Molecular Biology of the Gene

MOLECULAR BIOLOGY OF THE GENE MOLECULAR BIOLOGY OF THE GENE 20th in 1 century able to store . already information that knew that . stable 2 , , pertains to development that it can be so replicated (mutations genetic material was was known that DNA contains two with 1950 by it metabolic activities of structure and ↳ two undergo DNA as rare pyrimidine bases -o - established but structure still unknown four different - adenine purine bases with high accuracy transmitted to next generation provide genetic variability required for evolution with changes able to 3 . must be material genetic /organism cell ↳ researchers - types (A) quanine (G) of nucleotides thymine (T) , double have = , (C) Cytosine ving single ring have = O NHz & (A) thymine N O nitrogen-containing O 4 3 # N O H0P05CH2 Cy 1* O ②021 3 H guanine O O 4 3 g . . in each one is DNA rules . amount 1 NHz cytosine * C (C) G ②C W O HOPOSCH20g 1C # O ②021 roughly have 4 3 H # 1* Cy ②021 81 H 25 % of each type of nucleotide but most do not , DNA and T is about 31 %, so nucleotide content not fixed across A species = DNA does of consistent : A , T , G and (varies species , amount of A of four bases possible most DNA ↳ deoxyribose variability species Chargaft's only = base content of DNA species in humans have . H sugar 1 various spaces differs ↳ e 2 81 Cy , g 81 within 02 a H0P05CH2 of 1* C I N HzN Chargaff analyzed g # C (G) ↳ showed that some 4 g 81 CIA D base N HOPOSCH2 O C IN ↓N (T) CIA I Erwin C13 C adenine molecules provide for human chromosome - = from species T , and amount at each base pairs species of G nucleotide variability 140 million to = C position in DNA to sheer number of bases and length of Rosalind Franklin used ↳ ↳ found that if fibers are o when ↳ X-rays portions dark like based - on (and others) work how nucleotides constructed models and concluded outside , paired bases on , in center pattern some in definite manner arranged that DNA of the photograph portion of helix is repeated Watson and Crick were knew DNA is of nucleotides polymer molecule within is a double helix according 3' end > - P --- ---- fibers with sugar-phosphate backbones on the the inside 5' end G arranged into double helix a crossed (x) by separated can be diffraction pattern and bottom indicate that top did not know of DNA substance whose atoms are X-ray that DNA is indicated Franklin's (solid Crystal it results in X-rayed at structure , enough shape study concentrated viscous solution of DNA is obtained - > a diffraction pattern shows ↳ helical to C to their model , the two DNA strands are sugar-phosphate groups oriented in strand S S that are chained antiparallel together to make each directions opposite - each nucleotide has P phosphate group located at 5' position of sugar --- P T = - - - A S S nucleotides P 5' end 3' end to = antiparallel - one complementary ↳ antiparallel consistent > - two DNA base pairing spacing strand pairing runs = gives is located at 3 molecule 5' to 3 , together by linking within the other strand always bonded to ensures that bases replicated in 5 to 3' direction are by runs on sugar of one nucleotide preceding nucleotide parallel but other direction pyrimidine oriented Franklin's two purines together too always read in 5' to narrow , DNA must position 5'phosphate of directionality between strands was detected pyrimidines together too information stored free-oH phrine of strands joined properly , so they can interact diffraction pattern wide 3' direction - so DNA strand usually REPLICATION OF DNA DNA replication process of DNA molecule copying parental double helix DNA strand of each serves example for semiconservative replication parental double helix DNA after replication , each have green backbone each molecules (new strand) template for daughter sequence new strand nitrogen of parental in daughter find to out DNA double helix molecule that DNA replication contains old strand from DNA double helix 1) NA helicase at double helix has same base as daughter copy replication fork template strand ↳ because A pairs With T, G with C > - results in exact · and new strand daughter blue backbone (old and as - Meselson and Frank Stahl used radioactive isotopes of Matthew is = parental double helix three main events in replication DNA DNA : helicase ↳ creates two Protein Name Function DNA helicase Separates double-stranded DNA unwinds DNA , separates parental strands replication forks to