Download 18.3 Amino Acids - Haverford Alchemy

Outline
18.1 An Introduction to Biochemistry
18.2 Protein Structure and Function: An Overview
18.3 Amino Acids
18.4 Acid–Base Properties of Amino Acids
18.5 Handedness
18.6 Molecular Handedness and Amino Acids
18.7 Primary Protein Structure
18.8 Shape-Determining Interactions in Proteins
18.9 Secondary Protein Structure
18.10 Tertiary Protein Structure
18.11 Quaternary Protein Structure
18.12 Chemical Properties of Proteins
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Goals
1. What are the structural features of amino acids?
Be able to describe and recognize amino acid structures and
illustrate how they are connected in proteins.
2. What are the properties of amino acids?
Be able to describe how the properties of amino acids depend
on their side chains and how their ionic charges vary with pH.
3. Why do amino acids have “handedness?”
Be able to explain what is responsible for handedness and
recognize simple molecules that display this property.
4. What is the primary structure of a protein and what
conventions are used for drawing and naming primary
structures?
Be able to define protein primary structure, explain how
primary structures are represented, and draw and name a
simple protein structure, given its amino acid sequence
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Goals, Continued
5. What types of interactions determine the overall shapes
of proteins?
Be able to describe and recognize disulfide bonds, hydrogen
bonding along the protein backbone, and noncovalent
interactions between amino acid side chains in proteins.
6. What are the secondary and tertiary structures of
proteins?
Be able to define these structures and the attractive forces
that determine their nature, describe the α-helix and β-sheet
and distinguish between fibrous and globular proteins.
7. What is quaternary protein structure?
Be able to define quaternary structure, identify the forces
responsible for quaternary structure, and give examples of
proteins with quaternary structure.
© 2013 Pearson Education, Inc.
18.1 An Introduction to Biochemistry
• Biochemistry is the study of molecules and their
reactions in living organisms.
• Physicians are faced with biochemistry every
day; all diseases are associated with
abnormalities in biochemistry.
• Nutritionists evaluate dietary needs based on
biochemistry.
• The pharmaceutical industry designs molecules
that mimic or alter the action of biomolecules.
• The goal of biochemistry is to understand the
structures of biomolecules and the relationship
between their structures and functions.
© 2013 Pearson Education, Inc.
18.1 An Introduction to Biochemistry
• Biochemistry is the common ground for the life sciences,
where answers to fundamental questions are being
found at the molecular level.
• The principal classes of biomolecules are proteins,
carbohydrates, lipids, and nucleic acids.
• Biochemical reactions must continuously break down
food molecules, generate and store energy, build up new
biomolecules, and eliminate waste.
• Despite the huge size and complexity of some
biomolecules, their functional groups and chemical
reactions are no different from those of simpler organic
molecules.
• All the principles of chemistry introduced thus far
apply to biochemistry.
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18.1 An Introduction to Biochemistry
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18.2 Protein Structure and Function: An Overview
• Proteins are polymers of amino acids.
• Every amino acid contains an amine group (NH2), a
carboxyl group (COOH), and an R group called a side
chain, bonded to a central carbon atom.
• The central carbon is the alpha carbon.
• Amino acids in proteins are alphaamino (α-amino) acids because
the amine group in each is
connected to the alpha carbon.
• Each α-amino acid has a different
R group. This is what distinguishes
them from one another.
• R groups may be hydrocarbons, or
may contain a functional group.
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18.2 Protein Structure and Function: An Overview
• Two or more amino acids can link together by forming
amide bonds, which are known as peptide bonds when
they occur in proteins.
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18.2 Protein Structure and Function: An Overview
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Two amino acids form a dipeptide.
Three amino acids form a tripeptide.
Many amino acids together form a polypeptide.
Proteins have four levels of structure.
– Primary structure is the sequence of amino acids in a
protein chain.
– Secondary structure is the regular and repeating spatial
organization of neighboring segments of single protein
chains.
– Tertiary structure is the overall shape of a protein molecule
produced by regions of secondary structure combined with
the overall bending and folding of the protein chain.
– Quaternary structure refers to the overall structure of
proteins composed of more than one polypeptide.
