S Lecture (High-Points)

Today’s Lecture (High-Points)You can be identified by your own unique various regions Proteins energy sources to replicate DNA.[DNA is a very stable structure.] RNA can be used as record to tell how DNA is active(making proteins). [Amazing useful in biotechnology.] Clinical use of Diagnosing DNA Human history via DNA Sequencing Evolution and DNA Sequencing: What was cavemen like? What was the original life form?

Proteins catalyze DNA ReplicationDNA is stable: need to catalyze rxn with Proteins & dNTPs1. Helicase separates two strands.2. SSB proteins stabilize ssDNA so stays open.3. DNA polymerase adds new nucleotidesBut:One strand, (the leading strand) goes from 5’ 3, DNA polymeraseonly goes from 5’ 3’. No problem.Other strand (the lagging strand) goes from 3’ to 5’.It has to makeOkazaki fragments, 100-200 bp long.d: replication forkRNAprimer

Proteins catalyze DNA ReplicationLots of proteins involvedUse ATP & dNTP as energy sourcehttp://www.youtube.com/watch?feature player detailpage&v hC 8y8fNkCw

Clinical Applications of DNA(Mitotic) Chromosomes can be identified by theirunique DNA sequencesEach chromosome can be labeled uniquelyMitosis

Cytogenetic Analysis

Cytogenetics – KaryotypingCan tell the genetics of sex (XX, XY)

Prenatal ges/PrenatFig4.jpg

Cytogenetics – Prenatal DiagnosisTrisomy 21: “Down’s Syndrome”

Postnatal Genetic Diagnostics

Postnatal Genetic Diagnosis

Cancer Genetic Diagnostics

Cancer Genetic DiagnosisChromosomal Rearrangements can lead to Cancer

The location of genes on a chromosome can be determinedFluorescence in Situ Hybridization (FISH)Green- # 22 marker- 22q13Red- DiGeorge Syndrome region (if missing) at 22q11.2(Person has 2 normal)

FISHACBA). Chromosone 4 “painted”.B) From same person in A, but hybridized witha probe for the terminal part of chromosome4q. Only one green signal one chromosome4 is missing material from the terminal end of4q.C) Xcen chromosome 22Other: Steroid Sulfatase gene.Two X chromosomes, 1 St.Su. gene femalecarrier for Steroid Sulfatase sh.htm

RNASometimes want to look at Proteins to see what DNA is doing.Hard to see proteins—use RNADetails: 3 types of RNAMessenger RNA (mRNA): ―copy‖ of DNATransfer RNA– (tRNA) 3 bases of RNA amino acidRibosomal RNA—make protein using mRNA as copy

RNA has 3 different structures, names, and uses.mRNA, tRNA, rRNA1. Messenger RNA (mRNA)[ copy of DNA]2. transfer RNA (tRNA)[binds to amino acid andcodon for mRNA] 3 basescorrespond to uniqueamino acid.http://en.wikipedia.org/wiki/Messenger RNA3. ribosomal RNA (rRNA)[Makes up Ribosome, alongwith protein. Has catalyticactivity– can form peptidebond.We’ll go into nitty-gritty detailsabout how amino acids are linked together

Why are there 3 nucleotides/codon(amino acid)?Why not 2? 4?There are 20 a.a.: need or x3 (3x ?) tocode.With x3 , x 4, can code for 43 64amino acids.Degeneracy

RNA codon tableThis table shows the 64 codons and the amino acid each codon codes for.The direction is 5' to 3'.X A,U,G,C1stbase2nd baseUCAUUU (Phe/F)PhenylalanineUUC (Phe/F)PhenylalanineUUA (Leu/L)LeucineUUG (Leu/L)LeucineUCX (Ser/S)SerineCCUX (Leu/L)LeucineCCX (Pro/P)ProlineCAU (His/H)HistidineCAC (His/H)HistidineCAA (Gln/Q)GlutamineCAG (Gln/Q)GlutamineCGX (Arg/R)ArginineAAUU (Ile/I)IsoleucineAUC (Ile/I)IsoleucineAUA (Ile/I)IsoleucineACX (Thr/T)ThreonineAAU (Asn/N)AsparagineAAC (Asn/N)AsparagineAAA (Lys/K)LysineAAG (Lys/K)LysineAGU (Ser/S)SerineAGC (Ser/S)SerineAGA (Arg/R)ArginineAGG (Arg/R)ArginineGCX (Ala/A)AlanineGAU (Asp/D)Aspartic acidGAC (Asp/D)Aspartic acidGAA (Glu/E)Glutamic acidGAG (Glu/E)Glutamic acidGGX (Gly/G)GlycineUUAA Ochre (Stop)UAG Amber (Stop)AUG (Met/M)Methionine, StartGGUX (Val/V)ValineUAU (Tyr/Y)TyrosineUAC (Tyr/Y)TyrosineGUGU (Cys/C)CysteineUGC (Cys/C)CysteineUGA Opal (Stop)UGG (Trp/W)TryptophanNotice/Recall that 3 bases cause more than 1 AA.