more away from each other into single strands Single-stranded binding protein (SSB) it from DNA primase Synthesizes DNA Synthesizes polymerase separate Binds to single-stranded DNA and prevents re-forming strands ; a single-stranded binding short RNA primers DNA in the removes leading RNA primers ; and gaps with more DNA and lagging -o DNA filling the proofreads newly ligase Covalently attaches fragments in the lagging prevents them from does not adjacent Okazaki get replication to DNA primase puts begins DNA nucleotides DNA short Synthesis together polymerase also - in primers new on strands nucleotides complementary chain) proofreads strands to can correct DNA attach to separated helix replication so , - short strand of RNA , needed for begin for replication form re-forming new disturbed replication needs primer strand for proteins (SSB) , made DNA D) NA strands become template double helix mistakes DNA base polymerase recognizes RNA target, pairs with old strand (connects new parental strands are antiparallel antiparallel to parental strand must be daughter a each to each other strand ↳ DNA ↳ ↳ can leading only other new strand ↳ (lagging strand) is DNA goal be are DNA (with periodic replicated starts Okazaki = to fragments together -o results in two direction opposite in Lo polymerase DNA /stop) fragments converts short RNA polymerase replication continues synthesized fork has to be strand is , is easier 3' direction sequences into DNA double helix molecules (identical to each molecule S during phase of cell of these processes is either doubled before it before cell divides cancer made are in segments lagging Okazaki original copied that 5' to 5' to 3' in which ligase glues other and T so both new strands When DNA exposed it in short segments from 5' to 3 synthesized strand is synthesizes ↳ be , be can is sometimes treated with then by mistakenly used to create separated DNA has to be (before cycle exact start of Mitosis copy , or to make or meiosis) gamete for reproduction DNA has to cell division during replicated chemotherapeutic cancer cells to drugs that synthesize DNA mimic one of the four nucleotides in DNA replication stops cell dies , origin REPLICATION PROKARYOTIC VERSUS EUKARYOTIC bacteria single have circular loop chromosome o has to be replicated before cell divides ↳ in circular DNA molecules some molecule only ↳ in others in one , replication moves around DNA direction repai · Replicati replication fork replication bubble " & replication happens in two directions - ↳ replication process starts ↳ always at origin strands are 5 to 3' direction of replication separated and unwound ! * - , specific DNA site bacterial chromosome on polymerase binds to T , > T ↳ when of both opening DNA replication stops to begins copying polymerases , two process meet at termination copies of chromosomes are I > strand , region separated 1 > ! . parental in & & each side > new DNA duplexes Replication daughter in eukaryotes strand bacterial cell needs about 40 min to replicate complete chromosome ↳ some bacteria replication eukaryotes ↳ ↳ begins replication bubbles spread ↳ being DNA is Wherever ↳ DNA 20 min every replication in bidirectionally replicated origins RNA DNA Deoxyribose Bases A denine guanine , A denine , cytosine No number of ↳ in stem unregulated he can also makes check for accuracy - , of bacterial DNA acid) - ↳ uracil replaces length proofreads , - before previous , chromosome happens pairs/min) within hours replicate ends of chromosomes to -> Short DNA sequences , repeated over , prevents called telomerase (adds correct by enzyme loss negatively 100 , 000 base direction and - of DNA after successive rounds of replication e . g . uncontrolled cell division in cancer cells pairs -o it is making changed again accurate very several removing and DNA , can recognize mismatched nucleotides polymerase resumes : 1 mil 1 GENETIC CODE composed of nucleotides bases adenin (A) , does not form double helix (like DNA) Cytosine (C) quanin(G) thymine single-stranded linear , 000 base replication also slower (500-5 is unable daughter strand direction is polymerase polymer , but are added every by reversing it nucleotides contain ribose and is start replicated about 1 mistake remove to affects cell function nucleotide is removed RNA (ribonucleic RNA can fork lare composed of telomeres polymerase is (along length of shape-replication over and GENE EXPRESSION , RNA AND THE & replication