Living Parts

1
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
2
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
3
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
• http//www.cbc.umn.edu/mwd/cell_www/chapter2/memb
  rane.html

4
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

5
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

6
Nucleic Acids

• DNA polymers of deoxyribonucleic acids, ds
• Nucleotide
• 3 components base (purine/pyrimidine)
• sugar (ribose/deoxyribose)
• phosphate group

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

• Picture from on-line biology book
• http//www.emc.maricopa.edu/faculty/farabee/BIOBK/
  BioBookCHEM2.html

7
Protein-a chemical view

• A chain of amino acids folded in 3D

• Peptide
• Protein backbone
• N / C terminal

• Picture from on-line biology book

8
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

9
Protein a 3D view

• Bond length, bond angle fairly restricted

• Torsion angles on backbone
• ?(phi), ?(psi), ?(omega)

• ?, mostly plane(180, rare case 10in cis)
• ?, ?, free but with an average characteristic
  distribution- Ramachandran plot

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

10
Torsion Angles

• Dihedral angles

?(phi), ?(psi), ?(omega)
N
C
?
C
N
11
Secondary structures

• Helix - hydrogen bond (CO)i-(NH)i4
• ?-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

Picture from www.expasy.org site http//www.expasy
.org/swissmod/course/text/chapter1.htm

• Turn, loop/coil

12
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
13
From DNA to Protein

• Genome, genes, chromosome, proteome
• Overview of HGP

Picture from doegenomics.org http//www.ornl.gov/T
echResources/ Human_Genome/project/info.html

• Transcription (DNA-mRNA)
• Translation (mRNA-polypeptide)
• - Gene expression

14
Transcription

• Initiation, Elongation and Termination

• Central enzyme RNA polymerase

Picture from http//edtech.clas.pdx.edu/gene_expre
ssion_tutorial/transcription.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

15
Transcription in Eukaryotes

• More complicated process
• RNA Splicing intron and exon

Picture from http//www.intouchlive.com/home/frame
s.htm?http//www.intouchlive.com/cancergenetics/ge
nefx.htm3

• Alternative splicing diversity of proteins

16
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_expre
ssion_tutorial/translation.html
17
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/BiologyP
ages/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/BiologyP
ages/P/Promoter.html
18
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

19
Recombinant DNA technology

• Restriction enzyme, ligase

• Vector plasmid, bacteriophage (virus)

20
Recombinant DNA technology

• Cleave DNA

• Vector to carry DNA for cloning

• Transform bacteria

• An example

• Grow bacteria

• http//www.biology.arizona.edu/molecular_bio/probl
  em_sets/Recombinant_DNA_Technology/05t.html

• Screen for cloned DNA

• Revolutionized biology

21
Related techniques

• cDNA, vs. genomic DNA
• reverse transcriptase
• represent currently active mRNA population
• function, stage of the cell

• Polymerase Chain Reaction (PCR)
• in-vitro amplification of a region of DNA with
  known sequence
• primer, template
• DNA polymerase

22
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

23
X-ray crystallography
X-ray
Grow suitable crystals tricky Solving structure
mostly a mature technique
24
Cryoelectron 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