AP Biology Exam Review: DNA, Protein Synthesis & Biotechnology

Transcription

1 AP Bilgy Exam Review: DNA, Prtein Synthesis & Bitechnlgy Helpful Vides and Animatins: 1. Bzeman Bilgy: DNA Replicatin 2. Bzeman Bilgy: DNA and RNA - Part 1 3. Bzeman Bilgy: DNA and RNA - Part 2 4. Cld Spring Harbr Lab Animatin: Griffith / Avery, McCarty, and Macled Experiments 5. McGraw-Hill Animatin: Hershey Chase Experiment 6. Bzeman Bilgy: Transcriptin and Translatin 7. McGraw-Hill Animatin: Transcriptin 8. McGraw-Hill Animatin: Translatin 9. McGraw-Hill Animatin: Intrn Remval by Splicesmes cntaining snrnp's (small nuclear ribprteins) 10. McGraw-Hill Animatin: Lytic vs. Lysgenic Cycle f Viral Infectin 11. Sumanas Animatin: Life Cycle f HIV, a Retrvirus 12. McGraw-Hill Animatin: Bacterial Transductin Using a Temperate Phage 13. Bzeman Bilgy: Mechanisms f Genetic Variatin in Prkarytic vs. Eukarytic Cells 14. Sumanas Animatin: Trp Opern (Repressible Opern) 15. Sumanas Animatin: Lac Opern (Inducible Opern) 16. Bzeman Bilgy: Opern 17. Bzeman Bilgy: Gene Regulatin in Prkarytic vs. Eukarytic Cells 18. Sumanas Animatin: Gel Electrphresis 19. McGraw-Hill Animatin: Restrictin Enzymes (AKA Restrictin Endnucleases) 20. McGraw-Hill Animatin: Restrictin Fragment Length Plymrphisms 21. Sumanas Animatin: Plymerase Chain Reactin (PCR) 22. Cld Spring Harbr Lab Animatin: Bacterial Transfrmatin 23. Bzeman Bilgy: Respnse t External Envirnments Relevant Objectives: 27. Describe the structure f DNA 28. Describe the experiments leading t the discvery f DNA as the genetic material 29. Describe the prcess f DNA replicatin, including: leading and lagging strand, enzymes invlved in replicatin, the semicnservative mdel, primers, and telmeres 30. Describe hw mutatins in the DNA can arise and the prcess f DNA repair enzymes 31. Explain hw DNA is cnverted int a prtein. 32. Describe the prcess f transcriptin and hw this prduces a mdified mrna prduct based ff f DNA. 33. Describe the prcess f translatin and hw this leads t the prductin f a plypeptide frm an mrna sequence 34. Describe hw prteins are mdified and sent t the crrect lcatin 35. Explain the different types f mutatins and hw they can affect prtein frmatin 36. Describe the makeup f a virus 37. Explain hw viruses use hst cells t replicate 38. Be able t differentiate between the lytic and lysgenic phases f bacteriphage replicatin 39. Explain hw retrviruses differ frm ther viruses, and describe their mde f replicatin 40. Describe hw vaccines prevent viral infectin 41. Explain hw virids and prins can be infectius agents 42. Explain hw bacteria can transfer DNA (3 ways) and hw this influences evlutin 43. Explain hw bacteria can evlve quickly 55. Explain hw recmbinant DNA is made and inserted int an rganism 56. Describe the ptential uses fr recmbinant DNA technlgy 57. Explain hw t screen fr and select bacteria that has undergne transfrmatin fr intended gene 58. Explain what cdna is and describe the uses f cdna and DNA libraries 59. Describe the prcess f gel electrphresis and its uses 60. Describe the prcess f PCR and its uses 61. Explain why genetic engineering is a highly debated issue, and describe bth sides views n the tpic 82. Describe the rganizatin f an pern 83. Explain hw prkarytes regulate gene expressin using perns 84. Describe the difference between a repressible pern and an inducible pern, and give an example f each 85. Explain hw genes are regulated in eukarytes by the fllwing methds: DNA packaging, transcriptinal regulatin, psttranscriptinal regulatin, translatinal regulatin, pst-translatinal regulatin

