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Biochemistry I > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What are Enzymes?

A

A biological molecule that act to catalyze the wide range of reactions that take place with the cells. i.e. they speed up the rate of reactions.

They typically help transform one form of energy into a more useful form

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2
Q

What are enzymes made of?

A

Amino Acids linked together in one or more polypeptide chains

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3
Q

What is catalytic RNA?

A

Catalytic RNA is RNA molecules with enzyme activity- cats as an enzyme

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4
Q

Is it necessary to regulate enzyme activity? Why?

A

Yes, it is necessary. This is because these processes govern cell behaviour such as homeostasis. Also, the cell needs to change how much or product produced and reactants used up based on external and internal conditions! (operates only on a need basis)

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5
Q

How might enzymes be regulated?

A
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6
Q

What is Non- Covalent Regulation?

A
  • Feedback Inhibition
  • Allosterism
  • Protein-protein interaction
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7
Q

What is Covalent Regulation?

A
  • Reversible covalent modification (eg. phosphorylation)
  • Zymogen activation by proteolysis
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8
Q

What is Allosteric control?

A
  • Many enzymes contain sites- allosteric sites- (in addition to active sites) that are used for regulatory purposes. Such enzymes. Such enzymes are called allosteric enzymes.
  • Allosteric enzymes and proteins display cooperativity by the binding of effector molecules to the allosteric site.
  • eg. Haemoglobin
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9
Q

What is Reversible Covalent Modification?

A
  • The activity of many enzymes can be controlled and regulated by creating covalent bonds/ modification of that specific enzyme
  • Most common eg.- the attachment of a phosphoryl group onto the enzyme (using protein kinases) from ATP (phosphorylation).
                        protein kinase Enzyme + ATP ---------------------> Enzyme--P + ADP
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10
Q

What is Zymogen Activation by Proteolysis?

A
  • Many enzymes are produced in an inactive form and these enzymes are called zymogens or proenzymes.
  • In order to activate the, they are usually cleaved irreversibly by proteases at specific sites on the polypeptides.
  • Once activated, they can eventually be inactivated by the binding of some irreversible inhibitor.
  • eg. Digestive enzymes and the blood cascade enzymes typically use this form of regulation.
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11
Q

What is Enzyme Concentration?

A
  • Regulating the transcription of specific genes, which can control how much enzyme is produced. This can in turn regulate the overall level of activity due to some enzyme.
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12
Q

What are Cofactors?

A
  • A non-protein chemical compound that tightly and loosely binds with an enzyme or other protein molecules
  • Many enzymes would be inactive w/o the presence of some non-protein component referred to as a cofactor.
  • Apoenzyme + cofactor = haloenzyme
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13
Q

Types of Cofactors?

A

Two types:
1. An organic molecule referred to as a coenzyme (tightly bound cofactors are sometimes referred to as prosthetic groups like FAD (prosthetic group) vs NAD+ (coenzyme))

  1. A metal ion
    (a) metalloenzymes- superoxide dismutase (2Cu2+ & 2Zn2+) and carboxypeptidase A (Zn2+)
    (b) metal- activated enzyme- creatine kinase and enolase (Mg2+)
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14
Q

What are the Important “Must Know” coenzymes?

A
  • Coenzyme A (chemical group- acyl group, found in pantothenic acid, have a high energy -S bond)
  • Biocytin (chemical group- C02. found in Biotin, is a prosthetic group)
  • Lipoic Acid (chemical group- electrons and acyl groups, not required in diet, functions in acyl transfers)
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15
Q

How do we Classify Enzymes?

A
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16
Q

Why are enzymes necessary for life?

A

Enzymes help facilitate biochemical reactions in our bodies. They aid in everything from breathing to digestion. Having too little or too much of a certain enzyme can lead to health problems.

Consider that biological systems are typified by:
- Neutral pH
- Mild temperature
- Aqueous environment
Under these conditions, most reactions would take place only very slowly if at all

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17
Q

Specificity of Enzymes?

