Week # 9: Amino Acids and Proteins
Lectures - 23, 24, 25
http://www.elmhurst.edu/~chm/vchembook/565proteins.html
Concepts:
Classification of Amino Acids - polar, non-polar, acidic, basic, neutral
Synthesis of peptides and proteins
Protein Structure - primary, secondary, tertiary, quaternary
Denaturation - various agents to disrupt protein structure
Ques. 1. Use the following amino acids to answer the questions below:
ala, asp, arg, val, lys, leu, ser
a. Which amino acid is most polar?
b. Which amino acid is most non-polar?
c. Which amino acid gives an acidic solution?
d. Which amino acid gives a basic solution?
e. Which two amino acids form salt bridges between proteins?
f. Which two amino acids form hydrogen bonds between proteins?
g. Which two amino acids form hydrophobic interactions in proteins?
Ques. 2. Write a salt formation reaction with ser and val.
Ques. 3. Write the oxidation reaction of two cysteine amino acids.
Ques. 4: Use the above structures to answer the questions below:
a. Which amino acid is most polar?
b. Which amino acid is least polar?
c. Which amino acid has an acidic side chain?
d. Which amino acid has a basic side chain?
Ques. 5: Use the above structures to answer the questions below:
a. Which amino acid is most polar?
b. Which amino acid is least polar?
c. Which amino acid is the most polar looking only at thr and ser?
d. Which amino acid is the least polar looking only at asp and glu?
Ques. 6: Use the above structures to answer the questions below:
a. Which amino acid is most polar?
b. Which amino acid is least polar?
c. Which amino acid has an acidic side chain?
d. Which amino acid has an basic side chain?
e. Which amino acid side chain can not be considered for hydrogen bonding?
Ques. 7: Use the above structures to answer the questions below:
a. Which two amino acids may link in a salt bridge in tertiary protein structure?
b. Which two amino acids may link in hydrophobic interactions in tertiary protein
structure?
c. Which two amino acids may link in hydrogen bonding interactions in tertiary
protein structure?
Ques. 8: Use the above structures to answer the questions below
a. Which letter arrow points the end of the peptide that is the "amine" end?
b. Which letter arrow points the end of the peptide that is the "carboxyl" end?
c. Which letter arrow points to an amide or peptide bond?
Ques. 9. Write the peptide structures of:
a. ile-cys-thr.
b. Ala-Try-Gly-Phe
c. Ser-Cys-Ala-Gly
Ques. 10: Draw the optical isomers for: cys and ser.
O
cysteine
H2N
C
C
H 2C
OH
H
SH
Ques. 11. Explain the differences between primary, secondary, tertiary, and
quaternary protein structures by giving brief definitions of each. What types of
bonding are used in each?
Primary
Secondary
Tertiary
Quaternary
Ques. 12. Explain the difference between the alpha helix and the beta pleated
sheet protein structures. What are the differences in the hydrogen bonding?
http://www.elmhurst.edu/~chm/vchembook/566secprotein.html
Ques. 13. Define four types of bonding interactions which determine the tertiary
protein structure and give the type of bonding for each.
http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html
a.
b.
c.
d.
Ques. 14. Write the tertiary peptide structure showing ser and thr side chains
in hydrogen bonding.
Ques. 15. Write the tertiary peptide structure showing asp and arg side chains
as a salt bridge.
Ques. 16. List 4 amino acids which might be involved in non-polar hydrophobic
interactions.
Ques. 17: a. Write the tertiary peptide structure showing two cysteine side
chains as a disulfide bridge.
b. In the insulin structure above, how many disulfide links are present?
Ques. 18. What is the difference between fibrous and globular proteins?
Ques. 19. A. What is "heme"? Explain its structure and function in relation to
myoglobin and hemoglobin.
http://www.elmhurst.edu/~chm/vchembook/568globularprotein.html
Myoglobin:
Hemoglobin consists of four protein chains and four heme groups that carry oxygen from the
lungs to the tissue cells. Myoglobin consists of a single protein chain with 153 amino acids and
one heme group that stores oxygen in the muscle cells. Myoglobin has a stronger affinity for
oxygen then hemoglobin, which enables the oxygen to shift from one to the other.
The presence of myoglobin gives meat its bright red color. The tertiary structure is such that it
forms a "box-like" structure around heme. Heme is a series of flat, planar heterocyclic fivemember nitrogen rings attached to iron as shown in the above graphic.
The heme is held in position by the bonding of a nitrogen on a histidine side chain from the
protein to iron in heme. This histidine is shown in blue-gray on the left side of the heme. A second
histidine is in the vicinity on the opposite side of the heme but is not bonded.
There is one bonding position on iron ion for the attachment of oxygen diatomic molecule (red).
Note also that the oxygen is bonded at an angle to the plane of the heme.
Ques. 19B: Which type of protein structure is represented by the green ribbons?
Which type of protein structure is represented by bends and folds of the green
ribbons?
