1. Chemistry 121(001) Winter 2015
Introduction to Organic Chemistry and Biochemistry
Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
Office: 311 Carson Taylor Hall ; Phone: ;
Office Hours: MTW 8: :00 am;
ThF 9: :00 am 1:00 - 2:00 pm.
December 19, 2014: Test 1 (Chapters 12-13)
January 26 , 2015: Test 2 (Chapters 14-16)
February 13, 2015: Test 3 (Chapters 17-19)
March 2, 2015: Test 4 (Chapters 20-22
March 3 , 2015: Make Up Exam: Chapters 12-22)
Bring Scantron Sheet 882-E
CHEM 121 Winter 2015

2. Chapter 20 and GHW#10 Questions
Proteins and Peptides
CHEM 121 Winter 2015

3. Proteins
Naturally occurring bioorganic polyamide polymers containing a sequence of various combinations of 20 amino acids.
Amino acids contain the elements carbon, hydrogen, oxygen, and nitrogen and few also contain sulfur
Amino acids: Polyfunctional bioorganic compunds
Zwitterion form
R = 20 different alkyl, alcohols, amines , acids and heterocyclic amines
CHEM 121 Winter 2015

4. Handedness/Chirality of Amino Acids
CHEM 121 Winter 2015

5. Groups of Amino Acids based on R group
Hydrophobic (non-polar, neutral)
Polar, neutral
Polar Acidic
Polar Basic
CHEM 121 Winter 2015

6. 1) Hydrophobic (non-polar, neutral) (5 amino acids)
CHEM 121 Winter 2015

7. 1) Hydrophobic (non-polar, neutral) continued.. ( 4 amino acids)
G AL VaLI PPerMiT
CHEM 121 Winter 2015

8. 2) Hydrophilic (polar, neutral) continued..( 6 amino acids).
SeCTAsGulTy
CHEM 121 Winter 2015

9. 3) & 4) Polar amino acids (5 amino acids)
As Glue Hit Lady Argentina
CHEM 121 Winter 2015

10. Abbreviations glycine Gly G alanine Ala A valine Val V leucine Leu L
isoleucine Ile I
methionine Met M
phenylalanine Phe F
tryptophan Trp W
Proline Pro P
CHEM 121 Winter 2015

11. Electrically Charged (negative) Electrically Charged (positive)
Abbreviations
Non Polar
           
amino acid
three letter code
single letter code
glycine
Gly G
alanine
Ala A
valine
Val V
leucine
Leu L
isoleucine
Ile I
methionine
Met M
phenylalanine
Phe F
tryptophan
Trp W
proline
Pro P
Electrically Charged (negative)
     
Electrically Charged (positive)
           
aspartic acid
Asp D
glutamic acid
Glu E
lysine
Lys K
arginine
Arg R
histidine
His H
Non Polar Neutral
           
serine
Ser S
threonine
Thr T
cysteine
Cys C
tyrosine
Tyr Y
asparagine
Asn N
glutamine
Gln Q
CHEM 121 Winter 2015

12. 1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

13. 1) Give name, abbreviation and types (neutral, polar, non-polar, basic and acidic).

14. Protein Function
Enzymes - catalyze biological reactions (alcohol dehydrogenase, glucokinase)
Hormones - signals between cells (insulin, growth hormone)
Storage Proteins- store nutrients (ferritin storing iron in the liver)
Transport Proteins - transport nutrients through the body (hemoglobin transport of oxygen)
Structural Proteins- form structure of cells ( keratin, elastin, collagen)
Protective Proteins- have specific protective function (antibodies bind to foreign proteins)

15. 2) Draw the optical and L isomers for: cys.

16. 3) Use the following amino acids to answer the questions below:
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?

17. Primary protein structure
Proteins are polymers made up of amino acids.
Peptide bond - how the amino acids are
linked together to make
a protein. H |
H2NCCOOH R H |
H2NCCOOH R’
H O
| ||
H2N - C - C - | R H |
N - C - COOH
| |
H R’ +
+ H2O

18. 4) Draw the following: a) Dipeptide bond between ala and asp, and identify C- and N-terminal. b) Tripeptide, ile-cys-thr, and identify N- ( left) and C-terminal(right).

19. 4) Continued…. c) How many possible isomers are in the tripeptide formed with ile, cys and thr? Come up with a formula for linear chain with “ n” amino acids. d) Give the IUPAC name of the tripeptide with the sequence, ile-cys-thr.

20. 5) Use the structure to answer the questions below:
Which letter arrow points the end of the peptide that is the "amine“
end-N-terminal?
b) Which letter arrow points the end of the peptide that is the
"carboxyl" end, C-terminal?
c) Which letter arrow points to an amide or peptide bond?

21. Four levels of protein structure
1) Primary structure
The sequence of amino acids in a protein.
2) Secondary structure
Way that chains of amino acids are coiled or folded - (-helix, -sheet, random coil).
3) Tertiary structure
Way -helix, -sheet, random coils fold and coil.
4) Quaternary structure
Way that two or more peptide chains pack together.

22. Three levels of structure: telephone cord

23. Summary of protein structure
primary
secondary
H O
| ||
H2N - C - C | R H
N - C - COOH
| |
H R’’
- NH - C - C - R’
quaternary
tertiary

24. 6) 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

25. 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?

26. Alpha Helix

27. Alpha Helix

28. Beta Pleated Sheets

29. Beta Pleated Sheets

30. 8) Explain the difference between the alpha helix and the beta pleated sheet protein structures. What are the differences in the hydrogen bonding?

31. Fibrous Proteins
a) a- Keratin b) Collagen etc..