7 Nucleic Acid and Gene Expression

• Polynucleotides

  Both DNA and RNA are polymers of nucleotides
• Deoxyribonucleic acid (DNA) can be found in eukaryotes, prokaryotes, and some viruses. For eukaryotes, DNA is found in the nucleus, mitochondria, and chloroplasts
• Structure of a nucleotide

  • Individual nucleotides comprise pentose sugar (5-carbon), nitrogenous base, phosphate group
• Phosphate group


  • Confers a nucleic acid its negative charge and acidic character
• Nitrogenous base

  • Five types: adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U)
• Learning Outcomes

  • Describe the structure and roles of DNA and RNA (tRNA, rRNA, and mRNA)
  • Describe the process of DNA replication and how the end replication problem arises
  • Describe how the information on DNA is used to synthesize polypeptides in prokaryotes and eukaryotes
  • Describe the structure and organization of viral, prokaryotic, and eukaryotic genomes
• Pentose sugar

  • Two types: deoxyribose and ribose
• Types of nitrogenous bases

  • Adenine (A), Guanine (G), Cytosine (C), Thymine (T), Uracil (U)
• Monomers of DNA and RNA

  Deoxyribonucleotides and ribonucleotides, respectively
• Polymerisation of nucleotides

  DNA and RNA are formed from the polymerisation of deoxyribonucleotides
• Ribonucleic acid (RNA) are transcribed from DNA. There are three different types of RNA: Messenger RNA (mRNA), Ribosomal RNA (rRNA), Transfer RNA (tRNA)
• DNA and RNA are formed from the polymerisation of deoxyribonucleotides and ribonucleotides respectively
• Nucleotides polymerise

  Through consecutive condensation reactions between the phosphate group at carbon-5 of the pentose sugar of one nucleotide and the hydroxyl group at carbon-3 of the pentose sugar of the adjacent nucleotide to form a phosphodiester bond
• Due to complementary base pairing, the distance between the sugar-phosphate backbones of both strands is kept constant at the width of one base pair = 2nm
• Structure of DNA

  • Two polynucleotide strands coil around each other to form a double helix
  • Each chain is made of a sugar-phosphate backbone and nitrogenous bases that project into the centre of the helix
  • Chains are oriented in opposite directions (anti-parallel) to each other
  • Hydrogen bonds form between the nitrogenous base of one chain and the corresponding base of the opposite chain
• RNA is essential in living cells and viruses for the process of protein synthesis
• Transcription


  The process of making a strand of RNA using a single strand of DNA as a template
• Hydrogen bonds form between complementary bases


  • A=T (in DNA) or A=U (in RNA)
  • C≡G
• Phosphodiester bonds/linkages


  Strong covalent bonds which confer strength and stability to the nucleic acid
• Deoxyribonucleic acid (DNA) consists of two polynucleotide strands made up of many deoxyribonucleotides joined by phosphodiester bonds
• Nucleotide

  Involves two separate condensation reactions: 1) between the phosphate and pentose sugar, and 2) between the pentose sugar and nitrogenous base
• The number of adenine and thymine bases are approximately the same, and the same applies to the number of guanine and cytosine bases
• Translation

  Using messenger RNA (mRNA) as a template to produce a polypeptide
• Types of RNA

  • mRNA: messenger RNA
  • tRNA: transfer RNA
  • rRNA: ribosomal RNA
• Ribosomal RNA (rRNA)

  • Makes up approximately 80% of the total RNA in a cell
  • Complex molecule made up of double or single helices
  • Specific rRNA molecules associate with ribosomal proteins to form the small and large subunits of ribosomes
• Other types of RNA

  • microRNA (miRNA)
  • small interfering RNA (siRNA)
  • small nuclear RNA (snRNA)
• Transport of RNA strands to the cytosol

  RNA strands are transported to the cytosol through the nuclear pore
• Synthesis of rRNA in eukaryotes

  Synthesised in the nucleolus within the nucleus, then associates with ribosomal proteins to form ribosomal subunits which leave the nucleus via the nuclear pores
• RNA and DNA are different
• Ribosomes


  • Provide the structural framework for holding mRNA and tRNA in place
  • Contain the enzyme peptidyl transferase responsible for catalysing formation of peptide bonds in a polypeptide chain
• Ribosomal RNA in prokaryotes and eukaryotes


  Slightly different in terms of the rRNA and protein components that form the ribosome, but similar in structure
• Prokaryotic ribosomal assembly occurs in the cytoplasm due to the lack of membrane-bound organelles within these cells
• Ribosome assembly


  Small and large ribosomal subunits assemble to form a fully functioning ribosome during translation at the rough endoplasmic reticulum or in the cytosol
• Transfer RNA (tRNA)

  • Makes up approximately 15% of the total RNA in a cell
  • Single-stranded polynucleotide
  • Contains anticodons which are sequences of 3 nucleotides that are complementary to the codons on mRNA
  • Functions to carry a specific amino acid to a specific codon on the mRNA
• Messenger RNA (mRNA)


  • Makes up approximately 3–5% of the total RNA in a cell
  • Linear and single-stranded polynucleotide
  • Carries the DNA message from the nucleus to the cytosol in the form of a series of codons
  • Provides specific binding sites for complementary aminoacyl-tRNA complexes during translation
• In prokaryotes, ribosomal assembly occurs in the cytoplasm due to the lack of membrane-bound organelles within these cells
• DNA replication

  1. Both strands of DNA molecule are unwound and unzipped, and each strand acts as a template for synthesis of a new daughter DNA strand via complementary base pairing

  2. Hydrogen bonds form between the bases of the parent strand and the newly synthesized daughter strand to form a complete DNA molecule

  3. Both DNA molecules consist of one original parental strand and one newly synthesized daughter strand
• Mechanism of DNA replication - Step 1


  Unwinding of the DNA double helix before the start of DNA replication, free deoxyribonucleotides are synthesized in the cytoplasm, replication begins at a specific site called the origin of replication
• Evidence for semi-conservative replication was provided by Matthew Meselson and Franklin Stahl in 1958
• DNA replication is the process of making an exact copy of DNA to increase the amount of DNA prior to cell division