Download 9.3 The Three-Dimensional Structure of Proteins, Continued

Chapter 9 Lecture
General, Organic, and Biological
Chemistry: An Integrated Approach
Laura Frost, Todd Deal and Karen Timberlake
by Richard Triplett
Chapter 9
Proteins—Amides at Work
© 2011 Pearson Education, Inc.
Chapter Outline
9.1 Amino Acids
9.2 Protein Formation
9.3 The Three-Dimensional Structure of Proteins
9.4 Denaturation of Proteins
9.5 Examples of Biologically Important Proteins
© 2011 Pearson Education, Inc.
Chapter 9
2
Introduction
• Amino acids are the building blocks of proteins,
which have structural and functional properties
in our bodies.
• Proteins function as follows:
– They transport oxygen in the blood.
– They are the primary components of skin and
muscle.
– They work as defense mechanisms against
infection.
– They serve as biological catalysts called
enzymes.
– Most hormones are proteins.
© 2011 Pearson Education, Inc.
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Introduction, Continued
• Proteins are polymers of amino acids covalently
bonded in specific sequences.
• There are 20 commonly occurring amino acids
that make up proteins, and the order of amino
acids in proteins determines its structure and
biological function.
• When amino acids are covalently linked to one
another, this chain can twist and fold to form a
unique three-dimensional structure that has a
specific function.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look
Amino Acid Structure
• Amino acids contain two functional groups, a
protonated amine and carboxylic acid in the form
of a carboxylate group.
• These functional groups are bonded to a central
carbon atom known as the alpha () carbon,
and are referred to as alpha amino acids.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
• The  carbon is also bonded to a hydrogen atom
and a larger side chain. The side chain is unique
for each amino acid.
• The  carbon on all amino acids, except glycine,
is a chiral carbon because it has four different
groups bonded to it.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
• An amino acid, with a chiral center, has two
forms called enantiomers, which are
nonsuperimposable mirror images.
• When drawing the Fischer projection, the
carboxylate group is at the top of the structure
and the side chain (R group) is at the bottom.
• The protonated amine group can be on the lefthand side (L form) or right-hand side (D form) of
the structure.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
The L-amino acids are the building blocks for
proteins. Some D-amino acids occur in nature, but
not in proteins.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
•
•
•
The R group gives each amino acid its unique
identity and characteristics.
Twenty amino acids are found in most proteins.
There are 8 different families of organic
compounds represented in the structures of
different amino acids. They are as follows:
1.
2.
3.
4.
5.
6.
7.
8.
Alkanes
Aromatics
Alcohols
Phenols
Thiols
Amides
Carboxylic acids
Amines
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
•
The functional groups divide the amino acids
into the following four categories:
1.
2.
3.
4.
•
Nonpolar, consisting of nine amino acids
Polar, consisting of six amino acids
Acidic, consisting of two amino acids
Basic, consisting of three amino acids
There are 10 amino acids that are essential
amino acids because they cannot be
synthesized in the human body and must be
obtained in the diet.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
• The 10 essential amino acids are: valine,
leucine, isoleucine, phenylalanine, methionine,
tryptophan, threonine, histidine, lysine, and
arginine.
• Two of these amino acids, arginine and
histidine, are essential in children, but not adults.
• Nonessential amino acids can be synthesized in
the body from carbohydrates and amino acids.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
• Proteins that contain all the essential amino
acids are called complete proteins.
• Soybeans and most proteins found in animal
products are complete proteins.
• Some plant proteins are incomplete proteins
because they lack one or more essential amino
acid.
• Complete proteins can be obtained by
combining foods like rice and beans.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
The structure of the amino acids, including side
chains, names, functional groups, and
abbreviations are shown in the next few slides.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
© 2011 Pearson Education, Inc.
Chapter 9
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9.1 Amino Acids—A Second Look, Continued
© 2011 Pearson Education, Inc.
Chapter 9
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9.1 Amino Acids—A Second Look, Continued
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
Classification of Amino Acids
There are two classifications of amino acids
based on the side chains:
1. Nonpolar amino acids
2. Polar amino acids, which are further divided
into:
• Neutral amino acids
• Acidic amino acids
• Basic amino acids
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
Amino Acids Classified as Nonpolar
• Side chains consists entirely of carbon and
hydrogen.
• Carbon–hydrogen bond is nonpolar.
• Compounds composed of only carbon and
hydrogen are nonpolar and hydrophobic.
© 2011 Pearson Education, Inc.
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9.1 Amino Acids—A Second Look, Continued
Amino Acids Classified as Polar
• Contain functional groups, such as hydroxyl
(–OH) and amide (–CONH2).
• Side chains can form hydrogen bonds with
water.
• Side chains are hydrophilic.
• An exception is cysteine, which does not form
hydrogen bonds.
