Week 2: Thermo, IMF, Acids & Bases, and Amino Acids Flashcards
All cells require _______ to carry out life processes. _________ is the ultimate source of energy on the Earth.
energy
The Sun
Oxidation is _______
Reduction is ________
loss of electrons
gain of electrons
Many cellular process include the _________ of electrons
movement
Many biochemical reactions involve __________
oxidations and reductions (redox chemistry)
Thermodynamics is the study of ______ and ________
transformations
transfer of energy
Changes in energy are calculated as:
final minus the initial state
If change in free energy is negative (free energy decreases), reaction is:
energy ______
spontaneous (reaction or process takes place without outside intervention)
energy released to environment
If change in free energy is positive (free energy increases), reaction:
will not occur unless energy supplied
Processes that __________ are favored.
release energy (spontaneous reactions)
The term spontaneous means….
energetically favored. It does not necessarily mean fast.
First law of thermodynamics:
energy can neither be created nor destroyed
“you cant win” (no such thing as > 100%)
Second law of thermodynamics:
total entropy of system must increase over time
“you cant break even” (energy transfer < 100%)
The _______ and the ________ are examples of spontaneous processes because they represent an ________ in disorder and entropy of the Universe and have a negative _______ at constant temperature and pressure
the hydrolysis of ATP to ADP and Pi
the oxidation of glucose to CO2 and H2O by an organism
Spontaneous processes are the ones plants or animals use to ________ to the organism
provide energy
(often involving a break down or loss)
Nonspontaneous processes are the ones used to…
build up the compounds needed so we can later use the reactions that provide energy
the ________ and the _______ are examples of nonspontaneous processes
The phosphorylation of ADP to ATP (attachment of phosphate group_
production of glucose and O2 from CO2 and H2O in photosynthesis
An increase in entropy occurs when the final state has ________ than the initial state
more possible random arrangements
Assuming the value of ∆S is positive, an increase in temperature increases the _________ component to the overall energy change.
-∆G contribution of the entropy
Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? It appears that the solution is absorbing energy.
The heat exchange, getting colder, reflects only the enthalpy or ∆H component of the total energy change. The entropy change must be high enough to offset the enthalpy component and to add up to an overall -∆G.
When a reaction feels cold, it means energy is being _______ and ________
absorbed, used to power some change
Photosynthesis is _________, requiring light energy from the Sun. The complete aerobic oxidation of glucose is _______ and is a source of energy for many organisms, including humans. It would be reasonable to expect the two processes to take place _______ in order to ________ for the endergonic one.
endergonic
exergonic
differently
provide energy
Gibbs free energy (G, J/mol) is energy…
relevant to biochemical systems
Enthalpy (H, J/mol) is the…
heat content of a system
How does enthalpy relate to G?
Negative change in enthalpy contributes to a negative change in Gibbs free energy or a spontaneous reaction
equation of ∆G?
∆G = ∆H - T∆S
Entropy is the measure of the _______ and measure of ________
dispersion of the energy of the system
disorder or randomness
Conditions where ∆G will always be a negative value:
reaction is exothermic (∆H < 0)
entropy increases (∆S > 0)
the temp. is such that T∆S contributes significantly to making ∆G negative
_______ influences entropy changes
Temperature (T, units of K)
absolute temperature in Kelvin
∆G > 0, _______
nonspontaneous or endergonic
∆G < 0, ________
spontaneous or exergonic
energy absorbing
endergonic
energy releasing
exergonic
∆G = 0 indicates
equilibrium
Dynamic equilibrium is when movement and reactions…
proceed in the forward and reverse directions at the same rate
∆G is the change in free energy, indicates _____ and measure of ____ NOT ______
likelihood of reaction
equilibrium
NOT speed
Molecules are always…
in motion
exothermic:
heat released (-)
endothermic:
heat absorbed (+)
When two atoms with the same electronegativity form a bond, the electrons are shared _______ between the two atoms.
equally
The polar nature of ______ largely determines its _______ properties.
water
solvent
The unique fitness of water for ___________ determines the properties of many important biomolecules. Water can also act as ________, giving it great versatility in biochemical reactions.
an acid and as a base
Under what circumstance is a molecule that has a dipole not a polar molecule?
