Introductory Biochemistry BCH2601 Examination notes ⇌
Learning unit 1- Water, polarity, and pH
Electronegativity- measure of the tendency of an atom to attract electrons to it in a
chemical bond
Polar bonds- bonds in which two atoms have an unequal share in the bonding electrons
Nonpolar- refers to a bond in which two atoms share electrons evenly
Dipoles- molecules with positive and negative ends due to an uneven distribution of
electrons in bonds
Hydrophobic- tending not to dissolve in water
Hydrophobic interactions or bonds- attractions between molecules that are nonpolar
Amphipathic- refers to a molecule that has one end with a polar, water-soluble group and
another end with a nonpolar hydrocarbon group that is insoluble in water
Chemical structure of water
H2O molecule has a bent geometry with oxygen covalently attached to two hydrogens,
with a 104.3° angle between the hydrogens. The oxygen atom is highly electronegative
resulting in a net negative charge on the oxygen atom and a positive charge on each
hydrogen atom. Due to the asymmetrical geometry and uneven distribution of charge
between the atoms, one side of the water molecule has a slightly positive charge, and
the other side has a slightly negative charge- Polar molecules displaying dipole
moment.
Water is a polar solvent and will readily dissolve polar and ionic substances. The
charged ion interacts with the opposite partial charge on the water molecule in ionic
compounds- ion–dipole interaction. When water dissolves other polar molecules the partial
charge of one molecule will interact with the opposite partial charge of the other molecule,
forming a dipole–dipole interaction. Substances that easily dissolve in water are
hydrophilic. Nonpolar compounds cannot form ion–dipole and dipole–dipole
interactions and are insoluble in water- hydrophobic.
Hydrophilic Hydrophobic
Polar covalent compounds (e.g., alcohols Nonpolar covalent compounds (e.g.,
such as C2H5OH [ethanol] and ketones hydrocarbons such as C6H+4 [hexane])
such as (CH3)2C"O [acetone])
Amino acids, phosphate esters Fatty acids, cholesterol
Ionic compounds (e.g., KCl)
Sugars
Water molecules form hydrogen bonds with one another. A hydrogen bond occurs
between a hydrogen covalently bound to a highly electronegative atom, such as
oxygen, fluorine or nitrogen, and an unshared electron pair of electrons on another
highly electronegative atom.
A hydrogen bond is a noncovalent dipole–dipole attraction between two molecules. The
group with the electronegative atom polar covalently bonded to hydrogen (hydrogen
bond donor), and the electronegative atom that contributes the unpaired electrons
(hydrogen bond acceptor)- atom connected with broken lines.
,A single water molecule can form up to four hydrogen bonds. The central water
molecule is accepting two hydrogen bonds and donating two hydrogen bonds. In liquid
form each water molecule forms on average 3.5 hydrogen bonds with its
neighaemoglobinours.
Hydrogen bonds have a vital involvement in stabilizing the three-dimensional structures
of DNA (hydrogen bonds between complementary bases characterise the double-helical
structure of DNA), RNA (Transfer RNA also has a complex three-dimensional structure
,characterized by hydrogen-bonded regions), and proteins (gives rise to the α-helix and β-
pleated sheet conformations), etc.
Properties of water
Properties of water that result from hydrogen bonding
o Surface tension- hydrogen bonds lead to strong cohesive forces between the water
molecules and high surface tension of water.
o Elevated specific heat capacity.
o Elevated specific heat of vaporization.
o Higher density of liquid vs low density of solid water (ice)
o Elevated melting and boiling point.
o Cohesion
o Adhesion
o Hydrogen bonding also plays a role in the behaviour of water as a solvent. If a
polar solute can serve as a donor or an acceptor of hydrogen bonds, not only
can it form hydrogen bonds with water, but it can also be involved in
nonspecific dipole−dipole interactions.
Ice has a lower density than water because the orientation of hydrogen bonds in ice
results in the molecules having more space between them (right), making the ice
expand in size. Solid water (ice) can float on its liquid form (water).
