BCH 4024: Exam 1
What is [H2O]^2 equal to?
(55 M)^2
What is the formula for proton activity or (H+)?
(H+) = A[H+] Note that A is the activity coefficient
For most proteins, what percentage of AA's are aromatic?
1-2%
What is autoprotolysis?
A proton is transferred b/w 2 identical molecules (e.g. water) with one being the Bronsted acid and the other being the Bronsted base
How does a buffer adjust to the addition of H+?
A- + H+ <> HA
What type of chemical reaction is the formation of H-Bonds b/w H2O molecules?
Acid-Base
What do enzymes often have in this active sites?
Acids and bases
What is the Greek order that is used to signify the side chain carbons?
Alpha, Beta, Gamma, Delta, Epsilon
What are alpha amino acids (AA's)?
Always contain an amino group that is on the alpha carbon
How does the freezing of water relate to the carbon cycle?
As water freezes, it expands. This rips plants apart and allows C atoms to re-enter the cycle.
Where are buffers most effective?
At pH near their pKa, where there's an equally large pool of both weak acid and its conjugate base
What is the most important buffer system for acid-base homeostasis in humans?
Bicarbonate buffer system
What are the four principal buffers in humans?
Bicrabonate Orthophosphate ATP Proteins
In acid/base dynamics, which one acts as the proton donor? Proton acceptor?
Bronsted acid = proton donor Bronsted base = proton acceptor
How does bicarbonate (HCO3-) form?
CO2 + H2O <> H2CO3 <> HCO3- + H+ CO2 combines with water to form H2CO3, which then dissociates to form hydrogen ion and bicarbonate. This process is catalyzed by carbonic anhydrase. The system as a whole is a very powerful acid-base regulator when coupled with respiratory compensation.
What is the carbonic anhydrase covalent catalyzed hydrolysis reaction?
CO2(gas) + H2O <M> H2CO3 <> H3O+ + HCO3-
What type of enzyme uses a proton wire to shuttle H+ transfer in/out of its active site via proton hopping
Carbonic anhydrase (COVALENT HYDROLYSIS)
A catalyzed reaction reaches equilibrium within _____, while an uncatalyzed reaction reaches equilibrium _____,
Catalyzed = 1 sec Uncatalyzed = 30 years
Which hydrolysis reaction is catalyzed?
Covalent
What are two examples of polar, organic solvents?
DMF, THF
A(n) ____ in temperature = A(n) _____ in carbon recycling
Decrease in temperature = increase in carbon recycling
Do enzymes hydrate or dehydrate reactants?
Dehydrate
Know how to solve the Henderson-Hasselbalch equation in Lecture 1 Slide 13.
Done
What is the relationship between enzymes and side-reactions?
Enzymes can reduce potentially toxic side-reactions
What are the four transfer processes of the water cycle?
Evaporation Transpiration Precipitation Runoff
T/F: pH meters measure [H+]
F
T/F: pH of pure water is exactly 7.00
F
What is the glucose-6-phosphatase catalyzed hydrolysis reaction?
Glucose 6-phosphate <(H2O to HPO4)> Glucose
What regulates hexokinase in glucose phosphorylation?
Glucose-6-P. This acts as feedback regulation and turns off the enzyme.
Why is water's accessible melting point important?
It occurs in a temperature range that helps to sustain life on earth.
What AA's absorb UV light?
Phenylalanine Tyrosine Tryptophan
What are the AA's with aromatic side-chains?
Phenylalanine Tyrosine Tryptophan
In what type of solvents do nucleophilic reactions work the best?
Polar, organic solvents
DNA and RNA are _____.
Polyelectrolytes
What do pH meters measure?
Proton activity which is (H+)
In the acid-base formation of H-Bonds in H2O, which atoms are the proton donor and proton acceptor?
Proton donor: Hydrogen Proton acceptor: Oxygen
Where does runoff water eventually reach?
The ocean
What has determined where life began?
Water
When would pH = pKa?
When [A-] = [HA] So in that case, pH = pKa + 1 when [A-] = 10 * [HA}
What is acidosis?
When the blood has excess H+
What the mathematical requirement of neutrality?
[H3O+] = [OH-] = 10^-7 M
What is the lifetime of a hydrogen bond (H-bond)?
1-20 picoseconds
What are the two types of covalent hydrolysis catalyzed reactions?
1. Carbonic Anhydrase 2. Glucose 6-Phosphatase
What are the benefits of water having a low boiling point relative to earth's temperature?
1. Evaporative heat loss stabilizes body temperature 2. Moist atmosphere 3. Moves large amounts of water as clouds, precipitation, and run-off 4. Erosion remodeling Earth's landscape
What are the four key properties of water's structure?
1. High heat capacity 2. High BP relative to its molecular weight 3. High viscosity relative to its molecular weight 4. Strong interactions with ionic & nonpolar molecules
What are the four effects of enzymes?
1. Increase local concentration of reactants 2. Orient substrates to maximize reactivity 3. Stabilize reaction transition-states 4. Speed up reactions
What is the average number of H-Bonds of LIQUID water?
3.4
How many H-Bonds can a single water molecule make?
4
What is the average number of H-Bonds of ICE?
