MIT Biology Department
7.012: Introductory Biology - Fall 2004
Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel
Name__________________________
TA____________Section____
7.012 F’04 Problem Set 1 September 10th 2004
This completed problem set must be turned into the wooden box outside
Question 1
Problem sets will not be accepted late.
Solutions will appear on the web after the due time.
A.
a) Explain what an ion is.
b) Explain what a van der Waals force is.
c) Match the atoms and molecules listed below with the appropriate descriptive.
Choose from:
cation
anion
polar non-charged
nonpolar non-charged
ClH2O
Na+
CH4
d) Circle the “side chain” in each of the amino acids given below.
O
O
C
H C CH2CH 2
O
O
C
O
C
NH
+ 3
H
O-
C CH2 CH2 CH2CH 2
NH3+
NH
+ 3
GLUTAMIC ACID
LYSINE
O
O
C
C
H
C H
NH3
+
GLYCINE
O
O
H
C CH2 CH2
O
C
NH3
+
GLUTAMINE
NH2
e) Check the following terms to describe the side chains of the amino acids you circled
above.
Side Chain of…
Glutamic Acid
Charged
Non Charged
Polar
Non Polar
Hydrophobic
Hydrophilic
Lysine
Tyrosine
Asparagine
Glycine
Glutamine
f) Explain why ethane (C2H6) is a non-polar molecule while ethanol (C2H5 - OH) is a polar
molecule. (A diagram of each molecule may help.)
B.
a) What are two main differences between prokaryotic cells and eukaryotic cells?
b) Match the letter of the organelle on the left with the function or characteristic on
the right.
Complex or
Organelle
a. Mitochondria
b. Nucleus
c. Smooth Endoplasmic
Reticulum
d. Golgi Apparatus
e. Lysosome
f. Ribosome
g. Chloroplast
h. Nucleolus
Function or Characteristic
Site of lipid synthesis; where hydrophobic
toxins‡ water soluable and thus excretable
Digests macromolecules and degrades worn-out
organelles
Catalyzes protein synthesis
Contains all genomic DNA in eukaryotic cell
Uses sunlight to build sugar
Where ribosomal RNA is made
Prepares proteins for export from the cell
Powerhouse of the cell; where the Krebs Cycle
occurs
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Question 2
One day in lab while studying your favorite enzyme, Votase, you discover the following
potential interactions that could occur between this amazing enzyme and its substrate of
choice.
Gln
O
HO
Asp
C-O-
Substrate
Arg
H3 N
+
NH3+
Lys
H3C CH3
CH3
Ile
Votase
a) At each site between the chemical group on the substrate and the closest side chain of
an amino acid on Votase determine if a favorable interaction is likely to take place. If a
favorable interaction is likely to take place, give the name for the strongest direct
intermolecular interaction. Choose from ionic interaction, covalent bond, hydrogen bond,
and van der Waals force.
Amino Acid
Will a favorable
interaction take place?
Circle one.
Gln
Yes/No
Asp
Yes/No
Ile
Yes/No
Lys
Yes/No
Arg
Yes/No
If yes, Name the Strongest
Interaction
ionic interaction, covalent bond,
hydrogen bond, or van der
Waals force.
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b) For all cases where a potential interaction seemed unfavorable, explain why.
Question 3
a) In your continuing work with the enzyme votase you discover that the enzyme is also a
transmembrane protein (part of the protein crosses the lipid bilayer of the cell). Circle
the portion of the sequence below that you would expect to be the transmembrane region
of the protein.
+NH3 - glu - trp - asp - arg - his - asp - phe - glu - ser - gly – pro - thr - phe -
ile - trp - leu - ile - trp - leu - val - ile - ala – val - leu - phe - leu - leu - ile -
trp – ala - val - leu – arg - pro - gly - cys - ser - lys - ala - tyr - ala - lys -- val
- cys - ala - gly - cys - ser - asp - lys - gly - glu - COOH
b) Why will the section you circled be embedded in the membrane?
c) Draw a schematic of the phospholipid bilayer. Label the lipid hydrocarbon chains,
phosphate hydrophilic heads, and water.
4
Question 4
a) In the peptide below, circle the peptide bonds. What are the amino acids in this
peptide?
b) What is the name of the macromolecule below? ________________
c) What is the chemical difference between the pentose sugar in DNA and the pentose
sugar in RNA? (See page 48 in text book.)
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STRUCTURES OF AMINO ACIDS at pH 7.0
O
O
H
C CH3
ALANINE
(ala)
H
O
O
H
N
C
H
+
C
C CH2
NH3
+
O
N
C
H
H
H
ISOLEUCINE
(ile)
HISTIDINE
(his)
O-
O
C CH2CH2
CH3
H
NH3
+
H
OC H
C C CH3
NH OH
+ 3
THREONINE
(thr)
C CH2
C CH2
C CH3
NH3
+
CH3
O-
H
H
C CH2
NH3+
O-
O-
O
C
H
C CH2
OH
NH3
+
SERINE
(ser)
PROLINE
(pro)
H
C
H
H
H
H
O
O
NH3
+
TRYPTOPHAN
(trp)
C CH2CH2CH2CH2
NH3
+
H C CH2
CH2
H
N
CH2
H +
H
N
C
H
H
LYSINE
(lys)
O
H
O
C
H
PHENYLALANINE
(phe)
O
GLYCINE
(gly)
O
C
H
C H
NH3
+
C
NH3
+
METHIONINE
(met)
O
NH2
C
S
C
LEUCINE
(leu)
H
O-
O
C
H
H
C C CH2CH3
NH3 CH3
+
H
H
O
O
O
C
O
GLUTAMINE
(gln)
O
C H
O-
ASPARTIC ACID
(asp)
O
NH3
+
GLUTAMIC ACID
(glu)
CYSTEINE
(cys)
NH3
+
OC CH2CH2
O-
O
C CH2 C
NH2
C
H
C
H
ASPARAGINE
(asn)
O
NH3
+
NH3
+
C CH2 C
O
C CH2CH2
C
O
NH3
+
NH2
+
C
C CH2 SH
H
NH2
O-
O
C
H
C
ARGININE
(arg)
O
O
C CH2CH2CH2 N
O-
O
C
H
NH3
+
NH3
+
O
O
C
C
H
O
O
H
H
C
C
H
O
O
C CH2
OH
NH3
+
H
TYROSINE
(tyr)
H
H
C C
NH3 H
+
CH3
CH3
VALINE
(val)
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