Biology From gene to protein

Transcription

1 Biology From gene to protein Shorthand abbreviation of part of the DNA sequence of the SRY gene >gi ref XM_ Homo sapiens SRY (sex determining region Y chromosome) GGCATGTGAGCGGGAAGCCTAGGCTGCCAGCCGCGAGGACCGCACGGAGGAGGAGCAGG AGCGCGGAGCCGCGAGCCCCGAGCCCCGAGCCCGGCGCCTGGCTGAGTAGATGTCCATGA GGAGCCCCATCTCTGCCCAGCTGGCCCTGGATGGCGTTGGCACCATGGTGAACTGCACCAT CAAGTCAGAGGAGAAGAAAGAGCCTTGCCACGAGGCCCCCCAGGGCTCAGCCACTGCCGC TGAACCTCAGCCTGGAGACCCAGCCCGGGCCTCCCAGGATAGTGCTGACCCCCAAGCTCCA GCCCAGGGGAATTTCAGGGGCTCCTGGGACTGTAGCTCTCCAGAGGGTAATGGGTCCCCAG AACCCAAGAGACCAGGAGTGTCGGAGGCTGCCTCTGGAAGCCAGGAGAAGCTGGACTTCA ACCGAAATTTGAAAGAAGTGGTGCCAGCCATAGAGAAGCTGTTGTCCAGTGACTGGAAGG AGAGGTTTCTAGGAAGGAACTCTATGGAAGCCAAAGATGTCAAAGGGACCCAAGAGAGCC TAGCAGAGAAGGAGCTCCAGCTTCTGGTCATGATTCACCAGCTGTCCACCCTGCGGGACCA GCTCCTGACAGCC.. etc, etc, etc, Shorthand abbreviation of the protein sequence coded for by the SRY gene >gi emb CAD sex determining region Y [Homo sapiens] MQSYASAMLSVFNSDDYSPAVQENIPALRRSSSFLCTESCNSKYQCETGENS KGNVQDGVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEA EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPKNCSLLPADPASVLCSE VQLDNRLYRDDCTKATHSRMEHQLGHLPPINAASSPQQRDRY 1

2 Steps in the conversion of chemical information in DNA into the form of proteins Molecular terminology uses sames words that you might use for describing the copying over of an ancient manuscript [copying gene-sized segments] [conversion from one chemical language to another] transcription translation DNA mrna PROTEINS permanent, chemically stable copy temporary copy (often rapidly recycled) Jargon Review the permanent, chemically-stable copy of the genome mrna (messenger RNA): a temporary copy of a gene that is used by the protein synthesis apparatus Transcription: the synthesis of RNA using DNA as the template a) from the word transcribe which means to make a written copy RNA polymerase: catalyzes the synthesis of RNA: performs the chain elongation step 2

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4 The genome of an organism is an informational storage system or database The cell must be able to access the information in a highly specific manner: The cell must be able to express (transcribe and translate) a given gene a) at the appropriate time b) in the appropriate cells or tissues c) at the appropriate level (quantity) THE SRY GENE ON THE Y CHROMOSOME MUST BE EXPRESSED: DURING EMBRYONIC DEVELOPMENT (APPROPRIATE TIME) IN THE DEVELOPING GONAD (APPROPRIATE TISSUE) IN THE RIGHT AMOUNT TO EXERT ITS SEX-DETERMINING EFFECTS (APPROPRIATE QUANTITY) 4

5 RNA polymerase has features in common with DNA polymerase: Absolute requirement for a template: which directs the RNA polymerase according to the rules of complementary base pairing 5'---> 3' synthesis: enyzme adds onto the 3 end of the chain synthesis of RNA polymer is antiparallel to DNA template 5

6 RNA polymerase has features that are different from DNA polymerase: Does not require a primer (can start a polymerase chain) Copies only short segments of DNA Doesn't have a proofreading function -- doesn t correct errors 6

7 The chromosomes of all organisms are long, polymers of DNA DNA molecules are extremely long - we ve talked about this before! RNA polymerases copy short stretches of only one strand of the DNA 7

8 Presentation of the Drosophila genetic map in the publication reporting the complete genome sequence of Drosophila SCIENCE MARCH 24, 2000 How does an RNA polymerase recognize the position of a gene in the DNA polymer? How the the RNA polymerase know which DNA strand is the template? 8