2 Tpic Outline: 1. DNA Histry Be able t describe the experiments leading t the discvery f DNA as the cell s genetic material. Key scientists and experiments include Franklin, Watsn, Crick, Wilkins structure f DNA Griffith bacterial transfrmatin, genetic material Hershey / Chase sulfur and phsphrus tagged viruses, shwed DNA passed nt prteins Avery, MacLed, McCarty tried transfrmatin after kncking ut macrmlecules (RNA, DNA, prteins, lipids, carbhydrates) transfrmatin NOT successful if DNA kncked ut 2. Structure f DNA Dexyribse nucleic acid Duble helix (tw twisted stsrands) made f nucletides (mnmers) Nucletide = phsphate + 5C dexyribse sugar + nitrgen base Antiparallel strands- ne runs 3 t 5 the ther runs 5 t 3, sides f phsphates and sugars (backbne), rungs f paired bases with hydrgen bnds in between Purines (adenine, guanine; duble rings) pair with Pyrimidines (cytsine, uracil, thymine; single ring) A & T duble H bnd C & G triple H bnd 3. Lcatin f DNA In eukarytes DNA is fund in nucleus n multiple linear chrmsmes (a chrmsme IS a strand f DNA with prteins etc. assciated). In prkarytes DNA is nt in a nucleus and is usually a single circular chrmsme Prkarytes, viruses, and eukarytes (yeast) can cntain plasmids (small extra-chrmsmal DNA that is duble stranded DNA) 4. DNA replicatin Prcess f making exact cpies f DNA (i.e. fr mitsis r meisis) Prcess is semi cnservative (riginal strand is cpied) Steps A. Enzyme (helicase) unzip strands by breaking hydrgen bnds B. Spare nucletides are added bidirectinally t bnd cmplementarily with use f DNA plymerases (DNA pl) C. DNA pl nly can add t the 3 end f DNA and new DNA is made in the 5 t 3 directin D. Replicatin bubbles pen up and a replicatin frk is created because bubble is in half and it has ne side 3/5 and ne 5/3 E. RNA primers must be laid dwn t start prcess (RNA primase makes primers) F. Leading strand makes DNA cntinuusly (Read 3-75, laid dwn 5-73) G. Lagging strand makes DNA discntinuusly (Read 5-73, must flip strand t rient crrectly), Okazaki fragments H. Lagging strand requires enzyme (ligase) t fuse fragments 5. RNA Ribnucleic acid Single stranded, different sugar called ribse, different base called uracil INSTEAD f thymine Base pair rules in RNA, A-U and C-G messenger RNA r mrna carries infrmatin frm DNA t the ribsme transfer RNA r trna bind amin acids and are used in translatin at ribsme ribsmal RNA r rrna acts as an enzyme in the ribsme aiding in frming peptide bnds likely ne f the first enzymes (ribzyme)

3 6. Transcriptin making mrna in nucleus enzyme RNA pl reads the DNA in 3 t 5 directin and synthesizes cmplementary mrna in directin Ex. 3 t 5 DNA is ATG CAT then the 5 t 3 mrna made will be UAC GUA Steps A. Initiatin Prmter is where RNA pl binds and begins B. Elngatin adding f RNA nucletides, des nt stay attached t DNA C. Terminatin ends when RNA pl reaches a terminatin sequence 7. mrna editing intrns spliced ut (cut ut) using splicesmes (snrnp s) alternative splicing leads t many prteins frm ne mrna add plya tail t 3 add GTP cap t 5 each 3 nucletides are called a cdn g t ribsme (free r in rugh ER) 8. Translatin mrna cde is read and matched with trna (brings amin acids) t cnstruct a plypeptide using the ribsme Ex. mrna cdn is AAA then trna anticdn will be UUU and will have a crrespnding amin acid fr that cdn f mrna 3 steps: Initiatin, Elngatin, Terminatin (see ntes) If in ER then: plypeptide is released int ER, then t Glgi cmplex, vesicle t cell membrane, then excytsis (may be given signals fr exit/destinatin) Free ribsmes typically make prducts fr the cell and are nt exprted g t ther rganelles, used in cytplasmic reactins 9. Mutatins and Increasing Genetic Diversity Changes t the DNA sequence are nt all harmful, sme can increase genetic variability -7 mre pssible frms f traits s that nt all rganisms can be killed ff by any ne factr (ex: a disease that kills all tall peple) They can be spntaneus errrs in replicatin r they can be caused by mutagens (envirnmental factrs like radiatin, chemicals, cigarette smke, etc.) If a mutagen causes changes in genes that regulate the cell cycle/cell divisin it is cnsidered a carcingen (a cancer-causing factr) Sme mutatins are neutral (happen in intrns that d nt cde fr prteins) Sme mutatins are harmful (change prtein functin in a negative way) Types f Mutatins: A. Pint mutatin change in ne base pair f a gene (substitutin: replace ne base with anther) B. Silent changes ne base, but cdes fr the same amin acid (due t redundancy) C. Missense cdes fr anther amin acid (changes prtein sequence and usually functin) Example: sickle cell disease, ne T substituted fr A in the gene cding fr hemglbin prtein D. Nnsense cde changes t a stp cdn (makes a nnfunctinal prtein that is terminated early) E. Frameshift mutatin the mutatin effects all nucletides/cdn grupings farther alng the DNA/RNA cde, typically caused by insertin r deletin Insertin adding extra nucletides (causes a frameshift if yu are nt adding exactly three extra bases) Deletin remving nucletides (causes a frameshift if yu are nt remving exactly three bases) Example: O bld type allele invlves a deletin in the A bld type cde