© 2013 Pearson Education, Inc.
18.2 Protein Structure and Function: An Overview
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18.3 Amino Acids
• All of the proteins in living organisms are built
from 20 amino acids.
• Each amino acid has a three-letter shorthand
code.
• For 19 of these amino acids, only the identity
of the side chain attached to the carbon
differs.
• The remaining amino acid (proline) is a
secondary amine whose nitrogen and carbon
atoms are joined in a five-membered ring.
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18.3 Amino Acids
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18.3 Amino Acids
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18.3 Amino Acids
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18.3 Amino Acids
• The 20 α-amino acids that make up proteins
are classified as neutral, acidic, or basic,
depending on the nature of their side chains.
• The 15 neutral amino acids are further
divided into those with nonpolar side chains
and those with polar functional groups such
as amide or hydroxyl groups in their side
chains.
• The sequence of amino acids in a protein and
the chemical nature of their side chains
enables proteins to perform their functions.
© 2013 Pearson Education, Inc.
18.3 Amino Acids
• Noncovalent forces act between different
molecules or between different parts of the same
large molecule.
• The nonpolar side chains are described as
hydrophobic (water-fearing). To avoid aqueous
fluids, nonpolar side chains gather into clusters
to create a water-free environment.
• The polar, acidic, and basic side chains are
hydrophilic (water-loving). Attractions between
water molecules and hydrophilic groups on the
surface of folded proteins impart water solubility
to the proteins.
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18.4 Acid-Base Properties of Amino Acids
• Amino acids contain both an acidic group, —COOH and
a basic group, NH2.
• These two groups can undergo an intramolecular acid–
base reaction to form a zwitterion, a neutral ion with one
positive charge and one negative charge and is thus,
electrically neutral.
• This gives amino acids many of the physical properties
of salts: crystals, high melting points, and water
solubility.
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18.4 Acid-Base Properties of Amino Acids
• In acidic solution, amino acid zwitterions accept
protons on their basic —COO– groups to leave
only the positively charged —NH3+ groups.
• In basic solution, amino acid zwitterions lose
protons from their acidic —NH3+ groups to leave
only the negatively charged —COO– groups.
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18.4 Acid-Base Properties of Amino Acids
• The isoelectric point (pI) describes the pH at which a
sample of an amino acid has equal numbers of + and
– charges.
• At this point, the net charge of all the molecules of that
amino acid in a pure sample is zero.
• The pI for each amino acid is different, due to the
influence of the side chain.
• A few amino acids have isoelectric points that are not
near neutrality (pH 7). Since the side-chain groups of
these compounds are substantially ionized at
physiological pH of 7.4, these amino acids are usually
referred to by the names of the ions formed when the
groups in the side chains are ionized.
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18.4 Acid-Base Properties of Amino Acids
• Side chain interactions are important in
stabilizing protein structure thus, it is important
to be aware of their charges at physiological pH.
• Isoelectric points influence protein solubility and
determine which amino acids in an enzyme
participate directly in enzymatic reactions.
• Acidic and basic side chains are particularly
important because at physiological pH these
groups are fully charged and can participate not
only in ionic bonds within a protein chain, but
also transfer from one molecule to another
during reactions.
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18.5 Handedness
• The mirror images of your hand cannot be
superimposed on each other; one does not
completely fit on top of the other.
• Objects that have handedness in this manner
are said to be chiral (pronounced ky-ral,
from the Greek cheir, meaning “hand”)
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18.5 Handedness
• Not all objects are chiral. There is no such thing
as a right-handed tennis ball or a left-handed
coffee mug.
• Objects that lack handedness are said to be
nonchiral, or achiral. Their mirror images are
superimposable because they have a plane of
symmetry.
© 2013 Pearson Education, Inc.
18.6 Molecular Handedness and Amino Acids
• Alanine is a chiral molecule. Its mirror images
cannot be superimposed. As a result, alanine exists
in two forms that are mirror images of each other: a
“right-handed” form known as D-alanine and a “lefthanded” form known as L-alanine.
• Propane is an achiral molecule. The molecule and
its mirror image are identical and it has no left- and
right-handed isomers.
