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Chapter 1

1. What cells do?


(a) Form and build cells structure, and breakdown the unuseful structures
(b) Form its own extracellular matrix and its own glue, such collagen and
lamina basal, CAM (cell-adhesion molecules)
(c) Change shape and move, cytoskeleton
(d) Sense and send information in the form of signal molecules that is
affectes cells activity
(e) Regulate the gene expression to meet the changing needs, e.g. ideal
condition for transciption in E.coli is in the presence of glucose, but it
can also survive in lactose in a pinch.
(f) Grows and replicate, to reproduce the cells and inherited the gentic
material for survival.
(g) Cells die from aggravated assault or a programmed cell-suicide
(necessary to avoid the release of potentially toxic cell constituents)
(h) Generate energy in cellular metabolism, cell respiration.

2. Microorganism and virus involvement in human life, might be useful or


bring disease.

3. Cells and their part


(a) Cell biology reveals the size, shape, location and movement of the cells
(b) Biochemistry andbiophysics reveal the molecular structure and
chemistry purified cell constituents
(c) Genetics reveals the consequences of damage genes
(d) Genomics revelas differences in the structure and expression of the
entire genom
(e) Developmental biology reveals changes in the properties of cells as
they specialized

4. Mutation might be good, bad, or indifferent, depend on the mutation. Can


be inherited only if they are present in cells that potentially contribute to
the formation of offspring.

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

weakest molecular interactions, how can the geckos feet stick so


effectively?
Anwer:
Karena ikatan van der Waals terjadi akibat perbedaan dipol, ketika setae pada
kaki cicak mendekati dinding, interansi antara dipol setae dengan dinding
menguat sehingga kaki cicak bisa menapak pada dinding. Kemudian ketika
setae menjauhi permukaan dinding, makan ikatannya melemah dan terputus
ketika mencapai jarak tertentu sehingga kaki bisa dipindahkan ke tempat lain
saat cicak melangkah.
Lain halnya dengan ikatan kovalen yang kuat dan stabil, justru ikatan van der
Waals akan memungkinkan cicak untuk melangkah pada dinding.
Kaki cicak dapat menempel dengan baik pada dinding karena setae dalam
jumlah yang banyak memberikan interaksi dipol yang cukup kuat untuk
menahan bobot cicak pada dinding.

2. The K+ channel is an example of a transmembrane protein (a protein that


spans the phospholipid bilayer of the plasma membrane). What types of
amino acids are likely to be found (a) lining the channel through which K+
passes, (b) in contact with the hydrophobic core of the phospholipid
bilayer containing fatty acyl groups, (c) in the cytosolic domain of the
protein, and (d) in the extracellular domain of the protein?
Answer:
(a) Negatively charges aminos acids
(b) Hydrophobic, non-polar amino acids
(c) Hydrophilic amino acids
(d) Hydrophilic amino acids
3. V-M-Y-F-E-N: this is the single-letter amino acid abbreviation for a peptide.
What is the net charges of this peptide at pH 7.0? An enzyme called a
protein tyrosine kinase can attach phosphate to the hydroxyl groups of
tyrosine. What is the net chages of the peptide at pH 7.0 after it has been
phosphorylated by a tyrosine kinase? What is the likely source of the
phosphate utilized of the kinase for this reaction?

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.

5. In the 1960s, the drug thalidomide was prescribe to pregnant women to


treat morning sickness. However, thalidomide caused severe limb defects
in the children of some women who took the drug, and its used for
morning sickness was discontinued. It is now known that thalidmoide is
administered as a mixture of two stereoisomeric compounds, one of which
relieved morning morning sickness and the other of which was responsible
for the birth defects. What are stereoisomers? Why might two such closely
related compounds have such different physiologic effects?
Answer:
(a) Stereoisomers: isomer dari suatu atom, yang berbeda pada peletakan
spasial atom atau molekul yang mengelilinginya.
Khiral: atom C yang keempat elektron valensinya berikatan dengan gugus
yang berbeda-beda.
(b) Karena setiap atom pada yang berada dalam struktur suatu molekul
memiliki kemampan yang berbeda untuk berinteraksi dengan molekul
yang lainnya, sehingga suatu senyawa dengan isomer dapat memiliki
pengaruh yang berbeda pula untuk setiap isomernya.
Because the arrangement of atoms within their structure differs, yielding
their unique abilities to interact and chemically react with other molecules
(pg. 33).
6. Name the compound show below.