, Hydrogen bonding in water and how this influences the boiling and melting point- a
type of dipole-dipole interaction with permanent partial charges on hydrogen and oxygen
in water, leading to attraction of each other from separate molecules that require more
energy to break the attraction between molecules than a nonpolar compound that has only
weaker dipole-dipole or London dispersion forces making them harder to separate to
enter the gas phase.
List some organic molecules that can form hydrogen bonds with water. Alcohols,
ketones, and amines.
What is the difference between a polar and a nonpolar bond? A polar bond- bonding
electrons are not shared equally due to significantly different electronegativities,
resulting in unequal distribution of charge. In a nonpolar bond- similar electronegativities
of the atoms bonding and the electrons are therefore shared equally between the atoms,
resulting in no unequal distribution of charge.
Explain why hydrogen bonding does not occur between CH4 molecules. There is not a
large difference in electronegativities between carbon and hydrogen, and so the C–H bond
of CH4 will not be polar, as the electrons will be shared nearly equally between the two
atoms. For hydrogen bonding to occur there needs to be a hydrogen covalently bound to a
highly electronegative atom, and an unshared electron pair of electrons that can act at the
hydrogen bond acceptor. CH4 has neither of these characteristics. For hydrogen bonding to
occur there needs to be a polar compound.
Types of bonds
A covalent bond involves the sharing of one or more pairs of electrons between atoms.
Ionic bonds occur when one or more electrons from one atom are removed and
attached to another atom, resulting in positive and negative ions that are
electrostatically attracted to each other. Ionic and covalent bonds are the strongest types
of bonds.
Covalent Ionic
Bond formed between two non-metals with Bond formed by electrostatic force between
similar electronegativities. (oppositely charged ions) a non-metal and a
metal. Non-metals (-ve ion/ anion/
electronegative) are stronger than metals (+ve
ion/ cation/ electropositive) and can take electrons
very easily from metals.
Can be elements, e.g., H-H Only compounds, e.g., NaCl
Share electrons Transfer electrons (metal to non-metal)
Low melting and boiling point Very high melting and boiling point
E.g., Methane (CH4), hydrochloric acid (HCl) E.g., Sodium chloride (NaCl)
Learning unit 1- Water, polarity, and pH
Electronegativity- measure of the tendency of an atom to attract electrons to it in a
chemical bond
Polar bonds- bonds in which two atoms have an unequal share in the bonding electrons
Nonpolar- refers to a bond in which two atoms share electrons evenly
Dipoles- molecules with positive and negative ends due to an uneven distribution of
electrons in bonds
Hydrophobic- tending not to dissolve in water
Hydrophobic interactions or bonds- attractions between molecules that are nonpolar
Amphipathic- refers to a molecule that has one end with a polar, water-soluble group and
another end with a nonpolar hydrocarbon group that is insoluble in water
Chemical structure of water
H2O molecule has a bent geometry with oxygen covalently attached to two hydrogens,
with a 104.3° angle between the hydrogens. The oxygen atom is highly electronegative
resulting in a net negative charge on the oxygen atom and a positive charge on each
hydrogen atom. Due to the asymmetrical geometry and uneven distribution of charge
between the atoms, one side of the water molecule has a slightly positive charge, and
the other side has a slightly negative charge- Polar molecules displaying dipole
moment.
Water is a polar solvent and will readily dissolve polar and ionic substances. The
charged ion interacts with the opposite partial charge on the water molecule in ionic
compounds- ion–dipole interaction. When water dissolves other polar molecules the partial
charge of one molecule will interact with the opposite partial charge of the other molecule,
forming a dipole–dipole interaction. Substances that easily dissolve in water are
hydrophilic. Nonpolar compounds cannot form ion–dipole and dipole–dipole
interactions and are insoluble in water- hydrophobic.
Hydrophilic Hydrophobic
Polar covalent compounds (e.g., alcohols Nonpolar covalent compounds (e.g.,
such as C2H5OH [ethanol] and ketones hydrocarbons such as C6H+4 [hexane])
such as (CH3)2C"O [acetone])
Amino acids, phosphate esters Fatty acids, cholesterol
Ionic compounds (e.g., KCl)
Sugars
Water molecules form hydrogen bonds with one another. A hydrogen bond occurs
between a hydrogen covalently bound to a highly electronegative atom, such as
oxygen, fluorine or nitrogen, and an unshared electron pair of electrons on another
highly electronegative atom.
