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This 6 page Study Guide was uploaded by Emily Engelbrecht-Wiggans on Friday October 30, 2015. The Study Guide belongs to Biol 2002 at University of Minnesota taught by Dr. Peter Tiffin in Summer 2015. Since its upload, it has received 43 views. For similar materials see Foundations of Biology 1 in Biology at University of Minnesota.
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Date Created: 10/30/15
Chapter 16 How Genes Work I How Genes work a Particular alleles are associated with certain phenotypes alleles don t change from parent to offspring b Genes are found in chromosomes sequence of DNA that can be transcribed c Gene expression process of converting archived info into molecules 11 What do genes do a Knockouts are nonfunctioning alleles b Genes contain info needed to make an enzyme protein c Metabolic pathway series of steps to synthesize organic molecules 111 Central Dogma a DNAgtRNAgtproteins b Genotype determined by sequences of bases in DNA c Phenotype is the product of proteins the genotype produces d Exceptions i Many genes code for RNA that don t go to proteins ii Sometimes RNA ows back into DNA IV The Genetic Code Rules that specify the relationship between a sequence of nucleotides in DNA or RNA amp the sequence of amino acids in protein Triplet code 3base code provides more than enough quotwordsquot to code for all 20 amino acids Codon group of 3 bases that specifics a particular amino acid Reading frame sequence of codons Analyzing the code i Redundant amino acids can be coded by more than 1 codon ii Unambiguous codon always codes for same amino acid iii Nonoverlapping universal iv Conservative when several codons specify the same amino acid the first 2 bases in those codons are almost always identical making individuals less vulnerable to small errors in DNA sequence EDPPF Chapter 17 Transcription RNA Processing amp Translation 1 An Overview of Transcription a NTP making sugar ribose starts transcription b RNA polymerase cleaves off 2 phosphates amp catalyzes formation of phosphodiester linkage between 3 end of growing mRNA chain amp the new ribonucleoside monophosphate 5 to 3 matching c Energy from P bonds in nucleotide triphosphates that serve as substrates II Bacterial transcription a Sigma attaches to polymerase forms holoenzyme i Determines where amp direction of translation b Promoters recruit RNA polymerase 5 3 adds to 3 end i 4040 base pairs long has 10 box where transcription begins c Termination ends transcription in bacteria RNA folds into hairpin unreactive state 111 Eukaryotic Transcription a 3 polymerases b most promoters have a TATA box sequence c basal transcription factors assemble at promoter amp RNA polymerase follows no sigma d transcription ends variable distances from polyA signal IV RNA processing in Eukaryotes a Exons parts of premRNA that are expressed b lntrons get cut out from premRNA c Splicing removes introns in nucleus i Catalyzed by snRNA s working with complex proteins 1 Proteins amp macromolecule machine known as snRNP s ii snRNP s bind to 5 exonintron boundary iii other snRNP s arrive amp form splicosome iv intron forms a loop amp a single stranded stem lariat v lariat cut out phosphodiester links between exons d 5 cap and polyAtail i protect mRNA s from degradation by ribonucleases V Intro to Translation 5 3 a In bacteria RNA transcribedtranslated simultaneously b mRNA triplet specifies amino acid with adapter molecule VI Structure amp Function of Transfer RNA a Lshaped tertiary structure 1 leg has anticodon the other has amino acid b wobble pairingquot allowed in 3rd codon so 40 tRNA needed to translate the 61 codons VII Structure amp Function of Ribosomes a 3 tRNA s during synthesis move 1 position left as transcription occurs i tRNA s have amino acids covalently attached contain anticodon ii far right carries amino acid A site iii middle holds growing peptide chain P site iv no longer has amino acid attached about to leave E site b Initiating Transcription i mRNA binds to small ribosomal subunit ii initiator aminoacyl tRNA bearing fmet binds to start codon iii large subunit binds completing complex where peptidebond formation takes place c Elongation i Peptidebond formation occurs when tRNA s in EampA sites catalyzed by ribozymes ii Occurs 5 gt 3 d Terminating Translation i Stop codon release