2.1.2: Biological molecules
Water
What is a hydrogen bond?
● Interaction which occurs when a slightly negatively charged atom bonds to a slightly
positively charged atom
● The slightly negative and slightly positive atoms are known as dipoles
● Relatively weak interaction but occurs in high numbers
Many organic molecules contain oxygen and hydrogen bonded together in hydroxyl (OH)
groups and so are slightly polar eg. water molecules, which contain 2 of these hydroxyl groups
- Hydrogen bonding gives water its unique characteristics which are essential for life on
this planet
How does hydrogen bonding occur between water molecules?
● Water consists of two hydrogen atoms and one oxygen atom covalently
bonded together
● A water molecule is said to be dipolar (a polar molecule) because it has a
positive and negative pole (has regions of negativity and regions of
positivity as a result of the uneven distribution of electrons) yet has an
overall neutral electrical charge
- Why are the electrons distributed unevenly?
The electrons in the covalent bonds of a water molecule lie closer to the oxygen
nucleus than the hydrogen nuclei, because the
negative electrons in the electron pair
are more attracted to oxygen’s nucleus,
as it has eight protons (compared to the
one proton in hydrogen’s nucleus).
↓
This means that the oxygen atom is slightly
negatively charged, and the hydrogen atoms are slightly positively charged
Water molecules are therefore attracted to each other by weak hydrogen bonds, which form
between the oxygen and the hydrogen atoms of adjacent molecules
, ● Hydrogen bonds stabilise polymers - help them to retain their final shape, since they
are very large molecules
- Shape of polymers is crucial for their function, so hydrogen bonds are important
in maintaining their functioning eg. hydrogen bonds make the structure of DNA
more stable by holding the complementary strands together
- Enzymes are made of proteins, which are polymers - therefore if the temp on an
enzyme increases too much above the optimum, the hydrogen bonds in the active
site of the enzyme will break and the enzyme will denature (can’t fulfill function)
Property of water explained Link to water’s role in living organisms
Maximum density of water occurs at 4℃ because - Insulates organisms in water below (ice floating on a liquid water surface
when water freezes the space between molecules forms an insulating layer). Maintains the temperature of any water below
increases because when water molecules cool they it, so living organisms can survive below ice.
lose kinetic energy but still form a rigid, solid - Thaws more quickly on top
structure (ice) as hydrogen bonds don’t break easily - Difference in density allows nutrient cycling
- meaning ice is less dense than water, so this - Place for penguins & polar bears!
explains the expansion which occurs on freezing
- unusual that max density occurs as a liquid
Is a liquid between 0℃ and 100℃ - Provides a good habitat for living organisms to survive - in both
fresh-water and salt-water habitats (water is stable)
- Can act as a medium for transport and chemical reactions (see below)
- More accessible than gas
Has a high specific heat capacity because it requires - Thermoregulation - stable body temp for bodies with 70% water and
a lot of energy to overcome hydrogen bonds, so aquatic organisms
absorbs a lot of heat relative to its mass
(thermostable)
Has a high heat of vaporisation Water molecules cannot escape easily (temperature must be 100℃ for
bonds to break)
- Acts as an efficient coolant eg. as water moves through the plant in the
transpiration stream, sweating and panting. Necessary in prokaryotic and
eukaryotic cells for water to act as a coolant because the temperature
changes that occur during chemical reactions (due to the large amount of
energy required to overcome hydrogen bonding) must be buffered.
