Chemistry/Physics Flashcards
(133 cards)
1
Q
Chromatography “Separation and Purification methods” OCR: p. 112
A
- the primary reason for chemical separation during a chromatographic separation on cellulose is that the relative amount of hydrogen bonding to the stationary phase will determine the relative rate of migration of the various components in the sample
2
Q
The variety of opsins “How light and sound interact with matter”
A
enable the detection of different colors
3
Q
Retinal Binding Site
BR p. 48
A
hydrophobic environment (retinal is mainly carbon and hydrogen)
4
Q
Rf Values with developed chromatography plates “Separation and purification methods.”
A
- Rf is the ratio of the distance travelled by the analyte relative to the solvent front during a chromatographic separation. - equation: distance of substance investigated / distance of solvent front
5
Q
Stereospecific/ Stereospecific Reaction “Nature of molecules and intermolecular interactions.” OCR p. 45
A
- meaning rxn produces only one form of product - a rxn in which the stereochemistry of the reactant completely determines the stereochemistry of the product without any other option.
6
Q
Rhodopsin “Principles of chemical thermodynamics and kinetics.”
A
ATP (required for kinase activity): source of phosphate groups added to the molecule
7
Q
Hybridization States
- “Nature of molecules and intermolecular interactions.”
A
Steric Number = # bonded Atoms + Lone pairs
4 = sp^3
3 = sp^2 2= sp
8
Q
amine group “functional group” “Structure, function, and reactivity of biologically-relevant molecules.”
A
the functional group that forms during peptide bond formation is known as an amide group.
9
Q
Aldehyde functional group
A
10
Q
Carbonyl
A
11
Q
Ketone
A
12
Q
Acetal
A
13
Q
Hemiacetal
A
14
Q
Imine
A
15
Q
Enamine
A
16
Q
Aldol
A
17
Q
Alcohol
A
18
Q
Carboxylic Acid
A
19
Q
Amide
A
20
Q
Ester
A
21
Q
Lipase
BR: p. 48
A
hydrolyzes fatty acids
22
Q
Anhydride
A
23
Q
Phenol
A
24
Q
What affects rate of subsitution in a reaction?
OCR:
A
The rate of substitution of protonated alcohols is subject to steric hindrance. This inhibits the ability of nucleophiles to collide with the reacting electrophilic center and slows the rate of reaction.
25
pH
BCR p. 51
**pH = -log[H+]**
**[H+] = 10^-pH**
**pOH = -log[OH-]**
**pH + pOH = 14**
difference of 3 pH units = 1000-fold difference in **proton concentration**
26
If Reaction 2 (Figure 4) is repeated with HCl and the compound shown next to the reaction, which of the following compounds is NOT a direct product (without rearrangement)?
the structure shown in this response requires an additional shift of hydride atoms prior to elimination and is therefore NOT a direct product.
27
In a gas-liquid chromatograph, the first peak observed in the gc trace is attributable to which compound?
OCR p.123
Whichever compound will exhibit the lowest molecular weight and also the weakest intermolecular forces of attraction will therefore migrate the fastest and be the first peak in the gas chromatograph (gc) trace.
28
Acid Dissociation
BCR p. 69
- higher Ka (acid dissociation)/ lower pka: stronger acid
- acid dissociation: net positive charge vs net negative charge acid - the net negative charge will be weaker acid / dissociate to a smaller extent
29
Glycogen/Glycogenesis
BCR: p. 123
- Most glucose units in glycogen are linked by **α-1,4-glycosidic bonds**
**-**branching with glycogen: **α-1,6-glycosidic bond**
- Glycogen: polymer of glucose in muscle/liver cells
- Glycogenesis: glu-6-p→ isomerized in reversible rxn to glu-1-P w/ phosphoglucomutase → glu-1-p is activated w/ UTP to form UDP-glucose→ added to glycogen polymer by **glycogen synthase**
30
What is the product of the reaction of Compound 1 (nxt to rxn) with HBr by the pathway shown in Figure 3?
