Protein Tertiary Structure

Question 1

How Proteins Fold:

Answer 1

Proteins are composed of amino acids.

Amino acids are linked by peptide bonds to form the primary structure of a protein.

There are 20 different amino acids, each with
unique side chains.

The sequence of amino acids and the chemistry of the side chains determines how the protein folds which, in turn, determines the protein structure and function.

Question 2

There are four types of bonds found in
Tertiary and Quaternary structures:

Answer 2

1. Disulfide bridges
2. Salt bridges
3. Hydrogen bonding
4. Hydrophobic interactions

Question 3

It is important to realize that all four…

Answer 3

forces can be used for a protein to function in its specific role.

• If any or all of these forces are changed, the protein’s nature is also changed.
• The protein is then said to be denatured.

Question 4

Secondary structure of a protein is the…

Answer 4

arrangement of the polypeptide backbone of the protein in space.

Question 5

Secondary structure includes…

Answer 5

two kinds of repeating patterns: a-helix and b-sheet.

Question 6

(Secondary structure) Hydrogen bonding between backbone
atoms are…

Answer 6

responsible for both of these
secondary structures.

Question 7

Tertiary Protein Structure:

Answer 7

The overall three dimensional shape that results from the folding of a protein chain.

Question 8

Tertiary structure depends mainly on…

Answer 8

attractions of amino acid side chains that are far apart along the same backbone.

Question 9

Non-covalent interactions…

Answer 9

and disulfide covalent bonds govern tertiary structure.

Question 10

native state:

Answer 10

The shape in which a protein exists naturally in a living organism.

Question 11

Quaternary Protein Structure:

Answer 11

The way in which two or more polypeptide subunits associate to form a single threedimensional protein unit.

• Non-covalent forces are responsible for
  quaternary structure essential to the
  function of proteins.

Question 12

Protein Denaturation:

Answer 12

The loss of secondary, tertiary, or quaternary
protein structure due to disruption of noncovalent interactions and or disulfide bonds
BUT that leaves peptide bonds and primary
structure intact.

Question 13

Agents that causes denaturation:

Answer 13

Heat, Mechanical agitation, detergents, organic compounds, pH change, and inorganic salts.

Question 14

Heat Agent:

Answer 14

The weak side-chain attractions in
globular proteins are easily broken by heating. -e.g. cooking meat converts some of the insoluble collagens into soluble gelatin.

Question 15

Mechanical Agitation Agent:

Answer 15

• Most familiar example of denaturation of protein by mechanical agitation is the foaming that occurs during beating of egg whites.

Question 16

Detergents Agent:

Answer 16

Very low concentrations of
detergents can cause denaturation by disrupting the association of hydrophobic side chains.

Question 17

Organic compounds Agents;

Answer 17

Polar solvents such as acetone or ethanol can interfere with hydrogen bonding by competing for bonding sites.

Question 18

pH change Agents:

Answer 18

• Excess H+
  or OHions reacts
  with the basic or acidic side chains in amino
  acid residues and disrupts salt bridges.

Question 19

Inorganic salts Agents

Answer 19

• Sufficiently high
  concentrations of ions can disrupt salt bridges

Question 20

How does the unfolded protein adopt the
native state?

Answer 20

This has proven to be a very challenging
problem. It has been described as the
second half of the genetic code, or as the
3-dimensional code, as opposed to the
1-dimensional code of the nucleotide/amino
acid sequence.

-Predict 3D structure from primary
sequence

– Avoid misfolding related to human
diseases

– Design proteins with novel functions

Question 21

Anfinsen
Experiment

Answer 21

Denaturation of
ribunuclease A
(4 disulfide bonds) with
8 M Urea containing
b-mercaptoethanol to form
a random coil with no
activity

Urea – denatures
b-MeSH – reduces Cy

Question 22

After renaturation…

Answer 22

the refolded protein has native activity
despite the fact that there are 105 ways to renature the
protein.

Conclusion: All the information necessary for folding the
peptide chain into its native structure is contained in the
primary amino acid sequence of the peptide.

Question 23

Anfinsen Experiment: Remove b-mercaptoethanol only

Answer 23

oxidation of the sulfhydryl group, then
remove urea → scrambled protein, no
activity

• Further addition of trace amounts of b- mercaptoethanol converts the
  scrambled form into native form.
• Conclusion: The native form of a protein
  has the thermodynamically most stable
  structure.

Question 24

Quick Review: Tertiary Structure

Answer 24

*Specific overall shape of a protein

• Cross links between R groups of amino acids in
  chain

Disulphide
ionic
H bonds
hydrophobic

Question 25

Globular and Fibrous Proteins:

Answer 25

Globular proteins
“spherical” shape

Fibrous proteins
long, thin fibers

Question 26

Quaternary Structure

Answer 26

-Proteins with two or more chains

• Example is hemoglobin
  Carries oxygen in blood
  Four polypeptide chains
  Each chain has an iron-containing
  heme group to bind oxygen