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The Structures of DNA and RNA

The Structures of DNA and RNA. DNA is usually double-stranded, with adenine paired with thymine and guanine paired with cytosine . RNA is usually single-stranded and contains uracil in place of thymine. nucleo t ide = sugar + base + phosphate. nucleo s ide = sugar +base. When Do we

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The Structures of DNA and RNA

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  1. The Structures ofDNA and RNA DNA is usually double-stranded, with adenine paired with thymine and guanine paired with cytosine. RNA is usually single-stranded and contains uracil in place of thymine.

  2. nucleotide = sugar + base + phosphate nucleoside = sugar +base When Do we Find RNA Mixed with The DNA?

  3. Ribonucleotide Reductase

  4. Pyrimidines have the longer name and smaller base Purines have the shorter name and bigger base

  5. Structure of aPolynucleotide Chain Why do we Always talk about DNA going in the 5’ to 3’ direction?

  6. Deoxyribonucleotides What is dideoxyadenosine triphosphate (ddATP)? Why are dideoxynucleotides useful in Mol.Bio.?

  7. I hate when DNA is not depicted properly!

  8. Transcription and RNA Processing

  9. RNA Synthesis And Transport in Eukaryotes • Method: Pulse-Chase Labeling • At first, labeled RNA is exclusively in the nucleus. • Later, the labeled RNA is found in the cytoplasm.

  10. Awful representation

  11. Correct Representation of DNA

  12. RNA make a new “top strand”

  13. Modifications to Eukaryotic pre-mRNAs • A 7-Methyl guanosine cap is added to the 5’ end of the primary transcript by a 5’-5’ phosphate linkage. • A poly(A) tail (a 20-200 nucleotide polyadenosine tract) is added to the 3’ end of the transcript. The 3’ end is generated by cleavage rather than by termination. • When present, intron sequences are spliced out of the transcript.

  14. Eukaryotes Have Three RNA Polymerases Pol II is the only Polymerase that is routinely studied. Pol I and Pol III are very complicated.

  15. miRNA production

  16. A Typical RNA Polymerase II Promoter

  17. What does the word Promoter mean? It is the place at which RNA Pol II binds. But the word is incorrectly used to describe Enhancers plus Promoter.

  18. Initiation by RNA Polymerase II

  19. TFIID recognition site is TATAA How often is this site found in the genome? 1/45 Once every 1000 nucleotides 109 nucleotides or 106 times

  20. Transient transfection More Cells But on a per cell Basis expression levels of -gal is about the same

  21. Stable transfection

  22. The 7-Methyl Guanosine(7-MG) Cap

  23. The 3’ Poly(A) Tail AAUAAA

  24. Interrupted Genes in Eukaryotes: Exons and Introns Most eukaryotic genes contain noncoding sequences called introns that interrupt the coding sequences, or exons. The introns are excised from the RNA transcripts prior to their transport to the cytoplasm.

  25. Removal of Intron Sequences by RNA Splicing The noncoding introns are excised from gene transcripts by several different mechanisms.

  26. Excision of Intron Sequences

  27. Splicing • Removal of introns must be very precise. • Conserved sequences for removal of the introns of nuclear mRNA genes are minimal. • Dinucleotide sequences at the 5’ and 3’ ends of introns. • An A residue about 30 nucleotides upstream from the 3’ splice site is needed for lariat formation.

  28. Types of Intron Excision • The introns of tRNA precursors are excised by precise endonucleolytic cleavage and ligation reactions catalyzed by special splicing endonuclease and ligase activities. • The introns of nuclear pre-mRNA (hnRNA) transcripts are spliced out in two-step reactions carried out by spliceosomes.

  29. The Spliceosome • Five snRNAs: U1, U2, U4, U5, and U6 • Some snRNAs associate with proteins to form snRNAs (small nuclear ribonucleoproteins)

  30. What are Logo plots?

  31. Logo for a) Splice acceptor b) Splice Donor c) Initiator Met

  32. AG/GT CAG/NT exon 1 intron 1 exon 2 4 3 2 1 1 2 3 4 5 6 9 8 7 6 5 4 3 2 1 1 2

  33. Chapter 12Translation and the Genetic Code

  34. Protein Structure Proteins are complex macromolecules composed of 20 (?) different amino acids.

  35. Amino Acids • Proteins are made of polypeptides. • A polypeptide is a long chain of amino acids. • Amino acids have a free amino group, a free carboxyl group, and a side group (R).

  36. Peptide Bonds • Amino acids are joined by peptide bonds. • The carboxyl group of one amino acid is covalently attached to the amino group of the next amino acid.

  37. Protein Synthesis: Translation The genetic information in mRNA molecules is translated into the amino acid sequences of polypeptides according to the specifications of the genetic code.

  38. The Macromolecules of Translation • Polypeptides and rRNA molecules Euk: 28S, 18S, 5.8S, 5S • Amino-acid Activating Enzymes • tRNA Molecules • Soluble proteins involved in polypeptide chain initiation, elongation, and termination

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