1. DNA LECTURE PACKET 5 READING: CHAPTER 21 (PAGES 442-450) COPYRIGHT PEARSON EDUCATION 2008

2. Outline ▪ DNA - Structure - Replication ▪ RNA ▪ Protein production COPYRIGHT PEARSON EDUCATION 2008

3. What is DNA? ▪ Deoxyribonucleic acid, or DNA, is a double-stranded molecule that is the blueprint to making proteins. ▪ Chromosomes located inside the nucleus contains long coiled strands of DNA. ▪ The DNA is a long strand of nucleotides. COPYRIGHT PEARSON EDUCATION 2008

4. Nucleotides ▪ Nucleic acids (DNA and RNA) are made of nucleotides. ▪ Nucleotides have one phosphate, one sugar, and one nitrogenous base. COPYRIGHT PEARSON EDUCATION 2008

5. DNA ▪ DNA has four different bases. - Adenine (A), thymine (T), guanine (G), and cytosine (C) COPYRIGHT PEARSON EDUCATION 2008

6. DNA: double helix structure ▪ The sugars and phosphates link together by covalent bonds to form the rail on the outside. ▪ The sugars are covalently bound to a base. ▪ The bases form hydrogen bonds to keep the two strands together. COPYRIGHT PEARSON EDUCATION 2008

7. DNA: complementary base pairing ▪ The bases pair up in a specific manner: - Adenine (A) pairs with thymine (T) - Guanine (G) pairs with cytosine (C) ▪ Each base pair is held together by weak hydrogen bonds. ▪ Example: - If the original DNA strand was: TCAT… then the complementary strand would be AGTA COPYRIGHT PEARSON EDUCATION 2008

8. DNA: complementary base pairing COPYRIGHT PEARSON EDUCATION 2008

9. DNA: complementary base pairing ▪ Remember that on one strand, the base is covalently bonded to the sugar, which is covalently bonded to the phosphate group. ▪ Between the two strands, the bases are bonded together by weak hydrogen bonds. - A and T - C and G COPYRIGHT PEARSON EDUCATION 2008

10. DNA replication ▪ Before a cell divides, the parent cell needs to make a copy of the DNA. ▪ Each daughter cell receives a copy of the DNA. ▪ Replication of DNA is semi-conservative, meaning each new DNA molecule contains one strand of the original DNA and one strand of the new DNA. COPYRIGHT PEARSON EDUCATION 2008

11. DNA replication COPYRIGHT PEARSON EDUCATION 2008

12. DNA replication ▪ The incoming nucleotides have three phosphates, only one is used to bond to the sugar molecule. ▪ The energy needed to build the new DNA strand comes from taking the other two phosphates off. ▪ The energy gained from breaking the bonds is used to build the new bond. COPYRIGHT PEARSON EDUCATION 2008

13. If the original DNA strand was TCAA, what is the complementary? 1.TCAA 2.CGTT 3.AGTT 4.GACC COPYRIGHT PEARSON EDUCATION 2008

14. DNA replication: mutation ▪ Before a cell can divide, it must make a complete copy of the DNA. ▪ There are millions of bases that need to be added to the DNA strands, so there are many chances that something can go wrong. ▪ With the help of enzymes, the mistakes can be corrected. But not all mistakes can be corrected. COPYRIGHT PEARSON EDUCATION 2008

15. DNA replication: point mutation ▪ A point mutation is when just one base pair is paired incorrectly. COPYRIGHT PEARSON EDUCATION 2008

16. DNA replication: frameshift mutation ▪ A frameshift mutation can dramatically alter the protein being coded. - Deletion: A nucleotide, or a section, of the DNA is deleted. - Insertion: Extra base pairs are inserted. ▪ These two mutations can cause a big impact to downstream nucleotides (remember: amino acids are coded by three base pairs each). COPYRIGHT PEARSON EDUCATION 2008