OCR
(S)-1-bromo-1-deuteriopentane
because the incoming nucleophile displaces the leaving group form the opposite side of the reacting center during an SN2 reaction.
31
UDP
- deals with glycogen synthase
- contains uridine (nucleic acid used in RNA)
- structure of RNA contains ribose
- KNOW STRUCTURE OF RIBOSE
32
Phosphatase
- removes phosphate group from a protein
- removal of phosphate prior to gel electrophoresis --\> decrease in band intensity
33
thin lens equation
an object O is at a distance of three focal lengths from the center of a convex lens. What is the ratio of the height of the image to the height of the object?
- (1/o) + (1/i) = (1/f)
- magnification: -i/o
- if asked for ratio of height of image to height of object (given height of object): solve for i and then plug into magnification formula
- Object distance = 3f, focal length = f, image distance = i.
- 1/o + 1/i = 1/f --\> 1/3f + 1/i = 1/f. R
- 1/i = 1/f - 1/3f ==\> 1/i = 2/3f ==\> i = 1.5f.
Plug this into the magnification formula m = -i/o and you get 1.5f/3f = (1/2)
34
Gamma decay
occurs when nucleus emits photons
35
spontaneous vs nonspontaneous reactions
- spontaneous: negative ΔG, positive ΔS°, negative ΔH ( - reaction that create gaseous products from solids and liquids = positive ΔS°)
- nonspontaneous: positive ΔG, negative ΔS°, positive ΔH
36
net sum of chemical reactions
37
catalysts
If a homogeneous catalyst cannot be separated from the products at the end of a reaction: products will be contaminated with the catalyst
38
If solid catalyst is finely ground before it is added to the reaction mixture:
- Faster rxn rate: a greater surface area of catalyst will be exposed.
- grinding a heterogeneous catalyst increases the amount of catalyst available to the reaction and therefore increases its rate
39
V = IR
40
oxidation-reduction reactions / metal strips in solutions
GCR p. 268
this link is very helpful:
https: //chem.libretexts.org/Bookshelves/Analytical\_Chemistry/Supplemental\_Modules\_(Analytical\_Chemistry)/Electrochemistry/Redox\_Chemistry/Balancing\_Redox\_reactions
- putting a metal strip in a solution: if it results in a solid --\> metal strip is oxidized and the other ion has **higher reduction potential**...make two half-reactions and balance # e- (if solution is oxidized: e- go on right side) --\> add together to get new equation
- spontaneous reaction: E° is greater than zero; 1) make half-reaction equation and take values (reverse signs based on which ion is oxidized in solution)
41
42
common ion effect with solubility
GCR: p. 216
If you have a solution and solute in equilibrium, adding a common ion (an ion that is common with the dissolving solid) decreases the solubility of the solute. This is because Le Chatelier’s principle states the reaction will shift toward the left (toward the reactants) to relieve the stress of the excess product. When equilibrium is shifted toward the reactants, the solute precipitates.
43
molarity (M)
mol/V
M = molar concentration
n = moles solute
v = liters solution
44
Units of Power (P)
watt, defined as J/s = ft•lb/s = kg•m2/s3
45
Amino acid substitution / pKa
-naming: original amino acid, position, new amino acid
## Footnote
- pH is less than pKa of acidic group = acidic group is in protonated form
- pH is greater than pKa of acidic group = deprotonated form
- Acids with low pKa deprotonate easily
46
radioactive decay
GCR p. 53
alpha decay: large nucleus wants to become more stable by reducing # protons and neutrons **(atomic # -2; atomic mass -4)**
beta decay: when unstable nucleus contains too many neutrons --\> convert neutron to proton and electron **(atomic # +1)**
gamma decay: after the nucleus has undergone alpha or beta decay, it can "relax" to its ground state by emitting **photons (atomic # stays same)**
47
- **Oxidizing and Reducing Agents**
Ex question from mock MCAT 1 bio q. 53: When a strip of Zn is placed in a beaker containing 0.1 M HCl, H2(g) evolves. If a strip of Al is placed in a beaker containing 0.1 M HCl, does H2(g) evolve?
