4.1: Introduction to DNA EQ: How do we know that DNA is the source of heritable information and what is the structure of DNA? ----The first part of the lecture explains how we know DNA is the source of heritable information. It walks you through a series of experiments for which you need to understand the significance. ● Unde Unders rsta tand nd wha whatt a chr chrom omos osom ome e is is ● Know the signifi significance cance of Frederic Frederick k Griffith’s Griffith’s experim experiment ent (transfor (transformati mation) on) - what does his experiment experiment prove? prove? ● Know Know the signi signific ficanc ance e of the Hersh Hershey ey Chase Chase experi experimen mentt ○ Need to know know that a bacteriopha bacteriophage ge has two two parts (DNA (DNA and and protein) protein) to understan understand d the experime experiment nt ----NOW: We know that DNA is the source of heritable information. The next section of the lecture will go into the structure of DNA ● Know Know Char Charga gaff ff’s ’s rule rules s ○ Why is is it signif significant icant that these rules transcend transcend across across all specie species? s? ● Know the contri contributi bution on of Watson, Watson, Crick Crick,, Wilkins Wilkins and Frankl Franklin in ● Be able able to to expl explain ain the struct structure ure of DNA DNA ○ Suga Sugarr-ph phos osph phat ate e back backbo bone ne ○ Base Bases s (Cha (Charg rgaf aff’ f’s s rules rules of pai pairi ring ng)) ○ Double-helix 4.2: The Central Dogma EQ: How do the instructions encoded in DNA yield a protein? -----Now that we understand the structure of DNA, it is time to learn how it functions (how it carries heritable information information which become proteins we can see and use). ● Step Step 1: DNA DNA Rep Repli lica cati tion on ○ The goal of DNA DNA replicati replication on is to create create additional, additional, identic identical al double-st double-stranded randed DNA DNA molecules molecules.. ○ Understand Understand how how DNA replicate replicates s semi-conser semi-conservativ vatively ely (one strand strand is the templat template e (old) and another another strand strand is created (new)) = semi (half) conserved (saved) ■ Initiation ● Know Know the the sig signi nifi fica canc nce e of the the orig origin in ● Know the the significan significance ce of each each of the four four enzymes enzymes (DNA (DNA polymerase, polymerase, helic helicase, ase, primase primase and and topoisomerase) ● Know the direct direction ion of of replicati replication on (read (read 3’ to 5’, 5’, created created 5’ 5’ to 3’) 3’) ● Each strand strand is antiparall antiparallel el so they are read read in in opposite opposite directions directions ■ Elongation ● Understand Understand the issue issue of antipar antiparalle allell with with the the replic replication ation bubble bubble ○ Leadin Leading g strand strand and lagg lagging ing stra strand nd (Okaz (Okazaki aki frag fragmen ments) ts) ■ Termination ● DNA DNA replic replicati ation on ends ends when when entire entire stra strand nd has been been copi copied ed ● Unders Understan tand d the the signi signifi fican cance ce of of telom telomere eres s ● Understand Understand proofreadi proofreading ng as as a mechanism mechanism to reduce reduce mutation mutation rate ● Step Step 2: Tran Transc scri ript ptio ion n ○ The goal of transcr transcriptio iption n is to create create a single-stran single-stranded ded RNA molecul molecule e (mRNA) (mRNA) that can carry carry the informat information ion of DNA out of the nucleus and to the ribosomes. ■ Initiation ● Unders Understan tand d the the role role of of RNA RNA polyme polymeras rase e ● Understand Understand what what a promoter promoter is (usual (usually ly a character characteristi istic c DNA sequence sequence signal signalling ling where where transcription should start = TATATA) ● Know how how this this is process process is is similar similar and and different different between between eukaryote eukaryotes s and prokary prokaryotes otes hypothesize the significance of the similarities and differences ■ Elongation ● RNA RNA is prod produce uced d 5’ - 3’ 3’ (by (by readin reading g DNA DNA from from 3’ 3’ to 5’) 5’) ● Only Only one strand strand is made made - so no no laggi lagging ng stra strand nd ■ Termination ● Trans Transcri cripti ption on ends ends at the the end end of a trans transcri cripti ption on unit. unit. ● Step 2.5: Post-Trans Post-Transcrip criptiona tionall RNA RNA Processi Processing ng (eukary (eukaryotes otes only) ○ Understand Understand the significan significance ce of the 5’ 5’ cap cap and the poly-A poly-A tail
