Biology 124
BIOCHEMISTRY
Life, Chemistry and Water
Atomic structure
- Subatomic particles (neutrons, protons and electrons), energy levels, orbitals,
valence electrons and atomic structure
o Hydrogen: 1 proton in nucleus and 1 electron
o Carbon: 6 protons and 6 neutrons in nucleus with 2 then 4 electrons
- Atoms more stable when outer shell/orbital/valence electrons full of electrons (8)
o More stable configuration = chemical bonds between atoms
Chemical bonds – DNA and proteins
BONDS TYPE OF INTERATION STRENGH
Covalent Sharing of electron pairs
Ionic Attraction of opposite charges
Hydrogen Share H-atom
Van der Waal interaction Weak interaction between non-polar molecules
Ionic chemical bonds (transfer)
- Formed when ions with opposite charges (cations/anions) attract each other
o NaCl, MgCl2
- Valence electrons (outer most electrons/last orbit) are completely transferred to
other atoms (either lost or gained)
o When losing an electron: it becomes a positive ion and proton number is
constant (sodium Na)
o When gaining an electron: it becomes a negative ion and proton number is
constant (chlorine Cl)
o Forms a crystal lattice
Covalent chemical bonds (sharing)
- Formed when 2/more atoms share a valence electron pair (H2, O2, H2O2, CH4)
- Binding capacity is determined by atoms valence
- Strength depends on number of shared electrons
- Bonds indicated by pair of dots/single line
- Two types of bonds:
o Non-polar covalent bond – valence electrons shared equally (H2, O2, N2, CH4)
▪ Symmetrical tetrahedral shape
▪ Angle between atoms (between H and H of methane) is 109,5 degrees
o Polar covalent bonds – valence electrons not shared equally (H20)
▪ Asymmetrical shape
▪ Angle between atoms (between H and H of water) is 104,5 degrees
▪ Water: oxygen is slightly negative, and hydrogen is slightly positive
, Biology 124
• Oxygen more electronegative than hydrogen so valence
electron spends more time closer to oxygen atoms = two poles
- Type of bond between atoms depends on electronegativity
- When there is a triple bond (bonds increasing) it requires more energy to break it
Hydrogen chemical bonds
- Formed when a H atom (covalently bonded to an electronegative O or N atom) is
attracted by another electronegative O or N atom [ONLY]
- Special dipole-dipole interaction with direction
- Hydrogen bonds stabilise the secondary structures of proteins (helix structure)
- Oxygen stronger than hydrogen therefore valence electron of hydrogen spends more
time by oxygen (same with nitrogen) creating slightly negative and positive poles
- 1 water molecule can attract 4 other water molecules
Van der Waals chemical bonds
- Forces is weak attractions between non-polar molecules over short distances
(temporary positive/negative bonds)
- Constant motion of electrons = accumulation (by chance) in one part of molecule
o Leads to zones of positive and negative charge
- E.g. gecko toe, pads on seta and setae on toes
Properties of water with hydrogen bonds
- Water molecule has a strongly polar covalent bond between O (negaitve0 and the
2H (positive) atoms
- Water forms hydrogen bonds with other polar molecules (therefore solvent of life)
o Interaction with other water molecules = lattice
- Manifold property of water is due to the ability to form hydrogen bonds
Ability of water to form hydrogen bonds gives it 5 properties:
COHESION (STICKINESS)
- H20 attaches to any material to which it can form hydrogen bonds
- Cohesion: formation of hydrogen bonds with other water molecules
- Adhesion: formation of hydrogen bonds with other compounds (not H20)
- Biological consequences of cohesion:
o Creation of surface tension by unbalanced hydrogen bonding
o Spider supported by water surface tension
- Biological consequences of cohesion together with adhesion:
o Direction of water movement from roots to leaves – bark contains water
conducting cells and the water conducting cells contain cohesion between
the water molecules (as it is referring to water) and water molecule to bark
contains adhesion (as it is a hydrogen bonding not to water molecules)
TEMPERATURE CONTROL
