NAME ___________________________________
BIOLOGY 052, SECTION 006
EXAM 1
SPRING 2008
+ PRINT YOUR NAME AT THE TOP OF EVERY PAGE.
+ USE A PEN, NOT PENCIL.
+ SIGN THE HONOR PLEDGE AT THE END OF THE EXAM.
+ USE ONLY THE SPACE PROVIDED FOR YOUR ANSWER.
+ QUESTIONS WILL BE GRADED ON BOTH HOW CORRECT AND HOW COMPLETE YOUR
ANSWER IS.
1. (10 points) Match the definition below with its term from the following list:
alpha-helix
beta-sheet
binding site
coiled-coil
conformation
polypeptide backbone
primary structure
protein
protein domain
protein subunit
quaternary structure
secondary structure
side chain
tertiary structure
a. Three-dimensional relationship of the different polypeptide chains in a multi-subunit protein or
protein complex. >>>Quaternary structure
b. Common folding pattern in proteins in which a linear sequence of amino acids folds into a righthanded coil stabilized by internal hydrogen bonding between backbone atoms. >>> alpha-helix
c. Complex three-dimensional form of the protein. >>> Tertiary structure
d. Common structural motif in proteins in which different sections of the polypeptide chain run
alongside each other and are joined together by hydrogen bonding between atoms of the polypeptide
backbone. >>> beta-sheet
e. Regular local folding patterns in a protein, including alpha-helix and beta-sheet. >>Secondarystructure
2. (10 Points) Margarine is made from vegetable oil by a chemical process. Do you suppose this
process converts saturated fats to unsaturated ones, or vice versa? Explain your answer.
>>> Vegetable oil is converted to margarine by reduction of double bonds (by hydrogenation),
which converts unsaturated fatty acids to saturated ones. This change allows the fatty acid chains
in the lipid molecules to pack more tightly against one another, increasing the viscosity, turning oil
into margarine.
3. (10 points) Match the definition below with its term from the following list:
amphiphilic
black membrane
cholesterol
ganglioside
glycolipid
hydrophilic
hydrophobic
lipid bilayer
lipid droplet
liposome
phosphoglyceride
phospholipid
plasma membrane
a. Artificial phospholipid bilayer formed from an aqueous suspension of phospholipid molecules.
>>> Liposome
b. Describes a nonpolar molecule or part of a molecule that cannot form energetically favorable
interactions with water molecules and therefore does not dissolve in water. >>> Hydrophobic
c. Having both hydrophobic and hydrophilic regions, as in a phospholipid or detergent molecule.
>>> Amphiphilic or amphipathic
d. The main type of phospholipid in animal cell membranes, with to fatty acids and a polar head group
attached to a three-carbon glycerol backbone. >>> Phosphoglyceride
e. Lipid molecule with a characteristic four-ring steroid structure that is an important component of the
plasma membranes of animal cells. >>> Cholesterol
4. (10 points) Why are the maximum rates of transport by transporters and channels thought to be so
different?
>>> Specific solutes move through the membrane much more slowly via transporters than by
channels because transporters must bind the solute and undergo a series of conformational
changes to transfer the solute across the membrane. Transport through channels is much faster
because they are ion-specific pores that neither bind the ion nor undergo any conformational
changes in order to move it across the membrane.
5. (10 points) A signal sequence that directs proteins to the ER and nuclear localization sequences
differ with respect to their location within a polypeptide chain and subsequent processing. Briefly list
these differences and explain why they are essential for the function of these types of proteins.
>>> ER signal sequences are present at the N-terminus of a protein while an NLS may be
anywhere in the primary sequence of a protein. ER sequences are cleaved while NLS is not.
Cleavage of the ER SS occurs after translation and produces a soluble protein in the lumen of the
ER. NLS must be present within the protein throughout its lifetime so that nuclear proteins may
be imported following nuclear breakdown at each cell division.