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■ Why is this this only only useful useful for eukary eukaryote otes? s? ○ Exon splici splicing ng (removing (removing intron introns) s) - not much much is currentl currently y known about about introns introns and and why we have have them. them. Step tep 3: 3: Tr Transl ansla ation tion ○ The goal of transla translation tion is to create create protein protein from mRNA mRNA (which (which is carryin carrying g the instructi instructions ons from DNA) DNA) ○ Understand Understand the struct structure ure of of the ribosome ribosome (A (A site, site, P site site and and E site) site) ○ Understand Understand the the basic role role and structu structure re of tRNA tRNA (bringin (bringing g amino acids! acids! - specif specificit icity!) y!) ○ Know now wha whatt a codo codon n is is ■ Looking Looking at the codon codon chart chart (which (which will will be given to to you) notice notice there there are 64 codons codons but only only 20 amino amino acids which means there is redundancy - why might this be significant? ■ Know that the the codon codon chart is the same for for all life life - why why is this this signifi significant? cant? ○ Initiation ■ Start Start codon codon (AUG) (AUG) begins begins translat translation ion - which which means means Met Met is the first first amino amino acid alway always s ■ Understand Understand the role role of of anticodo anticodons ns on tRNA in bindin binding g to mRNA ○ Elongation ■ Understand Understand how how the mRNA moves through through the riboso ribosome me so more more codons codons can be be “read” “read” ■ Understand Understand how tRNA’s tRNA’s use use their their antico anticodons dons to “read” “read” the mRNA mRNA ■ Understand Understand that that tRNA tRNA are specifi specific c and will will only get get another another of the same same amino amino acid (once (once they have have “dropped off” their amino acid) ● Why is this this spec specifi ificit city y so so impo importa rtant? nt? ■ Understand Understand that that as amino amino acids acids are are being added added we we are creatin creating g peptide peptide bonds bonds between between them them = primary structure of a protein! ○ Termination ■ Stop co codon Mutations ○ Know the differe different nt types types of mutations mutations and and how they may affect affect a protein protein ○ Know Know tha thatt muta mutati tion ons s happ happen en in in DNA DNA
4.3: Mitosis EQ: How can one cell divide into two identical copies of itself and why is this necessary? ● Unde Unders rsta tand nd why why mito mitosi sis s is nece necess ssar ary y ● Understand Understand the phases phases of of the cell cycle: cycle: G1, S, G2 G2 and M, M, as well well as as G0 ● Get the the voc vocab ab fir first: st: ○ Know Know the differ differenc ence e between between chromo chromosom somes es and chrom chromati atids ds ○ Know Know the the differ differenc ence e betwee between n haploi haploid d and dipl diploid oid ○ Know when when the cell cell is haploid haploid and and when the the cell is diploid diploid in in the various various phases phases of the cell cell cycle cycle ● DO NOT MEMOR MEMORIZE IZE THE THE INDIVIDU INDIVIDUAL AL PHASES PHASES OF MITOS MITOSIS!! IS!!!!!! !!!!!!!! !!!!!! !! You do not need need to know these! these! ● Know the the overall overall flow from from one cell to two two cells - be able to explain explain how how many chromosom chromosomes es and chromatid chromatids s are at each stage
4.4: Cell Cycle Control EQ: How is the cell cycle (mitosis) controlled and what happens if these controls fail? ● Know the the function function of of checkpoint checkpoints s (overall) (overall) and and know what the the G1 checkpoi checkpoint nt does ● What What control controls s the checkp checkpoin oint? t? Intern Internal al and exter external nal cues! cues! ○ Internal Internal cues: cues: CdK, cyclin cyclin and MPF MPF (know the the function function of each and how the the concentratio concentration n cyclin cyclin and MPF would would affect the checkpoint) ○ External External cues: cues: proteins proteins created created by OTHE OTHER R cells cells or environmen environmental tal cues cues (overcrowdi (overcrowding, ng, etc) ● Canc Cancer er = unco uncont ntro roll lled ed cell cell div divis isio ion n ○ Mutations Mutations happen happen and there there are genes genes that are are present present to make make sure mutate mutated d cells don’t don’t divide divide - this this is what what checkpoint is for! ○ These genes, genes, the the ones that that make sure sure mutated mutated cells cells don’t don’t divide, divide, are called called proto-o proto-oncogen ncogenes es and tumor-suppressor genes ■ Proto Proto-on -oncog cogene enes: s: stimul stimulate ate cell cell divis division ion (gas (gas pedal) pedal) ■ Tumor-sup Tumor-suppress pressor or genes: genes: slow down cell division division (brake (brake pedal) pedal) ○ But what what happens happens if the proto-o proto-oncogen ncogenes es and tumortumor-suppr suppressor essor genes genes are are mutated mutated