9 What signals can we glean from this monotonous one-dimensional array of digit information? >gi gb U HUMHBB Human beta globin region on chromosome 11 TTGCAGATTAGTCCAGGCAGAAACAGTTAGATGTCCCCAGTTAACCTCCTATTTGACACCA CTGATTACCCCATTGATAGTCACACTTTGGGTTGTAAGTGACTTTTTATTTATTTGTATTTTT GACTGCATTAAGAGGTCTCTAGTTTTTTATCTCTTGTTTCCCAAAACCTAATAAGTAACTAA TGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATGA GCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTATATA TACACATATATATATATATTTTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAG AAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTGCATAT TCTGGAGACGCAGGAAGAGATCCATCTACATATCCCAAAGCTGAATTATGGTAGACAAAG CTCTTCCACTTTTAGTGCATCAATTTCTTATTTGTGTAATAAGAAAATTGGGAAAACGATCT TCAATATGCTTACCAAGCTGTGATTCCAAATATTACGTAAATACACTTGCAAAGGAGGATG TTTTTAGTAGCAATTTGTACTGATGGTATGGGGCCAAGAGATATATCTTAGAGGGAGGGCT GAGGGTTTGAAGTCCAACTCCTAAGCCAGTGCCAGAAGAGCCAAGGACAGGTACGGCTGT CATCACTTAGACCTCACCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAG CAGGGAGGGCAGGAGCCAGGGCTGGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTAC ATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCACCTGA CTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGG TGGTGAGGCCCTGGGCAGGTTGGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAG AAACTGGGCATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTG CCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCT TTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCT CATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGG GCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTT CAGGGTGAGTCTATGGGACCCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATG TCATAGGAAGGGGAGAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGC ATCAGTGTGGAAGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTT CTTTTGTTTAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGC CTTAACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAA ACTTTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTC ATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATG GGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTGCATT TGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTCTAATACTT TCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTTTGCACCATTC 9

10 What sort of sequence information defines the beginning and end of a gene? GO BACK and consider the molecular definition of a gene 10

11 MOLECULAR DEFINITION OF A GENE Segment of DNA composed of a transcribed region and adjacent regulatory region that controls transcription Generic Gene: contains a coding region, a promoter, and a regulatory region Coding region Sequence of DNA that specifies protein Promoter site on DNA to which the RNA polymerase binds this site tells the RNA polymerase where to start transcription 11

12 Regulatory region: site on DNA that affects the level of transcription of a particular gene -- that is, the quantity of mrna often involved in the temporal and/or spatial regulation of gene expression temporal = when the gene is transcribed spatial = where (in what cells and tissues) is the gene transcribed For example, specific regulatory sites near the hemoglobin genes specify that these genes should be transcribed only in red blood cells 12

13 How does the RNA polymerase know where to start transcribing a gene? How does it know which strand to use as the template? The genes promoter sequence is the key here 13

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15 >gi gb U HUMHBB Human beta globin region on chromosome 11 TTGCAGATTAGTCCAGGCAGAAACAGTTAGATGTCCCCAGTTAACCTCCTATTTGACACCA CTGATTACCCCATTGATAGTCACACTTTGGGTTGTAAGTGACTTTTTATTTATTTGTATTTTT GACTGCATTAAGAGGTCTCTAGTTTTTTATCTCTTGTTTCCCAAAACCTAATAAGTAACTAA TGCACAGAGCACATTGATTTGTATTTATTCTATTTTTAGACATAATTTATTAGCATGCATGA GCAAATTAAGAAAAACAACAACAAATGAATGCATATATATGTATATGTATGTGTGTATATA TACACATATATATATATATTTTTTTTCTTTTCTTACCAGAAGGTTTTAATCCAAATAAGGAG AAGATATGCTTAGAACTGAGGTAGAGTTTTCATCCATTCTGTCCTGTAAGTATTTTGCATAT TCTGGAGACGCAGGAAGAGATCCATCTACATATCCCAAAGCTGAATTATGGTAGACAAAG CTCTTCCACTTTTAGTGCATCAATTTCTTATTTGTGTAATAAGAAAATTGGGAAAACGATCT TCAATATGCTTACCAAGCTGTGATTCCAAATATTACGTAAATACACTTGCAAAGGAGGATG TTTTTAGTAGCAATTTGTACTGATGGTATGGGGCCAAGAGATATATCTTAGAGGGAGGGCT GAGGGTTTGAAGTCCAACTCCTAAGCCAGTGCCAGAAGAGCCAAGGACAGGTACGGCTGT CATCACTTAGACCTCACCCTGTGGAGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAG CAGGGAGGGCAGGAGCCAGGGCTGGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTAC ATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCACCTGA CTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGG TGGTGAGGCCCTGGGCAGGTTGGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAG AAACTGGGCATGTGGAGACAGAGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTG CCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCT TTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCT CATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGG GCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTT CAGGGTGAGTCTATGGGACCCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATG TCATAGGAAGGGGAGAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGC ATCAGTGTGGAAGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTT CTTTTGTTTAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGC CTTAACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAA ACTTTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTC ATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTATG GGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTGCATT TGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTCTAATACTT TCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTTTGCACCATTCT AAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATTTCTGCATATAAATATT TCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAATAGCAGCTACAATCCA GCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGATTATTCTGAGTCCAAGCTAG GCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCACAGCTCCTGGGCAACGTGCTG GTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATC AGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCT TGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGAT ATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGCAAT GATGTATTTAAATTATTTCTGAATATTTTACTAAAAAGGGAATGTGGGAGGTCAGTGCATTT AAAACATAAAGAAATGAAGAGCTAGTTCAAACCTTGGGAAAATACACTATATCTTAAACTC 15