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18.6 Molecular Handedness and Amino Acids
• Carbon forms four bonds oriented to the four
corners of an imaginary tetrahedron.
• In alanine, the central carbon atom is connected
to four different groups: a COO– group, an H
atom, an NH3+ group, and a CH3 group.
• Such a carbon is referred to as a chiral carbon
atom, or a chiral center.
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18.6 Molecular Handedness and Amino Acids
• The two mirror-image forms of a chiral molecule
like alanine are called enantiomers or optical
isomers (“optical” because of their effect on
polarized light).
• Enantiomers are one kind of stereoisomer,
compounds that have the same formula and
atoms with the same connections but different
spatial arrangements.
• Pairs of enantiomers have many of the same
physical properties: the same melting point,
solubility in water, isoelectric point, and density.
© 2013 Pearson Education, Inc.
18.6 Molecular Handedness and Amino Acids
• Pairs of enantiomers differ in their effect on polarized
light and in how they react with other molecules that are
also chiral.
• Pairs of enantiomers often differ in their biological
activity, odors, tastes, or activity as drugs.
• 19 of the 20 common amino acids are chiral. Only the Lenantiomers are found in proteins.
© 2013 Pearson Education, Inc.
18.7 Protein Primary Structure
• The primary structure of a protein is the
sequence in which its amino acids are lined up
and connected by peptide bonds.
• Along the backbone of a protein is a chain of
alternating peptide bonds and α-carbon atoms.
• The amino acid side chains are substituents
along the backbone, where they are bonded to
the carbon atoms.
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18.7 Protein Primary Structure
• The carbon and nitrogen atoms along the
backbone lie in a zigzag arrangement, with
tetrahedral bonding around the α-carbon atoms.
• The carbonyl-group double bond electrons are
shared with the adjacent C—N bond. This
sharing makes the C—N bond sufficiently like a
double bond that there is no rotation around it.
• The carbonyl group, the N—H group bonded to
it, and the two adjacent α-carbons form a rigid,
planar unit.
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18.7 Protein Primary Structure
• Two amino acids can form two different
dipeptides, X—Y and Y—X.
• Peptides and proteins are always written with
the aminoterminal amino acid (also called Nterminal) on the left and carboxyl-terminal
amino acid (C-terminal) on the right.
• The individual amino acids joined in the chain
are referred to as residues.
• A peptide is named by citing the amino acid
residues in order, starting at the N-terminus and
ending with the C-terminus.
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18.7 Protein Primary Structure
• The primary structure of a protein is the result of amino
acids being lined in precisely the correct order.
• So crucial is primary structure to function that the change
of only one amino acid can drastically alter a protein’s
biological properties.
• Sickle-cell anemia is the result of a single amino acid
substitution that replaces one amino acid (glutamate,
Glu) with another (valine, Val) in the hemoglobin
molecule.
• A hydrophobic pocket is exposed on the surface of the
hemoglobin and hydrophobic valine on another
hemoglobin molecule is drawn into this pocket.
• Insoluble fibrous chains are formed, forcing the cell into
a sickle shape.
© 2013 Pearson Education, Inc.
18.7 Protein Primary Structure
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Proteins in the Diet
Proteins are a necessary part of the daily diet because our bodies do not
store proteins like they do carbohydrates and fats.
9 of the 20 amino must be obtained in the diet. These are known as the
essential amino acids.
A complete protein source provides each of the nine essential amino acids.
Most meat and dairy products meet this requirement.
Traditional vegetarian food combinations provide complementary proteins.
– Grains are low in lysine and threonine, but contain methionine and tryptophan.
– Legumes (lentils, beans, and peas) supply lysine and threonine, but are low in
methionine and tryptophan. The two sources of protein complement each other.
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Disorders caused by inadequate protein intake are known as protein-energy
malnutrition (PEM).
– In kwashiorkor, protein is deficient although caloric intake may be adequate.
Children with kwashiorkor have an enlarged liver, and are underdeveloped.
– Marasmus is the result of starvation. It is identified with severe muscle wasting,
below-normal stature, and poor response to treatment.
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A reassessment of diet in developed countries is underway, with a focus on
disease prevention.
© 2013 Pearson Education, Inc.
