Chemistry 121(01) Winter 2014
Introduction to Organic Chemistry and Biochemistry
Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
E-mail: upali@latech.edu
Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;
Office Hours: MTW 9:00 am - 11:00 am;
TR 9:00 - 10:00 am & 1:00-2:00 pm.
December 20, Test 1 (Chapters 12-13)
January 27 Test 2 (Chapters 14-16)
February 14 Test 3 (Chapters 17-19)
February 26, Test 4 (Chapters 20-22)
February 27, 2014, Make Up Exam:
Bring Scantron Sheet 882-E
Chapter 20 and GHW#10
Questions
Proteins
Chapter
20:
Proteins
20.1 Characteristics of Proteins, 707
20.2 Amino Acids: The Building Blocks for Proteins, 708
20.3 Essential Amino Acids, 710
20.4 Chirality and Amino Acids, 711
20.5 Acid-Base Properties of Amino Acids, 711
20.6 Cysteine: A Chemically Unique Amino Acid, 714
20.7 Peptides, 714
20.8 Biochemically Important Small Peptides, 718
20.9 General Structural Characteristics of Proteins, 719
20.10 Primary Structure of Proteins, 720
20.11 Secondary Structure of Proteins, 723
20.12 Tertiary Structure of Proteins, 726
20.13 Quaternary Structure of Proteins, 730
20.14 Protein Hydrolysis, 730
20.15 Protein Denaturation, 732
20.16 Protein Classification Based on Shape, 733
20.17 Protein Classification Based on Function, 737
20.18 Glycoproteins, 740
20.19 Lipoproteins, 742
CHEM 121 Winter 2013
Silde 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 compounds
Zwitterion form
R = 20 different alkyl, alcohols, amines , acids and heterocyclic amines
Handedness/Chirality of Amino Acids
Groups of Amino Acids based on R group
• Hydrophobic (non-polar, neutral)
• Polar, neutral
• Polar Acidic
• Polar Basic
1) Hydrophobic (non-polar, neutral) (5 amino acids)
1) Hydrophobic (non-polar, neutral) continued..
( 4 amino acids)
2) Hydrophilic (polar, neutral) continued..( 6 amino acids).
3) & 4) Polar amino acids (5 amino acids)
Abbreviations
Nonpolar Amino Acids (hydrophobic) (9 amino acids)
1.
2.
3.
4.
5.
6.
7.
8.
9.
glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
Proline
Gly
Ala
Val
Leu
Ile
Met
Phe
Trp
Pro
G
A
V
L
I
M
F
W
P
Abbreviations
Polar (hydrophilic) 6 amino acids
1
2
3
4
5
6
serine
threonine
cysteine
tyrosine
asparagine
glutamine
Ser
Thr
Cys
Tyr
Asn
Gln
S
T
C (hydrophilic)
Polar
Y
N
Q
Abbreviations
Electrically charged (5 amino acids)
Polar (hydrophilic)
Electrically Charged (negative) (acidic)
1. Aspartic
2. Glutamic
Asp
Glu
D
E
Electrically Charged (positive) Basic
3. lysine
Lys
K
4. arginine
Arg
R
5. histidine
His
H
1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic).
1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic).
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)
2) Draw the optical and L isomers for: cys.
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?
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
H
| ||
|
H2N - C - C - N - C - COOH
|
| |
+ H2O
R
H R’
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 Cterminal(right).
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, ilecys-thr
.
5) Use the structure to answer the questions below:
a) 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?
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.
Three levels of structure: telephone cord
Summary of protein structure
primary
H O
H O
| ||
| ||
H2N - C - C - NH - C - C |
|
R
R’
tertiary
secondary
H
|
N - C - COOH
| |
H R’’
quaternary
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
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?
Alpha Helix
Alpha Helix
Beta Pleated Sheets
Beta Pleated Sheets
8) Explain the difference between the alpha helix and
the beta pleated sheet protein structures. What are
the differences in the hydrogen bonding?
Fibrous Proteins
a) - Keratin b) Collagen etc..