Molecular Biology:

• Theory of vitalism states that organic molecules could only be synthesised by living systems. Disproven by Wohler who artificially synthesised urea on accident. 

  Initial intention:

  AgOCN  + NH4Cl  → NH4OCN + AgCl

  What he got:

  AgOCN  + NH4Cl  → (NH2)CO(NH2) + AgCl
• Carbon atom can form 4 covalent bonds → diversity of stable compounds can exist (able to form x1, x2 and x3 bonds with another atom). Carbon atoms are also just the right, small size to fit in comfortably as parts of very large molecules, hence its ability to form large and complex molecules via covalent bonding (strongest bond). 
• Carb: CHO, Lipids: CHO, Proteins:  CHON sometimes S, Nucleic acids: CHONP
• Metabolism:

  • Catabolism
  • Breakdown of complex molecules into simpler molecules (releasing E)
  • Anabolism
  • Synthesis of complex molecules from simple molecules (req E)
• Amino acids are linked tgt by condensation to form polypeptides. 20 diff amino acids in polypeptides are synthesised on ribosomes. Amino acids can be linked tgt in any sequence → huge range of possible polypeptides. Diverse groups of proteins are formed from diff no. & seq of amino acids. General structure of amino acid is alpha carbon covalently bonded to 4 groups: H atom, amino group, carboxyl group & variable R group. 
• Since amino acids differ in R group, physical & chemical properties determine of R group uniqueness of each amino acid & polypeptide. 20 amino acids are used in the biosynthesis of proteins in cells. 2O → peptide bond* covalently joining the 2 amino acids & each monomer is then known as a residue.
• Amino acids can be joined to form: dipeptide (2 amino acid residues); tripeptide (3 amino acid residues); oligopeptide (≈ 3-10 amino acid residues); polypeptide (≥10). Ribosome joins amino acids by anabolic reaction aka condensation which links carboxyl group (-COOH) to amino group (-NH2) of another amino acid, w removal of 1 H
• Ribosomes are the molecules that facilitate formation of peptide bonds, meaning this is where polypeptides are synthesised. Also, read amino acid from Amino-terminus (N-terminus [free amino group ]) to Carboxyl-terminus (C-terminus [free carboxyl group ]). Ribosomes are the site of polypeptide synthesis but they need a template (messenger RNA), which is translated by transfer RNA molecules, which also carry specific amino acids.
• Genes are codes for making polypeptides. mRNA (messenger RNA) is a message containing a specific seq of bases from nucleus to ribosome in cytoplasm. 

  A polypeptide folds into a specific 3D conformation/ shape. RECALL: amino acids differ in R groups → seq of amino acids (seq of R groups) → type & location of chemical interactions → overall 3D conformation of protein.
• Protein structures:

  1. Primary structure: sequence of amino acids in a single polypeptide chain, maintained by peptide bonds

  2. Secondary structure: regular coiling/pleating of a single polypeptide chain, maintained by hydrogen bonds formed between CO and NH groups of the polypeptide backbone (R groups not involved)

  3. Tertiary structure: formed from more extensive folding and bending of a single polypeptide, leading to a unique 3D conformation of a protein, maintained by 4 types of interactions between R groups of adjacent or far apart amino acids

  4. Quaternary structure: association of two or more polypeptides to form a functional protein, each polypeptide chain known as a subunit, maintained by interactions like hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bonds
• Hemoglobin is an example of a protein consisting of 4 polypeptides, functioning to transport oxygen in blood from the lungs to the rest of the body, found in red blood cells
• Myoglobin's structure stops at the tertiary level
• 2 types of secondary structure:

  • α-helix
  • H bonds btw C=O group of nth amino acid and N-H group of (n+4)th amino acid in a single polypeptide chain enables the single polypeptide chain to be coiled into a regular coil.
  • Uses: found in keratin of claws, nails, hair
  • β-pleated sheet
  • H bonds btw C=O group of amino acid from one segment and N-H group of amino acid from an adj segment in a single polypeptide chain enables the single polypeptide chain to be folded into a flat sheet.
  • Uses: found in spider silk
• DNA (gene) → seq of amino acids → types and location of R groups & hence, the types and location of bond/chemical interactions → unique 3D conformation. Denaturation is loss of the protein molecules’s conformation → loss of function. Denaturation occurs from disruption of interactions that maintain the 3D struc of the protein. High ℃ ↑ kinetic energy and intramolecular vibrations → breaks interactions like H bonds. pH Δ affect ionisation of R-groups of charged amino acids and hence, ionic bonds.
• Fibrous proteins have structural roles while globular proteins have metabolic roles. 
• Rubisco:

  • Enzyme that catalyses the reaction fixing CO2 from the atmosphere by RuBP
  • Provides a source of carbon from compounds required by living organisms
  • Found in high concentrations in leaves and algal cells
• Insulin:

  • Hormone that signals many cells to absorb glucose to decrease glucose concentration in the blood
  • Affected cells have receptors (proteins) on their surface that insulin can bind to
  • Secreted by β cells in the pancreas and transported by the blood
• Immunoglobulin (antibody):

  • Recognizes and binds to antigens on pathogens to prevent them from attaching to specific host cell receptors and gaining entry into host cells
  • Antibodies mediate the destruction of pathogens by acting as a marker to phagocytes, which engulf the pathogens
• Rhodopsin:

  • Pigment that absorbs light
  • Membrane protein of rod cells in the retina, the light-sensitive region at the back of the eye
  • Rhodopsin consists of an opsin polypeptide surrounding a retinal prosthetic group
  • Retinal molecule absorbs a photon of light, changes shape, changes to the opsin, and the rod cell sends a nerve impulse to the brain
  • Can detect very low light intensities
• Collagen:

  • Forms a mesh of fibers in skin and blood vessel walls to resist tearing
  • Provides strength to tendons, ligaments, skin, and blood vessel walls
  • Forms part of teeth and bones to help prevent cracks and fractures
• Spider Silk:

  • The strongest kind of silk, supporting the weight of the spider
  • Draglines connect the spider to the web and act as safety lines in case the spider falls
  • Webs for catching prey use sticky silk that is elastic to prevent the prey from rebounding off the web
• Genome: all genes of a cell, tissue/ organism. It determines what proteins an organism can produce & is unique for most individuals (identical twins & clones share a genome). Environmental factors influence what proteins an organism needs to produce & in what qty. Eg factors would be nutrition, temperature, activity levels & anything else that affects cell activities.
• Proteome = genome + envi factors. All the proteins produced by a cell, tissue/ organism. Being a func involving both genome & the environment the organism is exposed, the proteome is both variable (over time) & unique to every individual (including identical twins & clones). It reveals what is happening in an organism at a particular time.
• Why is water polar:

  Oxygen is more electronegative than hydrogen → slightly more (-) charge near the oxygen atom in the covalent bond btw hydrogen & oxygen. e- are not shared equally. The unbonded e- repel each other & the water molecule forms a bend shape. ∴, water molecule has a net dipole, meaning that it is polar overall.
• Although intermolecular interactions are weaker than covalent bonds, H bonds restrict the movement of water molecules. E must be supplied to break these hydrogen bonds. A single hydrogen bond is not very strong but large number is very strong. Each water molecule bonds with 4 others in a tetrahedral arrangement.
• Water is cohesive & has high surface tension because of this. Water is also adhesive & similar to cohesive property: a single H bond is not strong but many is very strong. Water molecules ≈ to stick to other molecules that are charged or polar due to its dipolarity & ability to form H bonds. Capillary action is caused by the combination of adhesive forces causing water to stick to the surface (e.g. glass, wall of xylem vessel) & the cohesive forces between water molecules. Capillary action is helpful in the movement of water during transpiration and also when you drink using a straw. 
• Water also has thermal properties. Water has a high specific heat capacity. Water has a high boiling point & high latent heat of vaporisation (amt of E needed to Δ from a liquid to gas). Water has a high heat of fusion (amt of energy needed to be lost to change liquid water to ice). Thermal properties are due to many H bonds that can be formed/ broken to Δ the state of water or ˚C of water. 
• Water as a coolant:

  When water evaporates, it removes a lot of E from the organism’s body which is felt as a cooling sensation because excess heat E is removed from the body (high latent heat of vaporisation). The heat lost from leaves during evaporation of water via stomata prevents the leaves from overheating. It takes a lot of energy for water to change temperature (high heat capacity) which also helps aquatic habitats remain at fairly constant ˚C in hot summers.
• Water is a good solvent


  Due to polarity, water can dissolve many organic & inorganic substances that are charged. The polar attraction of large quantities of water molecules can interrupt ionic bonds to → dissociation of the ions. Substances that dissolve in water are hydrophilic, including polar molecules (e.g. glucose) and ions (e.g. sodium ions). Substances that water adheres to (e.g. cellulose) are also hydrophilic. Substances that are insoluble in water are hydrophobic.
• Carbohydrates are carbon-containing compounds that are hydrated. Hence, their general formula can be written as Cm(H2O)n, where m & n are variable whole numbers. 
• Monosaccharide:

  • Carbonyl group C=O (gives ability to reduce Cu2+ to Cu+ [Benedict’s test])
  • Soluble in H2O due to its many hydroxyl groups (polar) which can form H bonds w H2O (transported easily in transport systems)
  • Ring struc exhibit α & β isomerism → ↑ diversity of monosaccharides which can become building blocks for diff molecules. Only diff btw α & β is swap pos of hydroxyl group on the far right

  Eg: Deoxyribose & ribose. They are pentose sugar, ribose in RNA. Deoxyribose in DNA.
• Polysaccharide:

  • Formed by condensation of numerous monosaccharides (glycosidic bonds are formed btw molecules)
  • α is for storage (starch [plants] & glycogen [animals])
  • β is for structure (cellulose [plants])

  Starch: 2 forms of starch are amylose (unbranched) & amylopectin (branched). White ovals in the micrograph are granules of starch within a chloroplast of a plant cell.
• Polysaccharide (glycogen [animal’s storage polysaccharide]):

  • Struc similar to amylopectin but it is even more branched
  • Humans & other vertebrates store glycogen mainly in liver & muscle cells. Hydrolysis of glycogen in these cells gives glucose. Extensive branching gives a lot more ends for enzymes to work on
• Polysaccharide (cellulose [structural]):

  • Made up of  β glucose monomers, linked via β (1-4) glycosidic bonds 
  • Alternate β glucose monomers are rotated 180° (inverted) (NOT bond angle) with respect to each other → linear, unbranched molecule with hydroxyl groups projecting out in both directions
  • Cellulose chains which are parallel to each other are held together by intermolecular H bonds which form between these hydroxyl groups. Many of these cross-linked linear cellulose chains come together to form microfibril. A meshwork of such criss-crossing microfibrils form cellulose.
• Struc of cellulose determines its function:

  Due to unbranched & linear structure of cellulose chains, OH groups are free to H bond extensively with OH of other cellulose chains lying parallel to it forming cable-like units called microfibrils. Microfibrils have high tensile strength. As a macromolecule, cellulose has fewer OH groups available for H bonding with water as only the surface of microfibril is exposed to water & that is where free OH are still available, and this is insufficient to make cellulose soluble in water. 
• Triglyceride has glycerol & 3 fatty acids. Phospholipid has phosphate, glycerol & 2 fatty acids. Steroid has 4 fused hydrocarbon rings.
• Most animal fats contain saturated fatty acids. These fatty acids are closely packed & form extensive intermolecular interactions → high melting point (solidify at rtp). Fats from fish & plants ≈ unsaturated (x2 bond in their fatty acid chains). This → ↑ kinks in their struc prevents the chains from packing closely tgt, thus they cannot form extensive intermolecular interactions & ∴ they have a ↓ melting point (liquid at rtp).
• Glycerol is an alcohol w 3 C, each being an OH group. Glycerol is a polar molecule, meaning that it can form H bonds w water (soluble). Glycerol is viscous & has higher density than water. Glycerol + 3 fatty acids = triglyceride +3H2O (condensation rxn). 
• Lipids are more suitable for long-term energy storage than carbohydrates
• Triglycerides serve as good energy storage because 1g of triglyceride stores twice as much energy as 1g of glycogen or starch