4
What is vapor? (NOT THE SAME AS GAS)
A collection of molecules at a lower temperature
What is Le Chatelier's Principle?
A dynamic system compensates to stress
What is glucose phosphorylation?
A reaction where 40 nM hexokinase phosphorylates glucose at position-6, using ATP in the process
What is a hydrogen bond?
A stable interaction occurring b/w 2 atoms that share 1 H atom
What are the AA's that have nonpolar aliphatic R groups?
Glycine Alanine Valine Leucine Isoleucine Methionine Proline
What is the simplest amino acid?
Glycine. It is not optically active (symmetrical)
Which is longer: H-Bonds or covalent bonds?
H-Bonds
How does a buffer adjust to the addition of OH-?
HA + OH- <> A- + H2O
What are the traits of AA's with aromatic side-chains?
Hydrophobic Absorb UV light
Which hydrolysis reaction is uncatalyzed?
Ionic
What are the two types of hydrolysis reactions?
Ionic (uncatalyzed) Covalent (catalyzed)
How is erosion of Earth's landscape beneficial?
It increases surface area and exposes mineral nutrients
What is respiratory compensation?
It is compensation for the metabolic acid-base imbalances (either increase or decrease in HCO3) via the lungs. It is faster than metabolic compensation. An altered breathing rate modifies circulating [CO2].
What is the formula for the equilibrium constant?
K = ([H3O+][OH-])/[H2O]^2
What is the formula for Ka?
Ka = [H+][A-]/[HA]
How does the bicarbonate buffer system maintain acid-base homeostasis in humans?
Keeps a constant plasma pH by countering changes in acids, bases, anions, and metal ions.
What is the formula that relates K and Kw?
Kw = K * [H2O]^2
What is the formula for the equilibrium constant for water?
Kw = [H3O+][OH-] = 10^-14 M^2
Why are proteins always made of L AA's?
L's keep it going in one direction
In Fischer projections, what does the "L" denote?
Levo (LEFT)
In the formation of the bicarbonate buffer system, which molecule is the Lewis Acid? Bronsted Acid? Conjugate Base?
Lewis Acid = CO2 Bronsted Acid = H2CO3 CB = HCO3-
Which H-Bonds are stronger: linear or bent?
Linear (better to have three atoms aligned)
What does the bicarbonate buffer system take advantage of?
Metabolically produced CO2 in humans
What is the ionic hydrolysis uncatalyzed reaction?
NaCl + 8H2O <> Na+(H2O)4 + Cl-(H2O)4
In liquid water, do H-bonds stay the same/unbroken?
No, they are relentlessly made and broken. Thus, liquid water is a flickering/transient collection of W5 and very little W1
Are there free H+ in water?
No. Instead H+ is transferred to a neighboring H2O, making hydronium H3O+
In what way do enzymes operate as?
On/Off-switches
In glucose phosphorylation, where does hexokinase (HK) phosphorylate?
Position-6 in glucose
What is included in physiologic conditions?
Salty water Neutral pH Ambient temperature Atmospheric pressure
What type of alcohols are more reactive?
Secondary
Because of its strong polarity and interactions, what property of water is very high?
Specific Heat Capacity
T/F: In glucose phosphorylation, hexokinase ensures that only glucose-6-P forms.
T
T/F: Water undergoes rapid H+ dissociation/reassociation
T
Why does H-bonding give water such a high specific heat capacity?
The H-bonds give it a ton of stability to the point that water must be heated to 100 Celsius for all H-bonds to break.
What is hydrolysis?
The breaking of molecules by water
What is the water cycle?
The continuous exchange of water within the hydrosphere (atmosphere, soil water, surface water, groundwater, plants, animals)
What is thermal mass? Which property of water does it relate to?
Thermal mass is the ability to resist changes in temperature. It is related to water's high heat capacity.
What happens when the blood has acidosis (excess H+)?
These protons shift the equilibrium in favor of CO2 & H2O, which is breathed out and ultimately reduces body acidity.
How do protons move in liquid water?
They "hop" (never diffuse freely).
What is significant about the OH group of Tyrosine and the NH group of Tryptophan?
They both can form H-Bonds and play catalytic roles in some enzymes
How do enzymes allow metabolism to proceed under physiologic conditions?
They increase reactivity
What are the traits of AA's with nonpolar aliphatic R groups?
They tend to cluster together on the inside of proteins because they are nonpolar.
Why is water's deactivating role in nucleophilic reactions very beneficial to life?
Uncatalyzed reactions are very slow under physiologic conditions and requires enzyme catalysis that is specific and controllable. Prevents side reactions that could be toxic.
Boiling point only has ____ which is in equilibrium with steam
W1
Liquid water is a flickering/transient collection of ____ with very little ____.
W5; W1
How does water slow nucleophilic reactions?
Water crowds the electron-rich and electron-deficient reactants, ultimately deactivating them
What is water's role in nucleophilic reactions?
Water deactivates them, slowing them down
What are buffers?
Weak acids/bases that help stabilize pH. They obey Le Chatelier's Principle.
What is the formula for pH?
pH = -log10[H+]
What is the Henderson-Hasselbalch equation? (MEMORIZE)
pH = pKa + log [A-]/[HA]
What is the formula for pKa?
pKa = -logKa