C/P Flashcards
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
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
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.
4
Q
gas chromatography
A
mobile gas phase, stationary liquid phase. separation based on volatilities
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
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)
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
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
9
Q
degree of unsaturation
A
d= [2C + 2 - H]/2
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.`
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
12
Q
Gel electrophoresis
A
separate amino acids based on charge if pH > pI: NEGATIVE charge, move to + electrode if pH
13
Q
Epimer
A
diasteromers that differ at single chiral centre
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+
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)
16
Q
how are acetals formed
A
aldehydes react with alcohols in the presence of acid
17
Q
Elastic Potential energy
A
1/2kx^2
18
Q
effect of intermolecular attractions on potential and kinetic energies of particles
A
intermolecular attractions increase PE btw molecules, decreasing their KE
19
Q
atomic size periodic trend
A
increases down a family and to the LEFT across a period
20
Q
buoyant force equation
A
mg= pfluid* Vsubmerged *g m= pfluidVsub
21
Q
Specific gravity
A
SG= pfluid/pwater (density of water = 1000 kg/m^3)
22
Q
tautomers
A
isomers. structural difference is a shift of a H atom
23
Q
where does beta-oxidation occur? FA synthesis?
A
- mito matrix 2. cytoplasm
24
Q
what factor can change the equilibrium constant K
A
temperature only
25
when does total internal reflection occur
when angle of incidence is greater than critical angle
26
competitive inhibitor
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)
27
uncompetitive inhibitor
decreases KM and decrease VMax
28
lineweaver burke plot
slope: Km/Vmax y intercept: 1/Vmax x intercept: 1/km
29
noncompetitive inhibition- type of mixed.
same Km lower Vmax same x intercept, different Y intercept decrease slope
30
during the exponential phase of bacterial growth, bacteria reproduce by:
binary fission (conjugation & transduction increases genetic diversity, but doesn't affect population size.
31
oligonucleotide with a lower melting temp would have
few GC bonds because GC bp involve 3 H bonds, whereas AT involves only 2
32
effect of increased PTH
increased CA2+ levels
33
osmotic pressure
colligative property, depends only on the concentration of solute particles NOT their identity. depends on # of ions
34
amphoteric character of amino acids describes their ability to:
accept or donate a protein. act as acaid or base. forms dipolar ions
35
transformation (bacteria) and transduction and conjugation
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)
36
BBB
formed by enddothelial cells connected by tight junctions
37
Faraday
1 mole of charge
38
equation for charge (q) with voltage and capacitance and equation for energy with Q and V
and PE
q=CV
q=nE
PE=(1/2)QV
V=ED
39
byproduct of peptide formation, and its amu
H2O, 18 lol
40
The relative thermodynamic stability of isomeric organic compounds can be inferred from which type of experimental data?
heat of combustion, less heat = more stable
41
avogadro's number
= number of atoms in a mol 6.02x10^23
42
complex ion vs chelate
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.
43
how to do the electron configuation for metals with roman numerals (i.e Co(II))
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.
44
transferase
i,e, kinase catalyze transfer of P from ATP to target
45
anionic exchange column
binds anions (
46
EM spectrum (highest to lowest wavelength)
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
47
melting point and protein folding
Tm is the temperature at which 50% of the molecules are denatured or the fraction folded is 0.5
48
how many H bond donours/acceptors do each a.a. have?
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
49
reducing sugar
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
50
specific activity and yield
specific activity (units/mg) represents a measure of solution purity, the activity units themselves provide the best measurement of yield
51
ternary complex
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
52
which peptide would be more likely to make a covalently bonded dimer
LOOK FOR CYSTEINE\< indicates that disulfide-link could occur
53
which alcohol cannot be readily oxidized
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
54
E vs Z
e: pririoty groups on opposite side of double bond
55
london dispersion
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
56
amber codon
stop codon
57
amine
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
amide
also, the conjugate base of an amine is also called an "amide"
i.e. R-NH-
"amide has got Carbonyl by its side"
59
Imine
intimidating, cause it has a double bond... lol
60
carbamate
get all your mates
carbonyl, oxygen, and nitrogen
61
NaBH4
reduces ketones/aaldehydes to alcohols
62
lactone
class of cyclic organic esters, often formed by reaction of carboxylic acid with hydroxyl group or halogen in same molecule.