Is this nucleotide a component of DNA, RNA or both?


Name one other function of this compound.
Answer:
RNA.
Function:
-

Carries genetic information


mRNA transfer genetic information from DNA
tRNA coupled with amino acids to translate mRNA into protein
signal recognition particle

7. The chemical basis of blood-group specificity resides in the carbohydrates


displayed on the surfac of red blood cells. Carbohydrates have the
potential for great structural diversity. Indeed, the structural complexity of
the oligoseccharides that can be formed from four sugars is greater than

for oligopeptides from four amino acids. What properties od carbohydrate


make this great structural diversity possible?
Answer:
Karena, ikatan peptida hanya memiliki satu model ikatan, sementara ikatan
glikosida memiliki dua model,yaitu ikatan (1,6) dan ikatan (1,4)

8. Ammonia (NH3) is a weak base that under acidic condition become


protonated to he ammonium in in the following reactoin:
NH3 + H+ NH4+
NH3 freely permeates biological membranes, including thise lysosomes.
The lysosomes is a subcellular organelle with pH about 4.5-5.0; the pH of
cytoplasm is ~ 7.0. What is the effect on the pH of the fluid content of
lysosomes when cells are exposed to ammonia?
Note: protonated
ammonia does not diffuse freely accros membranes.
Answer:
pH dalam lisososm tidak terpengaruh oleh masuknya ion amonia, karena
amonia bersifat buffer di mana ion proton dari amonia tersebut akan
berinteraksi dengan larutan yang ada di dalam lisosom, sehingga ion
positifnya tidak lepas ke lingkungan (tidak menambah keasaman).

9. Consider the binding reaction L + R LR, where L is a ligand and R is its


receptor. When 1 x 10-3 M L is added to a solution containing 5 x 10 -2 M R,
90% of the L binds to form LR. What is the K eq of this reaction? How will the
Keq be affected by the addition of a protein that catalyzes this binding
reaction? What is the Kd?
L + R LR
[L] = 1 x 10-3 M
[R] = 5 x 10-2 M
90% L M
Kd = 10-9
Kd = ([L][R]) / ([LR])
10-9 = ( (1 x 10-3) x (5 x 10-2) ) / [LR]
[LR] = 5 x 104
Keq = ([LR]) / ([L][R]) = 109
Jika ditambah dengan katalis, Keq tidak berubah.

10.The Go for the reaction X + Y XY is 1000 cal/mol. What is the G at


25oC (298 K) starting with 0.01 M each X, Y and XY? Suggest two ways one
could make this reaction energetically favorable.
Answer:
(a) G = Go + RT ln Q
G = Go + RT ln ([P] / [R])
G = - 1000
(0.01/0.01.0.01)

cal/mol

(1.987

cal/degree.mol)(298

degree)

ln

G = - 1000 cal/mol + (529.162)(4.6)


G = - 1000 cal/mol + 2434.1452 = 1134.1452 cal/mol
(b) Increase the entrophy (S) enough or raise the temperature so that T.S
term can overcome the positive H
11.What is the ionization state of phosphoric acid in the cytoplasm? Why is
phosphoric acid such a physiologically important compound?
Answer:
HPO4 - H+ + PO42Buffer mempertahankan keasaman di dalam sel agar kondisinya tetap
ideal untuk menjalankan fungsi-fungsi sel.
12.According to the health experts, saturated fatty acids, which come from
animal fats, are a major factor contributing to coronary heart disease.
What distinguishes a saturated fatty acids from unsaturated fatty acids,
and to what does the term saturated refer? Recently, trans unsaturated
fatty acids, or trans fats, which raise total cholesterol levels in the body,
have also been implicated in heart disease. How does the cis stereoisomer
differ from the trans configuration, and what effect does the cis
configuration have on the structure of the fatty acid chain?
Answer:
(a) Saturated = tidak ada ikatan rangkap
Unsaturated = ada minmal 1 ikatan rangkap
The chain of carbon atoms are fully saturated with hydrogen atoms.
(b) Trans : berseberangan
Cis : bersebelahan
When this oil is hydrogenated, it is not possible to control where the
hydrogen atoms are added to the structure. If both hydrogen atoms are
added to the same side of the structure, it is called a "Cis" fat. Cis fats
exist naturally and, because the hydrogen atoms are crowded on one side
of the molecule, they bend, allowing other chemicals and enzymes to bind
to them (bisa diuraikan).

