Basic cell and molecular biology
Lecture 1 – 23/09/2024
The cell’s selection of catalysts (components that make a reaction faster)
that collaborate to reproduce the entire collection before a cell divide
Cell makes genetic information, uses that to make proteins and nucleate
acids
Fertilized eggs do not look so different, but the outcome is entirely
different (because of the genetic program of the egg cells).
Most processes in a cell work similar in all organisms = unity of
biochemistry
All cells are enclosed in a plasma membrane. Phospholipids form bilayers
so they can separate between hydrophilic and hydrophobic elements. This
makes it possible to have an ‘inside’ and ‘outside’.
Sugar group, base and phosphate together form a nucleotide. DNA strand
consists of a series of nucleotides and DNA is a double-strand molecule of
which both sides are complementary.
The central dogma is the flow of genetic information
Often DNA to RNA to protein but it can be the other way around (via
reverse-transcriptase RNA transcribes to a DNA molecule)
Mutation of a gene can give two different types of a gene and give two
(still homologous) types for different species, but they are called
orthologs.
If the divergence happens after conception, it is called paralogs.
Isolation of ribosomes realized that the more RNA on the ribosomes differ
from each other, the further apart they are genetically and evolutionary.
Energy is needed to start life. It is likely that the first life was originated by
hydrothermal vents on the sea floor that were not volcanic driven, were
there were temperatures that could provide life.
LUCA = last universal common ancestor
The cell that we all derive from.
Recent analysis puts the start of life way further back than wat was
thought before (4.2 billion years ago).
Bacteria and archaea are by far the most common forms of lite, they are
single-cellular but can be shaped differently. They do not have organelles,
but they do organize their genetic information in a particular way.
,Eukaryotic cells are a lot more complex
Mitochondria probably evolved from bacteria by symbiosis
Bacteria and archaea are in proximity, and they have endosymbiosis,
eventually forming of new cellular compartments.
Asgard archaeaon were found to have a cell body but also ectosymbionts
and cell protrusions.
Chloroplasts also originated by the endosymbiosis of a certain cell
Generally, the genomes of eukaryotes are larger than the ones of
prokaryotes, but size of genome does not necessarily say anything of
complexity.
Many eukaryotes are not multi-cellular but live as solitary cells.
Model organisms
Viruses (bacteriophage) always must insert their genetic material into
a cell to pass it on (they cannot reproduce)
E. coli is often used as a model organism. There is a lot of knowledge
about it.
Another model organism is bakers’ yeast (saccharomyces cerevisiae)
It is important for the model to be cheap to grow, not harmful for humans
and have a small but strong genome
Sequencing of viruses has enabled us to quickly form a vaccine against
new variants of for example covid.
, Lecture 2 – 24/09/2024
The main elements in a cell are H, C, N and O (99%) the rest consists of
elements of salt and a very small number of irons and coppers.
the elements occurring in cells are lightweight
Processes cost or deliver energy, but not every process costs the same
amount of energy. Noncovalent bonds take less energy to break in water
than covalent bonds.
A covalent bond is a bond where two ions share electrons. An ionic
bond is a bond where the electron is transferred from one ion to another.
Noncovalent bonds
A polar bond in water causes the atoms to have a little bit of a
charge (asymmetrically distributed). The slightly positive H-atom attracts
the slightly negative O-atom. These hydrogen bonds are not that strong,
so they don’t share an electron.
Van der Waals interaction is when two atoms get close. Atoms
are always in motion, the moment they get close they start to interact a
little bit with each other. This is a very weak force, but the strength is in
numbers.
Hydrophobic interactions are when the atoms repulse from water
because the atoms stick together rather than dissolving in water.
Electrostatic interactions is either an ionic bond or an interaction
between charged groups. Outside of water these interactions are very
strong but in water their strength can decrease.
Organic molecules are carbon compounds made by cells
Inorganic molecules are not made by cells, for example water
The four families of small organic molecules
1. A sugar
2. An amino acid
3. A fatty acid
4. A nucleotide
Condensation reactions (where proteins are made) are energetically
unfavorable but a hydrolysis reaction (where proteins are broken up) is
energetically favorable.
Noncovalent bonds specify the precise shape of a macromolecule and its
binding to the other molecules. A stable folded conformation can
become an unstructured polymer chain by disrupting noncovalent bonds
(for example by heating it).
