Biological molecules

• Emulsion test (lipids)

  1. Use a measuring cylinder and measure out 5-10ml of ethanol into a test tube

  2. Add 2 drops of castor oil, shake vigorously, until oil has dissolved

  3. Pour this solution into a test tube half-filled with water

  4. A positive result for lipids is if the combined solutions form a milky white layer – this is an emulsion

  5. The alcohol mixes with the water, leaving the lipid to form an emulsion of microscopic droplets suspended on the surface
• Iodine test (Starch)

  1. Add 2cm3 of solution into a test tube

  2. Add 2 drops of iodine potassium iodide reagent (orange) into the sample solution

  3. Leave it for 5 minutes

  4. If starch is present, the solution will turn blue-black
• Biuret test (Proteins)

  1. Add 5cm3 of solution into a test tube

  2. Add equal amounts of biuret solution (5cm3) into the same test tube as the unknown solution. (1:1 ratio)

  3. Shake well and let it stand at room temperature for 5 minutes

  4. Observe the tubes for colour change in suspension

  5. Positive result: Blue -> purple (If the concentration of peptide bonds is low – such as when short-chain peptides are present - the color change is from blue to pink)
• Semi-quantitative Benedict's test on a reducing sugar solution

  1. Pour (volume)cm3 of (concentration) glucose (reducing sugar) solution into a boiling tube

  2. Add same volume of benedicts solution into a boiling tube using a measuring tube

  3. Heat the test tube carefully by placing it in a rack in a water bath heated to at least 80 degrees Celsius (80>)

  4. Leave it in for 3 minutes and record any observations: describe the colour change

  5. If reducing sugar is present, the solution will gradually turn through green, yellow and orange to red brown (as insoluble copper (II) oxide precipitate starts to form)

  6. Repeat steps for other glucose solutions

  7. Leave all these colour changes in a boiling tube rack to compare them to the unknown samples

  8. Repeat steps 1-4 for unknown sample, compare the endpoint colour to the standard solutions and record the estimated concentration of reducing sugar sample
• Test to identify the presence of non-reducing sugars, using acid hydrolysis and Benedict's solution

  1. Add dilute HCl to the sample and heat in a water bath 80°C> (Acid will hydrolyze any glycosidic bonds present, causing the non-reducing sugar to become a reducing sugar / non-reducing disaccharide -> 2 monosaccharides)

  2. Cool solution

  3. Neutralize the solution with NaOH

  4. Check if it's been neutralized by testing a sample with universal indictor

  5. Add benedicts solution to test tube and heat 80°C>

  6. Green/yellow/orange/brick-red precipitate = +ve result (if a colour change occurs, a non-reducing sugar is present)

  
• Hydrolyzation

  A chemical reaction in which a molecule of water breaks one or more chemical bonds
• Two monosaccharide units can be joined together by a glycosidic bond

  
• Monomers are the basic building blocks of larger organic molecules. Monosaccharides are the monomers that make up carbohydrates
• Role of covalent bonds in joining smaller molecules together to form polymers

  1. During condensation, covalent bonds form between monomers, which allow monomers to join into polymers

  2. Water is released or lost during condensation

  3. During covalent bonding there is a sharing of valence electrons to complete an octet (a group of eight electrons) around atoms

  
• Condensation of all monomers result in the formation of polymers: monosaccharides covalently bonded with glycosidic bonds to form polymer polysaccharides, amino acids covalently bonded with peptide binds to form polymer peptides, nucleotides covalently bond with phosphodiester bonds to form polymer polynucleotides

  
• Glucose, fructose and maltose are reducing sugars (+ galactose). All monosaccharides and polysaccharides, excluding sucrose, are reducing sugars. Sucrose is a non-reducing sugar
• Formation of a glycosidic bond by condensation

  1. Glycosidic bond is a condensation reaction between 2 sugar units (monosaccharides), where the H- in a hydroxyl group from one sugar reacts with the other hydroxyl group on another

  2. This allows an oxygen "bridge" between the two molecules holding them together, this bridge is called glycosidic bond

  3. Glycosidic bonds are covalently bonded

  4. Sucrose is made of a- glucose and b- fructose monosaccharides, forming a disaccharide

  5. Many monosaccharides joined by condensation reaction/glycosidic bonds form polysaccharides

  6. Water is released by the reaction

  
• Breakage of a glycosidic bond in polysaccharides and disaccharides by hydrolysis, with reference to the non-reducing sugar test


  1. To break glycosidic bonds you hydrolyze, add water to, the polysaccharide or disaccharide

  2. The water breaks the poly/di saccharide into its constituent monosaccharides

  3. One of the monosaccharides gain a hydroxyl group and the other gains a hydrogen

  4. In a non-reducing sugar test, dilute HCl is added to the sample which hydrolyzes any glycosidic bonds present

  5. The (sucrose) disaccharide is broken into (a-glucose and fructose) monosaccharides which are reducing sugars

  
• Polysaccharides are a good source of energy because they are very dense and are made up of many monosaccharides linked together + easy to hydrolyze
• Energy stored in polysaccharides is mobilized by hydrolysis by enzymes into glucose whenever it's needed

  
• Glucose by itself is not used as energy storage because it is very chemically reactive and would interfere with normal cellular metabolism, and it would also dissolve and make the contents of the cell too concentrated, lowering water potential, attracting unnecessary inflow of osmosis
• Triglycerides are non-polar hydrophobic molecules

  
• Saturated fatty acids


  • Only single covalent bonds between carbon atoms
  • Linear chain
  • Typical in animal fats

  
• Unsaturated fatty acids


  • The presence of 1 or more double covalent bonds between c-c bonds
  • Introduces kinks (not branch) into fatty acid chain
• Triglyceride


