Genes and How They Work

1. Genes and How They Work Chapter 15

2. The Nature of Genes Early ideas to explain how genes work came from studying human diseases. Archibald Garrod studied alkaptonuria, 1902 • Garrod recognized that the disease is inherited via a recessive allele • Garrod proposed that patients with the disease lacked a particular enzyme These ideas connected genes to enzymes.

3. The Nature of Genes Evidence for the function of genes came from studying fungus. George Beadle and Edward Tatum, 1941 • studied Neurospora crassa • used X-rays to damage the DNA in cells of Neurospora • looked for cells with a new (mutant) phenotype caused by the damaged DNA

4. The Nature of Genes Beadle and Tatum looked for fungal cells lacking specific enzymes. • The enzymes were required for the biochemical pathway producing the amino acid arginine. • They identified mutants deficient in each enzyme of the pathway.

6. The Nature of Genes Beadle and Tatum proposed that each enzyme of the arginine pathway was encoded by a separate gene. They proposed the one gene – one enzyme hypothesis. Today we know this as the one gene – one polypeptide hypothesis.

7. The Nature of Genes The central dogma of molecular biology states that information flows in one direction: DNA RNA protein Transcription is the flow of information from DNA to RNA. Translation is the flow of information from RNA to protein.

9. The Genetic Code Deciphering the genetic code required determining how 4 nucleotides (A, T, G, C) could encode more than 20 amino acids. Francis Crick and Sydney Brenner determined that the DNA is read in sets of 3 nucleotides for each amino acid.

11. The Genetic Code codon: set of 3 nucleotides that specifies a particular amino acid reading frame: the series of nucleotides read in sets of 3 (codon) • only 1 reading frame is correct for encoding the correct sequence of amino acids

12. The Genetic Code Marshall Nirenberg identified the codons that specify each amino acid. RNA molecules of only 1 nucleotide and of specific 3-base sequences were used to determine the amino acid encoded by each codon. The amino acids encoded by all 64 possible codons were determined.

14. The Genetic Code stop codons: 3 codons (UUA, UGA, UAG) in the genetic code used to terminate translation start codon: the codon (AUG) used to signify the start of translation The remainder of the code is degenerate meaning that some amino acids are specified by more than one codon.

15. Gene Expression Overview template strand: strand of the DNA double helix used to make RNA coding strand: strand of DNA that is complementary to the template strand RNA polymerase: the enzyme that synthesizes RNA from the DNA template

16. Gene Expression Overview Transcription proceeds through: • initiation – RNA polymerase identifies where to begin transcription • elongation – RNA nucleotides are added to the 3’ end of the new RNA • termination – RNA polymerase stops transcription when it encounters terminators in the DNA sequence

17. Gene Expression Overview • Translation proceeds through • initiation – mRNA, tRNA, and ribosome come together • elongation – tRNAs bring amino acids to the ribosome for incorporation into the polypeptide • termination – ribosome encounters a stop codon and releases polypeptide

18. Gene Expression Overview Gene expression requires the participation of multiple types of RNA: messenger RNA (mRNA) carries the information from DNA that encodes proteins ribosomal RNA (rRNA) is a structural component of the ribosome transfer RNA (tRNA) carries amino acids to the ribosome for translation

19. Gene Expression Overview Gene expression requires the participation of multiple types of RNA: small nuclear RNA (snRNA) are involved in processing pre-mRNA signal recognition particle (SRP) is composed of protein and RNA and involved in directing mRNA to the RER micro-RNA (miRNA) are very small and their role is not clear yet

20. Prokaryotic Transcription Prokaryotic cells contain a single type of RNA polymerase found in 2 forms: • core polymerase is capable of RNA elongation but not initiation • holoenzyme is composed of the core enzyme and the sigma factor which is required for transcription initiation

22. Prokaryotic Transcription A transcriptional unit extends from the promoter to the terminator. The promoter is composed of • a DNA sequence for the binding of RNA polymerase • the start site (+1) – the first base to be transcribed

23. Prokaryotic Transcription During elongation, the transcription bubble moves down the DNA template at a rate of 50 nucleotides/sec. The transcription bubble consists of • RNA polymerase • DNA template • growing RNA transcript

25. Prokaryotic Transcription Transcription stops when the transcription bubble encounters terminator sequences • this often includes a series of A-T base pairs In prokaryotes, transcription and translation are often coupled – occurring at the same time

28. Eukaryotic Transcription RNA polymerase Itranscribes rRNA. RNA polymerase II transcribes mRNA and some snRNA. RNA polymerase IIItranscribes tRNA and some other small RNAs. Each RNA polymerase recognizes its own promoter.

29. Eukaryotic Transcription Initiation of transcription of mRNA requires a series of transcription factors • transcription factors – proteins that act to bind RNA polymerase to the promoter and initiate transcription

30. Eukaryotic pre-mRNA Splicing In eukaryotes, the primary transcript must be modified by: • addition of a 5’ cap • addition of a 3’ poly-A tail • removal of non-coding sequences (introns)

31. Eukaryotic pre-mRNA Splicing The spliceosome is the organelle responsible for removing introns and splicing exons together. Small ribonucleoprotein particles (snRNPs)within the spliceosome recognize the intron-exon boundaries • introns – non-coding sequences • exons – sequences that will be translated

32. tRNA and Ribosomes tRNAmolecules carry amino acids to the ribosome for incorporation into a polypeptide • aminoacyl-tRNA synthetasesadd amino acids to the acceptor arm of tRNA • the anticodon loop contains 3 nucleotides complementary to mRNA codons

35. tRNA and Ribosomes The ribosome has multiple tRNA binding sites: • P site – binds the tRNA attached to the growing peptide chain • A site – binds the tRNA carrying the next amino acid • E site – binds the tRNA that carried the last amino acid

37. tRNA and Ribosomes The ribosome has two primary functions: • decode the mRNA • form peptide bonds peptidyl transferase is the enzymatic component of the ribosome which forms peptide bonds between amino acids

38. Translation In prokaryotes, initiation of translation requires the formation of the initiation complex including • an initiator tRNA charged with N-formylmethionine • the small ribosomal subunit • mRNA strand The ribosome binding sequence of mRNA is complementary to part of rRNA

40. Translation Elongation of translation involves the addition of amino acids • a charged tRNA binds to the A site if its anticodon is complementary to the codon at the A site • peptidyl transferase forms a peptide bond • the ribosome moves down the mRNA in a 5’ to 3’ direction

43. Translation There are fewer tRNAs than codons. Wobble pairing allows less stringent pairing between the 3’ base of the codon and the 5’ base of the anticodon. This allows fewer tRNAs to accommodate all codons.

44. Translation Elongation continues until the ribosome encounters a stop codon. Stop codons are recognized by release factors which release the polypeptide from the ribosome.

46. Translation In eukaryotes, translation may occur on ribosomes in the cytoplasm or on ribosomes of the RER. Signal sequences at the beginning of the polypeptide sequence bind to the signal recognition particle (SRP) The signal sequence and SRP are recognized by RER receptor proteins.

47. Translation The signal sequence/SRP holds the ribosome on the RER. As the polypeptide is synthesized it passes through a pore into the interior of the endoplasmic reticulum.

49. Mutation: Altered Genes Point mutations alter a single base. • base substitution mutations – substitute one base for another • transitionsor transversions • also called missense mutations • nonsense mutations – create stop codon • frameshift mutations – caused by insertion or deletion of a single base