GREASE THOSE WHEELS ( BIOLOGY )
#5 BIOLOGICAL MOLECULES
- carry out tests for reducing and non-reducing sugars (including semi-quantitative use of the Benedict’s test), the iodine in potassium iodide solution test for starch, the emulsion test for lipids and the biuret test for proteins;
- describe the ring forms of α-glucose and β-glucose;
- describe the formation and breakage of a glycosidic bond with reference both to polysaccharides and to disaccharides including sucrose;
- describe the molecular structure of polysaccharides including starch (amylose and amylopectin), glycogen and cellulose and relate these structures to their functions in living organisms;
- describe the molecular structure of a triglyceride and a phospholipid and relate these structures to their functions in living organisms;
- describe the structure of an amino acid and the formation and breakage of a peptide bond;
- explain the meaning of the terms primary structure, secondary structure, tertiary structure and quaternary structure of proteins and describe the types of bonding (hydrogen, ionic, disulfide and hydrophobic interactions) that hold the molecule in shape;
- describe the molecular structure of haemoglobin as an example of a globular protein, and of collagen as an example of a fibrous protein and relate these structures to their functions (the importance of iron in the haemoglobin molecule should be emphasised);
- describe and explain the roles of water in living organisms and as an environment for organisms;
- state one role of each of the following inorganic ions in living organisms: calcium, sodium, potassium, magnesium, chloride, nitrate, phosphate;
Yep! This chapter is about the molecules that your body utilizes everyday from the food you eat and the drinks you drink...good drinks that is...=D...This chapter has got the highest frequency in your MCQ paper...and you should know the tiniest of the details to score well...lets start!
First of all you need to know the basic food tests...
1. BENEDICT's TEST
1. BENEDICT's TEST
- Benedict's test is to indicate the presence of a reducing sugar, like glucose.
- Benedict's Reagent (aqueous sodium hydroxide, tartaric acid and aq. copper sulfate) has the sugar sample added to it.
- Upon gentle heating (for around 2 minutes) the following color changes occur if a reducing sugar is present...
- Blue > Green > Yellow > Orange > Brick Red \ Crimson.
- If no color change is observed then a variant of Benedict's test is performed.
- Hydrolysis with heated HCl is done first (breakage of glycosidic bonds, if present)
- Sodium Hydrogen Carbonate is then used to neutralize the mixture.
- Now th mixture is gently heated.
- If a colour change is observed then the sugar involved is most likely to be sucrose.
2. TEST FOR STARCH
- The sample to be tested is crushed in distilled water.
- Aqueous Potassium Iodide is then added over it.
- If starch is present then a blue-black colour originates; otherwise a reddish-brown colour is there.
3. ETHANOL EMULSION TEST
- This test is used to test the presence of lipids.
- Ethanol is added to the sample, the mixture is shaken.
- If upon the addition of water to the mixture, a foamy, white emulsion is seen at the surface then lipid is present.
4. BIURET's TEST
- It is used to detect the presence of peptide bonds or in other words, proteins.
- Biuret's Reagent (1% KOH \ NaOH, potassium sodium tartrate and a few drops of copper sulfate) is added to an aquous sample.
- If peptide bonds are present then a violet colour can be seen instead of the original blue colour.
5. THE USE OF COLORIMETRY
- The above tests are all qualitative, i.e, the confirm the presence of a chemical in the mixture. But how do we know about the quantity that s when colorimetry steps in; to carry out a quantitative test.
- Colorimeter measures the absorption of a specific wavelength of light by a solution. In this way, along with the presence of different coloured solutions of the same test, we get to know the average quantity of chemical present in the mixture.
Now let us look at the Carbohydrates first...
The king of carbohydrates is without doubt glucose. We would look into some carbohydrates in detail but lets have a look at the two isomers of glucose alpha and beta.
As you see above; there is only one fundamental difference between the two enatiomers of glucose, that is, the orientation of the OH-group on the 1st Carbon. In beta-glucose it is over the hydrogen while in alpha-glucose it is below the hydrogen at 1-Carbon.
Now lets talk about carbohydrates in general...
- The general formula for carbohydrates is n(CH2O).
- There are three main categories of carbohydrates.
- Monosaccharides
- They include Glucose, Fructose and Galactose.
- They all have the same molecular formula, i.e, C6H12O6 but differ in arrangement of molecules, i.e, they are isomers of each other.
- They are sweet, highly soluble and act as respiratory substrates and are easily transported due to small size.
