Glossary of Biochm chpt 6 (review test III)

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What is a cofactor?
An inorganic element that may be required for enzyme activity
What is a coenzyme?
An organic or organometallic molecule required for the action of certain enzymes
What is a prosthetic group?
-a group other than the protein groups
-bound to a protein and essential to it's activity
-tightly/covalently bound coenzyme or metal ion
What is a Holoenzyme?
An enzyme plus a group (cofactor)
What is an apoenzyme?
aka an apoprotein
-An enzyme (protein) alone without a cofactor group
What can modifying groups do?
They can activate or inactivate an enzyme?
List some examples of enzyme modification?
1. Phosphorylation
2. Glycosylation
3. Alkylation
What are some modifying grouops?
1. phosphoryl-
2. glycosyl-
Why are biomolecules stable?
Because bio-reactions are slow
-they need to be catalyzed
Keq and ^G indicate what? What do they not indicate?
-they indicate equilibrium
-nothing about rate
What do enzymes indicate about a reaction?
-rate only
-nothing to do with equilibrium
How do enzymes affect rate?
By lowering the activation energy
How is the substrate's size relative to enzyme?
the substrate is typically much smaller than the enzyme
What is an active site?
the region of an enzyme surface that binds a substrate molecule and catalytically transforms it, (aka catalytic site)
What is a substrate?
The specific compound acted upon by an enzyme
What is the rate limiting step in a multi-step rxn?
The slowest rxn/step
Equation for rate (velocity)? for one substrate and for 2?
1. V = k[S]
2. V = k[S1][S2]
In k=CTe^(-^G++/RT) what does a small change in ^G++ translate to?
it is a change in the activation energy and translates to a large change in k
How much do enzymes typically increase rxn rates by?
10^5-10^17 fold
^Gb = what mathematically?
the difference between the uncatalyzed and catalyzed ^G
How do you account for the 10^5-10^17 increase in k?
need ^Gb around 30-100kJ/mol, which is possible since weak interactions are typically 4-30 kj/mol each
-so approx. 10-20 of them are needed for the observed change in ^Gb
Binding energy is also related to what?
-the better a substrate fits into the active site of an enzyme the MORE WEAK INTERACTIONS it can form with the enzyme
-an enzyme leads to the greatest rate increases for the substrate that it matches (binds to) most closely
List 4 ways that Binding energy contributes to catalysis?
1. reducing entropy
2. desolvation
3. compensating for distortion
4. induced fit-change in enzyme conformation
Explain how reducing entropy relates to binding energy and contributes to catalysis?
brings molecules together
Explain how desolvation relates to binding energy and contr.s to catalysis?
removes bound water from substrates
Explain how compensating for distortion is related to binding energy and contributes to catalysis?
-it holds a substrate in a distorted conformation so that it is more likely to react
Explain "induced fit" and how it relates to binding energy and contibutes to catalysis?
binding energy can distort the enzyme itself making it a better catalyst
What are the 3 most common types of catalysts? Which one do most enzymes use?
1. acid-base
2. covalent
3 metals

-most enzymes employ more than one
Be aware that groups that accept protons generally look like what?
have negative charges or unpaired electrons
What does steady st. kinetics refer to?
assumes that within a few seconds that most of the substrate turns into an enzyme substrate complex and this is what goes on to react.
-ES rises to stdy conc. and remains at that point
substrate concentration
initial rxn velocity
maximum achievable Vo
the [S] at which Vo = 1/2 Vmax
the michaelis constant
Michaelis-Menten eqn?
Vo = (Vmax[S])/(Km+[S])
Where does Km = [S]
where Vo = 1/2 Vmax
rate constant for rate determining step

