors, when they are needed and give 3 types

A
  • some enzymes can only work if they have other non-protein molecules attached to them (cofactors)
  • Especially those catalysing oxygen-reduction reactions
  • Cofactors are a substance that has to be present to ensure that an enzyme-catalysed reaction takes place at the appropriate rate
    • Prosthetic groups, coenzymes, other cofactors (e.g. ions)
78
Q

Describe and explain prosthetic groups

A
  • cofactors that are bound permanently by covalent bonds to an enzyme
    • Either organic or inorganic??? CHECK
79
Q

Example of a prostetic group

A
  • the enzyme carbonic anhydrase contains a zinc ion (Zn+2) permanently bound as a prosthetic group to its active site
  • This enzyme is found in erythrocytes and catalyses the interconversion of carbon dioxide and water into carbonic acid, which then breaks down to protons and hydrogencarbonate ions in red blood cells
  • This reaction may proceed in either direction depending on concentration of substrate or product molecules
  • Reaction is vitally important as it enables carbon dioxide to be carried in the blood from respiring tissues to the lungs
  • Will only function with zinc ion

CO2 + H2O ⟶ H2CO3 ⟶ H+ + HCO3-

80
Q

Describe other cofactors (e.g. ions)

A
  • bind temporarily to an enzyme or substarte molecule
  • May ease the formation of ES complexes and thus increase ROR
  • Some act as co-substrates- they and the substrate together form the correct shape to bind to the AS of the enzyme
  • Some change the charge distribution on the surface of the substrate molecule or on the surface of the enzymes active site, and make the temporary bonds in the ES complex easier to form
  • inorganic
81
Q

What is an example of a cofactor (e.g. ions)

A
  • Enzyme amylase
  • Catalyses hydolysis reaction which breaks down the polysaccharide starch into the dissacheride maltose
  • Starch → maltose
  • Will only function when a chloride ion is present which temporarily binds it to ease the formation of ES complexes
82
Q

Describe coenzymes

A
  • organic non-protein molecules
  • bind temporarily to the active site of enzyme molecules, either just before or at the same time that the substrate binds
  • The coenzymes are chemically changed during the reaction, and they need to be recycled into their original state, sometimes by a different enzyme
  • Most are or are derived from water soluble vitamins
  • cosubstrates
  • Most contain AMP
  • Can bind permanently ???- CHECK
83
Q

Name 5 examples of vitamins, the coenzyme derived from them and the human deficiency disease a lack of them can cause

A
  • B12- cobalamin coenzymes- pernicious anaemia (progressive and fatal)
  • Folic acid- tetrahydrofolate- megablastic anaemia (large, irreguarly shaped erythrocytes)
  • Nicotinamide (B3)- NAD, NADP- pellagra (diarrhoea, dermatitis, dementia)
  • Pantothenate (B6)- coenzyme A- elevated blood-plasma triglyceride levels
    • Thiamine (B1)- thiamine pyroposphate- berberi (mental confusion, irregular heartbeat, muscular weakness, paralysis, and hear failure)
84
Q

Describe 1 specific example of a coenzyme

A
  • NAD and NADP are hydrogen acceptors
  • Both derivatives of nucleotides

Module 2- Foundations in Biology (7 decks)

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