• Polar acidic and basic amino acids have
charged side chains that can form ion–dipole
interactions with water. These amino acids
are more polar than those classified as polar
neutral.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation
• When two amino acids condense, a dipeptide is
formed.
• The carboxylate ion (–COO-) of one amino acid
reacts with the protonated amine (–NH3+) of a
second amino acid.
• A water molecule is lost and an amide functional
group is formed. An amide bond is formed
between the two amino acids.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation, Continued
When amino acids combine in a condensation
reaction, the amide bond that is formed between
them is called a peptide bond.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation, Continued
• The product formed during the condensation of
alanine and valine is known as a dipeptide,
which is represented as Ala—Val or AV.
• In this dipeptide, alanine is called the
N-terminus because it has an unreacted
-amino group.
• Valine is called the C-terminus because it has
an unreacted -carboxylate group.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation, Continued
• Structures are always written from N-terminus to
C-terminus.
• Two amino acids can combine in two ways
forming two different dipeptides.
• The two dipeptides formed from condensation of
Ala and Val are Ala—Val and Val—Ala. They are
structural isomers, different compounds, and
have different properties.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation, Continued
Peptides formed in the condensation of three
amino acids are known as tripeptides; ones
with four amino acids are tetrapeptides; ones
with five amino acids are pentapeptides; etc.
© 2011 Pearson Education, Inc.
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9.2 Protein Formation, Continued
• A polypeptide is a compound that is formed
when the number of amino acids increases.
• A biologically active polypeptide consisting of 50
or more amino acids is referred to as a protein.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins
•
Peptides and proteins have three-dimensional
shapes or structures.
•
Proteins have four levels of structure:
1.
2.
3.
4.
Primary (1o)
Secondary (2o)
Tertiary (3o)
Quaternary (4o)
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• Each level of protein structure is a result of
interactions between the amino acids of the
protein.
Primary Structure
• The primary structure is the order in which the
amino acids are joined together by peptide
bonds that forms the backbone from N-terminus
to C-terminus. The amino acid side chains are
substituents to this backbone.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• The order or sequence of amino acids in a
protein chain are important in determining its
structure and function.
• Arranging amino acids in a different order
creates a polypeptide or protein that no longer
has the same function as the initial sequence of
amino acids.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• For example, the eight amino acid peptide
angiotensin II, which is involved in normal blood
pressure regulation in humans, has the following
amino acid sequence:
Asp—Arg—Val—Tyr—Ile—His—Pro—Phe
• Any other order of amino acids in this peptide
would result in a peptide that would not function
as angiotensin II.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Secondary Structure
•
The secondary structure of a protein
describes repeating patterns of structure within
the three-dimensional structure of a protein.
•
The two most common secondary structures
are:
1. Alpha helix (helix)
2. Beta-pleated sheet (-pleated sheet)
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• The  helix is a coiled structure, and much like the
coil of a telephone cord, it is a right-handed coil.
• This coil is stabilized by hydrogen bonds between
the carbonyl oxygen of one amino acid and the
N—H hydrogen atom of another amino acid located
four amino acids from it in the primary structure.
• The coil is able to stretch and recoil, and is a strong
structure. The side chains project outward from the
axis of the helix.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
A secondary structure involves hydrogen bonding
along the backbone.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
The -pleated sheet is an extended structure in
which segments of the protein chain align to form
a zigzag structure.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• Strands called beta strands are held together
through hydrogen bonding interactions between
the backbone.
• The side chains of a -pleated sheet extend
above and below the sheet.
• The interactions of the side chains within the
secondary structure lead to the tertiary structure
of proteins.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Tertiary Structure
• The tertiary structure is the three-dimensional
structure of the protein.
• It involves twisting and folding of the polypeptide
chain caused by hydrophobic and hydrophilic
interactions between the side chains of the
amino acids.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• The nonpolar amino side chains end up in the
interior of the protein away from the aqueous
environment.
• The polar side chains appear on the surface of
the protein since they are attracted to the
aqueous surroundings.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
• Stabilization of the tertiary structure is by:
– Attractive forces between the side chains and
aqueous environment
– Attractive forces between side chains
themselves
• These attractive forces cause the protein to fold
into a specific three-dimensional shape.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Interactions in the tertiary structure involves:
• Nonpolar or hydrophobic interactions
• Polar or hydrophilic interactions
• Salt bridges (ionic interactions)
• Disulfide bonds, which are covalent bonds
formed between –SH groups of two cysteine
molecules.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Proteins are classified into groups based on their
three-dimensional shape.
• Globular proteins are compact, spherical
structures that are soluble in an aqueous
environment. Myoglobin, which stores oxygen
in muscle, is an example.
• Fibrous proteins are long, threadlike
structures that have high helical content.
