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MCAT Fuzzy Concepts > C/P > Flashcards

C/P Flashcards

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1
Q

TLC

A

separates compounds based on different polarities polar stationary phase (i.e. silica). more polar compounds interact with stationary phase, travel slower. Less polar compounds have affinity for mobile liquid phase. RF greater for NP compounds

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2
Q

size exclusion chromatography

A

Smaller molecules diffuse into the pores and their flow through the column is slowed according to their size, while larger molecules do not enter the pores and are eluted in the column’s void volume. As they pass through the column, molecules are eluted in order of decreasing molecular weight

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3
Q

affinity chromatography

A

target molecule trapped on stationary phase, washed to remove unwanted. target protein is eluted off the solid phase in a purified state.

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4
Q

gas chromatography

A

mobile gas phase, stationary liquid phase. separation based on volatilities

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5
Q

important stretch frequencies (IR)

A

Carbonyl: 1700 cm-1 alkenes: 1650 cm-1 OH: 3600-3200 cm-1 CH: 2850-3300 cm-1

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6
Q

UV Spectroscopy

A

used for monitoring transition metals- take on bright colours. AND to study highly conjugated pi-systems. if a substance absorbs a colour (i.e. red) it will appear the opposite colour (i.e. green)

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7
Q

IR spectroscopy

A

bond absorbs IR radiation, seen as peak in IR spectrum (low transmittance corresponds to absorbance) wavelength IR: 2.5 to 20 microns learn stretch frequencies

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8
Q

NMR Spectroscopy

A

light from radio frequency range. number of peaks = number of chemically nonequivalent protons in molecule eq= identical electronic enviro splitting pattern= how many protons are interacting with the protons in that set. splitting: n+1 where n is number of neighbouring non-equivalent H mathematical integration of the sets of peaks indicates # of protons. area under peak is proportional to number of protons

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9
Q

degree of unsaturation

A

d= [2C + 2 - H]/2

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10
Q

Shielding and chemical shift

A

Downfield: more deshielded upfield: less deshielded EN: EN atom close to a proton will decrease its electron density, and deshield it. Moves downfield Hybridization: greater s character of CH bond, less electron density, more deshielded/downfield Acidity: protons attached to heteroatoms (O, N) are deshielded.`

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11
Q

common HNMR chemical sift values

A

carboxylic acid: 10-12

aldehyde: 10
aromatic: 8

vinyl (Alkene): 6

RCHX: 3

alkyl: 1

carbon that has carbonyl next to it: 2.5

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12
Q

Gel electrophoresis

A

separate amino acids based on charge if pH > pI: NEGATIVE charge, move to + electrode if pH

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13
Q

Epimer

A

diasteromers that differ at single chiral centre

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14
Q

Benedict’s test

A

Benedict’s reagent = CU2+ any sugar that can be oxidized by this reagent is a reducing sugar, because it reduces Cu2+ to Cu+

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15
Q

Grignard Reagent

A

general formula: R-M+ electron rich, anionic C atoms. function as strong base or nucleophiles. i.e.: CH3CH2MgBr Carbonyl + Grignard = alcohol (with methyl/ethyl from the G.R. attached)

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16
Q

how are acetals formed

A

aldehydes react with alcohols in the presence of acid

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17
Q

Elastic Potential energy

A

1/2kx^2

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18
Q

effect of intermolecular attractions on potential and kinetic energies of particles

A

intermolecular attractions increase PE btw molecules, decreasing their KE

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19
Q

atomic size periodic trend

A

increases down a family and to the LEFT across a period

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20
Q

buoyant force equation

A

mg= pfluid* Vsubmerged *g m= pfluidVsub

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21
Q

Specific gravity

A

SG= pfluid/pwater (density of water = 1000 kg/m^3)

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22
Q

tautomers

A

isomers. structural difference is a shift of a H atom

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23
Q

where does beta-oxidation occur? FA synthesis?

