Topic 1 Biological molecules
1.1 Chemistry for life
Spec 1.6i Inorganic ions
- Nitrate ions (𝑁𝑂3− ) - to make DNA and amino acids, which are needed for growth.
- Calcium ions (𝐶𝑎2+ ) - to form calcium pectate for the middle lamellae.
- Magnesium ions (𝑀𝑔2+) - to produce chlorophyll.
- Phosphate ions (𝑃𝑂43− ) - to make ADP and ATP.
Spec 1.7i Water
- A dipole is a separation of charge in a polar molecule.
- Dipole nature of water molecules:
- Polar -> Hydrogen bonds are formed between water molecules when the positive dipole of the H
atoms of a water molecule are attracted to the negative dipole of the O atom of another water
molecule.
- High specific heat capacity because of hydrogen bonds - It takes a lot of energy to increase the
temperature of water as a lot of energy is used to break the hydrogen bonds between water
molecules -> unusually high boiling point.
- Acts as a temperature buffer in cells which enables organisms to resist fluctuations in core
temperature to maintain optimum enzyme activity and metabolism.
- If water temperature increases too drastically / is too high, there would be less dissolved
oxygen in the water for aquatic organisms and there would not be enough oxygen for
respiration.
- Polar universal solvent - dissolves and transports charged particles involved in intracellular and
extracellular reactions as a medium for many reactions and a transport medium.
- Surface tension (polar -> hydrogen bonds -> cohesive)
- An inward force at the water surface
- slows water loss due to transpiration in plants
- allows water to rise unusually high in narrow tubes coupled with adhesion, lowering
demand on root pressure
- allows some insects to skim across the water surface
- Incompressibility because of hydrogen bonds and being cohesive - provides turgidity to plant cells
and hydrostatic skeletons for some small animals like earthworms.
- Water is a liquid at room temperature and liquids cannot be compressed.
- The shape of the container/body changes as pressure increases.
- Maximum density at 4℃ - Ice is less dense than water and floats because it freezes at 0℃ and its
hydrogen bonds hold water molecules in fixed positions further away from each other. It insulates
water in arctic climates so aquatic organisms can survive.
,(Held by covalent bonds)
Associate w/ water
(compact for storage + insoluble so does not affect osmosis) for rapid hydrolysis
+turgidity to ->
polar
-> allows water molecules
through cell wall
,(𝑪𝒏 𝑯𝟐𝒏 𝑶𝟐 )
Property: Polar as a whole
Interacts with the aqueous env. and w/ each other
1.2 Biological molecules
, Spec 1.3 Proteins
- polar / hydrophilic
- Spec i. Structure of amino acid:
- amine group (𝑁𝐻2 )
- carboxyl group (-𝐶𝑂𝑂𝐻)
- R group that varies between each amino acid
- Small R groups enable proteins to be close together -> allows the formation of bonds
that hold the polypeptide chains together.
- C atom
- H atom
- Spec ii.
- A dipeptide is formed by the joining of two amino acid monomers between the amine group
of one amino acid and the carboxyl group of another by a peptide bond by condensation
through the removal of a water molecule in which the R group is not involved.
- A polypeptide is formed when more and more amino acids join to form a polypeptide chain
by peptide bonds by condensation through the removal of a water molecule.
- A protein is formed when a polypeptide folds, coils or associates with other polypeptide
chains.
- Spec iii.
- Hydrogen bonds
- weak bonds
- between slightly positive charges of H atoms of the amine group of amino acids and
tiny negative charges of O atoms of the carboxyl group of amino acids
- important in the folding and coiling of polypeptide chains in the formation of proteins
- Disulfide bonds
- stronger than hydrogen bonds, but occur less often
- between the two sulfur containing groups of two cysteine amino acids by a covalent
bond by oxidation (loss of electrons)
- important for holding the folded polypeptide chains in a protein in place
- Ionic bonds (known as salt bridges)
- strong bonds, but not as common as other bonds
- between positive and negative amino acid side chains
- important for connecting amino acid side chains in the tertiary structure of proteins
- These bonds are sensitive to changes in temperature and pH -> can break and cause a
protein to lose its specific 3D structure which determines its function that it is denatured.
- Spec iv.
- Primary structure
- the sequence of amino acids, which is a polypeptide chain, that is coded for DNA and
determines the tertiary structure.
- It determines the tertiary structure as amino acids determine the type of
bonds, such as hydrogen, ionic and disulfide bonds, formed.
- A different primary structure (caused by a different base sequence) has
different R groups and hence a different secondary and tertiary structure.
Active site of the enzyme would be different that substrates cannot bind to it
to form enzyme/substrate complexes.
- held by peptide bonds
- a charge may be resulted in a non-functional protein as the R group may not interact
correctly, changing the shape of the protein and thus that of the active site.