A

Enzymes are very specific due to the shapes of their active sites. Therefore,

Lock and Key Model
- In the lock and key model, the substrate fits precisely and perfectly into the active site due to their exact complimentary shapes

Induced Fit Model
- In the induced fit model, the shape of the enzyme’s active site is not exactly complimentary. However, upon binding of the substrate to active sites, the binding cases the active site to become complementary to the substrate
- More accurate explanation and understanding of active site binding.

18
Q

What types of active sites does an enzymes have?

A

Contains 2 distinct types of sites or regions

  1. Binding sites- link to specific groups in the substrate- ensure proper orientation
  2. Catalytic sites- promotes the rxn

NB: active sites are specific, small compared to the entire enzyme, contain microenvironments that only comprise of the substrates and resulting products

19
Q

What is Substrate Channeling?

A

The process in which the intermediate produced by one enzyme is transferred to the next enzyme without complete mixing with the bulk phase
Eg. Biotin does not take part in catalyzing the reactions but shuttles the product of one rxn to be the substrate of another rxn

20
Q

What are examples of Enzymes and their Active Sites?

A

*Serine Proteases
- all have an identical fold-> Beta barrels w the catalytic triad of Asp, His, Ser at the interface of the two domains
- three types- chymotrypsin (hydrophobic pocket), trypsin (salt bridge), Elastase (small hydrophobic pocket)

21
Q

What is the Collision Theory?

A

Molecules can only react if they come into contact (bond- forming distance) w/ each other

22
Q

What are the Factors that Affect the Collision Rate?

A
  1. Activation Energy- for a reaction to occur, colliding molecules must have sufficient energy to overcome a potential barrier- the energy of activation
  2. Transition State Theory (Eyring)- postulates the formation of an unstable intermediate
23
Q

What is Strain Mechanism Theory?

A

Postulates that distorted binding occurs- active site s almost complementary/ rigid

24
Q

What is Transition State Stabilization?

A
  • By binding substrates to their active sites, enzymes stabilize the structure of the transition state
  • Substrate bound undistorted
  • Enzyme-Substrate complex possesses unfavourable interactions
  • E-S complex -> Transition State -> Products
25
Q

What is the Rate of A Reaction? Catalysis?

A
  • The reaction rate is the change in concentration of the products made or the reactants used over the change in time.
  • The rate of a rxn is proportional to the products of the activities of each reactant ( rxn rate prop. (activity of A)^a x (activity of B)^b)
26
Q

What is the 1st Order Reaction Equation?

A
  • Proceeds at a rate prop. to the conc. of ONE reactant at constant T and P in a dilute solution.

v = d[A]/dt
= +d[P]/dt
= k[A]

27
Q

What is the 2nd Order Reaction Equation?

A
  • Proceeds at a rate prop. to the conc. of TWO reactants;

Where A+B–>P
v = -d[A]/dt
= -d[B]/dt
= +d[P]/dt
= K[A][B]

Where 2A–>P
v = -d[A]/dt
= +d[P]/dt
= k[A]^2

28
Q

What is Initial Velocity (Vo)? How is it used?

A
  • At any time, the reaction rate = the slope at that point
  • This rate is constant at the start of the rxn

Therefore, Initial velocity is the reactant rate at initial time.
Vo = [P]2 - [P]1/ t2 - t1

NB: Velocity is dependent on the initial concentrations.
Can only be found from the product conc. vs time graph

29
Q

What is the Importance Vo?

A
  • Concentrations of each reactant are known
  • No products present at initial time so no back rxn
30
Q

What is the General Equation for the hyperbolic curve?

A

Vo = Vmax [S]/ Km+[S]

NB: Vmax is the max velocity and Km is conc. of substrates @ 1/2Vmax

31
Q

How to find the Vmax and Km values?

A

Vmax is the max velocity and Km is conc. of substrates @ 1/2Vmax

Note: Km is a measure of the affinity of the enzyme for its substrate. That means it gives an indication of how well it converts its substrate to products. A high Km means the enzyme has a low affinity, a low Km means the enzyme has a high affinity.