If the dipole is cancelled out by another of equal and opposite orientation. The classic example is CO2. Each carbon-oxygen bond is a dipole, but the two cancel each other out and the molecule is nonpolar.
Which would you think would be a stronger interaction and why: an interaction between a sodium ion and the partial negative charge on the oxygen in ethanol, or the interaction between two ethanol molecules?
The sodium ion is a fully charged cation. Therefore, its interaction with the partial negative charge on the oxygen of ethanol would be stronger than the interaction of the same oxygen with a partially positive charge from the hydrogen of another ethanol molecule.
Which of the standard 20 amino acids can form disulfide bridges in protein structures?
Cysteine because it contains a thiol group in its side chain. A disulfide bridge is formed when a sulfur atom from one cysteine forms a single covalent bond with a sulfur atom from a second cysteine in a different part of the protein.
Isoleucine has _____.
Lysine has ______.
Aspartate has _____.
Leucine has _______.
a chiral center.
an amino group
a carboxylic acid
a branched hydrocarbon
Identify the polar amino acids, the basic amino acids, and the sulfur-containing amino acids in the peptide with the following amino acid sequence:
Arg-Gln-Tyr-Cys-Thr-Lys-Met-Ser
Polar amino acids include Asn, Gln, Ser, Thr, Cys, and Tyr.
Basic amino acids include Arg, His, and Lys.
The two sulfur-containing amino acids are Cys and Met.
Identify the nonpolar amino acids, the acidic amino acids, and the aromatic-group-containing amino acids in the peptide with the following amino acid sequence:
Asp-Gly-Met-Ala-Pro-Trp-Tyr-Ile
Nonpolar amino acids include Met, Trp, Ile, Phe, Leu, Val, Pro, Ala, and Gly.
Acidic amino acids include Asp and Glu.
The three aromatic-containing amino acids are Tyr, Phe, and Trp.
Any process that results in a _______ from the system is favored.
release of energy
adding energy to the system from its surroundings will result in an_______ of the system, which is ________.
increase in the energy
unfavorable
Biochemical reactions that are not favored are coupled with ________ in order for the overall process to occur.
favored reactions
The value for ΔG for the oxidation of glucose to CO2 and H2O by an organism is _______, due to the _______. Therefore, this is a _______.
negative
increase in disorder
spontaneous process
For the separation of a disaccharide into two monosaccharides, one would expect the entropy change in the reaction to be
______.
This entropy change is expected because…
positive
one disaccharide molecule can be randomized in fewer ways than two monosaccharides
The three van der Waals forces in order of decreasing strength are:
Dipole-dipole > Dipole-induced dipole > Induced dipole-induced dipole
_____ and ______ employ H-bonds within their internal structures to control and maintain their molecular shapes.
Proteins
nucleic acids
Ex. chromosomal DNA, transfer RNA, and hemoglobin
Most _____, like _______, do not require H-bonds to control their structures. They are good H-bond formers, though.
mono- and disaccharides
glucose and sucrose
________, do not form many H-bonds and thus do not employ H-bonds to control their structures.
Lipids, like triacylglycerols and cholesterol
Which of the following molecules can serve as both a hydrogen bond donor and acceptor?
CO2, (CH3CH2)2O, CH3OPO3^2-, CH3OH, H2O
CH3OH and H2O
The formation of a H-bond requires a pair of polarized bonds, one of which contains an electropositive H atom (the donor) and the other of which contains an electronegative atom with a free lone pair of electrons (the acceptor). Nitrogen and oxygen are often found to be acceptors in H-bonds, and these two atoms are often bound to the donor hydrogens.
C-H bonds are not polar and thus will not form H-bonds. Hydrocarbons contain only these sorts of bonds and thus are hydrophobic.
A conjugate acid will be identical to its conjugate base except for the presence of _______ on the conjugate acid at its acid dissociation site.
an extra hydrogen
Pregabalin is an acid with a pKa of 4.2; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine. Electrically neutral molecules can pass through a membrane more easily than can charged molecules.
Would you expect more pregabalin to be absorbed in the stomach, where the pH of gastric juice is about 1, or in the small intestine, where the pH is about 6?
More pregabalin will be absorbed in the stomach because pregabalin molecules will have a less negative average charge there than in the small intestine.
