2. Sample questions for the nucleic acid section
Nucleoside is a pyrimidine or
purine base
• A.covalently bonded to a
sugar
• B.ionically bonded to a sugar
• C.hydrogen bonded to a sugar
• D.none of the above
The sugar in RNA is ______ , the
sugar in DNA is _____
• A.deoxyribose, ribose
• B.ribose, deoxyribose
• C.ribose, phosphate
• D.ribose, uracil
3. Sample questions for the nucleic acid section
In gel electrophoresis, what
fragments will move most
quickly through a gel?
• A.Large fragments
• B.Small fragments
• C.Large genome
• D.None of these
Nucleotide bases and
aromatic amino acids
absorb light respectively at
• A.280 and 260 nm
• B.260 and 280 nm
• C.270 and 280 nm
• D.260 and 270 nm
4. Sample questions for the nucleic acid section
Which of the following is found
on RNA but not DNA?
• A.Uracil
• B.Deoxyribose
• C.Phosphate
• D.Adenine
Which is true about the pairing of
bases in the DNA molecule?
• A. purines always pair with
pyrimidines
• B. a single ring base pairs with
another single ring base
• C. a double ring base pairs with
another double ring base
• D. purines pair with purines and
pyrimidines with pyrimidines
5. Sample questions for the nucleic acid section
A messenger acid is 336 nucleotides
long, including the initiator and
termination codons. The maximum
number of amino acids in the
protein translated from this mRNA
is:
• A 999
• B 630
• C 330
• D 111
• E 110
With what mRNA codon would the
tRNA in the diagram be able to
form a codon-anticodon base
pairing interaction?
• A. 3'-AUG-5'
• B. 3'-GUA-5'
• C. 3'-CAU-5'
• D. 3'-UAC-5'
• E. 3'-UAG-5'
6. Sample questions for the nucleic acid section
• Of what units are nucleic acids constituted? What are the
chemical entities that compose that unit?
• What is the rule for the pairing of nitrogenous bases in
the DNA molecule? And in the RNA?
• For each of the following structures identify: the
carbohydrate (ribose or deoxyribose)?; nucleoside or a
nucleotide? DNA or a RNA system?
7. Enzymes
• substance that increase rates of a
chemical reaction
• does not effect equilibrium
• remain unchanged in overall process
• reactants bind to catalyst, products are
released
10. Enzymes increase product formation by
(1) lowering the energy barrier (activation energy) for the product to
form
(2) increases the favorable orientation of reactant molecules for
product formation to be successful (stabilize transition state
intermediate)
11. Enzymatic Catalysis
• Activation Energy (AE) –
The energy require to
reach transition state
from ground state.
• AE barrier must be
exceeded for reaction to
proceed.
• Lower AE barrier, the
more stable the transition
state (TS)
• The higher [TS], the move
likely the reaction will
proceed.
S Ts P
12. Catalytic Power
• Enzymes can accelerate reactions as
much as 1016 over uncatalyzed rates!
• Urease is a good example:
– Catalyzed rate: 3x104/sec
– Uncatalyzed rate: 3x10 -10/sec
– Ratio is 1x1014 !
13. Specificity
• Enzymes selectively recognize proper
substrates over other molecules
• Enzymes produce products in very high
yields - often much greater than 95%
• Specificity is controlled by structure - the
unique fit of substrate with enzyme
controls the selectivity for substrate and
the product yield
14. Classes of enzymes
1. Oxidoreductases = catalyze oxidation-reduction reactions
2. Transferases = catalyze transfer of functional groups from
one molecule to another.
3. Hydrolases = catalyze hydrolytic cleavage
4. Lyases = catalyze removal of a group from or addition of a
group to a double bond, or other cleavages involving
electron rearrangement.
5. Isomerases = catalyze intramolecular rearrangement.
6. Ligases = catalyze reactions in which two molecules are
joined.
Enzymes named for the substrates and type of reaction
15.
16. Co-enzymes
• Non-protein molecules that help enzymes
function
• Associate with active site of enzyme
• Enzyme + Co-enzyme =
holoenzyme (conjugated enzyme )
• Enzyme alone = apoenzyme
• Organic co-enzymes – thiamin, riboflavin,
niacin, biotin
• Inorganic co-enzymes – Mg ++, Fe++, Zn++, Mn++
17.
18. Increase in the hydrogen ion concentration
(pH) considerably influences the enzyme
activity
19.
20. Sample questions
What is the function of enzymes within living systems?
• A) structural elements
• B) neurotransmitters
• C) catalysts
• D) hormones
Enzymes have names that
• A) always end in -ase
• B) always end in -in
• C) can end either in -in or -ase
• D) can end in either -in or -ogen
21. Sample questions
The protein portion of a conjugated enzyme is called a(n)
• A) apoenzyme.
• B) coenzyme.
• C) holoenzyme.
• D) cofactor.
Which of the following could be a component of a conjugated enzyme?
• A) coenzyme
• B) cofactor
• C) apoenzyme
• D) more than one correct response
• E) no correct response
22. Sample questions
Enzyme cofactors that bind covalently at the active site of an enzyme
are referred to as _________.
• (a) cosubstrates.
• (b) prosthetic groups.
• (c) apoenzymes.
• (d) vitamins
23. Sample questions
Which of the following statements concerning the effect of temperature
change on an enzyme-catalyzed reaction is correct?
• A) An increase in temperature can stop the reaction by denaturing
the enzyme.
• B) An increase in temperature can increase the reaction rate by
increasing the speed at
• which molecules move.
• C) An increase in temperature to the optimum temperature
maximizes reaction rate.
