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SP MCAT Biochem > Enzymes > Flashcards

Enzymes Flashcards

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MCAT flashcards
1
Q

Catalysts

A
  • do not impact thermodynamics of a reaction
  • enthalpy (H) of reaction and equilibrium do not change
  • help reaction proceed at faster rate by lowering activation energy or changing the reaction mechanism
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2
Q

List key features of enzymes

A
  • lower activation energy (Ea) so forward and reverse rxns occur more often
  • increase rate of the rxn
  • no change in equilibrium constant
  • appear in both reactants and products b/c not consumed in the rxn
  • pH and temperature sensitve
  • no change in Gibbs Free Energy of rxn
  • specific for a particular rxn or class of rxns
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3
Q

What are the 6 different enzyme classifications?

A
  • LIL HOT*
  • Lyase
  • Isomerase
  • Ligase
  • Hydrolase
  • Oxidoreductase
  • Transferase
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4
Q

Oxidoreductase

A
  • catalyzes oxidation-reduction rxns
  • catalyze the transfer of electrons between biological molecules that contain elements like C, H, and O
  • often have cofactor like NAD+ or NADP+
  • electron donor is the reductant
  • electron acceptor is the oxidant
  • reducing a molecule means fewer bonds to oxygen and more bonds to hydrogen: A + H AH
  • oxidizing a molecule means more bonds to oxygen and less bonds to hydrogen: A + O AO
  • enzymes that have oxygen as the final electron acceptor include “oxidase” in their name
  • Ex. oxidases, reductases, peroxidases, dehydrogenases
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5
Q

Transferase

A
  • catalyze movement of a functional group from one molecule to another
  • kinases are an example of this and function in catalyzing the transfer of a phosphate group to another molecule
  • Ex. polymerases (shift nucleotides into growing chains of DNA or RNA), transaminases, methyltransferases, hexokinase
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6
Q

Hydrolase

A
  • catalyze the breaking of a compound into two molecules using the addition of H2O
  • AB + H20 –> AOH + BH
  • Ex. phosphatase (cleaves phosphate group in peptide bond), peptidase (breaks down proteins), nuclease (break down nucleic acids/DNA/RNA), lipase (break down lipids), protease (breaks peptide bonds within proteins), esterase (breaks esters often in lipids)
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7
Q

Lyase

A

-catalyze the cleavage of a single molecule into two products without the use of water
-also involved in cleavage of bonds (can cleave dbs to make single bonds)
-often form rings or multiple bonds to reform octets
- XABY –> AB (ring form) + XY
- A = B + XY
-common names: decarboxylase, lyase, synthase
-Ex. use of enzyme aldolase:
Fructose 1.6-bisphosphate DHAP + Glyc. 3-phosphate
-Ex. glycogen phosphorylase

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8
Q

Isomerase

A
  • catalyze the rearrangement of bonds within a molecule – intramolecular
  • have same chemical formulas with different connectivity
  • AB BA
  • catalyze reactions between stereoisomers and constitutional isomers
  • some can also be classified as oxidoreductases, transferases, or lyases
  • common names: mutase, racemase
  • Ex. triose phosphate isomerase, aconitase
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9
Q

Ligase

A
  • catalyze addition and synthesis reactions, generally between large similar molecules and often require ATP
  • X + Y + ATP –> XY + ADP +Pi
  • usually involved in nucleic acid synthesis or DNA synthesis/repair
  • the only enzyme class that absolutely needs ATP to function
  • common enzymes in this class: synthetase, carboxylase
  • Ex. DNA Ligase, carbonic anhydrase
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10
Q

Endergonic Reactions

A

requires energy input (delta G > 0)

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11
Q

Exergonic Reactions

A

energy is given off (delta G < 0)

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12
Q

What are the mechanisms of enzyme activity that lead to decreased activation engergy?

A
  • Transition State Stabilization: makes transition state exist longer, dissipation of torsional strain and favorable bond formation, inductive effects of the active site residues
  • Microenvironment Adjustments: keeps H2O away form molecule, adjusts local environment’s pH
  • Substrate Proximity Adjustments: increases frequency of collisions
  • Transient Covalent Bonding: substrates are vulnerable to nucleophilic attack so briefly contact active site residues
  • Reactant Destabilization: creation of torsional strain or hydrophobic-hydrophilic interactions that make the rxn favorable because molecules are in the wrong state
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13
Q

What stabilizes the spatial arrangement within the active site of an enzyme when a substrate is present?

