Chem/Phys Flashcards
1
Q
How is a peptide bond formed?
A
Lone pair of electrons on amino-terminus nucleophilically attacks the carbonyl carbon of another amino acid’s carboxy-terminus
2
Q
Primary structure of protein
A
Linear sequence of amino acids connected by peptide bonds
3
Q
Secondary structure of protein
A
Local structure consisting of alpha-helices and beta-pleated sheets.
Stabilized by hydrogen bonds
4
Q
Tertiary structure of protein
A
3D structure stabilized by hydrophobic interactions, acid-base interactions, hydrogen bonding and disulfide bonds.
R-groups contribute to polypeptide’s tertiary structure
5
Q
Quaternary structure of protein
A
Interactions between subunits.
Heat and solutes cause denaturation of quaternary structure
6
Q
Which amino acid is not chiral?
A
Glycine, therefore it is also not optically active
7
Q
Why is atomic oxygen highly reactive?
A
It is a free radical because it has unpaired valence electrons
8
Q
What do nucleophiles possess that make them highly reactive?
A
Unpaired electrons - this is why they are often negative
9
Q
What is the Grignard reaction used for?
A
Formation of carbon-carbon bonds
10
Q
What is the relationship between index of refraction and speed of light?
A
Smaller index = faster light
11
Q
How are Polysaccharides connected
A
Carbohydrate-carbohydrate glycosidic bonds
12
Q
Rate law notations
A
0th: rate=k
1st: rate=k[A]
2nd: rate=k[A][B] or Rate=k[A]^2
13
Q
What is the function of a buffer?
How many pKa’s does a triprotic acid have?
A
Resists changes in pH.
Triprotic acids have 3 pKa’s
14
Q
How is Rf values (in chromatography) related to polarity?
A
Silica plates are very polar. Therefore polar molecules will have lower Rf values while non polar molecules will have higher Rf values
15
Q
Enzymes ONLY affect what?
A
Reaction rate
16
Q
Which nucleic acid bases are purines?
A
Adenine & guanine
17
Q
Which nucleic acids are pyrimidines?
A
Uracil thymine and cytosine
18
Q
How do the bonds between A-T and C-G differ?
A
A-T has two hydrogen bonds
C-G has three hydrogen bonds
19
Q
What is the relationship between pH and CO2 in the body?
A
Increased CO2 = decreased pH
20
Q
What is the charge of the anode of an electrolytic cell?
Cathode?
A
Anode = positive
Cathode = negative
21
Q
What is the charge of the anode of an galvanic cell?
Cathode?
A
Anode = negative
Cathode = positive
22
Q
What is the charge of the anode of an gel electrophoresis?
Cathode?
A
Anode = positive
Cathode = negative
23
Q
Which way does electric CURRENT flow?
A
From positive to negative
In a simple circuit the flow of current is the opposite of the flow of electrons (electrons are attracted to the positive)
24
Q
Which way do electrons flow?
A
Anode to cathode ALWAYS
AN OX RED CAT
25
What is the charge of a cathode and anode in a simple circuit?
Anode = negative
Cathode = positive
26
How are acetal and hemiacetals formed?
Addition of an alcohol onto a carbonyl group of an aldehyde
27
Sound waves travel fastest through what kind of media?
Solid media
28
What is Gibbs free energy equation?
G = H - T(S)
29
What is the difference between observed rotation and specific rotation?
Specific rotation is a constant (unless chemical changes occur)
Observed rotation is simply the rotation one can see (like an Orgo student in a lab)
30
What does Benedict's test used for?
Testing for reducing sugars
31
What is a reducing sugar?
A reducing sugar has a hemiketal or hemiacteal group
32
What is the common ion effect?
The common ion effect is responsible for the reduction in the solubility of an ionic precipitate when a soluble compound containing one of the ions of the precipitate is added to the solution in equilibrium with the precipitate.
33
When does respiratory alkalosis occur?