• D) more than one correct response
• E) no correct response
25. Transition (TS) State Intermediate
• Transition state = unstable high-energy intermediate
• Rate of reaction depends on the frequency at which
reactants collide and form the TS
• Reactants must be in the correct orientation and collide
with sufficient energy to form TS
• Bonds are in the process of being formed and broken in
TS
• Short lived (10–14 to 10-13 secs)
26. Intermediates
• Intermediates are
stable.
• In reactions with
intermediates, 2 TS’s
are involved.
• The slowest step (rate
determining) has the
highest activation
energy barrier.
• Formation of
intermediate is the
slowest step.
27. •Enzyme binding of substrates decrease activation energy by
increasing the initial ground state (brings reactants into
correct orientation)
•Need to stabilize TS to lower activation energy barrier.
28. The Transition State
Understand the difference between DG
and DG‡
• The overall free energy change for a
reaction is related to the equilibrium
constant
• The free energy of activation for a reaction
is related to the rate constant
31. Sample questions
• A catalyst can promote product formation during a chemical reaction
by _____.
• (a) lowering the activation energy barrier.
• (b) stabilizing the transition state.
• (c) positioning reactants in the correct orientation.
• (d) bringing reactants together.
• (e) all of the above
Which of the following is characteristic of an enzyme catalyst?
• (a) It positions reactants in the correct orientation.
• (b) It lowers the activation energy barrier.
• (c) It binds the transition state tighter than the substrate.
• (d) all of the above
32. ES complex must not be too stable
Raising the energy of
ES will increase the
catalyzed rate
•This is accomplished
by loss of entropy due
to formation of ES and
destabilization of ES by
•strain
•distortion
•desolvation
33. Transition State Stabilization
• Equilibrium between ES <-> TS, enzyme drives
equilibrium towards TS
• Enzyme binds more tightly to TS than substrate
Transition
state analog
35. Active Sites
• The active site of an enzyme represents
as the small region at which the substrate
(s) binds and participates in the catalysis
• The active site is made up of amino acids,
known as catalytic residues
38. Sample questions
An enzyme active site is the location in the enzyme where
• A) protein side groups are brought together by bending and folding
to form a site for interactions with substrates
• B) the catalyst interactions with the enzyme
• C) catalyst molecules are generated
• D) the substrate creates the catalyst molecules
An enzyme active site is the location in an enzyme where substrate
molecules
• A) are generated.
• B) become catalysts.
• C) undergo change.
• D) more than one correct response
• E) no correct response
39. Common types of enzymatic
mechanisms
• Substitutions reactions
• Bond cleavage reactions
• Redox reactions
• Acid base catalysis
• Covalent catalysis
40. Substitution Rxns
• Nucleophillic Substitution–
O
C
R X
Y
O
R C
X
Y
• Direct Substitution
O
C
R Y
+ X
R1 R2
C
R3 Y
R1 R2
X C Y
X R3
Nucleophillic = e- rich
Electrophillic = e- poor
R1 R2
C
X R3
+ Y
transition state
41. Oxidation reduction (Redox) reactions
• Loose e- = oxidation (LEO)
• Gain e- = reduction (GER)
• Central to energy production
• If something oxidized something must be
reduced (reducing agent donates e- to
oxidizing agent)
• Oxidations = removal of hydrogen or
addition of oxygen or removal of e-
• In biological systems reducing agent is
usually a co-factor (NADH of NADPH)
42. Cleavage reactions
• Heterolytic vs homolytic cleavage
• Carbanion formation (retains both e-)
R3-C-H R3-C:- + H+
• Carbocation formation (lose both e-)
R3-C-H R3-C+ + H:-
Hydride ion
• Free radical formation (lose single e-)
R1-O-O-R2 R1-O* + *O-R2
43. Acid-Base Catalysis
X H : B X: H B
• Accelerates reaction by catalytic transfer of a proton
• Involves AA residues that can accept a proton
• Can remove proton from –OH, -NH, -CH, or –XH
• Creates a strong nucleophillic reactant (i.e. X:-)
44. X H : B X: H B
O
C
N
O
H H : B
O
C
OH
N
H
B
O
C
OH HN
: B
:
:
Acid-Base Catalysis
carbanion intermediate
45. Covalent Catalysis
• 20% of all enzymes employ covalent catalysis
A-X + B + E <-> BX + E + A
• A group from a substrate binds covalently to
enzyme
(A-X + E <-> A + X-E)
• The intermediate enzyme substrate complex (A-X)
then donates the group (X) to a second substrate
(B) (B + X-E <-> B-X + E)
46. Covalent Catalysis
Protein Kinases
ATP + E + Protein <-> ADP + E + Protein-P
1) A-P-P-P(ATP) + E-OH <-> A-P-P (ADP) + E-O-PO4
-
2) E-O-PO4
- + Protein-OH <-> E + Protein-O- PO4
-
47. The Serine Proteases
Trypsin, chymotrypsin, elastase, thrombin,
subtilisin, plasmin, TPA
• All involve a serine in catalysis - thus the name
• Ser is part of a "catalytic triad" of Ser, His, Asp
• Serine proteases are homologous, but locations
of the three crucial residues differ somewhat
• Substrate specificity determined by binding
pocket
48. A zymogen (or proenzyme) is an inactive enzyme precursor.
52. Serine proteases
the carbonyl oxygen becomes an oxyanion
Nucleophilic attack Protonation
53. The main chain NHs of Gly193 and Ser195 stabilize the negatively charged
oxyanion of the tetrahedral intermediate
54. The reaction pathway for serine protease peptide bond cleavage
The highest energy peak in the serine protease reaction pathway corresponds to the
covalent intermediate hydrolysis process, which is the slowest step in the reaction.
