Topic 2: Molecular Biology
Topic 2.1
Overview
Understandings
➔ Molecular biology explains living processes in terms of the chemical substances involved.
➔ Carbon atoms can form four bonds allowing a diversity of compounds to exist.
➔ Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
➔ Metabolism is the web of all the enzyme catalysed reactions in a cell or organism.
➔ Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.
➔ Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.
Applications
Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
Skills
➔ Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.
➔ Identification of biochemicals such as carbohydrate, lipid or protein from molecular diagrams.
Nature of Science
➔ Falsification of theories: the artificial synthesis of urea helped to falsify vitalism.
Notes
Understanding 1:
Molecular biology can be thought of as all of the chemical reactions within a living cell.
Molecules such as nucleic acids, which make up DNA and RNA, as well as proteins are important complex molecules
Many simple molecules such as water are vital
Application 1:
Urea is a simple, nitrogen-containing compound, component of urine. Produced when there is an excess of amino acids, as a way to excrete the nitrogen.
Is produced in liver, with enzymes catalysing the reaction
Then, is filtered out of the blood by the kidneys, and exits in urine
Can be synthesized artificially:
NH3 + CO2 → ammonium carbamate → urea + water
Is used as a nitrogen fertilizer on crops
Nature of Science 1:
Was widely believed that organic compounds in plants+animals could only be made with a "vital principle" - which was different than chemical or physical forces. Meant life/soul
Artificially synthesized in 1828 with silver isocyanate and ammonium chloride
Was the first organic compound to be artificially synthesized
Was evidence against the theory of vitalism
Understanding 2:
Many different types of organic compounds can form because the element carbon forms four covalent bonds
Understanding 3 and Skill 2:
Carbohydrates, lipids, proteins, and nucleic acids are the four organic compound types found within living things
Carbohydrates: C, H, O. Ratio of 2H per O
Lipids: insoluble in water. Broad group, such as steroids, waxes, fatty acids, triglycerides (a fat or oil which has three fatty acids and a glycerol). Contain less oxygen than carbohydrates, such as oleic acid (an unsaturated fatty acid) C18H34O2, or the steroid testosterone C19H28O2
Proteins: chain(s) of amino acids. Often contains C, H, O, N, and some also contain S
Nucleic acids: chains of nucleotides, containing C, H, O, N, P. Two types are RNA and DNA
Skill 1:
Drawing Ribose (C5H10O5)
Oxygen on top of ring
4 Carbons in ring and one forms side chain
Hydroxyl group points up on C1, down on C2+3
Drawing Glucose (C6H12O6)
5 carbons in the ring and 1 forming side chain
In Alpha glucose, the hydroxyls are down on C 1,2,4 and up on C3
In Beta glucose, the hydroxyl is up on C1 and C3 and down on C2+4
In both Alpha and Beta, there is a hydroxyl on C 6 (so five in total on each)
Drawing a saturated fatty acid
Carbons form an unbranched chain
Carbons bonded to each other through single bonds
Often between 14-20 carbons
There is a carboxyl group on one end
The other end is just hydrogen
All other carbons are bonded to two hydrogens
Drawing amino acids
C in centre
An amine group
Carboxyl group
Hydrogen atom(s)
R group
Understanding 4:
Metabolism is the sum of all reactions that occur in an organism
Consists of pathways where one type of molecule is transformed into another. There are chains and cycles
Understanding 5:
Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.
Examples
Protein synthesis using ribosomes
DNA synthesis during replication
Photosynthesis, production of glucose from CO2 and water
Synthesis of complex carbs such as starch, cellulose, glycogen
Understanding 6:
Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers
Examples:
Digestion of food
Cell respiration, oxidation of glucose and lipids into CO2 and water
Digestion of complex carbon compounds in dead organic matter by decomposers
Topic 2.2 Water
Understandings
➔ Water molecules are polar and hydrogen bonds form between them.
➔ Hydrogen bonding and dipolarity explain the adhesive, cohesive, thermal and solvent properties of water.
➔ Substances can be hydrophilic or hydrophobic
Nature of Science
➔ Use theories to explain natural phenomena: the theory that hydrogen bonds form between water molecules explains water’s properties.
Applications
➔ Comparison of the thermal properties of water with those of methane.
➔ Use of water as a coolant in sweat.
➔ Methods of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in relation to their solubility in water.
Understanding 1:
In water, oxygen is slightly negative and hydrogen is slightly positive, so hydrogen bonds form between water molecules
Hydrogen bonds are drawn in dotted lines between the negative O of one water molecule and positive H of another
Nature of Science 1:
Hydrogen bonds are still a theory, but they explain the behaviours of water, such as its solvent, thermal, cohesive, and adhesive properties
Understanding 2:
Cohesive properties
Cohesion refers to the binding together of two molecules of the same type
This is useful for water transport in plants: water is sucked through xylem vessels at low pressure
Adhesive properties
Hydrogen bonds form between water molecules and other polar molecules, causing them to stick
Useful in leaves, where water adheres to cellulose in cell walls. If water evaporates from the cell walls, adhesive forces cause water to be drawn to the nearest xylem vessel
Thermal properties:
High specific heat capacity
Hydrogen bonds restrict its motion and also cause more energy to be required to increase its motion (its temperature)
High latent heat of vaporization
Takes a lot of heat to vaporize and therefore is a good coolant
Hydrogen bonds need to be broken in order to vaporize it
High boiling point
its liquid state is in temps that most habitats on Earth have
Solvent properties
Polar nature means in forms around charged or polar molecules (preventing them from clumping together), keeping them in solution
Water forms hydrogen bonds with polar molecules
Cytoplasm is where many substances are dissolved and its where many chemical reactions of metabolism occurs
Understanding 3:
Polar molecules or compounds are hydrophilic
All substances that dissolve in water
All substances that water adheres to
All particles with positive or negative charges such as ions
Nonpolar molecules are hydrophobic
All lipids, including fats and oils
Application 1:
Methane is nonpolar, no hydrogen bonds
Water is polar
Application 2:
Why sweat cools your body:
The cooling is due to the body heat that is absorbed by the water (sweat).
The heat that is taken from your body is used to evaporate the water from your skin.
good example of the importance of high latent heat of vaporization.
Application 3:
Sodium chloride is ionic, travels dissolved in blood plasma as ions Na+ and Cl-
Amino acids have both + and - charges, solubility depends on R group, but all amino acids are soluble enough to be carried dissolved in plasma
Glucose is polar and freely soluble in water/blood plasma
Oxygen is nonpolar but small enough for some to dissolve. Solubility decreases as temperature increases. Not enough can be dissolved to support aerobic cell respiration, so it binds to haemoglobin in red blood cells
Source: Biology, 2014 Edition, Oxford, Andrew Allott and David Mindorff
Topic 2.6