IB TOPIC 2 | MOLECULAR BIOLOGY
2016 | SYJ0014
Topic 2.1: Molecular biology – Molecules to metabolism
Living organisms control their composition by a complex web of chemical reactions.
• Understanding: Molecular biology explains living processes in terms of the chemical substances involved.
Molecules and their interaction with each other (for example, genes and proteins) is central in understanding living process
The discovery of the structure of DNA started a revolution in biology that has transformed our understanding of living organisms
• Understanding: Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
Element composition: the 4 most common elements are hydrogen, carbon, oxygen and nitrogen
Covalent bond: bond formed when two adjacent atoms share a pair of electrons with one contributed by each atom
Character: covalent bonds are the strongest type of bond between atoms
Covalent bond in carbons: carbon atoms can form diverse compounds as it can form up to four covalent bonds
• Understanding: Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Four main classes of carbon compound in living organisms:
Carbohydrates: main energy source composed of carbon, hydrogen and oxygen (e.g. glucose, starch, glycogen)
Lipids: often used for storage class of molecules that are insoluble in water (e.g. steroids, fatty acids, triglyceride)
Proteins: molecule with diverse structure and function composed of one or more chains of amino acids (e.g. enzymes)
Nucleic acids: molecules composed of chains of nucleotides (e.g. RNA and DNA)
• Understanding: Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.
Metabolism: web of all the enzyme catalysed reactions in any cells; sum of all reactions in an organism
Metabolism consists of pathways by which one type of molecule is transformed into another
• Understanding: Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from
monomers by condensation reactions.
• Understanding: Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into
monomers.
Anabolism: synthesis of complex molecules from simpler molecules (this includes condensation)
Catabolism: breakdown of complex molecules into simpler molecules. (this includes hydrolysis)
Anabolism Catabolism
Reaction Condensation Hydrolysis
Reactant Smaller molecules Larger molecules
Product Larger molecules Smaller molecule
Example Protein synthesis with ribosome Digestion of food
DNA synthesis during replication Cell respiration
Photosynthesis Digestion of complex carbon compounds
Synthesis of complex carbohydrates
• Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
Urea: component of urine produced by the liver in an excess of amino acid
Purpose: liver converts amino acid into urea when excess protein is consumed
CO (NH2)2
Process of urea synthesis: NH3 + CO2 → (NH4)2CO3 → urea + H2O
Urea in vitalism: Friedrich Wohler artificially synthesized urea to disprove the vital principle
Urea in modern use: urea is produced artificially as nitrogen fertilizers on crops
• Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.
alpha–D-glucose D-ribose Saturated fatty acid Generalized amino acid
Diagram
In Beta, –OH and –H groups in 1’ are opposite
Formula C6H12O6 C5H10O5 Dependant on chain length Dependant on R-groups
Structure Six membered ring Five membered ring Unbranched chain Acidic group (COOH)
One carbon side chain (5’) One carbon side chain (4’) 14-20 carbon atom chain Basic group (NH2)
Hydroxyl group (1’,2’,3’,4’, Hydroxyl group (1’,2’,3’, 5’) Carboxyl group at the end 20 different R-group types
6’)
LAST EDITED 2017-03-15 | 1
, IB TOPIC 2 | MOLECULAR BIOLOGY
2016 | SYJ0014
• Skill: Identification of biochemical such as sugars, lipids or amino acids from molecular diagrams.
Sugars Lipids Amino acids
Presence of nitrogen Usually absent Usually absent Present
H:O ratio H:O has a 2:1 ratio Less oxygen than carbohydrates Irregular
Shape Often ring shaped Often straight chained Irregular
Other elements Usually only made of C, H, O May contain phosphorus May contain sulphur
• Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.
• Guidance: Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.
• Guidance: Sugars include monosaccharides and disaccharides.
• Guidance: Only one saturated fat is expected and its specific name is not necessary.
• Guidance: The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized.
• Guidance: Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of
steroids are not expected.
• Guidance: Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.
LAST EDITED 2017-03-15 | 2
, IB TOPIC 2 | MOLECULAR BIOLOGY
2016 | SYJ0014
Topic 2.2: Molecular biology – water
Water is the medium of life.
• Understanding: Water molecules are polar and hydrogen bonds form between them.
Structure of water molecules:
Composition: formed by a covalent bond between an oxygen two hydrogens
Polar character: bond between the H and O is a polar covalent bond due to electronegativity difference
Intermolecular force: electronegative difference between H and O causes hydrogen bonding in water
Hydrogen bonding: type of bonding weaker than other bonds, but stronger than other intermolecular forces
Impact on character of water: bonding makes water denser than ice, causing the latter to float
• Understanding: Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.
