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Summary of Lecture 1:

7.013 Recitation 1 2013

Origin of life: its unity and diversity: It is thought that earth evolved about 5 billion years ago and
was inhabitable for the first 1 billion years. As earth cooled down, organic molecules were formed and
the first evidence of life (prokaryotes) appeared about 3.8 billion years ago in oceans. Photosynthetic
organisms likely originated about 2.5 billion years ago. These organisms increased the oxygen
concentration on earth and influenced the evolution of multi-cellular aerobic organisms about 1 billion
years ago. The true multi-cellular organisms evolved about 500 million years ago. The organisms today
are classified into three major domains; bacteria, archaea and eukarya. Of these bacteria and archaea
are unicellular and prokaryotic (without nucleus) whereas eukarya are nucleated and mostly multicellular.
Because all living organisms have originated from a common ancestor they share a genetic makeup and
are comprised of cells as their building blocks. Many of the processes that occur in the simplest of cells
also occur in complex organisms. The examples of such processes are replication (making DNA from
DNA), transcription (making RNA from DNA) and translation (making proteins from mRNA) etc.
Thus, biologists can use model systems such as bacteria, yeast, flies and mice for their research
knowing that they can extend their conclusions to other organisms including the human beings.

Questions:
1. Organisms such as bacteria, yeasts, flies, mice and rabbits are used as model systems for different
biological experiments.
i.

Classify each of the above organisms as prokaryotic or eukaryotic.

ii.

Classify each of the above organisms as unicellular or multi-cellular.

2. Human beings are complex multi-cellular organisms made of different cell types each responsible for
specialized function. Compare three cell types: retinal cells, skin cells and unfertilized ova.
i.

Do all these cell types have the same set of genes and same number of chromosomes?

ii.

Are the genes expressed in the unfertilized egg same as the genes in the retinal cells?

iii.

Are the proteins in the retinal cells the same as the proteins in the skin cells?

7.013 Recitation 2 - 2013


Summary of Lectures 2 & 3:
Bonding: There are many types of bonds that hold molecules together. Covalent bonds result when
two atoms share a pair of electrons between them, such as the bonds between C and H in methane.
Ionic bonds occur between atoms with a very high difference in electronegativities. Hydrogen bonds
occur between polar molecules, such as molecules of water, because of the partial negative charge on
the O and the partial positive charge on the H i.e. difference in the electronegativity of O and H atoms.
Van der Waals forces are very weak forces that occur between all atoms because of random distribution
of electrons. Hydrophobic effects promote the association of hydrophobic molecules together in order
for them to avoid water and thereby increase entropy.

Biological macromolecules- Lipids and Carbohydrates: All the cells, whether prokaryotic or
eukaryotic, have biological polymers or macromolecules. They are composed of the same major classes
of macromolecules: lipids, carbohydrates, nucleic acids and proteins.
Lipids or fats are predominately hydrocarbon chains that are used as energy storage and insulation.
Lipids are hydrophobic in nature. Modified lipids form phospholipids, steroid hormones, cholesterol
and some vitamins. Cell membranes are composed of lipid bilayers, which separate the aqueous inside
of the cell (the cytoplasm) from the aqueous outside of the cell (the extra cellular environment). One
specific type of lipid, called phospholipids, has polar phosphate groups as heads and two long
hydrocarbon tails that are hydrophobic. Phospholipids form lipid bilayers in aqueous solutions that
expose the phosphate head groups on each side of the layer and hide the hydrophobic tails in between
the two rows of head groups. Cell membrane is selectively semi-permeable. Only small hydrophobic
molecules can pass through cell membranes. All large or polar or charged molecules must cross the
membrane through protein pores in the membrane.
Carbohydrates include monosaccharides and disaccharides like glucose and lactose. A monosaccharide
is composed of carbons flanked by H atoms or -OH groups and can be linear or have a ring structure.
Many monosaccharides are linked together to form polysaccharides like starch and cellulose.
Carbohydrates are used as an energy source, as a source for carbon, and can be attached to other
molecules to serve as recognition markers for the cell.

Questions:
1. Many glucose monomers can be linked together through glycosidic bonds to make polysaccharides
such as glycogen in animals and starch in plants. What is the advantage of storing carbohydrates as
polysaccharides as opposed to monosaccharides?

2. Oil is fluid at room temperature but butter is solid. Which types of fats (saturated/unsaturated)
predominate in oil and butter?

3. Each cell in an organism has a plasma membrane that defines its boundaries, however the plasma
membranes of different cell types show different fluidity. What factors determine the fluidity of the
plasma membrane?

4. When biomedical researchers design drugs that must enter cells to be effective, they often add
methyl (-CH3) groups, which make the drugs more likely to enter the cells. Why does this work?

