Tutorial 2 & 3 Page 1 of 26

Tutorial #2 & 3: Cellular Chemicals, Nucleotides & DNA;

Amino Acids & Proteins




This tutorial contains 3 sections:
A: Review of bond types and some chemical structures (Week of Sept 16)
B: Nucleic acids and DNA (Week of Sept 16)
C: Amino Acids and protein (Week of Sept 23)



To complete tutorial:

Read in ECB: Chapter 2 p39-79 including Panel 2-1 through 2-7; Chapter 3 p81-95
including Panel 3-1; Chapter 4 p119-140; Chapter 5 p171-179. It is strongly
recommended that you make study notes while reading the textbook. This will assist
you preparation for the midterms and the final exam.
If you are a visual learner, we suggest you prepare cue cards with an image of one of
the amino acids or nucleic acids on one and the properties, codes and other information
on the other side. These should help you memorize these structures and their
properties. You may also want to prepare cue cards with the different bond and
structure types.



After completion of the tutorial you should be able to:
Recognize the chemical and bond type of the chemical components of the cell.

Be able to draw and identify all the amino and nucleic acids, list their properties, the
types of bonds and the way polymers of these molecules form and interact.
Identify structure - functions relationships.




















BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 2 of 26



Part A: Cellular Chemical Components

Before the tutorial:
Review basic structures, bond type and formation in ECB Chapter 2: p39-50 and Panels
2-1, 2-2 and 2-7.


Key terms to help you study & review:


acids
alcohols
aldehydes
amides
amines
amino acid
Avogadros number
bases
carbonyl group
carboxyl group
carboxylic acids
condensation reaction
covalent bond
deoxyribonucleic acid
DNA
electrostatic attractions
esters
fatty acids
free energy
G
high energy bond
hydrogen bond
hydrolysis
hydrophilic
hydrophobic
hydroxyl group
isomer
ketones
lipid
monomer
nucleic acid
nucleotide
nucleoside
organic molecule
oxidation
pH
phosphoanhydride bond
phosphodiester bond
phosphoryl groups
purine
polymer
pyrimidine
reduction
ribonucleic acid
RNA
saturated
unsaturated
van der Waals forces


This section of the tutorial should be very brief review of some of the chemistry required for this
course. By the end of this section you should be able to define all the words listed above. This
applies to all the Key terms to help you study & review in all the tutorial documents.





Part B: Nucleic Acids & DNA

Before the tutorial:
Review basic nucleic acid structure in ECB Chapter 2 p56-58 and Panel 2-6
Review basic DNA and RNA structure in ECB Chapter 5 p172-179
Complete the pre-tutorial NA & Genes Worksheet.



BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 3 of 26

Objectives:
Review the basic structure of nucleotides and the nucleic acids DNA and RNA (All of this
you should have had in high school biology!)


Learn more about the similarity and difference in the structure of DNA and RNA and the
importance of these similarities and differences to their function.


Understand the importance of complementarity and polarity (directionality) for both DNA
and RNA (next week you will see the importance in protein primary structure).


Relate the chemical structure to function: understand the stabilizing forces,
hydrophobic/hydrophilic regions, and charge distribution. (Bonds are review from
CHM140 and high school biology and chemistry)


To complete the Worksheet you will need to know the basic structure of the nucleotides.


More specifically:
Distinguish purines from pyrimidines.

Know the names of the bases and be able to draw their structures.

Know the atom numbers for the sugar and bases as well as the 5 3 orientation of both DNA
and RNA molecules.

Know whether each of the 5 Watson-Crick bases is found in RNA or DNA or both.

Know which bases complement each other in DNA-DNA and DNA-RNA complexes.

Be able to draw and identify the bond and bond type in nucleic acid polymers.

Know the charge of the sugar-phosphate backbone in DNA & RNA as well as the charge
distribution (+, -, neutral) on a nucleotide pair, DNA helix and RNA.
Be able to identify the major and minor grooves on a base pair and on the DNA helix.

