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by: Ms. Griffin Franecki

Genetics BIOL222

Ms. Griffin Franecki
Penn State
GPA 3.99


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This 0 page Class Notes was uploaded by Ms. Griffin Franecki on Sunday November 1, 2015. The Class Notes belongs to BIOL222 at Pennsylvania State University taught by Staff in Fall. Since its upload, it has received 17 views. For similar materials see /class/233055/biol222-pennsylvania-state-university in Biology at Pennsylvania State University.


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Date Created: 11/01/15
Transforming Principle Frederick Griffith 1928 Figure 8 1 Streptococcus pneumonia Causes pneumonia in humans lethal in mice Strain 19S9normal virulent smooth colony Strain 29R9mutant avirulent rough colony 1 Boil S dead 2 Mix boiled S with live R inject mice 3 Mice die 4 Live S cells recovered from dead mice Interpretation cell debris from S converted live R to live S This process is called transformation Ave MacLeod and McCarty 1944 Figure 8 2 What is the transforming principle Separated various classes of compounds found in boiled S and tested each class for the ability to transform R9 S Only DNA caused transformation DNA encoded the smooth phenotype First demonstration that genes are composed of DNA Many scientists still thought protein was the hereditary material Hershey amp Chase blender experiment 1952 Figure 8 3 Used phage T2 Phosphorous P in DNA Sulfur S in protein Incorporate 3213 into T2 DNA or 35 S into T2 protein Infect E coli 3213 found inside the cell but not 35 S Conclusion DNA is the hereditary material Structure Of DNA DNA is J of 4 quot1 each 39 39 a different nitrogenous base linked to an identical r deoxyribose sugar and a phosphate Figure 8 4 Adenine A Guanine G9purines Cytosine C Thymine T pyrimidines 1 Chargaff s rules A TCGA B TA GC C AT GC 2 X ray crystal data indicating that DNA is long skinny and helical with two similar parts that are parallel to each other 3 Jim Watson amp Francis Crick solved the DNA structure in 1953 Nobel prize Double helix Each helix is composed of two antiparallel strands ie 5 9 and 33995 Each strand is composed of nucleotides held together by phosphodiester bonds that form between the phosphate from one nucleotide and the deoxyribose sugar from the neighboring nt A pairs with T 2 hydrogen bonds G pairs with C 3 hydrogen bonds Purines pair with pyrimidines Figures 8 8 8 5 One strand is complementary to the other B form DNA right hand helix Major and minor grooves Figure 8 9 Implications of DNA structure 1 Suggested a way for DNA replication 2 Suggested that a genetic code in DNA would specify the amino acid sequence in proteins chapter 9 DNA Replication DNA replication is semiconservative Figure 8 1 1 ie Each daughter duplex contains one parental and one newly synthesized daughter strand Parental strands of duplex must be unwound which requires breaking hydrogen bonds Each parental strand serves as a template or mold for synthesis of its complementary strand Figure 8 10 Replication Fork Region of unwound DNA where active replication is taking place Complementary base pairing provides the basis for fidelity of DNA replication ie each template base dictates the complementary base in the new strand Replication is a complex process that requires DNA template nucleotides DNA polymerase and several other enzymes and protein factors Mechanism Of DNA Replication Refer to Figure 8 20 and think 3 D DNA Polymerase catalyzes the reaction that incorporates each dNTP into the growing DNA strand one nt at a time Fig 8 21 Arthur Kornberg Nobel prize late 1950 s for identifying DNA polymerase I from E coli Template dATP dCTP gtReplicated DNA DNA dGTP dTTP dNTP dNMP incorporation pyrophosphate P P E coli 1 DNA Polymerase 193 enzyme activities A 5 93 polymerase activity B 3 95 exonuclease activity that removes mismatched base pairs bp C 5 93 exonuclease activity that degrades dsDNA 2 DNA Polymerase II and 1V9 DNA repair 3 DNA Polymerase III Major polymerase for