5. The structure of one lipid that can use to make up a lipid monolayer is shown below. Why would
you not need a bilayer (i.e. but instead could use a lipid monolayer) if you used this specific kind of
lipid to make up a cell membrane?
R2
R1

Note: R1 & R2 represent charged groups and represents bonds between C and H atoms.

6. The following diagram represents a substrate molecule bound to the active site of a protein. The R
groups from the amino acids in the proteins substrate-binding region are shown. Each of the four R
groups from the protein that interacts with the substrate is numbered on the figure below. For each
side chain, state the strongest type of interaction it could have with the substrate in the configuration
shown below. Your choices are: Covalent, Hydrophobic, Ionic, Hydrogen, and Van der Waals. Also classify
each R group as hydrophobic, polar or charged.
This is the simplest correct bonding
arrangement of the atoms and charges.

H
N
O

Solution

Substrate

H
H
H

C
H

C
C
H

C
C

H
C
C

Protein

H
H

H
H

C
H H
H
C
H C

C
H

a) Identify the amino acids (1), (3) and (4) in the schematic above.
b) Classify the amino acids that you have identified above as polar/nonpolar, charged/ uncharged and
hydrophilic/hydrophobic.
c) Complete the following table.
R Group

Interaction(s) of R Group with


Substrate

Classification of R Group

(1)
(3)
(4)

STRUCTURES OF AMINO ACIDS at pH 7.0


O

O
H

CH3

NH3
+

CH2CH2CH2 N

CH2 SH

H
N

C
C

C
N

H
H

O-

CH2CH2

CH2CH2

CH3

METHIONINE
(met)

CH2CH3

CH2

O-

H
CH3

NH3 OH
+

THREONINE
(thr)

CH2

OC

C
H
CH2

N
H +

O-

CH2

H
H

CH2CH2CH2CH2

LYSINE
(lys)

O
H

C
NH3
+

CH2

OH

NH3
+

CH2

SERINE
(ser)

PROLINE
(pro)

H
N

H
H

O
H

NH3
+

TRYPTOPHAN
(trp)

CH3

CH3

O
C

LEUCINE
(leu)

GLYCINE
(gly)
O

NH3
+

CH2

C
NH3
+

PHENYLALANINE
(phe)
O

OC H
C

C
NH3
+

O
C

O-

GLUTAMINE
(gln)
O

O
C

NH2

NH3
+

O
H

O-

ASPARTIC ACID
(asp)

NH3
+

ISOLEUCINE
(ile)

H
O-

CH2 C

NH3 CH3
+

HISTIDINE
(his)

CH2

NH3
+

C
NH3
+

O-

CH2CH2

NH2

ASPARAGINE
(asn)

GLUTAMIC ACID
(glu)

CYSTEINE
(cys)

CH2 C

NH3
+

NH3
+

NH2
+

NH2

O-

NH3
+

O-

ARGININE
(arg)

C
NH3
+

ALANINE
(ala)

O
C

C
CH2

OH

NH3
+
H

TYROSINE
(tyr)

CH3

NH3
+

CH3

VALINE
(val)

NH3+

7.013 Recitation 3 - 2013


Summary of Lecture 4:
Biological macromolecules- Nucleic acids and Proteins: Nucleic acids [Deoxyribonucleic acids (DNA)
/ Ribonucleic acids (RNA)] are polymers specialized for the storage, transfer and use of genetic
information. They are comprised of nucleotides (A, T, G, C and U) each of which has phosphate group,
a pentose sugar and a nitrogenous base. Polymers of nucleic acid are formed by linking the 5
phosphate group of incoming nucleotide to the 3 hydroxyl group on the pentose sugar of last
nucleotide in the growing nucleic acid strand. DNA is the hereditary material in the cell and is usually
double-stranded. The RNA is usually single-stranded and is of three major types: ribosomal (rRNA),
transfer (tRNA) and messenger (mRNA). The mRNA gets translated to proteins. In comparison, the
tRNA and rRNA are involved in the synthesis of proteins. Nucleotides also serve as energy sources
(ATP and GTP) and second messengers (cAMP) during intracellular or cell-cell signaling.
Proteins are linear chains of amino acids of which there are 20 distinct types. The order of the amino
acids in the chain dictates the shape that the protein will take and therefore the function of the protein
in the cell. There are 4 levels of protein structure: primary, secondary, tertiary and quaternary. The
precise sequence of amino acids in a polypeptide chain constitutes the primary structure of proteins. A
proteins secondary structure (- helix and - pleated sheets) is comprised of regular repeated spatial
patterns in different region of polypeptide chains and is predominantly stabilized by hydrogen bonds.
The different interactions between the side chain groups of the amino acids determine the 3dimensional tertiary structure of proteins. Quaternary structure results when two or more polypeptide
chains in a protein bind to and interact with each other. Proteins perform all possible functions within a
cell except storage of hereditary information. Proteins can be structural, can be used to transport
materials, can be used for locomotion of cells and be used as enzymes or biological catalysts. It is worth
mentioning that the RNA may also have enzymatic activity.

