Biochemistry
1. The foundations of biochemistry
1.1 Cellular Foundations
Eukaryotic cells contain membrane-enclosed organelles:
• Mitochondria: site of most of the energy-extracting reactions of the cell
• Endoplasmic reticulum & Golgi complexes: play central roles in the synthesis and processing
of lipids and membrane proteins
• Peroxisomes: inhere very long-chain fatty acids are oxidized
• Lysosomes: filled with digestive enzymes to degrade unneeded cellular debris (only animal
cells)
Plant cells contain in addition:
• Vacuoles: store large quantities of organic acids
• Chloroplasts: inhere sunlight drives the synthesis of ATP in the process of photosynthesis
1.3 Physical Foundations
Systems can be:
• Isolated: exchanges neither matter nor energy with its surroundings
• Closed: exchanges energy but not matter with its surroundings
• Open: exchanges both energy and matter with its surroundings (living organisms)
First law of thermodynamics: in any physical or chemical change, the total amount of energy in the
universe remains constant, although the form of the energy may change
Second law of thermodynamics: the total entropy of the universe is continually increasing
∆𝐺 = ∆𝐻 − 𝑇∆𝑆
• ∆𝐺: change in free-energy content during a chemical reaction in J/mol
• ∆𝐻: change in enthalpy (bonds) in J/mol
• ∆𝑆: change in entropy (disorder) J/molK
If ∆𝐺 > 0 the reaction is endergonic (unfavourable), if ∆𝐺 < 0 the reaction is exergonic (spontaneous).
The order in cells is obtained by coupling ender- and exergonic reactions.
If ∆𝐻 > 0 the reaction is endothermic, if ∆𝐻 < 0 the reaction is exothermic.
Living organisms preserve their internal order by taking from the surroundings free energy in the form
of nutrients or sunlight, and returning an equal amount of energy as heat and entropy.
In a reaction of the form 𝑎𝐴 + 𝑏𝐵 → 𝑐𝐶 + 𝑑𝐷 the equilibrium constant is given by:
[𝐶]𝑐𝑒𝑞 ∙[𝐷]𝑑
𝑒𝑞
𝐾𝑒𝑞 =
[𝐴]𝑎 𝑏
𝑒𝑞 ∙[𝐵]𝑒𝑞
In which 𝐾𝑒𝑞 is large when a reaction occurs spontaneously.
1
,2. Water
2.1 Weak Interactions in Aqueous systems
Hydrogen bonds:
• Form between any electronegative hydrogen acceptor and hydrogen bound to any
electronegative hydrogen donor
• Relatively weak (longer than covalent bonds)
• One water molecule can form 3.4 hydrogen bonds when in
liquid form (4 bonds in solid form)
• Strongest when the hydrogen donor and acceptor are in a
straight line
Amphipathic compounds: contain regions that are hydrophilic and regions
that are hydrophobic, these compounds form micelles in water
(hydrophobic interactions are no “real” interactions)
van der Waals interactions: weak interatomic interactions between the
electron clouds of two very close uncharged atoms
Noncovalent interactions are individually weak (continually forming and
breaking) relative to covalent bonds, the cumulative effect of many such
interactions can be very significant.
2.2 Ionization of Water, Weak Acids and Weak Bases
Proton hopping between a series of hydrogen-bonded water molecules results in an extremely rapid
net movement of a proton over a long distance, which results in exceptionally fast acid-base reactions.
