BIOL 1030 Introduction to Biology: Organismal Biology. Fall 2009 Sections B & D. Steve Thompson:

Transcription

1 BIOL 1030 Introduction to Biology: Organismal Biology. Fall 2009 Sections B & D Steve Thompson: stthompson@valdosta.edu 1

2 DNA transcription and regulation We ve seen how the principles of classical genetics affects the heredity of phenotypic traits, and we ve seen how DNA is duplicated and segregated in mitosis and meiosis, but where do all those proteins that make up a phenotype come from and how do they end up in the right place at the right time?! 2

3 Remember DNA s structure It s a double helix, where the... Rungs are base pairs joined by hydrogen bonds. And the bases... Adenine (A) pairs with thymine (T), and... Cytosine (C) pairs with guanine (G). The strands are complementary, and... They are oriented in opposite directions, 5 to 3, or 3 to 5. 3

4 This should be very familiar to you by now! 4

5 Biology s Central Dogma DNA RNA protein Transcription cell copies DNA to RNA. Translation RNA information used to manufacture proteins. In Eukaryotes transcription happens inside the nucleus, whereas translation happens outside it. 5

6 Here s an overview student_view0/chapter15/simple_gene_expression.html 6

7 Remember the two types of nucleic acid DNA and RNA. Not structural and catalytic RNA 7

8 And the way the base pairing works 8

9 We ll cover three types of RNA today Messenger RNA (mrna) carries information specific to a protein; three (DNA) RNA bases form a codon, specifying a particular amino acid. Ribosomal RNAs (rrna) combine with proteins to form a ribosome. Transfer RNA (trna) carries a specific amino acid to the ribosome. 9

10 One more time... 10

11 Transcription (DNA to RNA) has three major steps Initiation; Enzymes unwind DNA exposing template strand; RNA polymerase binds to promoter; Elongation; RNA polymerase moves 3 to 5 ; Termination; RNA polymerase reaches terminator sequence at end of gene; RNA separates may be mrna, trna, or rrna; DNA reforms helix. 11

12 Here are the steps of transcription illustrated, broken down into the three major events. 12

13 And here it is in animation animations/chapter12/stages_transcription.swf 13

14 mrna modification In Bacteria and Archaea, ribosomes begin translating mrna as soon as transcription is complete. This all happens in the cytosol of the cell. In eukaryotes mrna is usually altered. A 5 cap and a poly-a tail is added to enhance translation by helping the ribosome to attach. Why and how? And the biggy introns (intervening sequences) are removed, leaving exons, which are spliced together by spliceosomes. 14

15 mrna modification occurs in the nucleus in Eukaryotes. 15

16 Contrast this with Bacteria and Archaea Chapter12/process_gene_information.swf 16

17 On to translation mrna to protein 17

18 The universal genetic code: An mrna codon with three bases specifies an amino acid, and signals start and stop. But it s redundant! 18

19 Translation requires all three major types of RNA mrna contains the genetic information specifying an exact amino acid order in the codons encoded in an organism s DNA. trna specific trnas bring specific amino acids to the ribosome by pairing their anticodon to each mrna codon. Ribosome a combination of rrnas and proteins that make protein factories. 19

20 The trna has a clover-leaf shape with the amino acid site on the stem. 20

21 The ribosome has two major components. Here s an example from a random Eukaryote. It contains 82 proteins and four rrnas ( knell.edu/kfield/ organelles/ ribosome.html). 21

22 Translation also has three steps. Initiation: The mrna start codon binds to the small ribosomal subunit. The First trna (methionine) binds to mrna codon. Elongation: The large ribosomal subunit attaches to the complex. The trna corresponding to second codon attaches. Covalent bond (the peptide bond) forms between adjacent amino acids. The ribosome releases the empty first trna. The ribosome shifts down one codon, allowing the third trna to bind. The polypeptide grows one amino acid at a time. Termination: The stop codon (UGA, UAG, or UAA) is reached, and the... New polypeptide is released. 22

23 Here s an overview, starting with initiation. This all happens both free in the cytosol and bound on the outside of the ER membranes in Eukaryotes (and in mitochondria and chloroplasts). 23

24 And then the large subunit binds and elongation starts. 24

25 And finally a stop codon is reached and termination occurs. 25

26 Here s a nice overview animations/chapter12/translation.swf 26

27 The chain grows and multiple proteins are built at the same time. 27

28 And one more time, the whole process animations/chapter12/protein_synthesis.swf 28

29 Protein folding Proteins must achieve their final functional shape before they can work some regions attract or repel, enzymes catalyze bonding, chaperone proteins may stabilize the process. Errors in folding can lead to illness, e.g. prions. Some proteins must be altered. For example... Insulin has some amino acids removed. Many proteins don t work alone (quaternary structure). For example... Hemoglobin has four separate polypeptide subunits (two alpha and two beta in adult). 29

