1. Biological-Engineering for Beginners Biochemistry II: Proteins Leigh Casadaban and Alina Gatowski July 26, 2009

2. What are Proteins?  What are proteins made of?  Does every cell have the same proteins?

4. Structure of Proteins   Primary Structure:   Amino Acid Sequence   Secondary Structure:   Alpha Helix   Beta Sheet  Tertiary Structure:  Hydrophobic core  Disulfide bonds  Salt bridges  Quaternary Structure  Protein subunits form into complex

5. Structure of Amino Acids  Primary Structure is made of Amino Acids  Polypeptide Chain:  Peptide bond is an « amide bond »

6. Anatomy of an Amino Acid

7. Peptide Bond Formation

8. FUN FACT Essential Amino Acids need to come from the food we eat. phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, leucine, and lysine

9. Amino Acids

11. The genetic code  Use the genetic code to turn mRNA nucleotides to amino acids  Three nucleotides make up a codon  4x4x4 = 64, so why only 20 amino acids?

12. Degeneracy of the Genetic Code  The genetic code has redundancy but no ambiguity  GAA and GAG both specify glutamic acid (redundancy), neither of them specifies any other amino acid (no ambiguity)

14. CENTRAL DOGMA Transcription Translation

15. 20 Amino Acids  Amino acids form polypeptide chains  http://www.nclark.net/Amino Acids.ram

16. Point Mutations

17. Secondary Structure

18. Ramachandran plot  Dihedral angles  and  for amino acid residues in protein structure  Shows steric hindrance and conformation  Glycine can adopt angles in all four quadrants

20. Alanine (R) and Glycine (L)

21. Tertiary Structure 1.Disulfide bonds 2.Hydrophobic interactions 3.Hydrogen bonds 4.Ionic interactions

22. Quaternary Structure Quaternary structure refers to the association of multiple subunits. The subunits may be identical or different When they are different, each subunit tends to have a different function

23.  Primary Structure can predict fold?

24. R group function  Tyrosine  Phenylalanine  Tryptophan

25. Fun Facts  Aspartame is used in low-calorie artificial sweeteners: Equal, NutraSweet, and Canderel  It is 200 times sweeter than sugar, without the high energy value of sugar  Aspartame is the methyl ester of a phenylalanine/aspartic acid dipeptide