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and Function
20 possible groups
R
|
H2N--C--COOH
|
H
NH 3 C COO - NH 3 C COO -
NH 3 C CO NH C COO - H2 0
Different Amino Acid Classes
Alanine O O Cysteine
H2N C H2N C OH
OH
H C H C
C H Generic C H
H H HS H
Non-polar O Polar
Amine Acid
H2N C OH
O C O Histidine
Aspartic ?R
acid H C
H2N C H2N OH
OH
C H C
H
H C H
C
O C H C H
Basic
Acid OH NH
C
C
H+N
Glycine O Non-Polar MethionineO
H2N C H2N C
C
OH
Amino Acids H C
OH
H H Valine O C H
Leucine O H
H2N C C H
Alanine O OH H2N C OH
H C S H
H2N C H C
OH C H H3C
C C H
H
H3C CH3
H TryptophanO
C H C H
H2N C OH
H H H3C CH3
H C
PhenylalanineO
H
C IsoleucineO C
H2N OH
C H
C H2N OH
H Proline O
H H3C C
C H2N+
H NH C OH
H H C
H2C C
C H
H2C CH2 H
H3C H
Protein Structure
Polar Amino Acids
Serine O Threonine O Tyrosine O
HO Glutamine O
Cysteine O Asparagine O
H2N C OH
H2N C OH H2N C OH H C
H C C
H C H
H H H
C C
C H
HS H O C H O C H
NH2
NH2
Acidic Amino Acids
Aspartic O Glutamic O
acid acid
H2N C OH H2N C OH
H C H C
C H C H
H
O C H H
C
OH O C H
OH
Basic Amino Acids
Histidine O
H2N C OH Lysine O
H C
H H2N C OH
C
H C Arginine O
C H
C H
NH H H2N C
C OH
H C H C
C H
H+N H C H H
H C
C H
H C H
+H N H
3 C H
N H
+H N
2 C H
NH2
Protein Structure
Levels of Protein Organization
• Primary Structure - The sequence of amino
acids in the polypeptide chain
• Secondary Structure - The formation of
helices and b pleated sheets due to hydrogen
bonding between the peptide backbone
• Tertiary Structure - Folding of helices and
sheets influenced by R group bonding
• Quaternary Structure - The association of more
than one polypeptide into a protein complex
influenced by R group bonding
Levels of Protein Organization
Primary Structure
Met-Gly-Ala-Pro-His-Ile-Asp-Glu-Met-Ser-Thr-..
The sequence of amino acids in the primary structure determines the folding
of the molecule.
Protein Structure
Protein Secondary Structure
• The peptide backbone has areas of positive
charge and negative charge
• These areas can interact with one another to
form hydrogen bonds
• The result of these hydrogen bonds are two
types of structures:
helices
b pleated sheets
H Protein Secondary Structure:
N Helix
C H
C
O N
C H
C
H
O N +
C -
N C
H O H O
C H
O H N C N C OH
C
O N H C H C
C
O C H C H C H
H H HO H
H N
C
N C
C O
O
H Protein Secondary Structure:
N
C
C
H Helix
O N
C
C
H
H
O
N - +
C C H O H O
N O
C H
H N C N C OH
C
O N H C H C
C
C H C H C H
O H H HO H
H N
C
N C
C O
O
Protein Secondary Structure:
Helix
R
R groups stick R
R
R
out from the R
helix influencing R
R
higher levels of R
R
protein R
R
organization R
R
R
M
L Yeast Cytochrome C Oxidase
S
L
R
Subunit IV Leader
Q Neutral Non-polar
S The order of the amino acids
determines the hydrogen
Polar
I Basic
R bonding Acidic
F
F MLSLRQSIRFFKPATRTLCSSRYLL
K
P
T
A • This would localise specific classes of
R
amino acids in specific parts of the helix
T
L
C
S
S
R
Y
L
P
Protein Secondary Structure:
b Pleated Sheet
O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O
O H O H O H O H
C C N C C N C C N C C N
N C C N C C N C C N C C
H O H O H O H O
Protein Secondary Structure:
b Pleated Sheet
O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O
O H O H O H O H
C C N C C N C C N C C N
N C C N C C N C C N C C
H O H O H O H O
O H O H O H O H
C C C C
C C N C C N C C N C C N
N C N C N C N C
H O H O H O H O
Levels of Protein Organization
Tertiary Structure
• Tertiary structure results from the folding
of helices and b pleated sheets
• Factors influencing tertiary structure
include:
• Hydrophobic interactions
• Hydrogen bonding
• Disulphide bridges
• Ionic bonds
Hydrophobic interactions
Valine O
H2N C OH
H C
H Glycine O
C
CH3 H2N C OH
H3C
C
H H
Proline O
H2N+ C OH
H2C C
H2C CH2 H
Hydrogen Bonding
Asparagine O Glutamine O
H2N C H2N C OH
OH
C H C
H
H C H
C H
O C H C H
NH2 O C H
NH2
Hydrophilic Hydrophobic
Protein Folding
• The peptide bond allows for rotation
around it and therefore the protein can fold
and orient the R groups in favorable
positions
• Weak non-covalent interactions will hold
the protein in its functional shape – these
are weak and will take many to hold the
shape
Non-covalent Bonds in Proteins
Globular Proteins
•Hemoglobin
– 2 globin
subunits
– 2 b globin
subunits
Protein Assemblies
• Proteins can form very
large assemblies
• Can form long chains if
the protein has 2 binding
sites – link together as a
helix or a ring
• Actin fibers in muscles
and cytoskeleton – is
made from thousands of
actin molecules as a
helical fiber
Types of Proteins