30 Regulation control of gene expression Protein synthesis is fast and efficient, but it has a... Tremendous ATP requirement. For example E. coli spends 90% of it ATP on protein synthesis. Therefore,... Cells save energy by not producing unneeded proteins (plus differentiation). Only those proteins that are needed by that particular cell at that particular time are produced. 30

31 Operons in bacteria Operons are a group of genes plus their promoter and operator, which control the transcription of group as a whole. Promoter where RNA polymerase attaches. Operator DNA sequence where a repressor can bind to inhibit transcription. For example, the lac operon three lactose degrading enzymes plus their promoter and operator. Without lactose a repressor turns genes off. With lactose, a modified form of the sugar binds to the repressor causing it to fall off the promoter. Transcription can proceed. 31

32 Here s how the components are organized on the bacterial DNA. 32

33 And here s what happens without lactose around. 33

34 But with lactose in the environment... 34

35 Eukaryotes are way more complex! Different cell types must express different subsets of genes at different times (known as differentiation). Transcription factors (>2000 known in humans) are required for RNA polymerase to bind to a promotor. Signal transduction is one way of activating amd/or deactivating various transcription factors. And there s a slew of additional regulatory mechanisms, e.g.... Methylation, sirna, and... Alternative splicing. Plus... Many, many others! 35

36 Here s a way oversimplified view of how a transcription factor works. Many databases of these exist, e.g. DBD/index.cgi? Home and jaspar.cgb.ki.se/ 36

37 And here s an example of alternative splicing. This is how the 25,000 some human genes can encode a million or so different proteins! 37

38 38

39 And now for something completely different: Mutations... Are a change in a cell s DNA sequence. They can be good, bad, or silent (neutral). There are many types of mutation: One is a point mutation. This... Substitutes one DNA base for another (Single nucleotide polymorphism). If it occurs in an exon, it can be silent (synonymous) if the same amino acid is specified. Or it... Can be nonsense if it changes a codon into a stop. Or it... Can be missense (nonsynonymous) if it changes the amino acid, which, again, can be good, bad, or neutral. However, it may cause disease, e.g. sickle cell anemia (but this is a mutation that is inherited, i.e. it is in every cell of your body). 39

40 Most forms of sickle cell are a one amino acid change caused by a single base substitution. But you inherit this mutation, it doesn t occur in your blood! 40

41 Here s an example of a single point substitution (SNP) Chapter12/Mutation_by_base_substitution.swf 41

42 Another class of mutations are base insertions and deletions If these occur in an exon, and are not in multiples of three, then they will cause a... Frameshift mutation, which will usually destroy the encoded protein! An expanding repeat is another type the number of copies of a particular nucleotide sequence increases over several generations. If this occurs in an exon, and is in multiples of three, then it will cause an amino acid repeat sequence to expand, e.g. Huntington s chorea. Insertions and deletions can occur in crossing over during meiosis. Therefore, the progeny will have em. 42

43 Here s an example of what happens when you insert extra bases into an exon (reading frame). 43

44 An animation illustrates a simple insertion or deletion mutation that can occur during DNA replication. Chapter12/Addition_and_deletion_mutations.swf 44

45 And here s an example of an entire gene getting duplicated in one chromatid and deleted in the other during crossing over in meiosis. 45

46 Know the vocabulary! 46

47 Causes of mutation Spontaneous DNA replication errors can cause substitution (point), insertion, or deletion mutations. Meiotic error can cause duplication or deletion mutations, and... Chromosome inversion and translocations. Transposons are moveable, jumping gene DNA sequences that can insert themselves into a reading frame, interrupting its function. Mutation can be accelerated by mutagens external agents, e.g. radiation, and many different chemicals, e.g. tar in cigarettes! 47

48 Heritable mutations Somatic mutations occur in nonsex cells, i.e. all the cells of your body except those that create sperm or eggs through meiosis. Those are called germ cells. All cells derived (through mitosis) from a mutated somatic cell carry that mutation (e.g. cancer). The mutation is not passed to any offspring! Contrast this with a germline mutation. It is... Heritable, and will passed on in every gamete produced by that individual. Plus it will be passed on for every generation from that point on (according to the odds of classical genetics). Mutations are incredibly important! As they... Create new gene variants (alleles) that fuel evolution; e.g.... Random mutations can result in antibiotic resistant bacteria. 48