BCH4024 TEST 1 QUESTIONS WITH
COMPLETE SOLUTIONS
diffusion-limited process: - Answer-reaction rate is determined by how fast reactants
collide
the Protonation and deprotonation of macromolecules? - Answer-acid/base groups on
surface react immediately
acid/base groups deep inside may never ionize
hydrogen bonds of buried helices and beta-sheets require the "conformation breathing"
-local unfolding
Pepsin - Answer-a digestive enzyme secreted into gastric juice, having a pH of 1.5
allowing pepsin to act optimally
Trypsin - Answer-a digestive enzyme that acts in the small intestine, and has a pH
optimum that matches the neutral pH in the lumen of the small intestine.
Alkaline phosphatase - Answer-a hydrolytic enzyme that
operates well enough at neutral pH of intestine.
"Weak"
Noncovalent
Interactions - Answer--Individually weak, but the aggregate
effect is very significant
-Allows proteins & nucleic acids to fold & unfold
four types of noncovalent (weak) interaction among biomolecules in aques solvent -
Answer-1. hydrogen bonds between neutral groups and peptide bonds
2. ionic interactions such as attraction and repulsion
3. hydrophobic interactions
4. van der waals interactions
Gibbs Free energy (ΔG)
Strengths of Noncovalent Interactions - Answer-(-) to make;; (+) to break
Hydrogen Bonds
Strengths of Noncovalent Interactions - Answer-Intrinsically polar interaction
R-N-H•••••O=C-R
(acid base reaction)
,requires proton donor(EP) and proton acceptor (EN)
linear bond=strong H bond
bent bond=weak H bond
ΔG ≈ 4 - 40 kJ/mol
Electrostatic
Strengths of Noncovalent Interactions - Answer-Opposite Charges Attract
& Like Charges Repel
ΔG ≈ 4 - 40 kJ/mol
Salt bridge
Strengths of Noncovalent Interactions - Answer-H-bonding + Electrostatics
e.g. carboxylate (R-COO-) i protonated amine (R-NH3+)
ΔG ≈ 40 - 400 kJ/mol
Hydrophobic interactions
Strengths of Noncovalent Interactions - Answer-Displacement of water is driven by
favorable entropy
ΔG ≈ 0.4 - 4 kJ/mol
Pi stacking
Strengths of Noncovalent Interactions - Answer-Stacking of aromatic rings
greater e- delocalization
ΔG ≈ 0.4 - 4 kJ/mol
van der Waals interactions
Strengths of Noncovalent Interactions - Answer-Very weak forces between oscillating
dipoles.
ΔG ≈ 0.4 - 4 kJ/mol
Hydrogen Bonds
are found throughout Nature - Answer-between peptide groups in polypeptides
between complementary bases of DNA (T+A)
the properties
of the universal solvent
improve solubility
, Essential for biospecific recognition.
Easy to make & break (allows fast kinetics)
what are "NOT true bonds" - Answer-No overlapping of atomic or molecular orbitals
The Gibbs Equation - Answer-(ΔG = ΔH - TΔS)
Contrary to intuition, water binds tightly to apolar groups, such
that ΔHwater-binding << 0 (conversely: ΔHwater-release >> 0).
Hydrophobic interaction results in release of water molecules
increases randomness: ΔSwater-release >> 0.
Hydrophobic Interactions - Answer-The Gibbs Equation (ΔG = ΔH - TΔS) is guiding
Strictly speaking, these stabilizing interactions are NOT true bonds
Water - Answer-very polar; making hard to break bonds between molecules using more
energy
Clusters, liquid H2O is disordered cluster
-explaining: viscosity, High B.P., and Heat capacity.
Accessible Melting Point
Low B.P.