meet polymerase , cytosine pairing DNA activity telomerase ↳ when error rate , cells it preserves ends of chromosomes nucleotide and = by of replication they DNA guanine repeats after chromosome polymerase DNA copied until longer due Yes not origins there is a V D) ouble-stranded with base are , thymine Single-stranded telomeres round of DNA of replication speed up process Ribose uracil , , takes Sugar Helix in them , new at numerous eukaryotes individual many Strands - completed round is in divide like DNA , , and uracil (U) making DNA three RNA Major ↳ takes a transfer ↳ two ↓ acids to ribosomes amino RNA (URNA) ribosomes (with ribosomal make up steps needed copied then translation in = = base all of code unit to encode genetic code each genetic = ↳ . different 20 is key code is 3 . ↳ are that protein template DNA read by ribosome into amino acid protein-central , is synthesized supports body function produced converted into sequence of amino acids of the 20 amino acids amino one Sequence of needs to be biology amino acids in protein identified (fewer would not have acids) basis of biological life degenerate code is triplet codon , of molecular triplet of nucleotides have more than one codon arginine have 6 code different codons protects against potentially unambiguous has only one meaning has start and stop signals start but three stop signals each sequence dogma mRNA sequence determines (redundancy s of degeneracy code > - that unlocks leucine , serine , genetic ↳ DNA into codon has to be made up of three nucleotides ↳ most amino acids 2 is sequence code has to be at least a coding ↳ on polypeptides where into MRNA , tRNA , RNA DNA to RNA to for proteins code genetic . 1 based transcript nucleotide changes genetic ↳ , base by mRNA flow of information from ↓ molecule RNA in , polypeptide ↳ genes proteins) information stored to convert first transcription ↳ DNA is ↳ cytoplasm (tRNA) transfers ↳ DNA in nucleus to ribosomes in from message RNA ribosomal : (mRNA) RNA messenger types harmful mutations enough variety Second Base First Base U W A G Base UUL UCU LAU UGH phenylalanine serine tyrosine cysteine UUC UCC USC UGC serine tyrosine cysteine LUA UCA UAA UGA leucine serine Stop stop UUG UCG UAG UGG leucine serine stop tryptophan CUL CCU CAL CGH proline histidine arginine CUC CCC CAC CGC leucine proline histidine arginine CHA CCA CAA CGA leucine proline glutamine arginine CUG CCG CAG CGG leucine proline glutamine arginine AUL ACU 114 AGU isoleucine threonine asparagine serine AUC 1CC AAC AGC isoleucine threonine asparagine serine AUA ACA AAA AGA isoleucine threonine lysine arginine A CG AAG AGG methionine threonine lysine arginine GUU GCU GAL GGU valine alanine a spartate glycine GHC GCC GAC GGC valine alanine a spartate glycine GUA GCA GAA GGA valine alanine 9 lutamate glycine GUG GCG GAG GGG valine alanine 9 lutamate glycine A * UG G (start) GENE EXPRESSION Segment all of types DNA ↳ G ↳ H code within mitochondria , genetic chloroplasts and slightly different organisms share common some archaebacteria strong evidence that ancestor C ↳ A G makes possible to transfer it organism genes from one to another U C A G U C A G TRANSCRIPTION : serves as template for production of RNA molecule of RNA produced sequences of bases in exceptions) living organisms (few 2 A leucine code is universal to all genetic U phenylalanine C ↳ Third C gene by transcription are , mRNA eventually transcribed into mRNA molecule transcription during leads to production of protein based on complementary base pairing ↳ T in when with DNA-bA gene DNA that strand RNA Clike is MRNA (G-C A-PU) , transcribed , DNA helix nucleotides of strands - , template strand polymerase DNA in moves along unwinds and opposite to strand polymerase either strand of DNA can be template strand , complementary RNA nucleotides pair gene other strand is non template unzips in template or coding strand 5' direction - adds nucleotide only to 3' end polymerase RNA ↳ promotor defines to DNA RNA to polymerase stop sequence to formed ↳ is e . modified g. L receives cap cap modified = pre-mRNA exons in lower , in in DNA RNA polymerase = after into splicing , to side 3' to 5' direction until it transcribing stops comes and releases 5' end and tail at 3 end nucleotide that guanine helps mRNA initiate loading by hydrolytic enzymes (protein-coding regions) and mix of exons of ribosomes and start of (non-protein introns coding regions eukaryotes (introns in between will mRNA by "self-splicing" enzymatically splicing itself out of be spliced out introns removed pre-mRNA ribozyme Cenzyme addition of 5' cap and 3' of RNA) made poly-A tail (shRNAs) splice RNA and remove them to remove introns is mRNA ready to leave nucleus and translated protein scientists used to think introns were wasted presence of introns allows cell to choose which ↳ not ↳ all exons if gene in pre-mRNA has three exons space within exons make it into it can will go genes into - have several key functions 3 /depending alternative mRNA splicing final mRNA produce - in cell MRNA mRNA with exons 1 + 2 1+3, 1 , + 2 + environmental and c ll needs = RNA (rough form) leaving eukaryotic nucleus higher eukaryotes spliceosomes that contain small nuclear RNAs ↳ snRNAs can identify introns through complementary base pairing uses dangles off portion of pre-mRNA multicellular capable of spliceosome newest to be transcribed transcript in ↳ supposed only - Crest strand in template = helix is bound to DNA of pre-mRNA will be contained in mature eukaryotes ↳ infron is polymerase delays degradation of contains particularly only at that is , reads down DNA processed before or translation > - transcript RNA initiation transcription and strand initiates termination mRNA molecule called mRNA newly to is not as stable as two strands molecule that is associated with RNA elongation DNA direction of start and association RNA-DNA promoter of attaches to increases flexibility and efficiency of cell on snRNAs of spliceosomes that cut out introns are important for alternative ↳ bind with mRNA role in evolution of translation happens = encourages crossing new base over in eukaryotes translation of mRNA regulating translation pairing prevent during meiosis makes t - exon shuffling (plays possible genes of cytoplasm in involved in small molecules through complementary presence of introns also a (miRNAs) microRNAs produce introns some splicing cells eukaryotic a is the second step herded to express into gene protein ↳ sequence of into mRNA GENE EXPRESSION as polymerase they ribosome - o connects sequence of amino acids dictated by polypeptide information from nucleic acid RNA by is read codons in mRNA : language TRANSLATION finish does not have to gene's have access to is translated into amino acid language making promoter , RNA many mRNA one transcript before it polymerase molecules can starts another - as produce transcripts long at the time same ↳ makes it possible for all to produce thousands of copies of same mRNA molecule (and therefore same protein) faster some species of Aminata mushrooms produce toxin called ↳ inhibits function of tRNA molecules ↳ RNA polymerase a transfer amino acids single stranded nucleic acid hydrogen-bonded to one , at least one complementary ↳ e g . ↳ in . on flat cloverleaf (but and 3' end - genetic code opposite antiparallel tRNA has anticodon itself actually to found - creates regions where has three-dimensional in complementary bases specific specify shape) proteins end of molecule contains anticodon = group of 3 bases that is mRNA codon 5'AGG 3 - binds to 61 codons due to destruction of liver another tRNA molecule per 20 amino acids ↳ amino acid binds to quickly to ribosomes doubles back are ↳ structure drawn as leads to death x-amanitin MRNA 5'CUU3' amino acids , other 3 are to carries amino acid stop sequences leucine different 40 ~ ↳ less tRNA molecules , ↳ first ↳ third two positions in tRNA position can differing only wobble genetic amino code - wobble despite ensure that produce tRNA more than one codon hypothesis anticodon pair same pair with can Obey A-USG-C molecules can configuration recognize as many rule four separate codons as nucleotide in third effect helps amino acids will vary in most cells because some 1966 Francis Crick established in = codons tRNAs than found changes in DNA base resulting a sequences sequence of protein correct degenerate is acid-charging enzymes Caminoacyl-tRNA synthetase) attach the correct amino acid to correct tRNA molecule THE ROLE OF RIBOSOMAL RNA rRNA produced from ↳ rRNA more in nucleolus template with various packaged ↳ subunits DNA separately through nuclear eukaryotes other bigger than the into cytoplasm join together at start nucleus in Cone ribosomal subunits into two proteins of envelope pores - of translation When translation ribosomes ↳ tRNA begins , binding have binding ribosomes remain in site for sites