Chapter 5: Introduction to the Nucleic Acids

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1 Chapter 5: Introduction to the Nucleic Acids

2 DNA, RNA, and the Flow of Genetic Information DNA and RNA are long gpolymers Carry information that is passed on to the next generation Genetic information is stored in the sequence of bases along a nucleic acid chain Base pairing occurs Base pairs provide the mechanism for copying the genetic information in an existing nucleic acid chain to form a new chain.

3 Central Dogma of Information Flow DNA What is this? DNA RNA Protein Function What is this? What is this? What is this? The Genetic Code is Crucial!

4 General Schematic of a Nucleic Acid polymer.

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6 Sugar Differences

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8 Nitrogen Bases in the Nucleic Acids

9 Making a Nucleoside N-glycosidic bond

10 Nucleosides Combining Nitrogen bases with sugars RNA Adenosine Guanosine Cytidine Uridine DNA Deoxy- prefix Thymidine

11 Making a Nucleotide Adding a phosphate to the nucleoside structure.

12 Nucleotide Nomenclature 5 - nucleoside phosphate 5 - nucleotide

13 Adenosine 5 -triphosphate A.K.A

14 3 - deoxyguanosine monophosphate

15 Tedious Method to show the polymer

16 Short-Hand Method to show the polymer

17 The Very Short-Hand Method to P-5 ACG 5ACG 3-OH show the polymer By convention: nucleic acid polymers are always written with the 5 end to the left and the 3 end to the right. Polarity to these molecules l 5 3 ACG is DIFFERENT than GCA

18 Anatomy of the DNA helix Launch animation h k /DNA t Visit this link as a study guide!!!

19 Billions of nucleotides join to form Prokaryotes Genomes. Contain genes (coding regions) Control areas (regulatory regions) Eukaryotes Contain genes (coding regions) Control areas (regulatory regions) Useless ess stretches es of DNA (noncoding regions) Introns intervening sequences in DNA Exons - are the coding regions in Eukaryotes.

20 An E. coli s genome exposed!

21 Structure of DNA A 1950 s Race Maurice Wilkins and Rosalind Franklin James Watson and Francis Crick Building a structural model from scientific data and dhypotheses! Read their Paper!!! (link is on the class website)

22 X-ray Diffraction of DNA Rosalind Franklin s Data

23 Watson-Crick Model from the data 1. two helical polynucleotides coiled around a common axis 2. The sugar-phosphate backbones are on the outside and the bases lie on the inside 3. bases are perpendicular to the axis of the helix. 34 Angstrom repeat 10 bases/turn (bases separated by 3.4 Ang.) 4. diameter is 20 Angstroms.

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26 Chargaff s Results on Nucleotide Ratios

27 Paper, scissors, and Hydrogen Bonds The secret of the Base Pairs!

28 Nitrogen Base Stacking helps stabilize the helix. Weak forces

29 Genetic Molecule Copies are made of the DNA before each MITOSIS event. The enzyme that copies the DNA for the daughter cells is called DNA polymerase For humans, 3 billion bases have to be copied to form the new strands of DNA Very rapid, very accurate Only 1 mistake in every 1 million base pairs.

30 What was the mechanism of DNA Possibilities Conservative Semiconservative Replication? i How can you find out?

31 Semi-Conservative Replication Model

32 Meselson and Stahl Experiment Animation link:

33 Density Gradient equilibrium Sedimentation

34 light N-14 isotope Heavy N-15 isotope Hybrid 1/2 Heavy ½ light.

35 Semi-Conservative Replication Uses the following amazing enzymes: 1. Helicases/topoisomersase help to open up the double helix 2. RNA primase lays down a short RNA primer to provide replication enzymes with a 3 -OH. 3. DNA polymerase builds off of the RNA primers to incorporate nucleotide triphosphates into the new daughter strands.both quickly and accurately! 4. Exonucleases Removes the RNA primer from the daughter strands 5. Ligase will fill in the gaps and establish a new phosphodiester linkage between een the neighboring DNA fragments making all of the separate fragments one continuouse nucleic acid strand.

36 Semi-Conservative Replication in Action! Animation of DNA Replication Another animation of DNA replication Another animation of DNA replication REALLY COOL ANIMATION OF DNA PACKAGING AND REPLICATION!

37 Hypochroism of DNA

38 Helicases melt the helix in the cell! Here is melting outside the cell using heat

39 Circular DNA l

40 DNA can Supercoil.enzymes called Topoisomerases Deal with the supercoiling inside the cell. l

41 Stem Loop and Hairpin structures can occur within single stranded d nucleic acids

42 Single Stranded RNA can take on a variety of complex structures! (and Functions) Magnesium Ions often help stabilize Magnesium Ions often help stabilize The structures.

43 Same Molecule in 3-D

44 DNA is Replicated by Polymerase Enzymes What are the requirements?

45 Phosphodiester Bridge

46 RNA Genomes a carry-over from ancient days? Retrovirus Mechanism

47 Gene Expression and RNA

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52 Transcription Start Signals in prokaryotes

53 Transcription Start Signals in eukaryotes

54 Terminator sequence In prokaryotes The end of the gene Contains a hair pin Structure that tells the RNA polymerase to Stop transcription. Rho factor may also Be involved

55 Methyl Guanosine cap added to 5 end PolyA tail added to 3 end

56 Molecular ushers the Molecular ushers the Transfer RNAs

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58 Hydrogen Bonding is the link between mrna and protein sequences.

59 1. Three nucleotides encode an amino acid 2. The Code I nonoverlapping 3. The Code has no punctuation 4. The Genetic Code is degenerate.

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61 First amino acids in The prokaryotes

62 Translation Start Signals in prokaryotes

63 Translation Start Signals in eukaryotes

64 Animation of Translation: html

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