chromosomal replication Contains gt 20 different polypeptide subunits Initiation DNA pol requires a short DNA or RNA primer for initiation Primer creates a short DNARNA duplex Origin of Replication Fixed point where DNA replication begins dnaA protein disrupts H bonds at the origin ssDNA binding protein ssb9stabilizes ssDNA DNA Helicase Disrupts H bonds holding the two strands together at the replication fork Figure 8 20 Topoisomerase Creates or relaxes supercoils in DNA Primase Synthesizes an RNA primer z 30 nt complementary to the DNA resulting in a duplex RNA primer extended by DNA polymerase III Can t initiate without the primer Figure 8 27 Bidirectional Replication Replication proceeds in both directions thereby synthesizing both strands ending at the terminus Figure 8 22 Leading Strand synthesized continuously Figure 8 28 Lagging Strand synthesized in short discontinuous fragments Okazaki fragments Lagging strand grows in opposite direction of the replication fork Figure 8 30 DNA polymerase I removes RNA primer with its 5 93 exonuclease and fills in ssDNA gaps with 5 93 pol activity DNA Ligase Seals the nicks phosphodiester bonds after primers are removed Exonuclease Editing pol I and pol III possess 3 95 exonuclease activity that serves as a proofreading and editing function by removing mismatched bases incorporated by mistake Proofreading greatly enhances the fidelity of DNA replication Figure 8 38 DNA replication takes z 40 min in E coli about 1000 ntsec Eukaryotic DNA Replication Similar but more complex Telomerase adds simple DNA repeats to the end of the lagging strand because priming cannot occur Uses an RNA template Gradual telomere shortening is linked to cell death Replication takes z 14 hr yeast to z 200 hr in some cells Must coordinate replication of several chromosomes Replication occurs in S phase of the cell cycle Multiple points of origin in each chromosome z 400 for 17 yeast chromosomes Biochemical reactions are catalyzed by enzymes that have a 3 dimensional 3 D structure that are crucial for their function Genes specify the structure of proteins some of which are enzymes therefore genes determine phenotypes of the organism One GeneOne Enzyme Hypothesis Each gene specifies a particular enzyme Gene A Gene B Gene C xlz xlz xlz Enzyme A Enzyme B Enzyme C 1 4 4 final product Genes control biochemical reactions by controlling the production of enzymes If gene B is mutated inactive enzyme B the cell will only survive if supplied with compound 3 or 4 Some enzymes are composed of several different polypeptides All proteins are not enzymes structural and regulatory proteins Thus one gene one enzyme became one gene one polypeptide Protein Structure Proteins are macromolecules composed of amino acids AAs R HZN C COOH 20 different AAs each with a different H R group side chain Table 9 3 AAs are linked by peptide bonds condensation reaction Figure 9 3a Polypeptide several linked AAs Primary 1 Structure Linear array of AAs in a polypeptide Figure 9 7a Secondary 11 Structure Polypeptides fold into repeating structures by forming H bonds between the backbone carbonyl C20 and amino N H groups of different residues oc helix Figure 9 5 S sheet Figure 9 6 Tertiary 111 Structure93D structure of a polypeptide generated by H bonds ionic interactions VanDerWalls forces and disulfide bridges between AA R groups Figure 9 7c Quaternary 1V Structure Two or more folded polypeptides bound together forming a complex Figure 9 7d A change in 1 AA can alter or destroy protein function Some changes don t effect protein function HbA wild type Hbs sickle cell anemia Figure 9 13 Since genes determine the specific primary AA sequence of proteins they determine 11 111 1V as well Colinearity of Genes and Proteins Charles Yanofsky 1960s Linear sequence of nts in a gene 5 93 determines the linear sequence of AAs in a polypeptide N terminus C terminus Enzyme Function Catalyze chemical reactions by breaking and making chemical bonds Substrate molecules bind to a region of the enzyme called the active site AA changes in the active