facilitate mRNA , cytoplasm and three complementary or attach to sites for tRNA binding base endoplasmic reticulum pairing between tRNA anticodons and mRNA codons large ribosomal subunit has adjacent amino ↳ translation stops at ↳ from URNA (ribozyme) - creates peptide bond between acids peptide bond created normal enzyme activity many stop codon times - = polypeptide When complete , increases by polypeptide one amino acid at dissociates a time from complex , folds into its shape polypeptide as soon as twists and bends into polypeptide emerges definite shape based from ribosome on make up of amino acids - starts folding chaperone ↳ proteins with more than one protein and ER help in polypeptide to folding each subunit process folds first , then multiple ↳ When entire ribosomes attach and translate initial portion of mRNA complex of and mRNA codons of mRNA same has been translated multiple ribosomes = at same time together to can increases polymerase attach translation efficiency pair with anticodons of tRNA mRNA corresponding sequence of amino acids polypeptide two first initiation steps of translation require brings ↳ initiation large all translation factors ribosomal prokaryotes > - (like RNA ribosome , next by polyribosome one order of codons determines order of tRNA molecules at ribosome and in join STEPS TRANSLATION REQUIRES THREE in subunits final functional protein complex into ↳ Cytoplasm molecules in to energy components (proteins) required subunit small together to assemble small for start of protein ribosome 1. E 2 P . . A 3 = sites for more large ribosomal subunit complex ARNA peptide amino acid initiator tRNA tRNA binding similar , but - exit = = eukaryotes has three synthesis ribosomal subunit attaches to mRNA close to start codon (AUG) first tRNA (initiator) pairs with start codon ↳ initiation in ribosomal subunit , mRNA , initiator tRNA and carrying E site is for binds to P site next amino leaving +RNAs - only carries amino acid methionine acid enters ribosome through A site joins small subunit EXPRESSION SUMMARY OF GENE once a ↳ protein (or RNA) is made and requires transcription operating in cell - expressed has been gene and translation often modifications to protein happen after translation > - prepare protein for its specific function in cell translation ↳ some first happens ribosomes acids of amino ribosomes at (polyribosomes) stay free polypeptide act as cytoplasm in single -o peptide , some attached to rough ER polypeptide belongs indicates where in cell or if it has to be secreted from cell polypeptide processed transport that have to be of addition by vesicles carry lumen of secreted enter sugars proteins , phosphates , between or ER through a channel-other folded and further lipids and to organelles plasma membrane if necessary Elongation polypeptide ↳ additionally to mRNA tRNA with ↳ when length increases in to tRNAs , one elongation amino acid requires elongation factors - facilitate of binding tRNA attached is peptide at P site , tRNAC verifies that incoming to amino acid on tRNA on A site (part of large ribosomal unit) tRNA uses carrying appropriate amino acid arrives ata site a entire matches codon energy to transfer growing growing peptide peptide peptide bond formation - peptide one amino acid longer than before Translocation ↳ ↑ ribosome moves forward spent tRNA (now at new E , peptide-bearing cycle (complementary - repeated translocation) when ribosome reaches in now P site site) exits ribosome codon exposed at A site and complete tRNA at stop ready base rapid to receive another tRNA pairing of new tRNA , transfer of peptide chain rate (15x per second in E codon , termination occurs , . Coli) polypeptide is released is and create bund ↳ after anticodons codons within ribosome ribosome ribozyme at a time , transferred new peptide Termination final step of protein ↳ polypeptide one happens requires protein after release ↳ components that carried out protein synthesis are separated from another termination ↳ synthesis and assembled , at stop codon called polypeptide ribosome release is set - codon that does not code for amino acid a factor free - can begins dissociates into its two subunits polypeptide from bind at stop codon and to and take one three-dimensional to fold used again if cleave shape necessary proteins do work of cell ↳ proteomics metabolic = dedicated to pathways understanding structure of proteins and how they last tRNA function in