Chapter 10 Nucleotides and Nucleic Acids

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Chapter 10Nucleotides and Nucleic Acids
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Outline

• What are the structure and chemistry of
  nitrogenous bases?
• What are nucleosides?
• What are the structure and chemistry of
  nucleotides?
• What are nucleic acids?
• What are the different classes of nucleic Acids?
• Are nucleic acids susceptible to hydrolysis?

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Information Transfer in Cells
The fundamental process of information transfer
in cells.
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10.1 What Are the Structure and Chemistry of
Nitrogenous Bases?

• Know the basic structures
• Pyrimidines
• Cytosine (DNA, RNA)
• Uracil (RNA)
• Thymine (DNA)
• Purines
• Adenine (DNA, RNA)
• Guanine (DNA, RNA)

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10.1 What Are the Structure and Chemistry of
Nitrogenous Bases?
(a) The pyrimidine ring system by convention,
atoms are numbered as indicated.
(b) The purine ring system atoms numbered as
shown.
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10.1 What Are the Structure and Chemistry of
Nitrogenous Bases?
The common pyrimidine bases cytosine, uracil,
and thymine in the tautomeric forms predominant
at pH 7.
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10.1 What Are the Structure and Chemistry of
Nitrogenous Bases?
The common purine bases adenine and guanine
in the tautomeric forms predominant at pH 7.
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10.1 What Are the Structure and Chemistry of
Nitrogenous Bases?
Other naturally occurring purine derivatives
hypoxanthine, xanthine, and uric acid.
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The Properties of Pyrimidines and Purines Can Be
Traced to Their Electron-Rich Nature
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10.2 What Are Nucleosides?

• Structures to Know
• Nucleosides are compounds formed when a base is
  linked to a sugar via a glycosidic bond
• The sugars are pentoses
• D-ribose (in RNA)
• 2-deoxy-D-ribose (in DNA)
• The difference - 2'-OH vs 2'-H
• This difference affects secondary structure and
  stability

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10.2 What Are Nucleosides?
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10.2 What Are Nucleosides?

• The base is linked to the sugar via a glycosidic
  bond
• The carbon of the glycosidic bond is anomeric
• Named by adding -idine to the root name of a
  pyrimidine or -osine to the root name of a purine
  
• Sugars make nucleosides more water-soluble than
  free bases

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10.2 What Are Nucleosides?
The common ribonucleosides.
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10.3 What Is the Structure and Chemistry of
Nucleotides?

• Nucleotides are nucleoside phosphates
• Know the nomenclature
• "Nucleotide phosphate" is redundant!
• Most nucleotides are ribonucleotides
• Nucleotides are polyprotic acids

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10.3 What Is the Structure and Chemistry of
Nucleotides?
Structures of the four common ribonucleotides
AMP, GMP, CMP, and UMP. Also shown 3-AMP.
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10.3 What Is the Structure and Chemistry of
Nucleotides?
Figure 10.12 The cyclic nucleotide cAMP.
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10.3 What Is the Structure and Chemistry of
Nucleotides?
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Nucleoside 5'-Triphosphates Are Carriers of
Chemical Energy

• Nucleoside 5'-triphosphates are indispensable
  agents in metabolism because their phosphoric
  anhydride bonds are a source of chemical energy
• Bases serve as recognition units
• Cyclic nucleotides are signal molecules and
  regulators of cellular metabolism and
  reproduction
• ATP is central to energy metabolism
• GTP drives protein synthesis
• CTP drives lipid synthesis
• UTP drives carbohydrate metabolism

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Nucleoside 5'-Triphosphates Are Carriers of
Chemical Energy
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Nucleoside 5'-Triphosphates Are Carriers of
Chemical Energy
Figure 10.14 Phosphoryl, pyrophosphoryl, and
nucleotidyl group transfer, the major biochemical
reactions of nucleotides. Nucleotidyl group
transfer is shown here.
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10.4 What Are Nucleic Acids?

• Nucleic acids are linear polymers of nucleotides
  linked 3' to 5' by phosphodiester bridges
• Ribonucleic acid and deoxyribonucleic acid
• Know the shorthand notations
• Sequence is always read 5' to 3'
• In terms of genetic information, this corresponds
  to "N to C" in proteins

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10.4 What Are Nucleic Acids?
3',5'-Phosphodiester bridges link nucleotides
together to form polynucleotide chains. The
5'-ends of the chains are at the top the
3'-ends are at the bottom. RNA is shown here.
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10.4 What Are Nucleic Acids?
3,5-phosphodiester bridges link nucleotides
together to form polynucleotide chains. The
5-ends of the chains are at the top the
3-ends are at the bottom. DNA is shown here.
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10.5 What Are the Different Classes of Nucleic
Acids?