Know the role of covalent bonds, Hydrogen bonds, van der Waals forces, hydrophobic
interactions to stabilize DNA and RNA.


Key terms to help you study & review:


adenine
antiparallel and parallel
base pair
covalent bond
cytosine
deoxyribonucleic acid
deoxyribose
dinucleotide
glycosidic bond
guanine
hydrogen bond
hydrophilic
hydrophobic (& hydrophobic
interactions)
nucleoside
nucleotide
major groove (of B DNA helix
& on base pair)
minor groove (of B DNA helix
& on base pair)
oligonucleotide
phosphodiester bond
polynucleotide
purine
pyrimidine
ribonucleic acid
ribose
thymine
uracil
van der Waals forces


BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 4 of 26


Introduction:
In order to fully understand the functions of molecules, one must understand their structures. A better
understanding of the arrangement of these essential molecules will help to understand the differences
between them, as well as how further modifications can affect them.

Furthermore, understanding structures allows one to visualize complicated processes such as the
synthesis of DNA (replication), RNA (transcription) and protein (translation), which are essential
processes to molecular biology.


Nucleic Acids (DNA and RNA)

The role of DNA is long-term information storage.

Therefore, two key functions of DNA are replication and expression: when cells divide the DNA must
copy itself with minimal errors (replication) and the information stored on the molecule must be
accessible at the right time (expression). DNA is read (transcribed) to make RNA; RNA is then read
(translated) to make protein. You may find it easier to recall which is which if you remember that
transcription is still the same language (nucleic acid to nucleic acid: DNA to RNA), while translation
changes languages (nucleic acid to amino acid: mRNA to protein).


Throughout this tutorial, keep in mind the structural features of DNA which supports the two key features
which make it idea for containing the information of heredity: faithful replication and predictable
expression.


As a storage medium, DNA must have certain properties:
1. The molecule must be able to carry information.
2. The molecule must be readable. It is no use putting information into a storage medium if the
information cannot be retrieved.
3. The molecule must be stable and secure.
4. The information must be passed from generation to generation. Thus the molecule must be able
to remain essentially unchanged for many generations.


RNA molecules read and interpret the information in DNA. The role of RNA is for information transfer
and information decoding. RNA molecules are key players in the reactions that turn information into
useful work.


Figure 1:
Single nucleotide with base,
deoxyribose pentose sugar
and phosphate





Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are large polymers composed of
monomers called nucleotides (see figure 1 above); the nucleotide polymers are called polynucleotides

BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 5 of 26

(short polymers are called oligonucleotides). Two base covalently attached together are called a
dinucleotide. A nucl eotide has three components: a phosphate group, a five-carbon sugar molecule,
and an organic base. Nucleotides are linked by phosphodiester bonds: the hydroxyl group attached to
the 3 carbon of the sugar forms an ester bond to the phosphate attached to the 5 carbon of the sugar on
another nucleotide, releasing a molecule of water. The bases are side groups on the sugar-phosphate
backbone.


Similarities and differences between DNA and RNA
1. Both RNA and DNA are composed of repeated units. The repeating units of RNA are
ribonucleoside monophosphates and of DNA are 2'-deoxyribonucleoside monophosphates.


2. Both RNA and DNA form long, unbranched polynucleotide chains in which different purine or
pyrimidine bases are joined by N-glycosidic bonds to a repeating sugar-phosphate backbone.

3. The chains have a directionality called a polarity. The sequence of a nucleic acid is read from 5'
to 3'. For example the sequence of the RNA molecule is AUGC and of the DNA molecule is
ATGC (Figure 2).














Figure 2:
The 5' to 3' Polarity of both DNA and RNA
(from the Biochemistry, University of Western Ontario)





4. The base sequence carries the information, i.e. the sequence ATGC has different information that
AGCT even though the same bases are involved.