17. DNA replication: causes of mutation ▪ Random error ▪ Mutagens: chemicals that damage the DNA and cause mutations in replication - cigarette smoke - sunlight - many chemicals COPYRIGHT PEARSON EDUCATION 2008

18. DNA replication: results of mutation 1.Enzymes can repair the damage. 2.The cell may commit suicide (apoptosis). 3.The cell may replicate and the mutation becomes permanent. COPYRIGHT PEARSON EDUCATION 2008

19. DNA replication: good mutation COPYRIGHT PEARSON EDUCATION 2008 ▪ Evolution occurs because there is variation in DNA. Sometimes a mutation can produce changes that are good. ▪ If these mutations are better, they may allow the organism to survive longer and produce more offspring. The change can spread throughout the population.

20. Central dogma COPYRIGHT PEARSON EDUCATION 2008 ▪ DNA codes for RNA, which then codes for proteins. ▪ A gene directs the production of a specific protein. ▪ Transcription: DNA goes to RNA ▪ Translation: RNA goes to protein

21. What is the monomer unit of proteins? COPYRIGHT PEARSON EDUCATION 2008 1.Glucose 2.Nucleotide 3.Amino acid 4.Fatty acid

22. What bond connects the monomer units in a protein? COPYRIGHT PEARSON EDUCATION 2008 1.Hydrogen bond 2.Ionic bond 3.Peptide bond

23. Protein synthesis COPYRIGHT PEARSON EDUCATION 2008

24. DNA vs RNA COPYRIGHT PEARSON EDUCATION 2008

25. DNA vs RNA COPYRIGHT PEARSON EDUCATION 2008

26. Transcription COPYRIGHT PEARSON EDUCATION 2008 ▪ DNA codes for RNA, which then codes for proteins. ▪ The product of transcription is RNA. ▪ Transcription happens in the nucleus.

27. Transcription COPYRIGHT PEARSON EDUCATION 2008

28. Transcription: RNA Polymerase COPYRIGHT PEARSON EDUCATION 2008 ▪ RNA polymerase (similar to DNA polymerase) binds to a region on the DNA upstream from the gene called the promoter region. ▪ It brings complementary RNA nucleotides together and binds them into a chain. ▪ When the RNA transcript is complete, it will be released from the DNA. ▪ Note: The nucleotide containing uracil as the nitrogenous base is complementary to adenine.

29. Transcription: Post-transcriptional modification COPYRIGHT PEARSON EDUCATION 2008 1.Pre-mRNA splicing (removing the introns and leaving the exons). 2.Addition of a 5’ methylguanosine cap. This is important for export of the mRNA in addition to translation of mRNA. 3.Cleavage of the RNA transcript near the 3’ end. 4.Addition of a poly(A) tail. This contributes to the mRNA’s stability.

30. DNA is: ATCG. What is the complementary mRNA? COPYRIGHT PEARSON EDUCATION 2008 1.TAGC 2.UAGC 3.UACG 4.ATCG

31. Translation COPYRIGHT PEARSON EDUCATION 2008 ▪ Translation is the process of going from RNA to protein. ▪ The mRNA transcript will be read in groups of three. Codons are sequences of 3 bases on mRNA that specify 1 out of the 20 amino acids.

32. Translation COPYRIGHT PEARSON EDUCATION 2008 1.Mature mRNA leaves the nucleus through the pores. 2.mRNA docks with ribosomes. 3.tRNA brings amino acids to the ribosome. 4.The amino acids are bounded together by a peptide bond. 5.mRNA is then degreaded by endonucleases and exonucleases.

33. Translation: codons COPYRIGHT PEARSON EDUCATION 2008 ▪ Three mRNA bases (codon) code for one amino acid.

34. Translation: codons COPYRIGHT PEARSON EDUCATION 2008

35. Translation: tRNA COPYRIGHT PEARSON EDUCATION 2008 ▪ Translation uses transfer RNA (tRNA) to identify the codons and transport appropriate amino acids to the ribosome. ▪ The ribosome is where the amino acids are bounded together. ▪ One side of tRNA attaches to an amino acid, while the other side has complementary nucleotides to the codon, known as the anticodon. ▪ Anticodon is a three base sequence on the other end of the tRNA that is complementary to the codon of the mRNA.

