TA_____________
2009 Name_____________________________________
Section_______ 7.013 Problem Set 1
Please print out this problem set and answer the questions on the printout.
Answers to this problem set are to be turned in at the box outside 68-120
by 3:00, Friday Feb 13. Problem sets will not be accepted late.
Solutions will be posted at: http://stellar.mit.edu/S/course/7/sp09/7.013/index.html
Question 1
Complete the crossword puzzle by using the following keywords.
Cell junctions
chromosomes
cytoskeleton
cytosol
endoplasmic reticulum (ER)
eukaryotes
Nuclear membrane
extracellular matrix (ECM)
mitochondria
flagella
genes
lysosomes
nucleolus
nucleus
organelles
phospholipids
plasma membrane
prokaryotes
ribosomes
D ow n
2. A component of the cell that is involved in the synthesis of ribosomes.
5. A dynamic network of fibers that maintain cell shape and motility and play important roles
in intracellular transport and cell division.
6. Membrane lipids that possess a hydrophobic head and a hydrophilic tail.
7. Filamentous structure that is present between cells, provides them with anchorage and is
involved in intercellular communication. (Note: Use the abbreviation).
8. Organisms that do not contain a nucleus.
9. Location of proteins that form a channel to export mRNA from the nucleus into the cytosol.
11. Locations of the enzymes that digest the toxic substances produced within a cell.
14. Location of a protein that transports water in and out of the cells.
16. Discrete units of hereditary information.
Across
1. An organelle in a eukaryotic cell that is involved in the synthesis of ATP.
3. Cell structures comprised of proteins that are involved in cell-cell adhesion.
4. Part of eukaryotic cell where DNA is synthesized and stored.
10. The assemblies of rRNA and proteins that play a major role in protein synthesis.
12. The assemblies of DNA and proteins that carry hereditary information.
13. One location of protein synthesis in a cell. (Note: Use the abbreviation).
15. Membrane enclosed sacs in eukaryotic cells that have diverse functions.
17. Location of an enzyme that initiates the breakdown of glucose.
18. Organisms whose cells are nucleated.
19. Cellular appendages that propel the movement of sperms.
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Question 1 continued
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Question 2
You are given three unlabeled samples and asked to identify the cells in each sample as
bacteria, archaea, or eukaryote. Which cell types will fluoresce if the samples are stained
with
a) A fluorescent dye that recognizes a protein involved in ATP synthesis?
b) A fluorescent dye that recognizes a lysosomal protein?
c) The percentage of difference in DNA sequences between organisms is often used as a tool to
classify species into three major groups; bacteria, archaea and eukarya and to devise an
evolutionary tree as shown below.
Evolutionary time scale
i.
ii.
In the evolutionary tree drawn above, indicate the order of origin of the three groups by
filling the boxes.
On the schematic above, indicate where the mitochondria (as an organelle) might have
originated using an arrow(s).
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Section_______ TA_____________
Question 3
The major macromolecules present in the cell are deoxyribonucleic acid (DNA), ribonucleic
acid (RNA), carbohydrates, proteins and lipids. Each of these macromolecules is composed of
specific monomers that serve as their building blocks.
a) The following diagram represents a nucleotide that serves as a monomer for nucleic acids.
i.
Would you classify this nucleotide as a monomer for DNA or RNA? Explain.
ii.
Circle the part(s) of this monomer that will bond so that this will be added to the
growing end of the polymer and name the covalent bond that will be formed.
iii.
If the monomer drawn above comprises 28% of a double stranded nucleic acid, predict
the percentages of each of the other nucleotides present in the double stranded nucleic
acid. Explain your answer.
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Question 3 continued
iv.
If you modify the nucleic acid such that this monomer is reduced from 28% to 10%,
would that increase or decrease the amount of energy required to denature the
modified nucleic acid relative to the original polymer? Explain.
v.
Identify the primary role of this polymer in a cell.
b) Drawn below is a schematic of a transmembrane protein.
Extracellular
Cell membrane
Cytosolic side
i.
Of the 20 essential amino acids that make a protein, list those that you would expect to
find in a linear stretch that spans the lipid bilayer? Explain why you selected these
amino acids. (Note: A chart of the amino acids is provided as the last page of this problem set).
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Question 3 continued
ii.
Consider the following amino acid sequence that is a part of the protein.
Circle one peptide bond that holds together the primary structure of this protein.
Box the groups that provide unique properties to every amino acid drawn above.
iii.
Assuming that the mature protein is comprised of a single polypeptide chain what level
of protein structure will not be present in this protein? Explain.
iv .
