MIT Department of Biology
7.013: Introductory Biology - Spring 2005
Instructors: Professor Hazel Sive, Professor Tyler Jacks, Dr. Claudette Gardel
NAME________________________________TA______________Section #______
7.013 Spring 2005 Problem Set 1
FRIDAY February 11, 2004
Problem sets will NOT be accepted late.
Question 1
a) Circle the correct answer.
i) Homo sapiens emerged ____________years ago.
5,000
50,000
500,000
5,000,000
50,000,000
ii) There are __________________billion letters (bases) in the human genome.
one
three
thirty
3 hundred
iii) An alpha helix is an example of _________________structure.
primary
secondary
tertiary
quarternary
b) What are the four major types of biological molecules discussed in lecture? What
monomers make up these molecules? Give one important function of each type of
biological molecule in the cell.
Name of molecule
Monomer
One function of the Polymer
1
c) Name the molecules depicted below.
NH 2
N
-
O
N
adenine
O-
N
P
O CH 2
H
O
O
H
H
H
H
O
-
N
O P
O
CH
HN
O
H
N
O
H
H
H
H
O
-
3
thymine
O
H2 C
DNA
O
O
NH 2
P
O
N
O
N
adenine
N
H2 C
H
O
N
H
H
H
H
HO
NH2
N
-O
P
N
adenine
O-
N
O
CH2
H
O
O
H
H
H
OH
O
-
N
O P
O
O
HN
O
H2 C
H
O
N
H
H
H
O
-
RNA
uracil
O
O
NH2
OH
P
N
O
N
O
N
H2 C
H
O
H
H
H
OH
HO
+
NH 2
CH3
H C
3
CH
C
H
NH 2
C
C
O
C
H
C
O
C
(CH2 ) 2
H
N
C
H
NH 2
O
C
(CH2 ) 3
H
N
O
O
NH
CH2
+
H3N
adenine
N
C
O
Protein
CH 2
H
N
C
H
COO
d) Circle one peptide bond if there is any in the figures above.
2
Question 2
a) Draw the energy profile for this reaction. Refer to Chapter 6 in the textbook.
A + B ---------> C + D
ΔG
o'
= -3.4
kcal/mol
On the diagram be sure to…
1) show relative energy levels of the reactants and the products.
2) label the axes.
3) label reactants and products.
4) indicate the energy of activation.
5) indicate ΔG.
b) An enzyme _____________ the activation energy of a reaction.
lowers
raises
does not affect
c) An enzyme _____________the ΔG of a reaction.
lowers
raises
does not affect
d) Using a dashed line in the above diagram, draw the energy profile in the presence of an
enzyme.
3
Question 3
Some receptors are transmembrane proteins found on the cell surface.
Membrane
–
O
– O P O
O
H
H 2C
C
O
C O
CH2
CH2
CH2
CH2
CH2
H 2C
O
O P O
–
O
–
H
H
C H
O
C OO
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C O
O
C
H
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C OO
O
C HH
H
H
C
–
O
O P O
–
O
H
C H2C
O
O
C O C
–
O
O P O
–
O
H
H 2C
C
O
C O
CH2
CH2
CH2
CH2
CH2
CH2
H
C H
O
C O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C O
O
C
H
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C O
O
C H
H
CH2 CH2
C O C
O
C
H
O
C H2C
O
H
O P O
O –
–
H 2C
O
– O P O
O
–
H
H C
–
O
O P O –
H
O
C H 2C
O
O
O C O C
–
O
O P O
–
O
H
H2C
C
H
C H
O
O
C O C O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2 CH2
O C O C
O
H C
H
O
C H 2C
H
O
O P O
O –
–
CH2 CH2
C O C O
O
H2C
C
O
H
– O P O
–O
O
C H
H
–
O
O P O –
H
H
O
H C
C H2 C
O
O
O C O C
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2 CH 2
CH2
CH 2
CH2
CH 2
CH2
CH2
CH 2
CH 2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
O C O
O
H C
H
Membrane
extracellular
CH 2
CH 2
CH 2
CH 2
CH 2
CH 2
CH 2
C
O
C H2 C
H
O
O P O–
O
–
intracellular
Receptor
proteins
growth
factor
receptors
a) The majority of the molecules that constitute a membrane belong to what class of
macromolecules? ________________________________
b) Explain the important qualities/properties of these molecules that allow them to form
membranes.
4
A smaller schematic of the receptor is shown here.
= transmembrane region
]
Sequence from this region shown below
+
NH3 ···Ile-Val-Phe-Leu-Ala-Val-Trp-Met-Phe-Arg-Lys-Thr-His···COO
-
c) Which stretch of amino acids in the above sequence is within the interior of the
transmembrane region of the receptor? Circle these amino acids and briefly explain your
reasoning below.
