Tophat: Chapter 6 Hierarchical Protein Structure

Primary structure

The linear sequence of monomers.

Stabilizing forces for primary structure

Covalent bonds such as peptide bonds or phosphodiester linkages.

Secondary structure

Regular patterns of folding or coiling within the macromolecule, such as alpha helices and beta sheets in proteins.

Stabilizing forces for secondary structure

Hydrogen bonds between backbone groups.

Tertiary structure

The 3-D arrangement of the macromolecule driven by interactions between side chains.

Stabilizing forces for tertiary structure

Combination of IMF’s: hydrogen bonds, ionic interactions, hydrophobic interactions, van der waals forces, and disulfide bonds.

Quaternary structure

The arrangement of multiple macromolecule subunits into a functional complex. Subunit organization.

Stabilizing forces for quaternary structure

Hydrogen bonds, ionic interactions, hydrophobic interactions, van der waals forces, and covalent linkages.

What was the given example for the primary structure of a protein?

Bovine pancreatic ribonuclease A.

How many amino acid residues does bovine pancreatic ribonuclease A have?

124

What amino acid is missing from bovine pancreatic ribonuclease A?

Trp, tryptophan.

Is tryptophan (Trp) made in humans?

No

Where is tryptophan obtained for humans?

Diet.

What primary bond does bovine pancreatic ribonuclease A have and how many?

4 disulfide bridges.

What are the two main secondary structures for proteins?

Alpha helix and beta sheets. (also known as a beta pleated sheet)

What does a mixture of primary and secondary structures form in proteins?

Tertiary structure.

What is a tertiary structure in proteins?

Polypeptide chains.

What are the 4 ways to view the tertiary structure of a protein?

1. Backbone only

2. Backbone plus side chains

3. Ribbon Structure

4. Space-filling structure

What do multiple tertiary structures form?

Quaternary structure

What type of heteromer is hemoglobin?

Tetramer.

What tertiary structures are in hemoglobin?

Two alpha polypeptide chains and two beta polypeptide chains.

How are secondary structures in polypeptides form?

1. The atoms of the peptide bond ensemble lie in one plane.

2. Rotation can occur about either of the bonds linking the alpha carbon to its two amide planes.

Angle about the C-alpha and N bond are denoted with what?

Phi

Angle about the C alpha and C bond are denoted with what?

Psi

Is phi=0 degrees and psi= 180 degrees favorable or unfavorable?

Unfavorable

Is phi= 180 degrees and psi= 0 degrees favorable or unfavorable?

Unfavorable

Is phi= 0 degrees and psi= 0 degrees favorable or unfavorable?

Unfavorable

Is phi= -60 degrees and psi= 180 degrees favorable or unfavorable?

Favorable

What are the classes of secondary structures in proteins?

1. Alpha helices (right or left handed)

2. Other helices

3. Beta sheet (parallel or antiparallel)

4. Tight turns

How many residues per turn does the alpha helix have?

3.6

What is the rise per residue in the alpha helix?

1.5 angstroms, 0.15 nm.

What is the rise per turn in the alpha helix?

5.4 angstroms.

How many atoms does the backbone loop that is closed by any H bond in an alpha helix have?

13

What is the phi of an alpha helix?

-60 degrees

What is the psi of an alpha helix?

-45 degrees.

The alpha helix has a large net dipole moment, true or false and why?

True, this is because the arrangement of N-H and C=O groups along the helix axis.

What does it mean for the exposed N-H and C=O groups at the end of an alpha helixes to be capped?

The four N-H groups at the N terminal and the four C=O groups at the C terminal of an alpha helix lock partners for H-bond formation.

What is helix capping?

The formation of H bonds with other nearby donor and acceptor groups.

How do hydrophobic interactions and helix capping correlate?

Capping may also involve appropriate hydrophobic interactions that accommodate nonpolar side chains at the ends of helical segments.

What is the polarity of helices?

They can be polar, nonpolar, or amphiphilic.

What presentation can reveal if the alpha helices are polar, nonpolar, character of alpha helices.

Helical wheel presentation.

What amino acids are alpha helix forming?

1. A (Ala)

2. E (Glu)

3. F (Phe)

4. H (His)

5. I (Ile)

6. L (Leu)

7. M (Met)

8. Q (Gln)

9. R (Arg)

10. W (Trp)

11. Y (Tyr)

What is the beta pleated sheet composed of?

Beta strands.

What two ways can bets sheets be aligned?

Parallel or antiparallel.

What is the rise per residue in antiparallel beta sheets?

3.47 angstroms.

What is the rise per residue in parallel beta sheets?

3.25 angstroms.

How many residues per turn for both beta sheet configurations?

2

In a beta sheet diagram which ways to the arrows point regardless of configuration?

Blunt end for the N terminus and pointed end for the C terminus.

What was the example given in class for composites of alpha helices and beta sheets?

Spidersilk.