Enzymes and energy: An endergonic reaction (one with a positive G) cannot occur spontaneously,
although it may be coupled to an exergonic reaction. An exergonic reaction (one with a negative G)
can proceed spontaneously. Exergonic reactions do not necessarily proceed quickly; this highlights the
difference between thermodynamics and kinetics. The thermodynamics of the reaction are dictated by
the difference in free energy between the substrate and the products. The kinetics of the reaction is
determined by the transition stage and how much energy must be added to form the intermediate.
Enzymes lower the activation energy needed for a reaction to proceed, but do not change the free
energy of either the reactants or the products.
Enzymes are biological catalysts. They catalyze specific reactions and act by lowering the activation
energy of their reaction. Each enzyme has a specific 3-dimensional conformation and an active site to
which the substrate molecules can bind. The complex then gives rise to product (P) and the enzyme is
released in its original form to catalyze the reaction once again. Each enzyme is specific for a particular
reaction. Enzyme functioning may be regulated by various factors. These factors may include i.e.
prosthetic groups, metal ions / cofactors, coenzyme, substrate concentration, pH, temperature,
inhibitors, allosteric modulators and the feedback inhibition by the end product.

Questions:
1. Nucleic acids are of two major types: double helical DNA and single stranded RNA.
i.
Draw the chemical structure of a DNA molecule composed of three deoxy-ribonucleotides.
Label the 3 and 5 ends.

ii.

How is a nucleotide different from a nucleoside?

iii.

Why the two strands of DNA are anti-parallel to each other?

iv.

Why is RNA more reactive compared to a DNA?

v.

RNA is single stranded. However, it can have a very complex three-dimensional structure.
Certain regions of RNA may show intra- molecular base pairing. Is the base pairing observed in
RNA similar to or different from that in DNA?

2. A certain protein has this structure, where a line indicates a hydrophilic region and a box represents
a hydrophobic region.
Hydrophilic

Hydrophobic

i.

Why do you think the protein might fold this way when dissolved in salt water?

ii.

How do you think the protein might fold differently if it were dissolved in cooking oil?

3. You are studying a protein that comes from a bacterial species that lives in your gut. This protein
also has enzymatic function. If you boil this protein, you will disrupt Hydrogen bonds and ionic bonds,
but not covalent bonds. If this enzyme is most active (100% active) in the cytoplasm of a bacterial cell
(37oC) in your gut, what would be the effect of protease treatment on the activity of this protein?

4. Pepsin is a digestive enzyme that acts on proteins in stomach. This requires the presence of HCl for
its normal functioning.
i.

What may be the type of reaction catalyzed by pepsin?

ii.

Pepsin functions well in the stomach but it ceases to function in the intestine. Explain why
pepsin does not function in the intestine?

5. The formation, maturation and folding of secreted proteins takes place in the endoplasmic reticulum
and the golgi body. These steps normally occur without any error. However, very rarely a misfolded
protein may be produced which (if not destroyed) can lead to severe, life threatening diseases. How do
the cells normally get rid of these misfolded proteins?

6. Enzymes, which are usually proteins, act as biological catalysts. Of the properties mentioned in the
following table, state which are not changed by the enzymes.
Properties

Does enzyme change this property (Yes/No)?

G of reaction
Rate of reaction

7. Working in a research lab you happen to identify a novel protein. This protein serves as an enzyme,
which catalyses the following reaction.
A

B+ C

G = negative

You observe that if you increase the concentration of substrate A, there occurs a simultaneous increase
in the rate of reaction, but only up to a certain point. Explain why.

Summary of Lectures 5 - 7:

7.013 Recitation 4 -2012

Introduction to Genetics: Each double-stranded piece of DNA in a cell is a chromosome. A


eukaryotic cell usually contains 5-50 linear chromosomes. A chromosome is comprised of DNA and
histone proteins and usually has a few thousand genes on it, all in a row. A gene is a short region of
DNA (a few 1000 nucleotides) that encodes the RNA or a protein that has some specific cellular
function. Two alleles (or versions) of the same gene may differ at only a single nucleotide and often
affect the identity of only a single amino acid in the protein product of the gene. This single amino acid
change may alter a gene product such that it works differently or not at all. The changed function of
that protein may affect the phenotype of the organism possessing that allele; for instance, a single
nucleotide change in the DNA of a plant can result in wrinkled seeds instead of round seeds. The
genotype of an organism is the alleles possessed by that organism. The phenotype of an organism is
how that organism looks on the outside (round or wrinkled).

