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  1. 1. BIOLOGY: Today and Tomorrow, 4e starr evers starr Chapter 7 Gene Expression and Control
  2. 2. 7.1 Ricin and Your Ribosomes  The ability to make proteins is critical to all life processes  Seeds of the castor-oil plant contain the protein ricin, a deadly poison that inactivates ribosomes that assemble proteins  Ricin has been used by assassins, and is banned as a weapon under the Geneva Protocol
  3. 3. Seeds of the castor-oil plant
  4. 4. 7.2 DNA, RNA, and Gene Expression  A gene is a DNA sequence that encodes an RNA or protein product in the sequence of its nucleotide bases (A, T, G, C)  In transcription, enzymes use the gene’s DNA sequence as a template to assemble a strand of messenger RNA (mRNA)  In translation, the protein-building information in mRNA is decoded into a sequence of amino acids  The result is a polypeptide chain that folds into a protein
  5. 5. sugar– phosphate backbone base pair nucleotide base deoxyribonucleic acid DNA ribonucleic acid RNA DNA and RNA
  6. 6. Gene Expression  Gene expression involves transcription (DNA to mRNA), and translation (mRNA to protein)  Gene expression  Process by which the information in a gene becomes converted to an RNA or protein product  Proteins (enzymes) assemble other molecules and perform many functions that keep the cell alive
  7. 7. 7.3 Transcription: DNA to RNA  During transcription, a strand of DNA acts as a template upon which a strand of RNA is assembled from nucleotides  Base-pairing rules in DNA replication apply to RNA synthesis in transcription, but RNA uses uracil in place of thymine  The enzyme RNA polymerase, not DNA polymerase, adds nucleotides to the end of a growing RNA strand
  8. 8. Base Pairing in Transcription
  9. 9. The Process of Transcription  In transcription, RNA polymerase binds to a promoter in the DNA near a gene  Polymerase moves along the DNA, unwinding the DNA so it can read the base sequence  RNA polymerase links RNA nucleotides in the order determined by the base sequence of the gene  The new mRNA is a copy of the gene from which it was transcribed
  10. 10. RNA polymerase gene region binding site in DNA The enzyme RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. Only one of the two strands of DNA will be transcribed into RNA. 1 RNA polymerase binds to a promoter
  11. 11. RNA DNA winding up DNA unwinding The polymerase begins to move along the gene and unwind the DNA. As it does, it links RNA nucleotides in the order specified by the nucleotide sequence of the template DNA strand. The DNA winds up again after the polymerase passes. The structure of the “opened” DNA at the transcription site is called a transcription bubble, after its appearance. 2 RNA nucleotides are linked
  12. 12. direction of transcription Zooming in on the transcription bubble, we can see that RNA polymerase covalently bonds successive nucleotides into an RNA strand. The new strand is an RNA copy of the gene. 3 RNA nucleotides are linked
  13. 13. Three Genes Being Transcribed  Many polymerases transcribe a gene region at the same time RNA molecules DNA molecule
  14. 14. RNA Modifications  Eukaryotic cells modify their RNA before it leaves the nucleus  Sequences that stay in the RNA are exons  Introns are sequences removed during RNA processing  Exons can be spliced together in different combinations, so one gene may encode different proteins  After splicing, a tail of 50 to 300 adenines (poly-A tail) is added to the end of a new mRNA
  15. 15. gene promoter exon intron exon intron exon DNA transcription newly transcribed RNA exon intron exon intron exon exon exon exon poly-A tail finished mRNA Post-transcriptional modification of RNA
  16. 16. ANIMATED FIGURE: Pre-mRNA transcript processing
  17. 17. ANIMATED FIGURE: Gene transcription details
  18. 18. ANIMATED FIGURE: Negative control of the lactose operon
  19. 19. 7.4 RNA Players in Translation  Three types of RNA are involved in translation: mRNA, rRNA, and tRNA  mRNA produced by transcription carries protein-building information from DNA to the other two types of RNA for translation
  20. 20. mRNA and the Genetic Code  Information in mRNA consists of sets of three nucleotides (codons) that form “words” spelled with bases A, C, G, U  Sixty-four codons, most of which specify amino acids, constitute the genetic code  The sequence of three nucleotides in a base triplet determines which amino acid the codon specifies  The order of codons in mRNA determines the order of amino acids in the polypeptide that will be translated from it
  21. 21. Genetic Code  Twenty amino acids are encoded by the sixty-four codons in the genetic code  Some amino acids are specified by more than one codon  Other codons signal the beginning and end of a protein- coding sequence  Most organisms use the same code
  22. 22. The Genetic Code
  23. 23. a gene region in DNA transcription codon codon codon mRNA translation methionine (met) tyrosine (tyr) serine (ser) amino acid sequence Correspondence between DNA, RNA, and proteins
  24. 24. rRNA and tRNA – the Translators  Ribosomes consist of two subunits of rRNA and structural proteins  Ribosomes and transfer RNAs (tRNA) interact to translate an mRNA into a polypeptide  tRNA has two attachment sites  An anticodon base-pairs with an mRNA codon  An attachment site binds to an amino acid specified by the codon