Cohesion: attraction between two molecules of the same type (e.g. two water molecule)
Adhesion: attraction between two different polar molecules (i.e. water and other polar molecules)
Cohesive properties of water:
Cause: water has strong cohesion force due to hydrogen bonding
Application: assist water transport in plants in xylems through transpiration, high surface tension for water striders
Adhesive properties of water:
Cause: water has adhesion forces (weaker than cohesion) due to its polarity
Application: water adhesion inside the plant’s tube
Thermal properties of water:
Cause: water has unique thermal properties due to strong hydrogen bonding
High specific heat capacity: relatively high amount of heat required to raise the temperature
Description: large amounts of energy transfer needed to raise/lower temperature due to hydrogen bonding
Application: thermally stable habitat in water bodies in comparison to air or land
High latent heat of vaporization: relatively high amount of heat required to change phase from liquid to gas at its boiling point
Description: large amounts of energy transfer needed to break bonds between molecules due to hydrogen bonding
Application: coolant for living organisms
High boiling point: relatively high temperature at which its vapour pressure equal to the pressure of gas above it
Description: large amounts of energy transfer needed to break bonds between molecules due to hydrogen bonding
Application: liquid water can exist over a broad range of temperature (0°C to 100°C) found in most habitats
Solvent properties of water:
Cause: water can dissolve polar and ionic substances by forming hydration shells around them due to their polarity
Application: molecule and ion transport in blood, lymphatic and digestive systems
• Understanding: Substances can be hydrophilic or hydrophobic.
Hydrophilic: characteristics of particles that can dissolve in water; mostly polar molecules and molecules with charges
Hydrophobic: characteristics of particles that are insoluble in water; non-polar with no charges
Hydrophobic interaction: tendency of nonpolar molecules in a polar solvent (usually water) to interact with one another as more hydrogen
bonds can be formed by water when the hydrophobic molecules are in contact with each other
• Application: Comparison of the thermal properties of water with those of methane.
Methane: non-polar chemical compound with the chemical formula CH4 that does not for hydrogen bonds
Property Methane Water
Formula CH4 H2O
Molecular mass 16 18
Density 0.46g per cm3 1g per cm3
Specific heat capacity 2.2J per g per °C 4.2J per g per °C
Latent heat of vaporization 760 J/g 2,257J/g
Melting point -182°C 0°C
Boiling point -160°C 100°C
• Application: Use of water as a coolant in sweat.
Coolant: a substance that reduce the temperature of a system below a specified value by conducting away the heat
Biological coolant: the body releases sweat as a coolant in high temperature
Mechanism: the heat needed for the evaporation of water in sweat is taken from the tissues of the skin
Reason for use of water: water’s high latent of evaporation means that more heat is taken from the tissues of the skin
LAST EDITED 2017-03-15 | 3
2016 | SYJ0014
Topic 2.1: Molecular biology – Molecules to metabolism
Living organisms control their composition by a complex web of chemical reactions.
• Understanding: Molecular biology explains living processes in terms of the chemical substances involved.
Molecules and their interaction with each other (for example, genes and proteins) is central in understanding living process
The discovery of the structure of DNA started a revolution in biology that has transformed our understanding of living organisms
• Understanding: Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
Element composition: the 4 most common elements are hydrogen, carbon, oxygen and nitrogen
Covalent bond: bond formed when two adjacent atoms share a pair of electrons with one contributed by each atom
Character: covalent bonds are the strongest type of bond between atoms
Covalent bond in carbons: carbon atoms can form diverse compounds as it can form up to four covalent bonds
• Understanding: Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Four main classes of carbon compound in living organisms:
Carbohydrates: main energy source composed of carbon, hydrogen and oxygen (e.g. glucose, starch, glycogen)
Lipids: often used for storage class of molecules that are insoluble in water (e.g. steroids, fatty acids, triglyceride)
Proteins: molecule with diverse structure and function composed of one or more chains of amino acids (e.g. enzymes)
Nucleic acids: molecules composed of chains of nucleotides (e.g. RNA and DNA)
• Understanding: Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.
Metabolism: web of all the enzyme catalysed reactions in any cells; sum of all reactions in an organism
Metabolism consists of pathways by which one type of molecule is transformed into another
• Understanding: Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from
monomers by condensation reactions.
• Understanding: Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into
monomers.
Anabolism: synthesis of complex molecules from simpler molecules (this includes condensation)
Catabolism: breakdown of complex molecules into simpler molecules. (this includes hydrolysis)
Anabolism Catabolism
Reaction Condensation Hydrolysis
Reactant Smaller molecules Larger molecules
Product Larger molecules Smaller molecule
Example Protein synthesis with ribosome Digestion of food
DNA synthesis during replication Cell respiration
Photosynthesis Digestion of complex carbon compounds
Synthesis of complex carbohydrates
• Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
Urea: component of urine produced by the liver in an excess of amino acid
Purpose: liver converts amino acid into urea when excess protein is consumed
CO (NH2)2
Process of urea synthesis: NH3 + CO2 → (NH4)2CO3 → urea + H2O
Urea in vitalism: Friedrich Wohler artificially synthesized urea to disprove the vital principle
Urea in modern use: urea is produced artificially as nitrogen fertilizers on crops
• Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.
