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  1. The purine ring is a combination
    • pyrimidine ring
    • imidazole ring (like a histidine amino acid)
  2. How does the bases (Cytosine, Guanine, Adenine, Thymiine, and Uracil) differ?
    • Bases differ in terms of theside chains off of the rings.
    • The key sidechains are either amine (NH2), Oxy (=O) or methyl (CH3).
    • The nitrogens and oxygensgive lots of sites for hydrogen bonding (tohold things together)
  3. How do we get unusual bases in DNA and RNA?
    - The "core" nitrogenous bases found in DNA and RNA can be modified with different side chains, etc. into "unusual"bases

    • Base modifications seen often include
    • 1- Methylation
    • 2- Acetylation
    • 3- Glycosylation
    • 4- Reduction (i.e. change a keto to an alcohol; change a double bond to a single bond)

    -Example tRNA contain a high amount of unusual bases (e.g. dihydrouracil) and Pseudouridine
  4. Where do we find "unusual bases"? What is the function?
    • viral DNA and
    • transferRNAs (tRNA) or
    • certain regions of DNA
    • help to regulate how that site is recognized by
    • 1- nucleic acid binding factors and/or
    • 2- hydrolyzed by nucleic acid cleaving enzymes            (like proteases but with nucleic acid targets)
  5. Differences between nucleic acid and Protein
    • Having a much higher phosphorus content
    • Resistant to proteolysis
    • Composed of sugars, phosphate and nitrogen (now
    • called bases)
  6. Difference between Nucleoside and Nucleotide
    • Nucleoside (Furanose Sugar + Nitrogenous Base)
    • Nucletide (Nucleoside + Phosphate)
  7. Chargaff's rule
    • the amount of adenine (A) = thymine (T),
    • the amount of guanine (G) = cytosine (C)
    • (A + G) = (C + T)
  8. Nucleotides are linked to each other by
    - phosphate groups, which bind the 3' end of one sugar to the 5' end of the next sugar
  9. Nitrogenous base ring Numbering system
    • Pyrimidines (T, C, U): C1  (the Nitrogen that will bond with ribose sugar )
    • Purines (A, G): C1 is the nitrogen in the pyridine ring furthest removed from that nitrogen in the imidazole ring which will bind with ribose in a nucleoside
  10. What is the name of the sugar in DNA and RNA
    • The key sugar molecule of DNA and RNA is ribose
    • Ribose is a 5 carbon sugar with a furanose ring
  11. What are the difference between DNA and RNA in the sugar
    • DNA: has Deoxyribose (H in position 2)
    • RNA: has Ribose (OH in position 2)
  12. Why RNA is less stable than DNA?
    • Because it is more prone to hydrolysis.
    • The “extra” hydroxy (electronegative) pulls electrons away from the carbon to the oxygen, making the ribose ring more susceptible to hydrolysis by OH groups
  13. The nitrogenous bases will covalently bond to
    location of C3’ and C5 are 
    Image Upload 1
    • The nitrogenous bases will covalently bond to C1’ of ribose or deoxyribose
    • The location of C3’ and C5’ – these are the linkage sites that of polymerized nucleic acids
  14. Image Upload 2
    What is the name of this structure ?
    AMP (Adenosine Monophosphate)
  15. Image Upload 3
    What is the name of that structure?
    ADP (Adenosine Diphosphate)
  16. Image Upload 4
    What is the name of that Structure?
    Adenosine Triphosphate (ATP)
  17. Why Nucleotides are known as “nucleic acids”? 
    See the chart of ADPImage Upload 5
    • The phosphates confer a negative charge on the nucleotide.
    • These groups add protons (H+) to the environment, making it acidic
    • Hence, Nucleotides are known as “nucleic acids”
  18. How nucletide does contribute to many reactions of metabolism?
    • 1- They serve as sources of chemical energy (ATP & GTP)
    • Image Upload 6

    Image Upload 7

    - They participate in cellular signaling as secondary messengers (cyclic guanosine monophosphate (cGMP) and cyclic adenosine monophosphate (cAMP)

    - They are incorporated into important cofactors of enzymatic reactions (Coenzyme A, FAD, FMN, NAD+ and NADP+)

    • -They also serve as carriers of activated intermediates in the synthesis of some carbohydrates (UDP-glucose glycogen), lipids (CDP-choline phosphatidylcholine)
    • and conjugated proteins (glycoproteins UDP-galactose; GDP-mannose)
    • ex, glucose, you have to add energy by adding phosphate to make energy, that is why We need UDP
    • - You have to energize these molecules by use necleotides
    • Nucleotides can also be key regulatory compounds that can inhibit or activate key enzymes to drive or otherwise direct metabolic pathways
  19. Synthesis of Deoxynulceotides?
    Image Upload 8

    - The removal of the “oxy” at 2’-carbon uses an enzyme called Ribonucleotide Reductase (which “reduces” the carbon-oxygen bond by adding hydrogens)

    - Ribonucleotide reductase uses an important cofactor –Thioredoxin – which contributes two sulfhydril groups (SHs) to drive the reaction.