  A fat (lipid)

  
• Ester bond formation


  1. Reaction of an acid + and alcohol produces an ester with an ester bond by condensation reaction

  2. It is called triglyceride because it has 3 fatty acids forming ester bonds with glycerol

  3. The ester bonds are made when the –COOH (carboxyl) group of each amino acid reacts with the –OH (hydroxyl) group of the glycerol (alcohol) to form the ester bond –COO-

  4. Water is created in the reaction

  
• The tails vary in length depending on the different fatty acid chains
• There can be two types of fatty acid chains: saturated & unsaturated
• Hydrocarbon chain of fatty acids


  Non-polar, hydrophobic (meaning they are insoluble in water as they are water hating)
• Triglyceride


  A neutral fat

  
• Triglycerides are insoluble in water, soluble in ethanol


  This reflects the hydrophobic/non-polar nature of fatty acid chains

  
• Functions of triglycerides in living organisms

  • Excellent energy reserves, even more than carbohydrates as they are richer in C-H bonds (long hydrocarbon chains). Yields more ATP in oxidation via respiration than carbohydrates
  • Metabolic sources of water in dry habitats. Some animals may never drink but survive on their metabolic water from their fat intake
  • Large and insoluble in water (hydrophobic). This means that triglycerides can be stored in cells without affecting their osmosis. This, too, makes them excellent energy storage molecules
  • Insulation - Triglycerides stored beneath the body surface insulate mammals from the environment, keeping their bodies warm
  • Providing buoyancy - Aquatic mammals (e.g., seals) have a thick layer of fat underneath their skin to prevent them from sinking whenever they are underwater
• Phospholipid


  • One of the fatty acid molecules is replaced with a phosphate group
  • The phosphate group is hydrophilic and makes the head of the phospholipid molecule hydrophilic too
  • The 2 remaining hydrocarbon tails are still hydrophobic
• Amino acid


  • The generic structure of an amino acid is an amphoteric molecule
  • Amphoteric means that the molecule can act both as an acid and base
  • It contains a carboxyl group which is the acidic part that donates protons
  • It also contains an amino group that accepts protons and acts as a base
  • The R group varies for the 20 naturally occurring amino acids and are told apart depending on the R groups

  
• Peptide bond formation and breakage

  1. Peptide bond is formed when two amino acids join in a condensation reaction

  2. A peptide bond is covalent

  3. The hydroxide in the carboxyl group reacts with one of the hydrogens in the amino group, forming water

  4. A peptide bond is formed (-CONH) and the new molecule is called dipeptide. A molecule made of many dipeptides is called polypeptide

  5. For the breakage of the peptide bond, water is added through hydrolysis and breaks the peptide bond

  6. One oxygen and hydrogen bind with the carbon and the second hydrogen binds with nitrogen

  7. The breakage of amino acids by hydrolysis naturally happens in the stomach & in the small intestine

  
• Primary structure of proteins


  The sequence of amino acids in the polypeptide chain. They are held together by peptide bonds

  
• Secondary structure of proteins


  • Secondary structure is generated by formation of hydrogen bonds between atoms in the polypeptide backbone, which folds the chains into either alpha helices or beta-sheets
  • Hydrogen bonds have a regular pattern
  • The hydrogen bond forms between the CO- group of one amino acid and NH- group of another
  • In secondary structure, there are both a-helix AND b-pleated sheets
  • The a-helix is a coil formed by hydrogen bonding between every fourth amino acid
  • b-pleated sheet: pleated structure formed by 2 or more polypeptide chains lying parallel connceted by H+ bonds

  
• Tertiary structure of proteins


  • Overall 3-D shape of a polypeptide that results from the bonds formed between side chains/R groups
  • Further folding & coiling of secondary structure to form a unique 3D shape
  • Interactions between R groups
  • At least 2 correctly named bonds. E.g., hydrogen, disulfide, etc.

  
• Quaternary structure of proteins

  A protein made up of more than 1 polypeptide chain

  
• Types of interactions that hold protein molecules in shape

  • Covalent bonding (including disulfide)
  • Ionic bonding
  • Hydrogen bonding
  • Hydrophobic interactions

  
• Globular proteins are generally soluble and have physiological roles
• Fibrous proteins are generally insoluble and have structural roles
• Haemoglobin


  An example of a globular protein, including the formation of its quaternary structure from two alpha (α) chains (α–globin), two beta (β) chains (β–globin) and a haem group
• Structure of haemoglobin


  • Irregular amino acid sequence (primary structure)
  • 2 a-helix + 2 b-pleated sheets (secondary)
  • Globular (tertiary structure)
  • 4 polypeptide chains (quaternary)

  
• Functions of haemoglobin


  • Due to the presence of polar hydrophilic R groups facing the outside, the haemoglobin molecule is soluble in water because water molecules cluster the hydrophilic R groups and can form hydrogen + ion-dipole interactions
  • It is a spherical globular protein, made up of 4 polypeptide chains so it has a quaternary structure. Each chain is a protein known as globin. 2 types that make a haemoglobin: a-globin & b-globin. 2 haemoglobin chains are a-globin and the other 2 are b-globin. (Haemoglobin has a-helix and b-pleated sheets)
  • Each 4 polypeptide chain of haemoglobin contains a haem group (permanent part of protein molecule but not made of amino acid is called a prosthetic group)
  • Each haem group contains an Fe atom which can bind to one oxygen MOLECULE each. So, in total, one haemoglobin molecule can bind to 4 oxygen MOLECULES, and 8 oxygen ATOMS
  • The haem groups allow oxygen to bind to the haemoglobin so it can be carried in the blood to different tissues and organs in the body