SCI 102. HUMAN GENOME Transcription / Translation 24/03/2015 HUMAN GENOME PROJECT. Human Genome Project (HGP) Whose DNA samples were sequenced in HGP?

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1 SCI 102 HUMAN GENOME Transcription / Translation HUMAN GENOME PROJECT 26 June 2000; announcement for the completion of the first draft Prof. MÜGE TÜRET Bill Clinton (USA President), Francis Collins (HUGO-international group leader), and Craig Venter (Celera Genomics Corporation) Human Genome Project (HGP) Whose DNA samples were sequenced in HGP? Bill Clinton declared, This is the most important, most wondrous map ever produced by humankind. The project started in scientists from six countries Completed in 2003 (ahead of predicted time) HGP catalysed our understanding of human biology and disease. DNA samples sequenced in this international project were obtained from tissues of several anonymous donors from diverse backgrounds Nine human samples; 8 males and 1 female (Males have Y-chromosomes, females do not) By sequencing genomes of different individuals, they avoided mutations. To ensure privacy, the identities of donors were never made public. DNA sequence data 1

2 Genome sequences in public databases; E.coli (bacteria that live in our intestines), Yeast, Worm, Fruit fly (Drosophila), Arabidopsis, and 100s of others First complete genome sequence 1.8 million nucleotides of Hemophilus influenza Can cause pneumonia and meningitis published in 1995 The group that published the sequence was a private company (Celera Genomics) Reflecting the race between commercially and federally funded projects. GENOMICS TODAY TOTAL NUMBER OF NUMBER OF NUMBER OF REFERENCES SPECIES SPECIES SPECIES WITH (ESTIMATED) IDENTIFIED/ COMPLETE DESCRIBED GENOMES (APPROXIMATE) SEQUENCES* (ESTIMATED) BACTERIA, 100,000 to 10 million 12,000 (460 cultured 17,420 bacteria, 362 ARCHAEA Archaea) Archaea genomes FUNGI 1.5 million 100, Bacteria 2.6 Mb genes 1977 Yeast 13 Mb genes Genome Sequences INSECTS 10 million 1 million 98 PLANTS TERRESTRIAL VERTEBRATES, FISH 435,000 (land plants and green algae) 80,500 (5,500 mammalian) 300, ,345 (5, (80 mammalian) mammalian) 1998 C. Elegans 100 Mb genes MARINE INVERTEBRATES OTHER INVERTEBRATES 6.5 million 1.3 million 60 1 million nematode, 23,000 nematode, 17 nematode, several 1,300 Drosophila 21 Drosophila thousanddrosophila 2000 Human 3 Gb genes 2

3 First big surprise What is a genome? Before HGP, considering the size of the human genome, Estimated gene number was HGP revealed about genes for the human genome based on computer analysis Programs predicting the beginning and ending of the genes Our genome harbors only about 10X the number of genes in a bacterium!!!! Organisms have the same DNA content in all their cells (with exceptions like some blood cells). Total DNA content of a cell à genome Completion of genome sequences gave birth to a new field of biology GENOMICS Genetics is concerned with how individual genes function (has a smaller focus than genomics) Genomics monitors the coordinated activities of all genes in the genome (has a broader focus than genetics) What Is Genomics? Chromosomes Sequencing whole genomes of different species Collecting genome variations within a population To study how a genome responds to environmental changes Human chromosomes Packaging of DNA into chromosome Diagram of human chromosomes 3

4 DNA Double Helix Base pairing rule A always pairs with T C always pairs with G RNA molecules have U instead of T A pairs with U C pairs with G Space filling model of DNA DNA structure James Watson and Francis Crick unraveled the DNA structure If you are given the nucleotide sequence of one DNA strand you can predict the sequence in the second (complementary) strand More than three billion nucleotides Genes proteins The alphabet of the genome is made up of 4 letters; A, T, G, and C It is without space inbetween the nucleotides (continuous) Has no punctuations Lacks an index Prediction of protein sequence from DNA sequence 4

