Biochemistry Summary
Made by Aniek Hofstede
Disclaimer: this summary was made for the exam of 2018-2019, please check whether the chapters
you need to know are the same.
Inhoud
Chapter 1: The foundations of Biochemistry .......................................................................................... 2
Chapter 2: Water ..................................................................................................................................... 4
Chapter 3 (1): Amino acids ...................................................................................................................... 7
Chapter 3 (2): Working with proteins ................................................................................................... 10
Chapter 4: The 3D Structure of Proteins ............................................................................................... 13
Tertiary Structure of Fibrous Proteins ............................................................................................... 15
Chapter 5: Protein Function .................................................................................................................. 18
Chapter 6: Enzymes ............................................................................................................................... 24
Chapter 8: Nucleotides and Nucleic Acids............................................................................................. 28
Secondary structure of RNA .............................................................................................................. 32
Chapter 10: Lipids .................................................................................................................................. 35
Chapter 11 (1): Biological Membranes and Transport .......................................................................... 38
Chapter 11 (2): Transport Across Membranes ...................................................................................... 41
Part II: Bioenergetics and Metabolism .................................................................................................. 44
Chapter 13: Principles of Bioenergetics ................................................................................................ 44
Chapter 14: Glycolysis and Fermentation ............................................................................................. 47
Chapter 16: The Citric Acid Cycle (not done) ........................................................................................ 49
Chapter 17: Oxidation of Fatty Acids .................................................................................................... 50
Chapter 18: Amino Acid Oxidation ........................................................................................................ 51
Chapter 19: Oxidative Phosphorilation and Photophosphorylation (not done) ................................... 52
Chapter 24: Genes and Chromosomes.................................................................................................. 53
Chapter 25: DNA Metabolism ............................................................................................................... 55
Chapter 26: RNA metabolism ................................................................................................................ 58
Chapter 27: Protein Metabolism (plaatjes) ........................................................................................... 61
1
,Chapter 1: The foundations of Biochemistry
Cells have cell organelles. Endoplasmatic reticulum and Golgi complexes play a role in synthesis and
processing of lipids and membrane proteins. Peroxisomes is the place where very long-chain fatty
acids are oxidized. Lysosomes degrade unneeded cellular debris
Cell organelles can be separated by differential centrifugation. This is because larger particles
sediment more rapidly than small particles, and soluble material doesn’t sediment. This is why you
should choose the centrifugal speed carefully.
Metabolome: the entire collection of small molecules in a given cell under specific conditions
Metabolomics is the systematic characterization of the metabolome under very specific conditions
Macromolecules: mostly polymers with more than 5000 atoms. Shorter ones are oligomers.
The sum of all proteins is the cell’s proteome, proteomics is the systematic characterization of this
protein complement under specific conditions.
Genome: entire DNA of a cell (genomics)
Glycome: cell’s entire complement of carbohydrate containing molecules.
Lipidome: lipid containing molecules
Proteins and nucleic acids are linear polymers of simple monometric subunits, their sequences
contain information that gives each molecule their 3D structure and functions.
Isomers
Stereo isomers: same chemical bonds, different configuration
Cis-trans isomers
Enantiomers: stereoisomers that are mirror images (chiral center is asymmetric carbon), pairs of
stereo isomers that are no mirror images are called diastereomers.
Thermodynamics
ΔG=ΔH-TΔS ΔG: changes in free-energy content during chemical reactions
ΔH: change in enthalpy (number and kind of bonds)
T: absolute temperature
ΔS: change in entropy (disorder)
ΔG>0 endergonic reaction (unfavorable)
ΔG<0 exergonic reaction (spontaneous)
The cell maintains its ‘order’ by coupling endergonic and exergonic reactions together.
Entropy: randomness/disorder of the components of a chemical system. Life requires continual
maintenance of order to prevent nature’s tendency to increase disorder, to maintain order you have
to put in energy. Living organisms are highly ordered, thus with low entropy!
Chemical reactions proceed spontaneous until the equilibrium constant (Keq) is reached. The rate of
product formation is equal to the rate of the amount that is converted, no net change in
concentration of reactants and products.
2
,The Keq is connected to the free-energy change ΔG⁰
Most cellular reactions only proceed at useful rates because enzymes are present to catalyze them.
They lower the activation energy, ΔGⱡ, by stabilizing the transition state.
Catabolism, anabolism and metabolism.
A cell consists of cell organelles, these are small parts in the cells which have their own function to
help maintain the cell. Here are some of the cell organelles with its function:
• Plasma membrane: this defines the periphery of the cell, separating the contents from the
surroundings. It is composed of lipid and protein molecules that form a thin, tough,
hydrophobic barrier around the cell.
• Endoplasmic reticulum (rough): plays a central role in the synthesis and processing of
proteins.
• Endoplasmic reticulum (smooth): plays a central role in the synthesis and processing of lipids
and drug metabolism.
• Golgi complex: this processes, packages and targets proteins to other organelles or for
export.
• Lysosomes: these are filled with digestive enzymes to degrade unneeded cellular debris.
• Peroxisomes: in these, very long-chain fatty acids are oxidized.
