9.1 The Link between Genes and Proteins

1. 9.1 The Link between Genes and Proteins Chapter 9 Gene Expression and Gene Regulation • At the beginning of the 20th century, Garrod proposed that genetic disorders such as alkaptonuria result from biochemical alterations or “inborn errors of metabolism”

2. An Inborn Error of Metabolism • Alkaptonuria • An autosomal recessive trait with altered metabolism of homogentisic acid • Affected individuals do not produce the enzyme needed to metabolize this acid, and their urine turns black Fig. 9-1, p. 198

3. The Relationship Between Genes and Enzymes • Using Neurospora, Beadle and Tatum showed that mutations can produce a loss of enzyme activity and a mutant phenotype • Beadle proposed that genes control the synthesis of proteins and that protein function is responsible for producing the phenotype • Beadle and Tatum received the Nobel Prize in 1958

4. Genetic Information Is Stored in DNA • The information necessary to make proteins is encoded in the nucleotide sequence of DNA • Four DNA nucleotides must code for the 20 amino acids used to make proteins • Combinations of three nucleotides comprise codons that specify particular amino acids in a protein

5. Keep In Mind • The information necessary to make proteins is encoded in the nucleotide sequence of DNA

6. 9.2 The Genetic Code: The Key to Life • Information transferred from DNA to mRNA is encoded in a set of three nucleotides (codons) • Codons • Triplets of nucleotides in mRNA that encode the information for a specific amino acid in a protein • Of 64 possible codons, 61 code for amino acids, and 3 are stop codons • The codon AUG is a start codon and specifies methionine

7. The Genetic Code for Amino Acids Table 9-1, p. 199

8. Keep In Mind • The three nucleotides in a codon are a universal language specifying the same amino acid in almost all organisms

9. 9.3 Tracing the Flow of Genetic Information from Nucleus to Cytoplasm • Question: Where is DNA kept inside a cell? • Where does protein synthesis occur? • Transfer of information from the linear sequence of nucleotides in DNA to the linear sequence of amino acids in a protein occurs in two steps: transcription and translation

10. The Flow of Genetic Information • Transcription • Transfer of genetic information from the base sequence of DNA to the base sequence of RNA, mediated by RNA synthesis • Translation • Conversion of information encoded in the nucleotide sequence of an mRNA molecule into the linear sequence of amino acids in a protein

11. The Link Between Transcription and Translation • Messenger RNA (mRNA) • A single-stranded complementary copy of the nucleotide sequence in a gene

12. DNA Transcription pre-mRNA Cell mRNA processing Cytoplasm Nucleus mRNA Translation Polypeptide Fig. 9-2, p. 201

13. Interaction of Components • Transcription and translation require the interaction of ribosomes, mRNA, tRNA, amino acids, enzymes, and energy sources • Ribosomes are the sites on which protein synthesis occurs • tRNA molecules are adapters that recognize amino acids and the nucleotide sequence in mRNA

14. Keep In Mind • Genetic information for proteins, in the form of mRNA, moves from the nucleus to the cytoplasm, where it is translated into the amino acid sequence of a polypeptide

15. 9.4 Transcription Produces Genetic Messages • Transcription begins when DNA unwinds and one strand is used as template to make a pre-mRNA molecule • Transcription has three stages: initiation, elongation, and termination

16. Initiation and Termination • Promoter region • The region of a gene on a DNA molecule to which RNA polymerase binds and initiates transcription • Terminator Region • The nucleotide sequence at the end of a gene that signals the end of transcription

17. Transcription of a Gene

18. Transcription of a Gene

19. Gene region 5’ Promoter region RNA polymerase, the enzyme that catalyzes transcription (a) RNA polymerase binds to a promoter in the DNA, along with regulatory proteins (initiation). The binding positions the polymerase near a gene in the DNA. Only one strand of DNA provides a template for transcription of mRNA. Fig. 9-3a, p. 200

20. Newly forming RNA transcript DNA template winding up DNA template unwinding (b) The polymerase begins to move along the DNA and unwind it. As it does, it links RNA nucleotides into a strand of RNA in the order specified by the base sequence of the DNA (elongation). The DNA double helix rewinds after the polymerase passes. The structure of the “opened” DNA molecule at the transcription site is called a transcription bubble, after its appearance. Fig. 9-3b, p. 200

21. Transcription site Growing RNA transcript G (c) What happened in the gene region? RNA polymerase catalyzed the covalent bonding of many nucleotides to one another to form an RNA strand. The base sequence of the new RNA strand is complementary to the base sequence of its DNA template––a copy of the gene. Fig. 9-3c, p. 201

