Unformatted text preview: Lecture Set #3 What is today’s day of the week? Monday B. Tuesday C. Wednesday D. Thursday E. Friday
A. How many micrograms (μg) are in a milligram (mg)?
A. A. B. C. D. E. 10-2 μg 10-1 μg 10 μg 102 μg 103 μg What are proteins made of? Protein Structure and Function A. B. C. D. E. DNA RNA amino acids carbohydrates lipids Amino Acids Amino Acids
the “R” group
The side-chain sidegroups (R-groups) (R are what make amino acids different from each other; they have unique unique chemistries, chemistries, especially relative to how they interact with water and the pH of the surrounding fluid. R R The R-groups can be: RHydrophobic Hydrophobic Hydrophilic Hydrophilic
ECB2 2-21 Cooper 2.13 Bio 106 Fall 2009 Professor Owen 1 Lecture Set #3 Protein structure
The The pH of the environment governs the charges on the R-groups RA. B. C. D. These These charges plus the shape of the R-groups Rdetermines the overall 3-D shape of the protein E. How many different acids are commonly found in a protein? 12 14 17 20 24 ECB2 2-22 Peptide Bond
Amino Amino acids are linked together by peptide bonds The carbon atom from the carboxyl group of one amino amino acid binds with the nitrogen atom of the amino group from second amino acid Water is a byproduct
carboxyl group amino group Peptide bond
Creates Creates double bond characteristics • No rotation at peptide bond, but rotation possible at alpha carbon (the C attached to the R-group) Rno rotation no rotation Cooper 2.15 rotation! Note that the R−groups stick out from the backbone. ECB2 4-2 Bio 106 Fall 2009 Professor Owen Peptide bond The protein has defined ends: N-terminus (amino) and C-terminus (carboxyl) C- Protein Structure 2 Lecture Set #3 Amino Acids Different kinds of noncovalent bonds (hydrogen, ionic, etc.) determine noncovalent protein folding. Each is weak, but together create a strong bonding arrangement to hold the protein into a particular shape. Protein folding & bonds Hydrophilic (polar) Hydrophobic (nonpolar)
ECB3 4-3 ECB3 4-4 You should learn the names of the amino acids and their 3-letter abbreviations. 3- Protein folding Hydrophobic forces help proteins fold into compact conformations. In the folded conformation below, the polar (hydrophilic) amino acids are on the outside in an aqueous environment, while the nonpolar (hydrophobic) amino acids are isolated inside. H-bonds Stabilize Folded Shape ECB3 4-5 Protein Structure
Why shape is important
Many Many proteins work by binding reactions, so that the shape of the protein is inherently related to its function
ex ex : making new drugs X-ray Diffraction
X-ray diffraction pattern from a crystal of the protein protein myoglobin 3-D shape determination Problems in determining structure: 1. Proteins are very complex molecules -- procedures can be very tedious. 2. 3-D structure is not static. Methods/problems 1. X-ray diffraction used for 90% (NMR = 10%) X2. Specimen must be crystallized--growing can take years -crystallized--growing space best location to grow (microgravity) 3. Database now contains 27,000+ structures. Bio 106 Fall 2009 Professor Owen 3 Lecture Set #3 Example – Ras protein Prions Protein misfolding caused by a prion is infectious, causing other proteins to misfold. misfold.
Ras proteins binds GTP (blue).
(a) Ball & stick model, (b) schematic diagram with β strands and α helices
Lodish et al. 3-5 3D protein shape directed by DNA is changed!
ECB3 4-8 Spongiform Encephalitis Mad Cow Disease Sponge-like lesions in brain tissue. Kuru
Kuru is a fatal degenerative disorder of the central nervous system. Kuru has been found only among the Fore people and related ethnolinguistic groups in Papua New Guinea (kuru is a Fore word for "trembling," or "shivering"). Four levels of structure
The The specific order of the amino acids joined joined together by peptide bonds the the chain of polypeptides has identifiable ends: amino and carboxyl ends: amino and carboxyl (N & C) Kuru was linked to the ritual cannibalism that was practiced by these tribes. The brains of the elders were prepared and eaten by the women and children. • huge number of possible proteins • ex: 4 amino acids = 20 x 20 x 20 x 20 = 160,000 • avg. protein = 300 amino acids = 10390 The The order is determined from the DNA Bio 106 Fall 2009 Professor Owen 4 Lecture Set #3 Example of primary structure
peptide bond Primary protein structure determines the final shape The sequence of a the amino acids th will will determine the 3D shape of the protein. ECB2 2-22 MBOC3 3-25 Secondary Structure
Rotations Rotations at the α−carbons Brings Brings oxygens (from the CO) and hydrogens CO) and hydrogens (from the NH) together forming hydrogen bonds 2 specific structures: specific Alpha helix (α-helix)
Single Single polypeptide chain turns regularly about itself to make a rigid cylinder.
ex: ex: skin, hair, nails Form Form readily in biological structures Some Some proteins are all α-helix (ex: keratin), some have none, but very common in globular proteins alpha helix & beta-sheet betaFrom ECB3 Panel 4-1 α helix Regions of an α-helix are amphipathic, amphipathic with both a hydrophobic core and a hydrophilic exterior
Lodish et al. 3-6,7 Bio 106 Fall 2009 Professor Owen 5 ...
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