When you hyperventilate
34
When does delocalization of electrons occur
When resonance is present
35
How do you calculate formal charge
Valence - bonds - nonbonded electrons
36
What is cloud point?
The point where a solution is on the brink of precipitation.
Lowering temp or adding solute will cause precipitation
37
What is the difference between a dehydration and hydrolysis reaction
Dehydration reaction links two monomers together by releasing water
Hydrolysis breaks polymers apart using water
38
How do you determine how many stereoisomers are possible in a compound?
2^n
Where n is the number of chiral centers
39
How do you determine the centripetal force?
F = m(v^2/r)
40
Tertiary alcohols experience what kind of reaction when attacked by a nucleophile?
SN1 reaction
41
Primary alcohols experience what kind of reaction when attacked by a nucleophile?
SN2 reaction and therefore the absolute conversion is inversed
42
What is the difference in types of products SN1 reactions create versus sn2 products?
Sn1 = racemic mixture
Sn2 = optically active and inverted
43
What's the difference between an alpha particle and a helium atom
An alpha particle is simple the helium nucleus (no electrons)
44
What is the relationship between normality and molarity?
What is the molarity of a 1 N solution of HCl?
What is the molarity of a 30N solution of H2SO4?
Normality of a solution is the molarity multiplied by the number of equivalents per mole
HCl has a molarity of 1 M
H2SO4 has a molarity of 15 M
45
How is current related to time?
Current = charge/time
46
How are cations formed in regard to principal quantum number?
Electrons are removed beginning with highest principal quantum number
I.e: 4s2 before 3d10
47
What is a Lewis base?
A Lewis acid?
A Lewis base is an electron donor
A Lewis acid is an electron acceptor
48
What is a Brønsted-Lowry acid?
A Brønsted-Lowry base?
Brønsted-Lowry acid = proton (H+) donor
Brønsted-Lowry base = proton acceptor
49
What is a saturated solution?
A solution in which no more solvent can be dissolved
50
What is the first step in stoichiometry problems?
Convert the mass to moles
51
What is a colloid?
Suspension of particles that are larger in size than that of an individual molecule
52
What color has the highest frequency?
What color has the highest wavelength?
Frequency = purple
Wavelength = red
53
What is the unit of a Watt
Joules/second
54
How does resistance relate to resistivity?
Resistance = p(L)/A
55
What is superheating of a liquid?
Heating a liquid under pressure above its boiling point without vaporization
56
What does a red litmus color represent?
What does a blue litmus color represent?
Red = acidic
Blue = basic
57
In aqueous solutions what does H2CO3 decompose to?
H2O and CO2
58
What is an aliphatic compound?
A compound that is not aromatic - it is a straight chain compound
59
What is tautomerization?
Tautomerization involves the movement of atoms typically H. Resonance deals with the delocalization of electrons
60
What does the reactivity of a metal depend on?
Ionization potential
61
What are the best leaving groups?
What are the worst leaving groups?
Best leaving groups = weak bases
Worst leaving groups = strong bases
62
How does an acid differ from its conjugate base?
By the presence of a H+
63
What occurs if the solubility product of a compound is exceeded?
A precipitate will form
64
What does a low ksp mean in regards to water solubility?
Low ksp = low solubility in water
65
When does a liquid boil in regards to its vapor pressure and atmospheric pressure?
A liquid will boil when the vapor pressure = atmospheric pressure
66
How many electrons can fit in the s, p, d and f orbitals?
S= 2
P= 6
D= 10
F= 14
67
In titration, how do the moles of analyte compare to the moles of titrant at the equivalence point?
Moles analyte = moles titrant at equivalence point
68
What are the 3 kinematics equations?
Vf = Vo + at
Xf = Vot + 1/2 at^2
V^2 =Vo^2 + 2a(Xf-Xo)
69
What does Newton's third law state?
For every force there must be an equal and opposite force
70
What are the bond angles for a sp, sp2, sp3 molecule?
