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137 Cards in this Set

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Poiseulle’s Law
Q = (pi * r^4 * ∆Pressure) / (8 * viscosity * length)
conversion from liter
1 L = 1 quart
1 L = (1000 gm)/(18 gm/mole) = 55.5 moles/L
dielectric effect
a shielding effect where a slightly (-) charge is neutralized by a (+) charge due to polarity
If you decrease order (increase entropy), what happens to energy change?
-decreasing order is equivalent to going from high energy to low energy (spontaneous reaction)
-reactions want less order
Gibbs free energy (∆G)
∆G = ∆H (heat) – T∆S (randomness)
osmotic pressure
osP = ([conc] * R * T) / (MW)
T is in kelvins (K = 273 + C)
Keq
Keq = [products] / [reactants]
pK & Keq of lactic acid
Keq = 1.38 * 10^-4
pK = 3.86
pK & Keq of ammonia
Keq = 5.62 *10^-10
pK = 9.25
Henderson-Hasselbalch Equation
pH = pK + log [A-]/[HA] (conj. base/conj. acid)
pK’s of phosphoric acid (H3PO4)
pK1 = 2.1
pK2 = 7.2
pK3 = 10.0
pH of the body
pH = 7.4
*when the cell metabolizes products, the body’s pH decreases and becomes acidic
*INC in CO2 levels decreases pH and causes the body to become acidic
pK of carbonic acid
pK = 6.1
CO2 + H20  H2CO3  H+ + HCO3-
essential amino acids
F, V, T, W, I, M, H, R, L, K
polar amino acids
G, S, T, C, Y, D, N, E, Q, H, R, K
nonpolar amino acids
A, V, L, I, M, F, W, P
ordering of molecules for determining chirality
1) COOH
2) NH3
3) R
4) H
have 1 and 3 at up and down, away and have 2 and 4 at left and right, towards
pK’s of amino acids other than acidic and basic ones
pK = 2.5 (for COOH)
pK = 9.5 (for NH2)
pK for acidic amino acids (ASP + GLU)
pK = 2.5 (for COOH)
pK = 4.5 (for acidic proton)
pK = 9.5 (for NH2)
pK for basic amino acid Lys
pK = 2.5 (for COOH)
pK = 9.5 (for NH2)
pK = 10.5 (for basic proton)
pK for basic amino acid Arg
pK = 2.5 (for COOH)
pK = 9.5 (for NH2)
pK = 12.5 (for basic proton)
pK for basic amino acid His
pK = 2.5 (for COOH)
pK = 6.0 (for basic proton)
pK = 9.5 (for NH2)
molecule used for cation exchange chromatography
CMC-carboxy methyl cellulose, (-) charge
molecule used for anion exchange chromatography
DEAE-diethyl amino ethane, (+) charge
how to detect whether or not an amino acid is a primary or secondary amine
use ninhydrin
primary amines -> purple
secondary amines -> yellow
beer-lambert law
used in detection spectroscopy
abs = a (std absorbance) * c (concentration) * l (length of cuvette)

abs. detects the density of a compound (think iced tea and amount of sugar)

blood sugar levels determined using this
conditions for obtaining aa residues
6 N HCL, 100 C, 24 hr
properties of peptide bonds
1. short
2. planar
3. trigonal
4. share electrons
5. don’t rotate -> trans in peptides
6. covalent

partial double bond character
(has 1.32 angstrom length)