site usually results in inactivity Lock and key model Figure 9 20a Induced fit model Figure 9 20b Many human diseases are caused by blocks in biochemical pathways Table 9 4 Genetics Explained by Biochemistry Recessive allele produces a non functional enzyme a Dominant allele produces a functional enzyme A Negativedominant9 Non functional because one mutant subunit inactivates the entire complex Temperature Sensitive Alleles Substitution of an AA 1 Permissive Temperature Produces a functional protein 2 Nonpermissive Temperature Non functional protein Active site of enzyme unravels at high temp Figure 9 22 Genetic Ratios P AAbb white X aaBB white xl F1 AaBb purple xl F2 9 A B purple 3 A bb white 97 ratio 3 aaB white Complementation 1 aabb white A allele B allele xl xl white enz A white enz B purple precursor 1 gtprecursor 2 gtpigment Transcription RNA polymerase RNAP9catalyzes RNA synthesis 5 93 from one strand of the DNA double helix template strand by complementary base pairing Figures 10 6a 10 1 1 Ribose 2 OH replaces deoxyribose p 300 A C G U Uracil9U replaces T RNA is considered single stranded but it does base pair G C 3 H bonds A U 2 H bonds GCgtAUgtGU G U 2 H bonds 3 Classes of RNA rRNA ribosomal RNA9Component of ribosomes 168 238 SS tRNA transfer RNA9Brings AAs to ribosome during translation mRNA messenger RNA9Intermediate that transfers the genetic information from DNA to proteins Directs protein synthesis RNA pol transcribes the template strand of the DNA RNA is the same sequence as the non template strand except U replaces T In prokaryotes a single RNA polymerase synthesizes rRNA tRNA mRNA RNA can be monocistronic one gene or polycistronic more than one gene Figure 10 6a Holoenzyme ocz mo 6 subunits Core enzyme ocz oo 5 subunits S 39 beta and beta 9polymerization activity 0L2 alpha9interacts with transcription factors chapter 11 00 omega9facilitates RNAP assembly 0 sigma9binds to promoter sequences Different 0 factors allow recognition of different promoter sequences Transcription 3 stages9lnitiation Elongation Termination Initiation Promoter Nucleotide sequence that O recognizes TTGACA TATAAT 1 start of transcript 35 z 17 nt 10 5 8 nt RNA polymerase holoenzyme binds to the promoter unwinds the DNA and catalyzes the incorporation of incoming NTPs via DNA complementarity DNA 339G C A T 5 RNA 5 C G U A3 Energy provided by cleavage of high energy triphosphate as in DNA replication Figure 10 10 Elongation Shortly after initiation s is usually released Transcription continues with the core enzyme Elongation is also subject to regulation Chapter 11 Figure 10 90 Termination RNA pol recognizes signals to terminate transcription Eukaryotes different Rhoindependent termination G C rich RNA stem loop followed by several U residues RNA polymerase dissociates from DNA template and releases the transcript when it encounters this signal Figure 10 12 Rhodependent termination Rho binds to a rut Rho utilization sequence in the nascent transcript C rich sequence Rho translocates along the RNA until it catches RNA polymerase and causes transcription to terminate Figure 10 13a b 0 ATP hydrolysis for translocation Eukaryotic Transcription Transcription in nucleus translation in cytoplasm usually ie RNA is transported from nucleus to cytoplasm RNA pol I rRNA RNA pol II mRNA the vast majority are monocistronic RNA pol III tRNA snRNA Transcription is similar to prokaryotes except different promoter sequences and more RNA polymerase subunits Eukaryotic RNA Processing In the nucleus Figure 10 15 1 5 cap added 7 methyl G Figure 10 15b 2 Poly A tail added to 3 end of transcript Figure 10 15de PolyA tails are also added to prokaryotic mRNA 3 Splicing removes introns Figure 10 17 exon intron exon9exon exon intron Splicng Small nuclear ribonucleoprotein complexes snRNPs catalyze removal of introns Via splicing Some introns are self splicing RNA quotenzymequot called a riboyme Tom Cech Nobel Prize 1989 Also occurs in a few phage transcripts and bacterial tRNAs Introns allow rapid generation of new genes by exon shuf ing thus new