32
Q

What is the Michaelis-Menten Assumption?

A

k1[E][S] = k-1[ES]

This is because on a Vo vs conc. of substrate graph, the beginning of the graph is linear @ initial velocity and initial time meaning that enzyme and substrate would react to form an enzyme substrate complex which would form the the enzyme and products but there would be little production of products hence the initial velocity is based on the [ES].

33
Q

What is the Michaelis-Menten Equation?

A

Vo= Vmax x [S]/Km + [S]

34
Q

What is the Significance of the Michaelis-Menten Equation?

A
  • Derived wrt a single substrate- enzyme (cat rxn)
  • 1 substrate binding site (>1 but w/o interaction)
  • 1 product formed
  • 1 intermediate complex
35
Q

What is the Lineweaver- Burk Plot and The Eadie-Hofstee and Hanes Plots Equation?

A

1/Vo = Km/Vmax x 1/[S] + 1/Vmax
NB: y = m x + c

NB:

36
Q

What is Enzyme Inhibition? What are the types?

A

A molecule that disrupts the normal reaction pathway between an enzyme and a substrate.
- Inhibitors usually act through binding w/ the enzyme
- Can be removed by dialysis (or simple dilution)- Reversible Iinhibition
- The degree of inhibition remains constant - rapid equil.

Three types of Reversible Inhibition:
- Competitive
- Uncompetitive
- Noncompetitive

37
Q

What is Competitive Inhibition?

A
  • Usually the inhibitor closely resembles the substrate
  • Binds but resembles the formation of a dead-end complex
  • The inhibitor therefore competes for the active site with the substrate
  • Vmax for the rxn is unchanged but the apparent Km is increased
  • Eg 1. Kaletra is a drug used to treat HIV that uses a competitive inhibitor of HIV protease
  • Eg 2. Substrates for the liver enzyme, alcohol dehydrogenase- converts alcohol (ethanol, methanol, polyethylene glycol- antifreeze) into acid (acetic, formic, glycolic acids)
38
Q

What is Uncompetitive Inhibition?

A
  • These inhibitors bind only to the ES complex
  • That means that the inhibitor does not bind to active site but to another site on the enzyme after the ES complex has been formed
  • Since inhibitor and subs are not competing for the same site, inhibition cannot be overcome by increasing substrate concentration
  • Both Km and Vmax are altered
  • Eg. Inhibition of arylsulphatase by hydrazine
39
Q

What is Noncompetitive Inhibition?

A
  • The inhibitor binds to both the free enzyme (E) and the ES complex w/ equal affinity (it binds to everybody!)
  • That means that the inhibitor binds to both the enzyme before the ES complex is formed and also after the ES complex is formed
  • Inhibition cannot be overcome by high substrate concentrations
  • Inhibition reduced substrate turnover through formation of a catalytically inactive ESI complex
40
Q

Recap of Reversible Inhibition…

A

(Screenshot of graph from slides)

41
Q

What are Isozymes - Lactate Dehydrogenase Isozymes?

A
  • Each of two or more enzymes with identical function but different structure
  • LDH is a tetramer made of repeats of 2 subunits- LDHA (subunit A) and LDHB (subunit B)
  • As a result, there are 5 different isozymes- different forms of the same enzyme which catalyze the same rxn
  • Eg. Pyruvate to Lactate
42
Q

What is Irreversible Inhibition- Suicide Inhibition?

A
  • The inhibitor tends to form a covalent bond with the enzymes and permanently alters its shape, so much so that it is unable to catalyze that rxn
    Eg. Penicillin - This drug forms a covalent bond with an essential serine residue in the active site of the bacterial enzyme- transpeptidase- the native enzyme cross links peptidoglycan chains during cell wall synthesis
  • Therefore, penicillin inhibits the transpeptidase from forming these cross links and as a result the cell wall becomes too weak causing it to burst and the cell dies

Biochemistry I (6 decks)

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