Chapter II: Molecular biology
1.1 Molecules to metabolism
Biochemistry: branch of organic chemistry (chemistry of carbon compounds) explaining the chemistry
characteristics of living organisms.
All living organisms are made up of molecules that can be classifies into four types:
→ Carbohydrates, Proteins, lipids and nucleic acids = interact to carry out metabolism of cell!
e.g. insulin (protein) glucose and membrane channels (carbohydrates), phospholipid (lipid), DNA (nucleic
acid).
Carbon-based life
Organic compounds: carbohydrates, proteins, lipids and nucleic acids (most contain carbon) → molecules
from which all living thigs are composed. Ex: Not all compounds containing carbon are classified as organic
e.g. carbon dioxide. → CARBON = keystone element for life on earth.
→ Carbon (4 VE) = shares electrons = 4 covalent bonds!
→ other molecules in addition to carbon: hydrogen, oxygen, nitrogen and phosphorus = form covalent
bonds with carbon and with each other!
Biochemical compounds that are important to living organisms
Category Building blocks Subcategory Example
Carbohydrates Monosaccharides Monosaccharides Glucose, galactose,
fructose
Disaccharides Maltose, lactose,
sucrose
Polysaccharides Starch, glycogen,
cellulose, chitin
Proteins Amino acids Enzymes, antibodies,
peptide hormones
Lipids Glycerol, fatty acids, Triglycerides Fat stored in adipose
phosphate groups cells
Phospholipids Lipids forming a bilayer
in cell membranes
Steroids Some hormones
Nucleic acids Nucleotides DNA, RNA, ATP
Metabolism: reactions controlled by enzymes:
Within a cell, thousands of molecules collide with each other and sometimes, these molecular collisions
provide enough energy to reactants for them to undergo a chemical reaction.
→ all of these enzyme-catalysed reactions (collisions) comprise cell’s metabolism
Factors such as identity, orientation and speed determine whether a reaction occurs or not.
→ use of enzymes to make reactions more likely: Enzymes have a specific shape into which a
reactant can fit = reactant locks on to ‘active site’ of the enzymes.
E.g.: ATP formation: 𝐀𝐃𝐏 + 𝐏𝟏 → 𝐀𝐓𝐏
1. ATP is synthesised from the bonding of ADP to a phosphate group + requires energy
2. Odds of these two reactants colliding at the right place is really small = enzyme acts as catalyst
3. ADP and phosphate group lock on to active site = reaction takes place = reactants become covalently
bonded to each other = ATP is formed
4. ATP is released from active site and enzyme is ready for new catalysis
→ enzyme enables reaction to occur at a higher reaction rate and less energy is required
Other reactions catalysed by enzymes include: replication of DNA (in preparation of mitosis), the synthesis of
RNA, synthesis of proteins (bonding AA to each other), cell respiration, photosynthesis
Metabolism = catabolism + anabolism
Catabolism: Conversion of large, complex molecules into smaller, simpler molecular forms (BB) → food into
building blocks
, = Hydrolysis reactions: require a water molecule as a reactant, water is split, covalent bonds broken
e.g. starch + (many) water molecules → (many) glucose molecules
protein + (many) water molecules → (many) polypeptides
Anabolism: Conversion of small, simple molecules into larger, more complex molecules.
→ building blocks recycled again somewhere in body into larger molecules.
= Condensation reactions: water molecule(s) is released as part of reaction, covalent bonds are formed
(require different enzyme)
e.g. glucose molecules → starch + (many) water molecules
Nature of science – vitalism
Belief that living and inanimate things are different because living organisms contain a
vitalistic element. Also, organic molecules could only be produced by living organisms.
E.g. production of urea: → belief that it could only be produced by living organisms
1828: production of urea by mixing two inorganic substances. = vitalism was discredited
Fig.3: ribose
Fig. 1: Alpha-D-glucose
Fig. 2: Beta-D-glucose
Fig. 4: generalised fatty acid Fig. 5: generalised amino acid
1.2 Water
The structure of water molecules and the resulting polarity:
Water = solvent of life
→ Cytoplasm and water environments = aqueous solutions
- Covalent bonds between oxygen and hydrogen = polar
covalent bonds (results from an unequal sharing of electrons)
- Slightly negative charge at oxygen end and slightly positive
charge at hydrogen ends
= opposite charges = polar molecule
- This dipolarity is the reason why water reacts with itself and other molecules in interesting ways.
1. Cohesive properties = attraction to each other
Whenever two molecules are near to each other, the positive end of one attracts the negative end
of another = hydrogen bond
→ when below freezing point: molecular motion slows down, hydrogen bonds become locked
and ice crystals form.
→ liquid water: faster molecular motion, hydrogen bonds are continuously reformed.
Ephemeral hydrogen bonding explains: formation of water droplets, surface tensions, water
moving as ‘columns’ in vascular plant tissues.