18.8 Shape-Determining Interactions in Proteins
HYDROGEN BONDS ALONG THE BACKBONE
Hydrogen bonds form between the hydrogen atoms
in the N—H groups and the oxygen atoms in the
C=O groups along protein backbones.
HYDROGEN BONDS OF R GROUPS WITH EACH
OTHER OR WITH BACKBONE ATOMS
• Some amino acid side chains contain atoms that
can form hydrogen bonds. These can connect
different parts of a protein molecule
• Often hydrogen-bonding side chains are present on
the surface of a folded protein, where they can form
hydrogen-bonds with surrounding water molecules.
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18.8 Shape-Determining Interactions in Proteins
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18.8 Shape-Determining Interactions in Proteins
IONIC ATTRACTIONS BETWEEN
R GROUPS (SALT BRIDGES)
• Ionized acidic and basic side chains will create salt bridges.
HYDROPHOBIC INTERACTIONS
BETWEEN R GROUPS
• Hydrocarbon side chains are attracted to each other by dispersion
forces to create a water-free pocket. Although individual attractions
are weak, their large number in proteins plays a major role in
stabilizing the folded structures.
COVALENT SULFUR–SULFUR BONDS
• Cysteine amino acid residues have side chains containing thiol
functional groups S-OH that can react to form sulfur–sulfur bonds.
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18.8 Shape-Determining Interactions in Proteins
Protein Analysis by Electrophoresis
• Protein molecules in solution can be separated from each other by
taking advantage of their net charges.
• In the electric field between two electrodes, a positively charged
particle moves toward the negative electrode and a negatively
charged particle moves toward the positive electrode. This
movement is electrophoresis.
• The net charge on a protein is determined by how many acidic or
basic side-chains are ionized, and this depends on the pH.
• By varying the nature of the buffer, proteins can be separated in a
variety of ways, including by their molecular weight.
• Once the separation is complete, the proteins are made visible by
the addition of a dye.
• Electrophoresis is routinely used in the clinical laboratory for
determining which proteins are present, and in what amounts in a
blood sample.
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18.8 Shape-Determining Interactions in Proteins
Protein Analysis by Electrophoresis
• Normal adult hemoglobin (HbA) and hemoglobin showing the
inherited sickle-cell trait (HbS) differ in their net charges.
• HbA and HbS move different distances during
electrophoresis.
• A normal individual has only HbA.
• An individual with sickle-cell anemia
has no HbA.
• An individual with sickle-cell trait has
roughly equal amounts of HbA and
HbS.
• HbA and HbS have negative charges
of different magnitudes because HbS
has two fewer Glu residues than HbA.
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18.9 Secondary Protein Structure
Alpha-helix
• The coil is held in place by
hydrogen bonds between each
carbonyloxygen and the amide
hydrogen four amino acid
residues above it.
• The chain is a right-handed coil
(shown separately on the right),
and the hydrogen bonds lie
parallel to the vertical axis.
• Viewed from the top into the
center of the helix, the side
chains point to the exterior of the
helix.
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18.9 Secondary Protein Structure
Beta-sheet
• The hydrogen bonds stabilize
interactions between
neighboring protein chains.
• The protein chains usually lie
side by side so that alternating
chains run from the N-terminal
end to the C-terminal end and
from the C-terminal end to the
N-terminal end (known as the
antiparallel arrangement).
• A pair of stacked pleated
sheets illustrate how the R
groups point above and below
the sheets.
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18.9 Secondary Protein Structure
• Fibrous protein is a tough, insoluble protein
whose protein chains form fibers or sheets.
– Wool, hair, and fingernails are made of fibrous
proteins known as keratins which are composed of αhelices twisted together into small fibrils that are in
turn twisted into larger and larger bundles.
– Natural silk and spider webs are made of fibroin,
composed of stacks of β-sheets. The R groups must
be relatively small, so fibroin contains regions of
alternating glycine and alanine. The sheets stack so
that sides with the smaller glycine hydrogens face
each other and sides with the larger alanine methyl
groups face each other.
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18.9 Secondary Protein Structure
• Globular protein is water-soluble protein whose
chain is folded in a compact shape with hydrophilic
groups on the outside.
