III. DNA, Protein Synthesis, and Mitosis A. DNA and RNA Structure

1. III. DNA, Protein Synthesis, and Mitosis A. DNA and RNA Structure DNA is the genetic material in all forms of life (eubacteria, archaea, protists, plants, fungi, and animals). Those quasi-living viruses vary in their genetic material. Some have double-stranded DNA (ds-DNA) like living systems, while others have ss-DNA, ss-RNA, and ds-RNA. RNA performs a wide array of functions in living systems. Many of these functions have only been discovered in the last few years.

2. A. DNA and RNA Structure 1. monomers are “nucleotides” three parts: - pentose sugar - nitrogenous base - phosphate group PO4 binds to the 5’ carbon

3. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ Between the PO4 (which always has free H+ ions binding and unbinding) of the free nucleotide and the –OH group on the 3’ carbon of the last sugar in the chain. OH OH O-P-O O H2O OH Energy released by cleaving the diphosphate group can be used to power the dehydration synthesis reaction

4. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) a. bases are complementary b. the strands are anti-parallel: they are aligned with opposite polarity 5’

5. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein

6. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. R-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA

7. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. r-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA c. t-RNA is made the same way, and brings amino acids to the ribosome

8. A. DNA and RNA Structure 1. monomers are “nucleotides” 2. polymerization occurs by ‘dehydration synthesis’ 3. most DNA exists as a ‘double-helix’ (ds-DNA) 4. RNA performs a wide variety of functions in living cells: a. m-RNA is a ‘copy’ of a gene, read by the ribosome to make a protein b. r-RNA is made the same way, is IN the Ribosome, and ‘reads’ the m-RNA c. t-RNA is made the same way, and brings amino acids to the ribosome d. mi-RNA (micro-RNA) and si-RNA (small interfering RNA) bind to m-RNA and splice it; inhibiting the synthesis of its protein. This is a regulatory function.

9. Cell Biology B. Protein Synthesis

10. B. Protein Synthesis Why is this important? Well…what do proteins DO?

11. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this isTRANSCRIPTION (t-RNA) (r-RNA) U G C U G A C U A C U (m-RNA)

12. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION (t-RNA) (r-RNA) U G C U G A C U A C U (m-RNA) Eukaryotic RNA and some prokaryotic RNA have regions cut out… this is RNA SPLICING

13. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C R-RNA is complexed with proteins to form ribosomes. Specific t-RNA’s bind to specific amino acids. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome

14. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C The ribosome reads the m-RNA. Based on the sequence of nitrogenous bases in the m-RNA, a specific sequence of amino acids (carried to the ribosome by t-RNA’s) is linked together to form a protein. This is TRANSLATION. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome

15. Protein Synthesis A. Overview A T G C T G A C T A C T G T A C G A CT G A T G A C The protein product may be modified (have a sugar, lipid, nucleic acid, or another protein added) and/or spliced to become a functional protein. This is POST-TRANSLATIONAL MODIFICATION. (t-RNA) (r-RNA) U G C U G A C U A C U Amino acid (m-RNA) ribosome glycoprotein

16. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ “TAG A CAT” message makes ‘sense’ “ATC T GTA” ‘nonsense’ limited by complementation

17. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription a. The message is on one strand of the double helix - the sense strand: 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon In all eukaryotic genes and in some prokaryotic sequences, there are introns and exons. There may be multiple introns of varying length in a gene. Genes may be several thousand base-pairs long. This is a simplified example!

18. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. Promoter 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation.

19. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase. Promoter 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon • Strand separate • RNA Polymerase can only synthesize RNA in a 5’3’ direction, so they only read the anti-parallel, 3’5’ strand (‘sense’ strand).

20. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription

21. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T G C A U GUUU G C C A A U AUG A U G A T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Initial RNA PRODUCT:

22. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription c. Transcription ends at a sequence called the 'terminator'. Promoter Terminator 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon Initial RNA PRODUCT: G C A U GUUU G C C A A U AUG A U G A

23. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing G C A U GUUU G C C A A U AUG A U G A exon intron exon Introns are spliced out, and exons are spliced together. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”. Initial RNA PRODUCT:

24. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing AUG A G C A U GUUU G C C A A U U G A This final RNA may be complexed with proteins to form a ribosome (if it is r-RNA), or it may bind amino acids (if it is t-RNA), or it may be read by a ribosome, if it is m-RNA and a recipe for a protein. intron exon exon Final RNA PRODUCT:

25. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA: G C A U G U U U G C C A A U U G A

26. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. M-RNA: G C A U G U U U G C C A A U U G A It then reads down the m-RNA, one base at a time, until an ‘AUG’ sequence (start codon) is positioned in the first reactive site.

27. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. Meth M-RNA: G C A U G U U U G C C A A U U G A

28. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site Meth Phe M-RNA: G C A U G U U U G C C A A U U G A

29. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site d. Translocation reactions occur Phe Meth M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

30. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds Ala Asn Meth Phe M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

31. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds Asn Meth Phe Ala M-RNA: G C A U G U U U G C C A A U U G A The amino acids are bound and the ribosome moves 3-bases “downstream”

32. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation e. polymerization proceeds f. termination of translation Meth Phe Ala Asn M-RNA: G C A U G U U U G C C A A U U G A Some 3-base codon have no corresponding t-RNA. These are stop codons, because translocation does not add an amino acid; rather, it ends the chain.

33. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis 1. Transcription 2. Transcript Processing 3. Translation 4. Post-Translational Modifications Meth Phe Ala Asn Most initial proteins need to be modified to be functional. Most need to have the methionine cleaved off; others have sugar, lipids, nucleic acids, or other proteins are added.

34. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription - DNA bound to histones can’t be accessed by RNA Polymerase - but the location of histones changes, making genes accessible (or inaccessible) Initially, the orange gene is “off”, and the green gene is “on” Now the orange gene is “on” and the green gene is “off”.

35. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription Promoter 3’ 5’ sense A C T A T A C G T A C A A A C G G T T A T A C T A C T T T T G A T A T G C A T G T T T G C C A A T A T G A T G A A A nonsense 5’ 3’ exon intron exon RNA POLY Transcription factors can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these transcription factors. So cells can respond genetically to changes in their environment.

36. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing Cut not made G C A U GUUU G C C A A U AUG A U G A U A U A exon intron exon Initial RNA PRODUCT: Mi-RNA’s and si-RNA’s are small RNA molecules that can bind to m-RNA and disrupt correct spicing, creating non-functional m-RNA’s.

37. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation Meth Phe M-RNA: G C A U G U U U U G A A A U U G A Incorrect splicing can result in a ‘premature’ stop codon, terminating translation early, resulting in a non-functional protein.

38. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification Meth Phe Ala Asn The patterns of cleavage and modification can vary.

39. VI. Protein Synthesis A. Overview B. The Process of Protein Synthesis C. Regulation of Protein Synthesis 1. Regulation of Transcription 2. Transcript Processing 3. Regulating Translation 4. Regulating Post-Translational Modification Affected by other cells Affected by other genes Affected by the environment Protein ? Gene activity is responsive to cellular and environmental cues

40. Cell Division A. The Cell Cycle INTERPHASE S (DNA synthesis) LE 12-5 G1 Mitosis Cytokinesis G2 MITOTIC (M) PHASE

41. A. The Cell Cycle     1.  Interphase: a.  G1: high metabolic activity (protein synthesis) chromosomes diffuse; one DNA double helix per chromosome

42. A. The Cell Cycle     1.  Interphase: Some cell types are "stuck" in this stage when they mature... it is only "stem cells" that keep dividing.  In some tissues, all stem cells  eventually mature, so the tissue can't regenerate (neurons)

43. LE 12-15 G0 G1 checkpoint G1 G1 If a cell does not receive a go-ahead signal at the G1 checkpoint, the cell exits the cell cycle and goes into G0, a nondividing state. If a cell receives a go-ahead signal at the G1 checkpoint, the cell continues on in the cell cycle.

44. VII. CELL REPRODUCTION Overview: Why Reproduce? A. The Cell Cycle     1.  Interphase a. G1 b. S Chromosome duplication (including DNA synthesis) Centromere Sister chromatids

45. VII. CELL REPRODUCTION Overview: Why Reproduce? A. The Cell Cycle     1.  Interphase a. G1 b. S c. G2

46. VII. CELL REPRODUCTION Overview: Why Reproduce? A. The Cell Cycle     1.  Interphase 2. Mitosis

47. INTERPHASE PROPHASE PROMETAPHASE Kinetochore Centrosomes (with centriole pairs Early mitotic spindle Chromatin (duplicated) Aster Fragments of nuclear envelope Nonkinetochore microtubules Centromere LE 12-6aa Nucleus Plasma membrane Chromosome, consisting of two sister chromatids Kinetochore microtubule Nuclear envelope

48. METAPHASE ANAPHASE TELOPHASE Nucleolus forming Metaphase plate Cleavage furrow LE 12-6ba Nuclear envelope forming Centrosome at one spindle pole Daughter chromosomes Spindle

49. VII. CELL REPRODUCTION Overview: Why Reproduce? A. The Cell Cycle B. DNA Replication C. Mitosis G2 OF INTERPHASE PROPHASE PROMETAPHASE

50. VII. CELL REPRODUCTION Overview: Why Reproduce? A. The Cell Cycle B. DNA Replication C. Mitosis LE 12-6da TELOPHASE AND CYTOKINESIS METAPHASE ANAPHASE