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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, thetypes of bonds and the way polymers of these molecules form and interact.

Identify structure - functions relationships.

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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 acidAvogadros number

bases

carbonyl group

carboxyl group

carboxylic acids

condensation reaction

covalent bond

deoxyribonucleic acid

DNAelectrostatic attractions

esters

fatty acids

free energy

G

high energy bond

hydrogen bondhydrolysis

hydrophilic

hydrophobic

hydroxyl group

isomer

ketones

lipid

monomer

nucleic acidnucleotide

nucleoside

organic molecule

oxidation

pH

phosphoanhydride bond

phosphodiester bondphosphoryl groups

purine

polymer

pyrimidine

reduction

ribonucleic acid

RNA

saturated

unsaturatedvan 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 & DNABefore 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.


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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 theimportance of these similarities and differences to their function.

Understand the importance of complementarity and polarity (directionality) for both DNAand 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 fromCHM140 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.


adenine

antiparallel and parallel

base paircovalent bond

cytosine

deoxyribonucleic acid

deoxyribose

dinucleotide

glycosidic bond

guanine

hydrogen bond

hydrophilic

hydrophobic (& hydrophobicinteractions)

nucleoside

nucleotide

major groove (of B DNA helix

& on base pair)

minor groove (of B DNA helix

& on base pair)

oligonucleotide

phosphodiester bond

polynucleotidepurine

pyrimidine

ribonucleic acid

ribose

thymine

uracil

van der Waals forces


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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 in formation 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 po lynuc leotides


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(short polymers are called oligonucleotides ). Two base covalently attached together are called a

dinucleotide. A nucleotide 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 3carbonof 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 RNA1. 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' nucleosidemonophosphates.

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

doublehelix is formed by complementary base pairs (AT and GC). This base pairing

provides away to correct errors; one of the bases of the pair can be a template to replace an

incorrect ormissing base on the other strand.


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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 basepairs.

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

twistedwith 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'!


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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

guaninecytosine (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 Nucleos ides:

Table 1 Names of the deoxyribose bases (DNA)

DefinitionsBases

Adenine (A) Guanine (G) Cytosine (C) Thym ine(T)

Deoxynuc leoside:

deoxyribosea base

Deoxyadenosine

(dA)

Deoxyguanosine

(dG)

Deoxycytidine

(dC)

Deoxythymidine

(dT)

Deoxynuc leotide

a phosphate,

a deoxyribose

abase

Deoxyadenylate Deoxyguanylate Deoxycytidylate Deoxythymidylate


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Table 2 Names of the ribose bases (RNA)

DefinitionsBases

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 isperformed by adenlyate kinase; this enzyme transfers the -phosphate group from one ADP to

the otherADP,forming ATP and AMP. Another enzyme, adenlyate cyclase, forms cAMP fromAMP.

Chemical bonds and other stabilizing forcesSeveral 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 madeup of water molecules (called the spine of hydration).

Helical configurationDNA 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.


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Figure 5:

Comparison of the three forms

of the DNA double helix

Side

EndA-DNA B-DNA Z-DNA

(from: http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/Nucleic_Acids/nucacid_structure.html . Linkis 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 20o

6o

7o

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.


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air

lar


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 minor 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 bindto 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 minorgrove 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)

MajorGroove

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)

MinorGroove

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 5 and 3ends of each anti-parallel strand.


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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?

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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 aB-DNA.

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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? Another way to analyze this, is to think 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,

wouldyou expect the GC (guanine-cytosine) content to be higher or lower in bacteria A than bacteria B

and why?


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12. Consider the following sequences:

DNA RNA

'

A '

G

G

T

CC

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 aP; put a square around the base with a free hydroxyl groupand labelwith OH.

(c) Down the right side of the DNA sequence above, write out the

complementary RNA sequence and label the 5' and 3' ends oftheRNA.

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 anessential 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):


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(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.


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Know the names of all 20 amino acids, the 1 and three letter code for each amino acid and be

able todraw 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.


allosteric(alpha) helix

aliphatic

amphipathic

anti-parallel

(beta) sheet

coil-coiled

covalent bonds

disulfide bond

fibrous proteins

globular proteinhydrogen bonds

hydrophilic

hydrophobic

ionic bonds

kinases

ligand

non-polar

parallel

peptide bond

phosphatasephosphorylases

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:

Am ino Ac id codes Properties Structure (un-ionized form)

Alanine Ala A

non-polar

aliphatic

hydrophobic

neutral

Arginine Arg R

polarhydrophilic

charged

(+)


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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


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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

hydrophobicneutral

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


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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.


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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


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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?


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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.


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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


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