Bài giảng Molecular Biology - Chapter 3 An Introduction to Gene Function

Molecular BiologyFifth EditionChapter 3An Introduction to Gene FunctionLecture PowerPoint to accompanyRobert F. WeaverCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.13.1 Storing InformationProducing a protein from DNA involves both transcription and translationA codon is the 3 base sequence that determines what amino acid is usedTemplate strand is the DNA strand that is used to generate the mRNANontemplate strand is not used in transcription2Protein StructureProteins are chain-like polymers of small subunits, called amino acidsDNA has 4 different nucleotides (A,G, C, T)Proteins have 20 different amino acids with:An amino groupA hydroxyl groupA hydrogen atomA specific side chain3PolypeptidesAmino acids are joined together via peptide bondsChains of amino acids are called polypeptidesProteins are composed of 1 or more polypeptidesPolypeptides have polarityFree amino group at one end is the amino- or N-terminusFree hydroxyl group at the other end is the carboxyl- or C-terminus4Types of Protein Structure (4)The linear order of amino acids is a protein’s primary structureInteraction of the amino acids’ amino and carboxyl groups gives rise to the secondary structure of a proteinSecondary structure is the result of amino acid and carboxyl group hydrogen bonding among near neighborsCommon types of secondary structure:a-helixb-sheet5Helical Secondary StructureIn a-helix secondary structure polypeptide backbone groups H bond with each otherThe dashed lines indicate hydrogen bonds between nearby amino acids6Sheet Secondary StructureThe b-sheet pattern of 2° structure also occurs when polypeptide backbone groups form H bonds In the sheet configuration, extended polypeptide chains are packed side by sideThis side-by-side packing creates a sheet appearance7Tertiary StructureThe total three-dimensional shape of a polypeptide is its tertiary structure A prominent aspect of this structure is the interaction of the amino acid side chainsThe globular form of a polypeptide is a roughly spherical structure8Protein DomainsCompact structural regions of a protein are referred to as domains Immunoglobulins provide an example of 4 globular domainsDomains may contain common structural-functional motifs Zinc fingerHydrophobic pocketQuaternary structure is the interaction of 2 or more polypeptides9SummaryProteins are polymers of amino acids linked through peptide bondsThe sequence of amino acids in a polypeptide (primary structure) gives rise to that molecule’s: Local shape (secondary structure)Overall shape (tertiary structure)Interaction with other polypeptides (quaternary structure)10Protein FunctionProteins:Provide the structure that help give cells integrity and shapeServe as hormones carrying signals from one cell to anotherBind and carry substancesControl the activities of genesServe as enzymes that catalyze hundreds of chemical reactions11Relationship Between Genes and Proteins1902 Dr. Garrod suggested a link between a human disease and a recessive geneIf a single gene controlled the production of an enzyme, lack of that enzyme could result in the buildup of homogentisic acid which is excreted in the urineShould the gene responsible for the enzyme be defective, then the enzyme would likely also be defective12One-Gene/One-PolypeptideOver time many experiments (i.e., Beadle and Tatum) have built on Garrod’s initial workMany enzymes contain more than one polypeptide chain and each polypeptide is usually encoded in one geneThese observations have lead to the one gene one polypeptide hypothesis:Most genes contain the information for making one polypeptide13Information CarrierIn the 1950s and 1960s, the concept that messenger RNA carries information from gene to ribosome was developedAn intermediate carrier was needed as DNA is found in the nucleus, while proteins are made in the cytoplasmTherefore, some type of molecule must move the information from the DNA in the nucleus to the site of protein synthesis in the cytoplasm14Discovery of Messenger RNARibosomes are the cytoplasmic site of protein synthesisJacob and colleagues proposed that messengers, an alternative of non-specialized ribosomes, translate unstable RNAsThese messengers are independent RNAs that move information from genes to ribosomes15Experiment to Test the mRNA Hypothesis16Crick and Jacob ExperimentsRadio-labeled phage RNA in experiments was found to be associated with old ribosomes whose rRNA was made before infectionrRNA doesn’t carry information from DNAA different class of unstable RNAs associate transiently with ribosomes17SummaryMessenger RNAs carry the genetic information from the genes to the ribosomes, which then synthesize polypeptides18TranscriptionTranscription follows the same base-pairing rules as DNA replicationRemember U replaces T in RNAThis base-pairing pattern ensures that the RNA transcript is a faithful copy of the geneFor transcription to occur at a significant rate, its reaction is enzyme mediatedThe enzyme directing transcription is called RNA polymerase19Synthesis of RNA20Phases of TranscriptionTranscription occursin three phases:InitiationElongationTermination21InitiationRNA polymerase recognizes a specific region, the promoter, which lies just upstream of geneThe polymerase binds tightly to the promoter causing localized separation of the two DNA strandsThe polymerase starts building the RNA chain by adding ribonucleotidesAfter several ribonucleotides are joined together the enzyme leaves the promoter and elongation begins22ElongationRNA polymerase directs the addition of ribonucleotides in the 5’ to 3’ directionMovement of the polymerase along the DNA template causes the “bubble” of separated DNA strands to move alsoAs the RNA polymerase proceeds along the DNA, the two DNA strands that have opened for the “bubble” reform the double helix behind the transciptional machinery 23Transcription and DNA ReplicationTwo fundamental differences between transcription and DNA replicationRNA polymerase only makes one RNA strand during transcription, it copies only one DNA strand in a given geneThis makes transcription asymmetricalReplication is semiconservativeDNA melting is limited and transient during transcription, but the separation is permanent in