4 10. Viruses prtein cating with nucleic acids (ssdna, ssrna, dsdna r dsrna) inside. Needs hst t replicate. Viral Replicatin Viruses inject DNA r RNA int hst cell Viruses have highly efficient replicative capabilities that allw fr rapid evlutin Viruses replicate via the lytic cycle, allwing ne virus t prduce many prgeny simultaneusly Virus replicatin allws fr mutatins t ccur thrugh usual hst pathways. RNA viruses lack replicatin errr-checking mechanisms, and thus have higher rates f mutatin Related viruses can cmbine/recmbine infrmatin if they infect the same hst cell Sme viruses are able t integrate int the hst DNA and establish a latent (lysgenic) infectin HIV is a well-studied system where the rapid evlutin f a virus within the hst cntributes t the pathgenicity f viral infectin. Genetic infrmatin in retrviruses is a special case and has an alternate flw f infrmatin: frm RNA t DNA, made pssible by reverse transcriptase, an enzyme that cpies the viral RNA genme int DNA. This DNA integrates int the hst genme and becmes transcribed and translated fr the assembly f new viral prgeny. 11. Bacterial Reprductin and Genetic Recmbinatin Transfrmatin bacteria uptakes DNA frm anther bacteria Transductin virus transfers DNA between tw bacteria Cnjugatin bacterial sex Transpsitin jumping genes 12. Prkarytic Gene Regulatin Bacteria are prkarytic with a single circular chrmsme Bacteria express all the genes needed fr a prduct (mre than ne gene at a time) Organizatin includes the prmter regin f DNA, peratr, and structural genes Trp pern = repressible; anablic pathway; used t make enzymes that help make tryptphan if nne is present Repressr is naturally INACTIVE s it will make tryptphan Repressr nly becmes ACTIVE when trp (called crepressr) is in excess and binds t repressr changing its shape Lac pern = inducible; catablic pathway; used t make enzyme t break dwn lactse when it is available Repressr is naturally ACTIVE s it will blck gene transcriptin unless lactse (called inducer) binds and makes repressr INACTIVE 13. Eukarytic Gene Regulatin Enhancers- Areas n genme that are nn-cding that are lcated at a distance frm a prmter Transcriptin factrs / activatrs can bind t these areas and cause transcriptin f certain genes (turns n) mrna Degradatin by RNAi - mrna has a life span in the cytplasm (can last a few hurs t a week) (turns ff) RNA prcessing (intrn splicing, 3 ply a tail, 5 cap) (turn n and alter expressin) Histne Acetylatin (turn n) DNA methylatin (turn ff) Translatin Repressrs (turn ff) Psttranslatinal mdificatins- flding, cleaving, etc. (alter expressin) 14. Creatin f Recmbinant DNA and Bacterial Transfrmatin Tlkit includes plasmid (piece f rund DNA frm bacteria/yeast) r ther vectr such as viruses; restrictin enzymes; hst cell (usually bacteria like E. cli) Restrictin enzymes cut genes at restrictin sites t make blunt r sticky ends Cut gene f interest with same enzyme t get same ends Use ligase t seal gene f interest int the plasmid Insert vectr int hst Used t clne and make cpies r t prduce a freign prtein such as HGH r insulin

5 15. Plymerase Chain Reactin (PCR) Used t make large amunts f clnes f DNA withut using a hst; heat which pens; use a primer t mark the place in the sequence where Taq plymerase begins replicatin; cl; repeat 16. Gel Electrphresis Used t lk at unique pattern created by fragments f DNA; cut DNA using enzyme; lad int a gel; turn n electricity; DNA runs frm negative t psitive; larger chunks mve less; unique fr each persn if testing variable areas f DNA (ex: RFLP s); can be used fr prtein r mrna t