• Their structures, which vary widely with their
functions, are not regular.
• Sections of α-helix and β-sheet are usually present.
• Hydrophilic side chains on the outer surfaces of
globular proteins account for their water solubility,
allowing them to travel through body fluids.
• Many globular proteins are enzymes.
• The overall shapes of globular proteins represent
another level of structure, tertiary structure.
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18.10 Tertiary Protein Structure
• The way in which an entire protein chain is coiled
and folded into its specific three-dimensional shape
is the protein’s tertiary protein structure.
• Each protein molecule folds in a distinctive manner
that is determined by its primary structure and
results in its maximum stability.
• A protein with the shape in which it functions in living
systems is known as a native protein.
• A protein composed only of amino acid residues is a
simple protein.
• Tertiary structure is drawn in a style that shows the
combination of α-helix and β-sheet regions, the
loops connecting them, and disulfide bonds.
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18.10 Tertiary Protein Structure
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18.10 Tertiary Protein Structure
• Conjugated
proteins are aided in
their function by an
associated non–
amino acid unit.
• The oxygen-carrying
portion of myoglobin
has a heme group
embedded within the
polypeptide chain.
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18.11 Quaternary Protein Structure
• Quaternary protein structure is the way in
which two or more protein chains aggregate to
form large, ordered structures.
• Polypeptides are primarily held together by
noncovalent forces, but covalent bonds and
non–amino acid portions may also be
incorporated.
© 2013 Pearson Education, Inc.
18.11 Quaternary Protein Structure
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HEMOGLOBIN
Hemoglobin is a conjugated quaternary protein
composed of four polypeptide chains (two each of two
polypeptides called α-chain and β-chain) held together
by hydrophobic interactions and four heme groups.
The α-chains have 141 amino acids, and the β-chains
have 146 amino acids.
The heme groups each contain an iron. Hemoglobin is
the oxygen carrier in red blood cells. In the lungs, O2
binds to Fe2+ so that each hemoglobin can carry a
maximum of four O2 molecules.
In tissues in need of oxygen, O2 is released, and CO2 is
picked up and carried back to the lungs.
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18.11 Quaternary Protein Structure
Figure 18.8 Heme and hemoglobin, a protein with quaternary
structure. (a) The polypeptides are shown in purple, green, blue,
and yellow, with their heme units in red. Each polypeptide
resembles myoglobin in structure. (b) A heme unit is present in each
of the four polypeptides in hemoglobin.
© 2013 Pearson Education, Inc.
18.11 Quaternary Protein Structure
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COLLAGEN
Collagen is the major constituent
of connective tissues.
The basic structural unit of
collagen (tropocollagen) is three
intertwined chains of about 1000
amino acids each. Each chain is
loosely coiled in a left-handed
(counterclockwise) direction.
Three of these coiled chains wrap
around one another (in a
clockwise direction) to form a stiff,
triple helix in which the chains are
held together by hydrogen bonds.
All collagens have a glycine every
three residues, and prolines are
hydroxylated in a reaction that
requires vitamin C.
© 2013 Pearson Education, Inc.
18.11 Quaternary Protein Structure
Protein Structure Summary
• Primary structure is the sequence of amino acids connected by peptide bonds
in the polypeptide chain; for example, Asp-Arg-Val-Tyr.
• Secondary structure is the arrangement in space of the polypeptide chain,
which includes the regular patterns of the α-helices and the β-sheet motifs (held
together by hydrogen bonds between backbone carbonyl and amino groups in
amino acid residues) plus the loops and coils that connect these segments.
• Tertiary structure is the folding of a protein molecule into a specific threedimensional shape held together by noncovalent interactions primarily between
amino acid side chains that can be quite far apart along the backbone and, in
some cases, by disulfide bonds between side-chain thiol groups.
• Quaternary structure is two or more protein chains assembled in a larger
three-dimensional structure held together by noncovalent interactions.
Classes of Proteins Summary
• Fibrous proteins are tough, insoluble, and composed of fibers and sheets.
• Globular proteins are water-soluble and have chains folded into compact
shapes.
• Simple proteins contain only amino acid residues.
• Conjugated proteins include one or more non–amino acid units.