At pH ~ 1 pregabalin’s carboxylic acid will be dominantly protonated, meaning that the charge on pregabalin in the stomach will be less negative than the charge on pregabalin in the small intestine. Thus, pregabalin in the stomach will more easily cross the stomach membrane than it will be able to cross the small intestine membrane.
The key to selecting a good buffer for biochemical reactions is twofold:
- the pH of the chosen buffer should be close to the optimal pH for the biochemical reaction
- the buffer should not interact with the components of the biochemical reaction.
The details of the makeup of the buffer are irrelevant. Only the pKa value and the degree of interaction with the reaction of interest are important.
Calculate the pH of a buffer solution prepared by mixing 50.0 mL of 1.25 M lactic acid and 25.0 mL of 0.75 M sodium lactate.
(The pKa for lactic acid is 3.86. The molar mass for lactic acid is 90.1 g/mol and the molar mass for sodium lactate is 112.1 g/mol.)
3.34
buffers works best when the _______ equals the _______
pH of the solution
pKa of the buffer
Electronegativity is the measure of force of an atom’s __________ in a chemical bond
attraction for shared electrons
Oxygen and nitrogen are more electronegative than ___
carbon and hydrogen
Electronegativity often relates to ______ as ___________
reactivity
nucleophiles/electrophiles
Electrons are _______ in polar bonds
unequally shared
Polar bonds:
more _____ found closer to one atom
______ generated
Due to difference in __________ of atoms
negative charge
partial dipole
electronegativity
Dipole is a measure of __________
Arrow points to ________
polarity of chemical bond
center of electronegativity
van der Waals radius is the distance between ______ and ________
nucleus of atom
its effective electronic surface
CO2 has ____ but is _____ overall due to ______
polar bonds
nonpolar
linear geometry
In a nonpolar bond, two atoms share electrons ______
evenly
Ionic bonds is the attraction of ________, held together by ________
Ex?
opposite charges
(+) and (-) ions
Ex. salt crystals
Salt bridge (_______)
attraction of _______
_______ attraction
_______ in biomolecules
charged functional groups
opposite charges
electrostatic attraction
Ionic bond in biomolecules
Bond between negatively charged carboxyl group and positively charged amine group is an example of ______
salt bridge
Ion-dipole interactions is when ions ____ interact with ____
in solution
molecules that have dipoles
-KCl dissolved in H2O is an example of?
_______ potassium ions interact with _______ and _______ chloride ions interact with _______
Ion-dipole interaction
Positively charged potassium ions
negative dipoles on oxygen
negatively charged chloride ions
positive dipoles on the hydrogens
Bonding occurs with the _____ of radii
overlap
the ______ the overlap, the ______ the bond distance, the ______ the bond
greater
shorter
stronger
3 types of van der Waals interactions:
Dipole-dipole
Dipole-induced dipole
Induced dipole-induced dipole (London dispersion forces)
van der Waals forces:
______ associations
______ attraction of ______
NOT ________
noncovalent
weak, dipoles
NOT electrostatic interactions of charged ions (NO NET CHARGE)
strengths of bonds found in biochem:
______ play vital role in biological systems and structures
Covalent (O-H)
Covalent (C-H)
Ionic interactions
Ion-dipole, Hydrogen bonds (equal)
van der Waals interaction
weaker forces
Hydrophilic (_______)
* Tending ______ in water
* Examples - ________
water-loving
to dissolve
Ionic and polar substances
Hydrophobic (______)
* Tending ______ in water
* Hydrophobic interactions: _____
* Examples: ________
water-hating
not to dissolve
Attractions between nonpolar molecules
hexane or other alkanes
Amphipathic (amphi = ______)
* Molecule that contains…
“both”
both hydrophobic and hydrophilic regions
Micelle formation by amphipathic molecules:
______ in water:
______ buried inside
_______ on surface
Formation depends on…
spherical arrangement
hydrophobic parts buried inside
hydrophilic parts on surface
attraction between temporary induced dipoles
Water has unique properties for a molecule its size, such as….
This is due to the ______ possible between water molecules.
a very high boiling point and melting point.
extensive hydrogen bonding
Stronger hydrogen bond =
Weaker hydrogen bond =
linear
non-linear
What are some macromolecules that have hydrogen bonds as a part of their structures?