, Biology 124
- Hydrogen bonds needs a lot of energy to break the bonds and then needs a lot of
energy to evaporate
- High specific heat: amount of energy (heat) which must be absorbed/released to get
a change of 1 degree per 1 g of substance. All hydrogen bonds must break =
increases kinetic energy and breaks free therefore gas. Biological consequences:
o H20 stabilises body temperature and gives resistance to overheating
o Large volumes of water influence climate coastal regions and stabilise ocean
and coastal temperatures
- High heat of vaporisation: amount of energy (heat) which is required to convert 1 g
of fluid water to gas. Biological consequences:
o Body gets rid of heat through evaporation of sweat (H20) from skin surface
o Evaporating H20 during transpiration overcomes overheating of plant tissue
o Evaporation of surface H20 contributes to stabilisation of water temperatures
FROZEN H20 (ICE) FLOATS
- H20 is less dense in solid (hydrogen bond lattice of ice) form than liquid forming a
o Lower density of ice due to formation of stable hydrogen bonds (more rigid
whereas hydrogen bond liquid water lattice moves direction and flows)
o Ice floats so there are more gaps/spaces than liquid and is therefore less
dense (lighter) than water as water has less gaps
- Biological consequences of ice floating:
o Ice insulates fluid water underneath = life existence under frozen surface
CREATES POLAR AND NON-POLAR ENVIRONMENTS
- These environments are critical to organisation of cells
- Liquid water lattice (polar) resists invasion of non-polar molecules (forces of non-
polar associations). Polar: water and non-polar: oil
- Polar/charged molecules cause competing attraction
o Opens a cavity into which polar/charged molecules can move
- Biological consequences:
o Biological membrane arounds cells and organelles are kept intact by water
SERVES AS A SOLVENT
- H20 is a good solvent – forms hydrogen bonds and a hydration layer
- H20 sticks to polar molecules
o Hydrophilic = attraction by water (dissolve in water)
- H20 repels non-polar molecules
o Hydrophobic = repelled by water (not dissolve in water – oil)
- H20 is a good solvent because of its polarity and ability to form hydrogen bonds
(hydration layer)
- Biological consequences:
o Bodily fluids (blood and saliva) contain water with different polar
components (proteins, sugar, DNA and ions) are dissolved – hydrophilic
, Biology 124
▪ Ionic and polar regions on the proteins surface attract H20 molecules
when purple lysozyme is in an aqueous environment
Water ionisation and pH
- Water can dissociate:
o H20 – OH- + H+ (proton)
o [H+] = [OH-] in pure water so [H+] in pure water = 10-7 M (25°C)
▪ [H+] = [OH-] = 10-7 M therefore [H+] [OH-] = 10-14 M
- pH scale describes how acidic or basic (alkaline) a solution is
o pH expressed in terms of [H+] therefore pH = -log[H+]/[H+] = 10-pH
o logarithmic scale of 0-14 (a pH unit = 10-fold different in [H+])
Acids and bases
- Acid: substance which increases the solutions [H+] giving off H+ ions to the solution
and completely ionises
o HCl - H+ + Cl-
o pH values are lower than 7 = acidic
- Base: substance which decreases the solutions [H+] by binding H+ ions to the solution
or releasing OH- ions into the solution and completely dissociates
o NH3 (ammonia) + H+ - NH4+ (ammonium)
o NaOH – Na+ + OH-
o pH values are above 7 = basic
Buffers
- Solution able to resist changes to pH when strong
acid or base is added
- They reduce variability of the [H+] and [OH-] of the
solution (blood) by taking H+ ions out of the
solution (binding them) if there are too many or
giving H+ ions to the solution if there are too few to
prevent fluctuations
- pH stays constant
- E.g. stabilisation of blood pH by carbonic acid
Chemical bonds with C-atoms
- Skeleton of biological molecules consists of C atoms
attached to other C atoms or other atoms (H, N, O and S)
- Tetravalency of C atoms makes diverse structures
o Hydrogen: 1 valence electron
o Oxygen: 2 valence electrons
Functional groups
- It is reactive groups of atoms that are coupled to a C atom framework (backbone)