- Fructose is a monomer of sucrose and also is a component of nectar and also aids the synthesis of insulin.
- Galactose is a monomer of lactose and also constitutes nectar.
- Disaccharides
- They form when two monosaccharides join together via a glycosidic bond in a condensation reaction. (see above). Remember that this process can be reversed by the addition of water, i.e, by dilute Sulfuric Acid.
- They include, sucrose, maltose and lactose.
- Combination of two alpha-glucose molecules gives maltose (reducing sugar)
- Combination of an alpha-glucose and a fructose molecule yields sucrose; which acts as a storage (onion) and transport material for plants. (non-reducing sugar).
- When an alpha-glucose and a galactose molecule combine then lactose (non-reducing sugar) or milk sugar results which makes up about 5% of mammalian milk.
- Polysaccharides
- They are formed when many monomer units are linked together, in contrast of the two linked to form a disaccharide.
- Most prominent polysaccharides and their structures and functions are discussed below...
- Starch is a polysaccharide forming from the linking together of alpha-glucose monomers. It contains both 1-4 glycosidic linkages (amylose) (see above 1st) and 1-6 glycosidic linkages (amylopectin) that branches it. Due to this branching it is very compact, thus suitable for storage and aids enzyme activity. Moreover its insolubility in water helps the cell to retain it for future use. However starch is mostly used by plants for storage.
- Glycogen also forms from the linkages of alpha-glucose monomers; but is relatively more branched and more compact. It is used for storage by animals.
- Cellulose has a beta-glucose as its single units. It contains more than 10000 beta-glucose monomers linked together by glycosidic bonds and cross-linkages (hydrogen bonds b/w H--O) which allows it to provide structural support to cells in the from of cell walls. (see below)
Now lets peek at the lipid family...
- Class of organic molecules that is insoluble in water and have a high percentage of Hydrogen and Carbon and relatively low proportion of oxygen thus they release more energy than both carbohydrates and proteins.
- Lipids are formed when three fatty acid molecules combine with a tri-glycerol molecule. In a dehydration \ condensation reaction. To reverse this process hydrolysis is required.
- There are two types of fatty acids; unsaturated (having C-C double bonds) and saturated (having no C-C double bonds)
- The process of the formation of a lipid molecule is outlined in the diagram above.
- Some uses of fats are..
- As a source of energy use.
- Storage in adipose tissues to provide insulation and protection from mechanical injury to vital organs.
- Helping aqueous organisms to stay buoyant.
- They can also be used as an energy storage option because of their insolubility and compactness.
- Component of cell membrane in the form of phospolipid molecules.
- A variant of the lipid molecule is the essential...phospholipid. In which one fatty acid in a lipid molecule is replaced by a phosphate group. The process that leads to it is also out lined below.
Now lets get down to the most important organic molecule of our body...without doubt the most important class of organic molecules (their name suggests that, Greek for first rank!!) that is synonymous with the world survival. Let me introduce to the proud and boastful..Proteins *clap**clap*...
- The consist of simpler units, i.e monomers, Amino Acids, joined together by peptide linkages.
- The two terminal ends of a polypeptide have a carboxyl and amine group respectively.
- The sequence of amino acids in a protein is encoded by the base sequence (codons) in our genome.
- They are basically organic compounds that have Nitrogen in them.
- The primary or initial formation of a straight chain polypeptide is outline below...
- Protein chain(s) can also arrange themselves in a secondary 3-D structures. There are two main types of it.
- The Alpha Helix (in which there are hydrogen bonds between Carbonyl and N-H groups on adjacent turns, a typical alpha helix is about 11 amino acids long, they are soluble, an example can be a portion of the protein that makes up our hairs and nails; Keratin)
- A Beta-Pleated Sheet (in which there are also hydrogen bonds between the two groups specified above; the only different been that they exist between neighboring anti-parallel chains, they are insoluble, an example can be the silk thread a spider weaves.)
- Secondary structure elemetns can be folded into a more specific tertiary structure.
- The protein is held in a series of tucks and bends by the following bonds...
- Hydrogen Bonds (Weakest)
- Ionic Bonds (Weaker)
- Disulfide Linkages (Strong)
- As well as Hydro-interactins with the hydrophilic R groups (with some sugar molecules attached and stuff) are displayed on the outside while hydrophobic R groups are buried within.