- Because Zn has higher reduction potential, since H2 gas evolves when in the presence of Zn(s), and Al(s) has an even higher oxidation potential than Zn(s), we know that H2 gas must evolve - or in other words, H+ must be reduced - when in the presence of Al(s).
(If Zn can reduce H+, then Al definitely can because it's stronger than Zn.)
Note:
The more negative the reaction potential --\> stronger reducing agent
48
nuclear localization signal
BR p. 176
- larger proteins cannot pass freely through nuclear pores and are excluded from nuclear interior unless they contain **sequence of basic amino acids**
**-** if they have sequence = translated on cytoplasmic ribosomes and then imported into the nucleus by specific transport mechanisms
- basically a signal that guides a protein molecule to the nucleus; useful to up/down regulate certain cellular processes and products
- permits proteins to enter the nucleus (not likely for transmembrane protein)
49
signal sequence
- what allows proteins to enter the **rough ER** (proteins that are either going to be secreted from the cell or perform their function within the cell membrane)
- transmembrane proteins: located in cell membrane (enter the endomembrane system by docking at the rough ER w/ signal sequence)
- definition: short sequence of AA (usually found at N-terminus) of a protein being translated, that directs the ribosome and its associated mRNA to the membranes of rough ER where translation will be completed; found on membrane-bound proteins, secreted proteins, and proteins destined for other organelles
50
mature mRNA
- has been spliced and processed; ready for translation
- not likely to contain introns or promoter sequences!
51
Transmembrane domains
similar to signal sequence, but they are located in middle of protein, not removed after translation, and occur on integral membrane proteins
52
Metric Units
There are 6 MCAT-relevant base units
53
Prefixes
6 prefixes, symbol, and "multiple"
54
Molarity
moles of solute per liter of solution
most common way of expressing solution concentrations
55
Liter units
1000L = 1m^3
1L = 1000cm^3
1mL = 1cm^3 = 1cc
56
Angstrom
unit of length = 10^-10 m
used with atomic radii and bond lengths
57
order of magnitude
Q: By how many order of magnitude is a centimeter longer than an angstrom?
An **order of magnitude** is a factor of 10.
Since 1cm = 10^-2 m and 1 Angstrom = 10^-10, a centimeter is 8 factors of ten greater than an angstrom.
58
Density
of a substance is its mass per volume
p = mass/volume = m/v
In SI units: (kg/m^3)
In chem: (g/cm^3)
g/cm^3 --\> multiple by 1000 --\> kg/m^3
59
Empirical formula
the smallest whole numbers that give the same ratio of atoms
to go from molecular formula to emperical, divide subscripts by their greatest common factor
60
Know the general "look" of these polyatmoic ions
61
formula weight
atomic mass unit
- is the sum of the atomic weights of all the atoms in the molecule
- is the unit for atomic weight (amu)
62
atomic number (Z)
- # protons
63
mass number (A)
protons + # neutrons
64
isotope
elements differ in # neutrons (different mass numbers)
65
molecular weight
when a compoudn exists as discrete molecules, this term is used instead of formula weight
ex) H2O molecular weight: 2(1) + 16 = 18
ex) NaCl formula weight (which is usually used to ionic compounds): 23 + 35.5 = 58.5
66
half-life
GCR p 59
67
mole
Avogador's number
- 6.02 x 10^23 "entities"
- Na or No
- A's number is the link between atmoic mass units and grams
- # moles = mass in grams / molecular weight (MW)
68
How to find percent composition by mass?
