Module 1 - Biochemistry

• Polymer synthesis in a cell

  1. Dehydration (condensation) reactions

  2. Dehydration removes water molecule forming new bonds between monomers

  3. One monomer added by each dehydration reaction, only at one end, one at a time

  4. Energy is required to make larger molecules from smaller ones (second rule of thermodynamics)
• Activated monomer

  Energy is added to the monomer by an earlier reaction
• Enzymes


  • Catalyse the dehydration reactions
  • Different enzymes for each type of polymer
• Protein synthesis of secreted and non secreted proteins

  1. Signal peptide on protein is recognised by the ribosome as to where the protein is secreted outside or for the endomembrane system

  2. Signal sequence directs polypeptides

  3. Signal peptide is chopped off after it informs the cell as it is no longer needed and may alter the proteins final structure and folding
• Secreted proteins


  • Have a hydrophobic signal peptide
  • That binds to a signal recognition particle (SRP)
  • Translation is stopped
• Cell signalling process


  1. Signal reception - Signal molecule interacts with receptor protein in plasma membrane, causing change in shape, starting relay of molecules

  2. Signal transduction - Relay of molecules is the transduction process

  3. Cellular response - Transduction pathway ends when a response is activated
• A change of just one amino acid can have a significant impact
• Cell transduction pathway

  1. Binding of signalling molecule to receptor will trigger enzyme activity

  2. Eg. Kinase enzymes that add phosphate groups to other proteins

  3. The triggered enzyme cascade, will amplify the signal which requires energy to do
• Hypothesis


  Specific to a singular observation
• Theory


  Big picture explanation, supported by many experiments and observations over time
• Differences between prokaryotic and eukaryotic cells


  • Prokaryotes - no genuine nucleus, no membrane-bound organelles, no true cytoskeleton
  • Eukaryotic cells - Genuine nucleus, Membrane-bound organelles, True cytoskeleton
• Covalent bonds


  Breaking a covalent bond requires a chemical reaction
• Weak covalent interactions


  • Molecules retain their chemical identity
  • Interactions are reversible and usually short lived
  • More permanent interactions result from large numbers of weak interactions
• Types of weak interactions in biological molecules

  • Hydrogen bonds
  • Hydrophobic interactions
  • Van der Waals interactions
  • Ionic interactions
• Hydrogen bonds


  Attraction between slightly negative and positive regions between molecules
• Hydrophobic interactions


  Tendency of non-polar molecules to congregate in water
• Van der Waals interactions

  Weak attractive, non covalent forces that occur when atoms come close enough to their outer shells, to have a slight attraction
• Ionic interactions


  Attractive or repulsive interactions between ions in a solution or charged parts of a molecule
• Strands of nucleic acids are anti-parallel and run in opposite directions
• Phospholipids


  • Amphipathic, have both a hydrophobic and a hydrophilic region
  • Self-organising molecules
  • No covalent bonds between phospholipid molecules
  • Hydrophobic interactions keep the fatty acid tails away from the water
• Electron microscopy (SEM and TEM)

  • Limit of resolution: 2nm
  • Uses an electron beam, as opposed to visible light
  • Uses heavy metals as a stain, therefore specimen is not alive
  • Lenses are made from electromagnets
  • Cell ultrastructure is visible
  • TEM - thin sections, SEM - 3D surface scanning
• Brightfield light microscopy


  • Uses visible light
  • Simple and less expensive
  • Stains can be used to increase contrast and make images clearer
  • Resolution limit: 200nm/0.2um
• Confocal light microscopy


  • '3D' fluorescence microscopy
  • Optical sections
  • Objects closer to the lens will be sharp, but above and below the focus will be less clear
  • Confocal imaging makes a 3D model allowing for overall image clarity
• Fluorescence light microscopy


  • Specimen will absorb UV light via fluorescent dyes
  • UV dyes are used
  • Shown as visible light
• Starch


  Has a 1-4 linkage of alpha glucose monomers
• Cellulose


  Has a beta 1-4 linkage, and because of this beta glucose molecules have to alternate direction, allowing it to become a linear polymer
• Hydrophobic effect


  When water and oil are in contact, the molecules arrange themselves to minimise the contact between the two
• Induced fit model


  • The enzyme changes its conformation to aid the reaction and the substrate binding to it
  • After the reaction, the reactants are released and the enzyme catalyses a new reaction
  • The substrate is held in the active site by weak interactions
• Purines and pyrimidines


  • Pyrimidines - Cytosine, Uracil, Thymine
  • Purines - Adenine, Guanine
• Pyrimidines and purines


  • Molecules containing nitrogen, that also act as a base
  • Pyrimidines are smaller, purines are bigger double ring structures
  • Able to donate electrons to other molecules, forming new molecules in the process
• Amino acid


  Monomer that is covalently bonded with other amino acids to make a polypeptide
• Polypeptide


  One or more amino acids covalently bonded
• Protein


  One or more polypeptides folded into a 3D specific conformation, which becomes the functional form
• DNA has direction
• Energy storage in animals and plants

  • Starch - plant storage polysaccharide
  • Glycogen - animal storage polysaccharide
• Intracellular signal receptors


  • For example, a testosterone receptor
  • Receptor is activated by hormone binding
  • Moves to nucleus and activated genes
• Forming and testing hypothesis and the use of controls in experiments

  1. Hypothesis - possible explanation of an observation, must be testable

  2. Experiment must test one variable at time and have repeatable results

  3. Theory - a broad explanation which is supported by many observations and experiments

  4. A hypothesis can always be disproven, with another explanation, therefore use terms such as 'supported' or 'rejected'/'contradicted'

  5. A hypothesis is a TENTATIVE EXPLANATION and is falsifiable
• Phospholipid bilayer


  • Phospholipid molecules are not covalently bonded together, they are kept in place by hydrophobic and hydrophilic interactions
  • If a hole is made in the bilayer, the molecules will rearrange to fill the gap and restore the normal state of the membrane
• Cellulose structure


  • Glucose monomers are linked in unbranched chains by β-1,4 glycosidic linkages
  • Every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure
  • Provides shape and stability to the plant cell wall
• Starch structure


  • Compact shape allows for a large amount of energy to be stored and released without taking up too much space
  • Due to the position of the OH groups, the starch molecule is not very soluble, and so it will not interfere with the plant's water storage