C-N 1.49
C=N 1.27
Prosthetic Groups (of protein's primary structure)
Heavy Metals: Fe, Zn, Cd, Hg, Pb
when trying to estimate MW
1. find gms of Fe, divide by MW (55.5) to give moles of Fe in protein
2. 1 gm protein/# of moles of Fe in protein = min. MW
average aa MW
120 gm/mol
to find est. number of aa in a protein take min MW and divide by 120 gm/mol
Edman’s Reagent
PITC (phenyl iso thio cyanate) interacts with primary amines (thus the amino end of a protein, may also be lysine or tyrosine) and cleaves off one aa at that end, can do 40-50 residues in sequence
Sanger’s Reagent
DNFB (dinitro fluoro benzene), hydrolyzes entire peptide chain so get individual aa’s but not order, gives the aa on the NH2 end
Dansylation
dansyl chloride, has fluoresces, destroys other peptide bonds
aminopeptidase
chews peptide from amino end down, gives new sample every 15 secs
hydrazine
tags each aa except for the COOH terminal aa, so tells what aa is on the COOH end, breaks every peptide bond
trypsin and cleavage of aa’s
cleaves basic aa’s (lys, arg)
chymotrypsin and cleavage of aa’s
cleaves aromatic aa’s (Phe, Tyr, Trp), sometimes His
cyanogen bromide (CNBr) and cleavage of aa’s
cleaves methionine
To separate aa’s based on solubility/hydrophobicity:
TLC, reverse phase
To separate aa’s based on charge:
ion exchange
To separate aa’s based on size:
gel exclusion, ultracentrifugation, dialysis, PAGE
to separate aa’s based on function
affinity purification
reagent used to denature a protein
SDS (sodium dodecyl sulfate), a detergent that stretches protein lengthwise), adds (-) charge to every 2 aa's
sedimentation rate
S = MWt (1 – (volume*density)) / (friction = 6 * pi * viscosity * strokes radius)
s is dependent on mass and shape
what determines where R groups are relative to each other on an aa peptide
1. hydrophobic interactions (water, entropic effect) REPULSION (the primary driving force, all others are stabilizing forces)
2. ionic interactions (repulsion/ attraction) STABILIZATION
3. van der Waals forces (steric hinderance) REPULSION (bec. of space)
4. H-bonding (sharing of H+ between two electronegative atoms) STABILIZATION
alpha helix features
right handed, driving force is hydrophobicity, stabilizing fore is H-bonds parallel to axis, found in wool, hair, horns, hooves, fingernails, 5.4 Angstroms/turn, 3.6 aa/turn

*long rigid rods with not much flexibility
alpha helical breakers
1. run of negative charges on aa’s close to each other on folded alpha helix, causes repulsion
2. proline, causes a loss in twisting ability, may lead to beta turns
beta structure features
1. rich in alanines
2. extended
3. antiparallel or parallel
4. perpendicular H-bonds
5. forms sheets
6. found in silk

1.5 aa's per turn
beta turn
can turn anywhere, not just Beta sheets, can be alpha helical breakers, a proline, then a small R group (glycine), then a hydrophilic
structure of collagen
glycine, X (proline), Y, glycine, X (proline), Y…
perpendicular H-bonds
¼ stagger in bone due to collagen
has a 700 angstrom nucleation site (for hydroxyapatite (650 A), caused by hydrophobic interactions), and 2800 angstrom for collagen

