CHEM Optional B - Biochemistry

• What is Metabolism

  Sum of all the chemical reactions in an organism, can are broken up into two: Catabolism & Anabolism
• What is Catabolism

  Breaking up of large molecules to form smaller molecules (energy is released)
• What is Anabolism

  Building up of small molecules to form larger molecules (energy is required)
• What is Energy Coupling?

  The process of using energy released from one reaction to drive another reaction. For metabolism - it is that energy released from catabolic reactions is used in anabolic reactions.
• What form is energy released in a catabolic reaction? Examples of Catabolic reactions?

  ATP - ex includes Glucose breakdown in resp. = producing H2O and CO2 and oxidation of fatty acids
• What are precursors?

  the smaller molecules that get synthesized to form the larger molecules in an anabolic reaction (REQUIRES ATP)
• Photosynthesis

  Plants synthesize energy rich molecules such as carbohydrates (ANABOLISM) it is an endothermic reaction
• photosynthesis occurs in the presence of a light absorbing pigment :

  Chlorophyll
• Respiration (cellular)

  Occurs in cells of living organisms - energy rich molecules such as carbohydrates are broken down to produce CO2 and H2O. (RELEASING ENERGY IN THE PROCESS - CATABOLIC)
• equation for respiration

  C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O
• Condensation Reactions

  a chemical rxn where two molecules (monomers) react to form a larger molecule with the loss of a small molecule (usually water) forming a covalent bond.
• Bipolymers

  long chain molecules formed in condensation. rxns. each molecule (monomer) must have two reactive functional groups
• Hydrolysis Reactions:

  a chemical rxn in which a water molecule reacts with a large molecule breaking the covalent bond and forming two smaller molecules. OPPOSITE OF CONDENSATION RXN
• Proteins

  • they are biological molecules composed of amino acids:
• Amino Acids contains

  a carboxyl group (COOH), Amine group (NH2) and and R group, which differs for every amino acid.
• Structure of a 2-amino acid

  they bond in a condensation reaction, therefore yielding water by forming a peptide bond (amide link)
• the bonding of amino acids produces

  dipeptides, tripeptides, and polypeptides (also known as proteins)
• Zwitterions 


  formed by amino acids, they are molecules (electrically neutral) with a + or - charge formed when hydrogen from the carboxylic acid group bonds with nitrogen atom from the amine group
• Because of amino acids ability for form zwitterions they are

  Amphiprotic : meaning they can act a bronzed Lowry acid or base by donating or accepting a proton.
• Isoelectric point


  pH @ which an amino acid is electrically neutral
• pH that is less than the pH of the isoelectric point, the amino acid forms

  a cation (on amine group)
• pH that is greater than the pH of the isoelectric point, the amino acid forms

  an anion (on carboxyl group)
• Structure of proteins: Primary proteins 


  The primary structure refers to the sequence of amino acids in the polypeptide chain.
• Structure of proteins: secondary proteins 


  The folding of the polypeptide chain as a result of hydrogen bonding
• 2 types of secondary protein structure:

  1)alpha helix and 2) beta pleated sheets
• Structures of proteins: tertiary structure

  refers to the twisting and folding of the secondary structure to form a specific 3D shape (RESULTS OF INTERACTIONS FROM SIDE CHAINS)
• Structures of proteins: Quaternary structure 


  refers to the interactions between polypeptide chains Ex/ hemoglobin ( a polypeptide chain)
• Types of interactions found in different protein structures 


  Hydrogen interactions (LDF): between non polar side chains - Hydrogen Bonding: between polar side chains - Ionic bonding: between charged side chains- Disuflide bridges (covalent bonding): between the side chains of cysteine which contain a sulfhydryl group - Peptide bonds: between C=O and N-H
• Primary Protein structure: types of bonds and interactions

  peptide bonds between individual amino acids
• Secondary Protein structure: types of bonds and interactions 


  Hydrogen Bonding
• Tertiary Protein structure: types of bonds and interactions 



  LD forces, ionic bonds, hydrogen bonds, disulphide bridges, and peptide bonds
• Quaternary Protein structure: types of bonds and interactions 



  SAME AS TERTIARY - in between polypeptide bonds
• Fibrous proteins


  fibrous is long and narrow. their role is strucural (strength adn support) they are mostly insoluble in H2O. they are repetitive amino acid sequence. They are less sensitive to changes in pH and heat. examples: collagen and keratin
• Globular proteins 


  they are round/spherical. functional, meaning act as catalysis and good for transport. they are mostly soluble in H2O and they are more sensitive to changes in pH and heat. They are irregular sequences of amino acids. Examples include, hemoglobin, insulin, and catalase
• Proteins can be analyzed in what two methods?

  Chromatography and gel electrophoresis
• before proteins can be analyzed what must happen? 


  they must be broken down into their parts (component amino acids) this is done by hydrolysis reaction where the peptide bonds between amino acids are broken (by HCl)
• Paper chromatography in simple terms


  a technique used for the separation of compounds based on the differential solubility in the stationary phase and mobile phase (solvent)
• The position of each amino acids can be expressed as what?

  an Rf value, and can be compared by known values.
• Rf value formula (retention factor)


  = distance moved by amino acid/distance moment by solvent front
• Electrophroesis (gel) in simple terms

  a technique for the analysis ad separation of a mixture based on the movement of charged particles in an electric field ***charge of amino acid depends on the pH