proteins rRNA Processing 1E coll Not in book A 30S primary transcript is processed into 16S 23S 5S rRNAs 5 16S 23S 5S 3 RNase III is responsible for processing 16S and 23S RNase E is responsible for processing 5S Translation Conversion of genetic info encoded in mRNA into proteins Genetic Code Nucleotides are letters in the code Figure 10 27 3 nts form the words codons representing different AAs ie 3 nt triplet codon non overlapping 20 AAs and only 4 different nts 4364 words codons 64 triplet codons but only 20 amino acids Genetic code is redundant degenerate ie most AAs represented by more than one codon Reading Frame The frame in which the triplet codons specify the AAs in a protein eg 5 GCCAUACGCCUACUUGG 3 Frame 1 Frame 2 Frame 3 The genetic code is universal EXCEPT for a few differences in mitochondrial DNA and in the nuclear DNA of some protozoans Thus the genetic code is NOT universal tRNA Recognition of Codons Anticodons in tRNA recognize the codons in mRNA by base pairing Figure 10 28 tRNA and rRNA genes are genes that do not code for proteins Wobble Not a different tRNA for each codon In some cases the 3rd position in the anticodon 5 can pair with more bases than its normal complementary base eg GU Figure 10 28 Table 10 5 Stop Codons UAA UAG UGA Figure 10 27 No corresponding tRNA Signals the termination of protein synthesis tRNA Chargng ATP ADP AA1 tRNA1 gt AAl tRNA charged tRNA tRNA synthetase charged tRNA 2 aminoacylated tRNA tRNA synthetase is an enzyme that charges aminoacylates tRNA Ribosomes Huge complexes consisting of about SO prokaryotes or 80 eukaryotes polypeptides and rRNA Sites of protein synthesis translation Prokaryotes Figure lO 30a SOS subunit 3OS subunit97OS ribosome SOS subunit contains 23S and SS rRNA 3OS subunit contains 16S rRNA Eukaryotes Figure lO 30b 60S subunit 4OS subunit 80S ribosome 60S subunit contains 28S and SS AND S8S rRNA 4OS subunit contains 18S rRNA Translation initiation elongation termination Initiation Fig 10 33 Requires mRNA ribosomes charged tRNAs initiation factors In prokaryotes the first AA is N formylmethionine and is inserted by initiator tRNA tRNAme Uses normal met codon and anticodon Ribosome binding site rbs9 Sequence on mRNA Shine Dalgarno sequence is complementary to the 3 end of 16S rRNA 1 mRNA binds to the 30S ribosomal subunit by base pairing with the 3 end of the 16S rRNA 2 fMet tRNA binds to the P peptidyl site on 3OS 3 SOS ribosomal subunit binds97OS ribosome Elongation Requires elongation factors 1 Aminoacyl tRNA binds to the A site 2 Peptide bond is formed by peptidyltransferase Thistransfers the growing peptide chain to the AA at the A site Peptidyltransferase activity is part of 23S rRNA 3 Ribosome translocates by moving one codon along mRNA tRNA at P site is removed and newly formed peptidyl tRNA moves to P site 4 Process is repeated Figure 10 36 GTP hydrolysis drives ribosome assembly AA tRNA binding and ribosome translocation Termination 1 Release factors proteins recognize the stop codons Not tRNA 2 Polypeptide is released from ribosome by cleavage from tRNA 3 Ribosome dissociates into 2 subunits mRNA is released Figure 10 37 Animation 1002A In prokaryotes transcription and translation are coupled Important for transcription attenuation Chapter 11 Eukaryotes transcription in the nucleus Until recently it was assumed that translation only took place in the cytoplasm It now appears that translation can take place in the nucleus or cytoplasm Coupled transcription and translation Regulation of gene expression involves protein nucleic acid and protein protein interactions Regulation occurs at several levels H Initiation of transcription Repression Activation N Transcript elongation RNA pol Pausing and Arrest 9 Regulated Termination Attenuation Antitermination 4 mRNA stability Steady state level of mRNA 01 Efficiency of translation rbs Codon usage Operon Genetic unit of coordinate expression eg lacPOZYA Figure 11 1 Promoter P9 Specific nucleotide sequence 39 J by the sigma subunit 0 of RNA r eg 10 amp 35 sequences Different promoters are