Keratins, found in hair, nails, the scales of
reptiles, and collagen, are examples.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Quaternary Structure
• The quaternary structure is two or more
polypeptide chains interacting to form a
biologically active protein.
• Hemoglobin, an oxygen transport protein, is an
example of a protein with a quaternary structure.
– It consists of four polypeptide chains or
subunits.
– It has two identical alpha subunits and two
identical beta subunits.
– All four subunits must be present for the
protein to function as an oxygen carrier.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
Not all proteins have a quaternary structure.
© 2011 Pearson Education, Inc.
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9.3 The Three-Dimensional Structure
of Proteins, Continued
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins
• Denaturation is a process that disrupts
secondary, tertiary, and quaternary structures.
• The primary structure is not destroyed during
denaturation.
• Frying an egg is an example of denaturation by
heat. Heat disrupts intermolecular forces such
as hydrogen bonding and other polar
interactions.
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
Other denaturing agents:
• Changes in pH, which alters the ability of the
acidic and basic side chains to form salt
bridges
• Organic compounds, which will disrupt the
disulfide bonds
• Heavy metals that disrupt salt bridges and
disulfide bonds
• Mechanical agitation, which disrupts hydrogen
bonds and weak forces
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
A protein will lose its biological activity if it loses
its three-dimensional shape.
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
• Curling straight hair or straightening curly hair
requires protein denaturation.
• Both processes require disruption of disulfide
bonds found in the hair protein keratin.
• The disruption of disulfide bonds reshapes the
hair and forces the reformation of disulfide
bonds in new places.
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
Ammonium
thioglycolate, which
reduces (breaks)
disulfide bonds, and
hydrogen peroxide
(reforms disulfide
bonds) are two
chemical agents
used in hairstyling.
© 2011 Pearson Education, Inc.
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9.4 Denaturation of Proteins, Continued
• The process of denaturation is used as an
antidote for lead or mercury poisoning.
• Egg whites can be given to an individual who
has ingested a heavy metal. Egg whites are
denaturated by the heavy metals and a
precipitate is formed.
• Vomiting is induced to eliminate the metalprotein precipitate.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins
Collagen
• Collagen is the most abundant protein in the
body. One-third of the bodies protein is collagen.
• It is found in connective tissue like cartilage,
skin, blood vessels, and tendons.
• A special quaternary structure called a triple
helix forms the fibrous structure of collagen.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
• Each polypeptide chain of a triple helix is a lefthanded helix.
• Collagen primarily contains the amino acids
glycine, proline, alanine, and hydroxyproline.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
• Hydrogen bonds between the polypeptide chains in
collagen are formed through the hydroxyl group on
hydroxyproline.
• Proline is converted to hydroxyproline with the aid
of Vitamin C. A deficiency of Vitamin C causes
scurvy, which is a collagen malformation disease.
Scurvy can be reversed with a vitamin C diet.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
Hemoglobin
• Hemoglobin transports oxygen in blood.
• It is composed of two alpha subunits and two
beta subunits held together by hydrogen bonds,
hydrophobic interactions, and salt bridges.
• Each subunit contains a nonprotein part called a
prosthetic group, which is called a heme.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
• Each heme group binds an Fe2+, which binds O2,
so a molecule of hemoglobin can bind up to four
molecules of O2.
• When O2 binds to the Fe2+ of hemoglobin, the
shape of hemoglobin changes, which allows the
hemoglobin to hold on to the oxygen until it is
delivered to tissues. This change in shape is
known as a conformational change.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
After the oxygen is delivered to the tissues, the
shape of the hemoglobin changes back to its
pre-oxygenated form.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
Antibodies—Your Body’s Defense System
• Antibodies, also known as
immunoglobulins, are produced in our
bodies when a foreign agent like bacteria
enters.
• The foreign agent recognized by antibodies is
known as an antigen.
• Antibodies consists of four polypeptide chains
held together by disulfide bonds and
intermolecular forces.
• Antibodies are “Y” shaped. Antigens bind at
the top of each arm of the Y.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
Antibodies—Your Body’s Defense System,
Continued
The top of each Y has a unique primary
structure for a particular antigen and binds
only one antigen, which is then destroyed by
the immune system.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
Integral Membrane Proteins
• Integral membrane proteins span the nonpolar
region of a cell membrane and facilitate the
movement of polar substances across the
membrane.
• An important integral membrane protein involved
in electrolyte balance is the sodium potassium
pump (Na+/K+ ATPase).
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
• The sodium potassium pump protein is
composed of four polypeptide chains held
together by intermolecular forces.
• The side chains embedded in the nonpolar
region of the cell membrane are nonpolar,
allowing them to interact with the nonpolar
region of the membrane.
• The central cavity of the protein is lined with
polar amino acids, allowing polar molecules to
pass.
© 2011 Pearson Education, Inc.
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9.5 Examples of Biologically Important
Proteins, Continued
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