Biochem Exam 1

Front 1

Poiseulle’s Law

Back 1

Q = (pi * r^4 * ∆Pressure) / (8 * viscosity * length)

Front 2

conversion from liter

Back 2

1 L = 1 quart
1 L = (1000 gm)/(18 gm/mole) = 55.5 moles/L

Front 3

dielectric effect

Back 3

a shielding effect where a slightly (-) charge is neutralized by a (+) charge due to polarity

Front 4

If you decrease order (increase entropy), what happens to energy change?

Back 4

-decreasing order is equivalent to going from high energy to low energy (spontaneous reaction)
-reactions want less order

Front 5

Gibbs free energy (∆G)

Back 5

∆G = ∆H (heat) – T∆S (randomness)

Front 6

osmotic pressure

Back 6

osP = ([conc] * R * T) / (MW)
T is in kelvins (K = 273 + C)

Front 7

Keq

Back 7

Keq = [products] / [reactants]

Front 8

pK & Keq of lactic acid

Back 8

Keq = 1.38 * 10^-4
pK = 3.86

Front 9

pK & Keq of ammonia

Back 9

Keq = 5.62 *10^-10
pK = 9.25

Front 10

Henderson-Hasselbalch Equation

Back 10

pH = pK + log [A-]/[HA] (conj. base/conj. acid)

Front 11

pK’s of phosphoric acid (H3PO4)

Back 11

pK1 = 2.1
pK2 = 7.2
pK3 = 10.0

Front 12

pH of the body

Back 12

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

Front 13

pK of carbonic acid

Back 13

pK = 6.1
CO2 + H20  H2CO3  H+ + HCO3-

Front 14

essential amino acids

Back 14

F, V, T, W, I, M, H, R, L, K

Front 15

polar amino acids

Back 15

G, S, T, C, Y, D, N, E, Q, H, R, K

Front 16

nonpolar amino acids

Back 16

A, V, L, I, M, F, W, P

Front 17

ordering of molecules for determining chirality

Back 17

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

Front 18

pK’s of amino acids other than acidic and basic ones

Back 18

pK = 2.5 (for COOH)
pK = 9.5 (for NH2)

Front 19

pK for acidic amino acids (ASP + GLU)

Back 19

pK = 2.5 (for COOH)
pK = 4.5 (for acidic proton)
pK = 9.5 (for NH2)

Front 20

pK for basic amino acid Lys

Back 20

pK = 2.5 (for COOH)
pK = 9.5 (for NH2)
pK = 10.5 (for basic proton)

Front 21

pK for basic amino acid Arg

Back 21

pK = 2.5 (for COOH)
pK = 9.5 (for NH2)
pK = 12.5 (for basic proton)

Front 22

pK for basic amino acid His

Back 22

pK = 2.5 (for COOH)
pK = 6.0 (for basic proton)
pK = 9.5 (for NH2)

Front 23

molecule used for cation exchange chromatography

Back 23

CMC-carboxy methyl cellulose, (-) charge

Front 24

molecule used for anion exchange chromatography

Back 24

DEAE-diethyl amino ethane, (+) charge

Front 25

how to detect whether or not an amino acid is a primary or secondary amine

Back 25

use ninhydrin
primary amines -> purple
secondary amines -> yellow

Front 26

beer-lambert law

Back 26

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

Front 27

conditions for obtaining aa residues

Back 27

6 N HCL, 100 C, 24 hr

Front 28

properties of peptide bonds

Back 28

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

Front 29

Prosthetic Groups (of protein's primary structure)

Back 29

Heavy Metals: Fe, Zn, Cd, Hg, Pb

Front 30

when trying to estimate MW

Back 30

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

Front 31

average aa MW

Back 31

120 gm/mol
to find est. number of aa in a protein take min MW and divide by 120 gm/mol