A hydrogen bond is a noncovalent dipole–dipole attraction between two molecules. The
group with the electronegative atom polar covalently bonded to hydrogen (hydrogen
bond donor), and the electronegative atom that contributes the unpaired electrons
(hydrogen bond acceptor)- atom connected with broken lines.
,A single water molecule can form up to four hydrogen bonds. The central water
molecule is accepting two hydrogen bonds and donating two hydrogen bonds. In liquid
form each water molecule forms on average 3.5 hydrogen bonds with its
neighaemoglobinours.
Hydrogen bonds have a vital involvement in stabilizing the three-dimensional structures
of DNA (hydrogen bonds between complementary bases characterise the double-helical
structure of DNA), RNA (Transfer RNA also has a complex three-dimensional structure
,characterized by hydrogen-bonded regions), and proteins (gives rise to the α-helix and β-
pleated sheet conformations), etc.
Properties of water
Properties of water that result from hydrogen bonding
o Surface tension- hydrogen bonds lead to strong cohesive forces between the water
molecules and high surface tension of water.
o Elevated specific heat capacity.
o Elevated specific heat of vaporization.
o Higher density of liquid vs low density of solid water (ice)
o Elevated melting and boiling point.
o Cohesion
o Adhesion
o Hydrogen bonding also plays a role in the behaviour of water as a solvent. If a
polar solute can serve as a donor or an acceptor of hydrogen bonds, not only
can it form hydrogen bonds with water, but it can also be involved in
nonspecific dipole−dipole interactions.
Ice has a lower density than water because the orientation of hydrogen bonds in ice
results in the molecules having more space between them (right), making the ice
expand in size. Solid water (ice) can float on its liquid form (water).
, Hydrogen bonding in water and how this influences the boiling and melting point- a
type of dipole-dipole interaction with permanent partial charges on hydrogen and oxygen
in water, leading to attraction of each other from separate molecules that require more
energy to break the attraction between molecules than a nonpolar compound that has only
weaker dipole-dipole or London dispersion forces making them harder to separate to
enter the gas phase.
List some organic molecules that can form hydrogen bonds with water. Alcohols,
ketones, and amines.
What is the difference between a polar and a nonpolar bond? A polar bond- bonding
electrons are not shared equally due to significantly different electronegativities,
resulting in unequal distribution of charge. In a nonpolar bond- similar electronegativities
of the atoms bonding and the electrons are therefore shared equally between the atoms,
resulting in no unequal distribution of charge.
Explain why hydrogen bonding does not occur between CH4 molecules. There is not a
large difference in electronegativities between carbon and hydrogen, and so the C–H bond
of CH4 will not be polar, as the electrons will be shared nearly equally between the two
atoms. For hydrogen bonding to occur there needs to be a hydrogen covalently bound to a
highly electronegative atom, and an unshared electron pair of electrons that can act at the
hydrogen bond acceptor. CH4 has neither of these characteristics. For hydrogen bonding to
occur there needs to be a polar compound.
Types of bonds
A covalent bond involves the sharing of one or more pairs of electrons between atoms.
Ionic bonds occur when one or more electrons from one atom are removed and
attached to another atom, resulting in positive and negative ions that are
electrostatically attracted to each other. Ionic and covalent bonds are the strongest types
of bonds.
Covalent Ionic
Bond formed between two non-metals with Bond formed by electrostatic force between
similar electronegativities. (oppositely charged ions) a non-metal and a
metal. Non-metals (-ve ion/ anion/
electronegative) are stronger than metals (+ve
ion/ cation/ electropositive) and can take electrons
very easily from metals.
Can be elements, e.g., H-H Only compounds, e.g., NaCl
Share electrons Transfer electrons (metal to non-metal)
Low melting and boiling point Very high melting and boiling point
E.g., Methane (CH4), hydrochloric acid (HCl) E.g., Sodium chloride (NaCl)
