DNA and RNA

1. DNA and RNA Ch. 12 and 13

2. They were done to determine whether genes are made up of DNA or protein. He injected bacteria into mice in four separate experiments. Griffith’s Experiments

3. S bacteria caused pneumonia and death when injected. R bacteria had no visible effect. Heat killed S bacteria did no harm. Heat killed S and live R were injected and the mouse died of pneumonia. Streptococcus pneumonia bacteria were used. S strain was smooth and caused pneumonia. R strain was rough and did no harm. His results..

5. If the mice died with S and heat-killed S and R, but not when S was heat-killed or R by itself, then there had to be some transforming material that was transformed from the heat-killed S to living R changing it into S bacteria. What was this transforming material? DNA What can we conclude?

6. Repeated Griffith’s experiment. Discovered that it is the nucleic acid DNA stores and transmits the genetic information from one generation of an organism to the next. Oswald Avery

7. 2 experiments. Used bacteriophages (viruses) that injected radioactive material into bacteria. They they looked to see if the bacteria became radioactive. Phages with green radioactive DNA 32-P injected it into bacteria and the bacteria became radioactive. Phages with green radioactive protein 35-S injected it into bacteria and it did not become radioactive. Hershey and Chase’s Experiment What can we conclude?

9. Remember that the structure of a molecule is related to its function, so knowing what a molecule looks like gives researchers insight into how DNA works. What do you know about DNA? Deoxyribonucleic acid Double Helix 5’C sugar, Deoxyribose Phosphate Group 4 Nitrogen Bases First double helix structure built by Watson and Crick Published in 1953 DNA Structure Nucleotide

11. Purines- larger Adenine and Guanine Pyrimindines- smaller Cytosine and Thymine Purines and Pyrimidines make up the 4 N bases Pairing of the bases in the DNA structure: Chargaff’s Rule (amount of A = amount of T and amount of C =amount of G A—T C—G

12. Rosalind Franklin used X-ray diffraction to reveal the shape of DNA. Discovery of DNA: X-Ray evidence • The X-shaped pattern shows that the strands of DNA are twisted around each other.

13. The shape of DNA is that of a “twisted ladder”. The P group is attached to the sugar and that forms the backbone. The “rungs” of the DNA are the pairing of the bases. Watson and Crick Double Helix

14. DNA Replication Semi-conservative The DNA unzips. Enzymes split apart the base pairs and unwind the DNA. Free nucleotides in the cell find bases to pair up with on each side along the “open” DNA via DNA polymerase. The sugar-phosphate backbone completes the 2 new DNA strands. Each strand has a new and old strand. DNA Replication Simulation

15. In depth DNA Replication 1. Antiparallel strands. Replication is 5’ to 3’ 2.Topoisomerase (DNA gyrase) relieves superhelicity downstream of replication fork. 3. Helicase unwinds ds DNA. 4. Primase synthesizes the RNA primers for lagging strand, complexes with helicase. (not shown) 5. Ssb proteins keep DNA from reannealing. 6. DNA pol III polymerizes leading and lagging strand. 7. Lagging strand- okasaki fragments 8. DNA pol I- removes RNA primers and replaces with DNA. 9. DNA ligase seals gaps

17. A clone is a member of a population of genetically identical cells produced from a single cell. In 1997, Dolly the sheep was the first clone of an adult mammal. It took over 500 tries. Cloning Clone the Mouse

18. Human Cloning? Why or Why not?

19. Process when the organism’s genotype is translated into it’s phenotype. Remember that proteins are made up of chains of Amino Acids. How many a.a. are there? 2 Processes Transcription- DNA to RNA Translation- RNA Protein Protein Synthesis • 1.26 The genetic material in DNA molecules provides the instructions for assembling proteins. This works the same in nearly all life forms.

20. DNA Double Stranded Base Pairs (A-T, G-C) Deoxyribose sugar RNA Single Stranded Base Pairs (A-U, G-C) Uracil is used instead of Tymine Ribose Sugar DNA vs. RNA

22. RNA polymerase unwinds a section of DNA RNA polymerase binds unattached RNA nucleotides to complementary DNA strand at promoter region. A new strand of mRNA (messenger RNA) is made. DNA will signal RNA pol to leave and transcription stops. It occurs in the nucleus. Tutorial Transcription

23. Before mRNA can leave the nucleus, RNA must be spliced. It gets rid of introns and exons are spliced together. mRNA now leaves the nucleus and into the cytoplasm where it finds a ribosome. Introns- non-coding regions of DNA or RNA. Exons-coding regions RNA splicing

24. Codon- 3 base sequence of mRNA that codes for an amino acid. Anti-codon: complementary 3 base sequence to mRNA on a tRNA. rRNA- ribosome where amino acids are put together. tRNA (transfer RNA)- matches up anticodons to codons to make amino acids that form proteins. Things to Know before we go on.

