Download CHEM 121 Winter 2017

Chemistry 121 Winter 17
Introduction to Organic Chemistry and Biochemistry
Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
E-mail: [email protected]
Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;
Contact me trough e-mail if you have questions
Online Tests on Following days
December 16, 2016: Test 1 (Chapters 12-13)
January 23, 2017 : Test 2 (Chapters 14-16)
February 10, 2017 : Test 3 (Chapters 17-19)
February 22, 2017 : Test 4 (Chapters 20-22)
February 23, 2017: Make Up Exam: Chapters 12-22)
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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 (20) based on R group
• Non-polar, hydrophobic (neutral)(9)
• Polar, neutral (6)
• Polar, Acidic (2)
• Polar, Basic (3)
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1) Hydrophobic (non-polar, neutral) (5 amino acids of 9)
GA VaLI
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1) Hydrophobic (non-polar, neutral) continued..
( 4 amino acids)
ProsPher MinisTry
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2) Hydrophilic (polar, neutral) continued..( 6 amino acids).
See CysT As GluilTy
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3) Polar acidic &Basic (5 amino acids)
As Glue Hit Lady Argentina
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Abbreviations (non-poar)
glycine
alanine
valine
leucine
isoleucine
Proline
phenylalanine
methionine
tryptophan
Gly
Ala
Val
Leu
Ile
Pro
Phe
Met
Trp
G
A
V
L
I
P
F
M
W
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Abbreviations
Non Polar
amino acid
glycine
alanine
valine
leucine
isoleucine
proline
phenylalanine
methionine
tryptophan
three letter
code
Gly
Ala
Val
Leu
Ile
Pro
Phe
Met
Trp
single letter
code
G
A
V
L
I
P
F
M
W
Polar acidic
Electrically Charged (negative)
aspartic acid
glutamic acid
Asp
Glu
D
E
Polar acidic &Basic
Electrically Charged (positive)
histidine
His
H
lysine
Lys
K
arginine
Arg
R
Polar Neutral
serine
cysteine
threonine
asparagine
glutamine
tyrosine
Ser
Cys
Thr
Asn
Gln
Tyr
S
C
T
N
Q
Y
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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:
a. Which amino acid is polar neutral?
b. Which amino acid is the non-polar neutral?
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-cys-
.
thr
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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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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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Alpha Helix
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Fibrous Proteins
a) - Keratin b) Collagen etc..
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Beta Pleated Sheets
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