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Proteins
Concept 5.4: Proteins have many structures,
resulting in a wide range of functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
[Animations are listed on slides that follow the figure]
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Animation: Structural Proteins
Animation: Storage Proteins
Animation: Transport Proteins
Animation: Receptor Proteins
Animation: Contractile Proteins
Animation: Defensive Proteins
Animation: Enzymes
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Animation: Hormonal Proteins
Animation: Sensory Proteins
Animation: Gene Regulatory Proteins
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• Enzymes are a type of protein that acts as a
catalyst, speeding up chemical reactions
• Enzymes can perform their functions repeatedly,
functioning as workhorses that carry out the
processes of life
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-16
Substrate
(sucrose)
Glucose
Enzyme
(sucrose)
Fructose
Polypeptides
• Polypeptides are polymers of amino acids
• A protein consists of one or more polypeptides
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Amino Acid Monomers
• Amino acids are organic molecules with carboxyl
and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
• Cells use 20 amino acids to make thousands of
proteins
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-UN78
a carbon
Amino
group
Carboxyl
group
LE 5-17a
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Nonpolar
Methionine (Met)
Phenylalanine (Phe)
Tryptophan (Trp)
Proline (Pro)
LE 5-17b
Polar
Serine (Ser)
Threonine (Thr)
Cysteine (Cys)
Tyrosine (Tyr)
Asparagine (Asn) Glutamine (Gln)
LE 5-17c
Acidic
Basic
Electrically
charged
Aspartic acid (Asp) Glutamic acid (Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Amino Acid Polymers
• Amino acids are linked by peptide bonds
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few
monomers to more than a thousand
• Each polypeptide has a unique linear sequence of
amino acids
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Determining the Amino Acid Sequence of a
Polypeptide
• The amino acid sequences of polypeptides were
first determined by chemical methods
• Most of the steps involved in sequencing a
polypeptide are now automated
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein Conformation and Function
• A functional protein consists of one or more
polypeptides twisted, folded, and coiled into a
unique shape
• The sequence of amino acids determines a
protein’s three-dimensional conformation
• A protein’s conformation determines its function
• Ribbon models and space-filling models can
depict a protein’s conformation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-19
Groove
A ribbon model
Groove
A space-filling model
Four Levels of Protein Structure
• The primary structure of a protein is its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
Animation: Protein Structure Introduction
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-20
b pleated sheet
+H
3N
Amino end
Amino acid
subunits
a helix
• Primary structure, the sequence of amino acids in
a protein, is like the order of letters in a long word
• Primary structure is determined by inherited
genetic information
Animation: Primary Protein Structure
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-20a
Amino end
Amino acid
subunits
Carboxyl end
• The coils and folds of secondary structure result
from hydrogen bonds between repeating
constituents of the polypeptide backbone
• Typical secondary structures are a coil called an
alpha helix and a folded structure called a beta
pleated sheet
Animation: Secondary Protein Structure
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-20b
b pleated sheet
Amino acid
subunits
a helix
• Tertiary structure is determined by interactions
between R groups, rather than interactions
between backbone constituents
• These interactions between R groups include
hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions
• Strong covalent bonds called disulfide bridges
may reinforce the protein’s conformation
Animation: Tertiary Protein Structure
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-20d
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Ionic bond
• Quaternary structure results when two or more
polypeptide chains form one macromolecule
• Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope
• Hemoglobin is a globular protein consisting of four
polypeptides: two alpha and two beta chains
Animation: Quaternary Protein Structure
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LE 5-20e
Polypeptide
chain
b Chains
Iron
Heme
Polypeptide chain
Collagen
a Chains
Hemoglobin
Sickle-Cell Disease: A Simple Change in
Primary Structure
• A slight change in primary structure can affect a
protein’s conformation and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-21a
10 µm
Red blood Normal cells are
cell shape full of individual
hemoglobin
molecules, each
carrying oxygen.
10 µm
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
cell into sickle
shape.
LE 5-21b
Sickle-cell hemoglobin
Normal hemoglobin
Primary
structure
Val
His
1
2
Leu
Thr
3
4
Pro
Glu
5
6
Secondary
and tertiary
structures
7
b subunit
Quaternary Normal
hemoglobin
structure
(top view)
Primary
structure
Secondary
and tertiary
structures
Molecules do
not associate
with one
another; each
carries oxygen.
His
Leu
Thr
Pro
Val
Glu
1
2
3
4
5
6
7
Exposed
hydrophobic
region
b subunit
a
Quaternary
structure
b
Val
b
a
Function
Glu
Sickle-cell
hemoglobin
b
a
Function
Molecules
interact with
one another to
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
b
a
What Determines Protein Conformation?
• In addition to primary structure, physical and
chemical conditions can affect conformation
• Alternations in pH, salt concentration,
temperature, or other environmental factors can
cause a protein to unravel
• This loss of a protein’s native conformation is
called denaturation
• A denatured protein is biologically inactive
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-22
Denaturation
Normal protein
Denatured protein
Renaturation
The Protein-Folding Problem
• It is hard to predict a protein’s conformation from
its primary structure
• Most proteins probably go through several states
on their way to a stable conformation
• Chaperonins are protein molecules that assist the
proper folding of other proteins
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-23a
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
LE 5-23b
Polypeptide
Steps of Chaperonin
Action:
An unfolded polypeptide enters the
cylinder from one
end.
Correctly
folded
protein
The cap attaches, causing
the cylinder to change
shape in such a way that
it creates a hydrophilic
environment for the
folding of the polypeptide.
The cap comes
off, and the
properly folded
protein is released.
• Scientists use X-ray crystallography to determine
a protein’s conformation
• Another method is nuclear magnetic resonance
(NMR) spectroscopy, which does not require
protein crystallization
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 5-24a
X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-ray
source
X-ray
beam
Crystal
LE 5-24b
Nucleic acid
X-ray diffraction pattern
3D computer model
Protein