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Midterm 1 Study Guide-Bio 2

by: Bree Scalzo

Midterm 1 Study Guide-Bio 2 BIOSC

Marketplace > Biology > BIOSC > Midterm 1 Study Guide Bio 2
Bree Scalzo
Foundations of Biology 2
Dr. Swiganova

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About this Document

This study guide includes material form lectures 1-5. Some of the formatting got messed up for a few of the pictures so sorry in advanced! Happy Studying!
Foundations of Biology 2
Dr. Swiganova
Study Guide
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This 13 page Study Guide was uploaded by Bree Scalzo on Tuesday February 3, 2015. The Study Guide belongs to BIOSC at a university taught by Dr. Swiganova in Fall. Since its upload, it has received 451 views.


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Date Created: 02/03/15
if tiDi l 2 sample Lecture 1 DNA and the Gene Synthesis and Repair HiPm 39 Hepiicaiil ln b 3quot Wm 1 Vi fl i 39 if rgh 395 39 4 4 l4 Centrlluw W Hui 1 A MJ separately arena locations 0f 3 In F ii the 6 each sample J balm What is genetic info made of a Hershey and Chase experiment with radioactively labeled protein coats and DNA proved that genes consist of DNA 2 DNA structure a Double Helix b Antiparallel Watson and Crick c Chargoff s rule i AT and CG ii ACTG Hypothesized mechanisms for DNA Replication l a SemiconservativeTRUE b Conservative c Dispersive DNA Synthesis a Exergonic reaction Replication Bubble a The Origin of Replication sequences of nucleotides where the replication beings i Results in replication bubble formation ii Bidirectional Enzymes of DNA Synthesis a Helicaseopens of double helix b Toposiomeraserelieves twisting forces by cutting the helix and putting it back together c Single Stranded DNAbinding Proteinsstabilizes single strands of DNA so they do not reform the helix and hydrogen bonds d DNA polymeraseworks in 5 3 direction synthesizing new DNA e Primasesynthesize RNA primer short piece of RNA that allows replication to begin by DNA polymerase Leading Strand Vs Lagging Strand a Leading Strand L ConUnuous ii Steps 1 Helicase opens up DNA 2 Unwound by topoisomerase 3 Primase synthesizes RNA primer 4 Synthesis of leading strand beings b Lagging Strand i Discontinuous ii Steps 1 Primer is added 2 First fragment synthesized okazaki fragment 3 Second fragment synthesized 4 Primer replaced with bases by DNA polymerase 5 Gap closed by DNA ligase 333333333 8 Problems with copying the end of linear chromosomes a Unreplicated end 9 Telomere Replication l a Telomereend of chromosome b Telomeraseextends the unreplicated end twice so a primer can be added and rest of telomere can be synthesized 10 Repairing mistakes during DNA Synthesis a DNA polymerase can proofread and repair mistakes b Mismatch repair mechanismremove section from incorrect base and adds correct bases 11 Damage caused by environmental factors a Chemicals and UV radiation cause kinks i Nucleotide excision repair cuts out damaged section of DNA and replaces with correct bases 12 Xeloderma Pigmentosum a Autosomal recessive disorder where DNA repair mechanisms don t work Telomerase with its own RNA template V RNA primer F 39 l llll Sliding clamp Lecture 2 How Genes Work 1 OneGene OneEnzyme Hypothesis Beadle and Tatum then Srb and Horowitz a One gene codes for one enzyme genes contain instructions for making proteins 2 The Central Dogma a DNAtranscriptionmRNAtranslationprotein i Exceptions reverse transcriptase in HIV 3 Genetic Code a 4 characteristics L redundant ii unambiguous iii nearly universal iv conservative 4 Translating a Template is being read but coding strand indirectly gives you the mRNA b mRNAsame as coding strand but Uracil instead of Thymine 5 Mutation a Any permanent change in an organisms DNA create new alleles b Can be i Bene cialincreases tness ii Neutralno affect on tness iii Deleteriousharmful to organisms c Types of mutations i Pointsingle base change ii Silentcodon changes not the amino acid no affect iii Missensechanges amino acid speci ed iv Nonsensechange that results in early stop codon shortened polypeptide results and usually deleterious v Frameshiftaddition or deletion of a nucleotide reading frame is shifted almost always deleterious d Sickle cell anemiamutation in gene encoding for beta hemoglobin subunits 6 Chromosome eve mutation a Polyploidyan extra set of chromosomes in each set b Aneuploidyone extra chromosome in one set trisomy 21 c Inversionsparts of a chromosome is switched with another chromosome d Translocationregion of a chromosome is duplicated somewhere else e Deletionspart of a chromosome is deleted i Criduchatdeletion