Lecture 1

Self-organization of biological systems Self-organization of biological systems: self-assembly into compartments active transport molecular specificity

Cell types: 1. Cells are fundamental units of life 2. Cells use chemical or solar energy to function, grow, and reproduce 3. Cells are macromolecular factories 4. Cells move, divide (mitosis), and sense environmental conditions

Courtesy of Dr. Julian Heath.

©1982. Used by permission of Jones and Bartlett Publishers, Sudbury MA.

©1993. Used by permission of Springer-Verlag. Prokaryotic cells

©1993. Used by permission of Springer-Verlag.

Eukaryotic cells

(b) ©1980. Used by permission of Elsevier Science. Mitochondria are organelles that metabolize conversion of chemical energy from food into ATP.

Chromatin and cell nucleus

Chromatin under the microscope Electron micrograph of D.Melanogaster chromatin: arrays of regularly spaced nucleosomes, each ~80 A across. Section of a chromosome: central scaffold + lateral loops High-resolution image of a human chromosome

Structure of the nucleosome core particle (NCP) T.J.Richmond: K.Luger et al. Nature 1997 (2.8 Ǻ); T.J.Richmond & C.A.Davey Nature 2003 (1.9 Ǻ) Left-handed superhelix: 1.84 turns, 147 bp, R = 41.9 A, P = 25.9 A. PDB code: 1kx5

Molecular composition of bacterial cells by weight Molecular composition of bacterial cells by weight: Small molecules 74% water 70% amino acids, sugars, fatty acids, ions 4% Macromolecules 26% proteins 15% RNA 6% DNA 1% lipids 2% polysaccharides 2% Molecular “parts list”

©1991 Larry Gonick.

©1982, American Association for the Advancement of Science. Used by permission.

20 types of amino acids in proteins

Protein Data Base accession code 1VII ({C.J. McKnight, D.S. Doering, P.T. Matsudaira, P.S. Kim, J. Mol. Biol (1996)).

Protein 3D structure Protein Data Bank (PDB)

Elastic rod model DNA looping induced by a Lac repressor tetramer

Protein Data Base accession code 1EHZ (H. Shi and P.B. Moore, RNA (2000)).

©1993. Used by permission of Springer-Verlag.

Fatty acids Cellulose (polysaccharide)

Lecture 2

A single peptide (protein building block) A polypeptide chain

A tyrosine (TYR) amino acid (one of 20 naturally occurring amino acids)

Peptide torsion angles and secondary structure omega = 180 deg, phi & psi are variable minimize E({phi,psi}) – protein folding problem

Secondary structure elements: alpha & 3-10 helices

Secondary structure elements: beta sheets

Turns of the polypeptide chain

The Ramachandran plot

Side chain conformations

Protein 3D structure (second look) Protein Data Bank (PDB) Protein functions: enzymes, gene regulation

Protein folding: I

Protein folding: II

Microtubules (25 nm): cytoskeleton Actin filaments (F-actin; 7 nm): actin cortex

Cell membranes are crowded: channels, receptors, pumps, actin cortex attachment points

DNA & RNA

The genetic code

©1993. Used by permission of Springer-Verlag.