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Enzymes Flashcards

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1
Q

Importance of enzymes

A
  • inheratple disorders due to defficancy (pku) or excessive activity of gene (onka genes overactivity)
  • Important in diagnosing illnesses (heart attack - enzimes leak into blood)
  • drugs exert bilogical effects through interactions with enzymes (asprin, dec. inflamation)
  • used in chemical industry, food procesing, agraculture
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2
Q

Enzymes lower

A

activation energy

Catalyze reactions to high rates (107-1019 times greater)

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3
Q

Activation energy is the

A

ammount of energy required to convert 1 mol of substrait from ground state to transition state (top of hill - unstable)

is overcome with enzymes via an alternate pasthway

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4
Q

Enzymes do not

A

alter the standard free energy of rxm.

dosnt change thermodynamics, only kenetics

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5
Q

Phosphatases

A

Catalyze hydrolytic removal of a phosphate group from a molecule

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6
Q

Kinases

A

Catalyze the addition of phosphate group to molecule

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7
Q

ATPases

A

Hydrolyze ATP. Energy-harnessing ATPase activity as part of their function

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8
Q

GTPases

A

Hydrolyze GTP. Play a role in the regulation of cell processes

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9
Q

Proteases

A

Break down proteins, hydrolyze peptide bonds between amino acids

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10
Q

The active site brings substrates into favorable conformations with

A

several amino acid side chains directly involved in the coordination, making, and breaking of bonds.

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11
Q

the 3-D structure of the reactive center of an enzime is formed by the

A

the folded domains of the protein

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12
Q

The active site of enzymes generate a highly selective environment in which

A

specific chemical reactions occur without generating unwanted side reactions.

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13
Q

Substrate is

A

a reactant that binds to the active site

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14
Q

lock in key

A

complemeary exact fit

both rigid

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15
Q

induced fit

A

some flexability in enzyme shape

adjustments made allow for better fit (enhanced catalisis)

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16
Q

Hexokinase

A

Glucose + ATP (enzime)-> Glucose 6-Phosphate + ADP

Two-domain protein with a central binding cleft for glucose and ATP.

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17
Q

•Upon glucose binding to hexokinase there is an ~____ fold increase in the affinity of the enzyme for ATP.

A

50

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18
Q

(in Hexokinase) Glucose binding induces a significant

A

conformational change in the protein that brings the two opposing domains close together to form a high affinity binding cleft for the phospho-transfer reaction to occur.

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19
Q

strategies of Enzyme Catalysis

Align/Position Reactants to favor that transition state

A
  • fewer conformations to explore
  • Increase efficiency
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20
Q

strategies of Enzyme Catalysis

induced charge state

A

Amino acids in active site interact with reactants via charge, polarity

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21
Q

strategies of Enzyme Catalysis

Deform reactants (or strain)

A

force so that it resembles a transition state

  • Enzyme strains substrate
  • Forcing a transition state, favor reaction
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22
Q

Much of the energy required to lower activation energy is derived from

A

weak, non-covalent interactions between substrate and enzyme

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23
Q

Binding energy

A

energy relased, lowers activation energy

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24
Q

Enzymes are __

work in __

are not __

can be ___

A

are catalysts: Lower activation energy, promote the transition state (ie orient substrates, strain substrates, induce charge, induced fit)

Enzymes are highly specific to reactions they catalyze

Enzymes work in moderate temperatures (ex. body temp if too hot, denature protines)

Enzymes are Not consumed in reactions (more effecient to resuse the enzime)

