Chapter17and19.pdf BIOLOGY 108 - 0001
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Date Created: 11/07/15
Chapter 17 From Gene To Protein 171 Transcription and Translation Archibald Garrod first to suggest that genes dictate phenotype through enzymes that catalyze specific chemical reactions in the cell Genes provide instructions for making specific proteins RNA ribose instead of deoxyribose and uracil instead of thymine and single stranded bridge between genes and proteins Transcription synthesis of RNA using information in the DNA quotrewrittenquot in a new quotlanguagequot Messenger RNA mRNA carries genetic message from DNA to the proteinsynthesizing machinery of the cell Translation synthesis of a polypeptide using information in the mRNA translation of nucleotide sequence of mRNA molecule into amino acid sequence Ribosomes site of translation facilitate orderly linking of amino acids into polypeptide chains In Bacteria since prokaryotes do not have nuclei their DNA is not separated by a membrane from ribosomes so translation can occur while transcription is still in progress In Eukaryotes transcription occurs in the nucleus and mRNA is transported into cytoplasm translation occurs in the ribosomes in the cytoplasm Primary Transcript initial RNA transcript from any gene Summary genes program protein synthesis via genetic messages mRNA cells are governed by a molecular chain of command DNA gtRNA gtProtein Central Dogma T Triplet Code genetic instructions for a polypeptide chain are written in sets of 3 nucleotide quotwordsquot genetic code of 3 nucleotide quotwordsquot is transcribed into 3 nucleotide mRNA quotwordsquot then translated to amino acids Template Strand the one strand of DNA that is transcribed the other is not provides a template for sequence of nucleotides in RNA transcript same strand is used as the template every time the gene is transcribed DNA strand template I TRANSCRIPTION l l Codon TRANSLATION I Protein Amino acid Codons mRNA nucleotide triplets codes for specific amino acid OR DNA nucleotides of the nontemplate strand therefore identical to mRNA strand except T39s instead of Us Codons may be redundant two codes for one amino acid No codons are ambiguous no codon codes for more than one amino acid Reading Frame the ability to read codons in the correct groupings 172 A Closer Look At Transcription RNA Polymerase pries two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand can only assemble RNA polynucleotide in 5 39339 direction can start a chain of RNA nucleotides from scratch no primer needed Promoter DNA sequence where RNA polymerase attaches and initiates transcription Terminator sequence that signals end of transcription in bacteria Transcription Unit stretch of DNA that is transcribed into an RNA molecule Initiation Start Point nucleotide where RNA synthesis actually begins and extends dozens of pairs of nucleotides long Transcription Factors collection of proteins that mediates the binding of RNA polymerase and initiation of transcription attaches to the promoter Transcription Initiation Complex complex of transcription factors RNA polymerase II and the promoter Elongation RNA polymerase moves along DNA untwisting the double helix RNA nucleotides are paired RNA molecule peels away from DNA template DNA double helix reforms Termination in Bacteria Transcription goes through a terminator sequence of DNA which signals the end of transcription Termination in Eukaryotes RNA polymerase goes through a Polyadenylation Signal AAUAAA A ways down from this signal proteins cut it free from the polymerase releasing the mRNA stopping transcription 173 PostTranscription Eukaryotic Modi cation RNA Processing both ends of the primary transcript are altered certain interior RNA sections are cut out remaining parts are spliced together produces mRNA molecule ready for translation 539 Cap modified form of guanine added onto 539 end after transcription of first 2040 nucleotides PolyA Tail 50250 A nucleotides added to the 339 end 539 Cap and Poly ATail Functions facilitate export of mature mRNA from the nucleus help protect mRNA from degredation help ribosomes attach to the 539 end of mRNA once mRNA reaches cytoplasm UTR untranslated regions will not be translated into protein but function in ribosome binding RNA Splicing cut and paste job in which large portions of RNA molecule are cut out Introns noncoding segments of nucleotides that lie between coding regions Exons nucleotides that are coded and eventually expressed by being translated into amino acid sequences EXons EXit the nucleus and are EXpressed Introns are cut out of the molecule and exons are joined together Forms a continuous coding mRNA sequence RNA splicing Spliceosome several small nuclear ribonucleoproteins that are involved in carrying out premRNA splicing releases the intron which is rapidly degraded joins together exons snRNA RNA of small nuclear ribonucleoproteins or snRNP catalyzes these processes Ribozymes RNA molecules that function as enzymes Why can RNA sometimes function as an enzyme It39s single stranded so it can basepair with complementary region elsewhere on the same molecule some RNA bases contain functional groups essential for catalysis RNA can hydrogenbond with other nucleic acid molecules RNA or DNA Alternative RNA Splicing many genes are known to give rise to two or more