A
  1. mito matrix 2. cytoplasm
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24
Q

what factor can change the equilibrium constant K

A

temperature only

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25
Q

when does total internal reflection occur

A

when angle of incidence is greater than critical angle

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26
Q

competitive inhibitor

A

bind free enzyme, when bound can’t bind substrate but can be overcome with more substrate… therefore same Vmax but Km increases (lower affinity for S) same y intercept (1/max) but changes x intercept (1/km) and slope (km/vmax)

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27
Q

uncompetitive inhibitor

A

decreases KM and decrease VMax

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28
Q

lineweaver burke plot

A

slope: Km/Vmax y intercept: 1/Vmax x intercept: 1/km

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29
Q

noncompetitive inhibition- type of mixed.

A

same Km lower Vmax same x intercept, different Y intercept decrease slope

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30
Q

during the exponential phase of bacterial growth, bacteria reproduce by:

A

binary fission (conjugation & transduction increases genetic diversity, but doesn’t affect population size.

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31
Q

oligonucleotide with a lower melting temp would have

A

few GC bonds because GC bp involve 3 H bonds, whereas AT involves only 2

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32
Q

effect of increased PTH

A

increased CA2+ levels

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33
Q

osmotic pressure

A

colligative property, depends only on the concentration of solute particles NOT their identity. depends on # of ions

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34
Q

amphoteric character of amino acids describes their ability to:

A

accept or donate a protein. act as acaid or base. forms dipolar ions

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35
Q

transformation (bacteria) and transduction and conjugation

A

naked DNA, not a virus, is taken into a cell and changes the genetic characteristics of the cell (transduction is mediated by a virus, conjugation involes direct transfer of DNA between bacteria)

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36
Q

BBB

A

formed by enddothelial cells connected by tight junctions

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37
Q

Faraday

A

1 mole of charge

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38
Q

equation for charge (q) with voltage and capacitance and equation for energy with Q and V

and PE

A

q=CV

q=nE

PE=(1/2)QV

V=ED

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39
Q

byproduct of peptide formation, and its amu

A

H2O, 18 lol

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40
Q

The relative thermodynamic stability of isomeric organic compounds can be inferred from which type of experimental data?

A

heat of combustion, less heat = more stable

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41
Q

avogadro’s number

A

= number of atoms in a mol 6.02x10^23

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42
Q

complex ion vs chelate

A

A complex ion (or coordination complex) consists of a central ion coordinated to ligands. If a single ligand has 2 or more atoms that can bond to the central atom, it’s referred to as a polydentate ligand or chelating ligand. So a chelate is a specific type of coordination complex that you get when your central atom is coordinated to multiple atoms of the same ligand.

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43
Q

how to do the electron configuation for metals with roman numerals (i.e Co(II))

A

the numerals represent loss of electrons Co(II) is a dication and is formed from the atomic element by the loss of two 4s electrons.

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44
Q

transferase

A

i,e, kinase catalyze transfer of P from ATP to target

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45
Q

anionic exchange column

A

binds anions (

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46
Q

EM spectrum (highest to lowest wavelength)

A

radio (10^3)

microwave (10^-2)

infrared (10^-5)

visible (10^-6) UV (10^-8)

Xray ((10^-10)

Gamma (10^-12)

Visible light 750 nm (red) –> 350 nm (violet)

Raging Martians invaded venus using X-ray Guns

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47
Q

melting point and protein folding

A

Tm is the temperature at which 50% of the molecules are denatured or the fraction folded is 0.5

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48
Q

how many H bond donours/acceptors do each a.a. have?

A

Adenine contains 1 donor and 1 acceptor, thymine contains 1 donor and 1 acceptor, guanine contains 2 donors and 1 acceptor, and cytosine contains 1 donor and 2 acceptors

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49
Q

reducing sugar

A

A reducing sugar is one that can act as a reducing agent. Reducing sugars can be identified through the presence of a free anomeric carbon, meaning it is not in a glycosidic bond and has a free hydroxyl group

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50
Q

specific activity and yield

A

specific activity (units/mg) represents a measure of solution purity, the activity units themselves provide the best measurement of yield

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51
Q

ternary complex

A

protein complex containing three different molecules that are bound together. … A ternary complex can be a complex formed between two substrate molecules and an enzym

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52
Q

which peptide would be more likely to make a covalently bonded dimer

A

LOOK FOR CYSTEINE< indicates that disulfide-link could occur

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53
Q

which alcohol cannot be readily oxidized

A

tertiary. it involves C-C bond breaking primary can be oxidized to aldehyde, which can be oxidzed into carboxylic acid secondary can be oxidized to ketone