When a “LIGAND” binds to the extracellular domain of the receptor, a conformational
change occurs in the receptor. Ligand binding causes dimerization of two adjacent
receptors in the cell membrane. Upon dimerization, the intracellular domains of the
receptors become activated. See schematic below.
ligand
ligand
extracellullar ligandbinding domain
Receptor 1
Receptor 2
plasma
membrane
intracellular domain
inactive domains
active domains
5
c) Regions of the two receptors that interact upon dimerization are drawn below. In
parts (i - iv) below, name the strongest type of interaction (choose from; hydrogen bond,
ionic, covalent, van der Waals) that occurs between the side chains of the amino acids
indicated.
Receptor 1
Ala45
Asp68
Cys82
Cys36
CH2 S H
CH2
S
S
CH3
CH 2
C O
O
Ser53
CH 2 OH
+
H3N
CH2
CH2
CH 2
H2N
i)
Phe50 : Val98
ii)
Asp68 : Lys65
Lys65
C CH2 CH2
H3C
H3C
Interacting Side chains
Cys75
CH2 CH2 CH
2
O
Phe50
Receptor 2
CH
Gln12
Val98
Type of interaction
iii) Cys75 : Cys82
iv) Ser53 : Gln12
d) Gln12 is the 12th amino acid in primary sequence. Val 98 is the 98th amino acid in the
primary sequence. Explain how these amino acids are far apart in the primary sequence of
the protein yet are close to each other in the region of the protein diagrammed above.
6
e) Molecular interactions between the two receptors are important for dimerization.
Thus, substitution of certain amino acids in the protein can affect receptor dimerization.
Predict whether the receptors will or will not be able to dimerize given the substitutions
(i - iv) below. EXPLAIN your reasoning.
i) Asp68 → Arg
ii) Ser53 → Thr
iii) Phe50 → Asn
iv) Val98 → Ile
f) Substitution of one amino acid, Cys75 → Gly, leads to dimerization of the receptors
with or without ligand. Provide a brief explanation for this observation.
7
Question 4
You have identified a new, rapidly reproducing species of dog that you have named the “mitbull”. The
mitbull is diploid and two autosomal chromosomes are shown. One chromosome carries gene A with
two alleles designated A and a. The other chromosome carries gene B with two alleles designated B
and b.
a) Diagram mitosis in a heterozygous (AaBb) mitbull cell shown below. Draw your diagrams in the
outlines of the ovals adjacent to the stages. Include the alleles and the mitotic spindle in your
diagrams.
Mitbull cell
A
a
B
b
Prophase
Metaphase
8
Anaphase
Telophase
phase
b) Indicate the genotype of cells that would result after telophase. ____________
9
c) A cell in Metaphase I is shown below where a crossover event takes place. Diagram the
indicated stages in meiosis. Designate the alleles and the spindle.
AA
B
a a
Bb
b
Telophase I
Metaphase II
Telophase II
10
d) You determine another gene, gene D, maps 20 cM or map units away from gene A.
i) Given the cell with chromosome configuration below, what would be the genotypes of all the
gametes if a recombination takes place between A and D?
A
d
a
D
ii) Circle the genotypes of the recombinant gametes above.
iii) At what frequency do you expect each of the recombinant genotypes to occur?_________
STRUCTURES OF AMINO ACIDS at pH 7.0
O
O
C
H
H
NH3
+
O
H
NH3
+
O
O
H
N
C
H
C
C CH2
NH3
+
O
+
N
C
H
H
H
C C CH2CH3
O-
H
C CH2CH2
S
CH3
H
H
C C CH3
NH3 OH
+
THREONINE
(thr)
C CH2
C CH3
NH3
+
CH3
H
H
H
O-
H
C CH2
C
O-
O-
O
C
H
C CH2
OH
NH3
+
SERINE
(ser)
PROLINE
(pro)
H
N
H
H
H
H
O
O
NH3
+
TRYPTOPHAN
(trp)
NH3+
NH3
+
H C CH2
CH2
H
N
CH2
+
H
H
C CH2CH2CH2CH2
LYSINE
(lys)
O
H
O
C
H
LEUCINE
(leu)
C CH2
C
H
GLYCINE
(gly)
O
C
PHENYLALANINE
(phe)
O
C H
NH3
+
C
NH3
+
METHIONINE
(met)
H
NH2
C
NH3
+
O
OC H
H
H
O-
O
C
C
O
O
ISOLEUCINE
(ile)
HISTIDINE
(his)
O
O
C H
NH3 CH3
+
H
C
GLUTAMINE
(gln)
GLUTAMIC ACID
(glu)
CYSTEINE
(cys)
O
O
NH3
+
O-
ASPARTIC ACID
(asp)
O
C CH2CH2
O-
NH3
+
NH3
+
O-
H
C
O
C CH2 C
NH2
C
O
C CH2CH2
H
ASPARAGINE
(asn)
O
C
C CH2 SH
NH3
+
O-
O
C
O
C CH2 C
NH2
+
ARGININE
(arg)
C
H
C
H
NH2
O-
O
C
H
C CH2CH2CH2 N
NH3
+
ALANINE
(ala)
O
O
C
C CH3
O
O
O
H
H
H
O
O
C
C
C CH2
OH
NH3
+
H
TYROSINE
(tyr)
H
H
C C
NH3 H
+
CH3
CH3
VALINE
(val)
11