BIOCHEMISTRY
Life, Chemistry and Water
Atomic structure
- Subatomic particles (neutrons, protons and electrons), energy levels, orbitals,
valence electrons and atomic structure
o Hydrogen: 1 proton in nucleus and 1 electron
o Carbon: 6 protons and 6 neutrons in nucleus with 2 then 4 electrons
- Atoms more stable when outer shell/orbital/valence electrons full of electrons (8)
o More stable configuration = chemical bonds between atoms
Chemical bonds – DNA and proteins
BONDS TYPE OF INTERATION STRENGH
Covalent Sharing of electron pairs
Ionic Attraction of opposite charges
Hydrogen Share H-atom
Van der Waal interaction Weak interaction between non-polar molecules
Ionic chemical bonds (transfer)
- Formed when ions with opposite charges (cations/anions) attract each other
o NaCl, MgCl2
- Valence electrons (outer most electrons/last orbit) are completely transferred to
other atoms (either lost or gained)
o When losing an electron: it becomes a positive ion and proton number is
constant (sodium Na)
o When gaining an electron: it becomes a negative ion and proton number is
constant (chlorine Cl)
o Forms a crystal lattice
Covalent chemical bonds (sharing)
- Formed when 2/more atoms share a valence electron pair (H2, O2, H2O2, CH4)
- Binding capacity is determined by atoms valence
- Strength depends on number of shared electrons
- Bonds indicated by pair of dots/single line
- Two types of bonds:
o Non-polar covalent bond – valence electrons shared equally (H2, O2, N2, CH4)
▪ Symmetrical tetrahedral shape
▪ Angle between atoms (between H and H of methane) is 109,5 degrees
o Polar covalent bonds – valence electrons not shared equally (H20)
▪ Asymmetrical shape
▪ Angle between atoms (between H and H of water) is 104,5 degrees
▪ Water: oxygen is slightly negative, and hydrogen is slightly positive
, Biology 124
• Oxygen more electronegative than hydrogen so valence
electron spends more time closer to oxygen atoms = two poles
- Type of bond between atoms depends on electronegativity
- When there is a triple bond (bonds increasing) it requires more energy to break it
Hydrogen chemical bonds
- Formed when a H atom (covalently bonded to an electronegative O or N atom) is
attracted by another electronegative O or N atom [ONLY]
- Special dipole-dipole interaction with direction
- Hydrogen bonds stabilise the secondary structures of proteins (helix structure)
- Oxygen stronger than hydrogen therefore valence electron of hydrogen spends more
time by oxygen (same with nitrogen) creating slightly negative and positive poles
- 1 water molecule can attract 4 other water molecules
Van der Waals chemical bonds
- Forces is weak attractions between non-polar molecules over short distances
(temporary positive/negative bonds)
- Constant motion of electrons = accumulation (by chance) in one part of molecule
o Leads to zones of positive and negative charge
- E.g. gecko toe, pads on seta and setae on toes
Properties of water with hydrogen bonds
- Water molecule has a strongly polar covalent bond between O (negaitve0 and the
2H (positive) atoms
- Water forms hydrogen bonds with other polar molecules (therefore solvent of life)
o Interaction with other water molecules = lattice
- Manifold property of water is due to the ability to form hydrogen bonds
Ability of water to form hydrogen bonds gives it 5 properties:
COHESION (STICKINESS)
- H20 attaches to any material to which it can form hydrogen bonds
- Cohesion: formation of hydrogen bonds with other water molecules
- Adhesion: formation of hydrogen bonds with other compounds (not H20)
- Biological consequences of cohesion:
o Creation of surface tension by unbalanced hydrogen bonding
o Spider supported by water surface tension
- Biological consequences of cohesion together with adhesion:
o Direction of water movement from roots to leaves – bark contains water
conducting cells and the water conducting cells contain cohesion between
the water molecules (as it is referring to water) and water molecule to bark
contains adhesion (as it is a hydrogen bonding not to water molecules)
TEMPERATURE CONTROL
