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Chapter 16 Amino Acids, Proteins,
and Enzymes
1
16.4
Levels of Protein Structure
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Primary Structure of Proteins
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The primary structure of a protein is
• the particular sequence of amino acids
• the backbone of a peptide chain or protein
CH3
CH3
S
CH CH3
SH
CH2
CH O
CH2 O
CH2 O
H3N CH C N
CH C N
CH C N
CH C O-
H
H
H
CH3 O
Ala─Leu─Cys─Met
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Primary Structures
3
• The nonapeptides oxytocin and vasopressin have similar
primary structures.
• Only the amino acids at positions 3 and 8 differ.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Primary Structure of Insulin
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Insulin
• was the first protein to have its
primary structure determined
• has a primary structure of two
polypeptide chains linked by
disulfide bonds
• has a chain A with 21 amino acids and
a chain B with 30 amino acids
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Secondary Structure–Alpha Helix
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The secondary structure of an
alpha helix is
• a three-dimensional spatial arrangement
of amino acids in a polypeptide chain
• held by H bonds between the H of –N-H
group and the O of C=O of the fourth
amino acid down the chain
• a corkscrew shape that looks like a
coiled “telephone cord”
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Secondary Structure–
Beta-Pleated Sheet
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The secondary structure of a beta-pleated sheet
•
•
•
•
consists of polypeptide chains arranged side by side
has hydrogen bonds between chains
has R groups above and below the sheet
is typical of fibrous proteins, such as silk
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Secondary Structure–Beta-Pleated Sheet
7
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Secondary Structure–Triple Helix
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The secondary structure of a triple helix is
• three polypeptide chains woven together
• typical of collagen, connective tissue, skin, tendons,
and cartilage
Collagen fibers are triple helices of polypeptide chains held together
by hydrogen bonds.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Learning Check
9
Indicate the type of protein structure.
primary
beta-pleated sheet
alpha helix
triple helix
A. polypeptide chains held side by side by H bonds
B. sequence of amino acids in a polypeptide chain
C. corkscrew shape with H bonds between amino acids
D. three peptide chains woven like a rope
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Solution
10
A. polypeptide chains held side by side by H bonds
beta-pleated sheet
B. sequence of amino acids in a polypeptide chain
primary
C. corkscrew shape with H bonds between amino acids
alpha helix
D. three peptide chains woven like a rope
triple helix
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Tertiary Structure
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The tertiary structure
of a protein
• is an overall threedimensional shape.
• is determined by crosslinks, the attractions and
repulsions between the
side chains (R groups) of
the amino acids in a
peptide chain
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Cross-links in Tertiary Structures
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There are five types of cross-links in tertiary structures.
1. Hydrophobic interactions are interactions between two
nonpolar R groups. Within a protein, the amino acids with
nonpolar R groups move away from the aqueous environment to
form a hydrophobic center at the interior of the protein molecule.
2. Hydrophilic interactions are attractions between the
external aqueous environment and the R groups of polar amino
acids moving the polar amino acids toward the outer surface of
globular proteins where they form hydrogen bonds with water.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Cross-links in Tertiary Structures
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3. Salt bridges are ionic bonds between ionized R groups of
basic and acidic amino acids. For example, the ionized R
group of arginine, which has a positive charge, can form a salt
bridge (ionic bond) with the R group in aspartic acid, which
has a negative charge.
4. Hydrogen bonds form between H of a polar R group and
the O or N of another amino acid. For example, a hydrogen
bond can form between the groups of two serines or between
the of serine and the in the R group of glutamine.
5. Disulfide bonds are covalent bonds that form between the
groups of cysteines in a polypeptide chain.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Learning Check
14
Select the type of tertiary interaction.
disulfide
ionic
H bonds
hydrophobic
A.
B.
C.
D.
leucine and valine
two cysteines
aspartic acid and lysine
serine and threonine
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Solution
15
Select the type of tertiary interaction.
disulfide
ionic
H bonds
hydrophobic
A.
B.
C.
D.
leucine and valine
two cysteines
aspartic acid and lysine
serine and threonine
hydrophobic
disulfide
ionic
H bonds
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Globular Proteins
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Globular proteins
• have compact, spherical shapes
• carry out synthesis, transport,
and metabolism in the cells
• such as myoglobin store and
transport oxygen in muscle
The ribbon structure represents
the tertiary structure of myoglobin.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Myoglobin
Copyright © 2012 by Pearson Education, Inc.
Fibrous Proteins
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Fibrous proteins
• consist of long, fiber-like shapes
• such as alpha keratins make up hair,
wool, skin, and nails
• such as feathers contain beta
keratins with large amounts of
beta-pleated sheet structures
The fibrous proteins of -keratin
wrap together to for fibrils of hair
and wool.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Quaternary Structure
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The quaternary structure
• is the combination of two
or more protein units
• of hemoglobin consists of
four polypeptide chains as
subunits
• is stabilized by the same
interactions found in
tertiary structures
In the ribbon structure of hemoglobin, the
quaternary structure is made up of four
polypeptide subunits, two (red) are  chains
and two (blue) are  chains. The heme groups
(green) in the four subunits bind oxygen.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Summary of Protein Structural Levels
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Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Summary of Protein Structure
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Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Learning Check
21
Identify the level of protein structure.
primary
tertiary
A.
B.
C.
D.
E.
secondary
quaternary
beta-pleated sheet
order of amino acids in a protein
a protein with two or more peptide chains
the shape of a globular protein
disulfide bonds between R groups
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Solution
22
Identify the level of protein structure.
primary
tertiary
A.
B.
C.
D.
E.
secondary
quaternary
beta-pleated sheet
order of amino acids in a protein
a protein with two or more peptide chains
the shape of a globular protein
disulfide bonds between R groups
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
secondary
primary
quaternary
tertiary
tertiary
Copyright © 2012 by Pearson Education, Inc.
Denaturation
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Denaturation involves
• the disruption of bonds in the secondary, tertiary, and
quaternary protein structures
• heat and organic compounds that break apart H bonds
and disrupt hydrophobic interactions
• acids and bases that break H bonds between polar
R groups and disrupt ionic bonds
• heavy metal ions that react with S-S bonds to form solids
• agitation such as whipping that stretches peptide chains
until bonds break
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Applications of Denaturation
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Denaturation of protein occurs when
• an egg is cooked
• the skin is wiped with alcohol
• heat is used to cauterize
blood vessels
• instruments are sterilized
in autoclaves
Denaturation of egg protein occurs
when the bonds of the tertiary
structure are disrupted.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Applications of Denaturation
25
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Learning Check
26
Tannic acid is used to form a scab on a burn. An egg is hard
boiled by placing it in boiling water. What is similar about
these two events?
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.
Solution
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Tannic acid is used to form a scab on a burn. An egg is hard
boiled by placing it in boiling water. What is similar about
these two events?
Acid and heat cause the denaturation of protein. They
both break bonds in the secondary and tertiary structures
of proteins.
Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition
Copyright © 2012 by Pearson Education, Inc.