Organelles can be separated using differential diffusion. This is done by first homogenizing a tissue
to break cells and disperse their contents in an aqueous buffer. The large and the small particles in
the suspension can be separated by centrifugation at different speeds. Larger particles sediment
more rapidly than smaller particles. By careful choice of the conditions of centrifugation, subcellular
fractions can be separated for biochemical characterization.
3
, Chapter 2: Water
The most common hydrogen bond donating and accepting
groups are O-H and H-N. If the hydrogen bond is in the
same direction as the molecule it is strong, if it makes a
turn it is weaker.
Water and reactions
Water dissolves salts by hydrating and stabilizing the Na+ and Cl- ions, weakening the electrostatic
interactions between them and thus counteracting their tendency to associate in a crystalline lattice.
Water replaces the solute-solute hydrogen bonds linking the biomolecules to each other with solute-
water hydrogen bonds, thus screening the electrostatic interactions between the ions. Water is
effective in screening the interactions between dissolved ions because it has a high dielectric
constant, a property that shows the number of dipoles in a solvent.
As a salt dissolves, the ions acquire a greater freedom of motion. This is an increase in
entropy (randomness) thus this reaction is favorable, this is partly why they dissolve so easily.
Important gasses like CO2 and O2 are nonpolar. The movement of molecules from the
disordered gas phase into the aqua solution restricts their motion and the motion of the water
molecules and is therefore a decrease in entropy -> not favorable, so poorly soluble in water. For
transport in an organism they have for example hemoglobin. NH3, NO and H2S are also important
but are polar so dissolve pretty good.
Benzene and hexane also are not soluble. They interfere with the hydrogen bonding among
water molecules and do not compensate for it.
All molecules or ions in aquatic solutions interfere with the hydrogen bonds of water, but
polar/charged solutes compensate for lost water-water hydrogen bonds by forming new solute-
water bonds. Hydrophobic solutes do not offer such a compensation, their addition to water may
therefore result in a small gain of enthalpy; the breaking of hydrogen bonds between water
molecules takes up energy from the system, requiring the input of energy from the surrounding (a lot
of energy is needed for this reaction -> energetic unfavorable). Adding nonpolar compounds to water
also produces a measurable decrease in entropy.
An amphipathic compound contains regions that are polar and regions that are nonpolar. Part of it is
hydrophobic and part hydrophilic. Therefore are they able to create micelles (e.g. lipids).
The forces that holds the nonpolar regions together is sometimes referred to as hydrophobic
interactions, although the strength of the force is not caused by any attractions between them.
The entropy increases when a substrate binds to an enzyme -> favorable
4
Made by Aniek Hofstede
Disclaimer: this summary was made for the exam of 2018-2019, please check whether the chapters
you need to know are the same.
Inhoud
Chapter 1: The foundations of Biochemistry .......................................................................................... 2
Chapter 2: Water ..................................................................................................................................... 4
Chapter 3 (1): Amino acids ...................................................................................................................... 7
Chapter 3 (2): Working with proteins ................................................................................................... 10
Chapter 4: The 3D Structure of Proteins ............................................................................................... 13
Tertiary Structure of Fibrous Proteins ............................................................................................... 15
Chapter 5: Protein Function .................................................................................................................. 18
Chapter 6: Enzymes ............................................................................................................................... 24
Chapter 8: Nucleotides and Nucleic Acids............................................................................................. 28
Secondary structure of RNA .............................................................................................................. 32
Chapter 10: Lipids .................................................................................................................................. 35
Chapter 11 (1): Biological Membranes and Transport .......................................................................... 38
Chapter 11 (2): Transport Across Membranes ...................................................................................... 41
Part II: Bioenergetics and Metabolism .................................................................................................. 44
Chapter 13: Principles of Bioenergetics ................................................................................................ 44
Chapter 14: Glycolysis and Fermentation ............................................................................................. 47
Chapter 16: The Citric Acid Cycle (not done) ........................................................................................ 49
Chapter 17: Oxidation of Fatty Acids .................................................................................................... 50
Chapter 18: Amino Acid Oxidation ........................................................................................................ 51
Chapter 19: Oxidative Phosphorilation and Photophosphorylation (not done) ................................... 52
Chapter 24: Genes and Chromosomes.................................................................................................. 53
Chapter 25: DNA Metabolism ............................................................................................................... 55
Chapter 26: RNA metabolism ................................................................................................................ 58
Chapter 27: Protein Metabolism (plaatjes) ........................................................................................... 61
1
,Chapter 1: The foundations of Biochemistry
Cells have cell organelles. Endoplasmatic reticulum and Golgi complexes play a role in synthesis and
processing of lipids and membrane proteins. Peroxisomes is the place where very long-chain fatty
acids are oxidized. Lysosomes degrade unneeded cellular debris
Cell organelles can be separated by differential centrifugation. This is because larger particles
sediment more rapidly than small particles, and soluble material doesn’t sediment. This is why you
should choose the centrifugal speed carefully.
Metabolome: the entire collection of small molecules in a given cell under specific conditions
Metabolomics is the systematic characterization of the metabolome under very specific conditions
Macromolecules: mostly polymers with more than 5000 atoms. Shorter ones are oligomers.
