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Biochemistry > Exam 2 Material > Flashcards

Exam 2 Material Flashcards

1
Q

Vo

A
  • Initial velocity at the beginning of a reaction when the concentration of substrate greatly exceeds enzyme concentration
  • Vo=Vmax[S]/Km+[S]
  • dependent on the substrate concentration
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2
Q

Rate (velocity)

A

-Δ[A]/Δt or -Δ[B]/Δt or Δ[P]/Δt

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3
Q

High [S]

A
  • 0 order, Rate=k, independent of [S]

- No increase in the rate of the reaction when more substrate is added

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4
Q

Low [S]

A

-1st order, rate increases with [S], rate=k[S]

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5
Q

Steady State Assumptions

A
  • Concentration of substrate must be much greater than enzyme concentration
  • ES remains constant (rate of formation equal to ES breakdown)
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6
Q

Km

A
  • Michaelis constant
  • Km=k2+k-1/k1
  • Independent of substrate/enzyme concentration
  • Inverse measure of how well a substrate binds to an enzyme (small Km=tight binding, large Km=weak binding)
  • Km=[S] @1/2 Vmax (substrate concentration at one half of the max velocity=Km)
  • Km low-reaches 1/2Vmax at lower [S] bc of higher affinity
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7
Q

Kcat

A
  • The turnover number or catalytic constant
  • How fast ES complex proceeds to E+P
  • Equals the number of substrate molecules converted to product per unit time (=Vmax/total)
  • 1St order rate constant (sec^-1)
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8
Q

Kcat/Km

A
  • catalytic efficiency & specificity constant
  • enzymes preference for different substrates
  • Measures how enzyme performs when S is low
  • Reflects binding and catalytic events, how the velocity changes according to how often E and S combine
  • 2nd order (m^-1 S^-1)
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9
Q

Apparent Km

A

-measured value of Km in presence of inhibitor

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10
Q

Ki

A
  • Dissociation constant for the inhibitor

- Measure of binding affinity

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11
Q

Competitive inhibitor

A

-Vmax stays the same but Km changes

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12
Q

Transition state analogs

A
  • competitive inhibitors/compounds that resemble the transition state and block the active site
  • bind much stronger to the enzyme than simple substrate or product analogs
  • Cannot isolate transition state, just resemble
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13
Q

Noncompetitive inhibitors

A
  • Bind reversibly to the enzyme
  • Can bind, but wont form product
  • Inhibitor binds to a site other than the active site
  • Binding causes a change in the conformation of the active site so the substrate doesn’t efficiently form product
  • Can bind to E or ES complex
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14
Q

Pure noncompetitive inhibitors

A

-Bind to a site far from the active site and do not affect substrate binding (apparent Km stays the same)

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15
Q

Mixed inhibitors

A

-Similar to noncompetitive except binding of substrate or the inhibitor affects the enzyme’s binding affinity for the other
-Two Ki’s- one for E and one for ES (different)
-Binds close to active site and alters both catalysis and binding
-Apparent Km increases, the inhibitor binds to a site close to active site & DOES decrease substrate binding
-Vmax decreases
(looks like competitive and noncompetitive)

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16
Q

Uncompetitive inhibitors

A
  • Inhibitor binds to a site other than the active site but only when the substrate is bound (only binds to ES)
  • Distorts active site, prevents reaction from occurring
  • Apparent Km decreases, effectively increases affinity for the substrate
  • Vmax decreases, the effects of un-competitive inhibition cannot be overcome by increasing [S]
  • ES complex is constantly being depleted as inhibitor binds, producing ESI complexes
  • Shifts E+S->ES equilibrium to the right toward more ES formation where it will bind more substrate to the enzymes to create more ES
  • Leads to lower Km
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17
Q

Irreversible inhibitors

A
  • inhibitors covalently modify the active site=permanent inhibition. Must wait for more enzyme to be made
  • Ex: aspirin, nerve gas
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18
Q

Oganofluorophosphates

A
  • Used as insecticides and nerve gas
  • irreversible covalent inhibition of ACE by DIFP (an organofluorophosphate)
  • phosphorous atom of VX covalently binds to a serine hydroxyl group in active site of ACE (VX gas and ACE has similar structures-competitive)
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19
Q

Atropine

A
  • antidote to ACE inhibition, binds to acetylcholine receptors and acts as a competitive inhibitor in muscles
  • more ACE is made to eventually regain control of the system
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20
Q

Induction

A

-Increase in amount/expression of transcript for enzyme produced caused by an effector molecule

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21
Q

Repression

A

-Decrease in amount or expression of transcript for enzyme produced caused by an effector molecule

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22
Q

Proteasomes

A

-Protein degradation by proteases in the lysosome or in macromolecular complexes

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23
Q

Zymogens

A
  • Inactive precursor to an enzyme, activated by cleavage of a specific peptide bond
  • inactive until they reach the proper environment (chymotrypsinogen to chymotrypsin and trypsinogen to trypsin)
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24
Q

Insulin

A

-synthesized as a precursor protein, modified to mature form by proteolysis

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25
Q

Proinsulin synthesized where? Transported where?