spontaneously forms (esp. with vitamin A and physiological salts)
mercaptoethanol
CH3CH2SH used to reduce disulfide bonds to SH
quaternary structure
all interactions between multiple subunits are non-covalent (hydrophobic patches, ionic links or H-bonds)
anabolic vs. catabolic
anabolic (synthesis) or catabolic (degradation), cannot be used to determine the spontaneity of a reaction
gibbs free energy and spontaneity
∆G = (-) is spontaneous
∆G = 0 is at equilibrium
∆G = (+) is non-spontaneous
Standard State Conditions for ∆G
1 mole/L each reactant and product
fixed temperature
pH = 7.0
[H2O] = 55.5 moles/L
∆G°’ is inversely related to – Keq
∆G°’ equation (free energy at standard state)
∆G°’ = -RT lnKeq = cal/mol
where R = 1.987 cal/(mole K)
T = 298 K (room temperature
ln = 2.303 * log
or ∆G°’ = -1364 log Keq
actual free energy
∆G = ∆G°’ + RT ln ([P]/[R])
∆G°’ for glucose
∆G°’ = -4000 cal/gm
* 180 gm/mole
-720,000 cal/mole
Keq = 10^528
strategies that limit the ∆G°’ for glucose
1. operating close to equilibrium (DEC ∆G°’ for glucose)
2. stepwise processes (gradual breakdown of glucoses 6 carbons)
3. coupling reactions
4. high energy barriers
energy in esters
(-3 Kcal/mole), forms acid and alcohol (or amine if breaking down amide)
energy in thiol-esters
-6 to -8 Kcal/mole
energy in anhydrides
-7 to -10 Kcal/mole, ex: ATP
what accounts for the difference in energy between different compounds
entropic forces
1. 1 reactant  2 products (INC in entropy)
2. resonance stabilization of products (compared to reactants)
a. INC resonance, INC entropy, ~50% of energy
electronic forces
3. charge repulsion in ATP vs. ADP
4. charge separation in ATP vs. ADP
energy in guanidinum phosphates
-10 Kcal/mole
Creatine
made from Arginine, composed of Gly, Met, Arg
energy in enoyl phosphate
-14 Kcal/mole, lots of energy present because of presence of tautomer form (a eneol form and a keto form (of which is favored energetically))
oxidation states of C
methane  methanol  formaldehyde  formic acid  carbon dioxide
tightly ordered ---------------------------------------------------------> loosest
reduced -----------------------------------------------------------------> oxidized
energy in carbohydrates vs. fats
carbs have 4 Kcal/mole, have more partially oxidized carbons
fats have 9 Kcal/mole, have far more reduced C’s, more constrained, more energy
energy in NADH or FADH
-15 Kcal/mole
velocity of a reaction
dependent on the activation energy, v = k [R]
Keq in terms of kinetics and thermodynamics
Keq = [P]/[R] = kf/kr
velocity of a reaction (Michaelis-Menton equation)
v = vmax * ([S]) / (Km + [S])
max. velocity of a reaction
vmax = k3 * [Et]
Km =
Km = (k2 + k3) / (k1)
inverse of affinity
k2/k1
turnover term
k3/k1
to determine enzyme specificity or enzyme preference
Vmax/Km
Lineweaver-Burk eq
1/v = (Km/Vmax) * (1/[S]) + (1/Vmax)
x-intercept of Lineweaver-Burk plot
-1/Km
y-intercept of Lineweaver-Burk plot
1/Vmax
slope of Lineweaver-Burk plot
Km/Vmax
irreversible inhibitors
heavy metals and –SH groups (penicillin, Pb, Hg), when add to reaction, DEC Vmax but no effect on Km, works by binding to cysteine

ex: aspirin, it acetylates proteins and forms esters
competitive inhibitor
binds to initial enzyme, reversible, same Vmax, different Km
non-competitive inhibitor
inhibitor can bind to enzyme or ES complex, same Km, DEC Vmax, looks like irreversible, tell difference through dialysis and see if inhibitor comes off, inhibitor binds to different spot on enzyme from substrate
uncompetitive inhibitor
inhibitor binds to ES complex, DEC Km and Vmax
6 classes of enzymes
OTHLIL (oxido-reductases, transferases, hydrolases, lyases, isomerases, ligases)
Modification of amino acids (post-translational): hydroxylation
proline-found in urine during bone remodeling, important in collagen, hydroxylate C 3 or 4

lysine-hydroxylate C 4 or 5
Modification of amino acids (post-translational): esterifcation
1. acetylation-adding acetic acid
2. phosphorylation

aa's involved:
serine, threonine, tyrosine
what form of amino acid is found in humans?
L-form, it evolved the right turn alpha helix
racemization and example of such:
racemization-switching from the D to L form

EX: aspartic acid, racemizes @ 0.14%/year
Solvents used in TLC
polar: water
nonpolar: isopropanol, butanol, phenol
carboxypeptidase
similar to aminopeptidase but starts at the carboxy end and gives sample every 15 secs.
Piezo Electric Effect
found in inorganic systems, where crystals orient themselves perpendicular to a force
random coils
random in the sense that they are unpredictable, aa's in random coils are not rich in hydrophobics but have hydrophilics to react with the aqueous solution
Affinson's Experiment
looked at ribonuclease (which has 8 cysteines or 4 disulfide bonds) and determined the likely hood that those bonds would rejoin

expected: 1% chance they rejoined correctly and had activity

observed: 80% retained activity, hydrophobic forces drive the bonds together
creatinine
the spontaneous folding of creatine's COOH and NH2 end, is excreted through urine, detected during muscular damage
oxidation and reduction forms of atoms
"ic" oxidized
"ous" reduced
turnover constant/turnover number
k3
slowest step in the michalis-mentin equation
v = k3 [E*S] complex
First, Zero, and Mixed order reactions
first-low [S] concentrations
zero-high [S] concentrations
mixed-everywhere else
pseudo-first order reaction
is second order, but if hold [E] constant (replenish E during the reaction), makes it appear to be 1st order
ADH
has a higher affinity for ethanol (which has a product of acetaldehyde, which is safe) as opposed to methanol (which has a product of formaldehyde, which is toxic)
oxido-reductases
EX: ADH, LDH, oxygenase