factor lls A site freeing polypeptide e PostTranslational Modifications i Folding speeded up by molecular chaperons ii Chemical modifications ex sugarlipid added or P group addedremoved VIII Helpful Tidbits rRNa component of ribosomes most abundant form of RNA a mutation that deletes base pairs from the 1 site inhibits sigma from binding to promoter transcription RNA processing involve premRNA snRNA mRNA translation involves tRNA rRNa not used in protein synthesis RNA primers translation starts at start codon transcription begins near promoter Wrap99 Chapter 15 DNA amp the Gene Synthesis amp Repair 1 What are Genes Made of a Primary structure sugarphosphate backbone amp sequence of Ncontaining bases b Secondary structure of DNA i Deoxyribonucleotides link when phosphodiester bond forms between hydroxyl on 3 carbon with P group on 5 carbon 11 DNA Synthesis Hypothesis a Semiconservative replication parent strands separate amp used as template for daughter strands old 12 new CORRECT conservative replication bases turn out for replication 1 new amp old stys same c dispersive replication parent strands cut whenever one strand crosses over another so DNA synthesized in short sections by extending each of the cut parent strands to the next crossover stretches of old and new DNA 111 Model for DNA synthesis 5 3 a DNA polymerase catalyzes DNA synthesis Replication bubble forms at origin of replication amp grows in 2 directions during replication c Replication fork parent DNA double helix splits into 2 strands i Opened by DNA helicase breaks H bonds ii Singlestrand DNA binding proteins ssBP s prevent strands from rejoining iii Topoisomerase cuts DNA before fork to allow it to unwind amp then rejoins it d Leading Strand 5 to 3 i RNA primer bonded to template strand ii Primase synthesizes short RNA stretch to be DNA polymerase primer iii Sliding clamp follows DNA polymerase enzyme amp holds it in place on template strand e Lagging Strand i DNA polymerase 1 attaches to 3 end as it moves 5 to 3 removes RNA primer ii DNA ligase join Okazaki fragments iii Replisome proteins for DNA synthesis joined together in large macromolecule IV Replicating the Ends of Linear Chromosomes a Telomere region at end of eukaryotic chromosome b Telomerase prevents chromosome shortening lagging strand becomes slightly longer c Chromosomes without telomerase shorten every cell division until their telomeres reach critical length and can t divide any more V Repairing Mistakes amp DNA Damage a DNA polymerase proofreads active site can detect nucleotide shapes i Epsilon subunit on DNA polymerase 3 acts as an exonuclease removes deoxyribonucleotides from the ends of DNA strands b Mismatch repair i Mismatched bases are corrected after DNA synthesis is complete c Repairing Damaged DNA i Nucleotide exclusion repair enzyme recognizes thymine dimer another enzyme removes defective sequence amp replaces with correct sequences VI 164 Mutation Modifies Genes amp Chromosomes a mutation any permanent change in an organisms DNA creates new alleles rare b point mutation single base change i missense mutation causes amino acid change in protein ii silent mutation doesn t change amino acid sequence in protein iii frameshift mutation addition deletion of a nucleotide iv nonsense mutation codon specified by amino acids altered to stop codon c Chromosomal mutations i Olyploidy increase in of each type of chromosome ii Aneuploidy addition deletion of individual chromosome iii Inversion segments ipped amp rejoined iv Translocation segments become attached to a different chromosome v Deletion section of chromosome lost vi Duplication additional copies of a segment are present d Karyotype complete set of chromosomes in a cell VII 123 Control of the Cell Cycle a Variation in length of G1 phase i G1 checkpoint 1 Cell size adequate enough nutrients social signals present DNA undamaged b MPhase i Checkpoint 1 Regulates onset of anaphase chromosomes attached to spindle apparatus 2 Progression through M to G1 chromosomes properly separated amp MPF absent ii M phasepromoting factor MPF indices M phase in eukaryotes in cytoplasm 1 Contains protein kinase amp a cyclin a Kinases are regulatory proteins concentration constant b Cyclins concentration uctuate during cell cycle c Cyclindependant kinase CdK kinase in MPF only function when attached to cyclin only i Catalyzes phosphorylating