Branches of Genetics

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1 Branches of Genetics 1. Transmission genetics Classical genetics or Mendelian genetics 2. Molecular genetics chromosomes, DNA, regulation of gene expression recombinant DNA, biotechnology, bioinformatics, genomics, proteomics 3. Population, evolutionary genetics allelic frequencies in populations effects of migration study relatedness of taxa via DNA and protein analysis 4. Quantitative genetics effects of many genes

2 Model Organisms cheap to grow short generation time can control mating no ethical concerns many offspring variation (humans?)

3 Prokaryotic model organism Bacteria example: E. coli What is a prokaryote?

4 Eukaryotic model organism 1. Unicellular Saccharomyces cerevisiae Bakers yeast Chlamydomonas reinhardtii Green algae

5 2. Multicellular Neurospora crassa Orange bread mold C. elegans Nematode worm

6 Xenopus laevis big eggs Zebra danio transparent development

7 Arabidopsis thaliana small plant/mustard family Drosophila melanogaster Fruit fly Mus musculus

8 GENES IN VARIOUS ORGANISMS T4 bacteriophage (virus) = 200 genes E. coli = 400 genes, almost all DNA encodes proteins H. sapiens = ~ 20,000 genes, 98% of DNA is non-coding 8

9 Gene Expression Genes control phenotype Cellular environment affects gene expression Involves extensive intracellular signaling Tissue, development, disease specific 9

10 Transcription Copy DNA to make mrna DNA + RNA polymerase + nucleotides mrna template enzyme building blocks transcript 10

11 I. TRANSCRIPTION (prokaryotes) A. INITIATION RNA polymerase recognizes the promoter of the gene 11

12 The template strand is read 3 5 RNA polymerase acts 5 3 RNA polymerase transcribes double stranded DNA mrna 5 G 5 GGTATACCTACC3 coding/sense 3 CCATATGGATGG5 template 12

13 Promoters = regulatory elements upstream of coding region of gene (+1) recognized by RNA polymerase Upstream Downstream Prokaryotes: -10 box (Pribnow) and -35 box 13

14 Consensus sequence of promoters If promoter has a slightly different sequence, it will not be as strong in initiating transcription 14

15 B. ELONGATION of mrna transcript RNA pol - synthesizes mrna from template DNA DNA exposed one base at a time (transcription bubble) The template strand (3 > 5 ) is read to make mrna strand 15

16 Once the polymerase has moved, another polymerase molecule can initiate to make another mrna transcript. What does this mean? C. TERMINATION RNA pol loosens, mrna dissociates 16

17 contrast prokaryotes with eukaryotes PROKARYOTES 1. no nucleus 2. 1 RNA polymerase 3. cotranslation 4. Polycistronic mrna One promoter shared by a few genes 5. All of gene is coding = no modification of mrna 17

18 1. 3 RNA polymerases RNA pol I transcribes rrna genes eukaryotes RNA pol II transcribes mrna and snrnas RNA pol III transcribes trna genes 2. Split genes Genes have coding and non-coding sequences Non-coding removed from mrna Transcription and translation in separate compartments of the cell 18

19 Split genes in eukaryotes exons - coding (expressed sequences) introns = intervening sequences non-coding but transcribed into mrna 19

20 Chick collagen = 37kb with 50 introns mrna/dna hybrid shows introns as loops 20

21 3. Promoters TATA promoter at -25 Promoter proximal elements Basal element 21

22 Promoter (s) = recognized by RNA polymerase II UTR = untranslated region (transcribed, not translated) Introns = non coding sequences within gene Exons = coding regions <- upstream downstream -> Note start site of transcription versus start site of translation 22

23 4. Enhancers=DNA sequences enhance transcription rate up to from transcriptional start Upstream, downstream or within gene orientation independent 23

24 Review 4 types of genes and associated RNAs protein coding -> mrnas -> protein trna genes -> transfer RNAs brings aa to ribosomes during translation r RNA genes -> ribosomal RNAs Component of ribosomes snrna genes -> small nuclear RNAs Processes mrna 24