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

1. Regulation, to activate or inactivate several systems, like transcription


factor.
2. Protein structure, builds structure, such as actin filament.
3. Movement, as motor, like actin an myosin in muscle cells.
4. Catalysts, enzyme to increase the reaction rate.
5. Transport, provide channels or transporter for molecullar traffic.
6. Signaling, provide pathways for signaling.

1. The three-dimensional structure of a protein is determined by its primary,


secondary and tertiary structures. Define the primary, secondary and
tertiary structures. What are some of the common secondary structures?
What are the forces that hold together the secondary structure and
tertiary structures? What is the quarternary structure?
Answer:
(a) Primary structures: linear arrangements of amino acids.
Secondary structures: the core elements of protein architecture, stable
spatial arrangements of segment of a polipeptide chain held together by
hidrogen bonds between backbone amide and carbonyl groups. The
principal secondry structures are -helix, -turns and short U-shaped turns.
Tertiary structures: the overall folding conformation of a polypeptide chain,
the three-dimensional arrangements of all its amino acids residues which
are stabilized only by hydrogen bonds, primarily stabilized by hydrophobic
interaction between nonpolar side chains, together with hydrogen bonds
between polar side chains and peptide bonds.
(b) -helix, -turns and short U-shaped -turns
(c) hidrogen bonds
(d) multimeric protein consist of two or more polpeptide chains or subunit.
2. Proper folding of proteins is esential for biological activity. Describe the
roles of molecular chaperones and chaperonins in the folding of proteins.
Answer:

Chaperones binds and stabilized unfolded or partly folded proteins,


thereby preventing these proteins from aggregating an being degraded.
Molecular chaperonins form a small folding chamber into which an
unfolded protein can be sequestered, giving it time and an appropriate
environment to fold properly.
3. Proteins are degraded in cells. What is ubiquitin and what role does it play
in tagging proteins for degradation? What is the role of proteosomes in
protein degradation?
Answer:
(a) Ubiquitin marks cytosolic proteins for degrdation in proteosomes.
Ubiqitin is 76-residues of polypeptide that determined which proteins
are to be degraded by covalently bond.
- The
covalent
addition
of
a
single
ubiquitin
molecule
(monoubiquitination) to a lysine on a target protein
- The addition of multiple single ubiquitins (multiubiquitination)
- Linking the ubiquitin to the N-terminus of the target protein
- Polyubiquitination in which the ubiquitins are linked to one another
via another via their Lys-63 residue instead of the Lys-48 position