replication24TerminationAnalogous to the initiating activity of promoters, there are regions at the other end of genes that serve to terminate transcriptionThese terminators work with the RNA polymerase to loosen the association between the RNA product and the DNA templateAs a result, the RNA dissociates from the RNA polymerase and the DNA and transcription stops25Important Note about ConventionsRNA sequences are written 5’ to 3’, left to rightTranslation occurs 5’ to 3’ with ribosomes reading the message 5’ to 3’Genes are written so that transcription proceeds in a left to right directionThe gene’s promoter area lies just before the start area, said to be upstream of transcriptionGenes are therefore said to lie downstream of their promoters26SummaryTranscription takes place in three stages:InitiationElongationTerminationInitiation involves the binding of RNA polymerase to the promoter, local melting and forming the first few phosphodiester bondsDuring elongation, the RNA polymerase links together ribonucleotides in the 5’ to 3’ direction to make the rest of the RNAIn termination, the polymerase and RNA product dissociate from the DNA template27Translation - RibosomesRibosomes are protein synthesizing machinesRibosome subunits are designated with numbers such as 50S or 30SNumber is the sedimentation coefficient - a measure of speed with which the particles sediment through a solution spun in an ultracentrifuge based on mass and shapeEach ribosomal subunit contains RNA and protein28Ribosomal RNAThe two ribosomal subunits both contain ribosomal RNA (rRNA) molecules and a variety of proteinsrRNAs participate in protein synthesis but do NOT code for proteinsNo translation of rRNA occurs29SummaryRibosomes are the cell’s protein factoriesBacteria contain 70S ribosomesEach ribosome has 2 subunits50 S30 SEach subunit contains rRNA and many proteins30tRNA: Translation Adapter MoleculeGenerating protein from ribosomes requires change from the nucleic acid to amino acidThis change is described as translation from the nucleic acid base pair language to the amino acid languageCrick proposed that some type of adapter molecule was needed to provide the bridge for translation, perhaps a small RNAThe physical interface between the mRNA and the ribosome31Transfer RNA: Adapter MoleculeTransfer RNA is a small RNA that recognizes both RNA and amino acidsA cloverleaf model is used to illustrate tRNA structureThe 3’ end binds to a specific amino acid The anticodon loop contains a 3 base pair sequence that pairs with complementarity to a 3 base pair codon in mRNA32Codons and AnticodonsEnzymes that catalyze attachment of amino acid to tRNA are aminoacyl-tRNA synthetasesA triplet in mRNA is called a codonThe complementary sequence to a codon found in a tRNA is the anticodon33SummaryTwo important sites on tRNAs allow them to recognize both amino acids and nucleic acidsOne site binds covalently to an amino acidThe site contains an anticodon that base-pairs with a 3-bp codon in the mRNAtRNAs are capable of serving the adapter role and are the key to the mechanism of translation34Initiation of Protein SynthesisThe initiation codon (AUG) interacts with a special aminoacyl-tRNAIn eukaryotes this is methionyl-tRNAIn bacteria it is a derivative called N-formylmethionyl-tRNAPosition of the AUG codon:At start of message AUG is initiatorIn middle of message AUG is regular methionineShine-Dalgarno sequence lies just upstream of the AUG, functions to attract ribosomesUnique to bacteriaEukaryotes have special cap on 5’-end of mRNA35Translation ElongationDuring initiation the initiating aminoacyl-tRNA binds within the P site of the ribosome Elongation adds amino acids one at a time to the initiating amino acidThe first elongation step is binding second aminoacyl-tRNA to the A site on the ribosomeThis process requires:An elongation factor, EF-TuEnergy from GTPThe formation of a peptide bond between the amino acids36Overview of Translation Elongation37Termination of TranslationThree different codons (UAG, UAA, UGA) cause translation terminationProteins called release factors (not tRNAs) recognize these stop codons causingTranslation to stopThe release of the polypeptide chainThe initiation codon and termination codon at the ends of the mRNA define an open reading frame (ORF)38Structural Relationship Between Genes, mRNA and ProteinTranscription of DNA does not begin or end at same places as translationTranscription begins at the transcription initiation site dependent upon the promoter upstream of the geneTranslation begins at the start codon and ends at a stop codonTherefore mRNA has a 5’-untranslated region/ 5’-UTR and a 3’-UTR or portions of each end of the transcript that are untranslated393.2 ReplicationGenes replicate faithfullyThe Watson-Crick model for DNA replication assumes that as new strands of DNA are made, they follow the usual base-pairing rules of A with T and G with CSemiconservative replication produces new DNA with each daughter double helix having one parental strand and one new strand40Types of ReplicationAlternative theories of replication are:Semiconservative: each daughter has 1 parental and 1 new strandConservative: 2 parental strands stay togetherDispersive: DNA is fragmented, both new and old DNA coexist in the same strand413.3 MutationsGenes accumulate changes or mutationsMutation is essential for evolutionIf a nucleotide in a gene changes, likely a corresponding change will occur in an amino acid of that gene’s protein productIf a mutation results in a different codon for the same amino acid it is a silent mutationOften a new amino acid is structurally similar to the old and the change is conservative42Sickle Cell DiseaseSickle cell disease is a genetic disorderThe disease results from a single base change in the gene for b-globinThe altered base causes the insertion of an incorrect amino acid into the b-globin proteinThe altered protein results in distortion of red blood cells under low-oxygen conditionsThis disease illustrates that a change in a gene can cause a corresponding change in the protein product of the gene43Comparison of Sequences from Normal and Sickle-Cell b-globinThe glutamate codon, GAG, is changed to a valine codon, GUGChanging the gene by one base pair leads to a disastrous change in the protein product44