Kcat = Vmax / [Et] OR
Vmax = Kcat * [Et]
What does the turnover number refer to?
-it is the number of substrate molecules converted to a product in a given unit of time, on a single enzyme molecule, when the enzyme is saturated with substrate
List 4 types of reversible enzyme inhibition?
1. Competitive
2. Uncompetitive
3. Noncompetitive: rare
4. Mixed
Describe competitive inhibition?
Inhibitor and Substrate tries to bind to same site
How can competitive inhibition be overcome?
By adding large amounts of substrate
On plot of comp. inh. all lines meet where.
on x axis
Can other types of inhibition, besides competitive, be overcome?
Describe Uncompetitive inhibition?
Inh. binds to a site other that the active site of enzyme-substrate complex
-inh.s structure is different from substrates
-inhibitor cannot bind until substrate does
Describe mixed inhibition?
Inhibitor binds to a site other than the Active Site of the Enzyme alone or of the Enzyme-substrate complex
-inhibitor can bind whether substrate binds or not
-inhibitors structure is different from substrates
Is competitive inh. possible to overcome?
Is uncompetitive inh. possible to overcome?
Is mixed/noncompetitive inh. possible to overcome?
In competitive inh. the inhibitor binds to what?
the active site
In uncompetitive inh. the inh. binds to what?
other site
In mixed/noncompetitive inh. the inh. binds to what?
other site
In competitive inh. describe the structure of the inh.
similar to substrate
In uncomp. inh. describe the struc. of the inh.
different from the substrate
in mixed. noncomp. inh. describe the structure of the inh.
different from the substrate
In competitive inh. the inh. binds to what?
the enzyme alone
In uncomp. inh. the inh. binds to what?
the ES complex
In mixed/noncomp. inh. the inh. binds to what?
the enzyme alone or the ES
In competitive inh. the apparent Km does what?
In uncompetitive inh. the apparent Km does what?
In mixed/non-competitive inh. the apparent Km does what?
changes/unchanged (increases)
In competitive inh. the apparent Vmax does what?
Remains unchanged
In uncomp. inh. the apparent Vmax does what?
In mixed/noncomp. inh. the apparent Vmax does what?
Describe irreversible inhibitors?
-bind to or destroy an essential function of an enzyme
-they kill it
What are suicide inactivators?
a special class of irreversible inhibitors
-binds to enzyme as a normal substrate, but it is then converted to a reactive compound that compounds irreversibly with the enzyme, very specific, with few side effects
-kills the enzyme and itself
-very promising drug candidates
-ex. penicillin
Enzymes have pH optima, explain?
Enzymes typically want physiologic pH of about 7 BUT some, like pepsin, found in stomach acid work best at low pH...useless if moved to digestive tract
List 4 types of regulatory enzymes?
1. Allosteric
2. Regulated by covalent modification
3. Regulated by other regulatory enzymes
4. Activated by peptide cleavage
Describe allosteric regulatory enzymes?
-can be either inhibitory or stimulatory
-can be either homotropic or heterotropic
-changes sigmoidal curve...raises or lowers it
If an allosteric modulator/effector is inhibitory what does that mean?
it decreases the activity
-negative modulation
-lowers sigmoidal curve
If an allosteric modulator/effector is stimulatory what does it indicate?
-increase activity
-positive modulator
-will raise sigmoidal curvea
Feedback inh. is an example of what?
allosteric modulation
Key example of reversible covalent modification?
What is phosphorylation, describe the two different actions?
- inv. with enzymes regulated by reversible covalent modification
1. protein kinases: adds phosphoryl groups
2. Protein phosphatases: removes phos. groups
What is a Zymogen?
-Involved with enzymes modified by peptide cleavage
-it is an inactive precursor of an enzyme
What is a proenzyme?
Related to enzymes modified by peptide cleavage
-cleave zymogens
Give examples of zymogens to active proteins?
1. Inactive chymotrypsinogen is cleaved to become active chymotrypsin
2. inactive trypsinogen is cleave to become active trypsin
What reaction does chymotrypsin catalyze?
hydrolytic cleavage of a peptide bond
How does the reaction with chymotrypsin work?
acid-base and covalent catalysis
How does hexokinase work?
induced fit
How does enolase work?
metal ion
How does lysozome work
covalent and generalized acid base
What reaction does hexokinase catalyze?
interconversion of glucose and + ATP, and Glucose-6-phosphate + ADP
What reaction does enolase catalyze?
reversible dehydration of 2-phosphoenolpyruvate
What reaction does lysozome catalyze?
uses two successive nucleophilic displacement reactions
Chymotrypsin acts on polypeptides at points adjacent to Phe, Trp, and Tyr. Based on this structure and the function of the enzyme, how do you explain this specificity?
the hydrophobic pocket of chymotrypsin is an ideal binding site for an aromatic amino acid
How do you figure out the # residues?
Mr chymotrypsin?
about 25,000
Mr hexokinase?
about 108,000
Mr enolase?
about 93,000
Mr lysozome?
about 14,000
Why does water not have the same effect on hexokinase as glucose? Which one of the four factors contributing to binding energy is this an example of?
induced fit, h20 cannot form as many bonds, glucose can and it forms a structural change (glucose is the normal substrate of hexokinase)
-this is why it does not readily add PO4 to H20

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