Enzymes can be regulated

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25
Rate of ES formation =
rate of ES breakdown
26
V0
inital velocity of protine formation
27
Enzime same inc. \_\_\_
substrate
28
enzime becomes saturated
Vmax no longer increase velocity
29
Km
dissocation constant messure of affiity of an ezyme for substrate is a substrate concentration when velocity is half of its max
30
lowe Km
higher affenity for its substrate
31
higher Km
need more substrate to get same rate
32
Compedative inhibitor
compeets with substrate for active site Vmax dosent change (because compedative/both are like/are substrates)
33
Lysozyme is a natural
natural antibiiotic
34
Lysozyme catalizes
catalizes the cutting of polysaccharide chains in cell walls of bacteria catalizes a hydrolysis reaction: Adds water to bond between two adjacent sugar groups in polysaccharide chain, causing bond to break. Reaction is favorable
35
Lysozyme reaction
1. Sugar D is forced into **strained conformation (strained catalisis)** 2. Glu35 serves as an acid, **donates a H+** to sugar E **(acid base catalisis)** 3. Asp52 attacks C1 of Sugar D, **transient covalent bonds forms** between Asp and Sugar D. (nuc. attack, transient, strong bond formed but must go back) 4. **Hydrolysis** of glycosidic bond (sugar-sugar bond) 5. Glu35 **polarize**s water molecule, **oxygen attacks** C1 Carbon atom 6. **Covalent bond** broken between Asp and C1 (sugar D) 7. Hydrolysis **completed** 8. Lysozyme returned to initial state (EP formation)
36
Why does activity decrease above and below Ph optium for lysozyme?
Because when Ph dec. picks up proton and becomes non ioniced interfering with mechanism Ph increase glu35 releases proton, interfering with mechanism
37
Allosteric Regulation:
Regulatory molecule binds to a regulatory site (not active site) of enzyme. inhibit or activate enzyme - involves conformation changes site that can be regulated
38
Irreversible Inhibition:
Drug Targets
39
Post translational modifications:
Phosphorylation/Dephosphorylation reactions that regulate target proteins. add and removal of phaspate affects acitivity covalent motification
40
Proteolytic Processing:
Enzyme activation relies on cleavage of one or more peptide bonds
41
Nucleotide Regulation:
ATPases and GTPases
42
Most protines are
allosteric (enzymes, receptors, structural proteins, motor proteins)
43
Binding at one of the sites causes a | (allosteric regulation)
shift from one folded shape to a slightly different folded shape
44
linkage principle of allosteric regulation
when one binds it increases the affinity for the scond site (can be + or -)
45
Active site and regulatory site communicate so that
catalysis at the active site can be influenced by binding of a regulatory molecule at a separate site.
46
Feedback inhibition (negative feedback) in allosteric regulation
product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway
47
Allosteric Inhibition of Reaction
Presence of either ligand interferes with the binding of the other ligands prefer differnt conformation (neg. regulation)
48
Allosteric Activation of Reaction
favorable - promotes binding of second ligand ## Footnote Each ligand prefers same protein conformation, so each ligand increases the protein’s affinity for the other.
49
Allosteric regulation of ADP / ATP
ATP - inhibitor ADP - activator
50
Cooperative Allosteric Transition
The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining sites. allows hemoglobin to function substrate affects all sites
51
Hemoglobin Allosteric Transition Oxygenation of hemoglobin causes Hemoglobin alternates between shows a ___ dissociation curve due to
the dimers to slide by each other and rotate 15º Hemoglobin alternates between the two stable states- T (deoxy) and R (oxy) Hemoglobin shows a sigmoidal oxygen dissociation curve due to cooperative binding.
52
Asprin innactivates
irreversable inhibitor ## Footnote the **Cyclooxygenase enzyme** - acts as an acetylating agent where an **acetyl group is covalently attached** to a serine residue in the enzyme’s active site - Cyclooxygenase is required for prostaglandin and thromboxane synthesis. **Pain and Inflamation** - Long term usage blocks the formation of thromboxane in platelets. Used as an anticoagulant in the prevention of heart attack and stroke
53
Curcumin irreversibly inhibits \_\_\_
(active ingredient in tumeric) enzyme Aminopeptidase N (APN), an enzyme that promotes tumor growth and angiogenesis (blood vessel growth, feeds tummor)
54
Protein phosphorylation is \_\_ Expect it too\_\_ via
transfer of terminal phosphate group of ATP to target protein. 1) change enzyme activity (adds a neg charge) 2) Create binding site 3) mask binging site via protine kinase
55
Protein dephosphorylation via
Removal of phosphate from target protein protine phosphatase
56
Pyruvate Dehydrogenase
Key enzyme in Carbohydrate Metabolism
57
Reversable phosphorlation 2 examples
cell signaling - phospated sites/create binging sites Cyclin-Cdk complexes of cell-cycle control system - phophsatase targest protines involved in different stages
58
Regulation: By Proteolytic Processing
Some of enzymes and proteins are synthesized in inactive forms that become active following proteolytic processing and cleavage of the precursors hormaones are inactive, rly on proteolytic processing in cell where needed active when and where needed - important so that enzimes (ex. digestive) are not aftivated to early (ex. in the liver)
59
Preproinsulin must be processed into
mature insulin through a series of cleavage and folding steps.
60
C-peptide
has a much longer half-life in plasma (~30–35 minutes) than mature insulin (~5 minutes) can be used as a diagnositic to determin if someone is still making insulun
61
Enzymes that Couple Energy Transduction to Mechanical Work
Mechanical enzimes ATP binding hydrolosis relsease use all in movement
62
Different Classes of Mechanical Enzymes
Membrane transporters Molecular Motors / Machines (ATPases)
63
GTPase
GTP binding protine neucleotide regulators, molecular switch ON - GTP bouns OFF - GDP bound
64
GTPase regulation
GEF - guanine exchange factor - conformation change causes gdp to realse for fresh GTP GAP - GTPase activating protine - inducing hydrolosis of GTP to GDP

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