A
  • In ER, oxidizing environment-folded and disulfide bonds formed
  • Transported to the golgi apparatus, packaged into secretory vesicles, processed by proteases to form mature insulin
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26
Q

Reversible covalent modifications

A
  • phosphorylation of Ser, Thr, Tyr (uses ATP) & usually occurs in response to a stimulus
  • methylation of glu residues (used in bacteria as food sensor)
  • creation or reduction of disulfide bonds
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27
Q

Allosteric enzymes

A
  • Mostly multi subunit proteins with one or more active sites
  • bind other ligands at sites other than the active site
  • can be activated or inhibited by allosteric ligands, often control key reaction sin major pathways that must be regulated
  • Michealis menten kinetics do not apply to allosteric enzymes
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28
Q

Vo vs [S] graph shape for allosteric enzymes

A

Sigmoidal

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29
Q

Activators

A

-positive modulators that bind to allosteric site and stabilize the active conformation, reaction rate increased

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30
Q

Inhibitors

A

-negative modulators that bind to allosteric site that stabilizes the inactive conformation, reaction rate decreased

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31
Q

Cooperativity

A
  • Changes in the conformation of one subunit leads to conformational changes in adjacent subunits
  • Can be positive or negative
32
Q

Concerted allosteric model with activators and inhibitors

A
  • all subunits are changed at once from taut (T) to relaxed (R) or vice versa
  • activator shifts equilibrium in favor of the R, inhibitor shifts in favor of T
  • S binds much tighter to R than to T
  • cooperativity achieved because S binding increases the population of R, which increases the sites available to S
33
Q

Homotropic effectors

A

-binding of substrate influences the binding of more substrate

34
Q

Sequential Model

A
  • Binding of the ligand to one subunit triggers a conformational change that is passed to subsequent subunits
  • more complex model, allows for intermediate formations
35
Q

Sequential Reactions

A

-reaction cannot proceed until all substrates are bound to the enzyme active site, ordered and random

36
Q

Double-displacement reactions (ping pong)

A
  • First product is released before second substrate binds

- Enzyme is altered by first phase of the reaction

37
Q

Stabilizing the transition state

A

Lowers Ea and increases reaction rate

38
Q

Catalysis promoted by proximity, orientation and strain effects

A
  • enzyme brings substrate into close proximity with each other & catalytic groups (now not improbable collision of two molecules)
  • enzyme binds substrates with a specific orientation that aligns the substrates and catalytic groups (now not improbable that molecules collide in correct orientation)
  • enzymes freeze out transitional/rotational motion of substrates and catalytic groups
  • upon substrate binding, transition state makes better contact with enzyme than substrate
39
Q

Electrostatic Catalysis

A

charged enzyme functional groups in stabilizing otherwise unstable intermediates in the chemical mechanism

  • substrate binds to enzyme, water is excluded from active site (desolvation)-protects reactive groups from water
  • causes local dielectric constant to be lower-enhances electrostatic interactions in the active site(charge distribution helps position the substrate)
40
Q

General Acid-Base catalysis

A
  • proton transfer
  • enzyme avoids unstable high energy charged intermediates by donating a proton (general acid) or accepting a proton (general base)
  • if a group donates a proton, it has to get a different proton back by the end of a cycle
41
Q

Covalent Catalysis

A

-form between a nucleophilic group on the enzyme and an electrophilic group on the substrate

42
Q

Alkali metals role

A

-loosely bound and play structural roles

43
Q

Transition metals

A

-usually play a functional role in catalysis as a part of a functional group

44
Q

Metal Ion Catalysis

A
  • Hold substrate properly oriented by coordinate covalent bonds, substrate held in very specific geometry so reaction can proceed efficiently
  • enhances reaction by polarizing the scissle bond and stabilizing a negatively charged intermediate
45
Q

Prosthetic groups

A

-coenzymes that ARE covalently bound to an enzyme and therefore are always present

46
Q

epimers

A

stereoisomers that differ at only one carbon

47
Q

enantiomers

A

stereoisomers that are mirror images (D&L)