• DNA - one type, one purpose
• RNA - 3 (or 4) types, 3 (or 4) purposes
• ribosomal RNA - the basis of structure and
  function of ribosomes
• messenger RNA - carries the message for protein
  synthesis
• transfer RNA - carries the amino acids for
  protein synthesis
• Others
• Small nuclear RNA
• Small non-coding RNAs

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10.5 What Are the Different Classes of Nucleic
Acids?
The antiparallel nature of the DNA double helix.
The two chains have opposite orientations.
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The DNA Double Helix

• The double helix is stabilized by hydrogen bonds
• "Base pairs" arise from hydrogen bonds
• A-T G-C
• Erwin Chargaff had the pairing data, but didn't
  understand its implications
• Rosalind Franklin's X-ray fiber diffraction data
  was crucial
• Francis Crick showed that it was a helix
• James Watson figured out the H bonds

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The Base Pairs Postulated by Watson
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The Structure of DNA

• An antiparallel double helix
• Diameter of 2 nm
• Length of 1.6 million nm (E. coli)
• Compact and folded (E. coli cell is only 2000 nm
  long)
• Eukaryotic DNA wrapped around histone proteins to
  form nucleosomes
• Base pairs A-T, G-C

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The Structure of DNA
Replication of DNA gives identical progeny
molecules because base pairing is the mechanism
that determines the nucleotide sequence of each
newly synthesized strand.
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Messenger RNA Carries the Sequence Information
for Synthesis of a Protein

• Transcription product of DNA
• In prokaryotes, a single mRNA contains the
  information for synthesis of many proteins
• In eukaryotes, a single mRNA codes for just one
  protein, but structure is composed of introns and
  exons

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Messenger RNA Carries the Sequence Information
for Synthesis of a Protein
Transcription and translation of mRNA molecules
in prokaryotic versus eukaryotic cells. In
prokaryotes, a single mRNA molecule may contain
the information for the synthesis of several
polypeptide chains within its nucleotide
sequence.
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Messenger RNA Carries the Sequence Information
for Synthesis of a Protein
Transcription and translation of mRNA molecules
in prokaryotic versus eukaryotic
cells. Eukaryotic mRNAs encode only one
polypeptide but are more complex.
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Eukaryotic mRNA

• DNA is transcribed to produce heterogeneous
  nuclear RNA (hnRNA)
• mixed introns and exons with poly A
• intron intervening sequence
• exon coding sequence
• poly A tail - stability?
• Splicing produces final mRNA without introns

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Ribosomal RNA Provides the Structural and
Functional Foundation for Ribosomes

• Ribosomes are about 2/3 RNA, 1/3 protein
• rRNA serves as a scaffold for ribosomal proteins
• The different species of rRNA are referred to
  according to their sedimentation coefficients
• rRNAs typically contain certain modified
  nucleotides, including pseudouridine and
  ribothymidylic acid
• Briefly the genetic information in the
  nucleotide sequence of mRNA is translated into
  the amino acid sequence of a polypeptide chain by
  ribosomes

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Ribosomal RNA Provides the Structural and
Functional Foundation for Ribosomes
Ribosomal RNA has a complex secondary structure
due to many intrastrand H bonds. The gray line
here traces a polynucleotide chain consisting of
more than 1000 nucleotides. Aligned regions
represent H-bonded complementary base sequences.
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Ribosomal RNA Provides the Structural and
Functional Foundation for Ribosomes
The organization and composition of ribosomes.
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Transfer RNAs Carry Amino Acids to Ribosomes for
Use in Protein Synthesis

• Small polynucleotide chains - 73 to 94 residues
  each
• Several bases usually methylated
• Each a.a. has at least one unique tRNA which
  carries the a.a. to the ribosome
• 3'-terminal sequence is always CCA-3'-OH. The
  a.a. is attached in ester linkage to this 3'-OH.
• Aminoacyl tRNA molecules are the substrates of
  protein synthesis

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Transfer RNAs Carry Amino Acids to Ribosomes for
Use in Protein Synthesis
Transfer RNA also has a complex secondary
structure due to many intrastrand hydrogen bonds.
The black lines represent base-paired
nucleotides in the sequence.
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The Chemical Differences Between DNA and RNA Have
Biological Significance

• Two fundamental chemical differences distinguish
  DNA from RNA
• DNA contains 2-deoxyribose instead of ribose
• DNA contains thymine instead of uracil

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The Chemical Differences Between DNA and RNA Have
Biological Significance

• Why does DNA contain thymine?
• Cytosine spontaneously deaminates to form uracil
• Repair enzymes recognize these "mutations" and
  replace these Us with Cs
• But how would the repair enzymes distinguish
  natural U from mutant U?
• Nature solves this dilemma by using thymine
  (5-methyl-U) in place of uracil

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The Chemical Differences Between DNA and RNA Have
Biological Significance
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DNA RNA Differences?

• Why is DNA 2'-deoxy and RNA is not?
• Vicinal -OH groups (2' and 3') in RNA make it
  more susceptible to hydrolysis
• DNA, lacking 2'-OH is more stable
• This makes sense - the genetic material must be
  more stable
• RNA is designed to be used and then broken down

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Restriction Enzymes

• Bacteria have learned to "restrict" the
  possibility of attack from foreign DNA by means
  of "restriction enzymes"
• Type II and III restriction enzymes cleave DNA
  chains at selected sites
• Enzymes may recognize 4, 6 or more bases in
  selecting sites for cleavage
• An enzyme that recognizes a 6-base sequence is a
  "six-cutter"

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Type II Restriction Enzymes

• No ATP requirement
• Recognition sites in dsDNA have a 2-fold axis of
  symmetry
• Cleavage can leave staggered or "sticky" ends or
  can produce "blunt ends

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Type II Restriction Enzymes

• Names use 3-letter italicized code
• 1st letter - genus 2nd,3rd - species
• Following letter denotes strain
• EcoRI is the first restriction enzyme isolated
  from the R strain of E. coli

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Cleavage Sequences of Restriction Endonucleases
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Restriction Mapping of DNA
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Problems

• End of Chapter problems 1-14