The sum of all proteins is the cell’s proteome, proteomics is the systematic characterization of this
protein complement under specific conditions.
Genome: entire DNA of a cell (genomics)
Glycome: cell’s entire complement of carbohydrate containing molecules.
Lipidome: lipid containing molecules
Proteins and nucleic acids are linear polymers of simple monometric subunits, their sequences
contain information that gives each molecule their 3D structure and functions.
Isomers
Stereo isomers: same chemical bonds, different configuration
Cis-trans isomers
Enantiomers: stereoisomers that are mirror images (chiral center is asymmetric carbon), pairs of
stereo isomers that are no mirror images are called diastereomers.
Thermodynamics
ΔG=ΔH-TΔS ΔG: changes in free-energy content during chemical reactions
ΔH: change in enthalpy (number and kind of bonds)
T: absolute temperature
ΔS: change in entropy (disorder)
ΔG>0 endergonic reaction (unfavorable)
ΔG<0 exergonic reaction (spontaneous)
The cell maintains its ‘order’ by coupling endergonic and exergonic reactions together.
Entropy: randomness/disorder of the components of a chemical system. Life requires continual
maintenance of order to prevent nature’s tendency to increase disorder, to maintain order you have
to put in energy. Living organisms are highly ordered, thus with low entropy!
Chemical reactions proceed spontaneous until the equilibrium constant (Keq) is reached. The rate of
product formation is equal to the rate of the amount that is converted, no net change in
concentration of reactants and products.
2
,The Keq is connected to the free-energy change ΔG⁰
Most cellular reactions only proceed at useful rates because enzymes are present to catalyze them.
They lower the activation energy, ΔGⱡ, by stabilizing the transition state.
Catabolism, anabolism and metabolism.
A cell consists of cell organelles, these are small parts in the cells which have their own function to
help maintain the cell. Here are some of the cell organelles with its function:
• Plasma membrane: this defines the periphery of the cell, separating the contents from the
surroundings. It is composed of lipid and protein molecules that form a thin, tough,
hydrophobic barrier around the cell.
• Endoplasmic reticulum (rough): plays a central role in the synthesis and processing of
proteins.
• Endoplasmic reticulum (smooth): plays a central role in the synthesis and processing of lipids
and drug metabolism.
• Golgi complex: this processes, packages and targets proteins to other organelles or for
export.
• Lysosomes: these are filled with digestive enzymes to degrade unneeded cellular debris.
• Peroxisomes: in these, very long-chain fatty acids are oxidized.
Organelles can be separated using differential diffusion. This is done by first homogenizing a tissue
to break cells and disperse their contents in an aqueous buffer. The large and the small particles in
the suspension can be separated by centrifugation at different speeds. Larger particles sediment
more rapidly than smaller particles. By careful choice of the conditions of centrifugation, subcellular
fractions can be separated for biochemical characterization.
3
, Chapter 2: Water
The most common hydrogen bond donating and accepting
groups are O-H and H-N. If the hydrogen bond is in the
same direction as the molecule it is strong, if it makes a
turn it is weaker.
Water and reactions
Water dissolves salts by hydrating and stabilizing the Na+ and Cl- ions, weakening the electrostatic
interactions between them and thus counteracting their tendency to associate in a crystalline lattice.
Water replaces the solute-solute hydrogen bonds linking the biomolecules to each other with solute-
water hydrogen bonds, thus screening the electrostatic interactions between the ions. Water is
effective in screening the interactions between dissolved ions because it has a high dielectric
constant, a property that shows the number of dipoles in a solvent.
As a salt dissolves, the ions acquire a greater freedom of motion. This is an increase in
entropy (randomness) thus this reaction is favorable, this is partly why they dissolve so easily.
Important gasses like CO2 and O2 are nonpolar. The movement of molecules from the
disordered gas phase into the aqua solution restricts their motion and the motion of the water
molecules and is therefore a decrease in entropy -> not favorable, so poorly soluble in water. For
transport in an organism they have for example hemoglobin. NH3, NO and H2S are also important
but are polar so dissolve pretty good.
Benzene and hexane also are not soluble. They interfere with the hydrogen bonding among
water molecules and do not compensate for it.
All molecules or ions in aquatic solutions interfere with the hydrogen bonds of water, but
polar/charged solutes compensate for lost water-water hydrogen bonds by forming new solute-
water bonds. Hydrophobic solutes do not offer such a compensation, their addition to water may
therefore result in a small gain of enthalpy; the breaking of hydrogen bonds between water
molecules takes up energy from the system, requiring the input of energy from the surrounding (a lot
of energy is needed for this reaction -> energetic unfavorable). Adding nonpolar compounds to water
also produces a measurable decrease in entropy.
An amphipathic compound contains regions that are polar and regions that are nonpolar. Part of it is
hydrophobic and part hydrophilic. Therefore are they able to create micelles (e.g. lipids).
The forces that holds the nonpolar regions together is sometimes referred to as hydrophobic
interactions, although the strength of the force is not caused by any attractions between them.
The entropy increases when a substrate binds to an enzyme -> favorable
4
