Sample questions for BIO12 Exam 1

In addition to the questions below, I also gave relevant textbook questions, at the beginning
of the notes for eah leture! "lease also use these as pratie problems! I do not
reommend #ust looking at the answers for an$ of these questions, beause that will not
help $ou stud$! Instead, if $ou annot answer a question, go bak over $our lass notes and
the textbook, treating it as an open%book exam! In this wa$ $ou will stud$ the material
relevant to the question! &his is important beause, of ourse, $ou will not reeive these
exat questions on $our exam and so $ou have to know the topi rather than these speifi
questions!
1. True or False. 'orret the False.
__ __ a. An electron microscope is so named because it uses an electron beam rather than a
beam of light to visualize a specimen.
__ __ b. The greatest advantage of the electron microscope is that we can view live specimens at
very high magnification.
__ ___c. The greater the value for resolution (R! the better the resolving power of the
microscope.
__ ___d. Fluorescence microscopy involves an electron microscope e"uipped with special filters
for detecting a fluorescent dye.
__ ___e. #eavy metals are used to generate contrast in specimens viewed in an electron
microscope.
__ ___f. $sing %omars&i or '() optics gives the specimen a three*dimensional appearance.
__ ___g. (n images generated using a scanning electron microscope! the specimen has a three*
dimensional appearance.
__ ___h. Ribosomes are easily detected using special phase contrast optics.
+. ,ist the following in order of size.
'irle the item which has a diameter of appro-imately 1 m
a a protein
b a mitochondrion
c an atom
d the nucleus of a typical cell
e a nucleotide
f a water molecule
()*+ES& ______ ___ _____ ___ ____ ___ ____ ___ ___ ____ ____ smallest
.. (n class we previewed the names and functions of several organelles found in eu&aryotic
cells. )hoose any three organelles and give a brief! one sentence! description of their
functions.
/. Fill in the blan&.
a )ells are formed of organic molecules! all of which contain _________(name the element.
b 0hat molecule is released when a peptide bond forms between two amino acids1 _ ________.
2. 0hat is the difference between a polar covalent bond and an ionic bond1
3. Fill in each blan& below with the letter(s corresponding to the correct interaction(s or
bond(s. 4ach letter can be used once! more than once! or not at all. (f there is more than one
correct answer! list them all.

A. covalent bond!
5. ionic bond!
). hydrogen bond!
'. van der 0aals attraction!
4. hydrophilic interaction!
F. hydrophobic interaction.
%ame the bond or interaction....

a ...that holds molecules of %a)l (sodium chloride together __________
b ...between ad6acent amino acid residues in a polypeptide _____ ______
c ...that helps protein to fold into a .*dimensional shape _____ ______
d ...that is the predominant bond that stabilizes an alpha heli- _____ ______
e ...between water molecules in a glass of water _____________ _
7. 5y the time you get to your e-am! a slide show should have begun at the front of the room. The
slides are numbered and as& you "uestions. To practice this type of "uestion! use figures from your
te-t boo&.
a. 0hat type of microscope too& the images shown in Figure 18*19 (be specific1
b. 0hat type of microscope too& the image shown in Figure 9.72a (be specific1 0hat about Figure
9.72b1
c. 0hat type of microscope too& the images shown in Figure 1/../ (be specific1
d. 0hat type of microscope too& the images shown in Figure /.8a (be specific1
e. 0hat type of microscope too& the images shown in Figure 8.. (be specific1 0hat about 8..71
0hat about 8..+1
f. 0hat type of microscope too& the images shown in Figure 1/.+. (be specific1
8. :uppose that! in a given protein! at a specific position a positively charged amino acid is replaced by
a negatively charged amino acid.