The ion product of water (1 x 10-14) is given by:
𝐾𝑤 = [𝐻 + ] ∙ [𝑂𝐻 − ]
The relation between the pH and the H+ concentration of a solution is given by:
𝑝𝐻 = −𝑙𝑜𝑔[𝐻 + ] and [𝐻 + ] = 10−𝑝𝐻
For weak acids and bases the following relations hold:
[𝐻 + ]∙[𝐴− ]
𝐾𝑎 = and 𝑝𝐾𝑎 = −𝑙𝑜𝑔(𝐾𝑎 )
[𝐻𝐴]
• 𝐾𝑎 : acid dissociation constant (for a reaction between a weak acid and its conjugated base)
• 𝑝𝐾𝑎 : the pH at which the reaction results in 50% reactant and 50% product
• The stronger the acid, the higher its 𝐾𝑎 and the lower its 𝑝𝐾𝑎
Titration curve: a plot of the 𝑝𝐻 vs. amount of base (e.g. NaOH) added until the acid is neutralized
2.3 Buffering against pH Changes in Biological Systems
Buffers: consist of a weak acid (the proton donor) and its conjugate base (the proton acceptor), the
buffering region is equal to the 𝑝𝐾𝑎 ± 1
Henderson-Hasselbach equation:
[𝐴− ]
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
[𝐻𝐴]
This equation describes the shape of the titration curve of a weak acid.
2
, 3. Amino Acids, Peptides and Proteins
3.1 amino Acids
Primary structure: amino acid residues and their order
Secondary structure: local structural conformations
Tertiary structure: overall three-dimensional arrangement of all
atoms in a protein (whole polypeptide chain)
Quaternary structure: assembled subunits (multimers)
Amino acids:
• Are stereoisomers; Cα is chiral so they are enantiomers (mirror images) and
optically active
• Living organisms only have the L-convention (no D-convention)
• Notation: full name, 3-letter code or 1-letter code
• Carbon chain can be numbered with numbers or Greek letters
Classification of amino acids based on the side chain at 𝑝𝐻 7:
• Non-polar & aliphatic: hydrophobic
• Aromatic: relatively non-polar and hydrophobic (absorb ultraviolet light)
• Polar & uncharged: relatively hydrophilic and can form hydrogen bonds (2 cysteine residues
can form a covalent hydrophobic disulfide bond)
• Positively charged: hydrophilic
• Negatively charged: hydrophilic
Lambert-Beer Law:
𝐴 =𝜀∙𝑙∙𝑐
• Biomolecules that absorb light at characteristic wavelengths can be detected and identified
and there concentrations can be calculated (280 nm for amino acids)
3
1. The foundations of biochemistry
1.1 Cellular Foundations
Eukaryotic cells contain membrane-enclosed organelles:
• Mitochondria: site of most of the energy-extracting reactions of the cell
• Endoplasmic reticulum & Golgi complexes: play central roles in the synthesis and processing
of lipids and membrane proteins
• Peroxisomes: inhere very long-chain fatty acids are oxidized
• Lysosomes: filled with digestive enzymes to degrade unneeded cellular debris (only animal
cells)
Plant cells contain in addition:
• Vacuoles: store large quantities of organic acids
• Chloroplasts: inhere sunlight drives the synthesis of ATP in the process of photosynthesis
1.3 Physical Foundations
Systems can be:
• Isolated: exchanges neither matter nor energy with its surroundings
• Closed: exchanges energy but not matter with its surroundings
• Open: exchanges both energy and matter with its surroundings (living organisms)
First law of thermodynamics: in any physical or chemical change, the total amount of energy in the
universe remains constant, although the form of the energy may change
Second law of thermodynamics: the total entropy of the universe is continually increasing
∆𝐺 = ∆𝐻 − 𝑇∆𝑆
• ∆𝐺: change in free-energy content during a chemical reaction in J/mol
• ∆𝐻: change in enthalpy (bonds) in J/mol
• ∆𝑆: change in entropy (disorder) J/molK
If ∆𝐺 > 0 the reaction is endergonic (unfavourable), if ∆𝐺 < 0 the reaction is exergonic (spontaneous).
The order in cells is obtained by coupling ender- and exergonic reactions.
If ∆𝐻 > 0 the reaction is endothermic, if ∆𝐻 < 0 the reaction is exothermic.
Living organisms preserve their internal order by taking from the surroundings free energy in the form
of nutrients or sunlight, and returning an equal amount of energy as heat and entropy.