of far end of chromosome 5 Deletion 9 Duplicatio Lecture 3 Transcription 1 The process of transcription a Initiation b Elongation c Termination 2 Transcription a Reading the DNA and making RNA that is complementary to the template 3 RNA polymerase a Reads the DNA and forms base pairs which will eventually detach to make mRNA i Eukaryotes have 3 types prokaryotes have 1 ii In prokaryotes RNA polymerase binds with sigma protein to make holoenzyme 4 Promoters a Bacteria Recognition sites are 10 box TATAAT and 35 box sigma recognizes these and binds to DNA b Eukaryotes more diverse 2530 base pairs upstream TATA box basal transcription factors bind to DNA 5 Initiation a Sigma or basal transcription factors bind to promoter region on DNA and orients the DNA template inside RNA polymerase i Zipperunzips hydrogen bonds of mRNA bases and DNA ii Rudderseparated RNA from DNA b Sigmabtf is released and v synthesis continues 6 Elongation a Transcription elongated the mRNA 7 Termination a Prokaryotes mRNA forms hairpin structure b Eukaryotes recognition of a poyA sequence 8 RNA Processing in Eukaryotes a RNA splicing i Long segments of DNA are not coded in RNA make introns leaves and extrons stays loops made by snRNPs b quot Adding caps and tails to transcripts i 5 cap to 5 end poyZ tail on 3 end 1 prolongs the life span of mRNA in cell 2 called telomeres ends of the chromosomes 9 Introns a Are recycled in the cell or degraded by exoriboneclease b Alternative splicingsplicing of primary RNA transcripts form a single gene in different ways to produce different mature mRNAs and thus different peptides 913 FIT4 4 Gilli 1 O u n shuf ing Comparison Bacteria Eukaryotes RNA polymerase One Three each produces a different class of RNA Promoter structure Typically contains More variable often a 35 box and a includes a TATA box 10 box about 30 from the transcription start site Proteins involved Sigma different Many basal in recognizing versions of sigma transcription factors promoter bind to different promoters RNA processing None Extensive several processing steps occur in the nucleus before RNA is exported to the cytoplasm 1 enzymecatalyzed addition of 5 cap on mrNAs 2 Splicing intron removal by splisosome to produce mRNA 3 Enzyme catalyzed addition of 3 polyA tail on mRNAs Lecture 3 pt 2 Translation Translation a Bacteriatranscription and translat because no barrier ion occur simultaneously b Eukaryota nuclear envelop so translation in cytoplasm From mRNA to a polypeptide a mRNA is negatively charged and a need middle man i tRNA proposed by Crick Transfer RNA tRNA UL mino acids are hydrophobic so a Translated mRNA into a polypeptide Wobble Hypothesis a At 3rOI codon position may not hav allowing for variation Ribosomes a Have small and large subunit i Bacteria 16SrRNA in small ii Eukaryotes 18SrRNA in small 28SrRNAin large Initiation of Translation a mRNA binds to small subunit of ribosomes at recognition site i Bacteria SineDalegarno sequence 5 AGGAGGU3 Eukaryotes Kozak sequence 5 gccAGccAUGG3 b FMet rRNA binds c Large subunit binds i EExit PPeptide A Accepting 7 Elongation a Nterminus to Cterminus b Aminoacyl tRNA arrives c Peptide bind formation d Translocation repeat bd several times 8 Termination a Release factors bind to stop codon b Polypeptide is released c Ribosome subunit separates 9 Protein Destinations a Wide variety poly 39 bu Mf f binds to stop codon e complementary base pair 23rRNA in large A v 391 1 MIN BACTERIA Ribosome binding site Start codon mRNA 3 b 1 mRNA binds to small subunit The ribosome binding site sequence binds to a complementary sequence in an RNA molecule in the small subunit of the ribosome a null ku in 39a 4mm I hnn fan Aminoacyl tRNA 5 Small subunit of ribosome 2 Initiator aminoacyl tRNA binds to start codon 3 Large subunit of ribosome binds completing ribosome assembly Translation can now begin CESS ELONGATION 0F POLYPEPTIDES DURING TRANSLATION 2 Peptidebond formation The amino acid attached to e e nbosome ne codon 39downu e mRNA with the help of elongation tactth not showmjheit lfl rattached to the polypeptide Oh i anQ lie39s into the Psita The A sitei gjy WV e r agidcfjhe tRNA ln theA site 7 7 TRANSLATION Hydrolysis of l 0nd linkin tRNAa I m RN 5 3 2 Polypeptide and uncharged tRNAs 3 Ribosome subunits separate maa elgca ng ribosome reaches are released The subunits are ready to attach to the go 5 39 T39 protein release factor fills start codon of another messa e 10 Posttranslational modification was g mging the tRNA in the P site to the made chain a Proteolysiscuts the product b Glycosylationrecognition on cell membrane c Phosphorylationadding phosphate group Lecture 