it oxidizes or reduces a compound
oxygenase
EX: phenylalanine hydroxylase, turns phenylalanine into tyrosine
PKU
lack PH to make tyrosine, therefore there is an excess of phenylalanine in the body
transferases
all types of kinases, transfer a group from one compound to another

ex: creatine kinase, pyrophosphorylase
hydroxylases
uses H2O to break or form a bond

ex: peptidases, carbohydrase, nuclease, lipase, phosphotases
lyases
use H20 to break or form a double bond

ex: citric acid, fatty acid metabolism
isomerases
switch a group within a compound

mutases-internal transferase
epimerases-switch configuartion about a single atom
ligases
join atoms together, uses ATP
phosphatases
remove a PO4

ex: phosphoproteinphosphatase
pyrophosphorylases
break anhydride, form anhydride, used when you want to activate a sugar, release a pyrophosphate
pyrophosphatases
used to break down PPi into 2 PO4, makes sure pyrophosphorylase goes from left to right
phosphorylases
adds PO4 to bond and breaks a bond

ex: glycogen phosphorylase
How do enzymes work? How do they enhance the rate of a reaction?
1. entropic effects
2. strain
3. acid-base catalysis
4. covalent catalysis
entropic effects for enhancing reaction rate
ex: carbonic anhydrase

INC the likelihood that molecules will collide, affects the collicsion, proximity, orientation and orbital steering of reactants, has a 10-100X INC in rxn velocity
strain
ex: glucokinase, lysozyme

induced fit, causes a change in the enzyme or substrate that INC the likelihood of reaction, 10^4-10^5 INC`
acid-base catalysis
ex: lysozymes, carboxypeptidase, carbonic anhydrase

used to stabilize the charge of reactants, use Zn as cofactor that stabilizes the protein to break bond, INC 10^4-10^5
covalent catalysis (reversible)
ex: serine protease, chymotrypsin

have hydrophobic pocket, have covalent ES complex, INC rate by 10^4-10^5
covalent irreversible
zymogens, prohormones, collagen

make substances in active form and cleave or assemble when needed or in proper place
lactalbumin
protein-protein interactions, acts ass allosteric effector of GT to change configuration of GT

pituitary->prolactin->mammary tissue->lactalbumin + GT->UDP-Glu + Gal->lactose
protein kinase A
2 subunits: 2 catalitic and 2 regulatory, cAMP bind to regulatory to free active site on catalitic
creatine kinase
dimer

skeletal muscle-M-M, 95% of CK in serum
heart muscle-M-B, 2-3%, 10-12 in MI
brain tissue-B-B, <1%
LDH
pyruvate <=> lactate

heart-H-H-H-H
blood-H-H-H-L
liver/skeletal muscle-L-L-L-L

heart LDH has higher vmax/km for pyruvate, activated by pyruvate while L4 version is inhibited by high pyruvate

PYR + LDH -> PYR-LDH -> LACT + LDH
Hexokinase
HK, found in all tissues except liver, has a higher affinity for G-6-P than GK
Glucokinase
GK, found in liver, has a lower affinity for G6P
HK in brain
20* more than in other tissues
resting glucose levels
5*10^-3 M/L
GAVLIMP
0, 1, 3, 4, 4, 4, 4
FYW
ring, ring OH, 5 then ring
STC
CH2-OH, CH3-CH-OH, CH2-SH
KRH
4CH2 NH3+, 3CH2-N-C-N2, CH2-5-ring
DENQ
CH2COOH, CH2CH2COOH, CH2CONH2, CH2CH2CONH2
What is the normal bicarbonate to CO2 ratio ([HCO3-] / 0.03 x pCO2) at physiological pH?
24/(0.03*pCO2)

pCO2 = 40
The insulin receptor:
Undergoes autophosphorylation and Acquires kinase activity