Biochemistry CH2 Flashcards
The process of life primarily takes place in _____ _____ _______, which is commonly referred to as ________ ________
Water based environments
aqueous solutions
what can shutdown without water and turn back on with it (metabolism etc)`
sea monkeys
Daily water exchange of typical human
Intake:
900 mL beverage
800 mL food
300 mL metabolic
Output:
1050 mL urine output
100 mL feces
850 mL sweat
2000mL total each
Water is what hybridization shape is water?
Electron domain geometry?
bent - 104.5 bond angle
sp3 tetrahedral
Waters unique properties (dissolves)
dissolves ionic substances (NaCl)
dissolves hydrogen bonding substances (C-OH N-H, carbs proteins amino acids)
Many polar substances
What does water not dissolve
Oily molecules (vegetable oil, Italian salad dressing)
Water colligative properties
Melting point - salt melts ice (sodium chlorine ions)
Osmotic pressure - Water higher concentration -> lower concentration (omsosis)
Autoionization (water chemistry)
Water melting and boiling point (celcius) @ 18g/mol
0 degrees melting point
100 degrees boiling point
heat of vaporization
@ 18g/mol
amount of calories per gram of water that it takes to vaporize water from a liquid to a gas
540 cal/g
H2S
Sp3 tetrahedral
bent electron configuration
Which is more dense, liquid or solid water?
liquid (ice cubes float, why lakes freeze top down)
Does water have a high heat capacity?
yes, amount of heat that its able to absorb before it heats up or vaporizes
Water attractive properties
water is attracted to itself and other things like coaster and the glass
(non covalent forces)
put a little salt on napkin so water can dissolve the ions
What are the arrows point towards (what does it mean)
Pointing towards the electronegative atom.
Indicate the direction of the electron density. The direction the arrow is pointing shows that the atom its pointing to has a more significant share of the shared electrons, hence has negative charge.
H2S C6H14 and CCl4 has lower … than water
Lower melting point, boiling point,, and heat of vaporization (6-11x)
Forces that occur between two molecules are called
non covalent forces
both attractive and repulsive exist but focusing on attractive
ex: water on penny, water beading up on waxed car
the attraction between any two molecule results from the presence of
+ and - charges
In non covalent forces, these charges are nearly always…
Are theese charges permanent?
partial positive and partial negative
no
Why do partial charges exist?
Difference in polarity, it is a difference in electronegativity.
Three types of non-covalent forces:
Hydrogen bonding
Dipole-dipole forces
London dispersion forces
Dipole-dipole forces
Common in polar molecules
If atoms have an unequal sharing of electrons, this means
the bond is polar
one partial positive and one partial negative end
similar situation to magnets
How would several molecules of HCl align
(maximizes dipole-dipole interactions)
What is the strongest dipole-dipole interaction?
H bonding
Why is acetone (organic molecule) a liquid and not a gas at room temperature?
dipole-dipole interactions
What is the strongest class of intermolecular forces
dipole-dipole
Hydrogen bonding
Any one donor can act as any one acceptor, doesn’t have to be N to N or O to O.
These are…
How many hydrogen bonds does a single water molecule form when it freezes?
About 4, 3.7.
What is responsible for waters unique physical properties such as high boiling and melting point?
Hydrogen bonding - strongest non-covalent forces
Which non covalent force is the weakest
London dispersion forces
What are london dispersion forces
Temporary arrangement of electrons within a molecule, when they bunch up at one side/spot of a molecule
Which property results in non polar molecules being able to interact with other molecules
London forces
Why can non polar molecules exist as liquids or solids
london forces
Do larger or smaller atoms and molecules experience greater london forces?
Larger, more electrons
They also have higher melting and boiling points as a result.
Why can I2 be solid at room temperature, Br2 a liquid at room temperature while F2 and Cl2 are gases at room temperature?
Molecular weights
F2 - 38 g/mol
Cl2 - 70 g/mol
Br2 - 160 g/mol
I2 - 254 g/mol
Greater london forces yielding greater attractive forces because more electrons in larger molecules.
Interaction strength (kcal)
F = kq1q2/r^2
Ordered water molecules hydrogen bonding network
clathrate
Hydrophilic vs Hydrophobic
Hydrophilic - Water soluble (loves water).
Hydrophobic - Insoluble in water (hates water).
Hydrophobic effect
Packing of nonpolar regions to minimize the interactions with water while the polar region interacts with water.
Driving force behind this is the spontaneous drive of water to bind to itself through hydrogen bonds.
Water auto ionization, how much OH- and H+ is formed (molar)
1 * 10^-7 M
Can many things be auto ionized?
Yes
Write equilibrium constant expression for this reaction.
What happens in equilibrium reactions? (double arrows going opposite directions)
Forward and reverse reactions are happening simultaneously.
No net change when at equilibrium but still happening just at the same rate.
Write equilibrium constant for autoionization for water.
Neutral would be = 1E-7
H+ =-8 or lower eg 10^-9, 10^-10 etc, then it is basic.
if OH- is of the same values then its acidic.
pH scale (IMPORTANT)
Memory = H+ reflects the pH essentially
pH =
pH = -log[H+]
Some bacteria live in streams that are acidic (pH = 3.2). What is the [H+] of the water?