polypeptides depending on which segments are treated as exons during processing ex fruit y gender depends on differences on how males and females splice the RNA transcribed in certain genes Domains discrete structural and functional regions of proteins ex one domain may contain an active site another may allow binding to cellular membrane Presence of introns facilitates evolution of new and maybe beneficial proteins This is called exon shuf ing Increases probability of crossing over 174 A Closer Look At Translation Translation ow of genetic information from mRNA to protein Transfer RNA tRNA molecule that translates the series of codons along mRNA transfer amino acids from cytoplasmic pool to growing polypeptide in ribosome arrives at a ribosome with a specific amino acid at one end and an anticodon on the other anticodon basepairs with a complementary codon on mRNA each codon codes for a specific amino acid which will be added to the polypeptide chain used repeatedly translates in cytoplasm deposits amino acids at ribosome and returns to cytoplasm tRNA in Eukaryotes made in the nucleus and then travels to the cytoplasm where translation occurs twists and folds into a compact 3D structure LShaped one end of the L has the anticodon other end of the L has its 339 end attachment site for amino acid Molecular Recognition For Translation tRNA binds to an mRNA codon AminoacyltRNA Synthetases family of enzymes that matches up tRNA and amino acid active site fits only a specific amino acid and tRNA combination resulting aminoacyl tRNA charged tRNA is released from enzyme and delivers its amino acid to polypeptide chain on a ribosome pairing of tRNA anticodon with mRNA codon wobble versatility with anticodoncodon pairing exible base pairing Ribosomal RNA rRNA most abundant type of RNA 4 molecules per ribosome in Eukaryotes catalyst for peptide bond formation Robosomes 3 Binding Sites for tRNA P Site holds tRNA carrying growing polypeptide chain A Site holds tRNA carrying next amino acid to be added to the chain E Site exit site through which tRNA39s are discharged from the ribosome when polypeptide is complete it leaves the ribosome through an exit tunnel Stages of Polypeptide Construction Initiation brings together mRNA tRNA bearing the first amino acid of the polypeptide and two ribosome subunits small ribosomal subunit binds to mRNA and initiator tRNA tRNA initiator binds with mRNA start codon signaling the start of translation large ribosomal subunit joins this complex all brought together by initiation factors NTerminus initial amino acid CTerminus final amino acid Elongation amino acids are added one by one to the preVious amino acid at the CTerminus continues until a stop codon in the mRNA reaches site lKihr n39u x A 3939 I uimquothu Aminocnd ufpolypcptidc b O in I v 39tion An o Codnn recogm mR 1 39 y 39 quot 39 396 incoming aminonq39l tRNA of H binds to the codon in tho A site Ribosomc ready for 7 next nmi thththth cyl tRNA 5 e Translocation The tRNA in thr A silo is translomtml to the I site taking the mRNA along with it Mnmwhilc the tRNA in the l ill39 moves to g 9 Peptide bond formation The ribosome catalyzes the formation of i pcptidc bond between the new amino acid and the carbmyl end of the growing polypeptide Termination a release factor will bind directly to the stop codon in the A site adds a water molecule instead of an amino acid to the polypeptide chain this breaks the bond between the completed polypeptide chain and the tRNA in the P site polypeptide leaves the ribosome through the exit tunnel Polyribosomes strings of ribosomes that can translate RNA simultaneously making construction fast PostTranslational Modifications may be required before a protein can be actually functional Ribosomes all start out free in the cytosol polypeptide chains begin to be built in the cytosol and continue that way UNLESS it signals for the ribosome to bind itself to the ER Signal Peptide marks a polypeptide destined for the endomembrane system or for secretion SignalRecognition Particle proteinRNA complex that functions as an escort bringing the ribosome to a receptor protein built into the ER membrane m c MI39 MBRANl am xm m mm v fr J r l fr mumm i V nu Im 39 Elmqlml 39 39 u 139 wulu mu l w pm I U rumlnc m HHIJMIN IIIIUMIN Vlmtll W 1mm r am y r rm xfn o wk r 39 V 3 v J ll lli Rl UM N llil IWJ N 0 l m A 0 H w mi N l or H m y H Um irmw I my 1 I l Mm i m M Copyright 2009 Pearson Education Inc 175 Mutations The Ultimate Source of New Genes Point Mutations small scale mutations of one or a few nucleotide pairs cause of hereditary genetic disorders such as SickleCell NucleotidePair Substitution replacement of one nucleotide and its partner with another pair of nucleotides Silent Mutation when a substitution changes the codon into a different codon however due to codon redundancy results in the same amino acid no physical effect on phenotype Missense Mutations a substitution that leads to a different amino acid coded can have little to no effect benefits or detriments most common substitution mutation makes sense but not the right sense Nonsense Mutations a substitution that changes an amino acid codon into a stop codon causes translation to end prematurely Insertions and Deletions additions or losses of nucleotide pairs in a gene much more harmful than substitution mutations Frameshift Mutation