a. 'oes this represent a change in primary or secondary structure1
b. This change could also result in a change in tertiary structure. 4-plain why
9. 'uring the separation of proteins in an electrical field;
a. Treatment of the sample with what molecule ensures the components of the sample separate based on
molecular size1
b. 0hat property of proteins ensures their separation in the first dimension of a +*' gel1
1<. 'uring your internship at %A:A (%ational Aeronautics and :pace Administration one of the space
probes returns with a sample of organisms from =ars. (n order to transport it bac& to earth! the
sample was frozen in the water in which the organisms were found. (nitial tests were conducted by
the 5iochemical Analysis 'epartment of the Alien :pecimens $nit. The NASA scientists argue
about what the Mars organisms might look like. After a while, you speak up and say that they are
probably spherical cells with membranes composed of a lipid bilayer having transmembrane as well
as non-transmembrane proteins associated with it. The NASA officials are astounded and begin to
ask you so many questions that you only have time to provide BRIEF ANSWERS:
Your answers are based on your interpretation of the following data:
Molecule A: a phospholipid with two saturated FA chains about twice the length of those typically
found in terrestrial organisms. Only this single type of phospholipid was found in the organisms. No
cholesterol was found.
Molecule B: a protein composed of one 80-amino-acid-long polypeptide with a lipid group attached
to it.
Molecule C: a protein composed of one 240 amino-acid-long polypeptide shows one stretch of non-
polar residues that runs from amino acids 34-75.
a. Why did you suggest these organisms would be spherical and have lipid bilayers?
b. You think molecule C is likely an integral membrane protein, but molecule B is not. Why?
c. What indicated to you that there are proteins associated with the membrane that are not
transmembrane proteins?
The NASA officials want to thaw the sample but are worried about what this might do to the organisms.
With great confidence you tell them that it is OK to warm them up to at least room temperature.
However, you caution that if they go beyond room temperature, they should do so very slowly and
carefully because the organisms may be very sensitive to rapid temperature change.
d. List TWO reasons why you think the transition temperature of their membranes is likely to be higher
than room temperature, making it OK to warm the sample up that much.
e. List ONE reason why you think the phase transition of the membranes of these organisms might
happen very suddenly (which would be potentially dangerous to them).
f. What kind of interactions hold the membranes of these organisms together?
You have really impressed the Director, who puts the entire NASA research facility at your disposal.
The Director asks you to test your ideas about membrane fluidity and mobility in these organisms.
g. List ONE type of experiment you could perform to examine the mobility of molecules in the
membranes of the Mars organisms. (3 pts)
h. Do you think the overall mobility of the molecules in the membranes of the Mars organisms at room
temperature will be GREATER THAN or LESS THAN the mobility of molecules in the membranes
of organisms typically found on Earth ? Explain.
11a. List three model systems used in the study of cell biology.
b. List one reason why you think cell biologists study model organisms. (2 pts)
12a. In the FtsZ paper, the authors used the fluorescence microscope. Explain the modification of FtsZ
the authors used that allowed FtsZ to be detected by this type of microscopic technique?
12b. (n the discussion reading paper on Fts>! why did the authors bleach only half of the Fts> ring and
not the entire ring during the FRA? e-periment1
1.. @ou are handed a mi-ture of three proteins in a buffer at p# 7.<. The characteristics of each protein
are as follows; (1 #istone A=0B1.!<<<C p(B3.<D (+ ?rotein E A=0B2<!<<<C p(B3.<D! (. a
phosphorylated version of ?rotein E.
a. 5ased on the data provided! describe how you would separate this mi-ture of three proteins into three
fractions! each containing a purified protein1 @ou need to be relatively specific! i. e. naming a
techni"ue without e-plaining how it applies to this situation is not sufficient.
b. #ow would you assay the course of your purification to determine when the proteins were pure1
c. (f you made a fusion protein composed of ?rotein E and FF?! how might this change your
purification scheme outlined in 1.a above1
1/. 'efine the terms hydrophilic! polar! and amphipathic1
12. @ou are using two light microscopes with two different ob6ectives; ) (%.A. B 1.+ and B (%. A. B
<.3. (f A operates with green light ( B 2<< nm what of light would 5 need to operate with in
order to achieve the same resolution1 (+ pts
13. (n the space below! draw a tripeptide of your choice! showing all of the atomsC be sure to show the
structures of the %* and )* termini and the R*groups as they would be configured at p# 7.<! as well
as the names of the residues in your tripeptide. 'o not use glycine.