Mendels laws and monohybrid cross: A monohybrid cross is when you cross two true-breeding
(i.e. homozygous) organisms that differ by a single characteristic, such as plants that produce rounded
versus wrinkled seeds. The two organisms you cross are called the P (parental) generation. For
example, a cross between two individuals, which are both homozygous and differ from each other in
one gene can be represented as AA X aa. The offspring will all receive one allele from each parent and
will have the genoptye Aa. They will display whichever of the two phenotypes is dominant. If you
cross two F1 organisms together (Aa x Aa), you create the F2 generation. The ratios of different
genotypes and phenotypes within the F2 generation can be derived either by using the laws of basic
probability (the sum rule and the product rule) or by using a Punnett Square.

Dihybrid cross: A dihybrid cross is when you cross two true-breeding organisms that differ by two
characteristics, such as plants that produce rounded green (AABB) versus wrinkled yellow (aabb)
seeds. The F1 will be genotypically AaBb and will display the dominant shape and dominant color
phenotype. If you cross two F1 organisms together, you create the F2 generation. Each parent passes
on one of their two alleles at each gene to the new progeny, and thus the F2 will consist of a phenotypic
ratio of 9:3:3:1 (if the genes are independent from one another).

Cell division: Mitosis consists of four phases. In prophase, the chromosomes become condensed and
visible. In metaphase, the chromosomes all align along the central axis of the cell. In anaphase, the
sister chromatids separate from each other such that one copy of the genome goes to each daughter cell.
In telophase, the separated nuclei decondense their chromosomes so that you can no longer see
individual DNA molecules. Right after mitosis, cytokinesis occurs, which is the division of everything
else besides the nucleus (i.e. the cytoplasm and all of the organelles contained in the cytoplasm).
Meiosis has two divisions; meiosis 1 looks different from mitosis, but meiosis II looks similar to mitosis.
The result of meiosis is the production of haploid gamete cells such as eggs or sperm, each of which has
half the number of chromosomes as a diploid somatic cell.

Recombination and crossing over: Homologous recombination is the reciprocal exchange of DNA
between two homologous chromosomes that occurs only during metaphase of meiosis I. During
homologous recombination, two homologs (e.g. the chromosome #7 inherited from dad and the
chromosome #7 inherited from mom) break at the same place and switch ends with each other.
Homologous recombination results in a change in which alleles are on the same chromosomes together
(e.g. a cell with AB on the maternal homolog and ab on the paternal homolog can give rise to
gametes containing Ab or aB chromosomes). The two recombinants (Ab and aB) will always
be created in equal frequencies because one of each kind is created by a single recombination event.
Two genes can either be unlinked, completely linked or somewhat linked. Genes that are unlinked are
usually located on different chromosomes from each other or are located far apart from each other on
the same chromosome. Genes that are completely linked are very close to each other on the same
chromosome. Genes that are somewhat linked are located on the same chromosome with a map
distance of <50cM. Unlinked genes assort independently from each other; this means that an AaBb
parent would create their four possible gametes (AB, ab, Ab, and aB) each 25% of the time. Genes that

are completely linked always segregate with each other. This means that an AaBb parent would create
only two of the four possible gametes. Genes that are somewhat linked to each other show a pattern
that is in between what is seen for unlinked genes and completely linked genes.

Questions:
1. Below is pictured the nucleus from a skin cell taken from a mouse (named Mouse #1), with the
chromosomes shown in bold.
a) Is the cell haploid or diploid?

b) Lets say we blew up a region of the longest chromosome to look at its sequence at one small gene.

5-CCAGTATACGGATTACGTAC-3

5-CCAGTATACGGATTACGTAC-3

i.

Is Mouse #1 homozygous or heterozygous for this gene?

ii.

Now we zoom in on the same exact gene on the long chromosome in a cell from a mouse named
Mouse #2 and find that its two homologous chromosomes have the sequences:

5-CCAGTATACGGAGTACGTAC-3

5-CCAGTATACGGATTACGTAC-3

Sequence 1

Sequence 2

How might we write the genotypes of Mouse #1 and Mouse #2 if Sequence #1 encodes a
functional protein but Sequence #2 encodes a protein that no longer works? (Note: Use the upper
case or lowercase A while writing the genotypes).

2. Consider a humming bird whose body color is controlled by the B gene. These humming birds are
either green or yellow, where green color is dominant to yellow. Give the expected ratio (both
phenotypes and genotypes) of the offspring for the following crosses.
Genotypic ratio
Phenotypic ratio
Cross 1:

BB x BB

Offspring:

Cross 2:

bb x bb

Offspring:

Cross 3:

Bb X Bb

Offspring:

Cross 4:

Bb X bb

Offspring:

3. In a diploid cell (2n), that is undergoing cell division, draw a graph showing the variation in the
DNA content (n = haploid) against time for the mitosis and meiosis.

