Vocabulary

1. Vocabulary Replication -- copying DNA before cell division Transcription -- making an RNA copy (messenger RNA or mRNA) of DNA. Note -- Transcription involves copying in the same language (e.g., court transcription). Translation -- making a protein from the mRNA. Note -- The nucleic acid language is being translated into the protein language.

2. Clicker question DNA is transcribed into RNA in the _______.RNA is translated into protein in the _______. 1) Endoplasmic reticulum, Golgi apparatus 2) Golgi apparatus, Endoplasmic reticulum 3) Nucleus, cytoplasm 4) Cytoplasm, nucleus 5) Nucleus, nucleus 6) Cytoplasm, cytoplasm

3. mRNA is spliced before leaving the nucleus to remove non-coding regions (introns)

4. Definitions Intron -- Non-coding intervening sequence Exon -- Coding, or expressed, sequences Bacterial genes don�t have introns

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8. Evolutionary flexibility A way to control gene expression  BUT Cell has to maintain larger genome Cell throws out a large fraction of the RNA it synthesizes

9. WHY INTRONS?

10. We can translate because we know the code

12. How did Sydney Brenner rule out the possibility of an overlapping triplet code? 1) By noticing that an overlapping code would restrict which amino acids were next to each other, but finding no evidence for restrictions in protein sequences. 2) By realizing that an overlapping code would produce too many stop codons. 3) By sequencing RNA and proteins. By looking up the answer in Wikipedia. By asking a Bi1 student.

13. The genetic code is degenerate In addition, there are three stop codons (UAA, UGA and UAG) and one start codon (AUG)*. *AUG codes for methionine, which can also be in the middle of a protein.

14. Clicker question In which of the following would one find exceptions to the genetic code? 1) Mitochondria 2) Some yeast 3) Some ciliates 4) Some bacteria 5) Bi1 students 6) All of the above

15. Clicker question Why do mitochondria contain their own DNA? 1) Proteins cannot pass through the double membrane of a mitochondrion, therefore they have to be synthesized inside it. 2) Mitochondria originated from bacteria that were engulfed by an ancestral eukaryotic cell. They survived, gradually losing some, but not all, of their genes. 3) All intracellular organelles contain DNA, so mitochondria share this property with the endoplasmic reticulum and Golgi apparatus. 4) Because mitochondria are continuously dividing and fusing during the lifetime of the cell, localized transcription and translation allows them to respond quickly to metabolic needs of the cell. 5) To confuse Bi1 students.

16. Clicker question Why do mitochondria contain their own DNA? Mitochondria originated from bacteria that were engulfed by an ancestral eukaryotic cell. They survived, living in symbiosis with their host, gradually losing some, but not all, of their genes.

17. mRNA can be read in 3 different reading frames

18. Clicker question How would you design a system to pair an amino acid with its correct codon? 1) Evolve =20 different amino acid-carrying proteins that recognize triplet codons. 2) Design amino acids that bind specifically to their codon(s). 3) Evolve enzymes to attach amino acids to triplets of RNA. 4) Evolve =20 different �adapter� RNAs, each of which uses one region to recognize a particular codon and another region to bind the amino acid corresponding to that codon.

20. Clicker question 1) Three hairpins are formed due to short regions of complementary RNA, which basepair. 2) Some of the bases in tRNA are hydrophobic, so these form a hydrophobic core that is shielded from water. 3) The clover leaf structure maximizes the possible interactions between oppositely-charged basepairs. 4) tRNAs evolved from clover plants.

21. Translation

23. Translation in more detail

24. Incorporating unnatural amino acids into proteins In vivo nonsense suppression Nonsense mutations (those that introduce stop codons) can be �suppressed� by a suppressor tRNA (anti-codon recognizes a stop codon, but tRNA is coupled to an amino acid) Use organic chemistry to couple an unnatural amino acid to a suppressor tRNA Deliver unnatural amino acids to the ribosome Extend the genetic code beyond 20 amino acids! See Dennis Dougherty and David Tirrell (CCE) for more information

27. Ribosomes are 2/3 RNA, 1/3 protein

28. Translating polyribosomes

33. EXTRA SLIDES & MOVIES

34. tRNA synthetase couples an amino acid to its tRNA, then the tRNA anticodon base pairs with the appropriate codon on the mRNA

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37. RNA splicing mechanism movie

38. Initiator tRNA searches for the start signal along mRNA 07_32_initiation.jpg07_32_initiation.jpg

39. Propose a mechanism by which the highlighted areas could cause transcription to stop. 5) The first two sequences are inverted repeats of each other, thus a hairpin, which is a signal for termination.

40. How can tRNAs and other hairpin-containing RNAs be transcribed? Need stretch of Uridines in RNA after hairpin -- otherwise RNA polymerase slows down rather than terminates. Termination not precise -- transcripts contain different lengths of 3� untranslated regions. Sometimes terminator or anti-terminator proteins are involved.