Front 32

Edman’s Reagent

Back 32

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

Front 33

Sanger’s Reagent

Back 33

DNFB (dinitro fluoro benzene), hydrolyzes entire peptide chain so get individual aa’s but not order, gives the aa on the NH2 end

Front 34

Dansylation

Back 34

dansyl chloride, has fluoresces, destroys other peptide bonds

Front 35

aminopeptidase

Back 35

chews peptide from amino end down, gives new sample every 15 secs

Front 36

hydrazine

Back 36

tags each aa except for the COOH terminal aa, so tells what aa is on the COOH end, breaks every peptide bond

Front 37

trypsin and cleavage of aa’s

Back 37

cleaves basic aa’s (lys, arg)

Front 38

chymotrypsin and cleavage of aa’s

Back 38

cleaves aromatic aa’s (Phe, Tyr, Trp), sometimes His

Front 39

cyanogen bromide (CNBr) and cleavage of aa’s

Back 39

cleaves methionine

Front 40

To separate aa’s based on solubility/hydrophobicity:

Back 40

TLC, reverse phase

Front 41

To separate aa’s based on charge:

Back 41

ion exchange

Front 42

To separate aa’s based on size:

Back 42

gel exclusion, ultracentrifugation, dialysis, PAGE

Front 43

to separate aa’s based on function

Back 43

affinity purification

Front 44

reagent used to denature a protein

Back 44

SDS (sodium dodecyl sulfate), a detergent that stretches protein lengthwise), adds (-) charge to every 2 aa's

Front 45

sedimentation rate

Back 45

S = MWt (1 – (volume*density)) / (friction = 6 * pi * viscosity * strokes radius)
s is dependent on mass and shape

Front 46

what determines where R groups are relative to each other on an aa peptide

Back 46

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

Front 47

alpha helix features

Back 47

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

Front 48

alpha helical breakers

Back 48

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

Front 49

beta structure features

Back 49

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

Front 50

beta turn

Back 50

can turn anywhere, not just Beta sheets, can be alpha helical breakers, a proline, then a small R group (glycine), then a hydrophilic

Front 51

structure of collagen

Back 51

glycine, X (proline), Y, glycine, X (proline), Y…
perpendicular H-bonds

Front 52

¼ stagger in bone due to collagen

Back 52

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)

Front 53

mercaptoethanol

Back 53

CH3CH2SH used to reduce disulfide bonds to SH

Front 54

quaternary structure

Back 54

all interactions between multiple subunits are non-covalent (hydrophobic patches, ionic links or H-bonds)

Front 55

anabolic vs. catabolic

Back 55

anabolic (synthesis) or catabolic (degradation), cannot be used to determine the spontaneity of a reaction

Front 56

gibbs free energy and spontaneity

Back 56

∆G = (-) is spontaneous
∆G = 0 is at equilibrium
∆G = (+) is non-spontaneous

Front 57

Standard State Conditions for ∆G

Back 57

1 mole/L each reactant and product
fixed temperature
pH = 7.0
[H2O] = 55.5 moles/L
∆G°’ is inversely related to – Keq

Front 58

∆G°’ equation (free energy at standard state)

Back 58

∆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

Front 59

actual free energy

Back 59

∆G = ∆G°’ + RT ln ([P]/[R])

Front 60

∆G°’ for glucose

Back 60

∆G°’ = -4000 cal/gm
* 180 gm/mole
-720,000 cal/mole
Keq = 10^528

Front 61

strategies that limit the ∆G°’ for glucose

Back 61

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

Front 62

energy in esters

Back 62

(-3 Kcal/mole), forms acid and alcohol (or amine if breaking down amide)

Front 63

energy in thiol-esters

Back 63

-6 to -8 Kcal/mole

Front 64

energy in anhydrides

Back 64

-7 to -10 Kcal/mole, ex: ATP

Front 65

what accounts for the difference in energy between different compounds

Back 65

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

Front 66

energy in guanidinum phosphates

Back 66

-10 Kcal/mole

Front 67

Creatine

Back 67

made from Arginine, composed of Gly, Met, Arg

Front 68

energy in enoyl phosphate

Back 68

-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))