- a molecule's molecular or emperical formula can be used to determine the molecule's percent mass composition
ex) C2H2N
2(12) + 2(1) + 14 = 40
%C: 2(12)/40 = 60%
69
Concentration: Molarity (M)
expresses the concentration of a solution in terms of moles of solute per volume (in liters) of solution
Molarity (M) = # moles of solute / # liters of solution
concentratoin is denoted by enclosing the solute in brackets
70
Mole fraction
expresses the fraction of moles of a given substance
mole of fraction of S = Xs = # moles of substande S / total # moles of solution
useful way to express con when more than one solute is present; used when discussing composition of mixture of gases
71
Law of Conservation of Mass (or of Matter)
the amount of matter (mass) does not change in a chemical reaction
72
hydrogen absorption spectra
If a photon hits an atom and the energy of the photon is the same as the gap between two electron energy levels in the atom, then the electron in the lower energy level can absorb the photon and jump up to the higher energy level. If the photon energy does not correspond to the difference between two energy levels then the photon will not be absorbed (it can still be scattered).
## Footnote
The absorbed photons show up as **black lines** because the photons of these wavelengths have been absorbed and do not show up!! (gaps in space correspond to photons getting absorbed)
73
Stoichiometric coefficients
tell us in what proportion the reactants react and in what proporiton the products are formed
they preceed each compound
ex) 2 Al + 6 HCL --\> 2 & 6 are stoich coef
74
Balancing Equations
1) start with most complex molecule
2) do math lol
75
Stoichiometric relationships in balanced reactions
GCR: p. 44
know how to do equations like this
76
limiting reagent
GCR: p. 45
since we run out of this reactant first, it limits how much product the reaction can produce
know how to do probelms like this
77
Oxidation state (or oxidation number)
indicates how the atom's "ownership" of it's valence electrons changes when it forms a compound
ex) NaCl --\> Na+1 bc it "donates" an electron in the covalent bond between itself and Cl, while Cl accepts the e- and has a -1 oxidation state
The \_\_\_\_\_state of an atom is the "charge" it would have if the compound were ionic.
78
Rules for Assigning Oxidation States
Exception to rule 6: in peroxides (H2O2 or Na2 O2), O2 is in a -1 oxidation state
79
80
hydrogen emission spectra
- light getting emitted
LIGHT BANDS on dark screen
The amount of energy **absorbed** by the electron to move into a higher level is the same as the amount of energy **released** when returning to the original energy level.
- refer to hydrogen absorption spectra for more info
81
Order of Electronegativities
FONClBrISCH ("fawn-cull-brish")
most electronegative (F) --\> least (H)
Bonds from H to anyting not found in the list will give H a -1 oxidation state
82
E photon = hf = h (c/wavelength)
h = Planck's constant
- As energy goes up, wavelength decreases and frequency increases
83
In determining which reactant loses the –OH group, which of the following isotopic substitutions would be most useful?
Replace the hydroxyl oxygen of ethanol with O-18.
this experiment involves labeling a group which does not exchange with other groups present prior to reaction and will therefore give information about the true identity of the groups, which are exchanged during the reaction.
whether or not that O18 is in the final compound will give us the information we want. If it is in the compound, we know that the ethanol kept its -OH group and therefore acetic acid lost its -OH. If the O18 isn't in the compound, that means ethanol lost its -OH instead.
84
85
A person, whose eye has a lens-to-retina distance of 2.0 cm, can only clearly see objects that are closer than 1.0 m away. What is the strength S of the person’s eye lens? (Note: Use the thin lens formula .)
Physics
51D
the strength of the eye lens is equal to the inverse of the focal length of the eye lens. Its numerical value is given by -1+(0.02 m)-1=1 D+50 D=51 D.
86
how enzymes affect chemical reactions
BCR
the stabilization of the transition state, not the substrate, provides binding energy that is used to lower the activation energy.
87
Which of the following will decrease the percentage ionization of 1.0 M acetic acid, CH3CO2H(aq)?
GCR
Adding concentrated HCl(aq)
HCl is a strong acid that will increase the amount of H+ in solution and thus decrease the percentage of CH3CO2H that ionizes.