25 Initiation of transcription in eukaryotes 2 types of proteins required: 1. Transcription factors allow RNA pol II to bind promoter 2. RNA polymerase II 25

26 26

27 A. Addition of 7 methyl guanosine cap Added to 5 end of mrna transcript increases half life of mrna (stability) recognition site for ribosome binding 27

28 A. Addition of 7 methyl guanosine cap Added to 5 end of mrna transcript increases half life of mrna (stability) recognition site for ribosome binding 28

29 B. Addition of the Poly A tail Poly A tail Poly A tail of ~200 A s added to end of transcript Increases the half life of the mrna 29

30 C. Removal of introns 30

31 Splicing excises introns at specific exon/intron junction sites. Joins exons. 31

32 Components of the spliceosome snrnps + mrna = spliceosome Snurps are sn RNAs + proteins 32

33 Gene mutations and beta thalassemia Beta thalassemia Mutation beta globin gene Inherited blood disorder (autosomal recessive) Can cause mild severe anemia, poor appetite, slow growth, bone abnormalities, enlarged heart Nucleated (immature) red blood cells More than 200 mutations identified 33

34 Thalassemia B 0 no beta globin produced no Hb B + low Hb production 34

35 Single base change (point) mutations 35

36 Single base change (point) mutations 36

37 Cis elements and trans factors Cis elements DNA sequences near gene that are required for gene expression Example: Trans factors proteins that bind to cis elements Example: 37

38 VII. TRANSLATION 38

39 A. Translation end product = PROTEINS 1. Protein Facts a. Amino acid building block of protein 20 in nature 39

40 b. Peptide short stretch of amino acids c. Polypeptide the fully translated message d. Protein functional, 3D shape 40

41 2. Protein structure Primary structure sequence of aa Secondary structure spontaneous folds 41

42 Tertiary structure 3D Quaternary structure Some proteins have multiple subunits Example: hemoglobin 42

43 B. The genetic code Nirenberg and Khorana 1965 Nobel Prize 1. 4 nucleotide bases encode 20aa TRIPLET CODE 64 possible codons 43

44 2. Non-overlapping 3. Degenerate More than 1 codon per particular amino acid 4. Universal A few differences in mitochondria, yeast 44

45 Most polymorphisms are in the 3rd position of codon Why? 45

46 5. 61 sense codons start codon AUG (methionine) Initiation of translation All proteins start with met, in some removed post translation 6. 3 stop codons UAA, UAG, UGA 46

47 Which part is the 5 UTR of the mrna? 47

48 Example of the genetic code A partial mrna is as follows: 5 AGGAGGCUCGAACAUGUCAAUAUGCUUGUCCUGACGC 3 start site for translation? amino acid sequence upon translation? open reading frame? 48

49 C. Ribosomes translate the mrna to amino acid sequence 100,000s /cell protein + rrna 49

50 Polysome = many ribosomes can translate single message to produce many copies of protein 50

51 1. Initiation D. Translation steps mrna read 5 -> 3 initiating at AUG 51

52 2. Elongation trnas bring amino acid to ribosome 52

53 2 codons can sit in a ribosome at once 53

54 DNA coding A T G A C T A G C DNA template T A C T G A T C G A C C C C C A T A A T G A A A A T C mrna A U G A C U A G C U G G G G G U A U U A C U U U U A G trna Aa U A C U G A Tyr--- 54

55 trna cloverleaf structure how? wobble ->30 trnas for 61 codons 55

56 3. Termination of translation Stop codon 56

57 VIII. Post translation - to the endoplasmic reticulum for processing 57

58 IX. CONTROL OF GENE EXPRESSION 58

59 1.Hormonal control of gene expression 59

60 3. Splicing of mrna alternate splicing to form protein isoforms 60

61 4. mrna half life poly A tail and 5 cap. The longer the mrna is in the cytoplasm, the more protein 61

62 5. RNA interference (RNAi) Silencing of mrna (cytoplasm) by tiny dsrna! mrna degradation RNAi can selectively turn off disease gene expression 62

63 RNAi dsrna complementary to red eye pigment microinjected into Drosophila embryos 63