How does this [H+] compare with the bacteria living in milk (pH = 6.5)?
What is the pH of cytoplasm for a typical human cell, and what is it called?
7.4, physiological pH
Lysosomes have a pH of 5, physiological pH is 7.4, compare the concentration of H+ ions in lysosomes vs other organelles
Over 100x more H+ concentration in lysosomes vs other organelles. (around 250)
Three primary types of molecules that dissolve in water
Ionic - NaCO3 & KCl
Polar - HCl & acetone (and other ketones)
Hydrogen bonding - Acetic acid and sugar
What does Ka and pKa equal for this reaction?
pKa =
pKa = -log[Ka]
Acid Strength
HCl strongest
Methane weakest
Lower pKa stronger acid
CH4 has pKa of 52, how easily would the CH bond break?
Would almost never happen
What is a buffer?
Neutralizing any acid or base that will be put into the system.
Resists change in pH.
A buffer is most effective within __ pH unit of pKa. For example, what should the buffer be for a pKa of 3.86?
1 pH unit
2.86-4.86 buffer range most effective.
Buffering capacity
There is a limit to the amount of acid or base a buffer can neutralize.
If a buffer is 100mM then it has that much ability to be able to basorb H3O+ protons or OH-.
Bicarbonate buffer system
Help offset any reactions that try to change the pH of the cell.
Effective in the bloodstream
Also the phosphate system, both effective at pH 7.4.
Chemical reactions indicators
Light
- Heat exchange
Sound
Color change
- Bubble formation
Three Thermodynamic Values
H - Enthalpy - heat and heat transfer.
S - Entropy - Randomness and disorder, more entropy more disorder.
G - Gibbs Free Energy - G = H - TS
ΔG = H - TΔS
T = temp units of kelvin
If Gibbs free energy is (-) or (+) what does that mean?
(-): spontaneous
(+): nonspontaneous
Give an example of a positive entropy and negative entropy reaction
Positive - One molecule breaking into two (more disorder)
Negative - Two proteins coming together to form one (more order)
Give an example of a positive and negative enthalpy reaction
Positive - Heat flows in (endothermic)
Negative - Heat flows out (exothermic)
Example of a spontaneous reaction. (Gibbs negative value)
What supports non-spontaneous reactions
ATP
Example of a nonspontaneous reaction. (Gibbs negative value)
Movement of muscle proteins
is Glucose + ATP –> Glucose-6-P + ADP spontaneous or nonspontaneous?
Spontaneous (-) delta G
Delta H is positive if heat flows (into or out of) the reaction
into
In the uric acid example of icepack, is it spontaneous or nonspontaneous, delta H positive or negattive
Happened spontaneously, so delta G is negative, and delta H is positive because heat flowed into the reaction to produce the products. The ice pack is cold because the heat dissipates into the air, into the persons hand and into the reaction, which leaves the bag feeling cold.
The movement of muscle proteins is (spontaneous or nonspontaneous)
nonspontaneous
But the ATP that is coupled to these reactions permits contraction.
What is the shape of water
Bent
What is autoionization and how is it important for water
Autoionization is when a compound/molecule reacts with itself which results in the formation of ions.
Water: It is important to water because it forms an H3O+ acid ion and OH- is the base ion, which allows water to act as a weak acid or a weak base. Autoionization of water is very indicative of its the chemistry of water.
What is the concentration, in M, of water as a pure liquid?
55.5M
Define Keq
Equilibrium constant
Solids and liquids are left out of this equation. It tells us the extent of which the reaction proceeds in a forward direction.
Keq = products^coefficients / reactants^coefficients
Define Kw
Kw is the ion product, it tells us the relationship of the concentration of the acid ion and the base ion in water.
Kw = [H+][OH-] = 1*10^-14
Identify the acid, conjugate base, and proton in the following reaction.
A buffer system has a pKa of 6.5, what is the effective buffering range?
5.5 to 7.5
Calculate Ka value (equation)
Ka = [H+][A-] / [HA]
Weak acid A has a pKa of 3.2, while weak acid B has a pKa of 5.6. Is Weak acid A or B the stronger of the two?
Weak acid A is stronger than weak acid B because weak acid A has a stronger pKa value which means its a stronger acid.
Ice melts at room temperature. What is the sign for delta G in this reaction?
delta G will be negative, because the reaction is spontaneous
Entropy is gained times the temperature is greater than the enthalpy
Enthalpy is positive because the icecube is absorbing heat to melt but the enthalpy isnt greater than the temperature times the entropy, making the gibbs free energy negative
Butane combusts in the air by the following reaction:
C4H10 (l) + 6.5 O2 (g) —-> 4 CO2 (g) + 5 H2O (g)
What is the sign of delta G, delta H, and delta S in this reaction?
ΔG is negative, it is a spontaneous reaction, there isn’t a case where it couldn’t be negative mathematically because
ΔH is negative
ΔH is negative because heat is released
ΔS is positive because it is a disorderly reaction as more gases are produced
What is the role of ATP in helping a non-spontaneous reaction occur?
ATP is the energy source for the reaction, ATP has a large negative delta G that powers the nonspontaneous reactions.