Figure 5.275 3 Sugar-phosphatebackbonesHydrogen bondsBase pair joinedby hydrogenbonding3 5 (a) DNABase pair joinedby hydrogen bonding(b) Transfer RNA

RNA is made from DNAIntrons and exons in EukaryotesIn prokaryotes(messenger)In eukaryotesintron –”non-coding region” deleted1993 Nobel Prize in Medicine to Phillip Allen and Richard J. Robertshttp://en.wikipedia.org/wiki/Intron

b-globin gene ofHemoglobinexample of introns/exons

Exploring the new world of the genomewith DNA microarraysNature Genetics Supplement 21:33-37 (January 1999)

Molecular portraits of human breast tumoursGene chips can be used to follow genetic changes during cancer and cancer treatmentDifferent Tumors FIG. 1. Variation in expression of 1,753genes in 84 experimental samples.Affymetrix, 1992. Marriageof Silicon and Genes.Semiconductor manufacturingtechniques could be united withadvances in combinatorialchemistry to build vast amountsof biological data on a smallglass chip.Different Genes Data are presented in a matrix format: eachrow represents a single gene, and eachcolumn an experimental sample. Greensquares, transcript levels below the median;black squares, transcript levels equal to themedian; red squares, transcript levels greaterthan the median; grey squares, technicallyinadequate or missing data.Brown & Botstein, Nature, 406, 747, 2000

Gene Chips can be used to follow genetic changesduring development

Molecular Evolution can be determined by DNA Sequences or by protein sequences or by protein structures(Nice chapter in Berg, Tymoczko, Stryer, 5th ed.)You and parents have same DNA by 99.9%You and me (unrelated humans) are 99.4% the same.You and chimp: 99% the same.We are related to a cauliflower! (about 50% DNA similarity)Protein structures most closely related tofunction best.Can sometimes see similarities instructure even where a.a. or DNAsequences are very different hard totell.http://en.wikipedia.org/wiki/Common descentwww.famous-scientists.net/jane-goodall.html

(1/20)153 0Just as you and parent look alike cause you came fromparent, you and monkey you and cauliflower have acommon “parent”.

We are all relatedCauliflower, Whales, Chimps, Humans.Genes: Whale and Humans have similar DNA sequencefor Maleness.Figure 6-27 The sex-determination genes from humans and whales are unmistakablysimilar. Although their body plans are strikingly different, humans and whales are builtfrom the same proteins. Despite the length of time since humans and whales diverged, thenucleotide sequences of many of their genes are still closely similar. The sequences of apart of the gene encoding the protein that determines maleness in humans and in whalesare shown one above the other, and the positions where the two are identical are shaded.Essential Cell Biology, p. 215

Charles DarwinBig Ideas in Biology(Physics is about great laws biology has one.)"There is a grandeur in this view of life, with its severalpowers, having been originally breathed into a few forms orinto one‖-- Charles Darwin, Origin of Life, 1860.Evolution-- Life evolved from simpler forms--One of the best tested scientific theories aroundEvolution is a series of tricks/random eventsBuild complex beings from simpler partsOften many ways of doing thisOur life form is just one.Scientists now believe that the most recent common ancestor ofall currently living organisms appeared about 3.9 Billion yearsago.

The most commonly accepted location of the root of the treeof life is between a monophyletic domain Bacteria and a cladeformed by Archaea and Eukaryota of what is referred to as the"traditional tree of life" based on several molecular studiesstarting with Carl Woese.http://en.wikipedia.org/wiki/LUCA

Artificial SelectionAll dogs came from wolves but through artificialselection have bred certain dogs for certain traits.Common vegetablessuch as cabbage, kale,broccoli aredescendants of wildcabbage plant.http://en.wikipedia.org/wiki/Common descent

DNA SequencingDecoding 4,000 year old DNA (From Nature, 2009)Less 10 years after first living person’s DNA sequenced“Inuk” died on an island off Greenland calledQeqertasussuk. He left bits of hair and bone that thepermafrost preserved, including his complete genome.Inuk’s genes reveal he was a fairly young man, robustlybuilt to exist in a frigid climate, with A-positive blood,dark skin, brown eyes, and thick, black hair on a scalpgenetically susceptible to baldness. He was a palaeoEskimo, and by comparing his genome to other livingpeople, they deduced that he was member of the ArcticSaqqaq, the first known culture to settle in Greenlandwhose ancestors had trekked from Siberia around theArctic circle in pursuit of game.Contamination a big problem: The best place to find it is entombed in ice, where it ispreserved by the cold and protected from contamination. Hair doesn't as readily absorbcontaminants, and its surface can be bleached clean. They also tagged the millions offragments of extracted DNA with a barcode-like sequence to distinguish them fromstray modern human DNA.

Class evaluation1. What was the most interesting thing you learned in class today?2. What are you confused about?3. Related to today’s subject, what would you like to know moreabout?4. Any helpful comments.Answer, and turn in at the end of class.

Jan 12, 2002 · Messenger RNA (mRNA): ―copy‖ of DNA Transfer RNA– (tRNA) 3 bases of RNA amino acid Ribosomal RNA—make protein using mRNA as copy . RNA has 3 different structures, names, and uses. mRNA, tRNA, rRNA . Just as you and parent look alike cause you came f