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Mutate Mutated d proto-o proto-onco ncogen gene e = oncogene oncogene = alway always s on (alway (always s gas) Mutate Mutated d tumortumor-sup supore oresso ssorr gene = alway always s off (neve (neverr brake) brake)
4.5: Meiosis EQ: Where does variation in a population come from? ● The differen difference ce between between asexual asexual and sexual sexual reprodu reproduction ction (both (both in mechani mechanism sm and variabil variability) ity) ● Understand Understand the basics basics of fertili fertilizati zation on (haploid (haploid + haploid haploid = diploid) diploid) ○ These These haploi haploid d cells cells are calle called d gamete gametes s (aka: (aka: sperm sperm and egg) egg) Meiosis is the process of making these haploid cells! ● Know the differen difference ce between between sister chromati chromatids ds and homologous homologous chromosome chromosomes s (this vocabular vocabulary y is very challenging challenging,, but it is imperative that you know it before understanding meiosis) ○ Homologous Homologous pair = a pair of chromoso chromosomes mes (one (one from from mom mom and one from from dad) dad) ○ Sister Sister chromati chromatids ds = identical identical copies copies of each each chromosome chromosome (mom (mom and and dad) made made during during S phase phase ○ There are are two sets sets of non-siste non-sisterr chromatids chromatids in in one homologou homologous s pair. There There are are also two two sets of sister sister chromatids in one homologous pair. Did that make sense? ● Unders Understan tand d the the simpl simple e diagr diagram am of of meio meiosis sis ○ Know the the differenc difference e between between Meiosis Meiosis I and Meiosi Meiosis s II (remember (remember meiosi meiosis s just means means division division)) ○ Know there is no DNA replicati replication on between between meiosi meiosis s I and meiosis meiosis II ■ Why Why not? not? Wha Whatt are are we tryi trying ng to to make make? ? ● You do not not need to know every phase phase of meiosis. meiosis. Howeve However, r, you do do need to to know a couple couple of key point points: s: ○ Crossing Crossing over: over: when non-sist non-sister er chromatids chromatids in in a homologous homologous pair exchange exchange informa information tion from from the same gene gene ■ What hat is the the poin pointt? ■ Happe appens ns in mei meios osis is I ○ Independent Independent assortm assortment:A ent:Alignm lignment ent of homologous homologous pairs pairs during during meiosis meiosis I where each each homologous homologous pair pair lines up independently of the other homologous pairs (i.e. its not like all “mom” chromosomes on the left and all “dad” chromosomes on the right) ■ What hat is the the poin pointt? ● Sexual Sexual reproductio reproduction n is challenging challenging (requires (requires a mate - which require requires s energy) - wouldn’t wouldn’t think think it would be evolutiona evolutionarily rily advantageous over time. However...it is! WHY? ● Unde Unders rsta tand nd wha whatt a kar karyo yoty type pe is. is. ○ Know the differenc difference e betwee between n autosom autosomes es and and sex chromosome chromosomes s
