1. Tertiary Structure
A result of interactions between side (R) chains that are widely separated within the peptide chain
Covalent disulfide bonds - between 2 cysteine AA
Salt bridges - between AA w/ charged side chains
(acid & base AA)
Hydrogen bonds - between AA with polar R groups
Hydrophobic attractions - between NP side chains
Spatial relationship of 2˚ structures
Level responsible for 3-D orientation of proteins.
Thermodynamically most stable conformation of a protein.
May have intra-chain and inter-chain linkages

2. Tertiary protein structure bonding

3. Human insulin, a small two-chain protein: Tertiary structure has both intra-chain & inter-chain disulfide linkages.

4. 3o protein structure - Non-covalent R group interactions:
(a) electrostatic interaction
(b) hydrogen bonding
(c) hydrophobic interaction

5. Tertiary structure of the single-chain protein: myoglobin.
found mainly in
muscle tissue
where it serves
as an intracellular
storage site
for oxygen
Myoglobin
Myoglobin and hemoglobin are hemeproteins whose physiological importance is principally related to their ability to bind molecular oxygen. Myoglobin is a monomeric heme protein found mainly in muscle tissue where it serves as an intracellular storage site for oxygen. During periods of oxygen deprivation oxymyoglobin releases its bound oxygen which is then used for metabolic purposes. The tertiary structure of myoglobin is that of a typical water soluble globular protein. Its secondary structure is unusual in that it contains a very high proportion (75%) of a-helical secondary structure. A myoglobin polypeptide is comprised of 8 separate right handed a-helices, designated A through H, that are connected by short non helical regions. Amino acid R-groups packed into the interior of the molecule are predominantly hydrophobic in character while those exposed on the surface of the molecule are generally hydrophilic, thus making the molecule relatively water soluble.
Each myoglobin molecule contains one heme prosthetic group inserted into a hydrophobic cleft in the protein. Each heme residue contains one central coordinately bound iron atom that is normally in the Fe2+, or ferrous, oxidation state. The oxygen carried by hemeproteins is bound directly to the ferrous iron atom of the heme prosthetic group.

6. Quaternary structure:
Shape or structure from joining more than one protein molecule (protein subunits) together to make a larger protein complex.
Same non-covalent bonds as tertiary form:
Electrostatic interactions (Van der Waals)
Hydrophobic interactions
Hydrogen bonding
Quaternary structure is easily disrupted
Hydrophobic Forces
Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R-groups. It is the nature of the interaction of the different R-groups with the aqueous environment that plays the major role in shaping protein structure. The spontaneous folded state of globular proteins is a reflection of a balance between the opposing energetics of H-bonding between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups. The hydrophobicity of certain amino acid R-groups tends to drive them away from the exterior of proteins and into the interior. This driving force restricts the available conformations into which a protein may fold.

