C/P Flashcards
TLC
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
size exclusion chromatography
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
affinity chromatography
target molecule trapped on stationary phase, washed to remove unwanted. target protein is eluted off the solid phase in a purified state.
gas chromatography
mobile gas phase, stationary liquid phase. separation based on volatilities
important stretch frequencies (IR)
Carbonyl: 1700 cm-1 alkenes: 1650 cm-1 OH: 3600-3200 cm-1 CH: 2850-3300 cm-1
UV Spectroscopy
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)
IR spectroscopy
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
NMR Spectroscopy
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
degree of unsaturation
d= [2C + 2 - H]/2
Shielding and chemical shift
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.`
common HNMR chemical sift values
carboxylic acid: 10-12
aldehyde: 10
aromatic: 8
vinyl (Alkene): 6
RCHX: 3
alkyl: 1
carbon that has carbonyl next to it: 2.5
Gel electrophoresis
separate amino acids based on charge if pH > pI: NEGATIVE charge, move to + electrode if pH
Epimer
diasteromers that differ at single chiral centre
Benedict’s test
Benedict’s reagent = CU2+ any sugar that can be oxidized by this reagent is a reducing sugar, because it reduces Cu2+ to Cu+
Grignard Reagent
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)
how are acetals formed
aldehydes react with alcohols in the presence of acid
Elastic Potential energy
1/2kx^2
effect of intermolecular attractions on potential and kinetic energies of particles
intermolecular attractions increase PE btw molecules, decreasing their KE
atomic size periodic trend
increases down a family and to the LEFT across a period
buoyant force equation
mg= pfluid* Vsubmerged *g m= pfluidVsub
Specific gravity
SG= pfluid/pwater (density of water = 1000 kg/m^3)
tautomers
isomers. structural difference is a shift of a H atom
where does beta-oxidation occur? FA synthesis?
- mito matrix 2. cytoplasm
what factor can change the equilibrium constant K
temperature only
when does total internal reflection occur
when angle of incidence is greater than critical angle
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)
uncompetitive inhibitor
decreases KM and decrease VMax
lineweaver burke plot
slope: Km/Vmax y intercept: 1/Vmax x intercept: 1/km
noncompetitive inhibition- type of mixed.
same Km lower Vmax same x intercept, different Y intercept decrease slope
during the exponential phase of bacterial growth, bacteria reproduce by:
binary fission (conjugation & transduction increases genetic diversity, but doesn’t affect population size.
oligonucleotide with a lower melting temp would have
few GC bonds because GC bp involve 3 H bonds, whereas AT involves only 2
effect of increased PTH
increased CA2+ levels
osmotic pressure
colligative property, depends only on the concentration of solute particles NOT their identity. depends on # of ions
amphoteric character of amino acids describes their ability to:
accept or donate a protein. act as acaid or base. forms dipolar ions
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)
BBB
formed by enddothelial cells connected by tight junctions
Faraday
1 mole of charge
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
byproduct of peptide formation, and its amu
H2O, 18 lol
The relative thermodynamic stability of isomeric organic compounds can be inferred from which type of experimental data?
heat of combustion, less heat = more stable
avogadro’s number
= number of atoms in a mol 6.02x10^23
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.
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.
transferase
i,e, kinase catalyze transfer of P from ATP to target
anionic exchange column
binds anions (
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
melting point and protein folding
Tm is the temperature at which 50% of the molecules are denatured or the fraction folded is 0.5
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
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
specific activity and yield
specific activity (units/mg) represents a measure of solution purity, the activity units themselves provide the best measurement of yield
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
which peptide would be more likely to make a covalently bonded dimer
LOOK FOR CYSTEINE< indicates that disulfide-link could occur
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
E vs Z
e: pririoty groups on opposite side of double bond
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
amber codon
stop codon
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”
amide
also, the conjugate base of an amine is also called an “amide”
i.e. R-NH-
“amide has got Carbonyl by its side”
Imine
intimidating, cause it has a double bond… lol
carbamate
get all your mates
carbonyl, oxygen, and nitrogen
NaBH4
reduces ketones/aaldehydes to alcohols
lactone
class of cyclic organic esters, often formed by reaction of carboxylic acid with hydroxyl group or halogen in same molecule.