© 2013 Pearson Education, Inc.
18.11 Quaternary Protein Structure
Collagen: A Tale of Two Diseases
Scurvy
• Scurvy is experienced whenever fresh fruits and vegetables are not available
for long periods of time. Armies, navies, and medieval people in northern
regions in late winter were particularly susceptible to scurvy.
• Symptoms include joint pain and swelling, blackened bruises on the skin, and
swollen, bleeding gums accompanied by tooth loss.
• Lack of vitamin C leads to the formation of weak collagen. Since tropocollagen
is part of capillary walls, weak collagen leads to the spontaneous bruising,
bleeding, and soft tissue swelling that are characteristic of scurvy.
• In 1747, James Lind established that citrus prevented and cured scurvy on
long sea voyages, leading to British sailors being known as “Limeys.”
Osteogenesis Imperfecta
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The primary symptom of this disease is spontaneous broken bones.
Incorrectly synthesized collagen leads to weak bone structures. There is no
cure; current research is directed at understanding the underlying biochemical
defect in hopes of designing better treatment.
A definitive diagnosis requires genetic testing.
© 2013 Pearson Education, Inc.
18.12 Chemical Properties of Proteins
• In protein hydrolysis, peptide bonds are hydrolyzed to yield
amino acids.
• Digestion of proteins in the diet involves hydrolyzing peptide
bonds in the stomach and small intestine, where the process
is catalyzed by enzymes. Amino acids are absorbed through
the wall of the intestine.
• A chemist might hydrolyze a protein by heating it with
hydrochloric acid.
© 2013 Pearson Education, Inc.
18.12 Chemical Properties of Proteins
• Denaturation is the loss of secondary, tertiary, and quaternary
protein structure that leaves primary structure intact.
• Solubility is often decreased by denaturation. Enzymes lose their
catalytic activity and other proteins are not able to carry out
biological functions when denatured.
• Most denaturation is irreversible, but renaturation is accompanied by
recovery of biological activity.
• All the information needed to determine protein shape is present in
the primary structure.
• Misfolding of proteins leads to abnormal secondary and tertiary
structures that compromise the function of the protein.
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18.12 Chemical Properties of Proteins
• Heat—The weak side-chain attractions in globular proteins
are easily disrupted by heating.
• Mechanical agitation—The most familiar example of
denaturation by agitation is the foam produced by beating egg
whites. Denaturation of proteins at the surface of the air
bubbles stiffens the protein and causes the bubbles to be held
in place.
• Detergents—Even very low concentrations of detergents can
disrupt the association of hydrophobic side chains.
• Organic compounds—Polar solvents interfere with hydrogen
bonding by competing for bonding sites.
• pH change—Excess H+ or OH– ions react with basic or acidic
side chains in amino acid residues and disrupt salt bridges
• Inorganic salts—High concentrations of ions can disturb salt
bridges.
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18.12 Chemical Properties of Proteins
Prions: Proteins that Cause Disease
• Prions (pronounced pree-ons) are “proteinaceous infectious
particles.”
• They are associated with Creutzfeldt–Jakob disease (CJD), bovine
spongiform encephalopathy (BSE), scrapie in sheep; a chronic
wasting disease in elk and mule deer; and in humans kuru, and fatal
familial insomnia (FFI).
• Some well-supported facts about prions include:
– Humans and all animals tested thus far have a gene for making a normal
prion protein that resides in the brain.
– Alpha helices in normal prions are replaced by β-sheets, resulting in a
disease-causing prion.
– A misfolded prion can induce a normal prion to flip from the normal shape to
the disease-causing shape.
– The infectious nature of prions is not affected by heat or UV-radiation
treatment.
– Synthetic prions cause neurological disease in mice similar to mad cow
disease or CJD.
© 2013 Pearson Education, Inc.
Chapter Summary
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What are the structural features of amino acids?
Amino acids in body fluids have an ionized carboxylic acid group,
—COO–, an ionized amino group, NH3+, and a side-chain R group
bonded to a central carbon atom (the α-carbon).
Twenty different amino acids occur in proteins, connected by
peptide bonds (amide bonds) formed between the carboxyl group
of one amino acid and the amino group of the next.
