BCH 361 Midterm Study Questions correctly
answered to pass
1. What forces are
Intramolecular Forces: Covalent bonding is the sharing of
used when
electrons between molecules.
molecules react
with each other?
Intermolecular forces:
Hydrogen
Bonding Ionic
bonding
Van der Waal interactions
Dipole Interactions (dipole-dipole, induced dipole (ion, dipole))
2. What is a
hydrogen bond? An intermolecular force between Hydrogen and either Oxygen,
Nitro- gen, or fluorine.
3. What is an acid? In biochemical terms, an acid is a proton donator. It typically
has a low
pka, which is deprotonated at low pHs.
4. What is a base? In biochemical terms, a base is a proton donator. Typically, it
has a high
pKA, which means it is deprotonated at high pHs.
5. What is pKA? -log(ka). It measures how tightly a proton is bound to a
molecule. Low
pka means the molecule is deprotonated at low pH. A high
pKa means a molecule is deprotonated at high pH.
6. If the pH of a compound, or more of the conjugate
solution of a weak base form?
acid is high- er than
the pKa, will
there be more of the
acid form of the
,BCH 361 Midterm Study Questions correctly
answered to pass
Conjugate form because at the pH groups are deprotonated creating a conjugate base.
higher than pKA, the ionizable
7. If a compound has a pKa Ha/A =.00794. Use the Henderson-Hasselbach equation
to solve for
of 9.7 and the pH is 7.6, [A] /[HA].
what is the ratio of
the
,BCH 361 Midterm Study Questions correctly
answered to pass
acid and base form of ba- sic side chains?
the compound?
8. What does acid-base 14. Which Residues have acidic side
catalysis always chains?
involve?
9. What is the
difference between
general acid and
specific acid-base
catalysis?
10. What makes
something
nucleophilic?
11. What makes
something
electrophilic?
12. What roles do we
find Ser and Cys
residues having in
enzyme active sites?
Why doesn't Thr
behave in this way?
13. Which residues have
, BCH 361 Midterm Study Questions correctly
answered to pass
nucleophile in the Ser-His-Asp catalytic triad.
is not as strong of a nucleophile because it has a methyl group.
id-base catalysis always involves a weak The Methyl group is an electron donator; it can donate
acid or base and another proton electrons to the -OH group on Thr, making it less
acceptor or donator (depending on nucleophilic.
whether an acid or base is present).
Histidine (His/H)
ecific Acid-base catalysis only uses H+ Lysine (Lys/K)
(H3O+) or OH- ions part of water for Arginine (Arg/R)
catalysis. General Acid-Base catalysis
uses other weak acids and bases for Aspartate (Asp/D)
proton transfers. Glutamate
(Glu/E)
utron Deficient. Nucleophiles often carry a
negative charge, which they want to
neutralize by reacting with a
positively charged molecule.
ectron deficient. Electrophiles carry a positive
charge, which is neu- tralized by a
nucleophilic attack. In this attack,
electrons are transferred to the
electrophile. Electrophiles often carry
leaving groups, which leave after a
nucleophile covalently binds to the
molecule.
Ser and Cys residues the -OH groups
often act as nucleophiles. For
example, the Ser acts as the
answered to pass
1. What forces are
Intramolecular Forces: Covalent bonding is the sharing of
used when
electrons between molecules.
molecules react
with each other?
Intermolecular forces:
Hydrogen
Bonding Ionic
bonding
Van der Waal interactions
Dipole Interactions (dipole-dipole, induced dipole (ion, dipole))
2. What is a
hydrogen bond? An intermolecular force between Hydrogen and either Oxygen,
Nitro- gen, or fluorine.
3. What is an acid? In biochemical terms, an acid is a proton donator. It typically
has a low
pka, which is deprotonated at low pHs.
4. What is a base? In biochemical terms, a base is a proton donator. Typically, it
has a high
pKA, which means it is deprotonated at high pHs.
5. What is pKA? -log(ka). It measures how tightly a proton is bound to a
molecule. Low
pka means the molecule is deprotonated at low pH. A high
pKa means a molecule is deprotonated at high pH.
6. If the pH of a compound, or more of the conjugate
solution of a weak base form?
acid is high- er than
the pKa, will
there be more of the
acid form of the
,BCH 361 Midterm Study Questions correctly
answered to pass
Conjugate form because at the pH groups are deprotonated creating a conjugate base.
higher than pKA, the ionizable
7. If a compound has a pKa Ha/A =.00794. Use the Henderson-Hasselbach equation
to solve for
of 9.7 and the pH is 7.6, [A] /[HA].
what is the ratio of
the
,BCH 361 Midterm Study Questions correctly
answered to pass
acid and base form of ba- sic side chains?
the compound?
8. What does acid-base 14. Which Residues have acidic side
catalysis always chains?
involve?
9. What is the
difference between
general acid and
specific acid-base
catalysis?
10. What makes
something
nucleophilic?
11. What makes
something
electrophilic?
12. What roles do we
find Ser and Cys
residues having in
enzyme active sites?
Why doesn't Thr
behave in this way?
13. Which residues have
, BCH 361 Midterm Study Questions correctly
answered to pass
nucleophile in the Ser-His-Asp catalytic triad.
is not as strong of a nucleophile because it has a methyl group.
id-base catalysis always involves a weak The Methyl group is an electron donator; it can donate
acid or base and another proton electrons to the -OH group on Thr, making it less
acceptor or donator (depending on nucleophilic.
whether an acid or base is present).
Histidine (His/H)
ecific Acid-base catalysis only uses H+ Lysine (Lys/K)
(H3O+) or OH- ions part of water for Arginine (Arg/R)
catalysis. General Acid-Base catalysis
uses other weak acids and bases for Aspartate (Asp/D)
proton transfers. Glutamate
(Glu/E)
utron Deficient. Nucleophiles often carry a
negative charge, which they want to
neutralize by reacting with a
positively charged molecule.
ectron deficient. Electrophiles carry a positive
charge, which is neu- tralized by a
nucleophilic attack. In this attack,
electrons are transferred to the
electrophile. Electrophiles often carry
leaving groups, which leave after a
nucleophile covalently binds to the
molecule.
Ser and Cys residues the -OH groups
often act as nucleophiles. For
example, the Ser acts as the