recognized by alternative 0 factors Operator 09 Specific nucleotide sequence recognized by the repressor Often overlaps the promoter Sequence Structural Genes ZYA9Encode mRNAs proteins lac operon lacPOZYA gt1000 fold regulation Figure 11 1 Utilization of lactose as a carbon and energy source Induction Relief of Repression9requires inducer to inactivate repressor The lac operon is negatively regulated by LacI repressor In the absence of inducer lactose LacI binds to the operator and blocks RNA polymerase Inducer binds to repressor repressor can39t bind to operator RNA pol binds to promoter transcription translation Animation 1101A lacI39 9mutations in the lac gene that result in constitutive expression always on9caused by AA changes in the DNA binding domain of the protein lac is trans dominant with respect to lacI39 ie Wild type LacI can be supplied in trans diffusible product on a plasmid which complements the defect Figure 11 6 Animation 1101C lacIs mutated inducer binding domain of the repressor Ssuper repressor No induction by lactose or IPTG always off 6ch is trans recessive with respect to ads ie Wild type LacI is not able to bind to the operator if LaclS is already bound to operator DNA Figure 11 7 Animation 1101D lac009 operator constitutive mutations mutation in the operator DNA sequence prevents repressor binding always on lacOc mutations are cis dominant ie Wild type lacO supplied in trans has no effect on the operon containing the lacOc mutation Figure 11 8 Animation 1101B Activation Positive transcription initiation regulatory mechanisms activation require protein factor activator binding to allow maximum expression of the operon eg cAMP CAP control of lac operon Superimposed on the repressioninduction system Catabolite Repression glucose is used for carbon and energy source before other sugars are used Regulation is mediated by the catabolite activator protein CAP and cyclic adenosine monophosphate cAMP High glucose9low cAMP Low glucose9high cAMP cAMP binds to and activates CAP cAMP CAP complex activates expression of lac operon by binding near the promoter Bound CAP facilitates RNA pol binding by protein protein interactions with the oc subunits of RNA pol Figure 11 12a d Dual Positive and Negative Control eg arabinose operon CaraBAD Figure 11 16 Negative control mechanism In the absence of arabinose AraC binds to the initiator and to the operator resulting in the formation of a DNA loop DNA loop prevents transcription by blocking cAMP CAP complex and RNA pol binding Positive control mechanism 1 Arabinose binds to araC protein AraC 2 Arabinose AraC complex binds to initiator region near the promoter 3 cAMP CAP complex binding is also required 4 Binding of both complexes facilitates RNA pol binding to the promoter 5 Transcription of araBAD synthesis of enzymes utilization of arabinose as carbon and energy Source Feedback I 39 quot Renression and A quot Tryptophan biosynthesis in E coli trpEDCBA Figure 11 19 Feedback Inhibition High tryptophan Tryptophan binds to the first enzyme in the biosynthetic pathway TrpED complex This prevents enzyme activity which prevents tryptophan synthesis Negative Control ggepressionl trp repressor TrpR encoded by trpR High tmptophan 1 TrpR activated by tryptophan binding 2 Activated TrpR binds to operator 3 Prevents RNA pol binding 100 fold regulation 4 Transcrintion A 39 any 39 that results in premature termination of transcription trpR39 mRNA synthesized in the presence of tryptophan R emoval of tryptophan from the growth medium resulted in an additional 10 fold increase in trp mRNA Deletions identified the attenuator located in the trp mRNA leader Figure 11 20a Attenuation requires coupled transcription and translation Leader peptide encoded by a quotminiquot gene 14 AA Two tandem trp codons are present in the middle of the mini gene Figure 11 21 If high tryptophan high charged tRNAtrP Thus tandem trp codons are efficiently translated If low tryptophan low charged tRNAtrP Thus ribosome stalls at tandem trp codons 1 Initiation of transcription 2 RNA pol transiently