A
  • hydrogen bonding
  • ionic interactions
  • transient covalent bonds
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14
Q

Lock and Key Theory

A
  • describes enzyme-substrate binding
  • enzyme’s active site (lock) is already in correct configuration for substrate (key)
  • no alteration of tertiary or quaternary structure is necessary upon binding of substrate
  • problems with model: competitive inhibition (more than one key for a given lock), promiscuous reactivity, reverse catalysis
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15
Q

Induced Fit Model

A
  • describes enzyme-substrate binding
  • active site of enzyme molds itself around substrate only when substrate is present
  • tertiary or quaternary structure is necessary upon binding of substrate
  • more accurate model of the two
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16
Q

Coenzymes

A
  • extrinsic ORGANIC molecules that are necessary for protein function
  • many are adenine or vitamin derived
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17
Q

Prosthetic Groups

A
  • tightly bound cofactors or coenzymes that are necessary for enzyme function
  • Ex. cysteine residue on heme C
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18
Q

Ribozymes

A

biological catalysts that are composed of RNA instead of polypeptides

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19
Q

What 2 vitamins are soluble in water?

A

B, C

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20
Q

What 4 vitamins are soluble in fat?

A

K, E, D, A

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21
Q

Cofactors

A
  • INORGANIC molecules that are necessary for protein function
  • usually free metal ions but can be polyatomic
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22
Q

Haloenzymes

A

enzymes that have all necessary cofactors and coenzymes present

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23
Q

Apoenzyme

A

enzymes that do not have all cofactors and coenzymes present

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24
Q

The site where a protein binds essential cofactors is most likely to be characterized by:

A

an excess of negative charge which is because most cofactors are metal cations

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25
Q

What amino acid is found in the active site of chymotrypsin and what molecule does it bind?

A

Serine acts as the active site and it binds phynylalanine

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26
Q

What amino acid is found in the active site of trypsin and what molecule does it bind?

A

Aspartate acts as the active site and it binds lysine

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27
Q

Saturation Kinetics

A
  • point at which an enzyme can’t go any faster

- enzyme is working at max velocity (Vmax) which can only be increased by increasing the enzyme concentration

28
Q

Michaelis-Menten Constant (Km)

A
  • inherent measure of the affinity a substance has for an enzyme
  • used to compare two enzymes to see which would perform better
  • substrate concentration such that V=1/2Vmax – half of all enzyme active sites are full
29
Q

What do high values of Km represent?

A
  • low affinity enzyme substrate complexes (because it requires a higher substrate concentration to be 1/2 saturated)
  • slow enzyme rxns (decreased Vmax)
30
Q

What equation can be used if the reaction rate is equal to half of Vmax?

A

Km = [S]

31
Q

What does a low Km value represent?

A

high affinity for the substrate (low substrate concentration required for 1/2 enzyme saturation)

32
Q

What equation can be used when [S]&raquo_space;> Km (zeroth order region)?

A

V = Vmax

33
Q

What happens to the reaction rate when [S] > Km ?

A

reaction rate increases much slower as it approaches Vmax

34
Q

What equation can be used when [S] «< Km (first order region)?

A

V = (Vmax x [S] ) / Km

35
Q

Catalytic Efficiency

A
  • Kcat / Km
  • large Kcat (high turnover) or small Km (high substrate affinity) results in a higher efficiency – more efficient enzyme
  • “perfect” value of this is between 10^8 and 10^9
36
Q

Lineweaver-Burk Plots

A
  • double reciprocal graph of Michaelis-Menten equation
  • plot is used to determine the type of inhibitor that an enzyme is experiencing because Vmax and Km can be directly compared
  • -1/Km is the intercept of the line with the x-axis
  • 1/Vmax i the intercept of the line with the y-axis
37
Q

Cooperativity

A
  • graph shows sigmoidal (S-shaped) kinetics owing to cooperativity among substrate binding sites
  • these types of enzymes have multiple subunits and active sites
  • enzymes exist in two stages: low-affinity tense state (T) or high-affinity relaxed state (R)
  • Ex. hemoglobin
38
Q

What encourages transition from T state to R state?

A

substrate binding because it increases the likelihood of substrate binding by other subunits

39
Q

Hill’s Coefficient

A

numerical value that quantifies cooperativity

40
Q

Hill’s Coefficient > 1 :

A

positive binding is occurring –> after one ligand is bound the affinity of enzyme for more ligand binding is increased

41
Q

Hill’s Coefficient < 1 :

A

negative binding is occurring –> after one ligand is bound the affinity of enzyme for more ligands decreases

42
Q

Hill’s Coefficient = 1 :

A

enzyme doesn’t exhibit cooperative binding

43
Q

How does cooperativity work in hemoglobin?