63
lactam
this is beta lactam
cyclic amide
64
ester vs ether
65
ketone
66
aldehyde
67
ping pong
aka double displacement reaction. one product is formed and released before second substrate binds
68
buffer capacity
A buffer has a buffering capacity that is ±1 pH unit away from the pKa
69
refraction
light passes through the interface between optical media with different indices of refraction
n=c/v
70
diffraction
71
polarization
electric field vectors in same direction
72
definition of current
charge/time
Q/t
73
meso compound
contains chiral centres but is overall achiral
74
amino acids R/S
almost all are S
except cysteine is R
glycine is achiral
75
gel electrophoresis
separates based on charge, size, shape
## Footnote
**size:** smallest moves through quickest
**charge:** negatively charged travel toward positive end (anode) quicker
**Shape:** more aerodynamic moves faster
76
SDS-page
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
reducing SDS-Page
SDS denatures protein except at places with disulfide bonds. in order to break these, need to use reducing SDS-page
78
native-page
no SDS/reducing agent. gel is non-denaturing. protein remains in native shape
79
when to use different types of distillation
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
fingerprint region of IR spectrum
special range unique to certain compound. spans the region of wavenumbers 1500 to 500 cm-1
81
amino acid configuration
plus 1 letter codes
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
peptide bond formation
condensation (hehydration) reaction with Nu amino group attacking electrophlic carbonyl. peptide bonds broken via hydrolysis
83
D and L forms of same sugar are
enantiomers
84
diasteromer
differ at at least 1, but not all, chiral centres
includes:
epimer: differ at 1 centre
anomer: differ at anomeric C
85
fructose
86
sugars: α- or β-conformation
* 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
glucose structure
OH
H
OH
OH
88
galactose structure
OH
H
H
OH
89
mannose structure
H
H
OH
OH
think: mannose has 2 of the same letters. so its order going down the right is 2 letters repeating
90
common disaccharides
sucrose (glucose-α1,2-fructose)
lactose (galactose-β-1,4-glucose)
maltose (glucose-α-1,4-glucose)
91
nucleoside vs nucleotide
nucleoside: 5C sugar bound to a nitrogenous base
nucleotides: nucleoside bound to 1 to 3 phosphate
92
telomeres
end of chromosome. contain high GC content to prevent unraveling
93
centromers
located in the middle of chromosonmes, hold sister chromatids together, until separated during anaphase of mitosis. also contain high GC content
94
periodic trend summary
95
which elements are more stable with fewer than 8 e-
H (2)
He (2)
Li (2)
Be (4)
B (6)
96
formal charge
FC= #valence - 1/2 bonding e - # lone pair
97
complex ion (coordination compound)
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
combustion rxn
fuel, such as hydrocarbon, reacted with oxidant (i.e. O) to produce oxide and water
99
isothermal
adiabatic
isobaric
isovolumetric (isochoric)
isothermal: T remains constant
adiabatic: no heat exchange
isobaric: pressure constant
isovolumetric (isochoric): volume constant
100
state fxn
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
standard heat of reaction
∆H° rxn = (sum of ∆H° f of products) – (sum of ∆H° f of reactants)
102
Hess' Law
enthalpies of rxns are additive
reverse rxn has same magnitude but opposite sign
103
relationship of atm, mmHg, torr, Pa
1 atm = 760 mmHg = 760 torr = 100,000 Pa
104
Colligative properties:
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
Boyle's Law
PV=k
P1V1=P2V2
106
Charles Law
V/T = k or
V1/T1= V2/T2
107
Dalton’s law of partial pressures:
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
average molecular speed
109
Graham's Law of diffusion and effusion, equation
110
half-eq point of titration
The halfequivalence point defines pH = pKa
111
Henderson Hasselbach
pH= pKa + log [A-]/[Ha]
112
113
Standard reduction potential and Gibbs free energy equations for half-cells
emf = E˚ red, cathode – E˚ red, anode
∆G = –nFEcell
114
SN1 vs SN2
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
factors which determine nucleophilicty
**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
aprotic vs protic solvents and nucleophilicty
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
Leaving groups
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
conformational isomers
differ by rotation around a single (sigma) bond
119
staggered vs eclipsed conformations
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
enantiomers vs diasteromers (light)
121
how are alcohols synthesized
addition H2O to double bonds
SN1/SN2 rxns
reduction casrboxylic acids, aldehydes, ketones, esters
(aldehydes/ketones with NaBH4 or LiALH4, esters with LiAlH4)
122
how to look for ox/red in an organic rxn
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
good oxidizing agent
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
good reducing agents
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
PCC
oxidizes a primary alcohol into an aldehyde
126
Jones's Reagent
convert _secondary alcohols into carboxylic acid_s (alkali dichromatic salt and KMnO4 will as well)
JSC (junior science club, ***j**ones converts **s**econdary alc into **C**.A.*)
PPA (**p**rimary **P**PC, **A** is first letter)
127
mesylates/tosylates
Alcohols can be converted to mesylates or tosylates to make them better leaving groups for nucleophilic substitution reactions
128
how are alcohols used as protecting groups
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
acidity of phenol
pka approx 10
130
quinones/hydroxyquinones
treatment phenol with oxidizing agents produces quinones, which can be further oxidized into hydroxyquinones
131
ubiquinone
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
how are aldehydes synthesized
oxidation primary alcohols
ozonolysis alkenes
133
aldol condensation
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
carboxylic acids
pka, bp
pka = 4.5 (resonance stablized conjugate base)
BP higher than alcohol bc can form 2 H bonds
135
synthesizing carboxylic acids
oxidation primary alcohols with KMnO4
Hydrolysis of nitriles
136
how to form soap with C.A.
reacting C.A. with NaOH, arrange in micelles
137
carboxylic acid derivatives- rank based on descending reactivity
1. acyl halides
2. anhydrides- dehydration of 2 carboxylic acids
3. carboxlyc acids and esters
4. amides (least reactive)
138
strecker synthesis
reagents: Aldehyde, NH4Cl, KCN
**AMINO ACID SYNTHESIS**
strecker
A, N, K
SANK: Strecker sank the ship
139
Gabriel (Malonic-Ester) synthesis
Reagents: potassium phthalimide, diethyl bromomalonate
reaction in presence of base and alkyl halide
140
pyrophosphate
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
types of chromotography: which have NP mobile phase