5. The DNA backbone is more stable than RNA:
a. Especially in alkaline conditions the RNA polynucleotide is unstable because the 2' OH on the
RNA forms 2'3'phosphodiester intermediates which break down to a mix of 2' and 3' nucleoside
monophosphates.
b. The 2' deoxyribose allows the sugar to assume a lower energy conformation in the backbone.
This helps to increase the stability of DNA polynucleotides.
c. The integrity of information on the DNA molecule is more stable and more reliable. The DNA
double helix is formed by complementary base pairs (AT and GC). This base pairing
provides a way to correct errors; one of the bases of the pair can be a template to replace an
incorrect or missing base on the other strand.


BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 6 of 26


6. The natural state of DNA is a double-stranded helix with the two strands joined by hydrogen bonds
between complementary bases. The adenine-thymine (A-T) and guanine-cytosine (G-C) base-pair
complementarity is a consequence of the size, shape, and chemical composition of the bases.







Figure 3:
Complementarity:
Adenine-Thymine &
Cytosine-Guanine base pairs



















7. Base pair stability differs:
a. Notice the two H bonds in the AT base pair and three H bonds in the GC base pair. This
difference in H bonds is a significant contributing factor to the greater stability of GC base
pairs.
b. The sugar rings on the purine nucleotides are in slightly different conformations. The purine
and pyrimidine rings in the GC base pair are almost perfectly planar, but the AT rings are
twisted with respect to each other, and are not perfectly planar. GC bp stacks with their
neighbors better than AT base pairs, contributing to the energy that holds the double helix
together.


8. The two DNA strands of the helix run anti-parallel: one strand is oriented 5' to 3' and the other is
3' to 5'. The labeling convention for DNA strands is the 5' end is on the top left, 3' on the top right.
Because of predictable complementarity, usually DNA sequences are listed in a short form e.g.,
ATATATGC instead of writing out the sequence of both strands.


Example: (5') ATATATGC (3')
(3') TATATACG (5')
is usually written simply as ATATATGC! Where the orientation is rarely
labeled and it is assumed to be top strand, 5' to 3'!


BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 7 of 26


9. Unlike DNA, the primary structure of RNA is a single stranded polynucleotide; however, RNA
exists with extensive double-stranded regions particularly in tRNA and rRNA, but these double
stranded regions are intra-molecular rather than two complementary strands. Complementarity is
an important characteristic of RNA in DNA-RNA and RNA-RNA interactions. RNA base pairs are
guanine cytosine (G-C) as in DNA, but uracil (instead of thymine) pairs with adenine (U-A).
Uracil is a base found only in RNA while thymine is only in DNA.















Figure 4:
Comparison of thymine in
DNA (left) and uracil in RNA
(right) can you find the
difference?














Nomenclature of Nucleotides and Nucleosides:


Table 1 Names of the deoxyribose bases (DNA)

Definitions
Bases
Adenine (A) Guanine (G) Cytosine (C) Thymine(T)
Deoxynucleoside:
deoxyribose
a base

Deoxyadenosine
(dA)
Deoxyguanosine
(dG)
Deoxycytidine
(dC)

Deoxythymidine
(dT)
Deoxynucleotide
a phosphate,
a deoxyribose
a base


Deoxyadenylate

Deoxyguanylate

Deoxycytidylate


Deoxythymidylate




BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 8 of 26


Table 2 Names of the ribose bases (RNA)

Definitions
Bases
Adenine (A) Guanine (G) Cytosine (C) Uracyl (U)
Nucleoside
a ribose
a base


Adenosine


Guanosine

Cytidine

Uridine
Nucleotide
a phosphate
a ribose
a base



Adenylate



Guanylate


Cytidylate


Uridylate

(from http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/dnast.htm - a fun place to spend a few
moments!)