Use Le Châtelier’s principle to identify that adding a strong acid to a solution of weak acid will decrease the amount of ionization of the latter
88
When the current in a circuit increases and the resistance of the circuit remains constant, the voltage of the circuit:
Physics
increases
according to Ohm’s law, current is equal to voltage divided by resistance. If current increases and resistance is constant, then voltage increases as well.
89
light spectra
Red: 750 nm (longest wavelength)
Violet: 400 nm (shortest wavelength)
90
Knowing that the speed of light in the vitreous humor is 2.1 × 108 m/s, what is the index of refraction of the vitreous humor? (Note: The speed of light in a vacuum is 3.0 × 108 m/s.)
What is the index of refraction of a medium?
Physics
1.4
because the index of refraction of a medium is equal to the ratio of the speed of light in vacuum to the speed of light in the medium, thus it is equal to (3.0 x 108 m/s)/(2.1 x 108 m/s) = 1.4.
Index of refraction: n = c (speed of light in vacuum) / v (speed of light in medium)
91
electron shell vs subshell
shell (n): circular orbits, n=3 has higher energy than e- in 2nd shell
subshell: comprised of one or more orbitals ((s-f); each subshell contains one or more orbitals of the same energy (degenerate); subshell higher than s has multiple orbital orientations
half-filled and filled orbitals: most stable
92
The intensity of the radiation emitted by the oxygen sensor is directly proportional to the:
Physics
the energy of electromagnetic radiation is directly proportional to the number of photons, and the intensity of electromagnetic radiation is defined as energy emitted per unit time. Thus, intensity is directly proportional to the number of photons emitted.
E (energy of the photon) = h (a constant) f (frequency of wave)
\*\*\*\*need more info\*\*\*\*
93
electron configurations
transition metals ionize from their valence s subshell before their d subshell
94
diamagnetic vs paramagnetic
diamagnetic: atom has all of its e- spin-paired (at the end of the block!); repelled by magnetic fields
paramagnetic: e- are not all spin paired; attracted to magnetic fields
95
What is the **energy of the photons** emitted by the LED at a frequency of 610 THz? (Note: h = 6.6 × 10–34 J·s)
Physics
4.0 × 10–19 J
the energy of a photon of frequency 610 THz is equal to 6.6 x 10-34 J•s x 610 x 1012 Hz = 4 x 10-19 J.
\*\*equation isn't given\*\*
96
What percentage of standard atmospheric pressure is the pulse pressure of a healthy adult?
**Provided:** maximum and minimum blood pressures of a healthy adult (the systolic Psand the diastolic Pd pressures, respectively) are about Ps = 120 mmHg and Pd = 75 mm Hg.
Physics
6%
the pulse pressure in a healthy adult is (120 − 75) mmHg = 45 mmHg, and so the percentage is 45 mmHg/760 mmHg = 6%.
\*\*note that 760mm Hg wasn't provided in psg\*\*
97
maximum # e- that can be present in n=3 shell
18 e-
98
99
excited vs ground state
ground state: lowest energy configuration
excited state: any of an infinite # of configurations that have a higher energy than the lowest energy e- configuration (not an ion; e- are not lost or gained; they jump to higher energy levels within the atom)
100
What fraction of a 15^O sample decays in 10 min?
**Given:** the half-life of 15^O is 2 minutes
Physics - half-life
thus, 10 minutes = 5 half-lives. Therefore, only (1/2)5 = 1/32 of the sample will be left after 10 minutes, while 31/32 of the sample will decay.
\*\*need to go over\*\*
101
valence e-
to form a cation (and in general) atoms will always lose their valence e- (the ones from the highest n level) first
102
Compared to micellular Compound 1, Compound 2 is structurally more rigid as a result of _what type of interaction_?
**Given**: multiple molecules of micellular Compound 1 come together to form Compound 2, which is a solid. An oxidant causes the formation of Compound 2
BCR
It can be reasoned that the interaction described is intermolecular in nature. Multiple pieces of information (from the psg) point to the fact that the interaction is disulfide bond formation, including the fact that an oxidant causes the formation of Compound 2, which can be reversed by the addition of a reducing agent.
