Biology For IMAT: 1.biochemistry

Biology for IMAT
1.Biochemistry
Atomic structure
• Atoms consist of subatomic
particles: protons (positive
charge), electrons (negative
charge) and neutrons (no
charge)
• Atom in the elemental state:

protons = electrons → +=-
→NEUTRAL CHARGE
• Atom in the ground state:

when all the electrons are in
the lowest available energy
level
• If an atom absorbs energy, it's
actually its electrons that
absorb energy and therefore
move to a higher energy level.
• Then the atom is said to be in

the excited state.
• After that the electrons which

have absorbed the energy, go
back to the grounded state by
releasing the energy they
absorbed.
Isotopes
• Isotopes are atoms of one element that vary only in the

number of neutrons in the nucleus
• Chemically all isotopes of the same element are identical

because they have the same number of electrons in the
same configuration
• Some isotopes are radioactive (ex. Carbon-14, P-32, S-

35)
Bonding
• When two atomic nuclei attract the same electrons a

bond is formed.
• The atoms in a bond are in a lower energy lever therefore

in a more stable configuration. This is why energy is
released when a bond is formed.
• Energy must be supplied to break a bond.

Ions
• Atoms that have gained or lost electrons
• Anion: an atom that has gained electrons (negative

charge ex. Cl-)
• Cation: an atom that has lost electrons (positive charge

ex. Na+, Ca++)
Ionic bonds
• They result from the transfer of electrons.
• For example: NaCl
• Na has 1 electron in the outer shell
• Cl has 7 electrons in the outer shell
• Na gives its one electron to Cl and: Na becomes Na+ and

Cl becomes Cl-. These two are hold together because the
electron that has been transferred to Cl, is now attracted
by both nuclei (of Cl and Na)
Covalent bonds
• They form when atoms share electrons. The resulting
structure is called a molecule.
Covalent bonds
• Electronegativity is the tendency of atoms to attract
electrons.
• When two atoms have the same electronegativity they both

attract equally the shared pair of electrons and the bond is
called non polar covalent bond. (ex. H-H, Cl-Cl)
• When the two atoms in a molecule are different (example H-

Cl) each atom does not have the same electronegativity and
therefore the shared pair of electrons is not equally
attracted. This is because the shared pair of electrons is
attracted more from the more electronegative element (in
our case Cl). This is called a polar covalent bond.
Polar covalent bond
• In this case we can speculate
that the electron has shifted
away from the less
electronegative atom and it
has seemingly a slight positive
charge called δ+
• The more electronegative

atom has the shared pair
towards its side and therefore
has a slight negative charge
called δ-
Hydrophilic or hydrophobic?
• Hydrophilic= hydro (water) + philic (friend) : substances

that dissolve in water [polar substances are hydrophilic]
• Hydrophobic= hydro (water) + phobic (fear): substances

that are miscible (capable of being mixed) or will dissolve
in lipids [non polar substances are hydrophobic
Properties of water
Water has a high specific
heat
• Specific heat is the amount of heat a substance must

absorb to increase 1 gram of the substance by 1˚C
• This makes water more resistant to changes in

temperature
• Large bodies of water such as lakes and oceans are slow

to change temperature as environmental temperature
changes.
Hydrogen bonding
• The positive hydrogen of one molecule is attracted to the

negative oxygen of an adjacent molecule
Water has a high heat of
vaporisation
• The latent heat of vaporisation is a measure of the heat

energy needed to vaporise a liquid
• The energy transferred to water molecules during

vaporisation results in corresponding loss of energy from
their surroundings which therefore cool down.
• Cooling mechanism, as in sweating or panting in

mammals.
Water is a universal solvent
• Because water is a highly polar molecule, it dissolves all polar and
ionic substances
Water exhibits strong
cohesion tension
• Water molecules have very high cohesion - in other words

they tend to stick to each other
• This results in high surface tension.

Density and freezing
properties
• Ice is less dense than water

and therefore floats on liquid
water and insulates the water
under it
• Changes in the density of

water with temperature cause
currents, which help to
maintain the circulation of
nutrients in the oceans
pH
pH
• pH is a measure of acidity and alkalinity of a solution.
• pH = - log[H3O+] or pH = - log[H+]
• The pH must be kept stable. Even a slight change can be

harmful
• Biological systems regulate their pH through the presence

of buffers, substances that resist the changes in pH
• Most important buffer: bicarbonate ion (HCO-)

ISOMERS
Organic compounds that have the same molecular
formula but different structure
Structural
isomers
• Differ in the arrangement of
their atoms
Cis-Trans isomers
• They differ only in spatial

arrangement around double
bonds
Enantiomers
• Molecules that are mirror
images of each other
• The mirror images are called

L- and D- versions.
Carbohydrates
• The body uses carbohydrates for fuel and as building
materials
• They consist of three elements: O, H , C
• Three classes of carbohydrates: monosaccharides,

disaccharides and polysaccharides
Monosaccharides
• Glucose, galactose and fructose
• Chemical formula C6H12O6