(b) Proteosomes is anothe cells molecular machine. The numerous


proteasomes dispersed throughout the cell cytosol proteolytically
cleave ubiquitin tagged proteins in an ATP-dependent process that
yeilds short (7- to 8-residue) peptides and intact ubiquitin molecules.
4. Enzymes can catalyze chemical reactions. How do enzymes increase the
rate of a reaction? What constitutes the active site of an enzyme? For an
enzyme-catalyzed reaction, what are Km and Vmax? For enzyme X, the Km
for substrate A is 0.4 mM and substrate B is 0.01 mM. Which substrate has
a higher affinity for enzyme X?
Answer:
(a) By lowering the activation energy needed in the reaction.
(b) Active sites contains two functionally important regions, one that
recognizes and binds the substrate (or substrates) and another that
catalyzes the reaction after the substrate has been bound.
(c) Km is defines as the substrate concentration that yields a half-maximal
reaction rate ( Vmax) ans a measure of the affinity of an enzyme for its
substrate while Vmax is the maximal velocity of reaction at saturating
substate concentration.
(d) Km A = 0.4 mM
Km B = 0.01 mM
The smaller Km, the more avid an enzyme can bind substrate from a dilute
solution and the smaller the substrate concentration needed to reach halfmaximal velocity.
5. Motor proteins, such as myosin, convert energy into a mechanical force.
Describe the three general properties characteristics of motor proteins.
Describe the biochemical events that occur during one cycle of movement
of myosin relative to an actin filament.
(a) 3 general properties characteristics of motor protein
- The ability to tracnduce a source of energy, either ATP or an ion
gradient, into linear or rotary movement.
- The ability to bind and translocate along a cytoskeletal filament,
nicleic acid strand, or protein complex.
- Net movement in a given direction

(b) Operational model for the coupling of ATP hysrolisis to movement of


myosin along an actin filament.

6. The function of proteins can be regulated in a number of ways. What is


cooperativity, and how does it influence protein function? Describe how
protein phosphorylation and proteolytic cleavage can modulate protein
function.
Answer:
(a) Cooperativity: the binding of one ligand molecule affects the binding of
subsequent ligand molecules. This cooperativity permits many
multisubunit proteins to respond more efficiently to small changes in
ligand concentration than would otherwise be possible. In positive
cooperativity, sequential binding is enhanced; in negative
cooperativity, sequential binding is inhibited.
(b) Phosphorylation changes a proteins charge and generally leads to a
conformational change; these effects can significantly alter ligand
binding by a protein, leading to an increase or decrease in its activity.

Proteolytic cleavage irreversibly activates or inactivates some proteins.


7. A number of techniques can separate proteins on the basis of their
differences in mass. Describe the use of two of these techniques,
centrifugation and gel electrophoresis. The blood proteins tranferrins (MW
76 kDa) and lysozymes (MW 15 kDa) can be separated by rate zonal
centrifugation or SDS polyacrylamide gel electrophoresis. Which of the two
proteins will sediment faster during centrifugation? Which will migrate
faster during electrophoresis?
Answer:
(a) Centrifugation is used for two basic purposes, as apreparative technique
to separate one type or material from athers and as an analytical
technique to measure physiological properties of macromolecules. This
technique is used to separate particles and molecules that differ in mass
or density.
Electrophoresis separates molecules on the basis of their charge, mass
ratio. This technique separating molecules in a mixture under the
influence of an applied electric field. Dissolved molecules in an electric
field move or migrate, at a speed determined by their chage: mass ratio.
For example, if two molecules have the same mass and shape, the one
with the greater net charge will move faster toward an electrode.
(b) Transferrins
(c) Lysozymes
8. Chromatography is an analytical method used to separate proteins.
Describe the principles for separating proteins by gel filtration, ionexchange, and affinity chromatography.
Answer:
(a) Gel filtration: protein separation besed on its size.

(b) In ion-exchange chromatography, the proteins are separated on the


besis of differences in their charges.

(c) Affinity chromatography used the ability of proteins to bind specifically


to other molecules. In this techniques, ligand molecules that bind to
the protein of interest are covalently attached to the beads used to
form the column. Ligans can be enzyme substartes or other small
molecules that bind to specific proteins.

9. Various methods have been developed for detecting proteins. Describe


how radioisotope and autoradiography can be used for labeling and
detecting proteins. How does Western blotting detect proteins?
Answer:
(a) Radioisotopes
labeled
nucleotides
of
the
molecules
and
autoradiography detected the the radioactivity by overlaiding it with a
photographic emulsion sensitive to radiation. Autoradigraphy is
commonly used in various assays for detecting specific isolated DNA or
RNA sequences. Autoradiography is a semi0quantitative technique for
detecting radioactively labeled molecules in cells, tissues, or
electrophoresis gels.
(b) Western blotting, a powerful method for separating and detecting a
protein in a mixtures

10.Physical methods are often used to determine protein conformation.