Polymer of amino acids linked by peptide bonds
Lecture 1 – 23/09/2024
The cell’s selection of catalysts (components that make a reaction faster)
that collaborate to reproduce the entire collection before a cell divide
Cell makes genetic information, uses that to make proteins and nucleate
acids
Fertilized eggs do not look so different, but the outcome is entirely
different (because of the genetic program of the egg cells).
Most processes in a cell work similar in all organisms = unity of
biochemistry
All cells are enclosed in a plasma membrane. Phospholipids form bilayers
so they can separate between hydrophilic and hydrophobic elements. This
makes it possible to have an ‘inside’ and ‘outside’.
Sugar group, base and phosphate together form a nucleotide. DNA strand
consists of a series of nucleotides and DNA is a double-strand molecule of
which both sides are complementary.
The central dogma is the flow of genetic information
Often DNA to RNA to protein but it can be the other way around (via
reverse-transcriptase RNA transcribes to a DNA molecule)
Mutation of a gene can give two different types of a gene and give two
(still homologous) types for different species, but they are called
orthologs.
If the divergence happens after conception, it is called paralogs.
Isolation of ribosomes realized that the more RNA on the ribosomes differ
from each other, the further apart they are genetically and evolutionary.
Energy is needed to start life. It is likely that the first life was originated by
hydrothermal vents on the sea floor that were not volcanic driven, were
there were temperatures that could provide life.
LUCA = last universal common ancestor
The cell that we all derive from.
Recent analysis puts the start of life way further back than wat was
thought before (4.2 billion years ago).
Bacteria and archaea are by far the most common forms of lite, they are
single-cellular but can be shaped differently. They do not have organelles,
but they do organize their genetic information in a particular way.
,Eukaryotic cells are a lot more complex
Mitochondria probably evolved from bacteria by symbiosis
Bacteria and archaea are in proximity, and they have endosymbiosis,
eventually forming of new cellular compartments.
Asgard archaeaon were found to have a cell body but also ectosymbionts
and cell protrusions.
Chloroplasts also originated by the endosymbiosis of a certain cell
Generally, the genomes of eukaryotes are larger than the ones of
prokaryotes, but size of genome does not necessarily say anything of
complexity.
Many eukaryotes are not multi-cellular but live as solitary cells.
Model organisms
Viruses (bacteriophage) always must insert their genetic material into
a cell to pass it on (they cannot reproduce)
E. coli is often used as a model organism. There is a lot of knowledge
about it.
Another model organism is bakers’ yeast (saccharomyces cerevisiae)
It is important for the model to be cheap to grow, not harmful for humans
and have a small but strong genome
Sequencing of viruses has enabled us to quickly form a vaccine against
new variants of for example covid.
, Lecture 2 – 24/09/2024
The main elements in a cell are H, C, N and O (99%) the rest consists of
elements of salt and a very small number of irons and coppers.
the elements occurring in cells are lightweight
Processes cost or deliver energy, but not every process costs the same
amount of energy. Noncovalent bonds take less energy to break in water
than covalent bonds.
A covalent bond is a bond where two ions share electrons. An ionic
bond is a bond where the electron is transferred from one ion to another.
Noncovalent bonds
A polar bond in water causes the atoms to have a little bit of a
charge (asymmetrically distributed). The slightly positive H-atom attracts
the slightly negative O-atom. These hydrogen bonds are not that strong,
so they don’t share an electron.
Van der Waals interaction is when two atoms get close. Atoms
are always in motion, the moment they get close they start to interact a
little bit with each other. This is a very weak force, but the strength is in
numbers.
Hydrophobic interactions are when the atoms repulse from water
because the atoms stick together rather than dissolving in water.
Electrostatic interactions is either an ionic bond or an interaction
between charged groups. Outside of water these interactions are very
strong but in water their strength can decrease.
Organic molecules are carbon compounds made by cells
Inorganic molecules are not made by cells, for example water
The four families of small organic molecules
1. A sugar
2. An amino acid
3. A fatty acid
4. A nucleotide
Condensation reactions (where proteins are made) are energetically
unfavorable but a hydrolysis reaction (where proteins are broken up) is
energetically favorable.
Noncovalent bonds specify the precise shape of a macromolecule and its
binding to the other molecules. A stable folded conformation can
become an unstructured polymer chain by disrupting noncovalent bonds
(for example by heating it).
Polymer of amino acids linked by peptide bonds