NOTE: even though an adenine plus a base and a phosphate is termed adenylate, when two more
phosphates are added to make ATP we call it adenosine triphosphate. This has obviously led to ADP
being called adenosine diphosphate, which has invariably led to AMP being called adenosine
monophosphates, even though, from the table above, should be called adenylate! When reviewing the
literature, the terms such as adenylate and guanylate are mostly seen in the names of enzymes which
utilize the high energy phosphate bond of the NMP. For example, formation of ATP from 2 ADP
molecules is performed by adenlyate kinase; this enzyme transfers the -phosphate group from one ADP to
the other ADP, forming ATP and AMP. Another enzyme, adenlyate cyclase, forms cAMP from AMP.

Chemical bonds and other stabilizing forces
Several types of forces stabilize the DNA helix and RNA. In DNA, there are hydrogen bonds formed
between bases (adenine pairs with thymine by two hydrogen bonds, guanine pairs with cytosine by three
hydrogen bonds). Van der Waals forces, from stacking interactions between base pairs, form in both
DNA and RNA. Ionic bonds form between positive and negatively charged groups so that interactions
between the two negative phosphate backbones and cellular cations (or basic proteins) serve to shield
the negative charges on the phosphates, negating the electrostatic repulsion between the two
backbones. Hydrophobic interactions occur due to the strong association of nonpolar molecules (such
as the stacked bases) into aggregates to minimize their exposure to water. Hydrophobic interactions are
not classified as true bonds because they do not result from an attraction between hydrophobic
molecules. The B DNA helix is also stabilized by water molecules in the grooves of the helix. The minor
groove contains a string made up of water molecules (called the spine of hydration).


Helical configuration
DNA has been shown to exist in three helical configurations: A-DNA, B-DNA and Z-DNA.
Figure 5 below shows images for comparison of the three forms of DNA. The images are all for DNA
molecules containing 12 base pairs; all 3 helix axes are vertical.





BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 9 of 26



Figure 5:
Comparison of the three forms
of the DNA double helix








Side











End
A-DNA B-DNA Z-DNA










(from: http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/Nucleic_Acids/nucacid_structure.html. Link is no
longer active.)



Table 3: Comparison of the three forms of the DNA double helix

A-DNA B-DNA Z-DNA
Helical sense right handed right handed left handed
Diameter ~26 ~20 ~18
Base pairs/turn 11 10.5 12
Helix rise/base pair 2.6 3.4 3.7
Base tilt normal to helix axis 20
o
6
o
7
o


Notice the following features (as shown in the Table 3 and figure 5)
A helix is the shortest, the Z is the thinnest & tallest with a diameter of about 18 Angstrom, and the
B form is about 20 Angstrom in diameter.


A and B forms are right handed; Z form is left handed.



BIO206H5F University of Toronto Mississauga






air
lar
Tutorial 2 & 3 Page 10 of 26

In B and Z form the Watson-Crick base pairs are perpendicular to the helix axis, in the A form they
are slanted. (Swarna,1996)


B-DNA, a right-handed helix, is the predominant form found in living tissue. On the outside of the B-
DNA the spaces between the intertwined strands form two helical grooves of different widths called
the major groove and the mi nor groove for the wider and narrow groove respectively. The
conformation of these grooves is significant as this space, and the exposed side groups on the
bases, are able to bind to other molecules, particularly proteins.


Figure 6 shows where the major and minor groves are located on a B-DNA double helix. The groves
are the result of the bond angles between the base and the pentose sugar. Figure 7 shows the major
and minor grove location between on base pair.

Figure 6:
DNA helix major & minor grooves
(from figure 7-9, p236 Introduction to
Molecular Biology, eds Griffith et al)











Major
Groove


Figure 7:
Major and minor grooves on the A-T base pair
(from figure 7-8, p235 Introduction to
Molecular Biology, eds Griffith et al)







Minor
Groove






Study the three different helical structures in figure 5 and be able to identify the major and minor grooves
on the B-DNA, as well as the 5and 3 ends of each anti-parallel strand.









BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 11 of 26

Nucleic Acid Worksheet


1. What does DNA/RNA stand for? (correct spelling counts!)


DNA= _____________________________________________
RNA = ____________________________________________


2. Name and draw the four bases found in DNA. Be sure to include the atom numbers!














3. Name and draw the one base only found in RNA:














4. Why do the atoms in the sugar molecules have a prime () after the number?









5. Which of the base pairs in DNA is most stable and why?














BIO206H5F 2011 University of Toronto Mississauga
Tutorial 2 & 3 Page 12 of 26

6. Draw and label a GC and A T nucleotide pairs and label the bases, sugar, phosphate, plus number
the atoms on the purine nucleoside. Also label the major and minor grooves of each base pair.


























7. Using the figure below answer the following questions.

















(a) Label (name) the bases, and the 5' and 3' carbons; add the OH groups to form a deoxyribose base
pair.


(b) Using arrows on the figure draw and label the MAJOR and MINOR grooves. What are the bond
angles and why are they not 90?




(c) Briefly give a logical functional significance of the major and minor grooves in the 3-D helical structure
of a B-DNA.








BIO206H5F 2011 University of Toronto Mississauga
Tutorial 2 & 3 Page 13 of 26

8. Draw a ribose, # the carbon atoms, label the attachment site for the base. Circle the hydroxyl group
not present in DNA.









9. Draw and label uracil and thymine. What is the structural difference between uracil and thymine?














10. Why does uracil replace thymine in RNA? Anot her way t o anal yze t hi s, i s t o t hi nk about
why thymidine replaces uracil in DNA (This question is difficult but you need to understand the answer.




















11. If one strain of bacteria A is naturally found at 80C and another strain of bacteria B is found at 20C,
would you expect the GC (guanine-cytosine) content to be higher or lower in bacteria A than bacteria B
and why?
















BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 14 of 26

12. Consider the following sequences:
DNA RNA
' A '
G
G
T
C
C
A
' T '

(a) Label the 5' and 3' ends of the DNA

(b) Circle the base that has a free phosphate group and label with a
P; put a square around the base with a free hydroxyl group
and label with OH.

(c) Down the right side of the DNA sequence above, write out the
complementary RNA sequence and label the 5' and 3' ends of
the RNA.


13. What is a dinucleotide and how does it differ from a base pair?





14. Draw a dinucleotide with the bases thymine and adenine and how would it be written:








15. In the 1940s Erwin Chargaff made the remarkable observation that in samples of DNA from a wide
range of organisms the mole percent of G [G/(A+T+C+G)] was equal to the mole percent of C. This
was an essential clue to the structure of DNA.
(a) If the GC content of a DNA molecule is 56%, what are the percentages of the four bases?


A= _____; T= _____; G= ____; C= _____

(b) Human DNA contains 20% C on a molar basis. What are the mole percents of A, G, and T?


A= _____; T= _____; G= ____; C= _____

(c) What is the structural basis for Chargaffs rules?





(d) Why does RNA not obey Chargaffs rules?






16. Structure-function: Nomenclature is more than just a name! Nucleotides are important in both nucleic
acid synthesis and energy transfer:
(a) Which nucleotide triphosphates would be used in transcription (RNA synthesis):


BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 15 of 26




(b) Which nucleotide triphosphates would be used in replication (DNA synthesis):
(c) What nucleotides are used for energy transfer?


(d) Why is there no TTP?











Part C: Amino Acids & Proteins

Before the tutorial:
Review all 20 amino acid structures in ECB Chapter 2 p72-73 Panel 2-5.
Review basic protein structure in ECB Chapter 4 p121-140
Read about how proteins are controlled
Complete the pre-tutorial Worksheet.


Objectives:
Review the primary, secondary, tertiary, quaternary structure of protein


Understand the importance of complementarity and polarity (directionality) for
polypeptides and 3D protein.
Relate the chemical structure to function: understand the stabilizing forces,
hydrophobic/hydrophilic regions, and charge distribution.
Factors affecting conformation of 3D structure.
Begin to appreciate how proteins work.
Begin to appreciate how proteins are regulated.