7. Tertiary and quaternary structure of the oxygen-carrying protein hemoglobin.
When O2 binds to
Fe of Heme group,
tension on the
molecule pulls
an amino acid,
which alters the
3o structure –
Hemoglobin
Adult hemoglobin is a [a(2):b(2)] tetrameric hemeprotein found in erythrocytes where it is responsible for binding oxygen in the lung and transporting the bound oxygen throughout the body where it is used in aerobic metabolic pathways. For a description of the different types of hemoglobin tetramers see the section below on Hemoglobin Genes. Each subunit of a hemoglobin tetramer has a heme prosthetic group identical to that described for myoglobin. The common peptide subunits are designated a, b, g and d which are arranged into the most commonly occurring functional hemoglobins.
Although the secondary and tertiary structure of various hemoglobin subunits are similar, reflecting extensive homology in amino acid composition, the variations in amino acid composition that do exist impart marked differences in hemoglobin's oxygen carrying properties. In addition, the quaternary structure of hemoglobin leads to physiologically important allosteric interactions between the subunits, a property lacking in monomeric myoglobin which is otherwise very similar to the a-subunit of hemoglobin.
Comparison of the oxygen binding properties of myoglobin and hemoglobin illustrate the allosteric properties of hemoglobin that results from its quaternary structure and differentiate hemoglobin's oxygen binding properties from that of myoglobin. The curve of oxygen binding to hemoglobin is sigmoidal typical of allosteric proteins in which the substrate, in this case oxygen, is a positive homotropic effector. When oxygen binds to the first subunit of deoxyhemoglobin it increases the affinity of the remaining subunits for oxygen. As additional oxygen is bound to the second and third subunits oxygen binding is further, incrementally, strengthened, so that at the oxygen tension in lung alveoli, hemoglobin is fully saturated with oxygen. As oxyhemoglobin circulates to deoxygenated tissue, oxygen is incrementally unloaded and the affinity of hemoglobin for oxygen is reduced. Thus at the lowest oxygen tensions found in very active tissues the binding affinity of hemoglobin for oxygen is very low allowing maximal delivery of oxygen to the tissue. In contrast the oxygen binding curve for myoglobin is hyperbolic in character indicating the absence of allosteric interactions in this process.
The allosteric oxygen binding properties of hemoglobin arise directly from the interaction of oxygen with the iron atom of the heme prosthetic groups and the resultant effects of these interactions on the quaternary structure of the protein. When oxygen binds to an iron atom of deoxyhemoglobin it pulls the iron atom into the plane of the heme. Since the iron is also bound to histidine F8, this residue is also pulled toward the plane of the heme ring. The conformational change at histidine F8 is transmitted throughout the peptide backbone resulting in a significant change in tertiary structure of the entire subunit. Conformational changes at the subunit surface lead to a new set of binding interactions between adjacent subunits. The latter changes include disruption of salt bridges and formation of new hydrogen bonds and new hydrophobic interactions, all of which contribute to the new quaternary structure.
The latter changes in subunit interaction are transmitted, from the surface, to the heme binding pocket of a second deoxy subunit and result in easier access of oxygen to the iron atom of the second heme and thus a greater affinity of the hemoglobin molecule for a second oxygen molecule. The tertiary configuration of low affinity, deoxygenated hemoglobin (Hb) is known as the taut (T) state. Conversely, the quaternary structure of the fully oxygenated high affinity form of hemoglobin (HbO2) is known as the relaxed (R) state.
This in turn affects the 4o structure bonds Exposes more heme sites -
creates greater affinity for O2

8. Protein Structure R eview

9. Review part 1: can you… List the characteristics of proteins
Draw the basic structure of amino acids (a.a.)
Compare & contrast structural differences
between the 4 main classes of a.a.
Draw a peptide formation between a.a.
List characteristics of four levels of protein
structure (1o, 2o, 3o, and 4o)
An interesting game developed at the University of Washington that helps solve protein folding problems. It gives anyone a chance to participate in real solutions to this research. foldit instuctions Foldit game download

10. Types of Proteins Two major types - based on structural levels
Fibrous - peptide chains are arranged in long strands/sheets
Globular - peptide chains are folded into spherical/globular shapes

11. Fibrous versus Globular protein
Fibrous Proteins 
Have fiber-like structures – good structural material. Relatively insoluble in water.
Unaffected by moderate in temp and pH.
Subgroups within this category include:
Collagens & Elastins: the proteins of connective tissues. tendons and ligaments.
Keratins: proteins that are major components of
skin, hair, feathers and horn.
Fibrin: a protein formed when blood clots.
Myosin: a protein that makes up muscle tissue

12. Serve regulatory, maintenance and catalytic roles.
Globular Proteins 
In living organisms:
Serve regulatory, maintenance and catalytic roles.
Include hormones, antibodies, and enzymes.
Either dissolve or form colloidal suspensions in water.
Generally more sensitive to temperature & pH change
than fibrous protein counterparts.
Examples within this category include:
Insulin Regulatory – controls glucose levels
Hemoglobin Transport – moves O2 around body
Myoglobin Storage – stores O2 near muscles
Transferrin Transport – moves Fe in blood
Immunoglobulins Defense – attacks invading pathogens

13. Fibrous structural protein: Keratin
Nails Horn & Hoof feathers Hair
Keratin structural molecules are normally long and thin,
insoluble in water, very high tensile strength,and arranged to form fibers.
Composed of long rods, twisted together,
laid down in criss-cross matrix form.