alpha–D-glucose D-ribose Saturated fatty acid Generalized amino acid
Diagram
In Beta, –OH and –H groups in 1’ are opposite
Formula C6H12O6 C5H10O5 Dependant on chain length Dependant on R-groups
Structure Six membered ring Five membered ring Unbranched chain Acidic group (COOH)
One carbon side chain (5’) One carbon side chain (4’) 14-20 carbon atom chain Basic group (NH2)
Hydroxyl group (1’,2’,3’,4’, Hydroxyl group (1’,2’,3’, 5’) Carboxyl group at the end 20 different R-group types
6’)
LAST EDITED 2017-03-15 | 1
, IB TOPIC 2 | MOLECULAR BIOLOGY
2016 | SYJ0014
• Skill: Identification of biochemical such as sugars, lipids or amino acids from molecular diagrams.
Sugars Lipids Amino acids
Presence of nitrogen Usually absent Usually absent Present
H:O ratio H:O has a 2:1 ratio Less oxygen than carbohydrates Irregular
Shape Often ring shaped Often straight chained Irregular
Other elements Usually only made of C, H, O May contain phosphorus May contain sulphur
• Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.
• Guidance: Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.
• Guidance: Sugars include monosaccharides and disaccharides.
• Guidance: Only one saturated fat is expected and its specific name is not necessary.
• Guidance: The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized.
• Guidance: Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of
steroids are not expected.
• Guidance: Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.
LAST EDITED 2017-03-15 | 2
, IB TOPIC 2 | MOLECULAR BIOLOGY
2016 | SYJ0014
Topic 2.2: Molecular biology – water
Water is the medium of life.
• Understanding: Water molecules are polar and hydrogen bonds form between them.
Structure of water molecules:
Composition: formed by a covalent bond between an oxygen two hydrogens
Polar character: bond between the H and O is a polar covalent bond due to electronegativity difference
Intermolecular force: electronegative difference between H and O causes hydrogen bonding in water
Hydrogen bonding: type of bonding weaker than other bonds, but stronger than other intermolecular forces
Impact on character of water: bonding makes water denser than ice, causing the latter to float
• Understanding: Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.
Cohesion: attraction between two molecules of the same type (e.g. two water molecule)
Adhesion: attraction between two different polar molecules (i.e. water and other polar molecules)
Cohesive properties of water:
Cause: water has strong cohesion force due to hydrogen bonding
Application: assist water transport in plants in xylems through transpiration, high surface tension for water striders
Adhesive properties of water:
Cause: water has adhesion forces (weaker than cohesion) due to its polarity
Application: water adhesion inside the plant’s tube
Thermal properties of water:
Cause: water has unique thermal properties due to strong hydrogen bonding
High specific heat capacity: relatively high amount of heat required to raise the temperature
Description: large amounts of energy transfer needed to raise/lower temperature due to hydrogen bonding
Application: thermally stable habitat in water bodies in comparison to air or land
High latent heat of vaporization: relatively high amount of heat required to change phase from liquid to gas at its boiling point
Description: large amounts of energy transfer needed to break bonds between molecules due to hydrogen bonding
Application: coolant for living organisms
High boiling point: relatively high temperature at which its vapour pressure equal to the pressure of gas above it
Description: large amounts of energy transfer needed to break bonds between molecules due to hydrogen bonding
Application: liquid water can exist over a broad range of temperature (0°C to 100°C) found in most habitats
Solvent properties of water:
Cause: water can dissolve polar and ionic substances by forming hydration shells around them due to their polarity
Application: molecule and ion transport in blood, lymphatic and digestive systems
• Understanding: Substances can be hydrophilic or hydrophobic.
Hydrophilic: characteristics of particles that can dissolve in water; mostly polar molecules and molecules with charges
Hydrophobic: characteristics of particles that are insoluble in water; non-polar with no charges
Hydrophobic interaction: tendency of nonpolar molecules in a polar solvent (usually water) to interact with one another as more hydrogen
bonds can be formed by water when the hydrophobic molecules are in contact with each other
• Application: Comparison of the thermal properties of water with those of methane.
Methane: non-polar chemical compound with the chemical formula CH4 that does not for hydrogen bonds
Property Methane Water
Formula CH4 H2O
Molecular mass 16 18
Density 0.46g per cm3 1g per cm3
Specific heat capacity 2.2J per g per °C 4.2J per g per °C
Latent heat of vaporization 760 J/g 2,257J/g
Melting point -182°C 0°C
Boiling point -160°C 100°C
• Application: Use of water as a coolant in sweat.
Coolant: a substance that reduce the temperature of a system below a specified value by conducting away the heat
Biological coolant: the body releases sweat as a coolant in high temperature
Mechanism: the heat needed for the evaporation of water in sweat is taken from the tissues of the skin
Reason for use of water: water’s high latent of evaporation means that more heat is taken from the tissues of the skin
LAST EDITED 2017-03-15 | 3