What are the properties of amino acids?
Amino acid side chains have acidic or basic functional groups or
neutral groups that are either polar or nonpolar. In glycine, the
“side chain” is a hydrogen atom.
The dipolar ion in which the amino and carboxylic acid groups are
both ionized is known as a zwitterion.
For each amino acid, there is a distinctive isoelectric point—the
pH at which the numbers of positive and negative charges are
equal. At more acidic pH, some carboxylic acid groups are not
ionized; at more basic pH, some amino groups are not ionized.
© 2013 Pearson Education, Inc.
Chapter Summary, Continued
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Why do amino acids have “handedness?”
An object, including a molecule, has “handedness” —is chiral—when it
has no plane of symmetry and thus, has mirror images that cannot be
superimposed on each other.
A simple molecule can be identified as chiral if it contains a carbon atom
bonded to four different groups. All α-amino acids, except glycine, meet
this condition by having four different groups bonded to the α carbon.
What is the primary structure of a protein and what conventions are
used for drawing and naming primary structures?
Proteins are polymers of amino acids (polypeptides).
Their primary structure is the linear sequence in which the amino acids
are connected by peptide bonds. Using formulas or amino acid
abbreviations, the primary structures are written with the amino-terminal
end on the left and the carboxyl-terminal end on the right.
To name a peptide, the names of the amino acids are combined, starting
at the amino-terminal end, with the endings of all but the carboxylterminal amino acid changed to -yl.
Primary structures are often represented by combining three-letter
abbreviations for the amino acids.
© 2013 Pearson Education, Inc.
Chapter Summary, Continued
5. What types of interactions determine the overall
shapes of proteins?
• Protein chains are drawn into their distinctive and
biochemically active shapes by attractions between
atoms along their backbones and between atoms in sidechain groups.
• Hydrogen bonding can occur between the backbone
carbonyl groups and amide hydrogens of adjacent protein
chains.
• Noncovalent interactions between side chains include
ionic bonding between acidic and basic groups (salt
bridges), and hydrophobic interactions among nonpolar
groups.
• Covalent sulfur–sulfur bonds (disulfide bonds) can form
bridges between the side chains in cysteine.
© 2013 Pearson Education, Inc.
Chapter Summary, Continued
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What are the secondary and tertiary structures of proteins?
Secondary structures include the regular, repeating threedimensional structures held in place by hydrogen bonding between
backbone atoms within a chain or in adjacent chains.
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The α-helix is a coil with hydrogen bonding between carbonyl oxygen
atoms and amide hydrogen atoms four amino acid residues farther along
the same chain.
The β-sheet is a pleated sheet with adjacent protein-chain segments
connected by hydrogen bonding between peptide groups. The adjacent
chains in the β-sheet may be parts of the same protein chain or different
protein chains.
Secondary structure mainly determines the properties of fibrous
proteins, which are tough and insoluble.
Tertiary structure is the overall three-dimensional shape of a folded
protein chain.
Tertiary structure determines the properties of globular proteins,
which are water-soluble, with hydrophilic groups on the outside and
hydrophobic groups on the inside. Globular proteins often contain
regions of α-helix and/or β-sheet secondary structures.
© 2013 Pearson Education, Inc.
Chapter Summary, Continued
7.
What is quaternary protein structure?
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Proteins that incorporate more than one peptide chain are said to have
quaternary structure.
In a quaternary structure, two or more folded protein subunits are united
in a single structure by noncovalent interactions.
Hemoglobin, for example, consists of two pairs of subunits, with a
nonprotein heme molecule in each of the four subunits. Collagen is a
fibrous protein composed of protein chains twisted together in triple
helixes.
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8.
What chemical properties do proteins have?
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The peptide bonds are broken by hydrolysis, which may occur in acidic
solution or during enzyme-catalyzed digestion of proteins in food. The
end result of hydrolysis is production of the individual amino acids from
the protein.
Denaturation is the loss of overall structure by a protein while retaining its
primary structure. Among the agents that cause denaturation are heat,
mechanical agitation, pH change, and exposure to a variety of chemical
agents, including detergents.
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© 2013 Pearson Education, Inc.