Proteins and nucleic acids
hydrogen bonding has not been observed between ______ molecules because the ______ bond is not sufficiently _______ for greatly unequal distribution of electrons at its two ends. Also, there are no __________ to serve as _______.
CH4
C—H
polar
unshared pairs of electrons
hydrogen bond acceptors
For a bond to be called a hydrogen bond, it must have a hydrogen covalently bonded to…. This hydrogen then forms a hydrogen bond with another…
oxygen, nitrogen, or fluorine
________ bind to nucleic acids as a result of ________ to the negatively charged phosphate groups.
Positively charged ions
electrostatic attraction
Acids are compounds that _________ when dissolved in aqueous solution. In other words, they are ________.
release hydrogen ions (protons)
proton donors
Bases are compounds that are ________.
proton acceptors
pH is a measure of the ______ of the solution. The _____ the pH, the ________ the solution
acidity
lower
more acidic
pH = ?
Higher _____ means more acidic and means ______ value
-log[H +].
[H +]
lower pH
Higher Ka value…
stronger acid, more dissociation
effects of adding weak acid or base to water
only partial dissociation
pH at which group is 1/2 ionized?
when pH value equals pKa
[H +] =
10^-pH
[OH-] [H3O+] =
1 x 10^-14
Buffers work based on the nature of ________ that compose the buffer.
weak acids and their conjugate bases
If a source of extra hydrogen or hydroxide ion is added to a buffer solution, it reacts with buffer components and is neutralized.__________.
neutralized
H-H equation –>
pH = pKa + log ( [A-] / [HA] )
equal amounts of the acid and conjugate base pH =
pKa
Buffering capacity is the ability of a substance to _______ when ________ are added
resist changes in pH
acids or bases
______ buffer within cells
_______ buffer in blood
phosphate
carbonate
Since a __________ has both a positive and negative charge, it is able to act as both a base or an acid depending on the situation.
zwitterion
all amino acids are _______ molecules
polar
_______ is technically not an amino acid. _______ contains no chiral carbon atoms.
Proline
Glycine
Peptides are formed by reacting the ________ of one amino acid with the ________ of another amino acid in a ____________
carboxyl group
amino group
covalent (amide) bond.
Proteins consist of ________; the number of amino acids in a protein is usually _______.
polypeptide chains
100 or more
Peptides are molecules formed by linking _______ by ______
two to few dozen amino acids
amide bonds
The pKa of acetic acid is 4.76. Which statement is true at pH 4.0?
[A-] < [HA]
Which of the following molecules will not form hydrogen bonds?
HF
H2CO3
HCOOH
H2O
NH3
All of these can form hydrogen bonds.
Breaking bonds
Endothermic
Forming bonds
Exothermic
What are two characteristics of a molecule that can be a hydrogen bond acceptor?
1) Available non-bonding lone pair of electrons. Note that if this lone pair is involved in resonance, it will NOT
be available for hydrogen bonding.
2) Electronegative atom: The lone pair of electrons needs to be on one of Nitrogen, Oxygen, or Fluorine.
Hydrogen bonds are an _______ force, therefore…
intermolecular force
bond BETWEEN molecules not within a molecule
Hydrogen bonds can be accepted by a _______ of an ______
free lone pair
O, N, or F atom
When phospholipids are placed in water, is the process of bilayer formation spontaneous?
Yes – the entropy of the surroundings increases.
________ and _________ drives the spontaneous folding of proteins
Hydrophobic interaction, hydrogen bonding that increase surrounding entropy
Glycine is the most simple amino acid – its R group is just a hydrogen. Therefore, the only way it could
ever have a positive charge is…
if the pH is very low AND it is by itself.
ou work in a lab and your partner has just informed you that in his peptide chain (DRGRADNER), the
amine group of his Glycine has just been protonated and now has a positive charge. You become
confused. Why?
It is impossible due to the amine nitrogen being involved in a peptide bond.
Water is capable of forming ________ hydrogen bonds
4
A buffer solution is present when a ______ is in combination with ________.
Adding NaF and HCl in a beaker together would create a _______
weak acid, its conjugate base
For A, we are combining F- and HF – the weak acid HF is with its conjugate base F-, so this is considered a buffer
solution.
buffer solution
