Functional groups
Groups of atoms that give molecules which have similar properties
➔ Alkane
➔ Alkenes
➔ Alcohol
➔ Carboxylic acid
➔ Amines
➔ Ketones
➔ Esters
Amino acids
➔ Made of carbon, oxygen, nitrogen, hydrogen, sulfur
➔ Atoms form an amino group and carboxyl group which are both connected to the
alpha carbon and the side chain which determines the properties and varies between
amino acids
➔ Properties: hydrophobic, hydrophilic, charged amino acids (interact with other
charged amino acid side chains)
Primary structure
➔ Linear sequence of amino acids as encoded by DNA, amino acids in a protein are
joined by peptide bonds linking amino group of one amino acid to the carboxyl group
of another, releasing H2O
Secondary structure
➔ Alpha helices: Right handed coil stabilised by hydrogen bonds between amino group
and carboxyl group between adjacent amino acids
➔ Beta sheets: 2 x antiparallel sheets stabilized by hydrogen bonds between amino
acid group and carboxyl group of opposite sheets
● Seen in alzheimers and parkinsons patients
Tertiary structure
➔ Three dimensional shape of the protein chain, determined by the characteristics of
the side chains of the amino acids. Often hydrophobic inner and hydrophilic outer
Quaternary structure
➔ Two or more polypeptide chains come together to form one functional molecule with
several subunits
History of biochemistry
Foundations of the universe
➔ 14,000,000,000 years ago it is believed the big bang occurred, forming the primordial
universe
➔ The first gases were hydrogen and helium forming the first generation stars
➔ After 7 billion years, their high pressure and heat environment resulted in the
condensation and fusion of hydrogen and helium together to form heavier elements
including carbon, nitrogen and oxygen
, ➔ Large unstable stars became unstable and explode as supernovae, dispersing all the
elements throughout the universe, now, these elements are present in all biological
lifeforms
➔ Further billions of years later, second generation stars formed solar systems with
planetary systems incorporating the heavier elements
➔ The universe is homogeneous, all with the same foundational elements, essential for
the beginnings of life which reflects a common evolutionary ancestor of all biological
life on earth
Molecular composition of life
➔ We are comprised of four main elements, carbon, hydrogen, oxygen and nitrogen
➔ We are 70% water
➔ Carbon in particular is central in molecule
formation as it has an electronic structure forming
up to 4 covalent bonds. Can also form single,
double and triple bonds with different electronic
structure and geometries which provides
versatility, scaffolding and diversity in chemical
compounds
Role Elements
Tier 1 Have the ability to form Carbon, Nitrogen, hydrogen,
strong covalent bonds with oxygen
elements to make
molecules, most abundant
Tier 2 Essential components of ➔ Phosphorous,
biological molecules that sulphur
form covalent bonds and
ionic elements which ➔ Chloride, sodium,
maintain fluid and electrolyte magnesium,
balance and induction of potassium, calcium
membrane potential
Tier 3 and 4 Found in trace elements but
play critical roles e.g.
transition metals are found
and structural and catalytic
elements in many proteins
and in enzymatic catalysis
,Seeding life on earth
➔ Life on earth is dependent on water, the cooling of the primordial earth and
condensation of water provided an aqueous environment within which molecules
could begin to form
➔ A lack of gaseous oxygen and reducing atmosphere supported bond formation while
electrical discharges/high energy environments were provided by lightning and
volcanic events to give rise to organic molecules of life
➔ Primordial soup: 1953 Miller and Urey, water vapour and simple gaseous molecules
(e.g. ch4, nh3 and h2) combined and a spark given by an electrode which formed
complex molecules and over 20 amino acids required for life
Modular design of life - Macromolecules
➔ Biomolecules: DNA, carbohydrates and proteins (summation of organic monomers)
➔ Non-biopolymer: Lipids
➔ Biopolymers’ are formed via nucleophilic attack coupled with the elimination of water
(polymerization through condensation) while lipids are not produced through a
condensation reaction
Weak interactions of biology
➔ Non covalent interactions that can be broken and reformed easily due to the low
bond energy
➔ DNA, proteins and carbohydrates 3D structure is held together by weak (non
bonding) interactions.
