M1
Cells
o Energy source:
- Litotrophic: e from inorganic chemicals
- Phototrophic: e from sunlight
- Organotrophic: e from other cells and organic products
o Prokaryotes
- simple, one component
- cytoplasm with ‘lose’ floating DNA, ribosome etc.
o Eukaryotes
- complex, many membrane-bound compartments (organelles)
nucleus
- genetic information in nucleus
endoplasmatic reticulum
golgi apparatus
lysosome
o Multicellularity
- Cells stay together after cell division
budding off of 2 daughter cells doesn’t happen (cleavage furrow doesn’t close)
Filamenthous shape
Hollow sphere 3D ball of cells sphered together
- Individual cells aggregate
different individual cells form one cohesive unit (individual cells mold together)
o Specialization
o Different cells specialize depending on environment (multicellularity with
different functions)
Photo nitrogen spores
synthesis fixation
o Example: E.Coli has 1 cel type, humans have ~200 special cell types
Genes
o How do genes evolve
o Information changes
o New genes generated from pre-existing genes
(intragenetic) mutations
Gene duplication
DNA segment shuffling
Horizontal transfer
o Ortholog
o Homologous genes (similar sequence) with
same function in 2 species
through speciation
, o Paralog
Homologous genes (similar sequence) with
different function in same species
through gene duplication and divergence
o Complexity of genome
o Genome size of a species does not correlate with number of genes
noncoding ‘junk’ DNA in eukaryotic cells contains many regulatory elements
o Increased complexity: from prokaryote to eukaryote
o Number of genes in different species
o Range from 500 in pathogenic bacterium Mycoplasma
o To 31,000 in tiny water flea Daphnia
Model organisms
o Domains of life
o Archaea: single celled organism without cell wall (oerbacterie)
o Bacteria
o Eukaryote
o Evolutionary relationships
o Eukaryote phylogenetically more similar to archaea
o Eukaryote evolved from symbiosis
1. Anaerobic cell ( ‘ancestor’ of eukaryote) takes up aerobe bacteria
2. Bacteria becomes an organelle (mitochondria/chloroplast)
o Model organisms
! E.coli:
- bacteria
- model for studying basic cell
- simple and small genome
- cheap to grow
! Yeast
- simple eukaryote
- model for organelles, DNA replication and cell cycle
- small genome (for eukaryote) with strong genetics
- cheap to grow
! Fruit fly
- model for (developmental) genetics
- strong genetics, low frequency of gene duplication, long (experimental)
history
- cheap
! Mouse
- model for various things related to humans, similar to human
- strong genetics, long (experimental) history
- relatively cheap
Protozoan
- simple eukaryote
- model for cell movement
, - small genome, strong genetics
- cheap
Worm
- model for multicellular development
Plant
- model for plant development and physiology
Frog
- model for early egg development and cell cycle
- big eggs, outside mother, cell division without growth
Zebrafish
- model for various things of which vertebrate development
- similar to human genome
- strong genetics, translucent
Human
- model for disease and behaviour
- large dataset of naturally occurring mutants
M2:
Chemical bonds
o Covalent
- C-C bond
- shared electron
- covalent bond is ~100x stronger than thermal lecture
- breaking of covalent bond: catalyst
- create macromolecules
o Noncovalent
- transfer electron
- facilitate macromolecular interaction (formation of ribosome of proteins)
Hydrogen
- strongest when atoms are in straight line
- relatively weak force
- water: network of 2 H-bonds per H2O molecule
- connection between (positive) H and a little bit negative elements
Van der Waals
- at very short distance any two atoms show a weak bonding interaction due
to their fluctuating electrical charges
- will be attracted to each other
- very weak force
- important for macromolecules when many atoms are involved
- DNA
Ionic bond
- transfer of e- between atoms
- Ionic bonds result from the electrostatic attraction between the positive
and negative charges of ions
Hydrophobic forces (is not a bonding!)
