Living Parts•Prokaryotes, Eukaryotes

•Tissue – groups of cells together for certain specialized functions, differentiated cells

•Tissue – 14 major types of tissues in animalsepithelial, connective, nervous, muscle, etc.

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookAnimalTS.html

•Cell – over 200 types in a vertebrate

Long – eg. nerve cellsSome do not divide for ~ 100 yearsSome divide rapidly, ~ few hours

Components of a Cell (Eukaryotes)

Picture from on-line biology book, http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

~70% water4% small molecules15-20% proteins2-7% DNA/RNA4-7% membrane

Membrane• Lipid bi-layer

Phospholipids and other lipidshydrophilic, hydrophobic

• Small molecules and membrane-bond proteins

• Semi-permeable / Osmosis

N2, O2, water, glycerol, glucose, sucrose, Ions, etc. http://en.wikipedia.org/wiki/Cell_membrane

Picture from : http://www.cbc.umn.edu/~mwd/cell_www/chapter2/membrane.html

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 http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

Nucleus

• Nuclear membrane

• Nuclear envelope with pores

• DNA/RNA and some proteins

• A good reference site http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

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• http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

A (adenine)G (guanine)

C (cytosine)T (thymine, DNA)U (uracil, RNA)

RNA: in both nucleus and cytoplasm, ss3 types: mRNA, rRNA and tRNA

Protein-a chemical view

• A chain of amino acids folded in 3D

• Picture from on-line biology book

• PeptideProtein backbone

N / C terminal

Amino Acids• 20 types in nature

• Different properties – side chain

• Positively charged – Arg, His, Lys

• A good reference site http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html

• 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 http://www.expasy.org/swissmod/course/text/chapter1.htm

• , 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 (3.613) 1.5Å / residue -sheet is composed of multiple -strands

Picture from www.expasy.org sitehttp://www.expasy.org/swissmod/course/text/chapter1.htm

• 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: http://www.pdb.org

SCOP database – protein classification

From DNA to Protein

• Genome, genes, chromosome, proteome

• Overview of HGP

Picture from doegenomics.orghttp://www.ornl.gov/TechResources/Human_Genome/project/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 http://edtech.clas.pdx.edu/gene_expression_tutorial/transcription.html

Transcription in Eukaryotes • More complicated process• RNA Splicing – intron and exon

Picture from http://www.intouchlive.com/home/frames.htm?http://www.intouchlive.com/cancergenetics/genefx.htm&3

• Alternative splicing – diversity of proteins

Translation

Picture from http://edtech.clas.pdx.edu/gene_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 http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html

• 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

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html

Altering rate of transcriptionRate of transcript processing, stability of mRNA, efficiency of ribosome

• Various needs for gene expression

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html

• 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

• http://www.biology.arizona.edu/molecular_bio/problem_sets/Recombinant_DNA_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• http://en.wikipedia.org/wiki/

Polymerase_chain_reaction

• cDNA, vs. genomic DNA

reverse transcriptase

represent currently active mRNA population

function, stage of the cell

A cool animation http://www.maxanim.com/genetics/cDNA/cDNA.htm

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

Protein Crystals Diffraction data

Electron density mapStructure

Phase

Sequence

Grow suitable crystals – trickySolving 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

http://en.wikipedia.org/wiki/Cryo-electron_microscopy