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54
Q

E vs Z

A

e: pririoty groups on opposite side of double bond

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55
Q

london dispersion

A

temporary attractive force that results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipole All “real” molecules and atoms will exhibit London dispersion force occurs on NP

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56
Q

amber codon

A

stop codon

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57
Q

amine

A

R3N, where R= H, or C, but NO carbonyl and no more than 2/3 R can be H

\

“amine is mean and boring”

58
Q

amide

A

also, the conjugate base of an amine is also called an “amide”

i.e. R-NH-

“amide has got Carbonyl by its side”

59
Q

Imine

A

intimidating, cause it has a double bond… lol

60
Q

carbamate

A

get all your mates

carbonyl, oxygen, and nitrogen

61
Q

NaBH4

A

reduces ketones/aaldehydes to alcohols

62
Q

lactone

A

class of cyclic organic esters, often formed by reaction of carboxylic acid with hydroxyl group or halogen in same molecule.

63
Q

lactam

A

this is beta lactam

cyclic amide

64
Q

ester vs ether

A
65
Q

ketone

A
66
Q

aldehyde

A
67
Q

ping pong

A

aka double displacement reaction. one product is formed and released before second substrate binds

68
Q

buffer capacity

A

A buffer has a buffering capacity that is ±1 pH unit away from the pKa

69
Q

refraction

A

light passes through the interface between optical media with different indices of refraction

n=c/v

70
Q

diffraction

A
71
Q

polarization

A

electric field vectors in same direction

72
Q

definition of current

A

charge/time

Q/t

73
Q

meso compound

A

contains chiral centres but is overall achiral

74
Q

amino acids R/S

A

almost all are S

except cysteine is R

glycine is achiral

75
Q

gel electrophoresis

A

separates based on charge, size, shape

size: smallest moves through quickest

charge: negatively charged travel toward positive end (anode) quicker

Shape: more aerodynamic moves faster

76
Q

SDS-page

A

type of gel electro

USED IF U WANT TO SEPARATE PROTEINS JUST BY SIZE.

SDS denatures protein, adds number of negative charges proportional to protein size

77
Q

reducing SDS-Page

A

SDS denatures protein except at places with disulfide bonds. in order to break these, need to use reducing SDS-page

78
Q

native-page

A

no SDS/reducing agent. gel is non-denaturing. protein remains in native shape

79
Q

when to use different types of distillation

A

simple: both BP are under 150 C, and at least 25 C apart
fractional: BP are less than 25 apart,
vacuum: BP above 150 C

80
Q

fingerprint region of IR spectrum

A

special range unique to certain compound. spans the region of wavenumbers 1500 to 500 cm-1

81
Q

amino acid configuration

plus 1 letter codes

A

all are L except glycine

all are S (except cysteine)

FWY: aromatic

RHEKD: charged (DE=acidic), others basic

MP GAVIL: NP

CTS NQA: polar

82
Q

peptide bond formation

A

condensation (hehydration) reaction with Nu amino group attacking electrophlic carbonyl. peptide bonds broken via hydrolysis

83
Q

D and L forms of same sugar are

A

enantiomers

84
Q

diasteromer

A

differ at at least 1, but not all, chiral centres

includes:

epimer: differ at 1 centre
anomer: differ at anomeric C

85
Q

fructose

A
86
Q

sugars: α- or β-conformation

A
  • α-anomers have the –OH on the anomeric carbon trans to the free –CH2OH group.
  • β-anomers have the –OH on the anomeric carbon cis to the free –CH2OH group.
87
Q

glucose structure

A

OH

H

OH

OH

88
Q

galactose structure

A

OH

H

H

OH

89
Q

mannose structure

A

H

H

OH

OH

think: mannose has 2 of the same letters. so its order going down the right is 2 letters repeating

90
Q

common disaccharides

A

sucrose (glucose-α1,2-fructose)

lactose (galactose-β-1,4-glucose)

maltose (glucose-α-1,4-glucose)

