Chapter 20. Protiens
→ The protein
made by spiders
to produce a
web is a form of
silk that can be
exceptionally
strong.
Sections…
Chemistry 121 Winter 2009 LA Tech
Chp. 20-1
Chapter 20. Proteins
20.1 Characteristics of Proteins
20.2 Amino Acids: The Building Blocks for Proteins
20.3 Chirality and Amino Acids
20.4 Acid-Base Properties of Amino Acids
20.5 Cysteine: A Chemically Unique Amino Acid
20.6 Peptide Formation
20.7 Biochemically Important Small Peptides
20.8 General Structural Characteristics of Proteins
20.9 Primary Structure of Proteins
20.10 Secondary Structure of Proteins
20.11 Tertiary Structure of Proteins
20.12 Quaternary Structure of Proteins
20.13 Fibrous and Globular Proteins
20.14 Protein Hydrolysis
20.15 Protein Denaturation
20.16 Glycoproteins
20.17 Lipoproteins
Chemistry 121 Winter 2009 LA Tech
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Chapter 21. Protein and the Amino Acids
These are biopolymers that are constructed
from a limited set of amino acids.
They are the most plentiful organic
substances in the cell.
About half of the dry mass of a cell is
composed of proteins.
They serve a wide range of functions.
Chemistry 121 Winter 2009 LA Tech
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Protein function
Enzymes
biological catalysts.
Immunoglobulins
antibodies of immune system.
Transport
move materials around -hemoglobin for O2.
Regulatory hormones, control of metabolism.
Structural
Movement
coverings and support skin, tendons, hair, bone.
muscle, cilia, flagella.
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Types of Proteins
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Amino acids
All proteins are composed of amino acids.
Twenty common amino acids.
All are -amino acids.
Except for proline, primary amino- group is
attached to the  carbon - the carbon just after
the acid group.
General
Structure
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Handedness/Chirality of Amino Acids
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Amino acids
Because both acid and base groups are present, an
amino acid can form a +/- ion.
H
|
R-C-COOH
|
NH2
H
|
R-C-COO
|
NH3+
The position of the equilibrium is based on pH and the
type of amino acid. Called a zwitterion.
Chemistry 121 Winter 2009 LA Tech
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Some amino acid examples
alanine
H
|
CH3-C-COO|
+NH
3
H
|
CH3 -S-CH2-CH2-C-COO|
+NH
3
methionine
Chemistry 121 Winter 2009 LA Tech
valine
N
H
H3C H
\ |
HC-C-COO/ |
H3C +NH3
H
|
CH2-C-COO|
+NH
3
tryptophan
Chp. 20-9
Some amino acid examples
glycine
O
H
|
H-C-COO|
+NH
3
H
||
|
-O-C-CH -CH -C-COO2
2
|
+NH
3
glutamic acid
Chemistry 121 Winter 2009 LA Tech
H
|
HO-CH2-C-COO|
+NH
3
serine
O
H
||
|
H2N-C-CH2-C-COO|
+NH
3
asparagine
Chp. 20-10
Groups of Amino Acids
Hydrophobic
Polar, neutral
Negatively charged-Acidic
positively charged-Basic
Chemistry 121 Winter 2009 LA Tech
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Non-polar Amino Acids
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Ploar/Neutral Amino Acids
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Ploar Acidic/Basic Amino Acids
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Abbreviations
glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
Proline
Chemistry 121 Winter 2009 LA Tech
Gly
Ala
Val
Leu
Ile
Met
Phe
Trp
Pro
G
A
V
L
I
M
F
W
P
Chp. 20-15
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’
Chemistry 121 Winter 2009 LA Tech
H O
H
| ||
|
H2N - C - C - N - C - COOH
|
| |
+ H 2O
R
H R’
Chp. 20-16
Four levels of protein structure
Primary structure
The sequence of amino acids in a protein.
Secondary structure
Way that chains of amino acids are coiled or
folded - (-helix, -sheet, random coil).
Tertiary structure
Way -helix, -sheet, random coils fold and coil.
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
secondary
H O
H O
H
| ||
| ||
|
H2N - C - C- NH - C - C - N - C - COOH
|
|
| |
R
R’
H R’’
tertiary
Chemistry 121 Winter 2009 LA Tech
quaternary
Chp. 20-19
Primary structure
All proteins have the same covalent backbone.
H O
H O
H O
H
| ||
| ||
| ||
|
H2N - C - C - NH - C - C - NH - C - C - NH - C - COOH
|
|
|
|
R
R’
R’’
R’’’
Part of a protein.
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Separation of three amino acids
Separation of Lys, Phe, and Glu using electrophoresis after
hydrolysis of protein
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Secondary structure
Long chains of amino acids commonly fold or curl into
a regular repeating structure.
