Nucleotides/Nucleic%20Acids

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Nucleotides/Nucleic Acids

• Chapter 10

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Nucleotides

• Metabolic processes
• Signal transduction
• Enzyme cofactors
• Polymers nucleic acids (DNA, RNA)

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DNA

• String of nucleotides
• Genetic info
• Nucleotide sequences code for aa sequences of all
  cell proteins
• Thousands of genes per cell
• Gene sequence for a protein/peptide
• Held as chromosomes

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RNA

• Classes
• Ribosomal (rRNA)
• Messenger (mRNA)
• Transfer (tRNA)

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Nucleotide Structure

• Nitrogenous base (pur or pyr)
• Sugar (ribose or deoxyribose) nucleoside
• Phosphate nucleotide (Table 10-1)

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Table 10-1
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Bases (10-2)

• Purines double ring structure (Adenine,
  Guanine)
• Differ at C6 (A amino, G carbonyl)
• Differ at C2 (A unsubstituted, G amino)
• Both found in DNA, RNA

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Bases (contd)

• Pyrimidines single, 6-membered ring (Thymidine,
  Uridine, Cytosine)
• Differ at C4 (T, U carbonyl, C amino)
• Differ at C5 (T methyl, C, U unsubstituted)
• C found in DNA, RNA
• T found in DNA only
• U found in RNA only

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Fig. 10-1
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Fig. 10-2
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Sugars (10-3)

• Ribose, deoxyribose
• b furanose
• Connected to bases by N-glycosidic bond
• C1 hydroxyl of sugar ? N9 (purines) or N1
  (pyrimidines)
• Phosphorylation by O-glycosidic bond
• C5 hydroxyl of sugar ? PO32-

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Fig. 10-4
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Fig. 10-4 (contd)
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Nucleic Acid Backbone

• Arrangement of nucleotides/deoxynucleotides
• Covalent linkages of sugars through phosphates
  (10-7)
• 'Tide 1 3' hydroxyl joined to 5' phosphate of
  'tide 2
• Phosphodiester bridge

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Fig. 10-7
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• Convention write sequence 5' ? 3'
• 5' end free phosphate
• 3' end sugar w/ free hydroxyl
• Phosphate grps charged at neutral pH
• Hydrophilic (why?)
• All phosphodiester links have same orientation
• Represent by letters, vertical diagonal lines
  (p.330)

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p. 330
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Pur/Pyr Rings

• Highly conjugated, so resonance structures
• Planarity
• Absorb UV light (260 nm) (10-10)
• Hydrophobic

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Fig. 10-10
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• Stacking (10-15)
• Stabilized by intermolecular forces
• VdW, dipole-dipole
• Functional bases of grps impt
• Minimizes interactions w/ H2O

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• Stacked bases pair w/ adjacent bases (on another
  nucleic acid strand) (10-11)
• A pairs w/ T
• Stabilized by H-bonds
• G pairs w/ C
• Stabilized by H-bonds
• Steric factors also stabilize

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Fig. 10-11
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2o Structure of DNA a Helix

• Watson/Crick (10-15)
• B form
• X-ray diffraction

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• Antiparallel chains -- common axis
• Backbone on outside
• Stacked bases on inside of helix
• Bases
• ? helix axis
• ? planes of sugars
• Every 10 residues
• Two chains held together by H-bonds
• Pur/pyr pairings
• Sequence unrestricted

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Fig. 10-15
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Fig. 10-16
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Semiconservative Replication

• Due to complementarity of 2 strands
• Site of A (ex) on one strand gives info
• Predict sequence of second strand
• Replication 2 strands unwind (10-17)
• Each strand template
• Complementary strand synthd

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Fig. 10-17
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Other Forms of Helix (10-19)

• A Right hand helix
• Less hydrophilic solns
• More compact
• Greater diameter
• Z Left hand helix
• When long repeating seqs of alternating G,C
• Smaller diameter
• Found in prokaryotes, eukaryotes

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Fig. 10-19
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Palindromic Sequences, Repeats (10-20,21)

• Self-complementary sequences
• 3D structures
• Hairpin loop
• Cruciform
• Triplex (10-23)
• Found at sites of initiation of DNA metab events
• May be regulatory or signaling function

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Fig. 10-20
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Fig. 10-21
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Fig. 10-21
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Fig. 10-23
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RNAs Impt in Genetic Code ? Protein

• Ribosomes in cytoplasm synth prots for cell use
• Ribosomes made of rRNA proteins
• Genetic code for these prots in nucleus
• Jacob/Monod
• Incrd ribosome when prots synthd
• mRNA carries genetic info nucleus ? cytoplasm
• DNA ? mRNA transcription
• mRNAs templates specifying aa seq (translation)

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• mRNA length depends on length polypeptide
• Each aa coded by 3-nucleotide sequence
• Also noncoding sequences
• tRNAs used in translation

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RNA Single Stranded (10-25)

• Base-pairs w/ complementary DNA or RNA
• If RNA-RNA, A pairs w/ U
• G-U pairing possible
• Secondary structures can form (10-26)
• Intrastrand loops, turns
• Many 3D shapes for RNAs (10-27)
• Structure impt to function!!

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Fig. 10-25
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Fig. 10-26
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Fig. 10-27
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Fig. 10-28
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Nucleic Acid Chemistry

• Highly viscous at pH 7.0
• Viscosity decrd as temp, pH change
• Denaturation of secondary structure (10-29)
• Disruption of H-bonds, hydrophobic interactions
• Annealing possible
• Slow if strands completely separated

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Fig. 10-29
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• Use mpt to estimate base composition (10-30)
• Diff H-bonds hold A-T or G-C
• More energy needed to melt more tightly bound
  strands

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• Hybrid duplexes from strands of 2 diff species
• Regions reanneal ? hybrid duplexes
• Study homologous regions
• Compare similarities between species
• Also impt in identification of gene on chromosome

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Mutations

• Alteration of DNA ? permanent changes in genetic
  info
• Can ? cancer and/or impt in aging
• May be changes in pur/pyr structure (10-33)

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• Deamination
• Ex C ? U
• Depurination
• Hydrolysis glycosyl bond ? base hydrolyzed
• More common in purs
• Get apurinic site

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Fig. 10-33a
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Fig. 10-33b
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• T-T dimers (10-34)
• With UV radiation
• Excitation of p e-, esp in T
• Covalent interaction between 2 stacked Ts
• ? kinked strand

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Fig. 10-34
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• Chemical mutagens (10-35)
• React w/ pur/pyr bases ? altered structure
• Nitrous acid ? deamination
• Alkylating agents ? methd or ethd bases
• Block functl grps
• Block base pairing
• Cell has repair mechs

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Fig. 10-35
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Other Impt Functions of Nucleotides

• Source of chem energy
• ATP also GTP, UTP, CTP (10-40)
• DNA incs monophosphates
• These began as triphosphates
• Dephosphn ? energy
• Hydrolysis 2 anhydride bonds ? 30
  kJ/mole

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Fig. 10-40
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Fig. 10-41

• Coenzymes
• CoA, NAD, FAD (10-41)
• Impt in redox rxns

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Fig. 10-41
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Fig. 10-41
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• Second messengers
• Linked to receptors in cell membr
• When receptor occupied outside cell, get
  conforml changes of cell membr prots
• Activates cell membr prot/enz adenylate cyclase
• Result ATP ? cAMP (10-42)
• cAMP interacts w/ regulatory enzymes in cell
• Control rates, extents of rxns in many cell
  processes
• Get rxn cascades

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Fig. 10-42