Living Parts Prokaryotes, Eukaryotes Tissue – groups of cells together for certain specialized functions, differentiated cells Tissue – 14 major types of tissues in animals epithelial, connective, nervous, muscle, etc. Cell – over 200 types in a vertebrate Long – eg. nerve cells Some do not divide for ~ 100 years Some divide rapidly, ~ few hours

Components of a Cell (Eukaryotes) Picture from on-line biology book,on-line biology book, ~70% water 4% small molecules 15-20% proteins 2-7% DNA/RNA 4-7% membrane

Membrane Lipid bi-layer Phospholipids and other lipids hydrophilic, hydrophobic Small molecules and membrane-bond proteins Semi-permeable / Osmosis N2, O2, water, glycerol, glucose, sucrose, Ions, etc. Picture from :

Cytoplasm Cytoskeleton – fibrous protein complexes maintain shape, anchoring, moving actin filaments microtubules Ribosome – protein synthesis Mitochondrion – energy Endoplasmic reticulum (ER) – mesh of membrane, protein synthesis and transport Lysosomes, Golgi, vesicles etc. A good reference site good reference site

Nucleus Nuclear membrane Nuclear envelope with pores DNA/RNA and some proteins A good reference site good reference site

Nucleic Acids DNA – polymers of deoxyribonucleic acids, ds Nucleotide: 3 components: base (purine/pyrimidine) sugar (ribose/deoxyribose) phosphate group Picture from on-line biology book A (adenine) G (guanine) C (cytosine) T (thymine, DNA) U (uracil, RNA) RNA: in both nucleus and cytoplasm, ss 3 types: mRNA, rRNA and tRNA

Protein-a chemical view A chain of amino acids folded in 3D Picture from on-line biology bookon-line biology book Peptide Protein backbone N / C terminal

Amino Acids 20 types in nature Different properties – side chain Positively charged – Arg, His, Lys A good reference site good reference site Negatively charged – Asp, Glu Polar but uncharged – Ser, Thr (OH), Asn, Gln(CO) Special – Cys, Gly, Pro Hydrophobic – Ala, IIe, Leu, Met, Phe, Trp, Tyr, Val, Generally:

Protein – a 3D view Bond length, bond angle – fairly restricted Torsion angles on backbone –  (phi),  (psi),  (omega) Picture from , mostly plane(180°, rare case 10°in cis) , , free but with an average characteristic distribution- Ramachandran plot

Torsion Angles Dihedral angles  (phi),  (psi),  (omega) N C N C 

Secondary structures Helix - hydrogen bond (CO) i -(NH) i+4  -helix ( ) 1.5 Å / residue  -sheet is composed of multiple  -strands Picture from site Zig-zag backbone, side-chains opposite directions, ~30°/residue twist, mostly antiparallel Hydrogen bond between two  -strands Turn, loop/coil

Protein tertiary and quaternary structure Tertiary – 3D folding of a polypeptide chain involves non-local interaction Quaternary – multiple chains/multi subunits PDB: SCOP database SCOP database – protein classification

From DNA to Protein Genome, genes, chromosome, proteome Overview of HGP Picture from doegenomics.org echResources/ Human_Genome/proj ect/info.html Transcription (DNA-mRNA) Translation (mRNA-polypeptide) - Gene expression

Transcription Initiation, Elongation and Termination Central enzyme: RNA polymerase RNA polymerase bind to promoter site, e.g. in bacteria 35 BP upstream of start: RNA polymerase binding site (TTGACA) 10 BP upstream of start: box (TATAAT) - sigma factor site Promoter sequence determines transcription level Picture from _expression_tutorial/transcriptio n.html _expression_tutorial/transcriptio n.html

Transcription in Eukaryotes More complicated process RNA Splicing – intron and exon Picture from ww.intouchlive.com/cancergenetics/genefx.htm&3 Alternative splicing – diversity of proteins

Translation Picture from _expression_tutorial/translation. html _expression_tutorial/translation. html Ribosome bind upstream region of mRNA tRNA bind to specific amino acid (AUG) on mRNA to start tRNA brings a.a. to ribosome At least one tRNA exists for each amino acid Example of a tRNA Example of a tRNA Genetic coding What is a codon?

Regulation in gene expression Prokaryote – e.g. lac gene regulation Eukaryotes Basel promoter, upstream promoter Enhancer, silencer Transcription factors Altering rate of transcription Rate of transcript processing, stability of mRNA, efficiency of ribosome Various needs for gene expression Spatially and timely different steps in eukaryotes

Experimental techniques Identify size of protein/DNA e.g. gel electrophoreses Identify proteins e.g. using antibodies - structural Sequencing peptide e.g. mass spectrometry Sequencing DNA/RNA Determine some 3D protein structure Molecular cloning, producing large amount of genes and proteins

Recombinant DNA technology Restriction enzyme, ligase Vector – plasmid, bacteriophage (virus)

Recombinant DNA technology Cleave DNA Vector to carry DNA for cloning Transform bacteria Grow bacteria Screen for cloned DNA Revolutionized biology ar_bio/problem_sets/Recombinant_DN A_Technology/05t.htmlhttp:// ar_bio/problem_sets/Recombinant_DN A_Technology/05t.html An example

Related techniques Polymerase Chain Reaction (PCR) in-vitro amplification of a region of DNA with known sequence primer, template DNA polymerase ain_reactionhttp://en.wikipedia.org/wiki/Polymerase_ch ain_reaction cDNA, vs. genomic DNA reverse transcriptase represent currently active mRNA population function, stage of the cell A cool animation

Protein Structure Determination Nuclear Magnetic Resonance (NMR) small, multi-dimensional NMR X-ray crystallography soluble, medium size, some viruses usually difficult for large proteins Other developing methods e.g. electron cryomicroscopy Structural genomics

X-ray crystallography ProteinCrystalsDiffraction data Electron density mapStructure Phase Sequence Grow suitable crystals – tricky Solving structure – mostly a mature technique X-ray

Electron cryo-microscopy Non-crystalline – e.g. viruses, large complexes, helical objects 2D crystallography – e.g. membrane proteins Take 2D images using TEM Computationally build 3D structure Computationally more intensive