14. Keratinized stratified squamous epithelial layer: found only in skin!
Dead cell layers at surface.  Keratin effectively waterproofs cells. Blocks diffusion of nutrients & wastes.
Provides protection against  friction, microbial invasion, and desiccation.

15. Many cross-links create very little flexibility: horns, claws, hooves, or nails.
Fewer cross-links allows some stretching but returns to normal: wool, skin, and muscle proteins.

16. Fibrous structural protein: Collagen
Collagen most abundant protein in human body
Structural protein
Major component of the connective tissue:
sheaths muscles & attaches them to bone through tendons
or attaches skeletal elements together through cartilage
Collagen exists as a molecule that is tightly coiled about itself forming a secondary triple coil.
Collagen Structure
Collagen, a basic "building block" in the construction of animals, is referred to as a structural protein. It is fibrous in nature and is a major component of the connective tissue that sheaths muscles and attaches them to bone through tendons or that attaches skeletal elements together through cartilage. It also forms the bulk of the proteins found in hides and skin. When extracted from hide, tendon, cartilage, and bones, collagen becomes the primary component of glues. Fibrous proteins are well suited to their task of support and connection. They are formed from very long, thin fibers of amino acids covalently bonded in specific sequence. This sequence gives collagen a specific shape and strength that is a consequence of intramolecular hydrogen bonding. In the 1950s, Linus Pauling, Robert B. Corey, and H. R. Branson determined that collagen exists as a molecule that is tightly coiled about itself forming a secondary structure termed an -helix.2 Nearly half the amino acids of collagen are glycine and alanine, the smallest amino acids; this causes the collagen molecule to coil in such a manner that the small amino acids are in the center of the coil and the bulky, less mobile ones.-for example, hydroxyproline- are on the outside (table 2). Hydroxyproline's rigid structure causes a twist in the coil wherever it occurs. The -NH- and=0 groups of glycine and alanine from one coil will then hydrogen bond with similar sites on the other coils. The molecules bunch together in groups of three, forming a larger coil that gives collagen fibers their strength in living tissue.

17. The molecules bunch together in groups of three,
forming a larger coil (superhelical coil)
that gives collagen fibers their strength in living tissue.
Tendons

18. Collagen structure can be disrupted in diseases such as scurvy,
which is a lack of ascorbic acid, a cofactor
in the hydroxylation of proline (Hydroxyproline)
In addition, collagen structure is disrupted
in rheumatoid arthritis.

19. Myosin & Actin
Muscle proteins which allow for contraction of the muscle.
Myosin
Fibrous tail - two coiled -helices
Globular head - one at the end of each tail
Actin
A multimeric protein
Long fiber of connected globular proteins

20. Muscle tissue contracts and relaxes when triggered by electrical
stimuli from brain.
Muscle fibers bundled
together make up a
single muscle. Many
myofibrils make up
each fiber.
Myofibrils have
striations, formed by
arrangements of
protein molecules.
Muscle tissue contracts and relaxes when triggered by electrical stimuli from the brain, through the nerves. The electrical stimuli release calcium ions from a component in the muscle cell. The release of calcium ions initiates the muscle contraction. The contractions cause movement of the body.
Hundreds of muscle fibres, each up to several centimetres long, are bundled together to make up a single muscle. Many small myofibrils make up each fibre (Figure 5). The myofibrils have a characteristic pattern of transverse lines, called striations, that are formed by the arrangements of protein molecules.The protein molecules form filaments. There are two types of filament; thick and thin. Thick filaments contain myosin, thin filaments contain actin , troponin and tropomyosin. Scientists think that muscles contract by the two types of filament sliding over each other so that they overlap more (Figure 5). Figure 6 The sturcture of myosin in thick muscle filaments.Myosin is made up of six polypeptide chains. Four are low molecular mass (light) chains, and two are high molecular mass (heavy) chains. The two heavy chains are twisted together for part of their length to form a coiled rod. Each heavy chain ends in a globular head region, which also contains two light chains. The rod is a two stranded a-helical coiled coil (Figure 6).
In thick filaments the myosin molecules are twisted in a bundle with the heads pointing out in a regular way from the main body of the filament (Figure 7).
The protein forms filaments. 2 types of filament: thick & thin.
Thick filaments contain myosin; thin filaments contain
actin, troponin and tropomyosin.