Download Chapter 11. Protein Structure and Function

Chapter 11. Protein Structure and
Function
• 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.
• Enzymes
Protein function
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.
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.
 carbon
General
Structure
H
|
R-C-COOH
|
NH2
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.
Some amino acid examples
alanine
H
|
CH3-C-COO|
+NH
3
H
|
CH3 -S-CH2-CH2-C-COO|
+NH
3
methionine
valine
N
H
tryptophan
H3 C H
\ |
HC-C-COO/ |
H3C +NH3
H
|
CH2-C-COO|
+NH
3
Some amino acid examples
glycine
O
H
|
H-C-COO|
+NH
3
H
||
|
-O-C-CH -CH -C-COO2
2
|
+NH
3
glutamic acid
H
|
HO-CH2-C-COO|
+NH
3
serine
O
H
||
|
H2N-C-CH2-C-COO|
+NH
3
asparagine
Abbreviations
•
•
•
•
•
•
•
•
glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
Gly
Ala
Val
Leu
Ile
Met
Phe
Trp
G
A
V
L
I
M
F
W
Groups of Amino Acids
• Hydrophobic
• Polar, neutral
• Negatively charged
• positively charged
Primary protein structure
• Proteins are polymers made up of amino
acids.
• Peptide bond are
•
H
• H
|
H2NCCOOH +
|
R
|
H2NCCOOH
|
R’
how the amino acids
linked together to make
a protein. H O H
| ||
|
H2N - C - C - N - C - COOH
|
| |
R
H R’ + H2O
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.
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.
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, ...
-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.
-helix
QuickTime™ and a
Graphics decompressor
are needed to see this picture.
-helix
C
||
O
H
|
N
C
||
OH
|
HN
|
N
H
|
N
C H
|| |
O N
H
|
N
C
||
O
C
||
O H
|
C
H
|| H N
C |
O |
|| N
C
O
N
||
C
O
||
O
Every amide hydrogen
and carbonyl oxygen is
involved in a hydrogen
bond.
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.
Tropocollagen
-Pleated sheets
• Another secondary structure for protein.
• Held together by hydrogen bonding
between adjacent
sheets
of
protein.
R
R
C
|
R
C
|
R
H
|
N
C
||
O
|
C
C
||
O
N
|
H
R
H |
| C
N
O
||
C
O
||
C
H
|
N
C
|
R
N
| C
H |
R
|
C
C
||
O
H
|
N
C
||
O
N
|
H
R
| O
C ||
C
O
||
C
C
|
R
N
| C
H |
R
-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.
Beta sheet
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
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
Sulfide
crosslink
Tertiary structure
of proteins
Hydrophobic
interaction
-S-S-
-COO- H3N+-
Salt
bridge
Hydrogen
bonding
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
Quaternary structure
of proteins
Aggregate structure
This example
shows four
different proteins
and two prosthetic
groups.
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.
Heme
• myoglobin
• 1 heme group
• hemoglobin
• 4 heme groups
Myoglobin
Heme
Hemoglobin
2  chains
4 heme
2  chains
Oxygen Transport
Example - cytochrome C 550
Heme structure
Contains Fe2+
Used in
metabolism.
Aggregate of
proteins and
other structures.
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.
Comparison of normal and
sickle cell hemoglobin
Normal
Sickle
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
quaternary
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 -