This file contains all the subject matter (notes from the lectures, supplemented with the necessary material from the book) for the course Basic cell and molecular biology at the University of Groningen.
Samenvatting van de hoofdstukken 4, 5, 6 en deels 7 (t/m 7.3) - Cellen en weefsels
Summary Molecular Biology of the Cell 2 (book) (WBFA007-04)
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Rijksuniversiteit Groningen (RuG)
Biologie
Basic Cell and Molecular Biology (WBBY00105)
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Introduction to the cell
Lecture 1 (27/09)
Heredity: the parent organism hands down information specifying the characteristics that the
offspring will have → central to definition of life
Most life is single-celled; every multicellular organism was once a single cell → single cell is the
vehicle for all hereditary information.
Common characteristics to all cells Differences between different cells
Storage of hereditary information in DNA Different power sources:
→ DNA: long, paired polymer chains, formed by Organotrophic: obtain energy by feeding on
four nucleotides (deoxyribose + phosphate other living things or the organic chemicals they
produce
group + base)
Lithotrophic: obtain energy from energy-rich
systems of inorganic chemicals in the
environment
Phototrophic: obtain energy from sunlight
Replication of hereditary information by Diversity in shapes and sizes
templated polymerization
Transcription of portions of hereditary Prokaryotes and eukaryotes:
information into RNA Prokaryotes: no nucleus, small and simple in
→ outcome: RNA; a portion of hereditary info, appearance, independent or loosely organized
communities, cell wall, no organized internal
represented in A,C,G,U, guide the synthesis of
structure, varied in biochemical abilities
proteins based on genetic instructions in DNA
→ unicellular organism that does not have a
defined nucleus
Eukaryotes: nucleus, many membrane-bound
compartments, big, cytoskeleton, can engulf
other cells by phagocytosis (plant cells also
have a cell wall and chloroplasts)
→ unicellular or multicellular organisms that
does have cells with a defined nucleus
Usage of proteins as catalysts Number of genes
→ Proteins: polymer chains of amino acids; can - Smallest living organism has 530 genes
bind to molecules to act as enzymes to catalyze - Minimum number of genes in order to
live is around 300 genes
reactions to make/break covalent bonds;
because proteins/RNA are single stranded and
flexible, they can fold back on themselves
depending on sequence → lysozyme is catalyst
for polysaccharide digestion
→ Life is an autocatalytic, self-reproducing
process; feedback loop that connects
polynucleotides and proteins
, Translation of RNA into proteins
Each protein encoded by a specific gene
→ Gene: region of DNA (either corresponding to
a protein or RNA) that is transcribed as a single
unit and carries information for a discrete
hereditary characteristic; genome: totality of the
genetic information in a cell embodied in its
complete DNA sequence
Function as biochemical factories dealing with
the same basic molecular building blocks
Enclosed in plasma membrane across which
nutrients and waste materials must pass
Three domains of life: archaea (prokaryote), bacteria (prokaryote) and eukaryotes. Ancient archaeal
cell engulfed bacterium → archaea are more phylogenetically similar to eukaryotes than bacteria
are to either eukaryotes or prokaryotes.
- Essential genes for basic life functions are very similar among archaea, bacteria and
eukaryotes, while highly specialized genes vary; specialized genes are highly conserved → if
negative mutation occurs, the individual will be eliminated; in noncoding DNA changes can
accumulate
- New genes arise from preexisting genes:
1. Intragenic mutation → random modification in gene sequence
2. Gene duplication → a gene duplicates; one copy provides essential functions, while
the other is free to accumulate changes, causing it to get a different function → two
genes diverge in the course of evolution → repeated rounds can give rise to gene
families: sets of several similar genes, formed by duplication of a single original gene
→ Gene homology: gene inherited in two species by a common ancestor
- Orthologous genes: homologous genes with same function in different
species
- Paralogous genes: homologous genes with different function in the same
species
3. DNA segment shuffling → hybrid gene arises because of breaking and rejoining of
genes
4. Horizontal transfer: a piece of DNA can be transferred from one genome to another,
even to that of another species
The evolution of the eukaryotic cell
Anaerobic cell derived from an archaeon with primitive nucleus engulfed an aerobic bacterium →
symbiosis → aerobic bacterium became the mitochondrium → some cells also engulfed a
photosynthetic bacterium → chloroplasts formed
,Most eukaryotic cells are unicellular, but at some point in time multicellularity originated, caused by
one of two things:
1. Cells stayed together after cell division; either filamentous shape or hollow sphere; during
development of zygote cells keep dividing but staying together
2. Aggregation of individual cells; in times of food shortage, cells of the same amoeba can
aggregate together; at some point, the cells that aggregated together all got different
functions and became dependent on each other → multicellularity
Cell specialization
- There are prokaryotes that can specialize in certain environments
- Multicellular organisms have many different cell types
Cambrian explosion: probably due to lots of gene duplication, there was an enormous amount of
speciation in a short amount of time, but the increasing sizes of genomes were not a core factor,
because the size of the genome does not correlate with the amount of genes → eukaryotes often
have bigger genomes that vary more between species; lots of noncoding junk DNA that contains
regulatory elements
Model organisms
bacterium Escherichia coli (simple, small Metabolism, DNA replication, transcription,
genome, cheap to grow, protein purification → translation
isolation of protein to determine its function)
yeast Saccharomyces cerevisiae (simple organelles, DNA replication and cell cycle
eukaryote, small genome for eukaryote, strong
genetics, cheap to grow)
protozoan Dictyostelium discoideum (simple Cell movement
eukaryote, small genome, strong genetics,
cheap to grow)
worm Caenorhabditis elegans (major cell types, Multicellular development
exact lineage of fertilized egg to 959 cells of
adult is known, 302 neurons, all connections
identified)
plant Arabidopsis thaliana (small genome for a Plant physiology and development
plant, strong genetics, cheap to grow for a
plant)
fly Drosophila melanogaster (strong genetics, Genetics
low frequency of gene duplications, long
(experimental) history, cheap)
frog Rana pipiens or Xenopus laevis (big eggs, Early egg development and egg cycle
outside mother, cell division without growth)
zebrafish Danio rerio (strong genetics, Vertebrate development
translucent)
mouse Mus musculus (strong genetics similar to Disease and behaviour
human long (experimental) history (relatively)
, cheap)
human Homo sapiens (very large dataset of Disease and behaviour
naturally occurring mutants)
New species evolve by mutations in existing genes, which is why certain genes that are associated
with disease in humans can also be found in other species → medications can be tested on animals
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