Sp = 180
Sp2 = 120
Sp3 = 109.5
71
Acetone formula
C3H6O
72
What do each of these enzyme classes do?
```
Oxidoreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase
```
Oxidoreductase = oxidation or reduction reactions
Transferase = transfer of function groups
Hydrolase = Hydrolysis reaction
Lyase = cleavage without hydrolysis
Isomerase = create isomers (rearrangement of atoms within a molecule)
Ligase = Joining of two molecules using ATP
73
Where are the following IR spec peaks located?
Carbonly, Hydroxyl, Amine
Carbonly = 1700-1750
Hydroxyl = 3200-3500 (broad)
Amine = 3100-3500 (sharp)
74
What does k equal to in regards to
k = [products]/[reactants]
75
What is Hess's Law?
deltaH = ∑Hproducts - ∑Hreactants
76
What does a capacitor do?
Stores an electric charge
77
Microtubules are used in which of the following:
Meiosis
Mitosis
Vesicle transport
Microtubules are used in all 3
78
What is 1atm equal to in mm Hg and in Pa
1 atm = 760 mm Hg = 10^5 Pa,
79
What kind of images do diverging lens produce?
What kind of images do converging lens produce?
Diverging = SUV - smaller upright virtual
Converging = SIR EIR LIR no LUV
```
SIR = beyond R
EIR = object at R
LIR = object between R and F
no = at focal point
LUV = between f and lens
```
80
What is an example of a molecule that exhibits homotropic regulation?
Hemoglobin
81
Where is an indicators pKa?
Within one unit of the desired pH
82
What is the difference between a positive control and a negative control?
Positive control = response expected
Negative control = no response expected
83
How are work and KE related
W = change in KE
84
What is 1 Pa equivalent to?
1 N/m^2
85
1 L is equivalent to what?
1 m^3
86
1 J is equivalent to what?
1 N.m
87
How is velocity and pressure related?
Increased velocity = decreased pressure
88
What is the equation for flow?
Flow= Area x velocity
89
What is an acetyl group?
A methyl and carbonyl group is an acetyl group
90
What is the structure of a hydroquinone?
What is the structure of a quinone?
Hydroquinone = Aromatic ring with two hydroxyl groups on opposite ends
Quinone = Aromatic ring with two carboxyl groups on opposite ends
91
What is a benzene, phenol, acyl, aklyl?
Benzene = aromatic ring
Phenol = aromatic ring with hydroxyl group
Acyl = carbonyl group
Alykl = C-H group
92
What is an example of proteolytic cleavage?
Hydrolysis
93
Prefix -thiol deals with what atom?
Sulfur
94
How does frequency relate to energy?
Higher frequency = hihger nergy
95
What is the unit of Hz?
s^-1
96
What does a voltmeter do?
Measures voltage/potential difference in a circuit
97
What is the central atom of choline?
Nitrogen
98
What is the difference between thermodynamic control and kinetic control?
Thermodynamic control = lower energy state of product preferred, often seen in reversible rxns
Kinetic control = preferred product of rxn has lowest activation energy and is formed most quickly
99
What is the formula for Keq?
Keq = [products]/[reactants]
100
What is the formula relating G and Keq?
Delta G= -RT ln(Keq)
101
What are the bond angles associated with linear, trigonal planar, tetrahedral molecules?
Linear = 180
Trigonal planar = 120
Tetrahedral = 109.5
102
What do kinases do?
Catalyze the transfer of phosphate groups using ATP
103
What molecules are often intensely colored?
Molecules with delocalization of electrons
104
How do you measure catalytic efficiency?
Kcat/Km
High Kcat, low Km = high efficiency
105
What types of bonds link monosaccharides?
Glycosidic linkages link monosaccharides
106
What amino acids can participate in hydrogen bonds?
Amino acids with polar side chains
107
What kind of molecules bind to anion exchange columns? Cation exchange columns?
