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Chapter 2
Review of the concepts
1. The gecko is a reptile with an amazing ability to climb smooth surfaces
including glass. Recent discoveries indicate that geckos stick to smooth
surfaces via van der Waals interaction between septae on their feet and
the smooth surface. How is this method of stickiness advantageous over
covalent interaction? Given that van der Waals forces are among the
Answer:
(a) V = 0, M = 0, Y = 0, F = 0, E = -1, N = 0 net charges = -1
(b) Tyrosine (Y) = 0, tirosin kinase = enzim untuk menambahkan gugus fosfat
ke asam amino. Peptide V-M-Y-F-E-N-Phosphate net charges = -1 + (-1)
= -2
(c) ATP
4. Disulfide bonds help to stabilized the 3D stucture of proteins. What amino
acids are involved in the formation of disulfide bonds? Does the formation
of a disulfide bond increase or decrease entrophy (S)?
Answer:
(a) Cysteine
(b) G = H T.S
H = enthalpy, energi untuk membentuk ikatan
Jadi, kalau ikatan terbentuk H naik, S akan berkurang.
cal/mol
(1.987
cal/degree.mol)(298
degree)
ln
If, however one hydrogen atom adds to one side of the structure and the
other atom to the other side, it creates trans fats, like the one below. Trans
fats do not exist naturally, with a very few exceptions. Because the
structure is uncrowded, they do not bend and so other molecules and
enzymes find it more difficult to bind to them. The shape of the molecule
is therefore vital to its function, much in the same way as the shape of a
key is important for the operation of a lock.
13.Chemical modifications to amino acids contribute to the diversity and
function of proteins. For instance, -carboxylation of specific amino acid is
required to make some proteins biologically active. What particular amino
acid undergoes this modification, and what is the biological relevance?
Warfarin, a derivative of coumarin, which is present in many plants,
inhibits -carboxylation of this amino acid and was used in the past as a
rat poison. At present, it also used clinically in humans. What patients
might prescribes warfarin and why?
Answer:
(a) Glutamate, form blood-clotting factors such as prothrombin
(b) Warfarin = anticoagulant
Warfarin and related 4-hydroxycoumarin-containing molecules decrease
blood coagulation by inhibiting vitamin K epoxide reductase, an enzyme
that recycles oxidized vitamin K to its reduced form after it has
participated in the carboxylation of several blood coagulation proteins,
mainly prothrombin and factor VII. For this reason, drugs in this class are
also referred to as vitamin K antagonists.[2] When administered, these
drugs do not anticoagulate blood immediately. Instead, onset of their
effect requires about a day before clotting factors being normally made by
the liver have time to naturally disappear in metabolism, and the duration
of action of a single dose of racemic warfarin is 2 to 5 days. Under normal
pharmacological therapy the drugs are administered to decrease the
action of the clotting factors they affect by 30 to 50%. [3]
Warfarin is used to prevent blood clots from forming or growing larger in
your blood and blood vessels. It is prescribed for people with certain types
of irregular heartbeat, people with prosthetic (replacement or mechanical)
heart valves, and people who have suffered a heart attack. Warfarin is also
used to treat or prevent venous thrombosis (swelling and blood clot in a
vein) and pulmonary embolism (a blood clot in the lung). Warfarin is in a
class of medications called anticoagulants ('blood thinners'). It works by
decreasing the clotting ability of the blood.
Chapter 3
Protein function
b. You suspect that the drug may be inducing a protein kinase and so
repeat the experiment in part a in the presence of 32P-labeled
inorganic phosphate. In this experiment the two-dimensional gels
are exposed to x-ray film to detect the presence of 32P-labeled
proteins. The x-ray films are shown below. What do you conclude
from this experimant about the effect of the drug on proteins 1-7?