Chemistry 121(001) Winter 2015
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 8:00 - 10:00 am;
ThF 9:00 - 10:00 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
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Chapter 20 and GHW#10
Questions
Proteins and Peptides
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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
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Handedness/Chirality of Amino Acids
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Groups of Amino Acids based on R group
• Hydrophobic (non-polar, neutral)
• Polar, neutral
• Polar Acidic
• Polar Basic
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1) Hydrophobic (non-polar, neutral) (5 amino acids)
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1) Hydrophobic (non-polar, neutral) continued..
( 4 amino acids)
G AL VaLI PPerMiT
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2) Hydrophilic (polar, neutral) continued..( 6 amino acids).
SeCTAsGulTy
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3) & 4) Polar amino acids (5 amino acids)
As Glue Hit Lady Argentina
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Abbreviations
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
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Abbreviations
Non Polar
amino acid
glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
proline
three letter
code
Gly
Ala
Val
Leu
Ile
Met
Phe
Trp
Pro
single letter
code
G
A
V
L
I
M
F
W
P
Electrically Charged (negative)
aspartic acid
glutamic acid
Asp
Glu
D
E
Electrically Charged (positive)
lysine
arginine
histidine
Lys
Arg
His
K
R
H
Non Polar Neutral
serine
threonine
cysteine
tyrosine
asparagine
glutamine
Ser
Thr
Cys
Tyr
Asn
Gln
S
T
C
Y
N
Q
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1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic).
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1) Give name, abbreviation and types (neutral, polar, nonpolar, basic and acidic).
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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)
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2) Draw the optical and L isomers for: cys.
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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?
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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’
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4) Draw the following:
a) Dipeptide bond between ala and asp, and identify Cand N-terminal.
b) Tripeptide, ile-cys-thr, and identify N- ( left) and Cterminal(right).
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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-cysthr
.
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5) Use the structure to answer the questions below:
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?
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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.
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Three levels of structure: telephone cord
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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
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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
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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?
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Alpha Helix
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Alpha Helix
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Beta Pleated Sheets
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Beta Pleated Sheets
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8) Explain the difference between the alpha helix and the
beta pleated sheet protein structures. What are the
differences in the hydrogen bonding?
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Fibrous Proteins
a) - Keratin b) Collagen etc..
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