Nucleic Acids

• Nucleic Acids
• Nucleic Acids


  Molecules that have the remarkable property of replicating itself, and serve as the repository and transmitter of genetic information in every cell and organism

  
• Types of Nucleic Acids

  • DNA: Deoxyribonucleic Acid
  • RNA: Ribonucleic Acid

  
• DNA


  Found within cell nucleus, storage and transfer of genetic information

  
• RNA


  Occurs in all parts of cell, primary function is to synthesize the proteins
• Gene


  Segment of DNA which specifies the chain of amino acids that comprises the protein molecule

  
• Most human genes are ~1000–3500 nucleotide units long
• Human genome is about 20,000–25,000 genes
• The Central Dogma


  Genetic message is transcribed by mRNA and translated by tRNA and rRNA into thousands of different proteins

  
• Nucleotide


  Has three components: pentose sugar, phosphate group, heterocyclic base

  
• Nitrogen-Containing Heterocyclic Bases


  • Adenine
  • Guanine
  • Cytosine
  • Thymine
  • Uracil

  
• Nucleoside Formation


  Condensation reaction between a five-carbon monosaccharide and a purine or pyrimidine base derivative

  
• Nucleotide Formation


  Phosphate group is added to a nucleoside, attached to C5' position through a phosphoester bond

  
• Nucleotide Nomenclature


  • Adenylic acid or adenosine monophosphate (AMP)
  • Guanylic acid or guanosine monophosphate (GMP)
  • Cytidylic acid or cytidine monophosphate (CMP)
  • Uridylic acid or uridine monophosphate (UMP)
  • Deoxythymidylic acid or deoxythymidine monophosphate (dTMP)

  
• Primary Structure of Nucleic Acids

  Nucleotides linked in 3',5'- phosphodiester bonds, sugar-phosphate groups form the backbone

  
• Polynucleotides and the Nucleic Acids

  RNA: polynucleotide with ribose, phosphate, and one of the bases adenine, cytosine, guanine, or uracil

  DNA: polynucleotide with deoxyribose, phosphate, and one of the bases adenine, cytosine, guanine, or thymine

  
• Shorthand Structure of Polynucleotides

  Bases indicated by initials, ribose by straight line, phosphate by P

  
• DNA


  • High molecular weight, double-stranded polynucleotide, primary function is storage and transfer of genetic information

  
• Base Pairing in DNA

  Adenine always pairs with Thymine, Guanine with Cytosine

  
• Watson and Crick proved the DNA structure was a double helix whose chains were complementary and antiparallel

  
• DNA Double Helix


  • Stabilized by Chargaff's rule of base pairing, stacking interaction of hydrogen-bonded bases, hydrophobic interior and hydrophilic exterior

  
• Denaturation of DNA


  Loss of helical structure due to disruption of hydrogen bonds, can be caused by extremes of pH, heat, or chemicals
• Conformations of DNA


  • B-DNA
  • A-DNA
  • Z-DNA
• Types of DNA Sequences

  • Exons
  • Introns
  • Palindromes or inverted repeats
  • Cruciforms

  
• Replication of DNA Molecules

  Two identical DNA molecules are formed from one parent DNA molecule, with each daughter DNA molecule containing one parent DNA strand and one newly formed DNA strand

  
• DNA replication is semiconservative and mostly bidirectional
• Ack (cruciform)


  Perfect palindrome forms with exact base pairs; quasi palindrome, when not all will form hairpin loop
• Cruciform (or snapback)


  • As their name implies, are crosslike structures
  • When a DNA sequence contains a palindrome
• Replication of DNA Molecules

  1. DNA molecules produce exact duplicates of themselves

  2. The two strands of the DNA double helix unwind, the separated strands serve as templates for the formation of new DNA strands