22. pre-mRNA (d) At the end of the gene region, the last stretch of the new transcript unwinds and detaches from the DNA template (termination). Fig. 9-3d, p. 201

23. Pre-mRNA must Undergo Modification and Splicing • Transcription produces large mRNA precursor molecules called pre-mRNA • Pre-mRNA is processed in the nucleus to produce mature mRNA

24. Processing and Splicing mRNA • Cap • A modified base (guanine nucleotide) attached to the 5’ end of eukaryotic mRNA molecules • Poly-A tail • A series of A nucleotides added to the 3’end of mRNA molecules • Why protection? HIV?

25. Processing and Splicing mRNA • Introns • DNA sequences present in some genes that are transcribed, but are removed during processing and therefore are not present in mature mRNA • Exons • DNA sequences that are transcribed, joined with other exons during mRNA processing, and translated into the amino acid sequence of a protein

26. Steps in the Processing and Splicing of mRNA

27. Unit of transcription in DNA strand Exon Intron Exon Intron Exon Transcription into pre-mRNA Cap Poly-A tail Snipped out Snipped out Mature mRNA transcript Fig. 9-4, p. 202

28. Alternative Splicing

29. Smooth-muscle mRNA Exons 1–12 pre-mRNA Striated-muscle mRNA Fig. 9-5, p. 202

30. Mutations in Splicing Sites and Genetic Disorders • Splicing defects cause several human genetic disorders • One hemoglobin disorder, b-thalassemia, is due to mutations at the exon/intron region and lower splicing efficiency

31. 9.5 Translation Requires the Interaction of Several Components • Translation requires the interaction of mRNA, amino acids, ribosomes, tRNA molecules, and energy sources • Twenty different amino acids are the building blocks used to make proteins

32. Amino Acids Commonly Found in Proteins Table 9-2, p. 203

33. Amino Acid Structure • Amino group • A chemical group (NH2) found in amino acids and at one end of a polypeptide chain • Carboxyl group • A chemical group (COOH) found in amino acids and at one end of a polypeptide chain

34. Amino Acid Structure • R group • Each amino acid has a different side chain, called an R group • An R group can be positively or negatively charged or neutral

35. An Amino Acid

36. Amino group Carboxyl group (a) Amino acid Fig. 9-6a, p. 203

37. Linking Amino Acids to Form Polypeptides • Peptide bond • A covalent chemical link between the carboxyl group of one amino acid and the amino group of another amino acid • Polypeptide • A molecule made of amino acids joined together by peptide bonds

38. Polypeptides Have Two Different Ends • N-terminus • The end of a polypeptide or protein that has a free amino group • C-terminus • The end of a polypeptide or protein that has a free carboxyl group

39. Formation of a Peptide Bond

40. Amino acid 2 Amino acid 1 (b) Peptide bond Fig. 9-6b, p. 203

41. Ribosomes • Ribosomes • Cytoplasmic particles composed of two subunits that are the site of protein synthesis • Ribosomal RNA (rRNA) • RNA molecules that form part of the ribosome

42. Ribosomes: Small and Large Subunits

43. Tunnel Small ribosomal subunit Large ribosomal subunit + Intact ribosome Fig. 9-7, p. 204

44. tRNA • Transfer RNA (tRNA) • A small RNA molecule that contains a binding site for a specific type of amino acid and has a three-base segment known as an anticodon that base-pairs with a specific base sequence (the codon) in messenger RNA

45. tRNA • Anticodon • A group of three nucleotides in a tRNA molecule that pairs with a complementary sequence (known as a codon) in an mRNA molecule

46. Transfer RNA (tRNA)

47. Codon in mRNA A U U A G C Anticodon in tRNA tRNA molecule site for amino acid attachment OH Fig. 9-8, p. 204

48. Initiation: Ribosomes Bring mRNA and tRNA Together • Initiation complex • Formed by the combination of mRNA, initiation tRNA, and the small ribosome subunit • The first step in translation

49. Elongation: Forming a Polypeptide • Start codon • A codon present in mRNA that signals the location for translation to begin • The codon AUG functions as a start codon • The ribosome moves along the mRNA, linking amino acids and producing a growing polypeptide chain

50. Termination • Stop codon • A codon present in mRNA that signals the end of a growing polypeptide chain • The codons UAG, UGA, and UAA function as stop codons • At termination, the polypeptide is released from the ribosome and undergoes a conformational change to produce a functional protein