Biological molecules - FC

• Nucleotide

  Pentose sugar, nitrogenous base, phosphate group
• DNA

  Deoxyribose sugar
• RNA


  Ribose sugar
• Role of DNA in living cells

  • Base sequence of genes codes for functional RNA & amino acid sequence of polypeptides
  • Genetic information determines inherited characteristics = influences structure & function of organisms
• Role of RNA in living cells

  • mRNA: Complementary sequence to 1 gene from DNA with introns (non-coding regions) spliced out. codons can be translated into a poly peptide by ribosomes
  • rRNA: component of ribosomes (along with proteins)
  • tRNA: supplies complementary amino acid to mRNA codons during translation
• How polynucleotides form

  Condensation reactions between nucleotides, creating strong phosphodiester bonds (sugar-phosphate backbone)
• Structure of DNA

  • Double helix of 2 polynucleotide strands (deoxyribose)
  • H-bonds between complementary purine & pyrimidine base pairs on opposite strands
  • Adenine (A) + Thymine (T)
  • Guanine (G) + Cytosine (C)
• Purine

  1. ring bases (A & G)
• Pyrimidine

  1. ring bases (T & C & U)
• Complementary base pairs in DNA

  • 2 H-bonds between adenine (A) + thymine (T)
  • 3 H-bonds between guanine (G) + cytosine (C)
• Complementary base pairs in RNA

  • 2 H-bonds between adenine (A) + uracil (U)
  • 3 H-bonds between guanine (G) + cytosine (C)
• Structure of DNA

  • Sugar-phosphate backbone & many H-bonds provide stability
  • Long molecule stores lots of information
  • Helix is compact for storage in nucleus
  • Base sequence of triplets codes for amino acids
  • Double-stranded for semi-conservative replication
  • Complementary base pairing for accurate replication
  • Weak H-bonds break so strands separate for replication
• Structure of messenger RNA (mRNA)

  • Long ribose polynucleotide (but shorter than DNA)
  • Contains uracil instead of thymine
  • Single-stranded & linear (No complementary base pairing)
  • Codon sequence complementary to exons of 1 gene from 1 DNA strand
• Structure of RNA

  • Single strand of about 80 nucleotides folded into clover shape
  • Anticodon on one end and an amino acid binding site on the other
• Order of increasing length

  • tRNA
  • mRNA
  • DNA
• Scientists initially doubted that DNA carried the genetic code because it is a chemically simple molecule with few components
• Semiconservative DNA replication

  Strands from original DNA molecule act as a template, resulting in a new DNA molecule containing 1 old strand & 1 new strand
• Semiconservative DNA replication

  1. DNA helicase breaks H-bonds between base pairs

  2. Each strand acts as a template

  3. Free nucleotides attach to exposed bases by complementary base pairing

  4. DNA polymerase catalyses condensation reactions that join adjacent nucleotides on new strand

  5. H-bonds reform
• Meselson-Stahl experiment

  • Bacteria were grown in a medium containing heavy isotope 15N for many generations
  • Some bacteria were moved to a medium containing light isotope 14N. Samples were extracted after 1 & 2 cycles of DNA replication
  • Centrifuge formed a pellet. Heavier DNA (bases made form 15N) settled close to the bottom of the tube
• The Meselson-Stahl experiment validated semiconservative replication
• Adenosine triphosphate (ATP)

  Nucleotide derivative of adenine with 3 phosphate groups
• Role of ATP in cells

  • ATP hydrolase catalyses ATP → ADP + Pi
  • Energy released is coupled to metabolic reactions
  • Phosphate group phosphorylates compounds to make them more reactive
• How ATP is resynthesized in cells

  ATP synthase catalyses condensation reaction between ADP & Pi during photosynthesis & respiration
• Why ATP is suitable as the 'energy currency' in cells

  • High energy bonds between phosphate groups
  • Small amounts of energy released at a time = less energy wasted as heat
  • Readily resynthesized
  • Single-step hydrolysis= quick energy availability
• General structure of an amino acid

  • COOH carboxyl group
  • R variable side group consists of carbon chain and may include other functional groups e.g. benzene ring of -OH (alcohol)
  • NH2 amine/ Amio group
• How to test for proteins in a sample


  1. Biuret test confirms presence of peptide bond

  2. Add equal volume of sodium hydroxide to sample at room temp

  3. Add drops of dilute copper sulphate solution. swirl to mix

  4. Positive result: Colour changes form blue to purple

  5. Negative result: solution remains blue

  
• Amino acids

  • 20 amino acids
  • Differ only by side 'R' group
• How dipeptides and polypeptides form

  1. Condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water

  2. Dipeptide: 2 amino acids

  3. Polypeptide: 3 or more amino acids
• Levels of protein structure

  4 levels
• Primary Structure

  Sequence, number & type of amino acids in polypeptide, determined by sequence of codons on mRNA

  
• Secondary Structure

  Hydrogen bonds form between O 𝛿- (slightly negative) attached to -C=O & H 𝛿+ (slightly positive) attached to -NH
• Types of secondary protein structure

  • α-helix: All N-H bonds on the same side of protein chain, Spiral shape, H-bonds parallel to helical axis
  • β-pleated sheet: N-H and C=O groups alternate from one side to the other
• Tertiary Structure

  3D structure formed by further folding of polypeptide, disulfide bridges, ionic bonds, hydrogen bonds
• Bonds in tertiary protein structure

  • Disulfide bridges: strong covalent S-S bonds between molecules of the amino acid Cysteine
  • Ionic Bonds: relatively strong bonds between charged R groups (PH changes cause these bonds to break)
  • Hydrogen bonds: numerous and easily broken
• Quaternary Structure

  • Functional proteins may consist of more than one polypeptide
  • Precise 3D structure held together by the same types of bond as tertiary structure
  • May involve addition of prosthetic groups e.g. metal ions or phosphate groups
• Structure and function of globular proteins

  • Spherical and compact
  • Hydrophilic R groups face outwards and hydrophobic R groups face inward = usually water-soluble
  • Involved in metabolic processes e.g. Enzymes and haemoglobin
• Structure and function of Fibrous Proteins

  • Can Form long chains
  • Insoluble in water
  • Useful for structure and support e.g. collagen in skin
• How chromatography could be used to identify the amino acids in a mixture

  1. Use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent

  2. Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper and solubility in solvent

  3. Use revealing agent or UV light to see spots

  4. Calculate Rf values and math to database
• Enzymes

  • Biological catalysts for intra and extracellular reactions
  • Specific tertiary structure determines shape of active site, complementary to a specific substrate
  • Formation of enzyme- substrate (ES) complexes lowers activation energy of metabolic reactions
• Induced Fit Model of enzyme action

  • Shape of active site is not directly complementary to substrate and is flexible
  • Conformational changes enables ES complexes to form
  • This puts strain on substrate bonds, lowering activation energy