Proteins (in detail) (Pg. 40)

1. Proteins (in detail) (Pg. 40) • The most diverse molecules in living organisms and among the most important: gelatin, desserts, hair, antibodies, spider webs, blood clots, egg whites, tofu, and fingernails, etc. • Make up 50% of dry mass of most cells. • Structural building blocks • Functional molecules • Involved in almost anything that cells do. • 3D shape is directly related to their function. • Enzymes: catalysts  speed up chemical reactions so cells can sustain life. • Immunoglobins: protect animals against foreign microbes and cancer cells. • Hemoglobin: transports oxygen. • Protein carriers: move substances across cell membranes. • And much more!

2. DNA to PROTEIN • Genetic information in DNA codes specifically for production of proteins and nothing else. • All copies of the same gene produce the same protein.

3. Protein Structure • Monomer: amino acid. • Central carbon atom with an amino group, a carboxyl group, a hydrogen atom, and a side chain (R). • 20 different R groups, therefore 20 different AAs. • Amphiprotic: both acidic (carboxyl) and basic (amino) functional group. • When dissolved in water, carboxyl group donates an H+ ion to the amino group • Causes the carboxyl group to become (-) and amino (+). • Amino acids may have side chains that are polar (hydrophillic) or nonpolar (hydrophobic), acidic (contain a carboxyl) or basic (amino).

4. Nonpolar amino acids

5. Polar Amino Acids

6. Electrically charged (acidic/basic) amino acids Note: there are 8 essential amino acids: body cannot synthesize from simpler compounds: Tryptophan, methionine, valine, threonine, phenylalanine, leucine, isoleucine, lysine.

7. HW (to do for Monday): Amino Acid Memory Cards • 1) take a cue card and place it in `portrait` orientation towards you. • 2) fold the top down and bottom up about 1 inch from the edges. • 3) Draw an amino acid on the blank side of the cue card. • 4) write the name of the amino acid on one of the folded parts, and the short-hand notation on the other fold. • 5) write a few things about the amino acid on the side with lines. • 6) use these cue cards to study. Do not lose them! (attach them to your binder, put them in your pencil case, etc). You will be required to know all of the amino acids as well as their properties.

8. Formation of a Polypeptide • Proteins consist of one or more amino acid polymers (polypeptides) that have twisted and coiled into a specific shape. • Final shape: conformation  determined by the sequence of amino acids it contains. • Peptide bond: condensation reaction between amino group of one amino acid and carboxyl group of another amino acid, forming an amide • Functional group linkage is called an amide bond. • Polypeptides: constructed in the cytoplasm of cells through process called protein synthesis.

10. Polypeptides • Amino terminus: amino group at one end. • Carboxyl terminus: carboxyl group at other end. • Can be between a few to more than a thousand amino acids. • Sequence determines polypeptide’s 3D conformation  determines function. • Structural proteins: roughly linear: forms strands or sheets. • Globular proteins: 1+ polypeptide chains that coil and bend to form rounded, spherical shape • Many enzymes are globular.

12. Primary Structure • Primary Structure: unique sequence of amino acids in a polypeptide chain. • Amino acid referred to as a ‘residue.’ • First protein to be ‘decoded’ in terms of residue was insulin: Fredrick Sanger, 1958. • Determined by the nucleotide sequence of DNA. • Possible arrangement of polypeptides: • The number of possible arrangements of residues in a polypeptide are 20n . • Example: How many different 40- residue polypeptides are possible? __________________________________________________________________________________

13. Changing the sequence. • Changing the sequence by one amino acid could alter the 3D shape  protein loses it’s function, is rendered useless, or has a different function (rare). • Ex// Sickle cell anemia: single AA change in hemoglobin causes red blood cell to change shaped: flow is hindered, vessels clog.

14. Secondary Structure • During protein synthesis, AAs added to growing chain one at a time  coils, folds, bends at various locations. • Two main shapes form: • α-helix & β-pleated sheet.

15. α-helix • α-helix: hydrogen bond forms between the electronegative O of (C=O) of one peptide bond and the electropositive hydrogen of the amino group (N-H) four peptide bonds away • Ex// fibrous proteins - α-keratin: protein in hair.

16. β-pleated sheet • Two parts of polypeptide chain lie parallel to one another. • Hydrogen bonds form between oxygen atoms of C=O on one strand and hydrogen atoms of amino groups on adjacent strand. • Spiders are Crazy Cool! • silk contains large amounts of beta • pleated sheets  spiders secrete silk • in liquid form and then solidify when exposed • to air. Many H-bonds. Strength!

17. Tertiary Structure • Strong forces of attraction and repulsion between the polypeptide and its environment force it to undergo additional folding. • Chaperone proteins: aid growing polypeptide to fold into tertiary structure: deficiency: cystic fibrosis. • AAs with polar R groups (ex// serine, tyrosine, and glutamine) are attracted to water. • AAs containing nonpolar R groups (ex//valine and phenylalanine) are ‘repelled’ by water. Congregate in the interior of folded polypeptide, away from water. • Structure stabilized by number of R-group interactions. • H-bonds • ionic bonds (between oppositely charged side chains) • van der Waals forces between nonplar R groups. • Disulfide bridges: covalent bond between sulfur-containing R groups of cysteine residues. • Proline kinks: R group is attached to the amino group  forms a kink in the polypeptide.

19. Quaternary Structure • Sometimes 2+ polypeptide subunits combine to form a functional protein. • Collagen (skin, bones, tendons, ligaments) • Keratin (hair) • Hemoglobin (transports oxygen): four polypeptides in quaternary structure.

21. Denaturation • Proteins are made within a cell, in a mostly neutral pH. • Different environmental conditions may cause unravelling. • pH • temperature • Salt concentrations • Various chemicals and heat disrupt: • Hydrogen bonds • Ionic bonds • Disulfide bridges • Hydrophobic interactions • Will usually return to original orientation if denaturing agent is removed.

22. Denaturing (2) • Enzymes work within specific ranges of conditions • Thermophiles: (archaebacteria: live in water at about 100 degrees celcius) • Would die at room temperature  enzymes would denature. • Gastrin: digestive enzyme in the stomach works best at pH = 2, and denatured in small intestine where the pH = 10. • Fevers: prolonged fevers can denature proteins in brain and lead to seizures/death. • Preservatives: salt, sugar, curry, pickling  denatures proteins in bacteria that spoil food. • Straitening hair: temporarily denaturing proteins with heat. • Cooking meat: to denature fibrous proteins in muscle tissue.

23. PPs, Page 50. #19-29 ON MONDAY, MAKE SURE YOU HAVE THE FOLLOWING COMPLETED: • Any PPs from the text that I have assigned throughout the powerpoint. • Carbohydrate worksheet • Lipid worksheet. MONDAY: quiz on Carbohydrates and Proteins.