  25. 25. Ribosome Structure large subunit small subunit intact ribosome + =
  26. 26. anticodon A) Icon and model of the tRNA that carries the amino acid tryptophan. Each tRNA’s anticodon is complementary to an mRNA codon. Each also carries the amino acid specified by that codon. tRNA for Tryptophan
  27. 27. B) During translation, tRNAs dock at an intact ribosome (for clarity, only the small subunit is shown, in tan). Here, the anticodons of two tRNAs have base-paired with complementary codons on an mRNA (red). tRNAs dock at a ribosome
  28. 28. ANIMATED FIGURE: Structure of a ribosome
  29. 29. 7.5 Translating the Code: RNA to Protein  Translation (second part of protein synthesis) occurs in the cytoplasm of all cells:  mRNA is transcribed in the nucleus  In the cytoplasm a small ribosomal subunit binds to mRNA  Initiator tRNA base-pairs with the first mRNA codon  Large ribosomal subunit joins the small subunit  Ribosome assembles a polypeptide chain  Translation ends when the ribosome encounters a stop codon
  30. 30. Translation in Eukaryotes Transcription ribosome subunitsRNA transport tRNA 1 Convergence of RNAs mRNA Translation polypeptide 2 3 4
  31. 31. Ribosome assembles a polypeptide chain
  32. 32. Ribosome assembles a polypeptide chain
  33. 33. Ribosome assembles a polypeptide chain
  34. 34. ANIMATED FIGURE: Translation
  35. 35. 7.6 Mutated Genes and Their Products  Mutations are permanent changes in the nucleotide sequence of DNA, which may alter a gene product  A mutation that changes a gene’s product may have harmful effects  Example: Mutations that affect the proteins in hemoglobin reduce blood’s ability to carry oxygen
  36. 36. Types of Mutations  Base-pair substitution  Type of mutation in which a single base-pair changes  Example: Sickle cell anemia  Mutations that shift the reading frame of the mRNA codons:  Deletion of one or more base pairs  Insertion of one or more base pairs  Example: Beta thalassemia
  37. 37. A) Hemoglobin, an oxygen-binding protein in red blood cells. This protein consists of four polypeptides: two alpha globins (blue) and two beta globins (green). Each globin forms a pocket that cradles a type of cofactor called a heme (red ). Oxygen gas binds to the iron atom at the center of each heme. Mutations in Hemoglobin
  38. 38. B) Part of the DNA (blue), mRNA (brown), and amino acid sequence (green) of human beta globin. Numbers indicate the position of the nucleotide in the coding sequence of the mRNA. Mutations in Hemoglobin
  39. 39. C) A base-pair substitution replaces a thymine with an adenine. When the altered mRNA is translated, valine replaces glutamic acid as the sixth amino acid of the polypeptide. Hemoglobin with this form of beta globin is called HbS, or sickle hemoglobin. Mutations in Hemoglobin
  40. 40. D) A deletion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. The result is beta thalassemia, in which a person has an abnormally low amount of hemoglobin. Mutations in Hemoglobin
  41. 41. E) An insertion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. As in D, the outcome is beta thalassemia. Mutations in Hemoglobin
  42. 42. glutamic acid valine A) A base-pair substitution results in the abnormal beta globin chain of sickle hemoglobin (HbS). The sixth amino acid in such chains is valine, not glutamic acid. The difference causes HbS molecules to form rod-shaped clumps that distort normally round blood cells into sickle shapes. Sickle-Cell Anemia: A Base-Pair Substitution
  43. 43. sickled cell normal cell B) Left, the sickled cells clog small blood vessels, causing circulatory problems that result in damage to many organs. Destruction of the cells by the body’s immune system results in anemia. Right, Tionne “T- Boz” Watkins of the music group TLC is a celebrity spokesperson for the Sickle Cell Disease Association of America. She was diagnosed with sickle-cell anemia as a child. Sickle-Cell Anemia
  44. 44. What Causes Mutations?  Most mutations result from unrepaired DNA polymerase errors during DNA replication  Some natural and synthetic chemicals cause mutations in DNA (example: cigarette smoke)  Insertion mutations may be caused by transposable elements, which move within or between chromosomes
  45. 45. ANIMATED FIGURE: Base-pair substitution To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  46. 46. ANIMATION: Deletion To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  47. 47. ANIMATION: Frameshift mutation To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  48. 48. ANIMATED FIGURE: Sickle-cell anemia To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  49. 49. ANIMATED FIGURE: Controls of eukaryotic gene expression To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  50. 50. ANIMATION: X-chromosome inactivation To play movie you must be in Slide Show Mode PC Users: Please wait for content to load, then click to play Mac Users: CLICK HERE
  51. 51. 7.7 Eukaryotic Gene Controls  All cells in your body carry the same DNA  Some genes are transcribed by all cells, but most cells are specialized (differentiated) to use only certain genes  Which genes are expressed at a given time depends on the type of cell and conditions
