From DNA to Protein: Gene Expression

1. 10 From DNA to Protein: Gene Expression

2. Chapter 10 From DNA to Protein: Gene Expression • Key Concepts • 10.1 Genetics Shows That Genes Code for Proteins • 10.2 DNA Expression Begins with Its Transcription to RNA • 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins

3. Chapter 10 From DNA to Protein: Gene Expression • 10.4 Translation of the Genetic Code Is Mediated by tRNA and Ribosomes • 10.5 Proteins Are Modified after Translation

4. Chapter 10 Opening Question • How do antibiotics target bacterial protein synthesis?

5. Concept 10.1 Genetics Shows That Genes Code for Proteins • Identification of proteins as gene products began in the early 20th century. • Children with a rare disease called alkaptonuria had parents who were first cousins. • Garrod realized they must be homozygous for a recessive mutant gene. • He isolated homogentisic acid from the children, which accumulated in the blood, joints, and urine.

6. Concept 10.1 Genetics Shows That Genes Code for Proteins • Garrod speculated that homogentisic acid is normally broken down to a harmless product by an enzyme, but the dominant wild-type allele for the enzyme was mutated in alkaptonuria patients. • These and other studies led him to correlate one gene to one enzyme.

7. Concept 10.1 Genetics Shows That Genes Code for Proteins • Homogentisic acid is part of a biochemical pathway of protein breakdown. • Phenylketonuria is another genetic disease that involves this pathway. • The enzyme that converts phenylalanine to tyrosine is nonfunctional. • Untreated, it can lead to mental retardation, but is easily detected in newborns.

8. Figure 10.1 Metabolic Diseases and Enzymes

9. Concept 10.1 Genetics Shows That Genes Code for Proteins • Study of alkapatonuria and phenylketonuria led to the “one gene–one enzyme” hypothesis. • But studies of proteins made up of multiple polypeptides showed that this hypothesis was an oversimplification.

10. Concept 10.1 Genetics Shows That Genes Code for Proteins • Hemoglobin consists of 4 polypeptide chains. • Variations in human populations show hundreds of single amino acid alterations in the β-chains, such as the one that results in sickle-cell disease. • The one gene–one enzyme relationship has since been revised to the one gene–one polypeptide relationship.

11. Figure 10.2 Gene Mutations and Amino Acid Changes

12. Concept 10.1 Genetics Shows That Genes Code for Proteins • Not all genes code for polypeptides. • Some are transcribed to RNA but not translated to polypeptides; the RNAs have other functions. • Molecular biology: the study of nucleic acids and proteins; often focuses on gene expression

13. Concept 10.1 Genetics Shows That Genes Code for Proteins • Gene are expressed in two steps: • Transcription: information from a DNA sequence is copied to a complementary RNA sequence • Translation:converts the RNA sequence to an amino acid sequence

14. Concept 10.1 Genetics Shows That Genes Code for Proteins • Three types of RNA: • Messenger RNA (mRNA)—a DNA sequence is copied to produce a complementary mRNA strand, which moves to a ribosome to be translated. • The nucleotide sequence of the mRNA determines the sequence of amino acids in the polypeptide chain.

15. Concept 10.1 Genetics Shows That Genes Code for Proteins • Ribosomal RNA (rRNA), along with proteins, makes up ribosomes; one catalyzes peptide bond formation. • Transfer RNA (tRNA) binds to specific amino acids and to specific sequences on mRNA by base pairing. • tRNA recognizes which amino acid should be added next in a growing polypeptide and carries it to the ribosome.

16. Figure 10.3 From Gene to Protein

17. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Transcription requires several components: • A DNA template for base pairings • The 4 nucleoside triphosphates (ATP, GTP, CTP, UTP) • An RNA polymerase enzyme

18. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • RNA polymerases catalyze synthesis of RNA from the DNA template. • RNA polymerases are processive—a single enzyme–template binding results in polymerization of hundreds of RNA bases. • Unlike DNA polymerases, RNA polymerases do not need primers.

19. Figure 10.4 RNA Polymerase

20. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Transcription occurs in three steps: • Initiation • Elongation • Termination

21. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Initiation requires a promoter—a control sequence of DNA that tells RNA polymerase where to start transcription and which strand to transcribe. • Each promoter has a transcription initiation site. • Other proteins (sigma factors and transcription factors) bind “upstream” from the initiation site and help RNA polymerase bind and determine which genes are expressed.

22. Figure 10.5 DNA Is Transcribed to Form RNA (Part 1)

23. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Elongation: RNA polymerase unwinds DNA and reads template in 3′-to-5′ direction. • RNA polymerase adds nucleotides to the 3′ end of the new strand; the RNA transcript is antiparallel to the DNA template strand. • Uracil (not thymine) in the RNA molecule is paired with adenine in the DNA molecule. • RNA polymerases can proofread but allow more mistakes.

24. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Termination is specified by a specific DNA sequence. • Mechanisms of termination are complex and vary among different genes and organisms. • In eukaryotes, multiple proteins are involved in recognizing the termination sequence and separating the newly formed RNA from the DNA template and RNA polymerase.

25. Figure 10.5 DNA Is Transcribed to Form RNA (Part 2)

26. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Coding regions are sequences of DNA that are expressed as proteins. • In prokaryotes, most of the DNA is made up of coding regions. • In prokaryotes and viruses, several adjacent genes sometimes share one promoter.

27. Table 10.1

28. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • In eukaryotes each gene has its own promoter and most have noncoding sequences called introns. • The transcribed regions are exons. • Introns and exons both appear in the primary mRNA transcript (pre-mRNA); introns are removed from the final mRNA.

29. Figure 10.6 Transcription of a Eukaryotic Gene

30. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Nucleic acid hybridization can be used to locate introns. • Target DNA is denatured by heat to separate the strands. • It is then incubated with a probe—a nucleic acid strand from another source. • If the probe has a complementary sequence, it forms a hybrid with the DNA by base pairing.

31. Figure 10.7 Nucleic Acid Hybridization

32. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Researchers used this technique to examine the β-globin gene with previously isolated β-globin mRNA as the probe. • Viewing the hybridized molecules by electron microscopy, they saw that the introns formed loops—stretches of DNA that did not have complementary base sequences on the mature mRNA. • If pre-mRNA was used, the result was a linear matchup—complete hybridization.

33. Figure 10.8 Demonstrating the Existence of Introns

34. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Introns interrupt, but do not scramble, the DNA sequence of a gene. • Most eukaryotic genes contain introns.

35. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • The pre-mRNA is modified: • RNA splicing removes introns and splices exons together. • Consensus sequences are short sequences between exons and introns; they are first bound by snRNPs—small nuclear ribonucleoprotein particles.

36. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • Then other proteins accumulate to form a large RNA–protein complex called a spliceosome. • The complex cuts the pre-mRNA, releases the introns, and joins the exons together to produce mature mRNA.

37. Figure 10.9 The Spliceosome: An RNA Splicing Machine

38. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • In the disease beta thalassemia, a mutation at an intron consensus sequence in the β-globin gene prevents the pre-mRNA from being spliced correctly. • Nonfunctional β-globin mRNA is produced, resulting in severe anemia. • This is an example of how mutations are used to elucidate cause-and-effect relationships.

39. Concept 10.2 DNA Expression Begins with Its Transcription to RNA • The pre-mRNA is also modified at both ends: • A 5′ cap (G cap) is added to the 5′ end. It facilitates binding to a ribosome and prevents digestion by ribonucleases. • A poly A tail is added to the 3′ end. It assists in export from the nucleus and contributes to the stability of the mRNA. • IN-TEXT ART, p. 202

40. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • Translation of the nucleotide sequence of an mRNA into an amino acid sequence occurs at ribosomes. • In prokaryotes, transcription and translation are coupled: ribosomes often bind to an mRNA as it is being transcribed. • In eukaryotes, the nuclear envelope separates mRNA production and translation.

41. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • The genetic information is a series of sequential, nonoverlapping, three-letter “words” (3 bases) called codons. • Each codon specifies an amino acid. • Codons were first identified by using short artificial polynucleotides instead of complex mRNAs.

42. Figure 10.10 Deciphering the Genetic Code (Part 1)

43. Figure 10.10 Deciphering the Genetic Code (Part 2)

44. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • There are more codons than amino acids. • AUG codes for methionine and is also the start codon. • UAA, UAG, and UGA are stop codons. • For most amino acids, there is more than one codon; the genetic code is redundant. • But it is not ambiguous—each codon specifies only one amino acid.

45. Figure 10.11 The Genetic Code

46. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • The genetic code is nearly universal: the codons that specify amino acids are the same in all organisms. • A few exceptions occur in mitochondria, chloroplasts, and some protists. • The genetic code is ancient; it unifies life and indicates that all life came from a common ancestor. • It is also the basis for genetic engineering.

47. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • Point mutations also confirm the genetic code. • Point mutations in a coding region are compared with the amino acid sequences in the resulting polypeptides. • Silent mutations can occur because of redundancy • Example: CCG and CCU are both translated as proline (Pro).

48. Figure 10.12 Mutations (Part 1)

49. Figure 10.12 Mutations (Part 2)

50. Concept 10.3 The Genetic Code in RNA Is Translated into the Amino Acid Sequences of Proteins • Missense mutations result in a change in the amino acid sequence. • Example: GAU is translated as aspartic acid (Asp), whereas a mutation that results in GUU is translated as valine (Val).