4.6: Introduction to Mendelian Genetics EQ: How are traits inherited and expressed? ● You don’t don’t need to to know about about Mendel Mendel - however however you should should study study his experim experimental ental design design (e.g. (e.g. why why the peas were were chosen, what his control was, etc) because AP likes you to design your own experiments. It is helpful to look at a pristine example :) ● Know th this vo vocab: ○ True br breeding ○ F1, F2 ○ Cross ○ Wild-type ○ Monohybrid ○ Dihybrid ● Know what what an allele allele is (know that that a homologous homologous pair has has two alleles; alleles; sister sister chromati chromatids ds are copies copies of the same allele) allele) ○ Understand Understand the difference difference between between dominan dominantt and recessive recessive alleles alleles ■ Dominance Dominance does does NOT mean mean more more evolutionar evolutionarily ily advantag advantageous eous - it just just means means it will will appear appear in a heterozygous situation ■ Domina Dominance nce is predet predeterm ermine ined d and and cons constan tantt ● Revi Revisi sitt geno genoty type pe vers versus us phen phenot otyp ype e ○ Know Know hom homoz ozyg ygou ous s and and hete hetero rozy zygo gous us ● Know now Men Mende dell’s laws: aws: ○ Law of segregati segregation: on: alleles alleles segregate segregate during during meiosis meiosis randomly randomly into into gametes gametes (each (each gamete inherit inherits s only one allele) ○ Law of independen independentt assortment: assortment: Allel Alleles es are inherited inherited independe independently ntly of one another another (it (it is not like you you will inherit inherit all of mom’s alleles or all of dad’s alleles - it is a combo!) ■ This This is due to inde indepen penden dentt assortm assortment ent durin during g meiosi meiosis! s! ● Look at at how to solve solve the the genetics genetics problems problems as as we will will be be doing doing this this in class! class! ● Know Know what what a testcr testcross oss is and and why why itit is useful useful 4.7: Extensions to Mendelian Genetics Same EQ as above - just know that Mendel got us understanding how traits are inherited/expressed, but since his research we have found some exceptions. This does not mean Mendel’s laws are incorrect (actually, quite the contrary). It’s just that we have added additional rules and understanding. The beauty of science - it is always changing and getting better with new brains (like yours!) ● Understand Understand the followi following ng term term and how how they are are differen differentt from Mendel’s Mendel’s underst understandin anding g ○ Inco Incomp mple lete te domi domina nanc nce e ○ Codominance ○ Mul Multipl iple all alleles eles ○ Poly Polyge geni nic c inh inher erit itan ance ce ● What is the the benefit benefit of these different different types of inherit inheritance ance patter patterns? ns? ● Unders Understan tand d linked linked gene genes s (this (this is impo importa rtant! nt!!!! !!!!) !) ○ Linked Linked genes are are genes genes located located on the the same chromosome chromosome (and theref therefore ore the same allele) allele) ■ These These genes genes will will not separate separate except except during during crossing crossing over!! over!! ■ The closer closer the the genes are are to each other other on an allele, allele, the the higher higher the likeli likelihood hood they they will be be inherited inherited together (the less likely they will separate during crossing over) ● Gene mapping ○ Sex-linkag Sex-linkage e example example (recessive (recessive alleles alleles carried carried on the x-chrom x-chromosome osome)) --- ignore ignore the sexist sexist graphic graphic please please :) ● You don’t don’t need to to understand understand the the other example examples, s, per se (howev (however er they are are WILDLY WILDLY interesti interesting) ng) ● You do need to understa understand nd that there there are many excepti exceptions ons to Mendel’s Mendel’s rules rules and this is only only to increase increase variatio variation n (think evolution!) 4.8: Human Genetic Conditions EQ: What is the relationship between inheritance of traits and their effect on human health? ● Understand Understand the basics basics of a pedigr pedigree ee - we we will will be practic practicing ing these these in in class class ● Understand Understand the diffe difference rence between between dominan dominantt and recessive recessive condition conditions s ○ Explain Explain how how the the expressi expression on in phenotype phenotype varie varies s between between the two two
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○ Would it diffe differr if a recessiv recessive e conditi condition on was was on the x-chromoso x-chromosome? me? Know x-linked x-linked dominant dominant versus x-linked x-linked recessive recessive conditions conditions ○ How does does the the probabil probability ity of of expressio expression n vary vary between between men men and women women in in each? each? Know Know y-l y-lin inke ked d cond condit itio ions ns ○ Alwa Always ys domi domina nant nt (why (why?) ?) ○ Very Very unco uncomm mmon on (why (why?) ?)