of one active site turns on 2 active sites turns off negative feedback VIII 121 Cell Cycle a M phase Interphase G1 S chromosomes replicate G2 phases ggapgrowth IX 124 Cancer OutofControl Cell Division malignant tumors cancerous invasive benign tumors non cancerous noninvasive metastasis cancer calls that spread from primary tumor to secondary site cancer involves defects in G1 checkpoint committed to replicating DNA amp entering G2 social control i individual cells should only divide when it s best for whole organism G1 Checkpoint i Rb prevents progression to S phase ii G1 cyclinCdk complexes trigger progression to S phase X Extra helpful Tidbits a Proteins Ras amp p53 are often found to be defective in cancer cells allowing for uncontrolled growth hpogre Lh Chapter 18 Control of Gene Expression in Bacteria I An overview of Gene Regulation and Information Flow a Changes in gene expression allow bacterial cells ro respond to environmental changes b Transcription control DNA doesn t go to mRNA slow but most energy efficient c Translation control mRNA doesn t go to proteins d Posttranslational control proteins have to be activated to be functional quickest but energy costly e Inducer small molecule tat triggers transcription of a specific gene II Identifying Regulated Genes a Mutagens things that damage DNA and increase mutation rates b Constitutive transcription happens continuously c Replica plating technique for identifying mutant that cannot grow in particular conditions d Several genes are involved in lactose metabolism i Code proteins lacZ cleaves lactose lacY transports lactose into cell 1 Close together on gene could be transcribed together ii Regulatory protein lacl constitutive expression of lacZ amp lacY don t need inducer III Negative Control of Transcription a Repressor binds to DNA operator amp shuts down transcription b Positive control activator binds to DNA amp triggers transcription c The Operon Model i Operon set of coordinately regulated bacterial genes transcribed together into 1 mRNA cluster of genes with adjacent promoter amp operator ii lacA codes for enzyme transacetylase allows certain types of sugars to be exported from cell 1 adjacent to lacZ amp lacY 2 cotranscription adjacent genes transcribed into 1 mRNA initiated from single promoter on operon 3 allosteric regulation small molecule binds to protein amp causes change in its shape activity d glucose inhibits the transport of lactose into cell inducer exclusion e activity of key regulatory proteins is controlled by posttranslational modifications IV positive control of transcription a activator interacts with RNA polymerase to increase rate of initiating transcription V Global Gene Regulation coordinated regulation of man genes a Regulon a set of separate gens or operons that contain the same regulatory sequences and are controlled by a single type of regulatory protein b When an environmental change triggers the removal of the repressor protein from all the operators every gene on the regulon is transcribed Chapter 19 Control of Gene Expression in Eukaryotes 1 Differential Gene Expression creates different cell types 11 Gene Regulation in Eukaryotes An Overview a Control at transcription translation amp post translation but also i Chromatin structure of DNA wrapped around proteins 1 Must be remodeled before transcription ii RNA processing if different cells use diff splicing patterns diff genes are produced iii mRNA lifespan is regulated Ill Chromatin Remodeling a Basic Structure i Histone are most abundant DNA associated protein ii Nucleosome beads on the quotstringquot chromatin is the necklace 1 DNA wrapped 2 times around 8 histone core 2 Between pairs of nucelosomes there is a linker stretch of DNA 3 Histones pack tightly together into what s called a 30nm fiber 4 30nm fiber attached at intervals along length to form scaffold b Chromatin must decondense to expose the promoter RNA polymerase binds to i Protected from DNase which cuts DNA c Absence of histones promotes transcription d DNA Methytransferases add methyl CHs to cytosine residues in DNA alter chromatin i Actively transcribed genes have low levels of methylated Cp6 near promoters e Histone Modification i Histone code a particular combination of histone modifications set the state of chromatin condensation for a particular gene ii Histone acetyltransferases HATs add