48
Q

Diasteromers

A

stereoisomers that are not mirror images

49
Q

Anomers

A

stereoisomers that differ only at keto/aldo carbon

50
Q

mutorotation

A

Interconversion between alpha and beta anomers through the open chain form

51
Q

Starch Makeup

A
  • amylose and amylopectin
  • energy reservoir of plant cells & significant source of carbohydrate in the human diet
  • found in chloroplasts of plant cells
52
Q

Amylose

A

-repeating units of maltose-linear

53
Q

Amylopectin

A
  • Main backbone is amylose (linear) with D-glucose molecules in alpha 1->4 linkage
  • has branches connect to backbone and to each other by alpha 1->6 linkages
  • branch points every 25-30 glucoses
  • has one reducing end
  • has many non reducing ends
54
Q

Glycogen

A
  • Carbohydrate storage molecule in vertebrates (in liver and muscle cells)
  • Liver: source of glucose for maintaining blood glucose
  • Skeletal muscle: used to generate ATP during anaerobic muscle contraction
  • starch-branching every 25 units, glycogen- every 8 to 10, ie more branching=short term storage, can lose all in 24 hrs
55
Q

Branching

A
  • allows several sites for simultaneous synthesis and degradation
  • branching speeds up degradation
56
Q

McArdles Disease

A
  • Mutation in the muscle glycogen phosphorylase
  • autosomal recessive, premature stop codon
  • muscle cells can’t produce enough energy, so muscles become easily fatigued
57
Q

Lipids

A

Substances from living things that dissolve in nonpolar solvents-insoluble in water

  • storage molecules for energy
  • gets lots of energy from fat
  • stored in adipose tissue
58
Q

amphipathic

A

have both hydrophilic and hydrophobic parts (fatty acids)

59
Q

adipocytes

A
  • only function is to store fat (lipids)
  • found in oily droplets in the cytoplasm
  • rich source of energy
60
Q

Olestra

A
  • Chemically synthesized fat (TAG) substitute
  • Mixture of sugars and fatty acids
  • not absorbed or metabolized, therefore not caloric
61
Q

Saponification

A
  • boil animal fat with lye (NaOH) to make soap

- NAS process

62
Q

Orlistat

A
  • treat obesity by inhibiting lipid absorption->reduce calorie intake-fat isn’t digested
  • inhibits pancreas lipase
  • side effect: oily and loose stool
63
Q

Phospholipases 3 functions

A

-membrane remodeling, signal transduction, and digestion

64
Q

Lysolethian

A
  • One-legged phospholipids
  • snake venom
  • acts as detergent
  • dissolves membranes in red blood cells which causes them to rupture
65
Q

Sphingolipid

A
  • polar membrane lipid, glycerol is replaced by sphingosine, long chained amino alcohol
  • much more amphiphilic than tracylglycerols
66
Q

Sphingomyelin

A
  • found in most cell membranes, but most abundant in the myelin sheath of nerve cells
  • insulates nerve axons
67
Q

Glycolipids

A
  • cerebrosides and gangliosides, abundant in the brain and nervous system membranes
  • improper degradation results in metabolic disease
68
Q

Tay-Sachs Disease

A
  • Sphingolipid storage disease
  • deficiency in B hexosaminidase A
  • gangliosides accumulate in nerve cells, brain and spleen, lysosomes rupture
  • results in blindness, weakness, seizures and mental retardation. Death usually by age 3
69
Q

Gaucher Disease

A

Sphingolipid storage disease
-accumulation of glucocerebroside in lysosome in spleen, liver, kidneys, lungs, brain, bone marrow, white blood cells
-characterized by bruising, bone pain, fatigue, anemia, low blood platelets, and enlargement of the liver and spleen
IV enzyme replacement therapy effective

70
Q

Cardiac Glycosides

A
  • sugar derivatives of steroids
  • increase cardiac muscle contraction
  • can be toxic but also medicinally important (digitalis)
71
Q

Hydropathy plots

A

-display the hydrophobic and hydrophilic regions of a protein sequence and predict the structure based on these regions

72
Q

Plasma membrane is added to membrane by vesicles from

A

ER & Golgi

73
Q

3 steps of membrane transport

A

-binding, change in shape of protein, release

74
Q

Carrier proteins different from channel because

A

they move small numbers of molecules at a time

75
Q

P glycoprotein

A
  • ATP binding cassette transporter
  • likely evolved as defense mechanism against harmful substances
  • pumps out harmful xenobiotics
  • protective function
  • in blood brain barrier, precludes access of anti-cancer, anti-HIV, anti-psychotic and other therapies to the brain
  • present in liver, small intestine and colon, limits the flow of drugs into the bloodstream

Biochemistry (3 decks)

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