pauses at stem loop 12 pause structure Figure 11 20a 3 Ribosome initiates translation of the leader peptide thereby releasing the paused RNA pol complex Results in coupled transcription translation If tryptophan excess Figure 11 20b 4 Ribosome translates tandem trp codons and continues to the stop codon in stem part 1 Thus the ribosome interacts with stem part 2 5 Transcription continues Stem loop 23 antiterminator structure does not form because the ribosome blocks its formation 6 Stem loop 34 forms Rho independent terminator promoting transcription termination If limiting tryptophan Figure 11 20c 4 Ribosome stalls at tandem trp codons No interaction with stem part 2 5 As transcription continues stem loop 23 antiterminator forms thereby preventing terminator 34 formation 6 Transcription continues into the tip structural genes transcriptional read through The decision to terminate transcription or to allow transcription to proceed into the structural genes depends on whether the antiterminator or terminator forms This in turn depends on whether the ribosome can translate the tandem tip codons This in turn depends on the availability of charged tRNAtrP This in turn depends on the tryptophan in the cell Everything depends on which of the mutually exclusive RNA II structures form Translational Regulation A Codon usage rare codons slow up translation resulting in lower expression levels Protein binding to the ribosome binding site rbs blocks initiation of translation by blocking ribosome binding Sequestration of the RES in an RNA secondary structure mRNA is unable to base pair with the 3 end of 16S rRNA Prevents translation initiation Gene Regulation in Eukaryotes All mRNAs are transcribed by RNA pol II Eukaryotic Promoters Required for initiation Figure 11 25 GGGCGG CCATT TATA 1 TATA box TATA binding protein TBP Directs RNA pol to initiate transcription downstream CAT box and G C box Not present in all cases Positions can vary from promoter to promoter All 3 elements are recognized by protein factors to enable RNA pol to bind and initiate transcription Enhancers Greatly increase transcription initiation at promoters Regulatory proteins bind to enhancer elements 1 Can be several kb away from promoter 2 Can be in either orientation 3 Can be 5 or 339 of promoter 4 Can be tissue specific eg DNA binding protein only present in some cell types Leads to differential gene expression Different genes expressed in different tissues Steroid hormones somewhat analogous to bacterial cAMP Effect gene expression of a subset of genes eg Estrogen activates transcription by binding to an activator protein that binds to a tissue specific enhancer TBP and TBP associated factors TAFs constitute TFHD TFIID and other TFII complexes constitute the general basal transcription factors Figure 11 29a These factors interact with RNA pol and form a preinitiation complex via protein nucleic acid and protein protein interactions Many TAFs and trans acting factors activators have 2 domains 1 DNA binding domain 2 Transcription activation domain ie interact with other protein factors Initiation complex Figure 11 28 Ordered assembly of an enormous complex consisting of several factors including the basal factors activators and RNA pol Forms a DNA loop via protein protein interactions bringing together the active complex DNABinding Motifs HelixTurnHelix One of the two oc helices interacts with the major groove of the double helix Figure 11 40 Zinc Finger Zinc atom complexed by histidine and cysteine residues Figure 11 41 Leucine Zipper Protein dimers form by hydrophobic interactions between leucine residues spaced 7 AAs apart present in each subunit HelixLoopHelix Form dimers without a zipper Interface between dimers formed by interactions between the 2 helices and the loop Leucine zippers and helix loop helix proteins can be homodimers or heterodimers Heterodimers increase the number of usable DNA sequences and the variety of protein combinations that can be used to turn genes on and off


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