103
The graph below shows the relationship between the predominant form of iron as a function of solution pH and applied potential. Based on the graph, which of the following statements is true?
GCR
At a potential of –0.44 V, the equilibrium between Fe and Fe2+ is independent of solution pH below pH 6.
At an applied potential of −0.44V and pH below 6, there is an equilibrium between Fe(s) and Fe2+(aq), as shown by the line of demarcation. The fact that this line moves horizontally with increasing pH up until pH = 6 means that this equilibrium is unaffected by changing the pH.
104
Trends
elements in same group show similar reactivity (all have same # e- in outermost shell)
metalloids: possess qualities of metals and nonmetals
105
Which of the following types of orbitals of the central atom are involved in bonding in octahedral compounds?
GCR
d2 sp3
octahedral compounds have six σ bonds and no lone pairs. According to valence bond theory, the central atom requires the hybridization of six atomic orbitals, d2sp3.
106
"Ideal Gas"
GCR
since a property of an “ideal” gas is that it is composed of particles that have negligible volume and do not exert intermolecular forces, individual molecular volume and intermolecular forces are negligible.
107
108
109
Periodic Trends - radius
as we go across a period, e- are added, but new shells are not --\> e- feel greater effective nuclear charge --\> radius decreases
as we go down a group, as new shells are added --\> v e- experience increased shielding (smaller effective nuclear charge)--\> RADIUS decreases
if we form an ion, the radius will decrease as e- are removed (the ones that are left are drawn in more closely to the nucleus); radius will increase as e- are added
110
periodic trends - IE
across a period / up a group: IE (amt of energy necessary to remove least tightly bound e- from isolated atom) increases since v e- are more tightly bound
- decreases from R to L due to decrease in effective nuclear charge
- amt of energy needed to remove the least tightly bound electron from the outermost energy level of an atom (be aware: atom in full octet is stable and doesn't want to remove 2nd least tightly bound e- for second ionization energy)
- first ionization energy: creates ion with +1, then +2, etc
111
electronegativity
ability of atom to attract e- to itself in covalent bond
(greater tendency to attract e- --\> greater electronegativity
- increases from L to R and from bottom to top
**F \> O \> N \> Cl \> Br \> I \> S \> C =(ish) H**
112
shielding effect
113
Z eff = effective nuclear charge
Z - core e-
114
if voltage in a tube is adjusted to provide circulating gas atoms with energy equal to a certain voltage, then species w/ ionization energy less than that will be ionized!
115
diatomic vs elemental gas
- greater stability (higher ionization potential) of diatomic
- use of most energetic e- to form bonds, stabilizing them in molecule
- bonds wouldn't form if they didn't increase electronic stability of atom (if arrangement is higher in energy --\> fly apart)
116
kinetic energy (example with cyclist)
if a cyclist collides with a tree:
The cyclist’s kinetic energy just before the impact will be converted into elastic and inelastic energy of deformation upon impact (related to the area under the stress versus strain curve) to cause damage to the tree and to the cyclist.
Decreasing this kinetic energy will result in a less violent collision. Because KE = (1/2)mv2, a decrease in the cyclist’s velocity would have the greatest effect (since v is squared) in lowering his KE.
117
The concentration of ketone bodies in the blood is expected to be increased the most in:
a person with untreated type 1 diabetes
- An individual with untreated type 1 diabetes would have decreased glucose inside of cells, leading to cellular “starvation,” even though blood glucose is high. This would cause the breakdown of fats for energy, leading to ketosis, and often dangerous increases in ketosis
note: Ketone bodies are increased when carbohydrates are lacking and the body switches to utilizing fats for energy.