lactam
this is beta lactam
cyclic amide
ester vs ether
ketone
aldehyde
ping pong
aka double displacement reaction. one product is formed and released before second substrate binds
buffer capacity
A buffer has a buffering capacity that is ±1 pH unit away from the pKa
refraction
light passes through the interface between optical media with different indices of refraction
n=c/v
diffraction
polarization
electric field vectors in same direction
definition of current
charge/time
Q/t
meso compound
contains chiral centres but is overall achiral
amino acids R/S
almost all are S
except cysteine is R
glycine is achiral
gel electrophoresis
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
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
reducing SDS-Page
SDS denatures protein except at places with disulfide bonds. in order to break these, need to use reducing SDS-page
native-page
no SDS/reducing agent. gel is non-denaturing. protein remains in native shape
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
fingerprint region of IR spectrum
special range unique to certain compound. spans the region of wavenumbers 1500 to 500 cm-1
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
peptide bond formation
condensation (hehydration) reaction with Nu amino group attacking electrophlic carbonyl. peptide bonds broken via hydrolysis
D and L forms of same sugar are
enantiomers
diasteromer
differ at at least 1, but not all, chiral centres
includes:
epimer: differ at 1 centre
anomer: differ at anomeric C
fructose
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.
glucose structure
OH
H
OH
OH
galactose structure
OH
H
H
OH
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
common disaccharides
sucrose (glucose-α1,2-fructose)
lactose (galactose-β-1,4-glucose)
maltose (glucose-α-1,4-glucose)
nucleoside vs nucleotide
nucleoside: 5C sugar bound to a nitrogenous base
nucleotides: nucleoside bound to 1 to 3 phosphate
telomeres
end of chromosome. contain high GC content to prevent unraveling
centromers
located in the middle of chromosonmes, hold sister chromatids together, until separated during anaphase of mitosis. also contain high GC content
periodic trend summary
which elements are more stable with fewer than 8 e-
H (2)
He (2)
Li (2)
Be (4)
B (6)
formal charge
FC= #valence - 1/2 bonding e - # lone pair
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
combustion rxn
fuel, such as hydrocarbon, reacted with oxidant (i.e. O) to produce oxide and water
isothermal
adiabatic
isobaric
isovolumetric (isochoric)
isothermal: T remains constant
adiabatic: no heat exchange
isobaric: pressure constant
isovolumetric (isochoric): volume constant
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
standard heat of reaction
∆H° rxn = (sum of ∆H° f of products) – (sum of ∆H° f of reactants)
Hess’ Law
enthalpies of rxns are additive
reverse rxn has same magnitude but opposite sign
relationship of atm, mmHg, torr, Pa
1 atm = 760 mmHg = 760 torr = 100,000 Pa
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.
Boyle’s Law
PV=k
P1V1=P2V2
Charles Law
V/T = k or
V1/T1= V2/T2
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)
average molecular speed
Graham’s Law of diffusion and effusion, equation
half-eq point of titration
The halfequivalence point defines pH = pKa
Henderson Hasselbach
pH= pKa + log [A-]/[Ha]
Standard reduction potential and Gibbs free energy equations for half-cells
emf = E˚ red, cathode – E˚ red, anode
∆G = –nFEcell
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
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
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
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
conformational isomers
differ by rotation around a single (sigma) bond
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
enantiomers vs diasteromers (light)
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)
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
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-).
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.
PCC
oxidizes a primary alcohol into an aldehyde
Jones’s Reagent
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)
mesylates/tosylates
Alcohols can be converted to mesylates or tosylates to make them better leaving groups for nucleophilic substitution reactions
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
acidity of phenol
pka approx 10
quinones/hydroxyquinones
treatment phenol with oxidizing agents produces quinones, which can be further oxidized into hydroxyquinones
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.
how are aldehydes synthesized
oxidation primary alcohols
ozonolysis alkenes
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
carboxylic acids
pka, bp
pka = 4.5 (resonance stablized conjugate base)
BP higher than alcohol bc can form 2 H bonds
synthesizing carboxylic acids
oxidation primary alcohols with KMnO4
Hydrolysis of nitriles
how to form soap with C.A.
reacting C.A. with NaOH, arrange in micelles
carboxylic acid derivatives- rank based on descending reactivity
- acyl halides
- anhydrides- dehydration of 2 carboxylic acids
- carboxlyc acids and esters
- amides (least reactive)
strecker synthesis
reagents: Aldehyde, NH4Cl, KCN
AMINO ACID SYNTHESIS
strecker
A, N, K
SANK: Strecker sank the ship
Gabriel (Malonic-Ester) synthesis
Reagents: potassium phthalimide, diethyl bromomalonate
reaction in presence of base and alkyl halide
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).
types of chromotography: which have NP mobile phase