A

binding of first O2 to Fe increases polarity and makes other Fe more available to bind O2

44
Q

What local conditions effect enzyme activity?

A
  • temperature
  • pH
  • salinity
45
Q

What are the effects of temperature on enzyme activity?

A
  • enzyme rxns double in velocity every 10 degrees Celsius until optimum temperature is reached
  • enzyme denatures at high temperatures past the optimum temperature
46
Q

What are the effects of pH on enzyme activity?

A
  • impact on ionization of active site and can lead to enzyme denaturation
  • optimal enzyme pH in human blood: 7.4 (if pH is less than this then termed acidemia)
47
Q

What is the ideal pH of a gastric enzyme?

A

2

48
Q

What is the ideal pH of a pancreatic enzyme?

A

8.5

49
Q

What are the effects of salinity on enzyme activity?

A

increasing levels of salt in vitro (in lab) can disrupt H-bonds and ionic bonds causing a change in enzyme conformation and denaturation

50
Q

Feedback Regulation

A

process by which enzymes are subject to regulation by products further down a given metabolic pathway

51
Q

Feed-Forward Regulation

A

when enzymes are regulated by intermediates that precede the enzyme in the pathway

52
Q

Feedback Inhibition

A

regulatory mechanism where catalytic activity of enzyme is inhibited by high levels of product later in the same pathway

53
Q

What are the 4 types of reversible inhibition?

A
  • competitive
  • noncompetitive
  • mixed
  • uncompetitive
54
Q

Competitive Inhibition

A
  • inhibitor is similar to the substrate and binds at the active site
  • overcome by adding more substrate
  • Vmax is unchanged
  • Km increases
55
Q

Noncompetitive Inhibition

A
  • inhibitor binds to allosteric site which induces a change in enzyme conformation
  • inhibitors bind with equal affinity to enzyme and ES complex
  • Vmax is decreased
  • Km is unchanged
56
Q

Allosteric Sites

A

non-catalytic regions of the enzyme that bind regulators

57
Q

Mixed Inhibition

A
  • inhibitor binds at allosteric site
  • inhibitor binds with unequal affinity to enzyme and ES complex
  • Vmax is decreased
  • Km increases (decreased affinity) if inhibitor preferentially binds to enzyme
  • Km decreases (increased affinity) if inhibitor preferentially binds to the ES complex
58
Q

Uncompetitive Inhibition

A
  • inhibitor binds to allosteric site after ES complex is formed
  • inhibitor only binds to ES complex
  • both Vmax and Km decrease
59
Q

Irreversible Inhibition

A

-alters enzyme in such a way that the active site is unavailable for a prolonged duration or permanently

60
Q

Allosteric Enzymes

A
  • multiple binding sites (active site + regulatory sites)
  • alternate between active and inactive form
  • bind allosteric activators or inhibitors which both cause conformational shift in protein
61
Q

Covalently Modified Enzymes

A
  • activated by phosphorylation
  • deactivated by dephosphorylation
  • glycosylation: covalent attachment of sugar moieties; tag an enzyme for in-cell transport or modify protein activity and selectivity
62
Q

Zymogens

A
  • secreted in inactive form and are activated by cleavage
  • contain a catalytic (active) domain and a regulatory domain
  • have suffix -ogen
63
Q

What are intrinsic parameters of an enzyme?

A
  • parameters that “belong” to the enzyme and won’t change even if the concentration of enzyme changes – NOT dependent on [E]
  • includes: Km, Kcat, catalytic efficiency
64
Q

What are extrinsic parameters of an enzyme?

A
  • parameters that can change as enzyme concentration changes – dependent on [E]
  • includes: Vmax
65
Q

Ordered Sequential Binding

A
  • substrates must bind in correct order for product(s) to form
  • must bind substrates before product can be made
66
Q

Randon Sequential Binding

A

-all substrates must be bound before product(s) can be formed, BUT substrates can bind in any order and products can be released in any order

67
Q

Ping Pong Binding

A
  • release some products before you bind all substrates
  • only forms binary complex (enzyme + substrate), NEVER forms tertiary complex (enzyme + substrate + inhibitor + …)
  • Ex) Aspartate + alpha-KG OAA + Glutamate

SP MCAT Biochem (16 decks)

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