118
relative refractory period
greater depolarization is needed to reach threshold
119
hyperpolarized vs depolarized cell at rest
cells that are hyperpolarized at rest are more difficult to depolarize to threshold
cells that are slightly depolarized at rest would be easier to depolarize to threshold
120
chemical synapse
example: neurohormone; hormone goes from modified nerve cell to into the blood
## Footnote
secrete NT from vesicles to postsynaptic membrane
121
ketoacidosis
decrease in blood pH due to the buildup of ketone bodies; An individual with ketoacidosis would be expected to exhibit compensatory mechanisms that can return blood pH to normal.
- Since blood pH is low, the body would drive towards expelling as much CO2 as possible by hyperventilating (**increased respiratory rate**)
122
bond between two sugar molecules:
**α-glycosidic linkage**
The bond between the two sugars in the diagram is an α-glycosidic linkage, because the anomeric carbon of glucose is pointing down
When β-glycosidic linkages are formed the linkage “locks” the carbohydrate in the β position, where the OH and CH2OH groups are on the same side of the ring
123
ionic bond
bond caused by the electrostatic attraction between two oppositely charged ions
124
Phosphodiester bonds
covalent bonds formed between a phosphate group and pentose sugar that utilize two ester linkages; used to form backbone of nucleic acids
125
Which one of the following compounds would be most soluble in ethanol?
CH4
HCOOH
CH3(CH2)16COOH
CH2Cl(CH2)16CH3
**Formic acid (**HCOOH) **is a highly polar molecule, making it soluble in the polar alcoholic solvent.**
Ch4 and CH2Cl(CH2)16CH3 cannot hydrogen bond with ethanol, and
CH3(CH2)16COOH has a long (18-C) nonpolar chain. Therefore, it will be less soluble in ethanol.
126
oxidative decarboxylation
C-3 hydroxyl group in 6-phosphogluconate is oxidized to a ketone, promoting the loss of the carboxyl group at C-1, which is lost as CO2.
127
esterification
a reaction between alcohols and carboxylic acids that results in ester formation
128
aldol condensation
the reaction of an enol and a carbonyl, which through a series of steps results in the synthesis of carbon-carbon bonds
129
hydrolysis
cleavage that results from the addition of water
130
thermodynamic equilibrium with unfolding and folding protein structure (q. 52 from mock MCAT course test 2)
A thermodynamic equilibrium between folded and unfolded scr SH3 can be achieved through the application of shearing forces.
- the thermodynamics of unfolding are slightly endergonic in the absence of force, but with the application of force, the final value of the free energy decreases, as shown in Figure 1b. Somewhere in this process ΔG will be 0 and the system will be at thermodynamic equilibrium.
131
urea w/ protein unfolding
Urea acts to stabilize the denatured state of scr SH3 by associating with backbone polar groups and charged side chains.
- unfolding will cause entropy to increase, not decrease, due to the disordering effect of unfolding
- Based on its structure, urea, CO(NH2)2, will interact with the polar moieties of a protein via hydrogen bonding, which include the peptide backbone and polar residues (charged or uncharged). By disabling intramolecular hydrogen bonding urea is capable of stabilizing the denatured state of a protein
- urea is not a reducing agent and will not affect disulfide bonds!
- note: Proteins can be denatured by urea through several processes. One method involves direct interaction whereby urea hydrogen bonds to polarized areas of charge, such as peptide groups. This mutual influence weakens the intermolecular bonds and interactions, weakening the overall secondary and tertiary structure. Once gradual protein unfolding occurs, water and urea can access more easily the hydrophobic inner core of the protein in question, speeding up the denaturation process.
132
anticodon sequence on the tRNA for the start codon
5’-CAU-3’
133
retention time in gas chromatography
A low retention time in gas chromatography is associated with a volatile (low boiling point) compound, while a high Rf in thin-layer chromatography is associated with a nonpolar compound
**the best answer for this question is a nonpolar compound with a low boiling point** (alcohols will have high boiling points due to their ability to hydrogen bond, and compounds with more carbons and less branching will have a higher boiling point because it has greater London dispersion forces)
- Non-polar compounds move up the plate most rapidly (higher Rf value), whereas polar substances travel up the TLC plate slowly or not at all (lower Rf value)