4 Control of Gene Expression in Bacteria 1 Trade off between different mechanisms of regulation or gene expression a Transcriptional controlenergetically favorable slow b Translational controlenergy ef cient response time in the middle c Posttranslational controlenergetically unfavorable fast 2 Regulation of transcription in Bacteria a Positiveuses activator makes transcription more likely to occur b Negativecalled repressor binder to operator and prevents transcription i Examples of regulatory decisions catabolic pathway lac operon or biosynthetic pathway tryptophan operon 3 Regulatory Proteins in bacteria a Repressor proteins bind to operators b Activator proteins bind to activatorbinding sites 4 Expressing genes coding for enzymes a Constitutivealways on glycolytic pathway b Induciblesynthesized only when needed c Repressible produced but can be turned off production of amino acids i What is the evolutionary basis for these types of gene control 1 Energy conservation 5 Lactose uptake by bacteria a Lactose serves as inducer for lac operon i 3 types of lactose metabolism mutants n b causuu th WY quotl all mducert39je comr39l repressor and I a 1 U l t l andmg neg n it model v 1 ed the mull of the Nag mmaf dsu WM ex give model of nele tommh Perm Dne 0f the key thm yl Was th la 2156 and galacmslde llc lllltase Stiller inscribed into a shingle r1111 A TD39QQM oined the term opemn tor a m we ling ial genes that are transcribed to st 00 enough the grout of games involveznm I termed the lac operon inlay Called MA was found to be adjacml Y ibed as part of the same Opemn milling ti IIIII 4 Repressor bound to lblockstranscripilon I again cannot cleave lactose 2 lacY cannot import lactose into cell 3 lacl cleave lactose constitutively b Gene involved in lactose metabolismLac Operon 6 Negative Control of lac operon a Lactose absent repressor present transcription stopped b Lactose present repressor present transcription continues c Lactose presentabsent repressor absent transcription conUnues i lacl is constitutively expressed because energetically favorable to keep the gene off 7 Role of Glucose a If present in system represses lac operon function 8 FROM LECTURE 4 SUPPLEMENT Permease Bgalactosidase a Which one of the answers in the table Answer No lactose No lactose correctly shoes the gene expreSSIon of lactose lactose this partially diploid E coli mutant IPOCZ Y39A 39 15050 PO Z Y A Answer A Why In the whether lactose is present or not the rst cell will always produce lacZ Bgalactosidase because the operator is mutated But because lacY is mutated it will not produce permease no matter what For this we have to look over at the other cell The lacY permease works so in the presence of lactose because lactose takes away the repressor So it will not produce permease if lactose is not preset to take the repressor off of the gene 9 The Trypotophan Operon a Negative control quotonquot by default b Repressor required tryptophan to bind to DNA blocking transcription i Tryptophan acts as corepressor 10 Arbinose Operon a Positive and negative transcriptional control i No arabinose presentforms a loop and does not express genes ii Arabinose presentloops disassembles and l expresses araB araA and araD 11 Global gene regulation a Regulonsset of genes or operons with same regulatory sequences controlled by a single type of regulatory protein can be under positive or negative control 12 ToxR regulon of Vibrio Cholerae a ToxR responds to environmental stimuli to ensure maximum damage Uses TCP to stay in intestines 13 Twocomponent signal transduction system of E coli a Responses to osmolarity so cell does not shrivelburst i ompCsmaller pores so favorable when in high osmotic pressures ii ompFlarger ports so favorable when in diluted environment 1 ompR response disrupts transcription so ompF or ompC isn t made Lecture 5 Gene Expression ln Eukaryotes 1 Mechanisms unique to Eukaryotes a lntrons extrons splisosomes mRNA stability 5 cap and 3 tail 2 Chromatin Remodeling a H1 proteins bring histones wrapped with DNA together to make Chromatin i If DNA is in condensed form gene expression is tuned off default condition 3 DNA Methylation alters chromatin mechanisms a DNA methyltransferasecatalyzes transfer of methyl group to cytosine residues on DNA results in condensation therefore no gene expression 4 Histone modi cation can increase or decrease chromatin condensation a Examples of Functional groups added to histones methyl phosphate short polypeptide acyetl b Histone acetylation i Adding acetyl groups on lysine residues on histones causes decondensation promotes gene expression 5 Chromatin remodeling complexes cause