Doug Raiford Lesson 14

 Reminder  Involved in virtually every chemical reaction ▪ Enzymes catalyze reactions  Structure ▪ muscle, keratins (skin, fur, nails, etc), actin and myosin (muscle), collagens (tendons, hides), etc. DNA  RNA  Protein transcriptiontranslation Sequence  Structure  Function 6/9/20162Proteins

 Translation  Forms peptide bonds  Dehydration process  Residue  N side: amine  C side: acid  Hence: amino acid Peptide bond 6/9/20163Proteins

 Amino acids are differentiated by their side chains  Chemical properties  Hydrophobicity/hydrophilicity  Polarity  Acidity/Bassicity 6/9/20164Proteins

Proline severely limits allowable conformations! ValPheAlaLeuIle Pro Met 6/9/20165Proteins

Asp Glu Arg Lys 6/9/20166Proteins His

6/9/20167Proteins SerThr Tyr Cys AsnGln

6/9/20168Proteins Trp Gly

 6/9/20169Proteins    almost always 180 

6/9/201610Proteins  4 atoms on same plane

 Two common arrangements show-up over and over  Alpha helix  Beta sheet  Constitute secondary structure 6/9/2016Proteins11 RNase P

6/9/201612Proteins       60°  Hydrogen bonds between C=O of residue n, and NH of residue n+4

 Fit nicely in the grooves of DNA  Globular proteins are often mostly helices  Or coiled coils 6/9/2016Proteins13

6/9/201614Proteins    -135,   +135°; stretched out  R groups are above and below  Form hydrogen bonds with the adjacent strands

6/9/2016Proteins15  Pleated  R groups above and below  Means nature can dictate the chemical properties of the surface of the sheet  BTW: terminology — C-terminus  Similar to 5’-3’

 Can be parallel or anti-parallel 6/9/201616Proteins

6/9/201617Proteins  Anti-parallel is slightly energetically favored

 In middle of sheet  Large aromatic residues (Tyr, Phe and Trp) and β-branched amino acids (Thr, Val, Ile) favored 6/9/2016Proteins18  On edges, aa’s like proline, very non-reactive  Prevents aggregation  Mutations that cause aggregation: prions  Alzheimer's: amaloid plaque

 Some of the coolest proteins  Porins (aqua porins allow water into cells) 6/9/2016Proteins19

 Secondary structure elements are connected by regions of turns and loops (or coils)  Turns – short regions of non- , non-  conformation  Loops – larger stretches with no secondary structure. Often disordered. 6/9/201620Proteins Disordered loops Often Link domains Solvent exposed Vary greatly in length and composition from homolog to homolog Rich in polar and charged amino acids Why?

 G. N. Ramachandran – first calculations of sterically allowed regions of phi and psi  Note the structural importance of glycine Observed (non-glycine) Observed (glycine) Calculated 6/9/201621Proteins

 Chaperone proteins  Sucks in a protein into chamber  Provides safe environment to fold  Top closes like an iris  Allosteric enzyme  Termed "heat shock" proteins  Heat destabilizes proteins 6/9/2016Proteins22

 Active transport (pumps)  ATPase pumps (ATP provides energy to transport solutes across membrane)  Calcium  ATP synthase  Proton gradient provides energy for ATP synthesis  =en&fs=1&rel=0 =en&fs=1&rel=0 6/9/2016Proteins23

 No really!  yer_detailpage&v=4jtmOZaIvS0 yer_detailpage&v=4jtmOZaIvS0 6/9/2016Proteins24

6/9/201625Proteins