2.1.3 Nucleic Acids

• DNA

  Deoxyribonucleic acid; self replicating material that is present in living organisms as the main component of chromatin, Carrier of genetic information; polynucleotide consisting of repeating nucleotide units. Chromatin in the nucleus, or plasmid in prokaryotes.
• RNA

  Three types; tRNA (transfer RNA; cytoplasm, translation), mRNA (messenger RNA; nucleus, transcription), rRNA (ribosomal RNA, ribosomes). Ribonucleic acid; present in all living cells. Acts as a messenger carrying instructions from DNA for controlling the synthesis of proteins.
• Nucleotide

  Organic molecules that acts as the monomer for forming nucleic acids like DNA and RNA. Composed of: nitrogenous base, five carbon ring sugar (pentose sugar) and at least one phosphate group; phosophorylate nucleotides have more than one.
• Nitrogenous bases

  Five to know: Adenine, Guanine, Thymine, Cytosine, Uracil. Nitrogen containing biological compounds that are the components of nucelotides; constitute the basic building blocks of nucleic acids.
• Phosphodiester bonds

  Bond between pentose sugar groups and phosphate groups (sugar of one nucleotide, phosphate of another); forms sugar-phosphate backbone of DNA and RNA.
• Nucleotide vs Nucleic Acid

  Nucelotide is the monomer of a nucleic acid; nucleic acid is many nucleotides linked together by phosphodiester bonds. RNA has one sugar phosphate backbone, DNA has two. They have complementary base pairs (hydrogen bonds) between the bases; A-T; C-G; A-U. They are long and large.
• DNA Labelled Diagram

  Phosphate group; deoxyribose sugar; O; A, T, C, G nitrogenous base.

  
• RNA Labelled Diagram

  Phosphate group; ribose sugar; OH; A, U, C, G nitrogenous base.

  
• RNA & DNA Similarities

  Both contain a phosphate group and a sugar phosphate backbone; both are polymers/polynucleotides; both long chains; both made of nucleotides; both have phosphodiester bonds; both have base pairs.
• RNA & DNA Differences

  RNA is single stranded; straight chain; shorter; uracil base; different monomers; one sugar phosphate backbone. DNA is double stranded with anti-parallel strands; helix structure; longer; thymine base; different monomers; two sugar phosphate backbones.
• Carbons where linkages form?

  Carbon 1 is associated with the nitrogenous bases; Carbon 5 is associated with the phosphate group.
• Two types of nitrogenous bases?

  Purines: Contain double carbon rings; adenine and guanine. Pyrimidines: Contain single carbon rings; thymine, cytosine and uracil.
• Complementary base pair rules

  Base pairs occur between a purine and pyrimidine, through a hydrogen bond. Adenine always pairs with thymine or uracil; Guanine always pairs with cytosine. C-G forms three hydrogen bonds; A-T, A-U form two hydrogen bonds - less energy is required to split this base pair.
• Carbon Orientation

  5' - the direction in which carbon 5 is facing the terminal nucleotide. 3' - the direction in which carbon 3 is facing the terminal nucleotide. Used for antiparallel structures describes the direction an enzyme moves in semi conservation replication of DNA (s phase in interphase)
• ATP

  Adenosine Triphosphate - has a triphosphate group with very high enthalpy bonds. It is a phosphorylated nucleotide, adding of phosphate makes it very reactive. Produced by anaerobic and aerobic respiration. Aerobic respiration; 1 mol. of glucose = 32ATP, mitochondria. Anaerobic respiration; 1 mol. of glucose = 2ATP, cytoplasm.
• Energy from ATP?

  ATP is hydrolysed to form ADP and a phosphate ion, releasing energy. ATP + H20 —> ADP + P1 + energy. (P1 = inorganic phosphate)
• ATP base

  Base is always adenine.
• Properties of ATP

  Small, moves easily in and out of cells; water soluble, energy requiring processes happen in aqueous environments; contains bonds between phosphates with intermediate energy, large enough to be useful for cellular reactions, not large enough to be wasted thermal energy; releases energy in small quantities, energy is not wasted as heat; easily regenerated, can be recharged with energy.
• Method of extracting DNA

  DNA and detergent solution should be boiled for a few minutes to break down surface membrane; move to ice bath so DNA structure is not disrupted; use protease enzymes to break down proteins in DNA (histones); mix with ethanol to form a DNA precipitate and two distinct layers of solution.
• DNA Replication

  DNA helicase unzips the DNA by breaking hydrogen bonds between bases. Free floating DNA nucleotides line up along the template strand according to complementary base pairing. In the leading strand, DNA polymerase catalyses the condensation reaction to create phosphodiester bonds between nucleotides. In the lagging strand, DNA polymerase catalyses the condensation reaction to create phosphodiester bonds between the nucleotides in okazaki fragments; sealed by DNA ligase.
• DNA Polymerase

  Catalyses condensation reaction between new nucleotides to form phosphodiester bonds; only works in 5' to 3' direction.
• DNA Helicase

  Unzips DNA by breaking hydrogen bonds between polynucleotide strands.
• DNA ligase

  Joins Okazaki fragments together.
• Okazaki Fragments

  Small sections of DNA that are formed during discontinuous synthesis of the lagging strand during DNA replication.
• Sense Strand

  Codes for the protein to be synthesised; runs from 5' to 3'
• Antisense strand

  3' to 5' - complementary copy of the sense strand; does not code for protein. Acts as template strand; complementary RNA has same sequence as the sense strand.
• Transcription

  Free RNA nucleotides pair with complementary base pairs on antisense strand (T replaces U, U binds with A on template strand). RNA polymerase forms phosphodiester bonds between RNA molecules. Transcription stops at the end of the gene; complete short RNA strand is called mRNA. mRNA detaches from template and leaves through nuclear pore, double helix reforms. mRNA travels to ribosome in the cytoplasm.
• Transcription & DNA Replication Similarities

  Both have template and coding strand; both rely on base pairings; both unzip DNA with DNA helicase; both form phosphodiester bonds.
• Transcription and DNA Replication Differences

  Transcription uses uracil, DNA Replications uses thymine; Transcription has promoter and terminator region; DNA Replication forms phosphodiester bonds between DNA nucleotides, transcription between RNA nucleotides; DNA replication involves DNA ligase binding okazaki fragments. Transcription, mRNA leaves the nucleus; DNA replication product stays in the nucleus.
• Exon


  Coding region of mRNA
• Intron

  Non-coding region of mRNA
• Pre-mRNA

  mRNA that has been transcribed but not yet modified
• Splicosome

  Machinery used to splice pre-mRNA
• Why splice?

  To remove introns
• Translation

  mRNA binds to ribosome subunit. tRNA anticodon (usually UAC) binds to start codon of mRNA (usually AUG) with amino acid attached; second tRNA molecules attaches to next triplet codon of mRNA with another amino acid attached. Two amino acids form peptide bond. First tRNA triplet leaves, allowing another tRNA to go through the same process. Process continues until the stop codon is reached.
• Degenerate Code

  More than one triplet of base codes for one amino acids; universal and non overlapping - each DNA/RNA nucleotide will only sit within a single triplet/codon.