Inhoudsopgave:
College 1: chemical evolution 2
College 2: DNA structure and replication 4
College 3: DNA transcription 8
College 4: Life of a protein (1) 12
College 5: Life of a protein (2) 16
College 6: Structure and function 17
College 7: Cell cell communication 21
College 8: DNA variation in individuals 23
College 9: DNA variation in populations 24
Pagina 1 van 24
,College 1: Chemical evolution
What is life?
• Aristotle: life is something that grows and maintains itself and reproduces
• Erwin Schrödinger: self assembling system that fights nature’s tendency toward chaos
• Gerard Joyce: life is a self-sustaining system capable of Darwinian evolution (NASA adopted
this definition)
General characteristics organisms —> fundamental systems:
1. Metabolism coupled to energy produciton
2. Production of biocatalysts based on genetic information (blueprint)
3. System for duplication of genetic information (High Fidelity)
Science = system to explain and predict phenomena
In order to predict, we use a empirical cycle of:
observation/measurement/reasoning —> theory —> prediction
Where do I come from? several theories:
1. Biological evolution
1. Charles Darwin: on the origin of species (1859)
2. all forms of life originated from common ancestors by natural selection
3. ‘survival of the fittest’ (implies variation)
2. Biogenesis
1. Louis Pasteur (1822-1895)
2. Life evolves from another life (each life comes out of an egg)
3. Abiogenesis = the generation of life from lifeless matter
1. First there was no life, so somewhere life must have come from
2. How did the first life originate?
3. What did it look like?
Big Bang
• Time = 0, infinitely high temperature, density
• It takes 300,000 years to form first atomic nuceli (H, He)
• After 1,000,000 years: formation of stars, ….
We need water, because you can make dissolved stuff with water; medium to let a biological and
chemical reaction happen.
Reducing atmosphere = atmosphere consisting of hydrogen, methane and carbon-dioxide
Oparin-Haldane hypothesis (1920s):
Aleksandr Oparin (USSR, 1924):
In a reducing atmosphere, and the presence of a proper energy source (UV light or electrical
discharges), a wide variety of small organic molecules would arise.
John Haldane (VS, 1929):
Primordial Soup functioned as a huge organic chemistry lab, driven by solar power.
Creating a primordial soup and tested what was in it after some time. A lot of amino acids were
found in the primordial soup, which are essential building blocks for life.
Enzymes (proteins) are essential in biochemistry:
Pagina 2 van 24
, Biochemical ((bio)organic) reactions do not or very slowly proceed in the absence of catalysts.
How to solve? we need a molecule that:
◦ Is an information carrier
◦ Is a product
◦ Can replicate itself
◦ Can be easily made
◦ Gives rise to variation
—> Ribonucleic acids (RNA) are such molecules
Purine: A, G
Pyrimidine: T, C, U
rRNA: essential part of the ribosomes, responsible for protein synthesis in the cell.
Ribosome = 2/3 RNA + 1/3 protein
Ribozyme can stick to a RNA message and cut it into smaller and cleaved RNA messages.
Can we make RNA molecules from the early eart building blocks, can we form them spontaneously?
• From small organic molecules
• Warmth
• UV radiation
• Glycoaldehyde (40 C + 1 day)
RNA —> sugar, phosphate, base
RNA building blocks —> RNA polymers —> self-making systems
Compartimentalisation:
• Make independent units —> individuals
• Lipids —> plasma membranes
• Transport mechanisms
—> Important because different compartiments can "meet" each other.
Many hiastuses & problems in RNA world hypothesis:
• Small molecules must be added in a certain order, because otherwise you get tarmac
catastrophe.
• Low concentrations —> processes proceed very slowly, because with a low concentration
there is a larger distance between molecules which makes the proces go very slowly.
Iron-Suphur theory —> we had some mineral (Iron & sulphur atoms), which led to the formation
energy via redox chemistry. This energy enables the formation of organic molecules
(macromolecules) out of inorganic material. —> Formation of macromolecules requires energy,
which iron and sulphur can produce.
Catalytic surface:
• Local higher concentrations of reactants
• Molecules alligned for reactions —> higher chance of succes
Problem: Origin of homochirality
• Two important building blocks in biochemistry (surgars and amino acids) are chiral
(asymmetrical). Achiral objects have a plain of symmetry. Assymetry: image is not the same
as the mirror image.