Structure is a result of hydrogen bonding between
amino acids within the protein.
Common secondary structures are:
 - helix
 - pleated sheet
Secondary structure adds new properties to a protein
like strength, flexibility, ...
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-helix
H
|
N
C
||
O
H
|
N
H
C
|
||
C H
N
OH
|| |
C
O N
|
||
C
HN
O
||
|
O H
N C
|
H
|| H N
C |
O |
|| N
C
O
N
||
C
O
||
O
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Every amide hydrogen and
carbonyl oxygen is
involved in a hydrogen
bond.
Chp. 20-23
Representations of the helix secondary structure
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-helix
One common type of
secondary structure.
Properties of an -helix include
strength and low solubility in
water.
Originally proposed by
Pauling and Corey in 1951.
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The coiled-coil structures
The coiled-coil
structure of the
fibrous protein beta
kerotin.
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Collagen
Family of related proteins.
About one third of all protein in humans.
Structural protein
Provides strength to bones, tendon, skin, blood
vessels.
Forms triple helix - tropocollagen.
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Collagen
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-Pleated sheets
Another secondary structure for
protein.
Held together by hydrogen bonding
between adjacent sheets of
protein.
C
|
R
C
|
R
H
|
N
R
|
C
C
||
O
R
H |
| C
N
C
||
O
N
|
H
O
||
C
O
||
C
C
|
R
N
| C
H |
R
Chemistry 121 Winter 2009 LA Tech
H
|
N
C
||
O
R
|
C
N
|
H
R
H | O
| C ||
C
N
C
||
O
O
||
C
C
|
R
N
| C
H |
R
The hydrogen bonding
between the carbonyl
oxygen atom of one
peptide linkage and the
amide hydrogen atom
of another peptide
linkage.
Chp. 20-29
-Pleated sheets
Silk fibroin - main protein of silk is an example
of a  pleated sheet structure.
Composed primarily of glycine and alanine.
Stack like corrugated cardboard for extra strength.
Chemistry 121 Winter 2009 LA Tech
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-Pleated sheets
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Tertiary structure of proteins
Fibrous proteins
• insoluble in water
• form used by connective tissues
• silk, collagen, -keratins
Globular proteins
•
•
•
soluble in water
form used by cell proteins
3-D structure - tertiary
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Tertiary structure of proteins
Results from interaction of side chains.
The protein folds into a tertiary structure.
Possible side chain interactions:
Similar solubilities
Ionic attractions
Electrostatic attraction between + and sidechains
Covalent bonding
Chemistry 121 Winter 2009 LA Tech
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Tertiary Structure
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Tertiary Structure of Proteins
Sulfide
crosslink
Hydrophobic
interaction
-S-S-
-COO- H3N+-
Salt
bridge
Chemistry 121 Winter 2009 LA Tech
Hydrogen
bonding
Chp. 20-35
Four types of interactions between amino acid R groups
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Quaternary structure of proteins
Many proteins are not single peptide strands.
They are combinations of several proteins
- aggregate of smaller globular proteins.
Conjugated protein - incorporate another type of
group that performs a specific function.
prosthetic group
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Quaternary structure of proteins
Aggregate structure
This example
shows four
different proteins
and two prosthetic
groups.
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Hemoglobin and Myoglobin
Hemoglobin
Oxygen transport protein of red blood cells.
Myoglobin
Oxygen storage protein of skeletal muscles.
As with the cytochrome example, both proteins
use heme groups. It acts as the binding site
for molecular oxygen.
Chemistry 121 Winter 2009 LA Tech
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Heme
myoglobin
1 heme group
hemoglobin
4 heme groups
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Myoglobin
Heme
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Hemoglobin
2  chains
4 heme
2  chains
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Oxygen Transport
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Example - cytochrome C 550
Heme structure
Contains Fe2+
Used in
metabolism.
Aggregate of
proteins and
other structures.
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Sickle cell anemia
Defective gene results in production of mutant
hemoglobin.
Still transports oxygen but results in deformed
blood cells - elongated, sickle shaped.
Difficult to pass through capillaries. Causes
organ damage, reduced circulation.
Affects 0.4 % of African-American.
Chemistry 121 Winter 2009 LA Tech
Chp. 20-45
Comparison of normal and sickle cell hemoglobin
Normal
Chemistry 121 Winter 2009 LA Tech
Sickle
Chp. 20-46
Denaturation of Proteins
The loss of secondary, tertiary, and quaternary
structures
1) pH extremes.
2). Heat 3). Mechanical Agitation (foaming)
4). Detergents
5). Organic Solvents
6). Inorganic Salts -
Chemistry 121 Winter 2009 LA Tech
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Heat-Denaturation of Proteins
Chemistry 121 Winter 2009 LA Tech
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Permanent for Hair
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