Anions bind to anion exchange columns
Cations bind to cation exchange columns
108
What needs more salt to be eluted from an anion exchange column: a highly negative molecule, or a weakly negative molecule
A Highly negative molecule needs more salt to be eluted from an anion exchange column
109
What parameter must be satisfied when measuring Kcat?
Substrate concentration must be saturating when measuring Kcat
110
What is the visible light spectrum in nm?
What color has the lowest wavelength?
Approx 400-700nm
Purple has the lowest wavelength (and therefore highest frequency)
111
What makes a good leaving group?
What are some examples of common leaving groups?
Being able to retain electron after a bond breaks (heterolysis)
Common leaving groups = weak bases, large groups with resonance (delocalization of electrons), and large groups with electron-withdrawing atoms
112
What is HF a weak acid?
Because F is so electronegative it binds very tightly to F and therefore takes a lot of energy to break the bond
113
How many units does a homotetramer have?
4 units
114
What does a reducing SDS-PAGE do?
Denatures proteins and eliminates quaternary structure
115
How carbons numbered in rings?
Based on N positions (where lowest N is first)
116
What molecules move the farthest in SDS-PAGE
small molecules move farthest
117
What is native electrophoresis?
What molecules travel farthest?
In native electrophoresis, molecules are not denatured
Smaller molecules travel farthest
118
What are hydronium molecules found in?
OH- molecules?
Hydronium = acids
OH- = bases
119
What nucleotide has the highest molecular weight?
Guanine
120
What is a key example of a non-reducing sugar?
Sucrose
121
How is Kcat related to Vmax
Higher Kcat = higher Vmax
122
What kind of amino acids can form peptide bonds?
Positively charged amino acids (Lysine) can acts as amine group
123
What amino acids can create covalent bonds?
Cysteine can create covalent bonds though disulfide bridges
124
What is a ternary complex?
A ternary complex is protein complex containing three different molecules that are bound together.
125
What do the quantum numbers: n. l, ml, and ms represrent
n= shell (value = [n=1,2,3]) max number of electrons in energy level = 2n^2
l= subshell (l= n-1) max number of elcetron in subsell = 4l +2
ml= orbiatal (bewteen +l and -l)
ms= spin (+1/2 or -1/2)
126
What atom is key for a pyrrole?
Nitrogen (N)
127
What is the formula for buoyant force?
Fb = pgVsubmerged
128
What is Bernoulli's equation?
P + 1/2(density)(velocity^2) + density(g)(h) = constant
or
Pressure + kinetic energy + potential energy = constant
129
What is fundamental frequency?
The lowest frequency produced by an object
130
Which harmonic has the longest wavelength?
1st harmonic
131
How many different substituents do stereocenters need to be attached to?
4 different group. Lone pair of electrons can count as a group!
132
What is avogadro's number?
6.023 x 10^23
133
What is dipole moment?
The mathematical product of the separation of the ends of a dipole and the magnitude of the charges
Dipolar ions (ions with positive and negative ends) will have greater dipole moments
134
How do saturated and unsaturated bonds differ?
Unsaturated bonds have double bonds (and are kinked) Saturated bonds are not kinked as they only contain single bonds
135
What is acid dissociation constant?
Ka (different from affinity constant) measures strength of an acid. Higher Ka = stronger acid
136
What is an ideal gas?
An ideal gas is a hypothetical gas that occupies negligible space and has no interactions (therefore obey gas laws exactly)
137
What oxidation state are molecules in when they are bonded to themselves?
0
i.e Ag has an oxidation state of 0
138
D-group elements are what kind of elements?
Transition metals (think s, p, d, f)
139
Is a galvanic cell spontaneous or nonspontaneous?
What about an electrolytic cell?
Galvanic = spontaneous
Electrolytic = nonspontaneous
140
How does reduction potential (E) relate to G (spontaneity)?
Reduction potential and spontaneity are inversely related
141
During recrystallization do you want to cool the solution slowly or quickly?
Lots of solvent or minimal solvent?
Cool solution SLOWLY
MINIMAL solvent
142
What is the unit for Pa?