    - Thioredoxin gets “recycled” (reduced back to 2 free –SH groups) by NADPH + H +
  20. What is the key enzyme in controlling the supply of deoxyribonucleotides ?
    • - Ribonucleotide Reductase is a key enzyme for controlling
    • the supply of deoxyribonucleotides (and hence for controlling cell replication)
    • Image Upload 9
  21. Function of Hydroxyurea
    Image Upload 10

    - Hydroxyurea reduces production of deoxyribonucleotides by inhibiting Ribonucleotide Reductase.
  22. What is Hydroxyurea is used for ?
    • - Hydroxyurea is used in the treatment of cancers like chronic myelogenous leukemia and in treating sickle cell disease
    • - Hydroxyurea reduces production of deoxyribonucleotides by inhibiting Ribonucleotide Reductase.
    • Image Upload 11
  23. What is attached in 3 and 5 end of DNA?
    • 5 end have free phophate 
    • 3 end have free hydroxyl- not attached to other nucleotides
  24. What is the direction of linkage in DNA and RNA? and the bases
    • Phosphodiester bonds from 3-5 direction
    • Bases written in sequence from 5-3
  25. How the phosphodiester bonds can be cleaved?
    • Hydrolytically by chemicals, or
    • Hydrolyzed enzymatically by family of nucleases
    • (deoxyribonucleases for DNA and ribonucleases for RNA)
  26. ...................drug attached to AT-rich region of the minor groove of DNA
    Pentamidine analog drug
  27. What stabilize the structure of the double Helix?
    • Nucleotide Base Pairing - Driven by and Stabilized by Hydrogen bonds
    • Hydrophobic pi (p)-stacking due to the aromatic nature of the nitrogenous bases, while hydrophilic basses are outside
  28. How do you seperate the two strands of DNA?
    • 1- Changing the pH of the solution, or by
    • 2- Heating
    • The DNA will “melt” (denature) when sufficient heat is added. This is called the “melting temperature”
    • The phosphodiester bonds are maintained (are NOT broken) by heating.
    • When the DNA is cooled, it will re-form the double strand,This is called "renaturation or reannealing"
  29. What are the major structural forms of DNA?
    • The B-form 
    •          (righ-handes helix- 10 nucleotide- 3600turn)
    •           seen in DNA complexes
    • The A form
    •           (right-handed helix- 11 nucleotide)
    •           form from partially dehydration of B-form
    •           seen in DNA-RNA and RNA-RNA complexes
    •  The Z form
    •            (left-handed helix- 12 base pairs)
    •             seen in deoxyribophophate backbone
  30. Linear and Circular DNA molecules
    • - In the nucleus of eukaryote.
    • Linear dsDNA+ histon proteins= chromatin

    • - In the mitochnondria
    • dsDNA form a closed circular molecule

    • - In prokaryotic 
    • supercoiled DNA+ non- histone protein= nucleoid

    • - In bacteria 
    • small, circular, 
    • extra-chromosomal DNA molecules called plasmids.
    • Plasmids carry genetic information and can replicate independently of chromosomes
  31. Where is DNA founded in the eukaryotic cells?
    • DNA is present in chromosomes in the nucleus and in the mitochondria of eukaryotic cell
    • - DNA+histone= chromatin------chromosome
  32. Central Dogma
    • The flow of information from DNA to RNA to Protein
    • The Master Plan” for an organism is stored in the DNA
    • RNA, however, that translates the information into working molecules that “carry out” the master plan
    • Image Upload 12
  33. What regulate the transcribtion?
    The sequence of bases in DNA will define where transcription enzymes

    RNA polymerases enzymes will regulate which areas of DNA to transcribe, , where to start , how much of the DNA to transcribe and where to stop transcription
  34. Similarities between RNA and DNA
    • All three types of RNA are unbranched polymeric molecules
    • Composed of nucleoside monophosphates
    • Linked by phosphodiester bonds
  35. RNA differes from DNA in
    • Having Ribose, rather than Deoxyribose sugar
    • Having Uracil instead of Thiamine
    • Existing as a Single Strand that folds back on itself into complex structures
  36. A main role of the nucleolus (a suborganelle within the nucleus) is
    • Synthesize rRNA 
    • Assemble ribosomes
  37. rRNA are found in association with many proteins as components of a complex structure known as a
  38. Some rRNAs have enzyme like activities, catalyzing
    reactions. RNA with catalytic activity is called a
  39. Function for mRNAImage Upload 13
    Carries the genetic information from the nuclear DNA to the cytosol (where protein synthesis occurs)

    Polycistronic: the message for more than one protein is included in a single mRNA (prokaryotes and viruses)

    • mRNA contain added 5’ “ends” and 3’ “ends” that are not turned into proteins.
    • The 3’ end is covered with a long sequence of adenine bases (a “poly A tail”).
    • The 5” end has a cap, and often has a leader sequence that helps the synthesized protein sequester into subcellular organelles and fold properly
  40. Monocistronic
    Each coding sequence has its own starting and ending region
  41. polycistronic
    Sometimes, the message for more than one protein is included in a single mRNA (often seen in prokaryotes and viruses)
  42. How do you get mature tRNA from pre tRNA?
    • tRNAs are also synthesized as long precursors that must be shortened by ribonucleases
    • Modifications include:
    • Removing sequences from both the 5’ and the 3’ ends
    • Removing an “intron” from the spot where the anti-codon loop will form
    • Adding a –CCA sequence to the 3’ end of tRNA (at the spot where the amino acids will be “carried”)
    • Reducing certain Uracil structures to make Dihydrouracil; rearranging the way bases are linked to the riboses (i.e. Pseudouridine)
  43. What are the steps in converting mRNA from pre-mRNA?
    • - The first “processing” reaction is to put a “Cap” on the 5’ end.
    • - The cap is a Methylated Guanosine triphosphate that is placed “backwards” on the 5’ terminal ribose 

    • - Next, add a poly-Adenosine (Poly-A) tail to the 3’ end of mRNA. From 40-200 “A”s are
    • added after transcription is finished (post-transcription).
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