Meiosis

Mitosis
4n
4n

DNA
content

DNA
content

2n

2n

n
Time (hrs)

II

Time (hrs)

4. A schematic of a diploid nucleus prior to DNA replication is drawn below. It contains two pairs of
chromosomes (2n = 4).

The genotype of the cell above is DdEeFf, where the D and E loci are on the large chromosome and the
F locus is on the small chromosome. This cell was taken from an F1 organism that resulted from the
cross of two true-breeding parents such that Parent 1 is DDeeFF and Parent 2 is ddEEff. Draw and
align the chromosomes as they could be when in metaphase of meiosis I. Include the D, d, E, e, F, and f
alleles on the drawing and assume no recombination. Given your drawing, draw the chromosomes in
each of the two products resulting from meiosis I. Include the D, d, E, e, F, and f alleles on the drawing.

10

5. Tomato plants can be tall or short and have notched or smooth leaves. You cross a tall, smooth
leafed plant with a short, notched leafed plant. All of the progeny are tall, and notched leafed.
a) Which traits are dominant and which are recessive?
b) What are the genotypes of the two true-breeding parents? Use the letters H or h to represent the alleles
of the height gene and the letters S or s to represent the alleles of the leaf gene. In each case, use the uppercase
letter for the allele associated with the dominant phenotype and the lower case letter for the allele associated with
the recessive phenotype.
c) Two tall, notched F1 plants were crossed.
i.
Diagram this cross.

ii.

If these two traits are unlinked, what ratio of phenotype do you expect in the F2 generation?

6. In fruit flies, the B/b gene and the G/g gene are linked. In one specific fly whose genotype is
GgBb, B is linked to g on the maternal chromosome #2, and b is linked to G on the paternal
chromosome #2. Note: This is a practice question related to lecture 8.
i.
List all parental type (non-recombinant) gametes by genotype that could be produced by this
GgBb fly.

ii.

List all recombinant gametes by genotype that could be produced by this GgBb fly.

iii.

Say that 40% of all gametes produced by the GgBb fly are Bg. What percentage of all gametes
produced by this fly are recombinants?

iv.

As the recombination frequency between two genes on the same chromosome rises, does the
physical distance between those two genes lower or rise?

11

Section 1-Solution key:


1. Organisms such as bacteria, yeasts, flies, mice and rabbits are used as model systems for different
biological experiments.
iii.
Classify each of the above organisms as prokaryotic or eukaryotic.
Cells that lack a membrane bound nucleus and cell organelles are prokaryotic (i.e. bacteria) whereas cells with a
distinct nucleus and cell organelles are eukaryotic (i.e. yeasts, flies, mice and rabbits).
iv.
Classify each of the above organisms as unicellular or multi-cellular.
Bacterial and yeast cells are unicellular whereas flies, mice and rabbits are multi-cellular.
2. You are given three different cell types, each stained with a dye that specifically binds to
deoxyribonucleic acid (DNA). You observe these cells under the microscope. Classify them as
prokaryotic, eukaryotic, gametes or skin cells based on the following observation. If there is more than one
good choice, include all.
i.
ii.
iii.
iv.

Cells contain circular DNA. Prokaryotic mostly, but eukaryotic cells, gametes and skin cells may have
circular DNA in their mitochondria.
Cells contain DNA segments in a specific organelle. Eukaryotic, skin cells, gametes
Cells contain two copies of DNA segments in a specific organelle. Eukaryotic, skin cells
Cells contain single copy of DNA segments in a specific organelle. . Eukaryotic, gametes

3. Human beings are complex multi-cellular organisms made of different cell types each responsible for
specialized function. Compare three cell types: retinal cells, skin cells and unfertilized ova.
iv.
Do all these cell types have the same set of genes and same number of chromosomes?
All the cells in an organism are derived from a fertilized ovum and therefore have the SAME set of genes.
Unfertilized ovum, being haploid, has half the number of chromosomes as retinal and skin cells, which are diploid.
v.
Are the genes expressed in the unfertilized egg same as the genes in the retinal cells?
No, each cell expresses a unique combination of genes.
vi.
Are the proteins in the retinal cells the same as the proteins in the skin cells?
Although all cells in an organism have the same set of genes, the gene expression (a process by which DNA
directs the synthesis of proteins) is specific for each cell type and it determines cell structure and functions.
Therefore, although some proteins may be common to both retinal and skin cells (i.e. enzymes involved in
synthesizing ATP), both retinal and skin cells will have their own UNIQUE set of proteins, which regulate their
specific structure and functions.