Urey-Miller Experiment (1953):
DNA —> transcription (DNA-polymerase) —> mRNA —> translation (ribosome) —> proteins
Pagina 3 van 24
College 1: chemical evolution 2
College 2: DNA structure and replication 4
College 3: DNA transcription 8
College 4: Life of a protein (1) 12
College 5: Life of a protein (2) 16
College 6: Structure and function 17
College 7: Cell cell communication 21
College 8: DNA variation in individuals 23
College 9: DNA variation in populations 24
Pagina 1 van 24
,College 1: Chemical evolution
What is life?
• Aristotle: life is something that grows and maintains itself and reproduces
• Erwin Schrödinger: self assembling system that fights nature’s tendency toward chaos
• Gerard Joyce: life is a self-sustaining system capable of Darwinian evolution (NASA adopted
this definition)
General characteristics organisms —> fundamental systems:
1. Metabolism coupled to energy produciton
2. Production of biocatalysts based on genetic information (blueprint)
3. System for duplication of genetic information (High Fidelity)
Science = system to explain and predict phenomena
In order to predict, we use a empirical cycle of:
observation/measurement/reasoning —> theory —> prediction
Where do I come from? several theories:
1. Biological evolution
1. Charles Darwin: on the origin of species (1859)
2. all forms of life originated from common ancestors by natural selection
3. ‘survival of the fittest’ (implies variation)
2. Biogenesis
1. Louis Pasteur (1822-1895)
2. Life evolves from another life (each life comes out of an egg)
3. Abiogenesis = the generation of life from lifeless matter
1. First there was no life, so somewhere life must have come from
2. How did the first life originate?
3. What did it look like?
Big Bang
• Time = 0, infinitely high temperature, density
• It takes 300,000 years to form first atomic nuceli (H, He)
• After 1,000,000 years: formation of stars, ….
We need water, because you can make dissolved stuff with water; medium to let a biological and
chemical reaction happen.
Reducing atmosphere = atmosphere consisting of hydrogen, methane and carbon-dioxide
Oparin-Haldane hypothesis (1920s):
Aleksandr Oparin (USSR, 1924):
In a reducing atmosphere, and the presence of a proper energy source (UV light or electrical
discharges), a wide variety of small organic molecules would arise.
John Haldane (VS, 1929):
Primordial Soup functioned as a huge organic chemistry lab, driven by solar power.
Creating a primordial soup and tested what was in it after some time. A lot of amino acids were
found in the primordial soup, which are essential building blocks for life.
Enzymes (proteins) are essential in biochemistry:
Pagina 2 van 24
, Biochemical ((bio)organic) reactions do not or very slowly proceed in the absence of catalysts.
How to solve? we need a molecule that:
◦ Is an information carrier
◦ Is a product
◦ Can replicate itself
◦ Can be easily made
◦ Gives rise to variation
—> Ribonucleic acids (RNA) are such molecules
Purine: A, G
Pyrimidine: T, C, U
rRNA: essential part of the ribosomes, responsible for protein synthesis in the cell.
Ribosome = 2/3 RNA + 1/3 protein
Ribozyme can stick to a RNA message and cut it into smaller and cleaved RNA messages.
Can we make RNA molecules from the early eart building blocks, can we form them spontaneously?
• From small organic molecules
• Warmth
• UV radiation
• Glycoaldehyde (40 C + 1 day)
RNA —> sugar, phosphate, base
RNA building blocks —> RNA polymers —> self-making systems
Compartimentalisation:
• Make independent units —> individuals
• Lipids —> plasma membranes
• Transport mechanisms
—> Important because different compartiments can "meet" each other.
Many hiastuses & problems in RNA world hypothesis:
• Small molecules must be added in a certain order, because otherwise you get tarmac
catastrophe.
• Low concentrations —> processes proceed very slowly, because with a low concentration
there is a larger distance between molecules which makes the proces go very slowly.
Iron-Suphur theory —> we had some mineral (Iron & sulphur atoms), which led to the formation
energy via redox chemistry. This energy enables the formation of organic molecules
(macromolecules) out of inorganic material. —> Formation of macromolecules requires energy,
which iron and sulphur can produce.
Catalytic surface:
• Local higher concentrations of reactants
• Molecules alligned for reactions —> higher chance of succes
Problem: Origin of homochirality
• Two important building blocks in biochemistry (surgars and amino acids) are chiral
(asymmetrical). Achiral objects have a plain of symmetry. Assymetry: image is not the same
as the mirror image.
Urey-Miller Experiment (1953):
DNA —> transcription (DNA-polymerase) —> mRNA —> translation (ribosome) —> proteins
Pagina 3 van 24