Enzymes catalyze biological reactions by binding to specific substrates at their catalytic
site. The catalytic site of each enzyme is comprised of only a few amino acids, although
the enzyme as a whole includes many more amino acids that are not a part of its
catalytic site. Describe one role of the amino acids that are not a part of the catalytic site
of an enzyme.
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Section_______ TA_____________
Question 3 continued
c) Assume that the transmembrane protein in the schematic above is a glycoprotein and has a
carbohydrate part as shown below.
i.
ii.
Name the covalent bond marked by a circle in the diagram.
What molecule (Molecular weight = 18) is produced as a byproduct following the
breaking of the bond that you identified?
d) Below is the structure of cholesterol that serves as a precursor for the steroid hormones,
Vitamin D and is also an important component of the plasma membrane.
i.
On the diagram above, box the entire hydrophilic region(s) of this molecule.
ii.
On the diagram above, circle the entire hydrophobic region(s) of this molecule.
iii.
What bonds / interaction are most likely to form between cholesterol molecules?
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Name_____________________________________
Section_______ TA_____________
Question 4
Phosphofructokinase (PFK) is an enzyme in a multi-step pathway which harvests the energy
from carbohydrates and stores it in ATP. The transfer of a phosphate group from ATP is an
important reaction in a wide variety of biological processes. This enzyme binds to its ligand,
fructose-6-phosphate and catalyses its phosphorylation to fructose-1,6- bisphosphate by
transferring the phosphate group from ATP (ligand bound / active form). PFK exists as a
homotetramer in bacteria and mammals where each monomer possesses 2 similar domains.
One domain has an ATP binding pocket whereas the houses other the substrate-binding site
and the allosteric site (a regulatory binding site distinct from the active site, but that affects
enzyme activity). Deficiency in PFK leads to Tauri's disease that is characterized by severe
nausea, vomiting, muscle cramps in response to bursts of intense or vigorous exercise.
Computer modeling programs that are currently being used by the biologists to view the
structure and function of various proteins both in normal and diseased state. For this problem
you will need to use a computer to view the structure of PFK enzyme. To begin, go to the
site: http://web.mit.edu/star/biochem . This website has several links. In the left menu click
on Supplemental resources. Explore the links marked The Amino Acids, The Peptide
Bond, Secondary Structure, and Nucleotides and DNA. These contain models of different
macromolecules and will help you understand protein and structure. To help you learn how
to use the program, a tutorial is available under StarBiochem User Guide. When you are
ready to begin, click on Start. Once you have Star Biochem open, go to File and choose the
file 2PFK and click open in the dialog box. You will see a schematic of the 2PFK enzyme on
the left, and a menu on the right. Choose STRUCTURE from that menu. You may try
opening these files using Athena Station.
a) Choose Primary under the STRUCTURE menu. You will see two, independent structures
in 2PFK (an artifact of how the structural model was determined); please use one of these to
answer the following questions. How many amino acids comprise this enzyme?
b) Choose Secondary under the STRUCTURE menu. Again, use one of the two separate
structures in this file to answer the following questions.
i.
What are the different types of secondary structures that you can observe?
ii.
How many alpha- helices are there in 2PFK?
iii.
How many beta- sheets are there in 2PFK?
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Question 4 continued
iv.
The secondary structures are predominantly stabilized by hydrogen bonds. For each
type of secondary structure that you found, identify the part of the amino acids that
participates in the formation of the hydrogen bonds. Your choices are the SIDECHAIN
or the BACKBONE? (Note: Explore the STRUCTURE and the VIEW CONTROL menu
to answer this question).
c) Explore the STRUCTURE menu. Again, use one of the two separate structures in this file to
answer the following questions.
i.
ii.
How many peptide chains are present in the molecule?
What is the highest level of protein structure that you observe?
d) To explore the catalytic activity of PFK, open 2PFK, 1PFK and 6PFK in three separate
windows. (Note: You should click on start to open each window). Compare the three forms of
PFK by going through their STRUCTURE menu.
i.
Which of the three molecules represents the resting / ligand-unbound state of PFK?
ii.
Now compare the structure of the remaining two molecules that you did not select
while answering the question above. Identify which of the two molecules represent the
active state of PFK and which one represents the inactive state. Explain your choices.
(Note: Carefully compare the ligands that are bound to the enzyme while making your selection,
and review the information given in this problem about PFK. Also apply what you have learned
in lecture).
iii.
Deficiency in PFK leads to Tauri's disease, characterized by severe nausea, vomiting,
muscle cramps. Patients with this genetic disorder are advised not to exercise
vigorously. Explain how a reduced physical activity can help these patients.
