Ch 2 - Enzymes

Question 1

catalyst

Answer 1

• do not impact thermodynamics
• increase reaction rate
• lower activation energy
• does not alter equilibrium constant
• not consumed
• ph/temperature sensitive
• does not effect overall gibbs free energy
• specific

Question 2

oxidoreductases

Answer 2

• catalyze redox reactions
• cofactor electron carrier
• reductant - electron donor
• oxidant - electron acceptor
• named “dehydrogenase” or “reductase”
• oxygen at final electron acceptor is named “oxidase”

Question 3

transferases

Answer 3

• movement of functional group from one molecule to another
• kinases - transfer of phosphate group

Question 4

hydrolases

Answer 4

• break compound using addition of water
• phosphatase - cleave phosphate group off
• peptidase - break down protein
• nuclease - break down nucleic acid
• lipase - break down lipid

Question 5

lyases

Answer 5

• cleavage of single molecule into 2 products
• does not require water
• no redox
• can also cause synthesis of 2 molecules to 1
  
  • synthases

Question 6

isomerase

Answer 6

• rearrangement of bonds within molecule
• stereo and constitutional isomers
• can be classified as oxidoreductases, transferases, lyases

Question 7

ligases

Answer 7

• addition or synthesis reactions
• between larger molecules
• ofen require ATP
• smaller synthesis via lyases
• nucleic acid synthesis and repair

Question 8

enzyme substrate complex

Answer 8

• active site
• favorable microenvironment
  
  • charge/pH
  • stabilize transition state
  • bring reactive groups together
• account for selectivity and regulatory mechanism
• hydrogen bonds
• ionic interactions
• transient covalent bonds

Question 9

lock and key theory

Answer 9

• enzymes active site is already in correct conformation for substrate
  
  • no alteration to 3 or 4 structure

Question 10

Induced fit model

Answer 10

• substrate and enzyme change shape to fit together perfectly
  
  • requires energy and is endergonic
• release substrate and return to original shape
  
  • releases energy and is exergonic
• incorrect substrate will not cause correct shift in conformation of enzyme

Question 11

Cofactors and coenzymes

Answer 11

• cofactors - inorganic molecules or metal ions
  
  • ingested from diet
• coenzymes - small organic
  
  • vitamins, NAD+, FAD, CoA
  • B complex vitamins and vitamin C need to be replenished
• nonprotein molecules that the enzyme requires
• kept at low conc in cells
• apoenzyme - enzyme without them
• holoenzyme - with cofactor/coenzyme
• prosthetic group - tightly bound and required for function
• may require several cofactors or coenzymes

Question 12

v_max

Answer 12

• when enzyme reaches saturation
• adding more substrate will NOT increase the reaction rate
• only increasing [E] will increase the rate of reaction
• unit of moles of enzyme per second
• v_max = [E] k_cat
  
  • k_cat : number of substrate molecules converted to product per enzyme per second

Question 13

Michaelis Menten

Answer 13

• v = v_max [S] / (K_m + [S]
• K_m = [S] when v = v_max / 2
• K_m : substrate conc when half of the enzymes active sites are full
  
  • Michaelis constant
  • used to compare enzymes
  • higher means lower affinity and more substrate needed to be half saturated
  • lower means higher affinity because less substrate needed to fill half active sites
  • not altered by changing [E] or [S]
• when [S] << K_m then rate is highly effected by changes in [S]
• when [S] << K_m then rate is barely effected by changes in [S]

Question 14

catalytic efficiency

Answer 14

• k_cat / K_m
• efficiency of the enzyme
• low K_m and/or high k_cat

Question 15

Lineweaver - Burk Plot

Answer 15

• double reciprocal of michaelis menten
• x axis intercept : -1 / K_m
• y intercept : 1 / v_max
• used to determine type of inhibition
• plot of 1 / V (y axis) vs 1 / [S] (x axis)

Question 16

Cooperativity

Answer 16

• do not follow michaelis menten
• sigmoidal curve
• low affinity tense state (T)
• high affinity relaxed state (R)
• binding of substrate encourages transition of other subunits from T to R state
  
  • increases substrate binding
• also loss of substrate causes other subunits to change from R to T state and decrease binding
• often regulatory enzymes
• quantified by Hill’s coefficient

Question 17

Hill’s Coefficient

Answer 17

• quantifies cooperativity
• nature of cinding of molecule
• < 1 then positive cooperative
• < 1 negative cooperative
• = 1 does not exhibit cooperative properties

Question 18

temperature effect on enzyme

Answer 18

• rate doubles every 10 deg C until reaching optimal then sharply drops off
• falls sharply due to denaturation
• only some enzymes can regain function if cooled

Question 19

pH on enzymes

Answer 19

• effects ionization of active site
• can cause denaturation
• optimal pH varies depending on environment
  
  • stomach, blood, small intestine

Question 20

salinity effect

Answer 20

• small physiological effect
• in vitro - increase in salt can disrupt hydrogen bonds and ionic bonds
  
  • denaturation

Question 21

feedback regulation

Answer 21

• regulation by products further down the pathway
• feed forward regulation - regulated by intermediates that precede the enzyme in the pathway
• negative feedback - feedback inhbition, maintain homeostasis. Level of product determines enzyme activity
  
  • product may bind competitively bind to active site of first enzyme in the pathway

Question 22

Competitive Inhibition

Answer 22

• occupancy of the active site
• can be overcome by addition of substrate
• does not alter v_max
• increases K_m
  
  • [S] must be higher in order to reach half of mac velocity
• LB plot - same y intercept, different X intercept

Question 23

Noncompetitive inhbition

Answer 23

• bind to allosteric site NOT active site
• change enzyme conformation
• cannot be overcome by additional substrate
• bind equally well to enzyme or enzyme-substrate complex
• decrease v max
• does not alter Km
• same x intercept
• different y intercept

Question 24

mixed inhibition

Answer 24

• inhibitor can bind to enzyme or enzyme-substrate complex
  
  • different affinity for each
• bind to allosteric site
• alter Km
  
  • if prefers enzyme then increase Km
  • if prefers ES-complex then decrease Km
• either case, Vmax decrease
• on LB plot the inhibitor and no inhbitor lines cross off the axes

Question 25

Uncompetitive inhibitor

Answer 25

• only bind to ES complex
• prevent release of S from E
• bind to allosteric site
• lower Km AND v max
• conformational change when S binds to E allows for uncompetitive inhibitor to bind
• parallel lines on LB plot

Question 26

irreversible inhibition

Answer 26

• prime drug mechanism
• active site made unavailable for long time or enzyme permanently altered
• not easily overcome
• may have to transcribe and translate a new enzyme

Question 27

allosteric enzymes

Answer 27

• multiple binding sites
• alternate between active and inactive form
• allosteric activators or inhibitors bind to the allosteric site

Question 28

covalently modified enzymes

Answer 28

• activated or deactivated by phosphorylation or dephosphorylation
• ex. glycosylation - covalent attachment of sugar

Question 29

zymogens

Answer 29

• enzymes that are secreted in an inactive form
• catalytic domain and regulatory domain
• regulatory domain is removed or altered to expose active site
• ex. apoptotic enzymes and trypsinogen
• suffix -ogen