17. An enzyme has a G= of +< H= and a Ima- of 2< mmoles of productJminuteJHg of enzyme.
After e-posure to an inhibitor and analysis on a ,ineweaver * 5ur& plot the following values
are obtained; *1JG= B * <.<2 litersJHmole and 1JIma- B <.</ (mmoles of productJminuteJHg
of enzyme
*1
. 0hat class of inhibitor was used in the e-periment1 (/ pts
18. (n lecture you learned that a &ey distinguishing feature of the ? class of pump is that the
pump is actually phosphorylated. $sing the %aKJGK AT?ase as an e-ample! what role does
phosphorylation play in the function of this pump1 5e very specific.
19 a. (+ points ,ipid bilayers have asymmetric composition of fatty acids yet they are also very
dynamic. 4-plain how asymmetry is maintained despite the fluid nature of the bilayer.
b. (+ points 'iscuss + e-amples that demonstrate that water is integral to the formation of cell
structure and function.
+<. ) s$ntheti bilayer of pure phospholipid has been formed across a small hole in a partition
separating two a"ueous compartments as illustrated.
a 0hich side () or B is most similar to the cytoplasm with regards to ion concentrations1___
__
b 'oes the concentration of G
K
on side ) increase! decrease! or stay the same over time1
4-plain your answer.
c %ow 2< m= glucose is added to side )! 'oes the concentration of glucose on side ) increase!
decrease! or stay the same over time1 4-plain your answer.
+1. a 0hy is transport of a moleculeJ ion using either a symporter or antiporter considered
active transport whereas transport using a uniporter considered passive transport1
#+L
1/< m= %a)l
/< m= G)l
#+L
/< m= %a)l
1/< m= G)l
) B
?artition
S$ntheti bila$er of pure
phospholipid
b Five one e-ample of either a symporter or an antiporter. (nclude either a description or
labeled diagram to indicate in what membrane this transporter operates! what is being
transported and in what diretion across the membrane does transport occur. 'onMt forget to
include whether your e-ample is an antiporter or a symporter.
++. A friend is wor&ing in a lab in the cancer center at the medical school and is trying to localize
a novel oncoprotein by fusing it to FF?. :he is frustrated because it seems li&e her cells die
whenever she e-presses the FF?*fusion protein before she can even loo& at them under the
microscope.
a. (+ points 0hat is li&ely the problem with her e-periment1
b. (. points 0hat alternative approach would still allow her to localize her protein1 5riefly
e-plain the &ey steps to this approach.
+.. @ou are wor&ing at a marine lab on the )alifornia coast this summer and are studying an
endangered fish that migrates during the year from a river with fresh water in =e-ico north
through the ?acific Lcean to a saltwater bay in Alas&a. Fiven this fishMs diverse habitats! you are
interested in studying the dynamics of a plasma membrane %aK pump in the membrane.
a. (. points 0hat are three characteristics of membranes that may be modified as the fish swims
from =e-ico to Alas&a so as to maintain constant membrane fluidity in all conditions1 5riefly
e-plain why these changes will be important for maintenance.
b. (3 points @ou have cultured cells from this fish that e-press a fusion of FF? to a %aK pump.
@ou want to test the hypothesis that these fish will rapidly respond to changes in temperature by
remodeling their plasma membrane to maintain a constant fluidity. To test this! you will grow
cells with the FF?*%a pump at +<N ). @ou will then ta&e one third of the cells and shift them
down to 1<N) and you ta&e another third and shift them up to .<N). @ou leave the remaining
cells at +<N ). @ou then image your cells after 3< minutes at the different temperatures.
First! imagine that your hypothesis is wrong and the cells can not react "uic&ly to temperature
change.
?redict the results of a FRA? e-periment where you bleach a section of membrane in cells from
each temperature on the empty graph below. @ou should have a curve for each temperature. ?lot
this on the graph to the left.
Hypothesis incorrect Hypothesis correct
%ow! imagine your hypothesis is correct and these fish can react "uic&ly to temperature changes
in terms of maintaining their membrane fluidity. ?lot what the results of the e-periment would
loo& li&e if this was the case on the graph above on the right! again plotting a curve for each
temperature.
$se the space below to e-plain the reasoning for your answer;
c. (+ points 0hat are + possible sources of FF?*protein that could contribute to the recovery of
fluorescence and which of these is most relevant for interpreting this e-periment1