Ques. 20. What tertiary protein structures are disrupted by each of the
following in a denaturation type reaction:
http://www.elmhurst.edu/~chm/vchembook/568denaturation.html
acids
reducing agents
alcohol
heavy metal salts
A 70% alcohol solution is used as a disinfectant on the skin. This concentration
of alcohol is able to penetrate the bacterial cell wall and denature the proteins
and enzymes inside of the cell. A 95% alcohol solution merely coagulates the
protein on the outside of the cell wall and prevents any alcohol from entering the
cell.
Ques. 21. How does alcohol work as a disinfectant on the skin? In addition to
the tertiary structure shown below, what other types of structure is also disrupted
- be specific?
Ques. 22. What happens at the molecular level during the heat sterilization of
surgical instruments?
Acids and Bases Disrupt Salt Bridges:
Salt bridges result from the neutralization of an acid and amine on side chains.
Review reaction. The final interaction is ionic between the positive ammonium
group and the negative acid group. Any combination of the various acidic or
amine amino acid side chains will have this effect.
As might be expected, acids and bases disrupt salt bridges held together by ionic
charges. A type of double replacement reaction occurs where the positive and
negative ions in the salt change partners with the positive and negative ions in
the new acid or base added. This reaction occurs in the digestive system, when
the acidic gastric juices cause the curdling (coagulating) of milk.
Ques. 23: a. What other amino acids engage in making salt bridges? List all
possible acidic and basic amino acids.
b. Explain what happens if you were to accidentally get acid in your eyes or on
your skin. What happens at the molecular level?
Ques. 24: What is the difference between the hydrolysis and the denaturation of
a protein in terms of structures effected? Expalin why insulin can not be taken
orally, but must be injected?
Permanent Hair Wave:
http://www.elmhurst.edu/~chm/vchembook/568hairwave.html
Temporary Wave:
When the hair gets wet, water molecules intrude into the keratin strands. The
sheer numbers of water molecules are able to disrupt some of the hydrogen
bonds which also help to keep the alpha-helices aligned. The helices are able to
slip past each other and will retain a new shape in the hair drying process as new
hydrogen bonds are formed. The hair strands are able for a short time to
maintain the new curl in the hair.
Permanent Wave:
In the permanent wave process, a basic reducing substance (usually ammonium
thioglycolate) is first added to reduce and rupture some of the disulfide crosslinks.
The hair is then put on rollers or curlers. Since the alpha-helices are no longer
tightly cross-linked to each other, the alpha-helices can shift positions in relation
to each other. An oxidizing agent, usually a dilute solution of hydrogen peroxide,
(also called the neutralizer) is added to reform the disulfide bonds in their new
positions. The permanent will hold these new disulfide bond positions until the
hair grows out, since new hair growth is of course not treated.
Ques. 25: The interaction of two or more proteins chains is part of
___?___protein structure. The alpha helices are part of __?__ protein structure
and are held into shape by __?___ bonding.
Immunoglobin:
http://www.elmhurst.edu/~chm/vchembook/568immunoglobins.html
An immunoglobin is a specific protein called an antibody synthesized in response
to the presence of a foreign substance antigen). The antibody has a specific
molecular structure capable of recognizing a complementary molecular structure
on the antigen which might be some proteins, polysaccharides, and nucleic
acids. Small organic foreign molecules do not by themselves elicit antibody
formation unless they become bonded to one of the larger biomolecules listed
above.
Structural Details:
Immunoglobin G (IgG), the most common human immunoglobin, consists of two long "heavy"
chains shown as A - cyan and B - magenta in the graphic on the left. There are two disulfide
bonds very near the region where the "y" splits. This is also known as the hinge region.
Two short "light" chains shown as C - red and D - green are bonded to the main chains through a
single disulfide bond each. There are a variety of other disulfide bonds in other parts of the
molecule.
In the lower "bulge" region of the main A and B chains, there are two chains of carbohydrates
made of glucose and galactose. The carbohydrates are bonded to the protein chain through the
amino acid as asparagine. The is through the N of amide side chain to the carbon # 1 in the
glucose to make an N-glycosidic bond.
Antibody-Antigen Interaction:
The interaction of the antibody with an antigen causes a change in shape of the antibody. The
variable regions shown as black or gray in the graphic on the left are the areas of the receptor
site for the antigen.
This in turn may cause the exposure of another site, which then is responsible for the various
reactions elicited by the antibody to destroy the foreign substance. The interaction of antibodies
and antigens may produce a network type complex.
Above is displayed the 3-D structure of the V-A and V-C portions of the Fab
complexed with the heptapeptide antigen from HA. Examination of the antigen
binding pocket reveals that a pronounced conformational change has occurred
upon antigen binding. The pocket is deformed by the antigen, closing around it.
This is mostly caused by a shift in the orientation of V-A, represented by the gray
and red. The red is the orientation of Asp99 and Asn100.
Vaccinations:
The understanding of immunochemistry led to the use of vaccinations as
protection against various epidemic producing diseases such as small pox,
diphtheria, polio, and typhus. A vaccination works by injecting a small amount of
weakened disease producing virus into the body which elicits the production of
antibodies which eventually destroy the foreign substance. Subsequent invasions
of the body by this same virus are met and destroyed by the antibodies formed at
the time of vaccination.