To complete the Worksheet you will need to know the all the amino acid structures.


More specifically:
Distinguish the charged polar, uncharged polar and nonpolar amino acids.



BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 16 of 26

Know the names of all 20 amino acids, the 1 and three letter code for each amino acid and be
able to draw all their structures.
Be able to draw and identify the bond and bond type in peptides, as well as the -carbon for each
amino acid in the peptide.
Know the charge of a given peptide; whether it is hydrophilic or hydrophobic.

Be able to identify - helices, parallel -sheets and anti-parallel -sheets.

Know the levels of structure of a protein, including domains and motifs.

Know the role of covalent bonds, hydrogen bonds, van der Waals forces, hydrophobic
interactions to stabilize proteins.
Know the importance of small molecules in protein function.
Know how proteins can be regulated by kinases and phosphatases, as well as non-covalent
mechanisms that can induce allosteric changes in protein structure.




Key terms to help you study & review:
allosteric
(alpha) helix
aliphatic
amphipathic
anti-parallel
(beta) sheet
coil-coiled
covalent bonds
disulfide bond
fibrous proteins


globular protein
hydrogen bonds
hydrophilic
hydrophobic
ionic bonds
kinases
ligand
non-polar
parallel
peptide bond


phosphatase
phosphorylases
polar
primary structure
quaternary structure
secondary structure
tertiary structure
van der Waals forces


To help you learn all 20 amino acids and their properties, they are summarized in the table below:
Amino Acid codes Properties Structure (un-i onized form)


Alanine


Ala


A
non-polar
aliphatic
hydrophobic
neutral







Arginine






Arg






R



polar
hydrophilic
charged
(+)




BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 17 of 26

Amino Acid codes Properties Structure (un-i onized form)




Asparagine




Asn




N

polar
hydrophilic
neutral





Aspartate




Asp




D
polar
hydrophilic
charged
(-)




Cysteine



Cys



C
polar
hydrophobic
neutral





Glutamine




Gln




Q


polar
hydrophilic
neutral





Glutamate




Glu




E

polar
hydrophilic
charged
(-)



Glycine


Gly


G
non-polar
aliphatic
neutral




Histidine




His




H
polar
aromatic
hydrophilic
charged
(+)










BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 18 of 26

Amino Acid codes Properties Structure (un-i onized form)




Isoleucine




Ile




I
non-polar
aliphatic
hydrophobic
neutral





Leucine




Leu




L
non-polar
aliphatic
hydrophobic
neutral








Lysine







Lys







K




polar
hydrophilic
charged
(+)







Methionine




Met




M


non-polar
hydrophobic
neutral





Phenylalanine




Phe




F

non-polar
aromatic
hydrophobic
neutral





Proline




Pro




P

non-polar
hydrophobic
neutral






BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 19 of 26

Amino Acid codes Properties Structure (un-i onized form)



Serine



Ser



S
polar
hydrophilic
neutral




Threonine



Thr



T
polar
hydrophilic
neutral





Tryptophan




Trp




W

non-polar
aromatic
hydrophobic
neutral






Tyrosine





Tyr





Y


polar
aromatic
hydrophilic
neutral




Valine



Val



V
non-polar
aliphatic
hydrophobic
neutral



URLs you might find useful:
Alpha helix (right and left handed)
http://www.web-books.com/MoBio/Free/Ch2C4.htm#right


Biology Project University of Arizona Biochemistry
http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.html













BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 20 of 26

Worksheet:
1. Draw and label the two stereoisomers of the amino acid alanine. Circle the isomer which
is normally found in nature?















2. Draw the amino acids serine and aspartic acid. Show the condensation reaction joining
these two amino acids by a peptide bond. Include the following labels:
peptide bond carboxyl group amino group
carbon on each amino acid before and after the condensation reaction.