Section 2- Solution key:


1. Many glucose monomers can be linked together through glycosidic bonds to make polysaccharides
such as glycogen in animals and starch in plants. What is the advantage of storing carbohydrates as
polysaccharides as opposed to monosaccharides?
Polysaccharides are more compact and occupy less space compared to individually dispersed monosaccharides.
Also, if carbohydrates were stored as monosaccharides, instead of polysaccharides, they would exert much higher
osmotic pressure on the cell. For example 1000 glucose molecule would exert 1000 times the osmotic pressure of a
single glycogen molecule, causing water to move in. If it were not for polysaccharides most organisms would
expend a lot of time and energy expelling excess water from their cells.
2. Oil is fluid at room temperature but butter is solid. Which types of fats (saturated/unsaturated)
predominate in oil and butter?

12

Butter is comprised of saturated fatty acids that only have single bonds, which allow close packing. In
comparison, oil is comprised of unsaturated fatty acids that have one or more double bonds that hinder close
packing.
3. Each cell in an organism has a plasma membrane that defines its boundaries, however the plasma
membranes of different cell types show different fluidity. What factors determine the fluidity of the
plasma membrane?
This is defined by lipid composition and temperature. Fluidity of the membrane increases proportionately with an
increase in the unsaturated fatty acids, short chain fatty acids or phospholipids. It also increases with an increase
in temperature.
4. When biomedical researchers design drugs that must enter cells to be effective, they often add
methyl (-CH3) groups, which make the drugs more likely to enter the cells. Why does this work?
Plasma membrane is comprised of lipid bilayer with proteins embedded in it. Adding nonpolar, hydrophobic
methyl groups (-CH3) to the drug enhances the chances of the drug (which may otherwise be hydrophilic and
hence incompatible for the hydrophobic atmosphere provided by the lipid bilayer) to cross the lipid bilayer and
enter the cell to mediate its action.
5. The structure of one lipid that can use to make up a lipid monolayer is shown below. Why would
you not need a bilayer (i.e. but instead could use a lipid monolayer) if you used this specific kind of
lipid to make up a cell membrane?
R2
R1

Note: R1 & R2 represent charged groups and represents bonds between C and H atoms.
A cell membrane is comprised of lipid bilayer with proteins embedded in it. The hydrophobic tails of the lipids
molecules face each other and remain hidden in the non-aqueous interior of the lipid bilayer whereas the polar,
hydrophilic heads of the lipids molecules form the extracellular or cytosolic surface of the lipid bilayer. Since the
molecule shown in the schematic above has polar R1 and R2 groups at the two ends and a hydrophobic chain in
between, it can assemble with similar molecules to form a lipid monolayer that will have a hydrophobic interior
and hydrophilic exterior, as is observed in a cell membrane.
6. The following diagram represents a substrate molecule bound to the active site of a protein. The R
groups from the amino acids in the proteins substrate-binding region are shown. Each of the four R
groups from the protein that interacts with the substrate is numbered on the figure below. For each
side chain, state the strongest type of interaction it could have with the substrate in the configuration
shown below. Your choices are: Covalent, Hydrophobic, Ionic, Hydrogen, and Van der Waals. Also classify
each R group as hydrophobic, polar or charged.
This is the simplest correct bonding
arrangement of the atoms and charges.

H
N
O

Solution

Substrate

H
H
H

C
H

O
C
O

C
C
H

13

C
H

C
C

C
H

H
Protein

H
H

C
H H
H
C
H C
H

S
C
C

H
2

a) Identify the amino acids (1), (3) and (4) in the schematic above.
#1; asp, #3: val and #4:asn
b) Classify the amino acids that you have identified above as polar/nonpolar, charged/ uncharged and
hydrophilic/hydrophobic.
Asp is polar/ charged/hydrophilic, cys is polar/uncharged/hydrophilic, , val is nonpolar/ uncharged/hydrophobic
and asn is polar/uncharged/hydrophilic.
c) Complete the following table.
R Group
(1)
(3)
(4)

Interaction(s) of R Group with


Substrate
Ionic, (Hydrogen bonding also possible)
Hydrophobic / Van der Waals
Hydrogen bonding

Classification of R Group
Charged, polar, hydrophilic
Nonpolar, hydrophobic
Polar, hydrophilic

Section 3- Solution key:


1. Nucleic acids are of two major types: double helical DNA and single stranded RNA.
i.
Draw the chemical structure of a DNA molecule composed of three deoxy-ribonucleotides.
Label the 3 and 5 ends.

5P5

3
ii.
How is a nucleotide different from a nucleoside?
A nucleoside is comprised of a nucleic acid base (A, T, G, C, U) and ribose/deoxyribose sugar. In comparison, the
nucleotide has the base, sugar and the phosphate group.
iii.
Why the two strands of DNA are anti-parallel to each other?
The anti-parallel arrangement of the two strands in a DNA duplex allows the complementary bases to stack in a
manner that allows them to hydrogen bond with each other. This arrangement also ensures that both the strands
replicate in a 53 direction (you will learn more about this in your Molecular biology lectures).
iv.
Why is RNA more reactive compared to a DNA?
The extra OH group at the 2C of the ribose sugar allows RNA to be more reactive compared to DNA.

