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DNA The Nuclear genome consists of DNA in the nucleus of eukaryotic cells – this is what we typically think of as our Genome: A Genome is the unique set of chromosomes (or DNA) in one cell of an organism. • Humans have 2 sets of chromosomes (one from each parent: we are diploid.) • Our genome consists of 3 x109 base pairs • ~25,000 genes (no one knows exactly yet). Plant Cell Animal Cell Nucleus Chloroplast Mitochondrion Chloroplasts (photosynthesis machinery in plants, algae) have their own DNA (called the Plastid genome) • 7.5-25 x 103 base pairs • 100-1000 copies depending on whether the cell is actively dividing (more when dividing). • ~100 genes Mitochondria have their own DNA (called the Mitochondrial genome) • ~1.7 x 104 base pairs • several copies • ~40 genes Nucleic Acids •DNA •RNA DNA •Deoxyribonucleic acid •double helix •“intelligent molecule” •made of nucleotides One human cell Has ~1 meter of DNA DNA is partitioned into 46 separate linear molecules (chromosomes, 23 from each parent) Nucleus CELL All of it is crammed into the cell's nucleus (a few micrometers) Robert H. Austin, James P. Brody, Edward C. Cox, Thomas Duke and Wayne Volkmuth FEBRUARY 1997 PHYSICS TODAY image from the National Human Genome Research Institute (NHGRI) Genetic Illustrations. DNA 2 nm 11 nm 30 nm Chromatin 300 nm 700 nm Chromosome 1400 nm Richarddawkins.net Nucleotide •Sugar (deoxyribose) •Phosphate •Nitrogenous Base •adenine (A) •thymine (T) •cytosine (C) •guanine (G) •DNA is double-stranded •adenine is always across from thymine •cytosine is always across from guanine •bases are held across from each other by weak hydrogen bonds A T C G The Sugar in the “backbone” is RNA: ribose DNA: deoxyribose This OH group is replaced by H (hydrogen atom) in Deoxy-ribose 5’ 3’ DNA is anti-parallel: One strand is 5’to 3’ The strand across from it is 3’ to 5’ 3’ 5’ How do We Know the Structure of DNA? Watson & Crick 1953 Diffraction Patterns Reciprocal Space http://www.matter.org.uk/diffraction/geometry/3D_reciprocal_lattices.htm Click here for a groovy interactive experience (Grab and drag one of the white dots) X-ray crystallography revisited DNA X-ray diffraction pattern X-ray crystallography revisited 34 Angstroms X-ray crystallography revisited 3.4 Angstroms X-ray crystallography revisited X-ray crystallography revisited X-ray crystallography revisited X-ray crystallography revisited X-ray Diffraction pattern → Molecular Structure 1953 Discovery → Nobel Prize Wavelength of diffracted light should match size of object for optimal resolution Why x-rays? A DNA molecule • not a rigid, static structure (as x-ray diffraction pictures might suggest) • under constant thermal fluctuations local twisting, stretching, bending, and unwinding of the double-strands. X-ray crystallography revisited http://www.uic.edu/classes/phys/phys461/phys450/ANJUM04/ The most common DNA structure in solution is B-DNA. B Z DNA has several helical conformations A-DNA, Z-DNA, SDNA A Under conditions of • applied force • low hydration ... B-DNA Long and thin Most common in solution Right-handed helix 27.3 A diameter 3.4 A rise/base pair ~ 10 bases/turn A-DNA Short and broad Low hydration Right handed helix 25.5A diameter 2.3A rise/base pair ~11 bases/ turn Z-DNA Longer and thinner Left-handed helix 18.4 A diameter 3.8 A rise/base pair ~12 bases/ turn DNA Replication •2 strands of DNA “unzip” - separate •primers are placed on each strand •DNA polymerase (an enzyme) builds new strands of DNA, using the original strands as templates RNA •Ribonucleic acid •single stranded •also made of nucleotides RNA nucleotides •Sugar (ribose) •Phosphate •nitrogenous base •adenine •cytosine •guanine •uracil Types of RNA •mRNA: messenger RNA, carries the DNA code out of the nucleus to the ribosome •tRNA: transfer RNA, carries amino acids to the ribosome •rRNA: ribosomal RNA, part of the ribosome Transcription (making RNA) •DNA unzips •one strand of DNA acts as a template •RNA polymerase reads the DNA bases •RNA nucleotides are placed across from the complimentary DNA bases •RNA separates from DNA •DNA zips back up •The “code” of DNA is the order of the bases •The code is universal among organisms •DNA from one organism can be read in the cells of another organism