36. Translation: tRNA COPYRIGHT PEARSON EDUCATION 2008

37. Translation: rRNA COPYRIGHT PEARSON EDUCATION 2008 ▪ Ribosomal RNA (rRNA) consists of two RNA molecules and a protein. ▪ It is a ribosome that forms the peptide bond. ▪ rRNA is the enzymatic portion of the ribosome. ▪ Ribosomes are produced in the nucleolus.

38. Types of RNA and their functions COPYRIGHT PEARSON EDUCATION 2008

39. Ribosomes COPYRIGHT PEARSON EDUCATION 2008 ▪ There are three tRNA binding sites on ribosomes: E, P, and A.

40. Ribosomes COPYRIGHT PEARSON EDUCATION 2008 ▪ E site: last tRNA exits ▪ P site: chain is growing/polymerizing ▪ A site: tRNA sits to add next AA

41. Translation: initiation COPYRIGHT PEARSON EDUCATION 2008 1.mRNA binds to the small subunit of ribosome. 2.tRNA with methionine (MET) amino acid attached binds to the mRNA codon AUG at the “P site”. 3.Large subunit of ribosome attaches.

42. Translation: initiation COPYRIGHT PEARSON EDUCATION 2008

43. Translation: elongation COPYRIGHT PEARSON EDUCATION 2008 4. tRNA with the next amino acid attached binds to the mRNA codon at the “A site.” The bond between the tRNA and methionine amino acid is broken. 5. A peptide bond is formed between the MET amino acid and the second amino acid. 6. The transfer RNAs all move over one space on the ribosome (translocation).

44. Translation: elongation COPYRIGHT PEARSON EDUCATION 2008 7. Now the “free tRNA,” which used to hold the methionine amino acid is in the “E site,” ready to be released. 8. The tRNA with two amino acids is now in the “P site” and the “A site” is ready to receive another tRNA. 9. The next tRNA with the third amino acid is brought into the A site. 10. The “free tRNA” is released from the “E site.”

45. Translation: elongation COPYRIGHT PEARSON EDUCATION 2008

46. Translation: termination COPYRIGHT PEARSON EDUCATION 2008 11. When translation reaches a stop codon, no tRNA binds to the stop codon. 12. Instead, the polypeptide chain is released and the ribosome breaks apart, releasing the mRNA.

47. The genetic code COPYRIGHT PEARSON EDUCATION 2008

48. The genetic code COPYRIGHT PEARSON EDUCATION 2008

49. If the mRNA sequence is AUGCCCAAG, then the amino acid sequence is: COPYRIGHT PEARSON EDUCATION 2008 1.Start-Pro-Lys 2.Met-Pro-Lys 3.Met-Pro-Lys-Stop 4.Start-Pro-Lys-Stop

50. What molecule is produced in transcription? COPYRIGHT PEARSON EDUCATION 2008 1.Nucleotide 2.DNA 3.Polypeptide chain (protein) 4.Amino acid 5.mRNA

51. What molecule is produced in translation? COPYRIGHT PEARSON EDUCATION 2008 1.Nucleotide 2.DNA 3.Polypeptide chain (protein) 4.Amino acid 5.mRNA

52. Protein production COPYRIGHT PEARSON EDUCATION 2008 ▪ All polypeptide chains are produced in the ribosomes. ▪ Polypeptides/proteins that will be cytosolic are produced on free floating ribosomes. ▪ If the proteins are going to become membrane proteins or are going to be exported out of the cell, then the polypeptide chain will be produced in a ribosome that is brought to the ER.

53. Protein production summary COPYRIGHT PEARSON EDUCATION 2008