Chemical components of cells 1. Chemical bonds 2. Water and hydrogen bonds 3. Macromolecules: polysaccharides, proteins and nucleic acids Protein structure and function 1. Different levels of protein structures 2. α-helix and β-sheets 3. Methods to seperate and analyse proteins; from biochemistry to proteomics
Covalent bonds are characterized by particular geometries
Length and strength of chemical bonds
C=C double bonds are shorter and more rigid than C-C single bonds
Polar and nonpolar covalent bonds polar e.g. O-H, -N-H nonpolar e.g. -C-H
Hydrophobic forces
4 main families of organic molecules in cells
Macromolecules in cells
Macromolecules are made from monomeric subunits
Macromolecules are formed by adding subunits to one end (via condensation reactions) -> specific sequence of subunits
Condensation and hyrdrolysis
Polysaccharides
Structural polysaccarides Cellulose, cotton (glucose) Chitin (N-acetylglucosamine) Glycosaminoglycans, heparin
Protein structure and function
Amino acids, the subunits of proteins
Proteins consist of L-amino acids
Peptide bonds are rigid, planar units
The 20 amino acids found in proteins
The 4 levels of protein structure Primary structure Secondary structure Tertiary structure Quartiary structure
Polypeptide backbone and side chains
Noncovalent bonds specify the precise shape of a macromolecule
Noncovalent bonds fold proteins
Proteins fold into compact conformations Hydrophobic forces cluster hydrophobic side chains in the interior of the folded protein Polar side chains tend to arrange themselfes near the outside of the folded protein > hydrogen bonds with water
Hydrophilic (green) and hydrophobic (red) amino acid residues in a soluble protein Cytochrom c
H-bonds within a protein molecule
Disulfide bonds can help to stabilize a favored protein conformation S-S bonds are only found in extracellular proteins
Elastin polypeptide chains form crosslinked rubber-like elastic fibers
Insulin The hormone insulin was the first polypeptide for which the complete amino acid sequence could be determined.
The α-helix
A α-helix can cross a lipid bilayer Note: An α-helix is no channel! The space is occupied by the peptide backbone. To make a channel through a membrane, other (bigger) structures are required.
Long, rodlike coiled-coil structures Examples: α-keratin in skin, myosin in muscles
The β-sheet
Parallel and antiparallel β-sheets N-terminus C-terminus
Many proteins are folded into seperate functional domains camp-binding domain CAP (catabolite activator protein) DNA-binding domain
Protein domains and protein families
X-ray crystallography
Proteins are dynamic structures RuBisCO (Ribulose-1,5- bisphosphatcarboxylase) is the most abundant protein on Earth (in plant leaves); 10 kg per person on earth. RuBisCO catalyzes the first major step of carbon fixation.
Hemoglobin is formed as symetrical assembly of two different subunits
Jacob, Monod and Changeux discovered the regulatory importance of allosteric changes in the conformation of many enzymes
Proteins can bind to one another trough compementary charges on their surfaces
Proteins can pack to form a filament, a tube, or a spherical shell
The ribosome, a complex of about 90 macromolecules (RNA and proteins)
Structure of a spherical virus
The protein binding site is highly selective
Enzyme catalysis
Regulation of protein activity by phosphorylation The addition of a single phophate group with two negative charges can dramatically change the conformation of a protein
Methods used in protein chemistry
Homogentization
Centrifugation
Differential Centrifugation
Column chromatography
Different kinds of chromatography
Gel electrophoresis
IE and 2D-SDS-PAGE
Identification of proteins by mass spectroscopy
Genomics & Proteomics
Protein chips: Global analysis of protein activities
Nucleotides, subunits of DNA and RNA ATP nucleoside nucleotide
ATP is the energy carrier in cells
DNA
The DNA-helix In 1953, based on X-ray diffraction images taken by Rosalind Franklin and the information that the bases were paired, James D. Watson and Francis Crick suggested the DNA structure in the journal Nature. Experimental evidence for Watson and Crick's model were published in a series of five articles in the same issue of Nature.
Genomics Genome sizes of different organisms are very different
Important genome sequencing papers Mouse Nature. 420: 520-562. (5 December 2002) Human Nature. 409: 860-921. (15 February 2001) Arabidopsis - First Plant Sequenced Nature 408: 796-815. (14 December 2000) Fruit Fly Science. (24 March 2000) 287: 2185-95. Roundworm C. elegans - First Mutlicellular Eukaryote Sequenced Science. (11 December 1998) 282: 2012-8. Bacteria - E. coli Science. 277: 1453-1474. (5 September 1997) Yeast Science. (25 October 1996) 274: 546, 563-7. Bacteria - H. influenzae - First Free-living Organism to be Sequenced Science. (28 July 1995) 269: 496-512.
There are more than 600 genomes completey sequenced in 2007 See GOLD (genome online databases at http://www.genomesonline.org)
Genome sizes and gene numbers organism estimated size gene number average gene density Chromo -somes Homo sapiens (human) Rattus norvegicus (rat) Mus musculus (mouse) Drosophila melanogaster (fruit fly) Arabidopsis thaliana (plant) Caenorhabditis elegans (roundworm) Saccharomyces cerevisiae (yeast) Escherichia coli (bacteria) H. influenzae (bacteria) 2900 million bases ~30,000 1 gene per 100,000 bases 46 2,750 million bases ~30,000 1 gene per 100,000 bases 42 2500 million bases ~30,000 1 gene per 100,000 bases 40 180 million bases 13,600 1 gene per 9,000 bases 8 125 million bases 25,500 1 gene per 4000 bases 5 97 million bases 19,100 1 gene per 5000 bases 6 12 million bases 6300 1 gene per 2000 bases 16 4.7 million bases 3200 1 gene per 1400 bases 1 1.8 million bases 1700 1 gene per 1000 bases 1 Genome size does not correlate with evolutionary status, nor is the number of genes proportionate with genome size.
The future of DNA sequencing In May 2007, James D. Watson, the co-discoverer of the molecular structure of DNA, became the first person to receive his own complete personal genome sequenced. The cost was less than $1 million (0.03 cents per base). It took less than two months. It is realistic to expect that within the next ten years, rapid low-cost sequencing of human genomes will become a reality. Pharmacogenomics Genotyping