- repulsion from water causes apparent hydrophobic ‘bonding’
Cells
o Energy source:
- Litotrophic: e from inorganic chemicals
- Phototrophic: e from sunlight
- Organotrophic: e from other cells and organic products
o Prokaryotes
- simple, one component
- cytoplasm with ‘lose’ floating DNA, ribosome etc.
o Eukaryotes
- complex, many membrane-bound compartments (organelles)
nucleus
- genetic information in nucleus
endoplasmatic reticulum
golgi apparatus
lysosome
o Multicellularity
- Cells stay together after cell division
budding off of 2 daughter cells doesn’t happen (cleavage furrow doesn’t close)
Filamenthous shape
Hollow sphere 3D ball of cells sphered together
- Individual cells aggregate
different individual cells form one cohesive unit (individual cells mold together)
o Specialization
o Different cells specialize depending on environment (multicellularity with
different functions)
Photo nitrogen spores
synthesis fixation
o Example: E.Coli has 1 cel type, humans have ~200 special cell types
Genes
o How do genes evolve
o Information changes
o New genes generated from pre-existing genes
(intragenetic) mutations
Gene duplication
DNA segment shuffling
Horizontal transfer
o Ortholog
o Homologous genes (similar sequence) with
same function in 2 species
through speciation
, o Paralog
Homologous genes (similar sequence) with
different function in same species
through gene duplication and divergence
o Complexity of genome
o Genome size of a species does not correlate with number of genes
noncoding ‘junk’ DNA in eukaryotic cells contains many regulatory elements
o Increased complexity: from prokaryote to eukaryote
o Number of genes in different species
o Range from 500 in pathogenic bacterium Mycoplasma
o To 31,000 in tiny water flea Daphnia
Model organisms
o Domains of life
o Archaea: single celled organism without cell wall (oerbacterie)
o Bacteria
o Eukaryote
o Evolutionary relationships
o Eukaryote phylogenetically more similar to archaea
o Eukaryote evolved from symbiosis
1. Anaerobic cell ( ‘ancestor’ of eukaryote) takes up aerobe bacteria
2. Bacteria becomes an organelle (mitochondria/chloroplast)
o Model organisms
! E.coli:
- bacteria
- model for studying basic cell
- simple and small genome
- cheap to grow
! Yeast
- simple eukaryote
- model for organelles, DNA replication and cell cycle
- small genome (for eukaryote) with strong genetics
- cheap to grow
! Fruit fly
- model for (developmental) genetics
- strong genetics, low frequency of gene duplication, long (experimental)
history
- cheap
! Mouse
- model for various things related to humans, similar to human
- strong genetics, long (experimental) history
- relatively cheap
Protozoan
- simple eukaryote
- model for cell movement
, - small genome, strong genetics
- cheap
Worm
- model for multicellular development
Plant
- model for plant development and physiology
Frog
- model for early egg development and cell cycle
- big eggs, outside mother, cell division without growth
Zebrafish
- model for various things of which vertebrate development
- similar to human genome
- strong genetics, translucent
Human
- model for disease and behaviour
- large dataset of naturally occurring mutants
M2:
Chemical bonds
o Covalent
- C-C bond
- shared electron
- covalent bond is ~100x stronger than thermal lecture
- breaking of covalent bond: catalyst
- create macromolecules
o Noncovalent
- transfer electron
- facilitate macromolecular interaction (formation of ribosome of proteins)
Hydrogen
- strongest when atoms are in straight line
- relatively weak force
- water: network of 2 H-bonds per H2O molecule
- connection between (positive) H and a little bit negative elements
Van der Waals
- at very short distance any two atoms show a weak bonding interaction due
to their fluctuating electrical charges
- will be attracted to each other
- very weak force
- important for macromolecules when many atoms are involved
- DNA
Ionic bond
- transfer of e- between atoms
- Ionic bonds result from the electrostatic attraction between the positive
and negative charges of ions
Hydrophobic forces (is not a bonding!)
- repulsion from water causes apparent hydrophobic ‘bonding’