4.9: Regulation of Gene Expression EQ: How is gene expression controlled? This is a great final lesson as it forces us to review the concepts from the central dogma! PROKARYOTES: ● Prokaryot Prokaryotes es regulate regulate gene expressi expression on simply simply by not transcribi transcribing ng those genes genes (stop transcr transcripti iption on = stop translatio translation n = no proteins from the gene are made!) ● Operons Operons = a cluster cluster of genes that all all contri contribute bute to to one metabol metabolic ic task task ○ It is more more effici efficient ent to turn turn on/off on/off an operon as opposed opposed to each each individual individual gene ● Understand Understand the diffe difference rence between between inducib inducible le and and repress repressible ible operons operons ○ Induci Inducible ble = always always off, off, can be be induce induced d (or turned turned on) on) ○ Repres Repressib sible le = alway always s on, can can be repre represse ssed d (or turn turned ed off) off) ● Know the the lac operon operon as the model model example example of of an inducible inducible operon operon (know (know the mechan mechanism ism of how how it works works exactly) exactly) ○ The lac lac opero operon n is a set set of genes genes that that brea breakdo kdown wn lact lactose ose ■ If lactos lactose e is is abse absent, nt, the operon operon is off ■ If lactos lactose e is is pres present ent,, the the operon operon is on ■ The lac lac operon operon is is always always off, off, unle unless ss lacto lactose se is pres present ent ○ A repressor repressor is always always bound bound to the the operator operator (where (where RNA polyme polymerase rase would would attach attach)) ○ When lactose lactose is present, present, it binds binds to the repressor repressor (as (as allolactos allolactose) e) and its alloster allosteric ic site thereby thereby changing changing its its shape so it cannot bind to the operator. ■ This allows allows RNA polymerase polymerase to to transcrib transcribe e the genes genes necessar necessary y to digest digest lactose lactose ○ What What happen happens s to lacto lactose se when when the the genes genes are are transc transcrib ribed? ed? ■ What, What, eventu eventuall ally, y, happ happens ens to allo allolac lactos tose? e? ■ What, What, even eventua tuall lly, y, happ happens ens to the the repr repress essor? or? ■ What, What, eventu eventuall ally, y, happen happens s to to the the operon operon? ? ○ NEGAT NEGATIVE IVE FEEDB FEEDBAC ACK.. K...ho .homeo meosta stasis sis!! ● Know the the trp operon operon as the model model example example of an an repressibl repressible e operon operon (know the the mechanism mechanism of how how it works works exactly) exactly) ○ The trp trp operon operon is a set of genes genes that produce produce tryptophan tryptophan (when (when trypto tryptophan phan is is absent) absent) ■ If tryp tryptop tophan han is is absen absentt = the the oper operon on is is on or or off? off? ■ If tryp tryptop tophan han is is presen presentt = the the operon operon is is on or off? off? ■ Trp Trp opero operon n is usuall usually y on to make make trypto tryptopha phan n ○ When tryptop tryptophan han is present present it acts acts as a co-repre co-repressor, ssor, activa activating ting the the repressor repressor so itit can bind to to the operator operator (tryptophan binds to the repressor allosteric site changing it to an active form) ■ The operator operator become becomes s active active and can bind bind to the operato operator, r, thereby thereby inhibiti inhibiting ng RNA polyme polymerase rase from from transcribing the genes that