  3. Free nucleotides pair with the complementary bases on the separated strands of DNA

  4. When the process is completed two identical molecules of DNA are formed

  5. The newly synthesized DNA has one new DNA strand and old DNA strand

  6. Two daughter DNA molecules are produced from one parent DNA molecule, with each daughter DNA molecule containing one parent DNA strand and one newly formed DNA strand

  
• DNA replication


  • Semiconservative and mostly bidirectional
  • First step is the separation of the strands accomplished by helicase, which breaks the H-bonds between base pairs
  • Positive supercoiling results when H-bonds are broken, this is relieved by topoisomerase
  • When supercoiling is relieved, single-strand binding protein binds to the separated strands to keep them apart
  • Primase catalyzes synthesis of a 10-12 base piece of RNA to "prime" the DNA replication
  • DNA polymerase "reads" the parental strand or template, catalyzing the polymerization of a complementary daughter strand; the enzyme checks the correct base pairing and catalyzes the formation of phosphodiester linkages
• Replication of DNA Molecules - Leading Strand

  The DNA Polymerase, using dNTP's and Mg2+, cause the replication by base-pairing the 3'strand with free nucleotide units

  
• Replication of DNA Molecules - Lagging Strand

  1. The enzyme primase (using NTP's and Mg2+) puts primers on the lagging strand by forming short RNA strands through base-pairing of the 5'strand

  2. DNA Polymerase recognize, then lengthen the primers using dNTP's

  3. The primers are then removed by nucleotidase and further lengthening is done by DNA Polymerase resulting to an OKAZAKI STRAND

  4. The Okazaki strands are then linked together and sealed using the enzyme ligase leading to the formation of a NEW STRAND

  
• DNA replication usually occurs at multiple sites within a molecule (origin of replication) and the replication is bidirectional from these sites
• Multiple-site replication enables rapid DNA synthesis
• Two conditions must be satisfied for replication to take place with high fidelity and accuracy: a) normal electronic characteristics b) normal base sequence
• Protein Synthesis


  1. Transcription - a process by which DNA directs the synthesis of mRNA molecules

  2. Translation - a process in which mRNA is deciphered to synthesize a protein molecule
• Ribonucleic Acids (RNA)


  • The sugar unit in the backbone is ribose; the base thymine found in DNA is replaced by uracil
  • RNA is a single-stranded molecule; DNA is double-stranded (double helix)
  • A hairpin loop is produced when single-stranded RNA doubles back on itself, and complementary base pairing occurs
  • RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides

  
• Types of RNA Molecules

  • Heterogeneous nuclear RNA (hnRNA)
  • Small nuclear RNA (snRNA)
  • Messenger RNA (mRNA)
  • Ribosomal RNA (rRNA)
  • Transfer RNA (tRNA)

  
• Transcription: RNA Synthesis


  1. Biosynthesis of RNA by DNA-dependent RNA Polymerase on a DNA template; an information transfer process where one of the two DNA strands acts as a template, which is copied into a complementary RNA molecule

  2. Transcription of DNA into RNA is restricted to discrete regions or genes of DNA

  3. When a gene is transcribed, only one strand of the DNA serves as the template for RNA synthesis: the template strand, also called the sense strand; the nontemplate strand is called the coding strand, also called the antisense strand

  
• Transcription: RNA Synthesis - Steps

  1. RNA Polymerase recognizes promoter sites and enhancer sites on DNA

  2. RNA Polymerase requires a 5'-3' direction which can only be provided by the 3'strand of DNA

  3. RNA Polymerase, once it has spotted the portion to be transcribed, does the transcription in the 5' → 3' direction and uses NTP's and Mg2+

  4. Unwinding of DNA double helix by RNA polymerase to expose some bases (a gene)

  5. Alignment of free ribonucleotides along the exposed DNA strand (template) forming new base pairs

  6. RNA polymerase catalyzes the linkage of ribonucleotides one by one to form hnRNA molecule

  7. Transcription ends when the RNA polymerase enzyme encounters a stop signal on the DNA template