BCMP 201 Protein biochemistry

BCMP 201 Protein biochemistry BCMP 201 Protein biochemistry with emphasis on the interrelated roles of protein structure, catalytic activity, and macromolecular interactions in biological processes. The course is intended to provide the core background and perspective required to consider and dissect biological problems at a mechanistic, molecular level. 1

Central dogma of molecular biology: DNA RNA protein Central dogma of molecular biology: DNA RNA protein Central dogma of protein biochemistry: sequence structure function 2

sequence sequence alignment homology modeling hands-on session (Blast, other bioinformatics tools) structure physical interactions (covalent, noncovalent) 1 ary, 2 ary, 3 ary, 4 ary structure molecular visualization hands-on session (Pymol, other visualization tools) function enzymatic mechanisms chemical kinetics, thermodynamics BCMP 201 Tuesdays 9:00-10:30 am: Wednesday 4:30-6:00 pm: Lecture (Cannon Room, C Building) Methods lecture (TMEC) Discussion Section Hands-on session 3

BCMP 201 Discussion section (4x) - Each section will be guided by two TF s/instructors - Two research papers will be discussed - Two students will present presentation, each on one of the two papers - Papers will be posted one week in advance, with discussion questions BCMP 201 Problem sets (5x) - Each problem set will be posted one week before it s due (Wednesdays) - Students can work together 4

BCMP 201 Final exam - 24-hr take home - Students cannot work together BCMP 201 Final grade 30% section presentation 30% problem sets 30% final 10% section participation 5

BCMP 201 Course website http://cmcd.med.harvard.edu/activities/bcmp201/class Course directors Antoine van Oijen: James Chou: antoine_van_oijen@hms.harvard.edu james_chou@hms.harvard.edu Teaching fellows Irene Kim (head TF) Scott Aoki Amanda Rice Rebecca Roush Michelle Stewart Lecture 1: physical interactions, primary structure Length, time, and energy scales Covalent bonds Noncovalent bonds Amino acids and their basic properties 6

Length scales 7

Length scales 10 nm Insulin (pdb id: 2hlu; 5.8 kda) Ribosome (1fjf + 1jj2; ~ 4 Mda) Time scales 8

Energy scales 1 kj/mol ~ 0.24 kcal/mol Energy scales 1 mol of glucose = 180 grams 180 g x 16 kj = 2880 kj/mol (or about 691 kcals) (www.calorieking.com) 1 kj/mol ~ 0.24 kcal/mol 9

Energy scales ADP ATP Total quantity of ATP + ADP in human body is about 0.1 mol (about 50 g) Energy made available by hydrolysis ATP into ADP: only ~ 50 kj/mol Where does energy to power cells come from? Every ATP is recycled ~ 1,000 times/day (burning the equivalent of your body weight in ATP on any given day ) 1 kj/mol ~ 0.24 kcal/mol Molecular interactions and structural hierarchy 1 ary Covalent bonds 2 ary Hydrogen bonds 3 ary Hydrophobic effect 4 ary Hydrogen bonds Electrostatic interactions Hydrophobic effect 10

Covalent bonds # of electrons in outer shell Maximum # of electrons in outer shell 2 8 8 18 Element: H C N O S # of electrons needed to fill outer shell: 1 4 3 2 2..................... Lewis notation: H C N O S (Image from: http://serc.carleton.edu/images/usingdata/nasaimages/periodic-table.gif) Covalent bonds Atoms will favor as many bonds to fill up outer electron shells (the octet rule) ammonia water methane oxygen nitrogen 11

Common functional groups Covalent bond lengths and energies Bond Distance Energy (Å) (kj/mol) O-H 0.96 462 C-H 1.10 416 C-O 1.43 353 C-N 1.52 294 S-S 2.02 214 C=O 1.20 714 C=C 1.34 613 12

Electronegativity Electrons are shared unequally in polar covalent bonds Electronegativity values Bonding geometry Not only stoichiometry is important, also geometry 13

Configuration: chiral and achiral Configuration: stereoisomers 14

Configuration versus Conformation Configuration: fixed spatial arrangement Conformation: spatial arrangement that can change due to rotation around bonds Amino acids Amino acids link together to form proteins Amino acid Peptide 15

Amino acids Amino acids link together to form proteins amino group carboxyl group side group Amino acid Peptide Stereoisomerism in amino acids Amino acids in proteins are L-stereoisomers 16

Structures of the 20 common amino acids Hydrophobic amino acids 17

Aromatic amino acids Polar amino acids 18

Disulfide bonds Acidic amino acids 19

Basic amino acids Glycine 20

Side-chain pka s Histidine has pka close to neutral Peptide bond formation α-amino group is good nucleophile, but -OH is poor leaving group: At room temperature peptide-bond formation does not occur spontaneously 21

The peptide bond is planar Conformational freedom in polypeptides 2 rotational degrees of freedom: Φ and Ψ (Lecture 2: backbone conformations; secondary structure) 22

Conformational freedom in polypeptides Steric clashing of side groups prevents adjacent amino acids to be in the cis conformation Conformational freedom in polypeptides Glycine can adopt backbone conformations that are sterically impossible with other a.a. s Proline can undergo cis-trans isomerization more easily than other a.a. s 23

Covalent and noncovalent interactions Electrostatic forces Coulomb s law: F= q1q2 r 2D D is dielectric constant of medium! Electrostatic interactions effectively screened by water r q1 + q2 - (D=1 for vacuum D=80 for water) When in direct contact salt bridge 24

Hydrogen bonding Hydrogen bonding Oxygen is very electronegative Stabilization of ice by H-bonding 25

Hydrogen bonding H-bonds are highly directional Hydrophobic effect Apolar molecules tend to stick together to maximize hydrogen bonding in solute No physical interaction between hydrophobic molecules; instead a consequence of solute properties (entropy versus enthalpy in a few weeks) 26

Hydrophobic effect Amphiphatic molecules (polar on one end,apolar on the other) will self aggregate Driving force in protein folding (hydrophobic core; hydrophilic outside) Van der Waals forces Induced dipole-dipole interactions caused by movements of nuclei in electron clouds 27

Van der Waals forces Lennard-Jones potential: E(r) = A r 12 " B r 6 Van der Waals surfaces 28