2. Adhesive properties: attraction to other molecules
1.1 Molecules to metabolism
Biochemistry: branch of organic chemistry (chemistry of carbon compounds) explaining the chemistry
characteristics of living organisms.
All living organisms are made up of molecules that can be classifies into four types:
→ Carbohydrates, Proteins, lipids and nucleic acids = interact to carry out metabolism of cell!
e.g. insulin (protein) glucose and membrane channels (carbohydrates), phospholipid (lipid), DNA (nucleic
acid).
Carbon-based life
Organic compounds: carbohydrates, proteins, lipids and nucleic acids (most contain carbon) → molecules
from which all living thigs are composed. Ex: Not all compounds containing carbon are classified as organic
e.g. carbon dioxide. → CARBON = keystone element for life on earth.
→ Carbon (4 VE) = shares electrons = 4 covalent bonds!
→ other molecules in addition to carbon: hydrogen, oxygen, nitrogen and phosphorus = form covalent
bonds with carbon and with each other!
Biochemical compounds that are important to living organisms
Category Building blocks Subcategory Example
Carbohydrates Monosaccharides Monosaccharides Glucose, galactose,
fructose
Disaccharides Maltose, lactose,
sucrose
Polysaccharides Starch, glycogen,
cellulose, chitin
Proteins Amino acids Enzymes, antibodies,
peptide hormones
Lipids Glycerol, fatty acids, Triglycerides Fat stored in adipose
phosphate groups cells
Phospholipids Lipids forming a bilayer
in cell membranes
Steroids Some hormones
Nucleic acids Nucleotides DNA, RNA, ATP
Metabolism: reactions controlled by enzymes:
Within a cell, thousands of molecules collide with each other and sometimes, these molecular collisions
provide enough energy to reactants for them to undergo a chemical reaction.
→ all of these enzyme-catalysed reactions (collisions) comprise cell’s metabolism
Factors such as identity, orientation and speed determine whether a reaction occurs or not.
→ use of enzymes to make reactions more likely: Enzymes have a specific shape into which a
reactant can fit = reactant locks on to ‘active site’ of the enzymes.
E.g.: ATP formation: 𝐀𝐃𝐏 + 𝐏𝟏 → 𝐀𝐓𝐏
1. ATP is synthesised from the bonding of ADP to a phosphate group + requires energy
2. Odds of these two reactants colliding at the right place is really small = enzyme acts as catalyst
3. ADP and phosphate group lock on to active site = reaction takes place = reactants become covalently
bonded to each other = ATP is formed
4. ATP is released from active site and enzyme is ready for new catalysis
→ enzyme enables reaction to occur at a higher reaction rate and less energy is required
Other reactions catalysed by enzymes include: replication of DNA (in preparation of mitosis), the synthesis of
RNA, synthesis of proteins (bonding AA to each other), cell respiration, photosynthesis
Metabolism = catabolism + anabolism
Catabolism: Conversion of large, complex molecules into smaller, simpler molecular forms (BB) → food into
building blocks
, = Hydrolysis reactions: require a water molecule as a reactant, water is split, covalent bonds broken
e.g. starch + (many) water molecules → (many) glucose molecules
protein + (many) water molecules → (many) polypeptides
Anabolism: Conversion of small, simple molecules into larger, more complex molecules.
→ building blocks recycled again somewhere in body into larger molecules.
= Condensation reactions: water molecule(s) is released as part of reaction, covalent bonds are formed
(require different enzyme)
e.g. glucose molecules → starch + (many) water molecules
Nature of science – vitalism
Belief that living and inanimate things are different because living organisms contain a
vitalistic element. Also, organic molecules could only be produced by living organisms.
E.g. production of urea: → belief that it could only be produced by living organisms
1828: production of urea by mixing two inorganic substances. = vitalism was discredited
Fig.3: ribose
Fig. 1: Alpha-D-glucose
Fig. 2: Beta-D-glucose
Fig. 4: generalised fatty acid Fig. 5: generalised amino acid
1.2 Water
The structure of water molecules and the resulting polarity:
Water = solvent of life
→ Cytoplasm and water environments = aqueous solutions
- Covalent bonds between oxygen and hydrogen = polar
covalent bonds (results from an unequal sharing of electrons)
- Slightly negative charge at oxygen end and slightly positive
charge at hydrogen ends
= opposite charges = polar molecule
- This dipolarity is the reason why water reacts with itself and other molecules in interesting ways.
1. Cohesive properties = attraction to each other
Whenever two molecules are near to each other, the positive end of one attracts the negative end
of another = hydrogen bond
→ when below freezing point: molecular motion slows down, hydrogen bonds become locked
and ice crystals form.
→ liquid water: faster molecular motion, hydrogen bonds are continuously reformed.
Ephemeral hydrogen bonding explains: formation of water droplets, surface tensions, water
moving as ‘columns’ in vascular plant tissues.
2. Adhesive properties: attraction to other molecules