synthesize synthetic tryptophan (don’t need it if there is real tryptophan!) ○ Tryp Trypto toph phan an is need needed ed by the the cell cell ■ What What wil willl happ happen en to to it over over tim time? e? ■ What will happen to the the co-repre co-repressor? ssor? What about the repress repressor? or? ■ What What about about the operat operator or and and the the enti entire re oper operon? on? ● AGAIN AGAIN - negat negative ive feedba feedback ck (Hom (Homeos eostas tasis! is!)) ● Understand Understand the CAP/c CAP/cAMP AMP operon operon as an example example of “upregu “upregulati lation” on” EUKARYOTES: ● Eukaryotes Eukaryotes can regulat regulate e gene expression expression at every every step of central central dogma dogma (pre-tran (pre-transcri scription ption,, transcript transcription, ion, post-transcriptional, post-transcriptional, translation, etc) ● DNA access ○ Histone Histone protei proteins ns wrap wrap chromo chromosomes somes into tight, tight, compact compact structures structures.. ○ Only Only acces accessib sible le DNA DNA will will be tran transcr scribe ibed. d. ○ The way that histone histone protei proteins ns wrap wrap chromosome chromosomes s is heritable! heritable! ● Prere-tran transc scrript iption
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In order for for transcript transcription ion to happen, happen, certain certain transcri transcription ption factors factors need need to be present. present. No transcrip transcription tion factors factors at the promoter (TATA box), then no transcription ○ This is the the key key mechanis mechanism m by which which cells cells become become different differentiated iated ■ All of of your cells cells have have 100% 100% of your your DNA, DNA, but not not all the DNA DNA gets expressed expressed (it (it depends depends on the the transcription factors - which get separated during mitosis of embryo) Post Post-t -tra rans nscr crip ipti tion on ○ Altern Alternati ative ve splici splicing ng (intro (introns/ ns/exo exons) ns) Prere-tran transl slat atiion ○ Honestly Honestly - not not truly truly understo understood. od. Don’t Don’t worry worry about about this one - just just know know it exists. exists. Post ost-tra -trans nsllatio ation n ○ Unne Unneed eded ed pro prote tein ins s are are disc discar arde ded d Overall Overall - know that eukaryot eukaryotes es can regulate regulate gene gene regulati regulation on using more more methods methods than than prokaryotes prokaryotes
4.10: Biotechnology & Viruses EQ: What are ways that DNA can be manipulated? EQ: How do viruses replicate their own genetic material? ● Biot iotech echnolog logy: ○ know the basics basics (simple (simple,, simple simple basics) basics) of each technique technique and know know the difference difference betwee between n genetic testin testing g and genetic engineering. ● Viruses ○ Know that that a virus is an obligate obligate intrac intracellul ellular ar parasite parasite consisting consisting of two two parts (geneti (genetic c information information + protein protein coat) coat) ○ Know now wha whatt a phag phage e is is ■ Know the diffe difference rence between between lytic lytic and lysogen lysogenic ic reprod reproductiv uctive e cycles cycles ○ Know that that eukaryot eukaryotic ic viruses viruses can can either either have RNA or or DNA as genetic genetic materia materiall ■ Understand Understand the the differenc difference e in how each each is replicat replicated ed in the host host - which which has more more potential potential for error/mutation? ○ Unders Understan tand d the advant advantage age to to mutati mutation on for for virus viruses es