Front 69

oxidation states of C

Back 69

methane  methanol  formaldehyde  formic acid  carbon dioxide
tightly ordered ---------------------------------------------------------> loosest
reduced -----------------------------------------------------------------> oxidized

Front 70

energy in carbohydrates vs. fats

Back 70

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

Front 71

energy in NADH or FADH

Back 71

-15 Kcal/mole

Front 72

velocity of a reaction

Back 72

dependent on the activation energy, v = k [R]

Front 73

Keq in terms of kinetics and thermodynamics

Back 73

Keq = [P]/[R] = kf/kr

Front 74

velocity of a reaction (Michaelis-Menton equation)

Back 74

v = vmax * ([S]) / (Km + [S])

Front 75

max. velocity of a reaction

Back 75

vmax = k3 * [Et]

Front 76

Km =

Back 76

Km = (k2 + k3) / (k1)

Front 77

inverse of affinity

Back 77

k2/k1

Front 78

turnover term

Back 78

k3/k1

Front 79

to determine enzyme specificity or enzyme preference

Back 79

Vmax/Km

Front 80

Lineweaver-Burk eq

Back 80

1/v = (Km/Vmax) * (1/[S]) + (1/Vmax)

Front 81

x-intercept of Lineweaver-Burk plot

Back 81

-1/Km

Front 82

y-intercept of Lineweaver-Burk plot

Back 82

1/Vmax

Front 83

slope of Lineweaver-Burk plot

Back 83

Km/Vmax

Front 84

irreversible inhibitors

Back 84

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

Front 85

competitive inhibitor

Back 85

binds to initial enzyme, reversible, same Vmax, different Km

Front 86

non-competitive inhibitor

Back 86

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

Front 87

uncompetitive inhibitor

Back 87

inhibitor binds to ES complex, DEC Km and Vmax

Front 88

6 classes of enzymes

Back 88

OTHLIL (oxido-reductases, transferases, hydrolases, lyases, isomerases, ligases)

Front 89

Modification of amino acids (post-translational): hydroxylation

Back 89

proline-found in urine during bone remodeling, important in collagen, hydroxylate C 3 or 4

lysine-hydroxylate C 4 or 5

Front 90

Modification of amino acids (post-translational): esterifcation

Back 90

1. acetylation-adding acetic acid
2. phosphorylation

aa's involved:
serine, threonine, tyrosine

Front 91

what form of amino acid is found in humans?

Back 91

L-form, it evolved the right turn alpha helix

Front 92

racemization and example of such:

Back 92

racemization-switching from the D to L form

EX: aspartic acid, racemizes @ 0.14%/year

Front 93

Solvents used in TLC

Back 93

polar: water
nonpolar: isopropanol, butanol, phenol

Front 94

carboxypeptidase

Back 94

similar to aminopeptidase but starts at the carboxy end and gives sample every 15 secs.

Front 95

Piezo Electric Effect

Back 95

found in inorganic systems, where crystals orient themselves perpendicular to a force

Front 96

random coils

Back 96

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

Front 97

Affinson's Experiment

Back 97

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

Front 98

creatinine

Back 98

the spontaneous folding of creatine's COOH and NH2 end, is excreted through urine, detected during muscular damage

Front 99

oxidation and reduction forms of atoms

Back 99

"ic" oxidized
"ous" reduced

Front 100

turnover constant/turnover number

Back 100

k3

Front 101

slowest step in the michalis-mentin equation

Back 101

v = k3 [E*S] complex

Front 102

First, Zero, and Mixed order reactions

Back 102

first-low [S] concentrations
zero-high [S] concentrations
mixed-everywhere else

Front 103

pseudo-first order reaction

Back 103

is second order, but if hold [E] constant (replenish E during the reaction), makes it appear to be 1st order

