Transcript slides - ODU Computer Science

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.
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookAnimalTS.html
•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)
~70% water
4% small molecules
15-20% proteins
2-7% DNA/RNA
4-7% membrane
Picture from on-line biology book,
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html
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
http://en.wikipedia.org/wiki/Cell_membrane
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 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
C (cytosine)
T (thymine, DNA)
U (uracil, RNA)
RNA: in both nucleus and cytoplasm, ss
3 types: mRNA, rRNA and tRNA
•
Picture from on-line biology book
•
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
A (adenine)
G (guanine)
Protein-a chemical view
• A chain of amino
acids folded in 3D
• Peptide
Protein backbone
N / C terminal
• Picture from on-line biology
book
Amino Acids
• 20 types in nature
• Different properties – side chain
Generally:
• Positively charged – Arg, His, Lys
• 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,
• A good reference site http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCELL2.html
Protein – a 3D view
• Bond length, bond angle – fairly restricted
• Torsion angles on backbone
– (phi), (psi), (omega)
• , mostly plane(180°, rare case 10°in cis)
• , , free but with an average characteristic
distribution- Ramachandran plot
•
Picture from http://www.expasy.org/swissmod/course/text/chapter1.htm
Torsion Angles
• Dihedral angles
(phi), (psi), (omega)
N
C
 C
N
Secondary structures
• Helix - hydrogen bond (CO)i-(NH)i+4
-helix (3.613) 1.5Å / residue
• -sheet is composed of multiple -strands
•Hydrogen bond
between two -strands
• Zig-zag backbone, side-chains opposite directions
, ~30°/residue twist, mostly antiparallel
• Turn, loop/coil
Picture from www.expasy.org site
http://www.expasy.org/swissmod/course/text/chapter1.htm
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
• Transcription (DNA-mRNA)
• Translation (mRNA-polypeptide)
- Gene expression
Picture from
doegenomics.org
http://www.ornl.gov/T
echResources/
Human_Genome/proj
ect/info.html
Transcription
• Initiation, Elongation and Termination
• Central enzyme: RNA polymerase
Picture from
http://edtech.clas.pdx.edu/gene
_expression_tutorial/transcriptio
n.html
• 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
Transcription in Eukaryotes
• More complicated process
• RNA Splicing – intron and exon
Picture from
http://www.intouchlive.com/home/frames.htm?http://w
ww.intouchlive.com/cancergenetics/genefx.htm&3
• Alternative splicing – diversity of proteins
Translation
• Genetic coding
• What is a codon?
•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
Picture from
http://edtech.clas.pdx.edu/gene
_expression_tutorial/translation.
html
Regulation in gene expression
• Various needs for gene expression
• Spatially and timely different steps in eukaryotes
• Prokaryote – e.g. lac gene regulation
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html
• Eukaryotes
Altering rate of transcription
Rate of transcript processing, stability of mRNA,
efficiency of ribosome
• Basel promoter, upstream promoter
• Enhancer, silencer
• Transcription factors
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html
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
• An example
•
http://www.biology.arizona.edu/molecul
ar_bio/problem_sets/Recombinant_DN
A_Technology/05t.html
Related techniques
• 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
• 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_ch
ain_reaction
Protein Structure Determination
• X-ray crystallography
soluble, medium size, some viruses
usually difficult for large proteins
• Nuclear Magnetic Resonance (NMR)
small , multi-dimensional NMR
• Other developing methods
e.g. electron cryomicroscopy
• Structural genomics
X-ray crystallography
X-ray
Protein
Crystals
Diffraction data
Phase
Structure
Electron density map
Sequence
Grow suitable crystals – tricky
Solving structure – mostly a mature technique
Electron cryo-microscopy
• 2D crystallography – e.g. membrane proteins
• Non-crystalline
– e.g. viruses, large complexes, helical objects
• Take 2D images using TEM
• Computationally build 3D structure
• Computationally more intensive
http://en.wikipedia.org/wiki/Cryo-electron_microscopy