91
Q

nucleoside vs nucleotide

A

nucleoside: 5C sugar bound to a nitrogenous base
nucleotides: nucleoside bound to 1 to 3 phosphate

92
Q

telomeres

A

end of chromosome. contain high GC content to prevent unraveling

93
Q

centromers

A

located in the middle of chromosonmes, hold sister chromatids together, until separated during anaphase of mitosis. also contain high GC content

94
Q

periodic trend summary

A
95
Q

which elements are more stable with fewer than 8 e-

A

H (2)

He (2)

Li (2)

Be (4)

B (6)

96
Q

formal charge

A

FC= #valence - 1/2 bonding e - # lone pair

97
Q

complex ion (coordination compound)

A

Lewis acid-base adduct with a cation bonded to at least 1 electron pair donor.

donor molecules= ligand, use coordinate covalent bond

central cation can be bonded to the same ligand multiple times in a process called chelation

98
Q

combustion rxn

A

fuel, such as hydrocarbon, reacted with oxidant (i.e. O) to produce oxide and water

99
Q

isothermal

adiabatic

isobaric

isovolumetric (isochoric)

A

isothermal: T remains constant
adiabatic: no heat exchange
isobaric: pressure constant

isovolumetric (isochoric): volume constant

100
Q

state fxn

A

descirbed by the macroscopic properties of system. depend only on initial and final states, not path

i.e. pressure, density, volume, temperature, enthalpty, internal energy, free energy, entropy

101
Q

standard heat of reaction

A

∆H° rxn = (sum of ∆H° f of products) – (sum of ∆H° f of reactants)

102
Q

Hess’ Law

A

enthalpies of rxns are additive

reverse rxn has same magnitude but opposite sign

103
Q

relationship of atm, mmHg, torr, Pa

A

1 atm = 760 mmHg = 760 torr = 100,000 Pa

104
Q

Colligative properties:

A

physical properties derived solely from the number of particles present, not the nature of those particles.

These properties are usually associated with dilute solutions. Molality (m) must be used, in addition to the van ’t Hoff factor (i) for ionic compounds.

105
Q

Boyle’s Law

A

PV=k

P1V1=P2V2

106
Q

Charles Law

A

V/T = k or

V1/T1= V2/T2

107
Q

Dalton’s law of partial pressures:

A

total pressure of a gaseous mixture is equal to the sum of the partial pressures of the individual components

PT = PA + PB + PC +…

PA = PTXA

where XA = nA/nT (molesof A)/ (totalmoles)

108
Q

average molecular speed

A
109
Q

Graham’s Law of diffusion and effusion, equation

A
110
Q

half-eq point of titration

A

The halfequivalence point defines pH = pKa

111
Q

Henderson Hasselbach

A

pH= pKa + log [A-]/[Ha]

112
Q
A
113
Q

Standard reduction potential and Gibbs free energy equations for half-cells

A

emf = E˚ red, cathode – E˚ red, anode

∆G = –nFEcell

114
Q

SN1 vs SN2

A

SN1:

  • 30>20>10>methyl
  • POLAR PROTIC
  • 2 steps
  • racemic product
  • strong Nu not needed

SN2:

  • methyl>10>20>30
  • POLAR APROTIC
  • 1 step
  • inversion
  • strong Nu
115
Q

factors which determine nucleophilicty

A

Charge: increases with increasing electron density (negative charge)

EN: Nucleophilicty DECREASES with increasing EN, because these atoms are less likely to share their electron density

steric hinderance: bulkier = less Nu

solvent: polar solvents can inhibit nu by protonating nucleophile or H bonding

116
Q

aprotic vs protic solvents and nucleophilicty

A

in aprotic, nucleophilcty parallels basicity:

F>Cl>Br>I

in protic, good bases pick up protons and are worse nucleophiles:

I>Br>Cl>F

117
Q

Leaving groups

A

retain e after heterolysis

best LG are able to stabilize e

most common:

  • weak bases
  • large groups w resconance
  • Large groups with e withdrawing atoms
118
Q

conformational isomers

A

differ by rotation around a single (sigma) bond

119
Q

staggered vs eclipsed conformations

A

staggered: groups 60 degrees apart. largest groups are 180 apart in anti

lage groups are 60 apart in gauche

eclipsed: groups directly in front. total eclipse: large groups directly in front