acetyl groups to positive lysine 1 Results in decondensed chromatin iii Histone deacetylases HDACs remove acetyl groups from positive lysines f ChromatinRemoldeling Complexes i Macromolecular machines that harness ATP to reshape chromatin g Chromatin modifications can be inherited i Epigenetic inheritance collective term for pattern of inheritance due to differences other than differences in DNA sequences ii Regulatory region section of DNA involved in controlling activity of gene IV Initiating transcription Regulatory sequences amp regulatory proteins a TATA box most intensively studied eukaryotic promoter b TATAbinding protein TBP binds to TATA box type of basal transcription factor c Promoterproximal elements are regulatory sequences near the promoter i Coregulated genes share a regulatory DNA sequence that binds to the same regulatory protein ii Have sequences that are unique to specific sets of genes d Enhancers are regulatory sequences far from the promoter i Usually have binding sites for more than 1 protein ii Most genes have more than one enhancer iii Can work even if normal 5 to 3 is ipped or if moved to a new location iv Transcriptional activators regulatory proteins that being transcription after bings to the enhancers v Silencers DNA sequences that inhibit transcription e Transcription factors PROTIENS can recognize DNA bases that are partially exposed in the major and minor grooves of DNA helixes by differences in composition and shape f A model for Transcription initiation i Transcription factors must interact with regulatory proteins to initiate transcription ii Basal transcription factors 1 Proteins that interact with promoters and are not restricted to particular genes or cell types iii Mediator acts as a bridge between regulatory and basal transcription factors amp RNA polymerase iv Chromatin is dynamic DNA occasionally dissociates from nucleosomes g Steps i Transcriptional activators bind to DNA amp recruit chromatinremodeling complexes amp HATs ii Those open up swath of chromatin including promoter promoterproximal elements amp enhancers iii other transcriptional activators bind to newly exposed enhancers amp promoter proximal elements basal transcription factors bind to the promoter amp recruit RNA polymerase 2 iv mediator connects transcriptional activators amp basal transcription factors that are bound to DNA made possible through DNA looping RNA polymerase 2 can now begin transcription V PostTranscriptional Control a Splicing RNAs modifying lifespan of mRNAs altering the rate at which transcription is initiated activating or inactivating proteins after translation has occurred b mRNA stability amp RNA Interference i RNA interference when single stranded RNA held by protein complex binds to a complementary sequences in an mRNA this destroys either the mRNA or a block of the mRNA s translation ii Ubiquitin enzymes that mark cells to be destroyed iii Proteasome macromolecule that recognizes proteins with ubiquitin tag amp cuts them into short segments VI Comparison of Bacterial and Eukaryotic Gene Expression a DNA packaging Euk default DNA state is condense amp inactive bacteria is active b Complexity of transcription amp complexity of protein interactions in euk dwarfs bacteria s c Coordinated transcription i Bact genes organized into operons amp transcribed together from a single promoter ii Euk operons are rare scattered genes expressed together when same regulatory transcription factors trigger transcription of genes with same DNA reg sequences d Greater reliance on posttranscriptional control euk make greater use Bacteria sigma interacts with promoter f Euk basal transcription factors interact with promoters mediator required ubiquitination need to respond to signals from other cells much more than bacteria need to VII Linking Cancer with defects in gene regulation a Protooncogenes genes that stimulate cell division i Mutation of called an oncogene an allele that promotes cancer development b The p53 tumor suppressor i Codes for a regulatory transcription factor 1 cell cycle regulation DNA repair amp apoptosis ii guardian of the genomequot VIII Useful tidbits a Analogy promoter is the doorknob promoters of many operons are similar operator is the keyhole each door locked by a specific key the key is a specific regulatory protein D
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