Describe how x-ray crystallography, cryoelectron microscopy, and NMR
spectroscopy can be used to determine the shape of proteins.
Answer:
(a) X-ray crystallography is used to determine the 3D structures of proteins.
Beams of x-ray are passed through a protein crystal in which millions of
protein molecules are precisely aligned in a rigid array characteristics.
Atoms in the crystal scaterred the x-ray, produced a diffraction pattern to
discrete spots when they are intercepted by photographic film.

Disadvantage: hard to crystallize the proteins, particularly large


multisubunit proteins that requires a time-consuming trial-and-error effort
to find just the right conditions.
Advantage: provide the most detail structures.
(b) Cryoelectron microscopy, protein sample is rapidly frozen in liquid helium
to preserve its structure and then examined in the frozen, hydrated state.
Pictures are recorded in film by using a low dose of electron to prevent
radiation-induced damage to the structure. Recent edvances permit
researchers to generate molecular models that compare with thise derived
from x-ray crystallography.
Most useful for large protein complexes which are difficult to crystallize
(c) NMR (nuclear magnetic resonance) spectroscopy is used to study 3D
structures of small proteins containing about as masny as 200 amini acids.
In this technique, a concentrated protein solution is placed in a magnetic
field and the effetcs of different frequencies on the spin of different atoms
are measured. From the magnitude of the effect, the distances between
residues can be calculated; these distances are then used to generate a
model of the 3D structure of the protein. The advantage: limited to
proteins smaller than 20 kDa, acn be applied to protein domains.
11.Mass spectrometry is powerful tool in proteomics. What are four key
features of a mass spectrometer? Describe briefly how MALDI and 2DPAGE (two-dimensional polyacrilamide gel electrophoresis) could be used
to identify a protein expressed in cancer calls but not in normal healthy
cells.
Answer:
(a) Mass spectrophotometer, requires a method for ionizing the sample,
usualy a mixture of peptides or proteins, accelerating the molecular
ions, and then detecting the ions. In a laser desorption mass
spectrophotometer, the protein sample is mixed with an organic acid
and then dried on a metal target. Energy from a laser ionizes the
proteins, and an electric field accelerates the ions down a tube to a
detector. Alternatively, in an electrospray mass spectrometer. A fine

mist containing the sample is ionized and then introduced into a


separation chamber where the positively charged molecule are
accelerated by an electric field. In both instruments, the time of flight is
inversely proportional to its charge.
Ionization, acceleration, detection, molecular weight

(b) 2D-PAGE have been very useful in comparing the proteosomes in


undifferentiated and differentiated cells or in normal and cancer cells
because as many as 100 proteins can be resolved simultanously.
Analyze the data
Proteomics involves the global analysis of protein expressions. In one approach,
all the proteins in control cells and treated cells are extacted and subsequently
separated using two-dimensional gel electrophoresis. Typically, hundreds or
thousands of protein spots are resolved and the steady-state levels of each
protein are compared between control and treated cells. In the following exampe,
only a few protein spots ar shown for simplicity. Proteins are separated in the first
dimension on the basis of charge by isoelectric focusing (pH 4-10) and then
separated by size by SDS polyacrylamide gel electrophoresis. Proteins are
detected with a stain such as Coomassie blue and assigned numbers for
idntification.

a. Cells are treated with a drug (+ Drug) or left untreated (Control)


and then proteins are extracted and separated by two-dimensional
gel electrophoresis. The stained gels are shown below. What do you
conclude about the effect of the drug on the steady-state levels pf
proteins 1-7?

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?

c. To determine the cellular localization of proteins 1-7, the cells from


part a were separated into nuclear and cytoplasmic fractions by
differential centrifugation. Two-dimensional gels were run and the
stained gels are shown below. What do you conclude about the
cellular localization of proteins 1-7?

d. Summarize the overall proerties of proteins 1-7, combining the data


from parts a, b, and c. Describe how you could determine the
identitiy of any one of the proteins.