What secondary structure has a higher percentage in the radial of spider webs and why?

Beta sheets because the radial strands of the webs must be strong and rigid.

What secondary structure has a higher percentage in the circumferential strands of spider webs and why?

Alpha helices because the strands must be flexible.

What is the main function of the beta turn?

Allows the peptide chain to reverse directions.

How the carbonyl O and the amide proton react with a beta turn?

The carbonyl oxygen of one resid

What two amino acids are prevalent in beta turns.

Proline and Glycine.

How many principal forms of beta turns are there?

2

What characterizes the peptide segments between secondary structures?

Short and direct.

How do proteins form the most stable structures?

They fold.

How does stability arise in tertiary structures?

1. Formation of large number of intramolecular hydrogen bonds.

2. Reduction in the surface area accessible to solvent that occurs upon folding.

What two factors lie at the heart of the principles for how stability arises?

1. Proteins are typically a mixture of hydrophilic and hydrophobic amino acids.

2. The hydrophobic groups tend to cluster together in the folded interior of the protein.

What is the coilded coil?

A bundle of alpha helices wound into a left handed superhelix.

What is the number of residues per turn in the coiled coil?

3.5

How many residues does it take for the position of the side chains to repeat in a coiled coil?

7

What is alpha keratin?

A fibrous protein found in hair, fingernails, claws, horns, and beaks.

What is the sequence characteristics for alpha keratin.

1. Contains 311 to 314 residue long alpha helical rod segments capped with non helical N and C termini.

2. Primary structure of helical rods consists of 7 residue repeats. 1st and 4th are nonpolar.

What does this structure promote for alpha helices?

It promotes association of helices to form coiled coils.

What is the collagen triple helix the principle component of?

Connective tissue.

What amino acid is nearly 1 out of 3 in the collagen triple helix and why?

Glycine because the center of the helix fits glycine only.

What amino acids make 30% of residues in the collagen triple helix?

Pro and HyPro.

What stabilizes the collagen triple helix?

The interchain hydrogen bonds involving HyPro.

What unusual amino acids does collagen ahve?

1. 4-hydroxyproline

2. 3-hydroxyproline

3. 5-hydroxylysine

What is the rise per residue for the collagen triple helix?

2.9 angstroms.

How many residues per turn does the collagen triple helix have?

3.3

What are the different chains in the collagen triple helix called?

Fibrils.

How are fibrils further strengthened in the collagen triple helix?

Interchain lysine-lysine and interchain hydroxypyridinium crosslinks.

What are fibroin and beta keratin and where are they found?

They are proteins that form extensive beta sheets and are found in silk fibers and bird feathers.

What three amino acids are primary in fibroin and beta keratin?

Glycine, Alanine, and Serine

What allows for the glycine on one beta sheet to interact with glycine’s on another?

Residues of a beta sheet extend alternately above and below the plane of the sheet, this places all glycines on one side and all alanines and serines on the other.

What molecules are in the surface structure of a globular protein?

Water molecules.

What is the polarity of alpha helices on a protein surface?

They are normally amphiphilic with polar and charged residues facing the solvent and nonpolar residues facing the interior.

How stable is a typical folded protein?

Only marginally stable.

Why are proteins often only marginally stable?

Due to flexibility and motion which are important to protein function.

What is the Kd for two subunits?

10-8 to 10-16M.

What energy levels do the Kd of two subunits correspond to?

50-100 kJ/mol at 37 degrees celsius.

How does entropy change within the quaternary level of a protein?

It is gained due to the burying of hydrophobic groups which is very favorable and it is lost due to association which is unfavorable.

What are the components of the overall quaternary structure?

1. Stability: reduction of surface to volume ratio

2. Genetic economy and efficiency

3. Brings catalytic sites together

4. Cooperation

How many protein subunits does alcohol dehydrogenase have?

2

How many protein subunits does glyceraldehyde- 3- phosphate have?

4

How many protein subunits does lactate dehydrogenase have?

4

How many protein subunits does pyruvate kinase have?

4

How many protein subunits does hemoglobin have?

2+2

How many protein subunits does insulin have?

6

How many protein subunits does glutamine synthetase have?

12

Define isologous

Subunits are bound with a certain residue sequence but have different orientations. Head to head interactions: both sides of subunit have the same residue sequence ABCD connected in a mirror image pattern.

Define Heterlogous

Subunits are bound with 2 different residue sequences. Head to tail interaction: there are 2 distinct arrangements of residues that bind, the order of the residues do not need to be constant.

How can disulfide bonds occur in reference to molecules?

They can form intermolecularly (between 2 molecules) or intramolecularly (within 1 molecule).

What do hydrophobic interactions drive?

Protein folding.

Where do ionic interactions usually occur?

On the protein surface

Where are hydrogen bonds formed?

Wherever possible

In what enzyme do we see electrostatic (ionic) interaction?

IRAK-4