MIT Biology Department
7.012: Introductory Biology - Fall 2004
Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel
Name__________________________
Question 1
TA____________Section____
7.012 Problem Set 1 Solutions
A.
a) Explain what an ion is.
An ion is an electrically charged particle that forms when an atom gains or loses one or
more electrons.
b) Explain what a van der Waals force is.
A weak attraction between molecules resulting from a momentary shift of the electron density in a
molecule thus establishing a dipole moment. The dipoles induced by the effect of one molecule on the
others lead to a net electrostatic attraction.
c) Match the atoms and molecules listed below with the appropriate descriptive.
Choose from:
cation
anion
polar non-charged
nonpolar non-charged
Cl-
Anion
H2O
Polar non-charged
Na+
Cation
CH4
Nonpolar non-charged
d) Circle the “side chain” in each of the amino acids given below.
O
O
C
C
NH3
+
O-
GLUTAMIC ACID
O
H
O
H
O
C
H C
CH2
OH
NH3
+
H
TYROSINE
H
C
O
H C CH2CH 2
O
O
O
C
H C
NH3
+
H
C CH2 CH2 CH2CH 2
NH3
+
LYSINE
O
O
NH2
ASPARAGINE
H
C H
NH
+ 3
GLYCINE
O
O
C
C
O
CH2 C
NH3+
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
Lysine
Non Charged
√
√
Polar
Non Polar
Hydrophobic
Hydrophilic
√
√
√
√
√
√
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.)
Ethanol is a polar molecule because there is a partial charge separation associated with the bond
between the hydrogen and the oxygen. The higher electronegativity of oxygen pulls the electrons
in the bond closer to the oxygen resulting in a greater electron density around the oxygen. This
provides a slight negative charge for the oxygen and a slight positive charge for the carbon. The
molecule is polar because these opposite charges are separated at the two ends of the bond.
Ethane, on the other hand, is nonpolar because there are no such charge separations present in
this molecule. The electronegativity difference between carbon and hydrogen are not significant
enough to cause this type of charge separation.
B.
Match the letter of the organelle on the left with the function or characteristic on the right.
Complex or
Organelle
Function or Characteristic
a. Mitochondria
C
b. Nucleus
E
c. Smooth Endoplasmic
Reticulum
d. Golgi Apparatus
F
Site of lipid synthesis; where hydrophobic
toxins‡ water soluable and thus excretable
Digests macromolecules and degrades worn-out
organelles
Catalyzes protein synthesis
B
Contains all genomic DNA in eukaryotic cell
e. Lysosome
G
Uses sunlight to build sugar
f. Ribosome
H
Where ribosomal RNA is made
g. Chloroplast
D
Prepares proteins for export from the cell
h. Nucleolus
A
Powerhouse of the cell
2
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.
Strongest Interaction
ionic interaction, covalent
bond, hydrogen bond, or
van der Waals force.
Gln
Yes/No
hydrogen bond
Asp
Yes/No
ionic interaction
Ile
Yes/No
van der Waals
Lys
Yes/No
--
Arg
Yes/No
ionic interaction
b) For all cases where a potential interaction seemed unfavorable, explain why that interaction may be unfavorable.
The interaction between the side chain of lysine and the NH3+ group is unfavorable because both
are positively charged. The positive charge of the NH3+ group will repel and not attract the
positive charge of the lysine side chain.
3
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?
The lipid bilayer of the cell is largely nonpolar and thus it is expected that the region of the
protein that passes through this nonpolar layer will also be nonpolar due to the hydrophobic
effect. The section underlined above represents the largest stretch of nonpolar amino acids of
the residues given and would most likely be the transmembrane section.
c) Draw a schematic of the phospholipid bilayer. Label the lipid hydrocarbon chains,
phosphate hydrophilic heads, and water.
Cell Exterior
H2O
H2O
Hydrophilic Heads
H2O
Hydrocarbon
Chains
H2O
H2O
H2O
Cell Interior
4
Question 4
a) What is the chemical difference between the pentose sugar in DNA and the pentose sugar in RNA? (See
page 48 in text book.)
The sugar in RNA has a hydroxyl (-OH) group in the 2' position while the sugar in DNA has a
hydrogen in the 2' position.
b) In the peptide below, circle the peptide bonds. What are the amino acids in this
peptide? cysteine-alanine-tyrosine-phenylalanine
c) What is the name of the macromolecule below? ____Ribonucleic Acid (RNA)_______
5
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
+
O
H
OC H
C C CH3
NH OH
+ 3
THREONINE
(thr)
H
C CH2
C CH3
NH3
+
CH3
H
C CH2
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
C
PHENYLALANINE
(phe)
O
GLYCINE
(gly)
C
NH3
+
METHIONINE
(met)
NH3
+
O
C
S
C H
NH2
LEUCINE
(leu)
H
O-
O
C
H
H
C C CH2CH3
NH3 CH3
+
H
H
C
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
+
NH3
+
O
C CH2CH2
C
O
C CH2 C
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)
6