Alpha Helix

_ A rise/residue

_ residue/turn

_ A rise/turn

_ atoms in H Loop

_ Hecial Nomenclature

1.5 A rise/residue

3.6 residue/turn

5.4 A rise/turn

13 atoms in H Loop

3.6 subscript 10 Hecial Nomenclature

Characteristics of Alpha Helix

1. Side chains are oriented outwards with interactions between i and i + 3 residues.

2. stabilized by H-bonds from the backbone carbonyl, i, to the i + 4 amide.

3. The orientation of the peptide bond creates an electric dipole along the helix axis.

Beta Sheet Characteristics

1. Beta sheets are stabilized by H bonds between both parallel and anti-parallel strands. 

2. Beta sheets have a right handed twist that can form beta barrel structures.

3. Tight turns between beta strands are stabilized by H bonds. 

Rules for a coiled coil alpha helix

1. Following the format a-b-c-d-e-f-g...

'a' and 'd' must both be non-polar (hydrophobic) amino acids that are not the same.

eg. Ile-Gln-Gln-Leu-Glu-Arg-Asp

Characteristics of alpha Keratin

1. Coiled coil alpha helix

2. Cross linking with cytosine disulfide bonds gives keratin its strength.

(These bonds may be broken in a reducing environment)

Characteristics of Collagen

1. Collagen is composed of three left-handed helixes twisted in a right-hand superhelical rope-like structure.

2. Stablized by H bonds.

3. Lysyl oxidase is the only enzyme

implicated in the process of creating

cross-links.

Structure of Hemoglobin

1. The tetramer has dihedral symmetry, with two fold axes of symmetry.

2. The protomer interface has hydrophobic, H bond and ion pair interactions.

3. The strongest interactions are between A and B protomers.

4. Can be viewed as a dimer of ab dimers.

5. Disulfide bonds do not stablize the protomers.

Assists in protein folding.

1. peptide prolyl cis-trans isomerase

2. molecular chaperones

3. protein disulfide isomerase

4. heat shock proteins

Leads to negative cooperativity in the Hill plot.

1. Contamination of a protein sample with an inhibitor of ligand binding.

2. Binding of ligand by a multimeric protein decreases ligand affinity in other subunits.

3. Two or more binding sites in the same polypeptide chain with different affinities.

4. A heterogenous mixture of protein with varying affinities of ligand.

What is methemoglobin?

Hemoglobin with oxidized Fe3+ bound to heme which does not bind to O2.

What is the Bohr effect?

Coupling of oxygen binding and proton release i transition from T to R state.

What is the role of carbonic anhydrase?

Generation of bicarbonate which is soluble in blood plasma.

What is the product of the reaction between an alcohol and a ketone?

Hemiketal

Epimers

Sugars that differ in the configuration around one carbon

atom

Structure of monogalactosyliacylglycerol

Structure of phosphatidylcholine.

Structure of Beta-estradiol (an estrogen)

D-Glyceraldehyde