120
Q

enantiomers vs diasteromers (light)

A
121
Q

how are alcohols synthesized

A

addition H2O to double bonds

SN1/SN2 rxns

reduction casrboxylic acids, aldehydes, ketones, esters

(aldehydes/ketones with NaBH4 or LiALH4, esters with LiAlH4)

122
Q

how to look for ox/red in an organic rxn

A

Oxidation = loss of electrons, fewer bonds to hydrogens, more bonds to heteroatoms (O, N, halogens)

Reduction = gain of electrons, more bonds to hydrogens, fewer bonds to heteroatoms

123
Q

good oxidizing agent

A

high affinity for electrons (such as O2, O3, and Cl2) or unusually high oxidation states (like Mn7+ in permanganate, MnO4 —, and Cr6+ in chromate, CrO42-).

124
Q

good reducing agents

A

i.e. sodium, magnesium, aluminum, and zinc, which have low electronegativities and ionization energies.

Metal hydrides are also good reducing agents, like NaH, CaH2, LiAlH4, and NaBH4, because they contain the H– ion.

125
Q

PCC

A

oxidizes a primary alcohol into an aldehyde

126
Q

Jones’s Reagent

A

convert _secondary alcohols into carboxylic acid_s (alkali dichromatic salt and KMnO4 will as well)

JSC (junior science club, jones converts secondary alc into C.A.)

PPA (primary PPC, A is first letter)

127
Q

mesylates/tosylates

A

Alcohols can be converted to mesylates or tosylates to make them better leaving groups for nucleophilic substitution reactions

128
Q

how are alcohols used as protecting groups

A

Alcohols can be used as protecting groups for carbonyls, as reaction with a dialcohol forms an unreactive acetal. After other reactions, the protecting group can be removed with aqueous acid

129
Q

acidity of phenol

A

pka approx 10

130
Q

quinones/hydroxyquinones

A

treatment phenol with oxidizing agents produces quinones, which can be further oxidized into hydroxyquinones

131
Q

ubiquinone

A

Ubiquinone (aka coenzyme Q) is a vital electron carrier associated with Complexes I, II, and III of ETC

Ubiquinone can be reduced to ubiquinol, which can later be reoxidized to ubiquinone. This is sometimes called the Q cycle.

132
Q

how are aldehydes synthesized

A

oxidation primary alcohols

ozonolysis alkenes

133
Q

aldol condensation

A

aldehyde acts both as nucleophile (enol form) and an electrophile (keto form)

one carbonyl forms enolate, which attacks other carbonyl

after aldol is formed, dehydration rxn results in α,β-unsaturated carbonyl

134
Q

carboxylic acids

pka, bp

A

pka = 4.5 (resonance stablized conjugate base)

BP higher than alcohol bc can form 2 H bonds

135
Q

synthesizing carboxylic acids

A

oxidation primary alcohols with KMnO4

Hydrolysis of nitriles

136
Q

how to form soap with C.A.

A

reacting C.A. with NaOH, arrange in micelles

137
Q

carboxylic acid derivatives- rank based on descending reactivity

A
  1. acyl halides
  2. anhydrides- dehydration of 2 carboxylic acids
  3. carboxlyc acids and esters
  4. amides (least reactive)
138
Q

strecker synthesis

A

reagents: Aldehyde, NH4Cl, KCN

AMINO ACID SYNTHESIS

strecker

A, N, K

SANK: Strecker sank the ship

139
Q

Gabriel (Malonic-Ester) synthesis

A

Reagents: potassium phthalimide, diethyl bromomalonate

reaction in presence of base and alkyl halide

140
Q

pyrophosphate

A

P2O74–, which is released during the formation of phosphodiester bonds in DNA. Pyrophosphate is unstable in aqueous solution, and is hydrolyzed to form two molecules of inorganic phosphate

Phosphoric acid is a phosphate group or inorganic phosphate (Pi ). At physiologic pH, inorganic phosphate includes both hydrogen phosphate (HPO2– 4 ) and dihydrogen phosphate (H2PO– 4).

141
Q

types of chromotography: which have NP mobile phase

A

MCAT Fuzzy Concepts (4 decks)

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