Lecture 1Lecture 1

Self-organization of biological systemsSelf-organization of biological systems:

• self-assembly into compartments• active transport• molecular specificity

Cell types:Cell types:

1. Cells are fundamental units of life2. Cells use chemical or solar energy to function, grow, and reproduce3. Cells are macromolecular factories4. 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 cellsProkaryotic cells

©1993. Used by permission of Springer-Verlag.

Eukaryotic cellsEukaryotic 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 nucleusChromatin and cell nucleus

Chromatin under the microscopeChromatin under the microscope

Electron micrograph of D.Melanogasterchromatin: arrays of regularly spacednucleosomes, 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)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 weightMolecular 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. 260 126 (1996)).

Protein 3D structure

Protein Data Bank (PDB) http://www.rcsb.org

Elastic rod model

DNA looping induced by a Lac repressor tetramer

Protein Data Base accession code 1EHZ (H. Shi and P.B. Moore, RNA 6 1091 (2000)).

©1993. Used by permission of Springer-Verlag.

Fatty acids

Cellulose (polysaccharide)

Lecture 2Lecture 2

A single peptide (protein building block)

A polypeptide chain

A tyrosine (TYR) amino acid (one of 20 naturallyoccurring 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) http://www.rcsb.org

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.

©1993. Used by permission of Springer-Verlag.