Week # 9: Amino Acids and Proteins
Lectures - 23, 24, 25
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.
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?
Ques. 13. Define four types of bonding interactions which determine the tertiary protein structure and give the type of bonding for each.
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.
Myoglobin:
Hemoglobin consists of four protein chains and four hemegroups that carry oxygen from the lungs to the tissue cells. Myoglobin consists of a single protein chain with 153 aminoacids and one heme group that stores oxygen in the musclecells. Myoglobin has a stronger affinity for oxygen thenhemoglobin, which enables the oxygen to shift from one tothe 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, planarheterocyclic five-member nitrogen rings attached to iron asshown in the above graphic.
The heme is held in position by the bonding of a nitrogen on ahistidine side chain from the protein to iron in heme. Thishistidine is shown in blue-gray on the left side of the heme. Asecond histidine is in the vicinity on the opposite side of theheme but is not bonded.
There is one bonding position on iron ion for the attachmentof oxygen diatomic molecule (red). Note also that the oxygenis bonded at an angle to the plane of the heme.
Ques. 19B: Which type ofprotein structure is represented by the green ribbons?Which type of proteinstructure is represented by bendsand folds of the greenribbons?
Ques. 20. What tertiary protein structures are disrupted by each of the
following in a denaturation type reaction:
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 bacterialcell wall and denature the proteins and enzymes inside of thecell. A 95% alcohol solution merely coagulates the protein onthe outside of the cell wall and prevents any alcohol fromentering 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 andamine on side chains. Review reaction. The final interaction isionic between the positive ammonium group and the negativeacid group. Any combination of the various acidic or amineamino acid side chains will have this effect.
As might be expected, acids and bases disrupt salt bridges heldtogether by ionic charges. A type of double replacementreaction occurs where the positive and negative ions in the saltchange partners with the positive and negative ions in the newacid or base added. This reaction occurs in the digestivesystem, 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:
Temporary Wave:
When the hair gets wet, water molecules intrude into thekeratin strands. The sheer numbers of water molecules are ableto disrupt some of the hydrogen bonds which also help to keepthe alpha-helices aligned. The helices are able to slip past eachother and will retain a new shape in the hair drying process asnew hydrogen bonds are formed. The hair strands are able fora 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 cross-links.
The hair is then put on rollers orcurlers. Since the alpha-helices are no longer tightlycross-linked to each other, the alpha-helices can shift positionsin relation to each other. An oxidizing agent, usually a dilutesolution of hydrogen peroxide, (also called the neutralizer) isadded to reform the disulfide bonds in their new positions. Thepermanent will hold these new disulfide bond positions until thehair 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:
An immunoglobin is a specific protein called an antibodysynthesized in response to the presence of a foreign substanceantigen). The antibody has a specific molecular structurecapable of recognizing a complementary molecular structureon the antigen which might be some proteins, polysaccharides, and nucleic acids. Small organic foreignmolecules do not by themselves elicit antibody formationunless they become bonded to one of the larger biomoleculeslisted above.
Structural Details:
Immunoglobin G (IgG), the most common humanimmunoglobin, consists of two long "heavy" chains shown asA - cyan and B - magenta in the graphic on the left. There aretwo 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 arebonded to the main chains through a single disulfide bondeach. There are a variety of other disulfide bonds in otherparts of the molecule.
In the lower "bulge" region of the main A and B chains, thereare two chains of carbohydrates made of glucose andgalactose. The carbohydrates are bonded tothe protein chainthrough the amino acid as asparagine. The is through the N ofamide side chain to the carbon # 1 in the glucose to make anN-glycosidic bond.
Antibody-Antigen Interaction:
The interaction of the antibody with an antigen causes achange in shape of the antibody. The variable regions shownas black or gray in the graphic on the left are the areas of thereceptor site for the antigen.
This in turn may cause the exposure of another site, whichthen is responsible for the various reactions elicited by theantibody to destroy the foreign substance. The interaction ofantibodies and antigens may produce a network type complex.
Above is displayed the 3-D structure of the V-A and V-Cportions of the Fab complexed with the heptapeptide antigenfrom HA. Examination of the antigen binding pocket revealsthat a pronounced conformational change has occurred uponantigen binding. The pocket is deformed by the antigen, closing around it. This is mostly caused by a shift in theorientation of V-A, represented by the gray and red. The redis the orientation of Asp99 and Asn100.
Vaccinations:
The understanding of immunochemistry led to the use ofvaccinations as protection against various epidemic producingdiseases such as small pox, diphtheria, polio, and typhus. Avaccination works by injecting a small amount of weakeneddisease producing virus into the body which elicits theproduction of antibodies which eventually destroy the foreignsubstance. Subsequent invasions of the body by this samevirus are met and destroyed by the antibodies formed at thetime of vaccination.