Electronegativity
➔ Measure of the tendency of an atom to attract a shared pair of electrons/gain electron
density
➔ Difference in electronegativity between two atoms gives a polarized bond
➔ A dipole moment represents the polarity along a bond of electric charge and direction
➔ Dipole moment is drawn as an arrow from the high electron density atom to the low
electron density atom
➔ Multiple dipole moments can be summed vectorially to give the net dipole moment of
a molecule
Types of interactions
Interactions where the strength/energy of the interaction depends on the distance between
the atoms (r)
, ➔ Charge charge: Strong long range attraction = 1/r
● Full positive and full negative charges are attracted
➔ Charge-dipole interactions: 1/r^2
● Charged molecule interacts with a polar molecule that has a dipole moment
● Attraction between a full charge and a partial opposite charge on the polar
molecule
➔ Dipole dipole interaction: 1/r^3
● Two polar molecules orient themselves so their opposite dipole moments
interact
➔ Charge induced dipole interactions: 1/r^4
● When a fully charged group interacts with a non-polar group thus causing an
induced dipole moment
➔ Dipole induced dipole interaction: 1/r^5
● When a polar molecule with a permanent dipole interacts with a non-polar
molecule and induces a dipole.
➔ Van der Waals: 1/r^6
● When two non-polar molecules interact
● Due to the fluctuation in distribution of electrons causing induced dipoles
● Electron clouds give rise to mutually attractive dipoles
● Very weak but with great numbers (e.g. DNA) produces a very large
stabilizing force
Hydrogen bonding
➔ Slightly positive hydrogen bonded to an electronegative atom
interacts with another electronegative atom with a partial
negative charge.
➔ Has a smaller bond distance than we would expect of the sum of
the atom vdW radii
Chemistry in an aqueous environment
Unique universal water
➔ Hydrogen bonding ability and polar nature
➔ Two hydrogen atoms and two lone pairs of electrons gives it an ability to form four
hydrogen bonds with other molecules (mainly other water molecules)
➔ Thus it has an unusually high boiling point as well as a high heat of vaporization
resulting in heat being removed from our body when sweat evaporates and we cool
➔ Predominantly in the water state (meanwhile other similar sized molecules are
gaseous)
➔ High heat capacity resulting in a nearly constant temperature in large bodies of water
(temperature buffer) and difficult to freeze so requires a lot of energy
When ice forms the oxygen bonds to 4 hydrogens making a cage structure and thus
expanding, it is therefore less dense than water and sits above it
➔ The density of ice and the boiling point of water mean that most water on earth is in
the liquid form
Groups of atoms that give molecules which have similar properties
➔ Alkane
➔ Alkenes
➔ Alcohol
➔ Carboxylic acid
➔ Amines
➔ Ketones
➔ Esters
Amino acids
➔ Made of carbon, oxygen, nitrogen, hydrogen, sulfur
➔ Atoms form an amino group and carboxyl group which are both connected to the
alpha carbon and the side chain which determines the properties and varies between
amino acids
➔ Properties: hydrophobic, hydrophilic, charged amino acids (interact with other
charged amino acid side chains)
Primary structure
➔ Linear sequence of amino acids as encoded by DNA, amino acids in a protein are
joined by peptide bonds linking amino group of one amino acid to the carboxyl group
of another, releasing H2O
Secondary structure
➔ Alpha helices: Right handed coil stabilised by hydrogen bonds between amino group
and carboxyl group between adjacent amino acids
➔ Beta sheets: 2 x antiparallel sheets stabilized by hydrogen bonds between amino
acid group and carboxyl group of opposite sheets
● Seen in alzheimers and parkinsons patients
Tertiary structure
➔ Three dimensional shape of the protein chain, determined by the characteristics of
the side chains of the amino acids. Often hydrophobic inner and hydrophilic outer
Quaternary structure
➔ Two or more polypeptide chains come together to form one functional molecule with
several subunits
History of biochemistry
Foundations of the universe
➔ 14,000,000,000 years ago it is believed the big bang occurred, forming the primordial
universe
➔ The first gases were hydrogen and helium forming the first generation stars
➔ After 7 billion years, their high pressure and heat environment resulted in the
condensation and fusion of hydrogen and helium together to form heavier elements
including carbon, nitrogen and oxygen
, ➔ Large unstable stars became unstable and explode as supernovae, dispersing all the
elements throughout the universe, now, these elements are present in all biological
lifeforms
➔ Further billions of years later, second generation stars formed solar systems with
planetary systems incorporating the heavier elements
➔ The universe is homogeneous, all with the same foundational elements, essential for
the beginnings of life which reflects a common evolutionary ancestor of all biological
life on earth
Molecular composition of life
➔ We are comprised of four main elements, carbon, hydrogen, oxygen and nitrogen
➔ We are 70% water
➔ Carbon in particular is central in molecule
formation as it has an electronic structure forming
up to 4 covalent bonds. Can also form single,
double and triple bonds with different electronic
structure and geometries which provides
versatility, scaffolding and diversity in chemical
compounds
Role Elements
Tier 1 Have the ability to form Carbon, Nitrogen, hydrogen,
strong covalent bonds with oxygen
elements to make
molecules, most abundant
Tier 2 Essential components of ➔ Phosphorous,
biological molecules that sulphur
form covalent bonds and
ionic elements which ➔ Chloride, sodium,
maintain fluid and electrolyte magnesium,
balance and induction of potassium, calcium
membrane potential
Tier 3 and 4 Found in trace elements but
play critical roles e.g.