16 Useful Analogies? Genome: gigantic file cabinet -- crammed with thousands of files Chromosome: a folder with a set of specific files (1000 s) Gene: a specific file transcription: retrieving and photocopying a specific file mrna: the photocopy of the specific file promoter: a tab showing where a file is located -- or showing the beginning of a file 16

17 The Genetic Code What features must the chemical carrier of genetic information have? Chemical structure must explain how information is stored: Must be some inherent capacity for information storage Genetic information is stored in the specific sequence of nucleotide subunits: In other words the sequence GATTCG... means something different to the organism than the sequence GTACCG... 17

18 Shorthand abbreviation of part of the DNA sequence of the SRY gene >gi ref XM_ Homo sapiens SRY (sex determining region Y chromosome) GGCATGTGAGCGGGAAGCCTAGGCTGCCAGCCGCGAGGACCGCACGGAGGAGGAGCAGG AGCGCGGAGCCGCGAGCCCCGAGCCCCGAGCCCGGCGCCTGGCTGAGTAGATGTCCATGA GGAGCCCCATCTCTGCCCAGCTGGCCCTGGATGGCGTTGGCACCATGGTGAACTGCACCAT CAAGTCAGAGGAGAAGAAAGAGCCTTGCCACGAGGCCCCCCAGGGCTCAGCCACTGCCGC TGAACCTCAGCCTGGAGACCCAGCCCGGGCCTCCCAGGATAGTGCTGACCCCCAAGCTCCA GCCCAGGGGAATTTCAGGGGCTCCTGGGACTGTAGCTCTCCAGAGGGTAATGGGTCCCCAG AACCCAAGAGACCAGGAGTGTCGGAGGCTGCCTCTGGAAGCCAGGAGAAGCTGGACTTCA ACCGAAATTTGAAAGAAGTGGTGCCAGCCATAGAGAAGCTGTTGTCCAGTGACTGGAAGG AGAGGTTTCTAGGAAGGAACTCTATGGAAGCCAAAGATGTCAAAGGGACCCAAGAGAGCC TAGCAGAGAAGGAGCTCCAGCTTCTGGTCATGATTCACCAGCTGTCCACCCTGCGGGACCA GCTCCTGACAGCC.. etc, etc, etc, Shorthand abbreviation of the protein sequence coded for by the SRY gene >gi emb CAD sex determining region Y [Homo sapiens] MQSYASAMLSVFNSDDYSPAVQENIPALRRSSSFLCTESCNSKYQCETGENS KGNVQDGVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEA EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPKNCSLLPADPASVLCSE VQLDNRLYRDDCTKATHSRMEHQLGHLPPINAASSPQQRDRY What is the translation code? 18

19 The genetic code serves as the key to translating the chemical language of nucleic acids into the chemical language of amino acids Features of the genetic code: Triplet Code: each amino acid is specified by a codon consisting of 3 bases each position of the codon can have any one of the 4 purine or pyrimidine bases 4 3 = 64 combinations (more than enough to cover the 20 amino acids) 19

20 how does the cell interpret 5 AUG/GUU/UGG/CUC/AAA/UAG 3? Degenerate: 64 codons and 20 amino acids- many more codons than are needed most aa are specified by more than one codon (1-6) for many aa the first two codons are important but the third one is not 3 stop codons - specify the end of the polypeptide chain AUG is the starter codon 20

21 This code is Universal all organisms from bacteria to man use the same genetic code a few minor exceptions to this rule this means that the genetic code is very ancient (4+ billion years old) must have evolved to its current form in the last common ancestor of all organisms 21