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Name_____________________________________
Section_______ TA_____________
Question 5
The following diagram represents the active site of an enzyme (E1) that catalyzes the covalent
joining of two peptides (P1 and P2) together to make a large protein (P3) at neutral pH. You
are able to observe this in a test tube (in vitro).
P2
P1
Gln
Gly
Glu
1
Ala
4
3
Asp
2
Arg
His
Ser
E1
Note: The dashed lines represent the bonds (numbered 1-4) that are formed between the
amino acids of the enzyme (E1) and the substrate peptides (P1 and P2).
a) Complete the following table by stating the interactions between the amino acids that are
either located at the catalytic site of the enzyme (E1) or are a part of the two interacting
substrate peptides (P1 or P2). (Note: Your choices are hydrogen bond, Van der Waals forces, ionic
bonds, covalent bonds and hydrophobic interactions).
Bond # Amino acids
1
Ala (E1) - Gly (P1)
2
His (E1) Asp (P1)
3
Arg (E1) Glu (P2)
4
Interaction / bond
Ser(E1) Gln (P2)
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Section_______ TA_____________
Question 5 continued
b) Explain how the interaction of the enzyme with the substrates will be influenced if the
Arginine at the catalytic site undergoes the following substitutions:
i.
Arg changed to Trp?
ii.
Arg changed to Lys?
.
c) During an experiment, by mistake, you add a mystery compound, M to the original
reaction mixture and find that the reaction is completely inhibited. You then try to make the
reaction work by increasing the concentration of substrates P1 and P2. You find that the
reaction now does work. However as indicated on the diagram below, if you add an excess of
P1 and a normal amount of P2 together with M the reaction works, but if you have a normal
amount of P1 and an excess of P2 the reaction is not restored. Based on this information,
briefly explain how compound M inhibits the enzymatic reaction.
P1+ P2
E1
P3
P1+ P2 + Mystery component
E1
No reaction
P1 (excess)+ P2 (normal) + Mystery component
E1
P3
E1
P1 (normal)+ P2 (excess) + Mystery component
No reaction
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Section_______ TA_____________
Question 5 continued
d) Draw the energy profile of P1 + P2
P3 in the space provided below if
i.
Free energy (G) is negative.
ii.
Free energy (G) is positive.
iii.
Which of these reactions will require more free energy? Explain.
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Section_______ TA_____________
STRUCTURES OF AMINO ACIDS at pH 7.0
O
O
C
H
CH3
H
NH3
+
CH2CH2CH2 N
C
CH2 SH
H
NH3
+
O
H
N
C
O
+
C
CH2
NH3
+
N
C
H
H
H
OC
CH2CH2
S
CH3
H
CH2
C
NH3
+
H
H
O-
C
H
H
CH3
NH3 OH
+
THREONINE
(thr)
C
CH2
C
H
C
CH2
OH
NH3
+
SERINE
(ser)
PROLINE
(pro)
H
C
H
H
H
H
O
O
NH3
+
TRYPTOPHAN
(trp)
NH3+
O-
O
H C CH2
CH2
H
N
CH2
H+
H
N
C
OC
H
CH2CH2CH2CH2
LYSINE
(lys)
O
H
C
NH3
+
CH3
PHENYLALANINE
(phe)
O
O
OCH
H
CH3
LEUCINE
(leu)
CH2
NH3
+
METHIONINE
(met)
C
C
C
H
C
C
NH3
+
H
H
O
O
C
CH2CH3
O-
O
CH
NH3
+
GLYCINE
(gly)
O
O
ISOLEUCINE
(ile)
C
H
C
H
NH2
GLUTAMINE
(gln)
O
CH
C
C
C
NH3
+
NH3 CH3
+
H
HISTIDINE
(his)
O
O-
O
O
CH2CH2
O-
ASPARTIC ACID
(asp)
O
C
CH2 C
NH3
+
O-
H
GLUTAMIC ACID
(glu)
C
H
C
NH3
+
CYSTEINE
(cys)
O
CH2CH2
O
C
NH2
C
O
C
H
ASPARAGINE
(asn)
O
C
C
CH2 C
NH3
+
O-
O
C
O
C
NH2
+
ARGININE
(arg)
O
H
C
H
NH2
O-
O
C
H
C
NH3
+
ALANINE
(ala)
O
O
C
C
O
O
O
H
H
C
C
H
C
O
O
CH2
OH
NH3
+
H
TYROSINE
(tyr)
H
H
C
CH3
C
NH3 H
+
CH3
VALINE
(val)
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