1.1 Chemistry for life
Spec 1.6i Inorganic ions
- Nitrate ions (𝑁𝑂3− ) - to make DNA and amino acids, which are needed for growth.
- Calcium ions (𝐶𝑎2+ ) - to form calcium pectate for the middle lamellae.
- Magnesium ions (𝑀𝑔2+) - to produce chlorophyll.
- Phosphate ions (𝑃𝑂43− ) - to make ADP and ATP.
Spec 1.7i Water
- A dipole is a separation of charge in a polar molecule.
- Dipole nature of water molecules:
- Polar -> Hydrogen bonds are formed between water molecules when the positive dipole of the H
atoms of a water molecule are attracted to the negative dipole of the O atom of another water
molecule.
- High specific heat capacity because of hydrogen bonds - It takes a lot of energy to increase the
temperature of water as a lot of energy is used to break the hydrogen bonds between water
molecules -> unusually high boiling point.
- Acts as a temperature buffer in cells which enables organisms to resist fluctuations in core
temperature to maintain optimum enzyme activity and metabolism.
- If water temperature increases too drastically / is too high, there would be less dissolved
oxygen in the water for aquatic organisms and there would not be enough oxygen for
respiration.
- Polar universal solvent - dissolves and transports charged particles involved in intracellular and
extracellular reactions as a medium for many reactions and a transport medium.
- Surface tension (polar -> hydrogen bonds -> cohesive)
- An inward force at the water surface
- slows water loss due to transpiration in plants
- allows water to rise unusually high in narrow tubes coupled with adhesion, lowering
demand on root pressure
- allows some insects to skim across the water surface
- Incompressibility because of hydrogen bonds and being cohesive - provides turgidity to plant cells
and hydrostatic skeletons for some small animals like earthworms.
- Water is a liquid at room temperature and liquids cannot be compressed.
- The shape of the container/body changes as pressure increases.
- Maximum density at 4℃ - Ice is less dense than water and floats because it freezes at 0℃ and its
hydrogen bonds hold water molecules in fixed positions further away from each other. It insulates
water in arctic climates so aquatic organisms can survive.
,(Held by covalent bonds)
Associate w/ water
(compact for storage + insoluble so does not affect osmosis) for rapid hydrolysis
+turgidity to ->
polar
-> allows water molecules
through cell wall
,(𝑪𝒏 𝑯𝟐𝒏 𝑶𝟐 )
Property: Polar as a whole
Interacts with the aqueous env. and w/ each other
1.2 Biological molecules
, Spec 1.3 Proteins
- polar / hydrophilic
- Spec i. Structure of amino acid:
- amine group (𝑁𝐻2 )
- carboxyl group (-𝐶𝑂𝑂𝐻)
- R group that varies between each amino acid
- Small R groups enable proteins to be close together -> allows the formation of bonds
that hold the polypeptide chains together.
- C atom
- H atom
- Spec ii.
- A dipeptide is formed by the joining of two amino acid monomers between the amine group
of one amino acid and the carboxyl group of another by a peptide bond by condensation
through the removal of a water molecule in which the R group is not involved.
- A polypeptide is formed when more and more amino acids join to form a polypeptide chain
by peptide bonds by condensation through the removal of a water molecule.
- A protein is formed when a polypeptide folds, coils or associates with other polypeptide
chains.
- Spec iii.
- Hydrogen bonds
- weak bonds
- between slightly positive charges of H atoms of the amine group of amino acids and
tiny negative charges of O atoms of the carboxyl group of amino acids
- important in the folding and coiling of polypeptide chains in the formation of proteins
- Disulfide bonds
- stronger than hydrogen bonds, but occur less often
- between the two sulfur containing groups of two cysteine amino acids by a covalent
bond by oxidation (loss of electrons)
- important for holding the folded polypeptide chains in a protein in place
- Ionic bonds (known as salt bridges)
- strong bonds, but not as common as other bonds
- between positive and negative amino acid side chains
- important for connecting amino acid side chains in the tertiary structure of proteins
- These bonds are sensitive to changes in temperature and pH -> can break and cause a
protein to lose its specific 3D structure which determines its function that it is denatured.
- Spec iv.
- Primary structure
- the sequence of amino acids, which is a polypeptide chain, that is coded for DNA and
determines the tertiary structure.
- It determines the tertiary structure as amino acids determine the type of
bonds, such as hydrogen, ionic and disulfide bonds, formed.
- A different primary structure (caused by a different base sequence) has
different R groups and hence a different secondary and tertiary structure.
Active site of the enzyme would be different that substrates cannot bind to it
to form enzyme/substrate complexes.
- held by peptide bonds
- a charge may be resulted in a non-functional protein as the R group may not interact
correctly, changing the shape of the protein and thus that of the active site.