the triplet grouping of nucleotides becomes completely shifted making all nucleotides downstream from it to be grouped incorrectly Cause of Mutations DNA replication errors or recombinations Mutagens physical and chemical agents that can cause mutations ex Xrays UV rays etc most mutagens are carcinogenic cause cancer 176 The Universal Genetic Concept Bacterial and eukaryotic RNA polymerases differ significantly differences bacterial cells lack compartmental organization can simultaneously transcribe and translate Archael RNA polymerase resembles the three eukaryotic ones similarities sensitive to chemical inhibitors complex set of transcription factors Formal Genetic Definition A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule 191 Viruses Viral Structure made of an infectious particle consisting of nucleic acid enclosed by a protein coat and surrounded by a membranous envelope consist of double stranded DNA single stranded DNA double stranded RNA OR single stranded RNA Capsid protein shell enclosing a viral genome built from capsomeres come in various shapes Viral Envelopes membranous envelopes derived from membranes of a host cell that contain a virus Bacteriophages viruses that infect bacteria usually consist of more complex capsids 192 Virus Replication How viruses work A virus will latch onto a host cell and work its genome inside through endocytosis injection etc Once inside the viral proteins commandeer the host reprogramming the cell to copy viral nucleic acid and manufacture viral proteins The cell releases often by bursting the viruses The deathdamage to the host cell cause many of the human body39s symptoms of a virus The viruses released could infect other host cells spreading the viral infection 1 3939ir39us attaches tc a cell A 11 39 3 Nucleic acid DNA er en a 2 39v39ir39us penetrates cell membrane and injects nucleic acid EDNn cr39 RN A intc cell and released fr39cm the cell The hcst cell mag he destr39cg ed in the pr39ccess 3 iilir39al nucleic acid replicates using hcst cellular39 machiner39g 4 New vir39al p l nucleic acids are I I 39 quot quot3 packaged intc irir39al particles 39 39 I g Fm Lytic Cycle phage replicative cycle that results in the death of a host cell bacterium lyses and releases phages produced within the host cell Virulent Phage a phage that replicates only through the lytic cycle Lysogenic Cycle allows virus to remain dormant in a host cell for a long time all lysogenic viruses will eventually enter the lytic cell lysogenic ones are just sneakier Temperate Phage phages capable of using both lysogenic and lytic modes of replicating within bacteria Prophage viral DNA in the lysogenic cycle it is embedded in the host cell39s genome so the host cell is still reproducing but passing on the viral DNA eventually a signal will tell the prophage to detach and enter the lytic cycle Phage DNA r The phage attaches to a Daughter cell host cell and injects its DNA with prophage Many cell divisions produce a large population of quot 39 bacteria infected Occasionally a prophage exits the bacterial chromosome in 1 i initiating a lytic cycle 39 7 I39IZJII e x a flfrgff 39 Lytic cycle Phage DNA circularizes Bacterial Q chromosome I Lysogenic cycle The bacteim repoduces Certain factors The cell lyses releasing phages determine whether normally copying the prophage and transmitting it to daughter cells Prophage lytic cycle or Lysogenic cycle IS Induced is entered 8iquot tquot quot3 l39 quotlquot I x New phage DNA and proteins are PhageDNA integrates into the synthesized and assembled into phages baCter39a39 Chromosome com a prophage Double Stranded DNA Viruses ex Chicken Pox or Herpes much less deadly lower mutation rate Single Stranded RNA Viruses ex AIDSEbola much more deadly higher mutation rate RNA viruses embed themselves into the host39s genome making them much harder to get rid of Retroviruses viruses equipped with reverse transcriptase Reverse Transcriptase converts RNA into DNA present in HIV HIV Human Immunodeficiency Virus targets CD4 white blood cells 1 HIV fuses to white blood cell and inserts its capsid and RNA into the cell 2 Capsid degrades and RNA is exposed 3 HIV brings its own machinery the Reverse Transcriptase 4 HIV RNA is transcribed into DNA and moves into the nucleus to integrate with host DNA 5 Host DNAHIV DNA are transcribed and translated into a new viral protein the mature HIV 6 Mature HIV is released into the body to affect a new host cell 193 Pathogens in Animals and Plants Viroids VERY small viruses that infect plants inherited either from an outside source or it is passed on from a parent via infected seeds cause errors in the regulatory systems that control plant growth abnormal development or stunted growth Prions an infectious protein that has been misfolded usually in the brain when this misfolded protein encounters the healthy protein versions of themselves they induct them into their rebellious gang making them misfold as well example Mad Cow Disease Bacteria Characteristics Transformation bacteria can acquire DNA from its environment and incorporate it into its own genome can make bacteria resistant to antibiotics Transduction virus that infects bacteria and assumes some of the bacteria39s DNA Conjugation bacteria sex bacteria can transport information to another bacteria
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