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BChem
Biochemistry notes
| Question | Answer |
|---|---|
| Amino acids and protein structure | |
| • aa connected by peptide bonds | |
| o strong, covalent bonds, partial double bond characteristics, little rotation around bond axis | |
| o 4 levels of protein structure | |
| • primary –“most important” of the 4 | |
| case study in back addressing sickle cell | |
| • single aa change in beta hemoglobin affecting function | |
| • secondary structure | |
| • tertiary structure | |
| • only oligomeric proteins posses a quaternary structure | |
| • super secondary structure | |
| collections of secondary structures found together | |
| • luceine zipper, B pleated sheets and others | |
| o Athenson studies and denaturation of protiens | |
| • Denaturation and reforming of structures (reversal) | |
| o Globular and fibrous protiens | |
| • Globular | |
| Active, enzymes | |
| • Fibrous | |
| Non-polar/water insoluble amino acids | |
| Not water soluble | |
| More structural/supportive | |
| | |
| Generic amino acid structure | |
| • Amino group | |
| • Carboxylic acid group | |
| • Hydrogen | |
| Naturally ocuring amino acids are L form | |
| • All but glycine are chiral compounds | |
| o D or L form | |
| o L – rotate polarized light to the left | |
| o D – rotate polarized light to the right | |
| Ka: acid dissociation constant | |
| • How readly that functional group give up its proton | |
| • High Ka – functional group is readily dissociated | |
| pKa: High Ka = low pKa | |
| • high pKa = low Ka: will not give up proton easily | |
| Carbon side chains – non polar | |
| Amino acid residues make a dipeptide | |
| • Peptide bonds require energy | |
| o Strong, covalent bonds | |
| o Atoms involved are linear, planar | |
| o No rotation about peptide bond | |
| o Trans bonds | |
| • O and H groups located on opposite sides of bond | |
| • Reduces steric hindrance | |
| • R groups are also on opposite sides of bond | |
| o Every third bond in a protein is a peptide bond | |
| N terminal is always drawn on left, C terminal on right | |
| Peptides <50 AA | |
| Protiens >50 AA | |
| Levels of protein structure | |
| • Primary | |
| o Dictates how higher levels of protein structure follow | |
| • Secondary | |
| o Local recurring folding | |
| • Alpha helix | |
| Hydrogen bonds stabilize the alpha helix | |
| These H bonds are 4 AA residues apart | |
| • Proline & hydroxyl____ helix breakers | |
| • Helix binders | |
| • and Beta pleated sheets | |
| stabilized by H bonds in between sheets | |
| parallel | |
| • N, N, N terminal configuration | |
| or anti-parallel agrangements | |
| • N, C, N terminal configuration | |
| • More stable than parallel | |
| • Beta turns or beta bends | |
| Globular shapes need to bend or fold | |
| • Tertiary | |
| o Energetically favored arrangement | |
| o Often facilitated by molecular chaperones | |
| o Interactions involve R groups through noncovalent bonds | |
| o Anhydrous core found inside many enzymes | |
| o Bonds | |
| • Ionic, H, hydrophobic interactions, Van der Waals forces and disulfide bonds | |
| Disulfide bonds tend to be found in extracelluar proteins | |
| • Quaternary | |
| o Only applied to multi subunit proteins, oligomeric | |
| • Hemoglobin, insulin receptor | |
| • Supersecondary structures | |
| o Collections of secondary structures found together | |
| Denaturation | |
| • Athenson studies | |
| • Denatured proteins can be reformed as long as bonds are not broken | |
| Two families of Proteins | |
| Globular Proteins | |
| • Protein folds in such a way that hydrophobic – inside, philic – outside | |
| • Biological catylists/enzymes | |
| Fibrous Proteins | |
| • Structure | |
| • Found in muscle, tendons, etc. | |
| • | |
| Questions | |
| • | |
| Drop by and see doctor shaw |
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