N/m^2
143
What is the unit for Voltage?
J/C
144
What is the unit for Ampere's?
C/s
145
How does ionic radius differ from atomic radius?
Atomic radius increases towards bottom left corner of periodic table
Anions are much larger than neutral molecules
Cations are much smaller than neutral molecules
146
When do gases deviate from ideal gas law?
Low temperatures and high pressure
147
How do strong acids and bases behave in aqueous solutions?
They complete dissociate into their ions in aqueous solutions
148
How do weak acids and bases behave in aqueous solutions?
Weak acids and bases only partially dissociate
149
How does Ka (acid dissociation constant) relate to acid strength?
High Ka = strong acid
150
When will a precipitate form in regards to Ksp?
When the Ksp is exceeded a precipitate will form
151
What kind of charge does a axon possess?
A negative charge (as it conducts electricity - stores electrons)
152
Does the rule "like dissolves like" hold true for acids/bases?
No
153
What kind of solutions are bases dissolved in?
Bases can be dissolved in acidic solutions (neutralization)
Most bases are insoluble in water
154
What is the charge of the C-terminus?
N-terminus?
C-terminus = -1
N-terminus = +1
155
What occurs in an ionization reaction?
Ions are created
156
What occurs in a Lewis Acid/Base reaction?
Lewis acid and lewis base form to create a Lewis "complex"
157
What occurs in a redox reaction?
Oxidation state changes
158
If a buret is in cup of water, and the water level in the buret is higher than the cup of water, how does the pressure in the buret compare to the ambient pressure?
The pressure of gas in the buret is lower than ambient pressure
PV=nRT
(volume increased, so pressure decreases)
159
Hydrogen bonding occurs when?
When H is bonded to highly electronegative atoms (F, N O)
160
The principal quantum number is a measure of what?
Radial size of an electron cloud
161
What does it mean to exist in equilibrium?
Exist between two forms
162
Are 4 or 6 membered rings more thermodynamically preferable?
6 membered rings are more thermodynamically preferable
163
A C=C bond IR shift is approximately where?`
1600 cm^-1
164
What does the Doppler effect deal with?
Speed of sound and frequency change
165
What is the photoelectric effect?
E = hf
166
When temperature is increased is endothermic or exothermic reaction favored?
Endothermic reaction is preferred
167
What is the difference between fractional, simple and vacuum distillation?
Fractional = boiling points are less than 25 degrees apart
Simple = bp greater than 25 degrees
Vacuum = used to separate mixtures of very high boiling points
168
When do gases act ideally?
High temperature, low pressure
169
Azetropes must be separated by what kind of distillation?
Fractional distillation
Azetropes are also known as constant boiling mixtures
170
How do you determine the number of valence electrons on an atom?
Count the group number
171
What is the general formula for trigonal bipyramidal molecules?
Octahedral molecules?
Trigonal bipyramidal = PCl5
Octahedral SF6
172
Keq > 1 means what?
Keq
Keq > 1 means lots of products (shift right)
Keq
173
What is chelation?
When an atom (cation) is bonded convalently to the same ligand multiple times
174
What are the differences between isolated, closed an open systems in regards to thermochemistry?
Isolated = no exchange of energy or matter
Closed = no exchange of matter, but can exchange energy
Open = can exchange both matter and energy
175
What does a state function depend on?
State function depend on only the initial and final states of the system, no the path they take
i.e Temperature
176
What is the definition of Arrhenius acid and base?
Arrhenius acid = in aqueous solution, acid produces excess H+
Arrhenius base = in aqueous solution, base produces excess OH-
177
What is the pH of a solution when [H+] = 1 x 10^-3
pH = 3
178
Do galvanic or electrolytic cells have salt bridges?
Galvanic cells have salt bridges to allow electrons to flow between the half cells containing the anode and cathode
179
How do you calculate emf (standard reduction potential)
Ered, cat - Ered, anode
180
How can you calculate total pressure of a rxn based on partial pressures?