26. rRNA attaches to first codon on mRNA. A tRNA brings an a.a. to the rRNA with the anti-codon and matches it up with the codon. 3. A 2nd tRNA brings in the next one and then a peptide bond bonds the 2 a.a. together. It moves over and the 1st one leaves so the next one can come in. Translation http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/trad.htm

27. AUG- Methionine is the Start Codon. There are 3 Stop Codons: UAA, UAG, and UGA. Starting and Stopping Translation

29. Protein synthesis

30. When nucleotides are deleted or added, it changes the order or code of the codons, results in different a.a. Frameshift mutations (Gene mutation)

31. Occur when there is only one change in the nucleotide. It only changes one a.a. coded for. Point Mutations (Gene mutation)

32. Occurs when a large stretch of DNA is inserted into the gene. Multicolored corn 1.28b Genetic variation occurs from crossing over, jumping genes and deletion and duplication of genes. Jumping Genes (Transposons)

33. 1. ionizing radiation- gamma and X-rays 2. alkylating agents- carcinogens. If occur in somatic cells- only affects that cell. If occurs in gamete- passed on. Mutations arise?

34. When nondisjuction occurs in all chromosome pairs. Occurs often in plants and can make them “robust”. Polyploidy

35. Control over Genes Ch. 14

36. Control Over Genes • Regulatory proteins intervene before, during or after gene transcription or translation. Ie. Hormones, initiate changes in cell activities when they dock at suitable receptors. • Negative control- slow or stop gene action (repressor protein) • Positive control- promote or enhance it (activator protein)

37. Promotors- noncoding sequence that marks where to start transcription. RNA polymerase hops on. Enhancers- binding sites for activator proteins. Promoters and Enhancers

38. When genes are changed, the proteins they code for may change and this can affect cell structure and function,which changes a phenotype. The control of gene expression (protein synthesis), is different in prokaryotes and eukaryotes. Structure Determines Function

39. Prokaryotes Genes turn on and off primarily in response to changes in environmental factors. 1.1b Different parts of the genetic instructions are used in the different kinds of cells and are influenced by the cell’s environment and past history. Eukaryotes Gene regulation involves several complex systems. Most eukaryotic genes are controlled individually and have regulatory sequences that are much more complex. TATA box Gene Expression

40. Operons • A group of genes that operate together are known as operons. • In E.coli there are 4288 protein encoding genes that are turned off and on together. • Because the genes must be expressed in order for the bacterium to be able to use the sugar lactose as food, they are called lac operon.

41. The regulatory gene codes for production of the repressor that binds to DNA, preventing RNA pol from binding to the promoter. Protein synthesis can’t occur. Gene Regulation in Prokaryotes Lac genes (operon)- group of genes that operate together.

42. 2. Enzymes bind to the repressor and changes it’s shape so it can’t combine to DNA. Now, RNA pol can bind to promoter. The repressor is inactivated.

43. 3. RNA pol moves along DNA where mRNA is translated to produce product. When there is enough “product” in the cell, the repressor takes back original shape and turns genes back off. Was this negative or positive control? The Genes are On

44. An analogy to gene control would be when a house gets below a certain temp. the furnace kicks on and when it is hot enough it turns back off. What would the promoter be? Analogy of Gene Regulation in Prokaryotes

45. Positive control • The lac operon is controlled by activator protein called CAP . • RNA pol binds to promoter if CAP is there. • CAP is first activated by cAMP. • When glucose is scarce- CAP-cAMP complex forms and turn on lactose metabolism genes. • The lac operon is regulated by several factors including the availability of glucose and of lactose. Lactose can be degraded into glucose for the cell to use. If you have glucose, you don’t need to have lactose.

47. Gene Expression in Eukaryotes • TATA box is about 30 bp long and helps RNA polymerase to find position by marking a point just before the point for transcription to begin.

48. Eukaryotic Gene Controls • Controls before transcription • Controls of transcript processing • Controls at Translation • Controls after translation • Can you think of activities that need to be controlled at each of these points? • Prokaryotic- transcription.

49. Development and Differentiation • Differentiation- cells become specialized in structure and function. • Hox genes (Homeotic Genes)- control the differentiation of cells and tissue in the embryo. Clusters. A mutation can completely change the organs that develop in specific body parts. Legs instead of antennae on fruit fly can grow on head.

50. Hox gene clusters What do you recognize about where each gene controls in each organism?