Download 7.013 Spring 2005 Problem Set 1Solutions

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 1Solutions
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
Lipid
Fatty Acid,
Triglyceride
Hormones, Membranes, Energy
storage
Nucleic Acids
Nuceleotide
Carry information
Carbohaydrate
Sugar
Energy, Protein Modification,
Protein
Amino Acid
Enzymes, motility, structural roles
1
c) Name the molecules depicted below.
NH 2
N
-
O
N
adenine
O-
N
P
O CH 2
H
O
O
H
H
DNA
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
RNA
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
CH 2
H
N
C
H
Peptide, protein,
Protein
polypeptide
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.
Free Energy (G)
kcals/mole
Energy of
activation
fructose 6-phosphate
+ ATP
o
Δ G = -3.4 kcals/mole
fructose 1,6-bisphosphate
+ ADP
Reaction Progress
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? _______________________Lipid, Phospholipid_________
b) Explain the important qualities/properties of these molecules that allow them to form
membranes. Phospholipids possess hydrophilic “heads” and hydrophobic “tails” that allow them to assemble into a
bilayer containing a hydrophobic core when in an aqueous environment.They are Amphipathic. One hydrophilic end that
faces the aqueous solution, and one hydrophobhic end that faces another hydrophobic moiety on another molecule.
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.
The circled amino acids have hydrophobic side chains that reside within the hydrophobic
interior of the membrane.
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
CH 2
Cys75
CH2
CH2 CH2 CH
2
H2N
O
Phe50
Lys65
C CH2 CH2
H3C
H3C
Interacting Side chains
Receptor 2
CH
Gln12
Val98
Type of interaction
i)
Phe50 : Val98
van der Waals
ii)
Asp68 : Lys65
ionic
iii) Cys75 : Cys82
covalent
iv) Ser53 : Gln12
hydrogen
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.
When the protein folds into its final form, amino acid residues that are far apart in the primary structure
can be closely aligned to one another.
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
The receptors will not be able to dimerize because this substitution replaces a
negatively charged amino acid with a positively charged amino acid. The ionic bond
between Asp68 and Lys65 is disrupted, and a repulsion occurs.
ii) Ser53 → Thr
The receptors will be able to dimerize because this substitution replaces a polar amino
acid that can participate in hydrogen bonds with another such amino acid.
iii) Phe50 → Asn
The receptors will be able to dimerize even though this substitution replaces a
hydrophobic acid with a polar amino acid because the van der Waals forces remain.
(Within the region diagrammed, the close proximity of the charged species makes it
unlikely that hydrophobic interactions are a key force in the interaction between the
two receptors.)
iv) Val98 → Ile
The receptors will be able to dimerize because this substitution replaces a
hydrophobic acid with another hydrophobic amino acid and the van der Waals forces
remain.
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.
This substitution positions two cysteine residues opposite each other. These two residues
can form a disulfide bond and thus covalently link the two receptors together.
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
A A
a a
B
B
b
b
A A
Metaphase
a a
B
B
b
b
8
A
Anaphase
A
a
a
B
b
B
b
Telophase
phase
a
A
A
a
B
b
B
b
b) Indicate the genotype of cells that would result after telophase. _____AaBb_______
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
b
Bb
Telophase I
A
A
a
B
B
b
a
b
Metaphase II
A
a
B
B
A
b
a
b
Telophase II
A
B
a
B
A
b
a
b
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
a
a d
A d
a D
D
ii) Circle the genotypes of the recombinant gametes above.
iii) At what frequency do you expect each of the recombinant genotypes to occur? ___10%___
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