In a reaction of the form 𝑎𝐴 + 𝑏𝐵 → 𝑐𝐶 + 𝑑𝐷 the equilibrium constant is given by:
[𝐶]𝑐𝑒𝑞 ∙[𝐷]𝑑
𝑒𝑞
𝐾𝑒𝑞 =
[𝐴]𝑎 𝑏
𝑒𝑞 ∙[𝐵]𝑒𝑞
In which 𝐾𝑒𝑞 is large when a reaction occurs spontaneously.
1
,2. Water
2.1 Weak Interactions in Aqueous systems
Hydrogen bonds:
• Form between any electronegative hydrogen acceptor and hydrogen bound to any
electronegative hydrogen donor
• Relatively weak (longer than covalent bonds)
• One water molecule can form 3.4 hydrogen bonds when in
liquid form (4 bonds in solid form)
• Strongest when the hydrogen donor and acceptor are in a
straight line
Amphipathic compounds: contain regions that are hydrophilic and regions
that are hydrophobic, these compounds form micelles in water
(hydrophobic interactions are no “real” interactions)
van der Waals interactions: weak interatomic interactions between the
electron clouds of two very close uncharged atoms
Noncovalent interactions are individually weak (continually forming and
breaking) relative to covalent bonds, the cumulative effect of many such
interactions can be very significant.
2.2 Ionization of Water, Weak Acids and Weak Bases
Proton hopping between a series of hydrogen-bonded water molecules results in an extremely rapid
net movement of a proton over a long distance, which results in exceptionally fast acid-base reactions.
The ion product of water (1 x 10-14) is given by:
𝐾𝑤 = [𝐻 + ] ∙ [𝑂𝐻 − ]
The relation between the pH and the H+ concentration of a solution is given by:
𝑝𝐻 = −𝑙𝑜𝑔[𝐻 + ] and [𝐻 + ] = 10−𝑝𝐻
For weak acids and bases the following relations hold:
[𝐻 + ]∙[𝐴− ]
𝐾𝑎 = and 𝑝𝐾𝑎 = −𝑙𝑜𝑔(𝐾𝑎 )
[𝐻𝐴]
• 𝐾𝑎 : acid dissociation constant (for a reaction between a weak acid and its conjugated base)
• 𝑝𝐾𝑎 : the pH at which the reaction results in 50% reactant and 50% product
• The stronger the acid, the higher its 𝐾𝑎 and the lower its 𝑝𝐾𝑎
Titration curve: a plot of the 𝑝𝐻 vs. amount of base (e.g. NaOH) added until the acid is neutralized
2.3 Buffering against pH Changes in Biological Systems
Buffers: consist of a weak acid (the proton donor) and its conjugate base (the proton acceptor), the
buffering region is equal to the 𝑝𝐾𝑎 ± 1
Henderson-Hasselbach equation:
[𝐴− ]
𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔
[𝐻𝐴]
This equation describes the shape of the titration curve of a weak acid.
2
, 3. Amino Acids, Peptides and Proteins
3.1 amino Acids
Primary structure: amino acid residues and their order
Secondary structure: local structural conformations
Tertiary structure: overall three-dimensional arrangement of all
atoms in a protein (whole polypeptide chain)
Quaternary structure: assembled subunits (multimers)
Amino acids:
• Are stereoisomers; Cα is chiral so they are enantiomers (mirror images) and
optically active
• Living organisms only have the L-convention (no D-convention)
• Notation: full name, 3-letter code or 1-letter code
• Carbon chain can be numbered with numbers or Greek letters
Classification of amino acids based on the side chain at 𝑝𝐻 7:
• Non-polar & aliphatic: hydrophobic
• Aromatic: relatively non-polar and hydrophobic (absorb ultraviolet light)
• Polar & uncharged: relatively hydrophilic and can form hydrogen bonds (2 cysteine residues
can form a covalent hydrophobic disulfide bond)
• Positively charged: hydrophilic
• Negatively charged: hydrophilic
Lambert-Beer Law:
𝐴 =𝜀∙𝑙∙𝑐
• Biomolecules that absorb light at characteristic wavelengths can be detected and identified
and there concentrations can be calculated (280 nm for amino acids)
3