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v.

RNA is single stranded. However, it can have a very complex three-dimensional structure.
Certain regions of RNA may show intra- molecular base pairing. Is the base pairing observed in
RNA similar to or different from that in DNA?
Yes, the intra-molecular base pairing in RNA follows the same complementary base-pairing rule as DNA where
A forms two hydrogen bonds with U and C forms three hydrogen bonds with G.
2. A certain protein has this structure, where a line indicates a hydrophilic region and a box represents
a hydrophobic region.
Hydrophilic

Hydrophobic
iii.
Why do you think the protein might fold this way when dissolved in salt water?
The boxed hydrophobic regions try to hide in the non-aqueous interior away from the surrounding hydrophilic
environment of the salt water. In comparison, the hydrophilic regions, shown by the lines, remain exposed to the
salt water and may from hydrogen bonds and / or ionic bonds with the molecules in the surrounding
environment.
iv.
How do you think the protein might fold differently if it were dissolved in cooking oil?
The folding will be reversed. The boxed hydrophobic regions will be exposed and may undergo hydrophobic
interaction with the surrounding hydrophobic environment whereas the hydrophilic regions, shown by the lines,
will be hidden in the interior away from the surrounding hydrophobic environment.
3. You are studying a protein that comes from a bacterial species that lives in your gut. This protein
also has enzymatic function. If you boil this protein, you will disrupt Hydrogen bonds and ionic bonds,
but not covalent bonds. If this enzyme is most active (100% active) in the cytoplasm of a bacterial cell
(37oC) in your gut, what would be the effect of protease treatment on the activity of this protein?
Protease treatment will cleave the covalent peptide bonds that hold the amino acids of the proteins one after the
other to form its primary structure. The effect of such treatment is irreversible since the primary structure of the
protein is disrupted.
4. Pepsin is a digestive enzyme that acts on proteins in stomach. This requires the presence of HCl for
its normal functioning.
iii.
What may be the type of reaction catalyzed by pepsin?
Pepsin digests the proteins to small polypeptides at acidic pH.
iv.

Pepsin functions well in the stomach but it ceases to function in the intestine. Explain why
pepsin does not function in the intestine?
Each enzyme maintains its active three-dimensional conformation at a specific pH. The acidic pH in the stomach
is the required pH for pepsin activity whereas the alkaline pH of the intestine is not.
5. The formation, maturation and folding of secreted proteins takes place in the endoplasmic reticulum
and the golgi body. These steps normally occur without any error. However, very rarely a misfolded
protein may be produced which (if not destroyed) can lead to severe, life threatening diseases. How do
the cells normally get rid of these misfolded proteins?
The misfolded proteins are degraded by the lysosomal enzymes. Alternatively, they may bind to heat shock
proteins, which act as molecular chaperons to cage the misfolded proteins.

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6. Enzymes, which are usually proteins, act as biological catalysts. Of the properties mentioned in the
following table, state which are not changed by the enzymes.
Properties
G of reaction
Rate of reaction

Does enzyme change this property (Yes/No)?


No
Increases

7. Working in a research lab you happen to identify a novel protein. This protein serves as an enzyme,
which catalyses the following reaction.
A

B+ C

G = negative

You observe that if you increase the concentration of substrate A, there occurs a simultaneous increase
in the rate of reaction, but only up to a certain point. Explain why.
If you increase the substrate concentration, more substrate molecules will be available to bind to the active site of
the enzyme and get converted to products B and C. This causes an initial increase in the rate of enzyme-catalyzed
reaction. However, after some time, the active sites of all the available enzyme molecules are already saturated
with the substrate molecules i.e. enzyme itself becomes a limiting factor. At this point, even if the substrate
concentration is increased, there occurs no further increase in the rate of reaction i.e. reaction rate reaches a
plateau phase.

Section 4- Solution key:


1. Below is pictured the nucleus from a skin cell taken from a mouse (named Mouse #1), with the
chromosomes shown in bold.
a) Is the cell haploid or diploid?
It is diploid since the chromosomes are present in pairs.
b) Lets say we blew up a region of the longest chromosome to look at its sequence at one small gene.

5-CCAGTATACGGATTACGTAC-3

5-CCAGTATACGGATTACGTAC-3
iii.

Is Mouse #1 homozygous or heterozygous for this gene?

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It is homozygous since the sequence on the two homologous chromosomes provided in the schematic above is
identical.
iv.