  52. 52. Cell Differentiation  Cells differentiate when they start expressing a unique subset of their genes – controls over gene expression are the basis of differentiation  Differentiation  The process by which cells become specialized  Occurs as different cell lineages begin to express different subsets of their genes
  53. 53. Controlling Gene Expression  Controlling gene expression is critical for normal development and function of a eukaryotic body  All steps between transcription and delivery of gene product are regulated  Transcription factor  Protein that influences transcription by binding to DNA
  54. 54. Master Genes  Master gene  Gene encoding a product that affects the expression of many other genes  Controls an intricate task such as eye formation  Homeotic gene  Type of master gene that controls formation of specific body parts during development
  55. 55. Studying Homeotic Genes  Researchers study the function of a homeotic gene by altering its expression – by introducing a mutation or deleting it entirely (gene knockout)  Examples: antennapedia, dunce, tinman, groucho  Many homeotic genes are interchangeable among species  Example: eyeless gene in flies and PAX 6 gene in humans
  56. 56. A) A transcription factor—the protein product (gold ) of an insect gene called antennapedia attaches to a promoter sequence in a fragment of DNA. In cells of a fly embryo, the binding starts a cascade of cellular events that results in the formation of a leg. Example of gene control
  57. 57. B) Antennapedia is a homeotic gene whose expression in embryonic tissues of the insect thorax causes legs to form. A mutation that causes antennapedia to be expressed in the embryonic tissues of the head causes legs to form there too (left). Compare the head of the normal fly on the right. Example of gene control
  58. 58. Gene Knockout Experiment: Eyeless A) A fruit fly with a mutation in its eyeless gene develops with no eyes. B) Compare the large, round eyes of a normal fruit fly. C) Eyes form wherever the eyeless gene is expressed in fly embryos. Abnormal expression of the eyeless gene in this fly caused extra eyes to develop on its head and also on its wings.
  59. 59. PAX6 Gene Function  In humans and many other animals, the PAX6 gene affects eye formation D) Humans, mice, squids, and other animals have a gene called PAX6. In humans, PAX6 mutations result in missing irises, a condition called aniridia (left ). Compare a normal iris (right ). PAX6 is so similar to eyeless that it triggers eye development when expressed in fly embryos.
  60. 60. Sex Chromosome Genes  In mammals, males have only one X chromosome – females have two, but one is tightly condensed into a Barr body and not expressed  According to the theory of dosage compensation, X chromosome inactivation equalizes expression of X chromosome genes between the sexes
  61. 61. X Chromosome Inactivation A) Barr bodies. The photo on the left shows the nucleus of five XX cells. Inactivated X chromosomes— Barr bodies— appear as red spots. Compare the nucleus of two XY cells in the photo on the right
  62. 62. The Y Chromosome  The human X chromosome carries 1,336 genes  The human Y chromosome carries 307 genes, including SRY— the master gene for male sex determination  Triggers formation of testes  Testosterone produced by testes controls formation of male secondary traits  Absence of SRY gene in females triggers development of ovaries, female characteristics
  63. 63. SRY gene expressed no SRY present penis vaginal opening birth approaching B) An early human embryo appears neither male nor female. SRY gene expression determines whether male reproductive organs develop. Development of Human Reproductive Organs
  64. 64. Epigenetics  Transcription is affected by chromosome structure  Modifications that suppress gene expression:  Adding a methyl group (CH3) to a histone protein  Direct methylation of DNA nucleotides  Once a particular nucleotide has become methylated, it usually stays methylated in all of the cell’s descendants  Environmental factors, including the chemicals in cigarette smoke, add more methyl groups
  65. 65. Methyl group attached to a DNA nucleotide
  66. 66. Epigenetics  Methylation of parental chromosomes is normally “reset” in the first cell of the new individual  All parental methyl groups are not removed, so some methylations can be passed to future offspring  Boys are affected by lifestyle of individuals in the father’s line; girls, by individuals in the mother’s line  Heritable changes in gene expression that are not due to changes in underlying DNA sequence are epigenetic
  67. 67. An epigenetic effect  Grandsons of boys who endured a winter of famine tend to live longer than grandsons of boys who overate at the same age
  68. 68. 7.8 Ricin and Your Ribosomes (revisited)  Ricin is a ribosome-inactivating protein (RIP)  Toxic RIPs, including ricin, have one polypeptide chain that binds tightly to carbohydrates on plasma membranes  Once inside the cell, a second polypeptide inactivates the ribosomes, and the cell quickly dies  Other RIPs include Shiga toxin (dysentery) and E. coli O157:H7 (food poisoning)
  69. 69. Some RIPs ricin Shiga toxin E. coli enterotoxin
  70. 70. Digging Into Data: Paternal Grandmother’s Food Supply and Infant Mortality