6. (10 points) Match the definition below with its term from the following list:
bright-field microscope
cell doctrine
confocal microscope
dark-field microscope
differential-interference contrast microscope
fluorescence microscope
phase contrast microscope
photoactivation
transmission electron microscope
image processing
ion-sensitive indicator
light microscope
limit of resolution
microelectrode
optical tweezers
green fluorescent protein
scanning electron microscope
immunogold electron microscopy
a. The minimal separation between two objects before they appear distinct. >>> Limit of resolution
b. Fluorescent protein (from a jellyfish) that is widely used as a marker for monitoring the movement of
proteins in living cells. >>> green fluorescent protein
c. Similar to a light microscope but the illuminating light is passed through one set of filters before the
specimen, to select those wavelengths that excite the dye, and through another set of filters before it
reaches the eye, to select only those wavelengths emitted when the dye fluoresces.
>>> fluorescence microscope
d. Type of electron microscope that produces an image of the surface of an object. >> Scanning EM
e. Type of light microscope that produces a clear image of a given plane within a solid object.
>>> Confocal
7. (10 points) Match the definition below with its term from the following list:
adaptor protein
dynamin
clathrin-coated vesicle
transport vesicle
COPII-coated vesicle
clathrin
t-SNARE
cargo receptor
retromer
SNARE protein
v-SNARE
a. General term for a membrane-enclosed container that moves material membrane-enclosed
compartments within the cell. >>> transport vesicle
b. A protein that mediates binding between the clathrin coat and transmembrane proteins, including
transmembrane cargo receptors. >>> adaptor protein or adaptin
c. Cytosolic GTPase that binds to the neck of a clathrin-coated vesicle helps it to pinch off from the
membrane. >>> dynamin
d. Protein that facilitates vesicle transport, docking, and membrane fusion. >>> SNARE protein
e. General term for a transport vesicle that carries a distinctive cage of proteins covering its cytosolic
surface. >>> clathrin-coated vesicle
8. (10 points) Match the definition below with its term from the following list:
ATP synthase
chemiosmotic coupling
citric acid cycle
cristae
mitochondria
electron-transport chain
inner membrane
intermembrane space
matrix
electrochemical proton gradient
outer membrane
oxidative phosphorylation
proton-motive force
respiratory chain
a. The subcompartment formed between the inner and outer mitochondrial membranes.
>>> intermembrane space
b. Metabolic pathway that oxidizes acetyl groups to CO2. >>> citric acid OR Kreb's cycle
c. The result of a combined pH gradient and membrane potential. >>> proton-motive force
d. Enzyme in the inner mitochondrial membrane that catalyzes the formation of ATP from ADP and
inorganic phosphate. >>> ATP synthase
e. A sieve-like membrane surrounding the mitochondria that is permeable to molecules of 5000 daltons
or less. >>> outer membrane
9. (10 points) How is it possible for some molecules to be at equilibrium across a biological membrane
and yet not be at the same concentration on both sides? Provide an example of an ion that exhibits this
property.
>>> The equilibrium distribution of a molecule across a membrane depends on concentration and
membrane potential (the electrochemical gradient). A charged molecule will respond to both
components of the electrochemical gradient and will distribute accordingly. K+ ions, for example,
are at equilibrium across the plasma membrane even though they are 30-fold more concentrated
inside the cell. The difference in concentration is balanced by the membrane potential (negative
inside), which opposes the movement of cations to the outside of the cell.
10. (10 points) When the chemical dinitrophenol (DNP) is added to mitochondria, the inner membrane
becomes permeable to protons. When the drug valinomycin is added to mitochondria, the inner
membrane becomes permeable to potassium ions (K+).
a. How will the electrochemical proton gradient change in response to DNP?
b. How will it change in response to valinomycin?
>>> a. DNP will collapse the electrochemical proton gradient completely. Protons pumped across
the inner membrane will be carried back across the membrane by DNP, therefore no energy can
be stored across the membrane.
>>> b. K+ ions will be driven into the matrix by the electrical potential of the inner membrane
(negative inside, positive outside). The influx of positively charges K+ ions will abolish the
membrane's electrical potential without affecting the concentration component of the proton
gradient (the pH difference). As a result, only part of the driving force that makes it energetically
favorable for protons to flow back into the matrix will be lost.