Constant temperatures in cell must be maintained eg. optimum temp of
enzymes
,Very high latent heat of fusion - amount of energy - Prevents cell damage by formation of ice crystals
needed to change the state of 1 kg of the substance - Aquatic habitats remain habitable
without changing its temperature (lots of heat must
be removed before freezing occurs)
Water is a universal solvent (dissolves more Water’s ability to act as a solvent allows molecules to be dissolved in the
substances than any other common liquids) cytosol (the aqueous component of the cytoplasm) of
Water molecules - the solvent - surround the solute prokaryotes and eukaryotes. Solutes react more easily
molecules and keep them in a solution. when dissolved, so they are a medium for chemical
reactions/metabolic processes
Water is a polar molecule so Water makes an ideal transport medium for polar solutes because the
any other polar molecules polar molecules and ions which can be dissolved in it are able to be
or ions dissolve in water eg. transported easily around living organisms eg. glucose is transported in
NaCl (salt) blood transport system of animals
Non-polar substances are hydrophobic (can’t Important property of the phospholipid bilayer of the cell membrane
dissolve and are repelled by water) (gives the cell membrane its "water proof" nature and allows it to act as a
container for the cell and its contents)
Cohesion: hydrogen bonds between water Allow water molecules to flow together in a column against the force of
molecules meaning that the molecules stick together gravity - “capillary action”, which helps water to move up narrow tubes
- Cohesive forces mean reduced eg. xylem vessels in the vascular bundles of plants
compressibility - Reduced compressibility allows water to act as a medium for support
Adhesion: water adheres to a surface (because water (turgor pressure in plants, and hydroskeleton of earthworms, amniotic
molecules are attracted to charged fluid, support of whales in seas)
particles/surfaces, due to their dipolarity)
Very high surface tension: hydrogen bonds pull Helps some insects to walk on water and also helps water to move up the
molecules in at the surface because water molecules xylem tissue of plants without breaking up
at the surface with air orientate so that hydrogen
bonds face inwards, since water molecules are more
strongly cohesive to each other than they are to air
Very low viscosity (water molecules slide easily over - Allows osmosis
each other) - Lubricant: pleural fluid, mucus, synovial fluid (joints)
Colourless because has a high transmission of Photosynthesis of aquatic plants
visible light
, Chemical elements that make up biological molecules
● About 99% of all living things are made up of only 4 elements: carbon, hydrogen, oxygen
and nitrogen - these elements (+a few others eg. phosphorous and sulfur) are used to
build all the molecules found in living cells
Carbon atoms
● Organic molecules: molecules that contain carbon (all biomolecules except water)
- Life on this planet is often referred to as being ‘carbon-based’ because of this
Carbon atoms make a good building block because:
- The 4 electrons in the outer shell repel each other
- Therefore the outer electrons push away
- Shapes atom into a tetrahedron
Carbon atoms can share these 4 electrons (carbon’s 4 bond sites) with other atoms -
therefore sharing 4 pairs of electrons. This forms covalent bonds which are
stable and strong - meaning atoms can join together and form organic
molecules
● Carbon atoms can bond together and form:
- Chains (long chains eg. fatty acid or short chains eg. amino
acid)
- Branched chains
- Ring forms
- Double bond (forms 2 bonds with another atom eg. C=O in glucose)
- Covalently bond with oxygen, hydrogen, nitrogen +/or sulfur to make large
molecules
Hydrogen atoms
● Can only form 1 bond with another atom
Oxygen atoms
● Can form 2 bonds with other atoms
Nitrogen atoms
● Can form 3 bonds with other atoms
Water
What is a hydrogen bond?
● Interaction which occurs when a slightly negatively charged atom bonds to a slightly
positively charged atom
● The slightly negative and slightly positive atoms are known as dipoles
● Relatively weak interaction but occurs in high numbers
Many organic molecules contain oxygen and hydrogen bonded together in hydroxyl (OH)
groups and so are slightly polar eg. water molecules, which contain 2 of these hydroxyl groups
- Hydrogen bonding gives water its unique characteristics which are essential for life on
this planet
How does hydrogen bonding occur between water molecules?
● Water consists of two hydrogen atoms and one oxygen atom covalently
bonded together
● A water molecule is said to be dipolar (a polar molecule) because it has a
positive and negative pole (has regions of negativity and regions of
positivity as a result of the uneven distribution of electrons) yet has an
overall neutral electrical charge
- Why are the electrons distributed unevenly?
The electrons in the covalent bonds of a water molecule lie closer to the oxygen
nucleus than the hydrogen nuclei, because the
negative electrons in the electron pair
are more attracted to oxygen’s nucleus,
as it has eight protons (compared to the
one proton in hydrogen’s nucleus).
↓
This means that the oxygen atom is slightly
negatively charged, and the hydrogen atoms are slightly positively charged
Water molecules are therefore attracted to each other by weak hydrogen bonds, which form
between the oxygen and the hydrogen atoms of adjacent molecules
, ● Hydrogen bonds stabilise polymers - help them to retain their final shape, since they
are very large molecules
- Shape of polymers is crucial for their function, so hydrogen bonds are important
in maintaining their functioning eg. hydrogen bonds make the structure of DNA
more stable by holding the complementary strands together
- Enzymes are made of proteins, which are polymers - therefore if the temp on an
enzyme increases too much above the optimum, the hydrogen bonds in the active
site of the enzyme will break and the enzyme will denature (can’t fulfill function)
Property of water explained Link to water’s role in living organisms
Maximum density of water occurs at 4℃ because - Insulates organisms in water below (ice floating on a liquid water surface
when water freezes the space between molecules forms an insulating layer). Maintains the temperature of any water below
increases because when water molecules cool they it, so living organisms can survive below ice.