3. What are amphipathic polypeptides?








4. Label the C-terminal and N-terminal in the following polypeptide chain:


MET-VAL-HIS-LYS-ARG-THR-LEU-VAL-HIS


5. Explain what is meant by parallel and anti-parallel strands in DNA and in protein.












BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 21 of 26


6. Make 3x5 cards one for each of the 20 amino acids. On the front draw the structure with
the R group in a contrasting colour; on the back put the full name, 3-letter code, 1-letter
code and characteristics (hydrophobic, hydrophilic, polar, nonpolar, acidic, basic, sulfur
containing)
This is only a suggestion to help in learning the different amino acids!


7. On the figure below of a short polypeptide label the following:
a. N-terminus and the C-terminus (N, C)
b. All of the carbons (A) and circle them.
c. All the peptide bonds (P).
d. Each amino acid with the full name and the 3-letter code.






8. Distinguish between a polypeptide and a protein.







9. How are the properties of an helix different from a strand; how are they similar?







10. Draw as well as explain in words what the following abbreviations represent:
Cys-S-S-Cys


Ser-P



BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 22 of 26

11. Complete the following table comparing the properties of the structural levels of protein:

Structural level Structural description Bonding characteristics







12. What are the major properties that distinguish different amino acids from one another?
Create a table to classify each of the 20 amino acids into clusters of similar characteristics:
be able to identify an amino acid by its R group and classify it as polar (positive, negative,
uncharged), or nonpolar.










13. What are the properties of glycine, proline, and cysteine that distinguish these amino acids
from the others? How do these properties affect secondary structure?














BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 23 of 26

14. The human hemoglobin chain contains an helical structure. The primary sequence of
the amino acids in this region is:


pro-pro-val-glu-ala-ala-tyr-glu-lys-val-val-ala-gly-val-ala-asn-ala-leu-ala-his-lys-tyr-his


a. How many turns in the helix? How did to arrive at this number?








b. If each amino acid contributes 0.15 nm to the helix, what is the approximate length of
this helix?








c. Circle the hydrophobic amino acids.


d. Underline the hydrophilic amino acids.
e. Why is this alpha helix amphipathic?






15. Compare and contrast properties of fibrous and globular proteins and give examples for
each.




















BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 24 of 26

16. Consider the following amino acids:
Cys-S-S-Cys Gln Glu His
Ile Leu Lys Met
Phe Ser Ser-P Val

a. Which of the above amino acids would you expect to find more often exposed to the outside
of a globular protein?





b. Which amino acids would you expect to find more often in the centre of a globular protein?





c. Which ones would you expect to see more in fibrous proteins?





d. Which amino acids would most likely reside in the membrane-anchoring domain of a
protein?





17. Describe the role of the following chemical bonds/forces in stabilizing protein structure
and/or affecting the conformation:
Hydrogen Bonds




van Der Waals Forces





Ionic Bonds





Hydrophobic Interactions





Disulfide Bonds



BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 25 of 26




18. Define the following:
protein motif:










protein domain:








19. Explain why the following statements describe a motif or domain.
a. Proteins that bind calcium often have a helix-loop-helix structure with hydrophilic amino
acids at critical positions.





b. Regulatory protein CAP (catabolite activator protein).





c. DNA binding proteins.




d. Several proteins, including tissue plasminogen activator (tPA) and the digestive enzyme
chymotrypsin, have a 200 to 300 amino acid region that catalyzes the breakdown of
protein. This region is attached to the rest of the protein by an amino acid hinge.



e. Proteins that reside in membranes have long sequences of hydrophobic amino acids
that anchor the proteins in the lipid membrane.



f. Proteins that bind DNA are characterized by a zinc finger: a combination of one alpha
helix and two strands stabilized with a zinc atom. This structure fits into the groove of
DNA.


BIO206H5F University of Toronto Mississauga
Tutorial 2 & 3 Page 26 of 26


20. Draw and describe protein regulation by phosphorylation.



































































BIO206H5F University of Toronto Mississauga