Polarity
lifetime of H-Bond - Answer-1-20 ps (10^-12s)
Liquid H2O - Answer-Flickering Strucker
disordered collection of clusters
3.4 H-Bonds
*Structure and Hydrogen Bonding of H2O
Ice - Answer-4 H-Bonds
Expands and rips apart cellulosic and woody plants (The Carbon Cycle - Facilitates
biological turnover)
COMPLETE SOLUTIONS
diffusion-limited process: - Answer-reaction rate is determined by how fast reactants
collide
the Protonation and deprotonation of macromolecules? - Answer-acid/base groups on
surface react immediately
acid/base groups deep inside may never ionize
hydrogen bonds of buried helices and beta-sheets require the "conformation breathing"
-local unfolding
Pepsin - Answer-a digestive enzyme secreted into gastric juice, having a pH of 1.5
allowing pepsin to act optimally
Trypsin - Answer-a digestive enzyme that acts in the small intestine, and has a pH
optimum that matches the neutral pH in the lumen of the small intestine.
Alkaline phosphatase - Answer-a hydrolytic enzyme that
operates well enough at neutral pH of intestine.
"Weak"
Noncovalent
Interactions - Answer--Individually weak, but the aggregate
effect is very significant
-Allows proteins & nucleic acids to fold & unfold
four types of noncovalent (weak) interaction among biomolecules in aques solvent -
Answer-1. hydrogen bonds between neutral groups and peptide bonds
2. ionic interactions such as attraction and repulsion
3. hydrophobic interactions
4. van der waals interactions
Gibbs Free energy (ΔG)
Strengths of Noncovalent Interactions - Answer-(-) to make;; (+) to break
Hydrogen Bonds
Strengths of Noncovalent Interactions - Answer-Intrinsically polar interaction
R-N-H•••••O=C-R
(acid base reaction)
,requires proton donor(EP) and proton acceptor (EN)
linear bond=strong H bond
bent bond=weak H bond
ΔG ≈ 4 - 40 kJ/mol
Electrostatic
Strengths of Noncovalent Interactions - Answer-Opposite Charges Attract
& Like Charges Repel
ΔG ≈ 4 - 40 kJ/mol
Salt bridge
Strengths of Noncovalent Interactions - Answer-H-bonding + Electrostatics
e.g. carboxylate (R-COO-) i protonated amine (R-NH3+)
ΔG ≈ 40 - 400 kJ/mol
Hydrophobic interactions
Strengths of Noncovalent Interactions - Answer-Displacement of water is driven by
favorable entropy
ΔG ≈ 0.4 - 4 kJ/mol
Pi stacking
Strengths of Noncovalent Interactions - Answer-Stacking of aromatic rings
greater e- delocalization
ΔG ≈ 0.4 - 4 kJ/mol
van der Waals interactions
Strengths of Noncovalent Interactions - Answer-Very weak forces between oscillating
dipoles.
ΔG ≈ 0.4 - 4 kJ/mol
Hydrogen Bonds
are found throughout Nature - Answer-between peptide groups in polypeptides
between complementary bases of DNA (T+A)
the properties
of the universal solvent
improve solubility
, Essential for biospecific recognition.
Easy to make & break (allows fast kinetics)
what are "NOT true bonds" - Answer-No overlapping of atomic or molecular orbitals
The Gibbs Equation - Answer-(ΔG = ΔH - TΔS)
Contrary to intuition, water binds tightly to apolar groups, such
that ΔHwater-binding << 0 (conversely: ΔHwater-release >> 0).
Hydrophobic interaction results in release of water molecules
increases randomness: ΔSwater-release >> 0.
Hydrophobic Interactions - Answer-The Gibbs Equation (ΔG = ΔH - TΔS) is guiding
Strictly speaking, these stabilizing interactions are NOT true bonds
Water - Answer-very polar; making hard to break bonds between molecules using more
energy
Clusters, liquid H2O is disordered cluster
-explaining: viscosity, High B.P., and Heat capacity.
Accessible Melting Point
Low B.P.
Polarity
lifetime of H-Bond - Answer-1-20 ps (10^-12s)
Liquid H2O - Answer-Flickering Strucker
disordered collection of clusters
3.4 H-Bonds
*Structure and Hydrogen Bonding of H2O
Ice - Answer-4 H-Bonds
Expands and rips apart cellulosic and woody plants (The Carbon Cycle - Facilitates
biological turnover)