Dissacharides
• The consist of two monosaccharides joined together, with
the release of one molecule of water, by the process
known as dehydration synthesis or condensation
• glucose + glucose = maltose
• glucose + galactose = lactose
• glucose + fructose = sucrose

Polysaccharides
• They are macromolecules, polymers of carbohydrates and are
formed as many monosaccharides join together by
dehydration reactions.
• Cellulose: found in plants - makes up plant cell walls
• Starch: found in plants - two forms are amylose and

amylopectin - energy storage polysaccharide
• Chitin: found in animals - makes up exoskeleton in

arthropods
• Glycogen: found in animals - “animal starch” - it is stored in

liver and skeletal muscle
Lipids
• Diverse class of organic
compounds that include fats, oils,
waxes and steroids
• They are all hydrophobic
• They consist of 1 glycerol (alcohol)

and 3 fatty acids
• A fatty acid is a hydrocarbon chain

with a carboxyl group at one end.
Saturated fatty acids
• Come from animals
• Are solid at room temperature
• When ingested at large

quantities are linked to heart
disease
• Example: butter
• They contain single bonds

between carbon atoms
Unsaturated fatty acids
• Extracted from plants
• Liquid at room temperature
• Good dietary fats
• At least one double bond

between carbon atoms
• Exception: group of tropical

oils (coconut and palm oil) -
saturated - somewhat solid at
rt- unhealthy
Unsaturated fatty acids
• Monounsaturated: one double covalent bond and each of

the two carbons in this bond has only one hydrogen atom
bonded to it.
• A polyunsaturated fatty acid is like a monounsaturated

fatty acid except that there are two or more double
covalent bonds.
Triglycerides
• Fats and oils
Roles of triglycerides
• Energy reserves (storage product)
• Insulation
• Buoyancy (blubber in mammals like whales)
• Metabolic source of water

Desert kangaroo rat
Uses metabolism of food to provide most of the
water it needs
Phospholipids
• Looks like a lipid except one of the fatty acid chains is replaced by a
phosphate group
• The two fatty acid tails of the phospholipid are non polar and
hydrophobic and the phosphate head is hydrophilic
• Amphipathic molecule
• Modified lipids
Phospholipid bilayer
Steroids
• Lipids that do not have the

same general structure as
other lipids.
• Ex. cholesterol, testosterone,

estradiol, estrogen
• (some steroids are hormones,

and therefore lipids have
endocrine functions)

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Biology for IMAT

• Atom in the elemental state:

• Atom in the ground state:

• Then the atom is said to be in

• After that the electrons which

• Isotopes are atoms of one element that vary only in the

• Chemically all isotopes of the same element are identical

• Some isotopes are radioactive (ex. Carbon-14, P-32, S-

• When two atomic nuclei attract the same electrons a

• The atoms in a bond are in a lower energy lever therefore

• Energy must be supplied to break a bond.

• Atoms that have gained or lost electrons

• Anion: an atom that has gained electrons (negative

• Cation: an atom that has lost electrons (positive charge

• For example: NaCl

• Na has 1 electron in the outer shell

• Cl has 7 electrons in the outer shell

• Na gives its one electron to Cl and: Na becomes Na+ and

• When two atoms have the same electronegativity they both

• When the two atoms in a molecule are different (example H-

• The more electronegative

• Hydrophilic= hydro (water) + philic (friend) : substances

• Hydrophobic= hydro (water) + phobic (fear): substances

• Specific heat is the amount of heat a substance must

• This makes water more resistant to changes in

• Large bodies of water such as lakes and oceans are slow

• The positive hydrogen of one molecule is attracted to the

• The latent heat of vaporisation is a measure of the heat

• The energy transferred to water molecules during

• Cooling mechanism, as in sweating or panting in

• Water molecules have very high cohesion - in other words

• This results in high surface tension.

• Ice is less dense than water

• Changes in the density of

• The pH must be kept stable. Even a slight change can be

• Biological systems regulate their pH through the presence

• Most important buffer: bicarbonate ion (HCO-)

• They differ only in spatial

• The mirror images are called

• They consist of three elements: O, H , C

• Three classes of carbohydrates: monosaccharides,

• Glucose, galactose and fructose

• Chemical formula C6H12O6

• glucose + glucose = maltose

• glucose + galactose = lactose

• glucose + fructose = sucrose

• Cellulose: found in plants - makes up plant cell walls

• Starch: found in plants - two forms are amylose and

• Chitin: found in animals - makes up exoskeleton in

• Glycogen: found in animals - “animal starch” - it is stored in

• They are all hydrophobic

• They consist of 1 glycerol (alcohol)

• A fatty acid is a hydrocarbon chain

• Are solid at room temperature

• When ingested at large

• They contain single bonds

• Liquid at room temperature

• Good dietary fats