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The Exam:
This document at:
Friday Sept. 2
Will start at what time 8 AM
Will end at 10:55 AM, sharp
Format
No calculator needed.
Know scientific notation: 103 = 1000 10-3 = 0.001, 1/106 = 10-6
8 M- = 8 per molar
8 M-.sec- = 8 per molar per second
Closed notes/Closed book
Strongly weighted towards lectures.
Goal: Class average of 87%
Corrections to Homework + Key:
#9 E is also false
#14 Correct answer is E
#84 D is also a correct answer (chaperones DO affect folding rate)
#87: dissociation constant… not “equilibrium constant”
Ignore the “why doesn’t myoglobin form
sickle cell-like polymers?” question.
Cool Cool Logarithms:
Log(x/y) = Log x – Log y
Log (x . y) = Log x + Log y
Log xy = y . Log x
Same rules apply to ln
43.Since the equilibrium constant for peptide hydrolysis
is extremely favorable (in favor of bond cleavage), how can
it be that some proteins (like some of the proteins in the lens
of our eyes) are chemically stable for many years?
Concept of Kinetic Entrapment
57. Which of the following is NOT a
possible function of the proteolytic
processing of a protein?
a. plays roles in the process of
metastasis
b. plays roles in protecting protein
from hydrolysis
c. plays roles in peptide hormone
production
d. plays a role in zymogen
activation
e. plays roles in blood clotting
cascade
Homologs: Proteins that share significant sequence homology.
Orthologs: Different organisms, homologous, same function.
Paralogs: Same organism, homologous, but different functions.
91 Protein sequence motifs:
a. May be used as intracellular
organellar zip codes.
b. May be intimately linked to protein
function.
c. One example is the helix-loop-helix
motif.
d. May be signals to direct
posttranslational modification.
e. May serve as “signatures” which
allow membership in a particular
protein family to be predicted.
97. Which class of 1 substrate/1 inhibitor
kinetic scheme is most similar to the random
sequential scheme for a 2 substrate enzyme?
Random sequential reaction
Competitive Inhibition.
Random sequential reaction
Uncompetitive Inhibition
Random sequential reaction
Noncompetitive Inhibition
(Your text refers to this as “mixed” inhibition).
R
amino
NH2
C
acid
COOH
H
The free amino and carboxylic acid groups have pKa
NH3+
NH2
COOH
pKa ~ 9.4
COO
pKa ~ 2.2
R
+NH
3
C
COO-
H
“zwitterion”
-
Lipid Modification of Proteins
Other Forms of “Protein Stability”
Kinetic Stability (a.k.a. Thermal Stability)
“irreversible”
aggregation
Cellular Stability
Proteolyic
Degradation
Prion Diseases
A Special Class of Amyloid-Associated Disorders
The Human Prion Protein
Experimental 3-D Structure of
Core Domain of PrPC (healthy
form).
Speculative 3-D Structure
of the PrPSc (scrapies form)
Competing models for the molecular basis of prion infectivity.
Medical History
Of Prion Disorders
No need to memorize.
Prion Diseases: Transmissable Spongiform Encephalopathies (TSEs)
Scrapies (sheep)
Bovine Spongiform Encephalopathy (BSE, Mad Cow Disease)
Kuru
Creutzfeld-Jakob Disease (CJD)
Gerstmann-Straussler-Scheinker Syndrome
Fatal Familial Insomnia (which is not always familial)
These disease are characterized by the formation of PrPSc-containing
“spongiform” deposits in the brain (amyloid-like), ataxia, and a variety
of other devastating symptoms that lead to death.
Prion diseases can be triggered by:
Inherited and (most likely) sporadic mutations.
Transfer of infectious seed from one organism to another.
surgical procedures involving organs, tissues, fluids, or
molecules from infected organism
ingestion of tissue from infected organism.
Disease and Culture
Making Binding Data Linear
[L]
fR
=
Kd + [L]
y = m.x + b
[L]
1
1/Kd =
=
fR
[L]
fR Kd + fR [L]
1
=
fR Kd + fR [L]
1/Kd – fR/Kd =
+
fR
Kd
fR
[L]
m = slope (constant)
b = y intercept (constant)
y= exptl. variable
x= exptl. Variable
i.e.:
[L]
1
=
fR Kd
fR/[L] = y
fR = x
m = -1/Kd
b = 1/Kd
+ fR
[L]
intercept = 1/Kd
slope = -1/Kd
fR/[L]
0
0
fR
1.0
fR/[L] = 1/Kd – fR/Kd
Scatchard Equation
Hemoglobin has 4 binding
sites, which are positively
homocooperative.
The Hill equation:
[L]
fR =
fR
log
(1 – fR)
Kd,apparent + [L]
=  . log[L] - logKd,apparent
For a 150 lb. patient and …
… a 300 g/mol drug that binds
to a single protein target.
Kd
Milligrams of Drug to
Achieve 5 X Kd
1 nM
0.1
1 μM
100
1 mM
100,000
(this has been corrected
since the 8/31 review
session– the mgs were
right all along, but I had
left out the 5 when I showed
how it was calculated)
150 lbs X 454 grams/lb = 68,100 grams = 68 kg
Assume density = 1 g/ml
So… 68.1 kg = 68 liters = volume
1 micromolar = 10-6 molar
68 liters X 300 gram/mol X 10-6 moles/liter X 5 = 0.122 grams
= 122 mgs
It’s My Function!