nucleosomes to slide along DNA or histones to disintegrate from DNA thus promoting transcription a Chromatin remodeling can also be inherited 6 Transcription Regulation a Promoterproximal elements regulator sequences close to promoter speci c for different sets of genes b Regulator sequences can be located far from the promoter and even in an intron Enhancer FrauvI39I11ntilssrFEM a E Enhancer Enhaneer 39 l a lJpstreain Pr ml ter EZIII JI39I llntr39cin Exnn llintrun lEIEilI I Dorihall39ear r h proximal a element ncers a regulatory sequences can be far from promoter and even in introns or UTRs i unique to eukaryotes bind with activators can be on either the 3 or 5 side most genes have more than one can work in ipped orientation 3 5 ii comparative to active binding sites of prokaryotes 8 Transcription factors Activatorsbind to enhancers Repressorsbind to silencers Basal transcription factorsbind to promoters During development cells differentiate into a large variety of tissues yet all have the same genome What determines cell regulation i Speci c extracellular signal l speci c signal transduction response activation of speci c transcription factors regulation of speci c gene sets 9 How do Transcription factors recognize where to bind to DNA a Recognize speci c sequences of bases and shapes create by hydrogen bonds 10 What is a gene in Eukaryotes a Portion of DNA that codes for a functional polypeptide or RNA molecule i Differential gene expression in eukaryotes 1 Cellcell communication chromatin remodeling regulatory proteins bind to enhancers and silencers different sets of genes are expressed 006m 11 Transcription Initiation in Eukaryotes a Loosening up of DNA from histones through chromatin remodeling b Exposer of promoter and regulatory sequence c RNA polymerase and basal transcription factors bind around DNA d DNA looping by mediator by binding the enhancers and promoterproximal elements to it 12 Compare and Contrast basal transcription factors and regulatory transcription factors Basal Transcription Factors Regulatory Transcription Factors Bind to promoter Bind to enhancers silencers or promoterproximal elements Not speci c to particular genes or Speci c to particular genes sets or cell types cell types Essential for transcription to occur Regulatory effect modulate but no regulatory effect transcription 13 PostTranscriptional Control a Alternative splicing is the major regularity mechanism in multicellular eukaryotes is the splicing of primary RNA transcripts from a single gene in different ways to produce different mature RNAs and thus different polypeptides 14 RNA Interference a When a tiny singlestranded RNA held by a protein complex bind to complementary sequence of mRNA and destroys or blocks translation i Transcription creates a microRNA gene hairpin structure ii Double stranded erNA formed when enzyme in cytoplasm trims the RNA hairpin into a short double stranded RNA iii Mature RNA formed when binds to RNAinducing Silencing Complex RISC other half of RNA is degraded iv miRNA held by RISC binds to complementary sequence on target mRNA v RISC cuts or prevents transcription of mRNA 15 Other mechanisms to control translation Phosphorylation of regulatory proteins Posttranslational control 16 Cancer and Defects in Gene regulation Tumor suppressor genes Protooncogenes i P53 the guardian of the genomequot ii Prevent mutated cells from populating U9 U9 Bacteria vs Eukaryota Gene Regulation Level of Regulation Bacteria Euka ryotes Chromatin remodeling Limited packaging of DNA Remodeling not a major issue in regulating gene expression Extensive packaging of DNA Chromatin must be opened for transcription to begin Transcription Positive and negative control by regulator proteins that act at sites close to the promoter Sigma interacts with promoter Positive and negative control by regulatory proteins that act at sites closefar from the promoter Large basal transcription complex interacts with promoter Mediator complex required RNA processing None documented Extensive processing alternative splicing of introns addition of 5 and 3 caps mRNA stability 0 Some RNA 0 For many genes inference RNA interference documents limits life span or translation rate Translation 0 Regulatory Regulatory proteins bind to mRNAs andor ribosomes and affect translation rate proteins bind to mRNAs andor ribosome and affect translation rate Posttranslational modi cation Folding by chaperone Folding by chaperone proteins proteins 0 Chemical 0 Chemical modi cations may modi cation change activity 0 Ubiqination targets proteins for destruction by proteasome


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