1. Campbell and Reece Chapter 20

2.  made possible: Human Genome Project completed in 9 yrs (2001) by 2010 genomes of > 7,000 species

3.  DNA formed when segments of DNA from 2 different species are combined in vitro (in test tube)  useful for analyzing genes & gene expression

4.  manipulation of organisms or their components to produce useful products  includes selective breeding, using bacteria in fermentation

5.  the direct manipulation of genes for practical purposes

6.  useful for researcher to have just that portion of DNA working with 1 gene may be as small as 1/100,000 th of a chromosome  bacterial plasmids: circular DNA molecules that replicate separately from bacterial chromosome used by bacterium when environment changes

8.  used to cut DNA w/in short, specific nucleotide sequences (restriction sites)  set of dbl stranded DNA fragments with single stranded “sticky ends”

9.  sticky ends form H-bonds with sticky ends of C’ bases from other DNA: temporary bonds  DNA ligase make bonds permanent: makes covalent bonds in sugar- phosphate backbone

11.  http://www.dnalc.org/resources/animations/ restriction.html http://www.dnalc.org/resources/animations/ restriction.html  http://highered.mcgraw- hill.com/olcweb/cgi/pluginpop.cgi?it=swf::5 35::535::/sites/dl/free/0072437316/120078/bio3 7.swf::Restriction%20Endonucleases http://highered.mcgraw- hill.com/olcweb/cgi/pluginpop.cgi?it=swf::5 35::535::/sites/dl/free/0072437316/120078/bio3 7.swf::Restriction%20Endonucleases  http://www.dnalc.org/view/15476- Mechanism-of-Recombination-3D- animation-with-with-basic-narration.html http://www.dnalc.org/view/15476- Mechanism-of-Recombination-3D- animation-with-with-basic-narration.html

12.  name given original plasmid  dfn: a DNA molecule that can carry foreign DNA into host cell & replicate there  bacterial plasmids mostly used because 1. readily available from suppliers 2. can insert foreign DNA in vitro  bacterial cell 3. multiply rapidly

13.  http://highered.mcgraw- hill.com/sites/0072556781/student_view0/ chapter14/animation_quiz_2.html http://highered.mcgraw- hill.com/sites/0072556781/student_view0/ chapter14/animation_quiz_2.html

16.  large plasmids trimmed down so they contain just the genes necessary for replication  carry 100 – 300 kb (kilo base pairs), normal plasmid can insert vectors no larger than 10 kb

17. can make “libraries” using cDNA:

18.  each have advantages  Genomic library good if: looking for a gene but not sure where it is in a genome, or what kind of cell to look in if looking for introns or regulatory sequences as’c w/gene  cDNA library good if studying: specific protein sets of genes expressed in particular cell types changes in patterns of genes over life of cell (during development of organism)

19.  Nucleic Acid hybridization: process of base pairing between a gene & a C’ sequence on another nucleic acid molecule  C’ molecule = ssDNA or ssRNA = nucleic acid probe  probe is made that is C’ to known sequence in gene

22.  several technical difficulties hinder the expression of cloned eukaryotic genes in bacterial hosts  can substitute eukaryotic hosts: yeasts, some insect cell, some mammalian cells that have appropriate expression vectors: a cloning vector that contains a highly active bacterial promoter just upstream of restriction site where eukaryotic gene can be inserted allowing gene to be expressed in bacterial cell or have been genetically engineered to use in specific eukaryotic cells

23.  Polymerase Chain Reaction  amplifies specific target segment of DNA in vitro using primers that bracket the derived sequence, & a heat-resistant DNA polymerase, & nucleotides

25.  http://www.dnalc.org/view/15475-The- cycles-of-the-polymerase-chain-reaction- PCR-3D-animation-with-no-audio.html http://www.dnalc.org/view/15475-The- cycles-of-the-polymerase-chain-reaction- PCR-3D-animation-with-no-audio.html

27.  once you have many copies of a gene you can ask questions about its functions, where & when the gene is expressed, or how important is it to the organism

28.  uses a gel made of a polymer (agarose commonly)  gel acts like molecular sieve  separates nucleic acids or proteins based on charge and size  nucleic acids carry (-) charges on phosphate group so  (+) end of gel  as move the longer molecules impeded more by “sieve”

30.  fragments produced be restriction enzymes put thru gel electrophoresis  band pattern characteristic of starting molecule & restriction enzyme used  able to identify viruses & plasmids by their band patterns  then recover DNA from gels  1 way of getting pure samples of DNA – won’t work with DNA from eukaryotic cells: gel electrophoresis  smear not bands

