1. 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

2. These are examples of protein function
Proteins can do so many different things because they are chemically and physically versatile
Table 5-1

3. Enzymes are probably the most important type of protein
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

4. 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

5. 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

6. Some R groups are nonpolar or hydrophobic
Glycine
(Gly or G)
Alanine
(Ala or A)
Valine
(Val or V)
Leucine
(Leu or L)
Isoleucine
(Ile or I)
Figure 5.17 The 20 amino acids of proteins
Methionine
(Met or M)
Phenylalanine
(Phe or F)
Tryptophan
(Trp or W)
Proline
(Pro or P)

7. Some R groups are polar Serine (Ser or S) Threonine (Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Figure 5.17 The 20 amino acids of proteins

8. Some R groups are so polar that they have an electric charge
under cellular conditions
Acidic
Basic
Figure 5.17 The 20 amino acids of proteins
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)

9. 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

10. Peptide Bond Formation Condensation reaction Peptide bond (a)
Side chains or R groups
Peptide
bond
Figure 5.18 Making a polypeptide chain
Backbone
Amino end
(N-terminus)
Carboxyl end
(C-terminus)
(b)

11. 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

12. A ribbon model of lysozyme A space-filling model of lysozyme
Lysozyme is the name of one important protein
Groove
Groove
Figure 5.19 Structure of a protein, the enzyme lysozyme
A ribbon model of lysozyme
A space-filling model of lysozyme
Ribbon diagram shows position of backbone
Space filling shows all atoms

13. A protein’s structure determines its function
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
Figure 5.20 An antibody binding to a protein from a flu virus

14. 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)

15. 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

16. +H3N Primary Structure Amino end Amino acid subunits 1 5 10 15 20 25
Figure 5.21 Levels of protein structure—primary structure 20 25

17. 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
For the Cell Biology Video An Idealized Alpha Helix: No Sidechains, go to Animation and Video Files.
For the Cell Biology Video An Idealized Alpha Helix, go to Animation and Video Files.
For the Cell Biology Video An Idealized Beta Pleated Sheet Cartoon, go to Animation and Video Files.
For the Cell Biology Video An Idealized Beta Pleated Sheet, go to Animation and Video Files.

18. Also possible for a part of a protein to have no particular secondary
Secondary structure
Beta pleated sheet
Examples of
amino acid
subunits
Figure 5.21 Levels of protein structure—secondary structure
Alpha helix
Also possible for a part of a protein to have no particular secondary
structure

19. 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 widely-separated amino acids
Covalent bonds called disulfide bridges may reinforce the protein’s structure

20. Hydrophobic interactions and van der Waals interactions Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Figure 5.21 Levels of protein structure—tertiary and quaternary structures
Ionic bond

21. 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 non-amino acid chemical-iron)
Some polypeptides do not have any quaternary structure. Some have it only part of the time and not the rest

22. Polypeptide Beta Chains chain Iron Heme Alpha Chains Hemoglobin
Figure 5.21 Levels of protein structure—tertiary and quaternary structures
Heme
Alpha Chains
Hemoglobin
Collagen

23. Some images of
Quaternary
structure

24. 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 loses its ability to function properly

25. Denaturation Normal protein Denatured protein Renaturation
Figure 5.23 Denaturation and renaturation of a protein
Normal protein
Denatured protein
Renaturation

26. Cells have to devote significant attention to protein folding
Chaperonins or chaperone proteins are used to help correct folding occur

27. 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.
Chaperonin
(fully
assembled)