lose kinetic energy but still form a rigid, solid - Thaws more quickly on top
structure (ice) as hydrogen bonds don’t break easily - Difference in density allows nutrient cycling
- meaning ice is less dense than water, so this - Place for penguins & polar bears!
explains the expansion which occurs on freezing
- unusual that max density occurs as a liquid
Is a liquid between 0℃ and 100℃ - Provides a good habitat for living organisms to survive - in both
fresh-water and salt-water habitats (water is stable)
- Can act as a medium for transport and chemical reactions (see below)
- More accessible than gas
Has a high specific heat capacity because it requires - Thermoregulation - stable body temp for bodies with 70% water and
a lot of energy to overcome hydrogen bonds, so aquatic organisms
absorbs a lot of heat relative to its mass
(thermostable)
Has a high heat of vaporisation Water molecules cannot escape easily (temperature must be 100℃ for
bonds to break)
- Acts as an efficient coolant eg. as water moves through the plant in the
transpiration stream, sweating and panting. Necessary in prokaryotic and
eukaryotic cells for water to act as a coolant because the temperature
changes that occur during chemical reactions (due to the large amount of
energy required to overcome hydrogen bonding) must be buffered.
Constant temperatures in cell must be maintained eg. optimum temp of
enzymes
,Very high latent heat of fusion - amount of energy - Prevents cell damage by formation of ice crystals
needed to change the state of 1 kg of the substance - Aquatic habitats remain habitable
without changing its temperature (lots of heat must
be removed before freezing occurs)
Water is a universal solvent (dissolves more Water’s ability to act as a solvent allows molecules to be dissolved in the
substances than any other common liquids) cytosol (the aqueous component of the cytoplasm) of
Water molecules - the solvent - surround the solute prokaryotes and eukaryotes. Solutes react more easily
molecules and keep them in a solution. when dissolved, so they are a medium for chemical
reactions/metabolic processes
Water is a polar molecule so Water makes an ideal transport medium for polar solutes because the
any other polar molecules polar molecules and ions which can be dissolved in it are able to be
or ions dissolve in water eg. transported easily around living organisms eg. glucose is transported in
NaCl (salt) blood transport system of animals
Non-polar substances are hydrophobic (can’t Important property of the phospholipid bilayer of the cell membrane
dissolve and are repelled by water) (gives the cell membrane its "water proof" nature and allows it to act as a
container for the cell and its contents)
Cohesion: hydrogen bonds between water Allow water molecules to flow together in a column against the force of
molecules meaning that the molecules stick together gravity - “capillary action”, which helps water to move up narrow tubes
- Cohesive forces mean reduced eg. xylem vessels in the vascular bundles of plants
compressibility - Reduced compressibility allows water to act as a medium for support
Adhesion: water adheres to a surface (because water (turgor pressure in plants, and hydroskeleton of earthworms, amniotic
molecules are attracted to charged fluid, support of whales in seas)
particles/surfaces, due to their dipolarity)
Very high surface tension: hydrogen bonds pull Helps some insects to walk on water and also helps water to move up the
molecules in at the surface because water molecules xylem tissue of plants without breaking up
at the surface with air orientate so that hydrogen
bonds face inwards, since water molecules are more
strongly cohesive to each other than they are to air
Very low viscosity (water molecules slide easily over - Allows osmosis
each other) - Lubricant: pleural fluid, mucus, synovial fluid (joints)
Colourless because has a high transmission of Photosynthesis of aquatic plants
visible light
, Chemical elements that make up biological molecules
● About 99% of all living things are made up of only 4 elements: carbon, hydrogen, oxygen
and nitrogen - these elements (+a few others eg. phosphorous and sulfur) are used to
build all the molecules found in living cells
Carbon atoms
● Organic molecules: molecules that contain carbon (all biomolecules except water)
- Life on this planet is often referred to as being ‘carbon-based’ because of this
Carbon atoms make a good building block because:
- The 4 electrons in the outer shell repel each other
- Therefore the outer electrons push away
- Shapes atom into a tetrahedron
Carbon atoms can share these 4 electrons (carbon’s 4 bond sites) with other atoms -
therefore sharing 4 pairs of electrons. This forms covalent bonds which are
stable and strong - meaning atoms can join together and form organic
molecules
● Carbon atoms can bond together and form:
- Chains (long chains eg. fatty acid or short chains eg. amino
acid)
- Branched chains
- Ring forms
- Double bond (forms 2 bonds with another atom eg. C=O in glucose)
- Covalently bond with oxygen, hydrogen, nitrogen +/or sulfur to make large
molecules
Hydrogen atoms
● Can only form 1 bond with another atom
Oxygen atoms
● Can form 2 bonds with other atoms
Nitrogen atoms
● Can form 3 bonds with other atoms