Add partial pressures for all gases to get total pressure
| Dalton's Law
181
Is PCC an oxidizing agent or a reducing agent?
Oxidizing agent (weak)
182
What do oxidizing agents contain?
Oxygen
183
What do reducing agents contain?
Hydrogen
184
Which has a higher value, uk or us?
Static friction is greater than kinetic friction
185
What is the first harmonic also referred to as?
The fundamentals frequency
186
What does the number of peaks of a NMR graph indicate?
Number of distinct H neighbors. Peaks is greater than the number of neighbors (n+1)
187
What is emitted during a beta negative decay?
Electron!
188
What are the differences between cis and trans isomers?
Cis = same side
Trans = opposite side
Unsaturated fatty acids have greater kinks in cis!!
189
How many steps is SN1 reaction?
SN2
SN1 = 2 steps (therefore has carbocation intermediate)
SN2 = 1 step
190
What kind of reaction has a carbocation intermediate, SN1 or SN2?
SN1 - as it has two steps
191
Where does steric hindrance affect an alcohol?
Steric hindrance affects the central atom (not the peripheral atoms)
192
What does gas liquid chromatography separate mixtures based on?
Based on boiling points
193
What kind of molecules will migrate the fastest and cause the first peaks in GC?
Molecules with the lowest boiling points migrate the fastest and cause the first peaks
194
What kind of products are does SN2 produce?
Inverted products, optically active
195
What kind of products does SN1 produce?
Racemic products
196
What is deuterium?
Heavy hydrogen (isotope with double mass)
197
Which amino acids can be phosphorlyated easily?
Serine, threonine, tyrosine (amino acids with OH group)
198
How does the area of capillaries compare to the area of arteries?
Capillaries have more TOTAL area
199
What is the equation for refractive index?
n = c/v
c = speed of light, 3 x 10^8
200
What does a hydrophobic compound consist of?
A lot of C-H bonds
201
Where are the sources of phosphate groups for a kinase?
ATP, that is why ATP is used
202
What is uracil associated with?
RNA
203
How do charged anions behave in solution?
Charged anions are less likely to deprotonate in solution because they have high levels of attraction with positively charged hydrogens
204
What is the formula for magnification?
m = -i/ o
(-image)/object
205
What is most disordered: gas, liquid or solid?
Gas is most disordered
206
What are the two equations for standard cell potential?
Ecell = Ecat - E anode
Ecell = Ered - Eox
AN OX, RED CAT
207
Describe the spontaneity of an electrolytic cell?
Electrolytic cell is non-spontaneous (because it has a battery)
208
What does the common ion effect do?
Reduces solubility
209
What is a lactone?
A cyclic ester
210
How does a H NMR peak relate to the number of neighbors with hydrogen?
Peak = 1 greater than number of neighbors
211
What is a moiety?
Part of a molecule
212
What are the equations for fundamental frequency for a string, open pipe and closed pipe?
string = f = nv/2L
open = f = nv/2L
closed = f = nv/4L
213
What are the units for 0, 1 and 2 order reactions?
0 = M/s
1 = 1/s
2 = 1/M.s
214
What are the differences between 0, 1 and 2 order reactions?
0 = constant rate, independent of reactants
1 = rate proportional to concentration of one of the reactants
2 = rate proportional to square of concentration of one of reactants, or product of concentration of two of the reactants
215
What is another term for acetic acid?
Acetate
216
What is binding affinity characterized in Michelis-menten?
Km
217
Is coA chiral or achiral?
Achiral
218
What is the charge of an -OH at pH 7?
0, uncharged
219
What is the half-reaction for oxidaiton?
NADH = NAD+ + H+ + 2e-
220
What is molality?
Mols/kg
221
What is the ir frequency for c-c?
1200
222
What is the ir frequency for c=c?
1600
223
Shielded hydrogens are attached to what?
Less electronegative molecules
224
Deshielded means an atoms is attached to what?
A more electronegative atom