, Biology 124
- Hydrogen bonds needs a lot of energy to break the bonds and then needs a lot of
energy to evaporate
- High specific heat: amount of energy (heat) which must be absorbed/released to get
a change of 1 degree per 1 g of substance. All hydrogen bonds must break =
increases kinetic energy and breaks free therefore gas. Biological consequences:
o H20 stabilises body temperature and gives resistance to overheating
o Large volumes of water influence climate coastal regions and stabilise ocean
and coastal temperatures
- High heat of vaporisation: amount of energy (heat) which is required to convert 1 g
of fluid water to gas. Biological consequences:
o Body gets rid of heat through evaporation of sweat (H20) from skin surface
o Evaporating H20 during transpiration overcomes overheating of plant tissue
o Evaporation of surface H20 contributes to stabilisation of water temperatures
FROZEN H20 (ICE) FLOATS
- H20 is less dense in solid (hydrogen bond lattice of ice) form than liquid forming a
o Lower density of ice due to formation of stable hydrogen bonds (more rigid
whereas hydrogen bond liquid water lattice moves direction and flows)
o Ice floats so there are more gaps/spaces than liquid and is therefore less
dense (lighter) than water as water has less gaps
- Biological consequences of ice floating:
o Ice insulates fluid water underneath = life existence under frozen surface
CREATES POLAR AND NON-POLAR ENVIRONMENTS
- These environments are critical to organisation of cells
- Liquid water lattice (polar) resists invasion of non-polar molecules (forces of non-
polar associations). Polar: water and non-polar: oil
- Polar/charged molecules cause competing attraction
o Opens a cavity into which polar/charged molecules can move
- Biological consequences:
o Biological membrane arounds cells and organelles are kept intact by water
SERVES AS A SOLVENT
- H20 is a good solvent – forms hydrogen bonds and a hydration layer
- H20 sticks to polar molecules
o Hydrophilic = attraction by water (dissolve in water)
- H20 repels non-polar molecules
o Hydrophobic = repelled by water (not dissolve in water – oil)
- H20 is a good solvent because of its polarity and ability to form hydrogen bonds
(hydration layer)
- Biological consequences:
o Bodily fluids (blood and saliva) contain water with different polar
components (proteins, sugar, DNA and ions) are dissolved – hydrophilic
, Biology 124
▪ Ionic and polar regions on the proteins surface attract H20 molecules
when purple lysozyme is in an aqueous environment
Water ionisation and pH
- Water can dissociate:
o H20 – OH- + H+ (proton)
o [H+] = [OH-] in pure water so [H+] in pure water = 10-7 M (25°C)
▪ [H+] = [OH-] = 10-7 M therefore [H+] [OH-] = 10-14 M
- pH scale describes how acidic or basic (alkaline) a solution is
o pH expressed in terms of [H+] therefore pH = -log[H+]/[H+] = 10-pH
o logarithmic scale of 0-14 (a pH unit = 10-fold different in [H+])
Acids and bases
- Acid: substance which increases the solutions [H+] giving off H+ ions to the solution
and completely ionises
o HCl - H+ + Cl-
o pH values are lower than 7 = acidic
- Base: substance which decreases the solutions [H+] by binding H+ ions to the solution
or releasing OH- ions into the solution and completely dissociates
o NH3 (ammonia) + H+ - NH4+ (ammonium)
o NaOH – Na+ + OH-
o pH values are above 7 = basic
Buffers
- Solution able to resist changes to pH when strong
acid or base is added
- They reduce variability of the [H+] and [OH-] of the
solution (blood) by taking H+ ions out of the
solution (binding them) if there are too many or
giving H+ ions to the solution if there are too few to
prevent fluctuations
- pH stays constant
- E.g. stabilisation of blood pH by carbonic acid
Chemical bonds with C-atoms
- Skeleton of biological molecules consists of C atoms
attached to other C atoms or other atoms (H, N, O and S)
- Tetravalency of C atoms makes diverse structures
o Hydrogen: 1 valence electron
o Oxygen: 2 valence electrons
Functional groups
- It is reactive groups of atoms that are coupled to a C atom framework (backbone)