transition metals are found
and structural and catalytic
elements in many proteins
and in enzymatic catalysis
,Seeding life on earth
➔ Life on earth is dependent on water, the cooling of the primordial earth and
condensation of water provided an aqueous environment within which molecules
could begin to form
➔ A lack of gaseous oxygen and reducing atmosphere supported bond formation while
electrical discharges/high energy environments were provided by lightning and
volcanic events to give rise to organic molecules of life
➔ Primordial soup: 1953 Miller and Urey, water vapour and simple gaseous molecules
(e.g. ch4, nh3 and h2) combined and a spark given by an electrode which formed
complex molecules and over 20 amino acids required for life
Modular design of life - Macromolecules
➔ Biomolecules: DNA, carbohydrates and proteins (summation of organic monomers)
➔ Non-biopolymer: Lipids
➔ Biopolymers’ are formed via nucleophilic attack coupled with the elimination of water
(polymerization through condensation) while lipids are not produced through a
condensation reaction
Weak interactions of biology
➔ Non covalent interactions that can be broken and reformed easily due to the low
bond energy
➔ DNA, proteins and carbohydrates 3D structure is held together by weak (non
bonding) interactions.
Electronegativity
➔ Measure of the tendency of an atom to attract a shared pair of electrons/gain electron
density
➔ Difference in electronegativity between two atoms gives a polarized bond
➔ A dipole moment represents the polarity along a bond of electric charge and direction
➔ Dipole moment is drawn as an arrow from the high electron density atom to the low
electron density atom
➔ Multiple dipole moments can be summed vectorially to give the net dipole moment of
a molecule
Types of interactions
Interactions where the strength/energy of the interaction depends on the distance between
the atoms (r)
, ➔ Charge charge: Strong long range attraction = 1/r
● Full positive and full negative charges are attracted
➔ Charge-dipole interactions: 1/r^2
● Charged molecule interacts with a polar molecule that has a dipole moment
● Attraction between a full charge and a partial opposite charge on the polar
molecule
➔ Dipole dipole interaction: 1/r^3
● Two polar molecules orient themselves so their opposite dipole moments
interact
➔ Charge induced dipole interactions: 1/r^4
● When a fully charged group interacts with a non-polar group thus causing an
induced dipole moment
➔ Dipole induced dipole interaction: 1/r^5
● When a polar molecule with a permanent dipole interacts with a non-polar
molecule and induces a dipole.
➔ Van der Waals: 1/r^6
● When two non-polar molecules interact
● Due to the fluctuation in distribution of electrons causing induced dipoles
● Electron clouds give rise to mutually attractive dipoles
● Very weak but with great numbers (e.g. DNA) produces a very large
stabilizing force
Hydrogen bonding
➔ Slightly positive hydrogen bonded to an electronegative atom
interacts with another electronegative atom with a partial
negative charge.
➔ Has a smaller bond distance than we would expect of the sum of
the atom vdW radii
Chemistry in an aqueous environment
Unique universal water
➔ Hydrogen bonding ability and polar nature
➔ Two hydrogen atoms and two lone pairs of electrons gives it an ability to form four
hydrogen bonds with other molecules (mainly other water molecules)
➔ Thus it has an unusually high boiling point as well as a high heat of vaporization
resulting in heat being removed from our body when sweat evaporates and we cool
➔ Predominantly in the water state (meanwhile other similar sized molecules are
gaseous)
➔ High heat capacity resulting in a nearly constant temperature in large bodies of water
(temperature buffer) and difficult to freeze so requires a lot of energy
When ice forms the oxygen bonds to 4 hydrogens making a cage structure and thus
expanding, it is therefore less dense than water and sits above it
➔ The density of ice and the boiling point of water mean that most water on earth is in
the liquid form