32.  Restriction Fragment Length Polymorphism : single nucleotide polymorphism (SNP) that exists in the restriction site for a particular enzyme, making the site unrecognizable by that enzyme & changing lengths of the restriction fragments formed by digestion with that enzyme  found in coding & noncoding DNA

35.  used to detect certain nucleotide sequences w/in a complex DNA sample  compares the restriction fragments produced from different samples of genome DNA

37.  method used to sequence relatively short DNA fragments  done by automated sequencing machines

38.  technique: synthesizes a set of DNA strands C’ to original DNA fragment each strand starts with same primer & ends with dideoxyribonucleotide (ddNTP) incorporation of ddNTP terminates growing DNA strand because it lacks 3’ –OH group (site of attachment of next nucleotide) each ddNTP tagged with distinct fluorescent label so identity of nucleotide at end of each strand (ultimately entire strand) is identified

40.  in vitro hybridization with labeled probes looking for specific mRNAs  could be used to look at how expression of a gene changes during the embryonic development of organism  carry out gel electrophoresis on mRNA

42.  Reverse Transcriptase- Polymerase Chain Reaction quicker & more sensitive than Northern blotting isolates mRNA from different developmental stages of organism then add reverse transcriptase to make cDNA which serves as template for PCR amplification using primers from gene being studied bands will be in samples that originally contained the gene being studied

43.  alternative method used to determine which cells are expressing certain genes  done in living organism  probes labeled with fluorescent dyes

45.  uncover gene interactions  suggest correct therapeutic route in cancer treatments

46.  most common method used to determine function of gene: disable it & observe what happens  specific mutations introduced to cloned gene & then mutated gene returned to cell knocking out normal gene in the process

47.  RNA interference  method for silencing expression of selected genes  uses synthetic dsRNA molecules matching the sequence of gene to trigger breakdown of the gene’s mRNA or to block its translation

48.  important when studying groups of genes to determine how multiple genes interact (basis of systems biology, chap 21)  in humans considered unethical to block activity of genes

50.  used to analyze genomes of large #s of humans with certain phenotype or disease  test for genetic markers : DNA sequences that vary in a population uses SNPs (single nucleotide polymorphisms) single base pair site where variation is found in at least 1% of population few million in human genome

54.  as advances being made in DNA technology also working on technology to make multicellular organism from 1 cell producing genetically identical organism  1 st attempted late 1950’s

55.  Genomic Equivalence: an organism’s cells have the same genome proved when able to generate new organism from 1 cell used carrot (root) cells  cultured  adult plant

56.  totipotent: describing a cell that can give rise to all parts of the embryo & adult, as well as extraembryonic membranes in species that have them

57.  used in cloning animals  transplant nucleus from a differentiated animal cell  enucleated ova can sometimes give rise to clone

59.  Embryonic Stem Cells (ES) or Adult Stem Cells from animal embryos or adult tissues can reproduce & differentiate in vitro and in situ  ES cells are pluripotent : cell that can give rise to many but not all parts of an organism difficult to acquire

60.  ES cells currently donated by patients undergoing infertility treatment or from long term cell cultures established with cells isolated from donated embryos  when main objective is to produce ES to treat disease process called therapeutic cloning

61.  now scientists can “de-differentiate” cells returning them to pluripotent cells: called iPS: induces Pluripotent stem cells can do anything ES cells can do

62.  2 major uses 1. reprogram cells from patients with disease to become iPS cells then act as model cells for studying the disease & potential treatments Parkinson’s disease, type 1 diabetes 2. field of regenerative medicine patient‘s own cells used to regenerate damaged tissues

64.  introducing genes into afflicted individual (into somatic cells) for therapeutic purposes  useful for disorders caused by single gene defect (overall, relatively small # of all diseases)  for it to be permanent, treated cells must be the ones that continue to divide thru out patient’s life

66.  using Short Tandem Repeats (STRs) in DNA isolated from crime scenes leads to genetic profile strong evidence to prove suspect innocent or guilty used in paternity disputes identification of remains

67.  gene for desired protein inserted into bacterial genome and become tiny “factory” for making protein Insulin Digestive enzymes Growth Hormone

68.  genetically engineered microorganisms developed for oil spills or to degrade toxic waste materials Bacteria Algae Plants

69.  to improve productivity & food quality