1. Now playing: Frank Sinatra “My Way” A large part of modern biology is understanding large molecules like Proteins A large part of modern biology is understanding large molecules like Proteins

3. Websites: http://www.ncl.ox.ac.uk/dp/jjones1.html http://wizard.pharm.wayne.edu/biochem/prot.html.html Websites: http://www.ncl.ox.ac.uk/dp/jjones1.html http://wizard.pharm.wayne.edu/biochem/prot.html.html Goals: 1.Study polypeptides, peptide bonds & proteins. 2. Introduce 3-D, quaternary protein structure. 3. Relate proteins to genetics, science, agriculture and health. 3. Relate proteins to genetics, science, agriculture and health. Assignment: Read: chapters 3 & 5

4. Review: Molecule Building Blocks Small Molecules Chemical Bonds Macromolecules Sugars Covalent Polysaccharides Glycerol and fatty acids Covalent Lipids (fats) Amino acidsCovalent and peptide Proteins

6. Side chains (R groups) determine 20 different amino acids -Central carbon atom C -Amino group H H H H N N Amino group -Carboxyl group OH C C O O Carboxyl group R -Side chain (R) H H -Hydrogen atom Amino Acid Structure

7. Peptide bonds link Amino Acids together OH H H CCN O RH H CCN O R H H H CCN O R A Polypeptide = long chain of amino acids joined by peptide bonds Dehydration synthesis = losing a water

8. Protein conformation = 3-D Structure, peptide bonding is the Primary structure Protein =chain of amino acids Chemical Reaction Protein Conformation or Structure Determines Function

9. Primary Structure = AA’s make the Chain… AA Type

10. Amino Acids Building Blocks for ALL Proteins Non-Essential Amino Acids Glycine Alanine Aspartate Glutamate Asparagine Glutamine Arginine Tyrosine Systeine Serine Proline Non-Essential Amino Acids Glycine Alanine Aspartate Glutamate Asparagine Glutamine Arginine Tyrosine Systeine Serine Proline Assignment: Look up the essential amino acids Essential Amino Acids Phenylalanine Valine Threonine Tryptophan Isoleucine Methionine Histidine Leucine Lysine Essential Amino Acids Phenylalanine Valine Threonine Tryptophan Isoleucine Methionine Histidine Leucine Lysine

11. Side Chains: “R” H|H| Glycine Asparagine Cysteine Glutamic Acid Glutamine Arginine Aspartic Acid

12. Serine Alanine Lysine Proline Isoleucine Leucine Threonine Methionine Histidine

13. Tyrosine Tryptophan Valine Phenylalanine

14. Amino Acids Polarity or Charge helps Determine Binding… Polarity or Charge helps Determine Binding…

15. Amino Acids Each AA has a unique 1-letter and 3-letter code identifying it in the Protein’s chain…

16. Each AA has a unique 1-letter or a 3-letter code to identifying the Protein’s AA-chain 3-Letter Code in AA chain ProteinAA Chain Sequence The background shadow indicates similar binding or folding function. Single letter code

17. Primary Structure Amino acid sequence Peptide bonding H H HH C C O N R H H C C O N R H H C C O N R H C C O OH R

18. Protein Secondary Structure Is the pattern of hydrogen bonding in one polypeptide Pattern yields folding: 1-  helix or 2-  - pleated sheets Is the pattern of hydrogen bonding in one polypeptide Pattern yields folding: 1-  helix or 2-  - pleated sheets 1. Hydrogen bonds 2. Disulfide bonds (cysteine) 3. Hydrophobic forces 4. Ionic interactions Types of Bonding:

19. Types of Bonds Hydrogen bonds Disulfide bonds Hydrophobic forces Ionic interactions

20. Tertiary Structure = Folding Side Chains (R-groups) Tertiary Structure = Folding Side Chains (R-groups) Bonds: 1. Hydrogen bonds 2. Disulfide bonds (cysteine) 3. Hydrophobic forces 4. Ionic interactions

21. Quaternary Structure >1 polypeptide chain folded Multiple Proteins Folded Together >1 polypeptide chain folded Multiple Proteins Folded Together 1. Hydrogen bonds 2. Disulfide bonds (cysteine) 3. Hydrophobic forces 4. Ionic interactions Bonds: The core histone octamer: from Arents et al. (1991).

22. Proteins are Complex and Specific The complex primary sequence of amino acids in the protein’s chain can be symbolically represented as a “molecular language” that determines the “meaning” or structure of the protein. Protein structure specifies its function. Proteins function by binding to and interacting with their substrates to effect chemical reactions, cellular communication, pore formation, catalysis, etc. The complex primary sequence of amino acids in the protein’s chain can be symbolically represented as a “molecular language” that determines the “meaning” or structure of the protein. Protein structure specifies its function. Proteins function by binding to and interacting with their substrates to effect chemical reactions, cellular communication, pore formation, catalysis, etc.

23. “Life is a wave, in which no two consecutive moments of its existence is composed of the same particles.” -- John Tyndall (1820 - 1893) British draftsman, surveyor, physics professor, mathematician, geologist, atmospheric scientist, public lecturer, and mountaineer -- John Tyndall (1820 - 1893) British draftsman, surveyor, physics professor, mathematician, geologist, atmospheric scientist, public lecturer, and mountaineer