5 DNA and protein are colinear DNA sequence determines amino acid sequence in a point-to-point manner Gene Expression DNA à RNA à protein (central dogma) Synthesis of RNA from DNA template transcription Synthesis of protein from RNA template translation Colinearity of DNA and protein in the trpa gene of E. coli DNA opens up during transcription to create a transcription bubble Promoters contain a TATA box to signal +1 Geometry of RNA synthesis Alignment of some human gene sequences: Some human genes showing TATA-box promoter sequences near the transcription start site 5

6 Transcription and Translation RNA Cells are governed by a cellular chain of command DNA RNA protein Transcription Is the synthesis of RNA under the direction of DNA Produces messenger RNA (mrna) Translation Is the actual synthesis of a polypeptide, which occurs under the direction of mrna Occurs on ribosomes Table 17.1 Synthesis of an RNA Transcript - Initiation Promoters signal the initiation of RNA synthesis Transcription factors help eukaryotic RNA polymerase recognize promoter sequences Synthesis of an RNA Transcript - Elongation RNA polymerase synthesizes a single strand of RNA against the DNA template strand (antisense strand), adding nucleotides to the 3 end of the RNA chain As RNA polymerase moves along the DNA it continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides 6

7 Transcription Overview Specific sequences in the DNA signal termination of transcription When one of these is encountered by the polymerase, the RNA transcript is released from the DNA and the double helix can zip up again. Translation is the RNA-directed synthesis of a polypeptide Translation involves mrna Ribosomes - Ribosomal RNA Transfer RNA Genetic coding - codons Translation TRANSCRIPTION TRANSLATION DNA mrna Ribosome Polypeptide Polypeptide Trp Phe Amino acids trna with amino acid attached Ribosome Gly trna A G C A A A C C G Anticodon U G G U U U G G C 5ʹ mrna Codons 3ʹ The Genetic Code The Genetic Code Genetic information is encoded as a sequence of nonoverlapping base triplets, or codons Codons: 3 base code for the production of a specific amino acid, sequence of three of the four different nucleotides Since there are 4 bases and 3 positions in each codon, there are 4 x 4 x 4 = 64 possible codons 64 codons but only 20 amino acids, therefore most have more than 1 codon 3 of the 64 codons are used as STOP signals; they are found at the end of every gene and mark the end of the protein One codon is used as a START signal: it is at the start of every protein Universal: in all living organisms 7

8 The Genetic Code A codon in messenger RNA is either translated into an amino acid or serves as a translational start/stop signal Transfer RNA Consists of a single RNA strand that is only about 80 nucleotides long Each carries a specific amino acid on one end and has an anticodon on the other end A special group of enzymes pairs up the proper trna molecules with their corresponding amino acids. trna brings the amino acids to the ribosomes, Wobble decoding Charging of trna with amino acid Unique amino acid charging enzyme for each trna type 3 dimensional trna molecule is roughly L shaped Wobble decoding reduces the need for trna species Between 32 and 40 trnas typically needed 8

9 The ribosome has four RNA binding sites Building a Polypeptide mrna aa-trna (A-side) Peptitdyl-tRNA (P-side) Deacylated-tRNA (E-side) Ribosomes facilitate the specific coupling of trna anticodons with mrna codons during protein synthesis The 2 ribosomal subunits are constructed of proteins and RNA molecules named ribosomal RNA or rrna We can divide translation into three stages Initiation Elongation Termination The AUG start codon is recognized by methionyl-trna or Met Once the start codon has been identified, the ribosome incorporates amino acids into a polypeptide chain RNA is decoded by trna (transfer RNA) molecules, which each transport specific amino acids to the growing chain Translation ends when a stop codon (UAA, UAG, UGA) is reached Translation initiation Translation elongation 9

10 Translation termination Transcription & Translation video 10