Front 104

ADH

Back 104

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)

Front 105

oxido-reductases

Back 105

EX: ADH, LDH, oxygenase

it oxidizes or reduces a compound

Front 106

oxygenase

Back 106

EX: phenylalanine hydroxylase, turns phenylalanine into tyrosine

Front 107

PKU

Back 107

lack PH to make tyrosine, therefore there is an excess of phenylalanine in the body

Front 108

transferases

Back 108

all types of kinases, transfer a group from one compound to another

ex: creatine kinase, pyrophosphorylase

Front 109

hydroxylases

Back 109

uses H2O to break or form a bond

ex: peptidases, carbohydrase, nuclease, lipase, phosphotases

Front 110

lyases

Back 110

use H20 to break or form a double bond

ex: citric acid, fatty acid metabolism

Front 111

isomerases

Back 111

switch a group within a compound

mutases-internal transferase
epimerases-switch configuartion about a single atom

Front 112

ligases

Back 112

join atoms together, uses ATP

Front 113

phosphatases

Back 113

remove a PO4

ex: phosphoproteinphosphatase

Front 114

pyrophosphorylases

Back 114

break anhydride, form anhydride, used when you want to activate a sugar, release a pyrophosphate

Front 115

pyrophosphatases

Back 115

used to break down PPi into 2 PO4, makes sure pyrophosphorylase goes from left to right

Front 116

phosphorylases

Back 116

adds PO4 to bond and breaks a bond

ex: glycogen phosphorylase

Front 117

How do enzymes work? How do they enhance the rate of a reaction?

Back 117

1. entropic effects
2. strain
3. acid-base catalysis
4. covalent catalysis

Front 118

entropic effects for enhancing reaction rate

Back 118

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

Front 119

strain

Back 119

ex: glucokinase, lysozyme

induced fit, causes a change in the enzyme or substrate that INC the likelihood of reaction, 10^4-10^5 INC`

Front 120

acid-base catalysis

Back 120

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

Front 121

covalent catalysis (reversible)

Back 121

ex: serine protease, chymotrypsin

have hydrophobic pocket, have covalent ES complex, INC rate by 10^4-10^5

Front 122

covalent irreversible

Back 122

zymogens, prohormones, collagen

make substances in active form and cleave or assemble when needed or in proper place

Front 123

lactalbumin

Back 123

protein-protein interactions, acts ass allosteric effector of GT to change configuration of GT

pituitary->prolactin->mammary tissue->lactalbumin + GT->UDP-Glu + Gal->lactose

Front 124

protein kinase A

Back 124

2 subunits: 2 catalitic and 2 regulatory, cAMP bind to regulatory to free active site on catalitic

Front 125

creatine kinase

Back 125

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%

Front 126

LDH

Back 126

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

Front 127

Hexokinase

Back 127

HK, found in all tissues except liver, has a higher affinity for G-6-P than GK

Front 128

Glucokinase

Back 128

GK, found in liver, has a lower affinity for G6P

Front 129

HK in brain

Back 129

20* more than in other tissues

Front 130

resting glucose levels

Back 130

5*10^-3 M/L

Front 131

GAVLIMP

Back 131

0, 1, 3, 4, 4, 4, 4

Front 132

FYW

Back 132

ring, ring OH, 5 then ring

Front 133

STC

Back 133

CH2-OH, CH3-CH-OH, CH2-SH

Front 134

KRH

Back 134

4CH2 NH3+, 3CH2-N-C-N2, CH2-5-ring

Front 135

DENQ

Back 135

CH2COOH, CH2CH2COOH, CH2CONH2, CH2CH2CONH2

Front 136

What is the normal bicarbonate to CO2 ratio ([HCO3-] / 0.03 x pCO2) at physiological pH?

Back 136

24/(0.03*pCO2)

pCO2 = 40

Front 137

The insulin receptor:

Back 137

Undergoes autophosphorylation and Acquires kinase activity