- Tertiary structure plays a very important part in protein function because if the tertiary structure breaks down, as in denaturing, the protein cannot function. Similarly mutations in DNA (in a gene encoding for that protein) can causes that protein to have an altered tertiary structure thus making it useless such proteins usually...
- Are degraded in the cytoplasm.
- Protein kinesis cannot occur, i.e, the proteins cannot be delivered to the organelle/structure utilizing them (as in lysosomes).
- Some times the proteins, due to an improper orientation as in displaying hydrophobic R groups at the surface, can go insoluble and form deposits in the cells.
- Now let us move to the final and highest level of protein organization, the quaternary structure. In which more than one polypeptide chains (in precise ratios) are linked together (not bonded covalently, mind you!) with prosthetic (non-protein) group(s) in between. They are in a precise 3-D shape with two main classes.
- Globular Proteins (are globe like in structure, are soluble in water due to dipole-dipole interactions, are relatively unstable, i.e, easily denatured, the play chemical functions in the body like, catalyzing chemical reactions, in antibodies etc)
- An important member of the Globular class is haemoglobin. Which consists of four polypeptide chains containing two alpha-chains and two beta chains that have a heme (iron-containing) group each. The iron is in Fe2+ oxidation state that renders it capable in binding with an oxygen molecule, an oxidation to Fe3+ state renders the protein useless.
- Fibrous Proteins (are long filament-like protein structures and are insoluble in water due to the surface presentation of hydrophobic R groups. They are chemically inert and usually play structural roles as in Keratin (nails and hair), tendons and other connective tissues. Compared to globular proteins; they are less sensitive to environmental changes and tend to denature less readily)
- A very important component of this class of quaternary structure is, Collagen, the most abundant protein in our body; making up about 20-30% of our total protein count. It is made up of three separate alpha-helices twisted around each other The structure is held together by hydrogen bond between corresponding chains (the same N-H::::O=C ones) although some covalent bonds (aldol-histadine cross links and aldol cross-links) also exist. Glycine residues also give collagen its tensile strength as every third amino acid is small in the helices.
Now let us move to the different ions and their functions...
- Ca[+2]
- Major component of bones and teeth.
- Needed for muscle contractions and blood clotting
- Structural support in the form of calcium pectate in cell walls.
- Na[+]
- Utilized in nerve impulses.
- Maintaining an anion-cation balance across the cell membrane.
- Constituent of sap vacuole to aid turgidity.
- K[+]
- Movement of nerve impulses.
- Maintaining the anion-cation balance across the cell membrane.
- Necessary for photosynthesis, cell respiration and protein synthesis.
- Maintains plant turgidity.
- Mg[+2]
- Component of chlorophyll.
- Activator for some enzymes such as ATPase.
- Cl[-]
- Maintenance of anion-cation balance across a plasma membrane.
- Component of gastric juice (HCl)
- Utilized in Chloride shift, a process that aids in CO2 exchange by RBCs. it is an effort to maintain blood pH as HCO3- ions move out of the RBC.
- NO3[-]
- Amino acid synthesis (Nitrogen is required).
- Component of chlorophyll.
- PO4[-3]
- ATP synthesis.
- Oxidative Phosphorylation is mitochondria.
- Component of phospholip bilayer in cell membrane.
Now let us get to our final and vitally, the most important chemical compound to exist on our planet, life depends on it entirely...'no water no life'...
Lets talk about the functions of water...
Cohesion in the water molecules due to hydrogen bonds between adjacent water molecules results in a surface tension which allow aquatic organisms like pond skaters to walk over it. The polarity of a water molecule also makes it a universal solvent as it interacts with other charged bodies thus resulting in their dissolution. Additionally,. it plays an integral role in photosynthesis in plants and helps to maintain their erect posture. It is widely used by warm-blooded organisms as a tool for temperature control due to its high latent heat of vaporization thus a small amount of sweat can take away a large amount of heat upon vaporization. Moreover it has a high specific heat capacity which allows chemical processes in living organisms to take place within a short temperature range and protect us from temperature changes. Water also has a high heat of fusion and thus prevents our cells from freezing. Moreover, water is the transport medium for nearly every type of molecules in our body.
Water is colorless which allows life to exist in aquatic habitats as it allows sunlight to pass through and thus helps plants photosynthesize. The cohesion of water molecules and its adhesion to surrounding molecules allows plants to pull up water via the xylem vessels. Water also serves as a lubricant in our body; it is present in the synovial fluid in our joints and mucus in our URT.