Now we zoom in on the same exact gene on the long chromosome in a cell from a mouse named
Mouse #2 and find that its two homologous chromosomes have the sequences:

5-CCAGTATACGGAGTACGTAC-3

5-CCAGTATACGGATTACGTAC-3

Sequence 1

Sequence 2

How might we write the genotypes of Mouse #1 and Mouse #2 if Sequence #1 encodes a
functional protein but Sequence #2 encodes a protein that no longer works? (Note: Use the upper
case or lowercase A while writing the genotypes).
Mouse #1 = aa
Mouse #2: Aa
2. Consider a humming bird whose body color is controlled by the B gene. These humming birds are
either green or yellow, where green color is dominant to yellow. Give the expected ratio (both
phenotypes and genotypes) of the offspring for the following crosses.
Genotypic ratio
Phenotypic ratio
Cross 1:

BB x BB

Offspring:

All green

Cross 2:

bb x bb

Offspring:

All yellow

Cross 3:

Bb X Bb

Offspring:

1: 2: 1

Cross 4:

Bb X bb

Offspring:

1:1

3 Green : 1 Yellow

Green : Yellow

3. In a diploid cell (2n), that is undergoing cell division, draw a graph showing the variation in the
DNA content (n = haploid) against time for the mitosis and meiosis.

Meiosis

Mitosis
4n
4n

DNA
content

DNA
content

2n

2n

n
Time (hrs)

Time (hrs)

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II

4. A schematic of a diploid nucleus prior to DNA replication is drawn below. It contains two pairs of
chromosomes (2n = 4).

The genotype of the cell above is DdEeFf, where the D and E loci are on the large chromosome and the
F locus is on the small chromosome. This cell was taken from an F1 organism that resulted from the
cross of two true-breeding parents such that Parent 1 is DDeeFF and Parent 2 is ddEEff. Draw and
align the chromosomes as they could be when in metaphase of meiosis I. Include the D, d, E, e, F, and f
alleles on the drawing and assume no recombination. Given your drawing, draw the chromosomes in
each of the two products resulting from meiosis I. Include the D, d, E, e, F, and f alleles on the drawing.
D

Dd

e E

F F

Dd

e E

i) Metaphase of meiosis I

ii) Product 1 of meiosis I

F F

Product 2 of meiosis I

5. Tomato plants can be tall or short and have notched or smooth leaves. You cross a tall, smooth
leafed plant with a short, notched leafed plant. All of the progeny are tall, and notched leafed.
a) Which traits are dominant and which are recessive?
Dominant traits are tall and notched whereas the recessive traits are short and smooth.
b) What are the genotypes of the two true-breeding parents? Use the letters H or h to represent the alleles
of the height gene and the letters S or s to represent the alleles of the leaf gene. In each case, use the uppercase

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letter for the allele associated with the dominant phenotype and the lower case letter for the allele associated with
the recessive phenotype.
Tall, smooth leaf parent plant will have the genotype HHss whereas short, notched leaf parent plant will have the
genotype hhSS.
c) Two tall, notched F1 plants were crossed.
iii.
Diagram this cross.
HS
Hs
HS
HS HS
HS Hs
Tall, notched
Tall/notched
Hs
Hs HS
Hs Hs
Tall/notched
Tall/smooth
hS
hS HS
hS Hs
Tall/notched
Tall/notched
hs
hs HS
hs Hs
Tall/notched
Tall/smooth

hS
HS hS
Tall/notched
Hs hS
Tall/notched
hS hS
short/notched
hs hS
short/notched

hs
HS hs
Tall/notched
Hs hs
Tall/smooth
hS hs
short/notched
hs hs
Short/smooth

iv.

If these two traits are unlinked, what ratio of phenotype do you expect in the F2 generation?
Note: This is a practice question related to lecture 8.
Tall and notched (9): tall and smooth (3): short and notched (3): short and smooth (1)
6. In fruit flies, the B/b gene and the G/g gene are linked. In one specific fly whose genotype is
GgBb, B is linked to g on the maternal chromosome #2, and b is linked to G on the paternal
chromosome #2. Note: This is a practice question related to lecture 8.
i.
List all parental type (non-recombinant) gametes by genotype that could be produced by this
GgBb fly.
Non-recombinant gametes are Bg and bG.
ii.
List all recombinant gametes by genotype that could be produced by this GgBb fly.
Recombinant gametes are BG and bg.
iii.

Say that 40% of all gametes produced by the GgBb fly are Bg. What percentage of all gametes
produced by this fly are recombinants?
20% of the gametes are recombinants.
iv.
As the recombination frequency between two genes on the same chromosome rises, does the
physical distance between those two genes lower or rise?
Physical distance is directly proportional to the recombination frequency. So the distance increases with the
increase in recombination frequency.

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