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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
• Proteins have more chemical and physical
versatility than any other type of
macromolecule
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
These are examples of protein function
Proteins can do so many different things because
they are chemically and physically versatile
• Enzymes are probably the most important type
of protein. They act as catalysts to speed up
chemical reactions
• Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life
Proteins are polypeptides
• Polypeptides are polymers built from a set of
20 amino acid monomers
• All cells use the same set of 20 amino acids to
construct their proteins
• A protein consists of one or more polypeptides
Amino Acid Monomers
• Amino acids are small organic molecules with
both carboxyl and amino functional groups
• They also have side chains called R groups
• Amino acids differ based on R group properties
Some R groups are nonpolar or hydrophobic
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Some R groups are polar
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine Glutamine
(Asn or N) (Gln or Q)
Some R groups are so polar that they have an electric charge
under cellular conditions
Acidic
Aspartic acid Glutamic acid
(Glu or E)
(Asp or D)
Basic
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Amino Acids in Polymers
• A polypeptide is a polymer of amino acids that
are linked by peptide bonds
• Polypeptides range in length from a few to
more than a thousand monomers
• Each type of polypeptide has a unique linear
sequence of amino acids
Peptide
Bond
Formation
Peptide
bond
(a)
Condensation reaction
Side chains or R groups
Peptide
bond
Backbone
(b)
Amino end
(N-terminus)
Carboxyl end
(C-terminus)
Properties of Amino Acid Polymers
• Two distinct ends or termini: carboxy and
amino
• Backbone of peptide bonds, strong covalent
bond
• Chemical properties influenced by sum total of
R groups
• Exact order or sequence of amino acids
influences shape and biological properties
Lysozyme is the name of one important protein
Groove
Groove
A ribbon model of lysozyme
A space-filling model of lysozyme
Ribbon diagram shows position of backbone
Space filling shows all atoms
The sequence of amino acids determines a
protein’s three-dimensional structure
A protein’s structure determines its function
Antibody protein
Protein from flu virus
A Hierarchy of Four Levels of Protein Structure
• The primary structure of a protein is its unique
sequence of amino acids (1o)
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain (2o)
• Tertiary structure is determined by interactions
among various side chains (R groups) (3o)
• Quaternary structure results when a protein
consists of multiple polypeptide chains (4o)
• 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
Primary Structure
1
+H
5
3N
Amino end
10
Amino acid
subunits
15
20
25
• The coils and folds of secondary structure
result from hydrogen bonds between repeating
constituents of the polypeptide backbone
• Usually the interactions are among amino acids
that are close to one another in the primary
structure
• Typical secondary structures are a coil called
an  helix and a folded structure called a 
pleated sheet
Secondary structure
Beta pleated sheet
Examples of
amino acid
subunits
Alpha helix
Also possible for a part of a protein
to have no particular secondary
structure
• Tertiary structure is determined by interactions
between R groups, not between backbone
constituents (aka conformation or configuration)
• Refers to overall shape in space
• These interactions between R groups include
hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions
• May be interactions between R groups on widelyseparated amino acids
• Covalent bonds called disulfide bridges may
reinforce the protein’s structure
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 (the chains also associate with a nonamino acid chemical-iron)
• Some polypeptides do not have any quaternary
structure. Some have it only part of the time
and not the rest
Polypeptide
chain
Beta Chains
Iron
Heme
Alpha Chains
Hemoglobin
Collagen
Some images of
Quaternary
structure
What Determines Protein Structure?
• In addition to primary structure, physical and
chemical conditions can affect structure
• Alterations in pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
• This loss of a protein’s native structure is called
denaturation
• A denatured protein is biologically inactive
Denaturation
Normal protein
Renaturation
Denatured protein
Chaperonin
(fully
assembled)
An unfolded
polypeptide
enters the
cylinder
from
one end.
Cap attachment
causes the
cylinder to
change shape,
creating a
hydrophilic
environment
for polypeptide
folding.
The cap
comes off,
and the
properly
folded
protein is
released.
• Cells have to devote significant attention to
protein folding
• Chaperonins or chaperone proteins are
used to help correct folding occur