Basic Cell and Molecular Biology - Summary
Table of Contents
Molecular Biology
Lecture 1: Cell and genomes ................................................................................. 2
Lecture 2: Cell chemistry and proteins .................................................................... 5
Lecture 3: DNA, chromosomes ............................................................................. 10
Lecture 4: DNA replication and repair (part 1) ....................................................... 14
Lecture 5: DNA replication and repair (part 2) ....................................................... 18
Lecture 6: How cells read the genome: transcription ............................................ 24
Lecture 7: How cells read the genome: translation ............................................... 29
Lecture 8: Analyzing molecules: DNA ................................................................... 34
Cell Biology
Lecture 1
Lecture 1A: Microscopy ..................................................................................... 37
Lecture 1B: Membranes .................................................................................... 39
Lecture 2: Intracellular compartments and membrane sorting .............................. 42
Lecture 3: Intracellular membrane traffic .............................................................. 47
1
, Molecular biology
Lecture 1 Cells and genomes (3 pages)
Understanding cell biology
- Components
- Processes
Why cell biology
- Smallest form of life is a cell
- Most organisms are single cells
- Once in their life multicellular organisms were single cells
Comparing cells of all organisms
Common:
- Storage of information in DNA
How DNA is built up, double stranded DNA, DNA double helix
- Replication, transcription and translation
DNA > RNA > protein
- Each protein encoded by specific gene
DNA: genes encode information for molecules with a functionality
Gene: region of DNA that is transcribed as a single unit and carries
information for a discrete hereditary characteristic:
1) Single protein (or set of related proteins)
2) Single RNA (or set of single RNA’s)
- Proteins are catalysts
RNA and proteins fold into structures that can perform specific tasks
Lysozyme (protein) is a catalyst for polysaccharide digestion
- Enclosed by a membrane: internal and external environment
2
, Comparing cells of all organisms
Different:
- Source of energy
Lithotrophic: energy from (energy-rich) inorganic chemicals
Phototrophic: energy from sunlight
Organotrophic: energy from other cells and organic cell-products
- Diversity in shape and size
- Prokaryote or eukaryote
Prokaryote: one compartment
Eukaryote: many membrane-bound compartments (organelles)
Diversity in life forms: three domains of life
• Bacteria
• Archaea
• Eukaryotes
Archaea are phylogenetically more similar to eukaryotes than bacteria are
to either archaea or eukaryotes
- Number of genes (500 to 31.000)
Essential genes for basic life functions (such as rRNA genes) from archaea,
bacteria and eukaryotes are very similar
Many specialised genes are more variable in sequence
➢ Thus, some genes evolve rapidly; others are highly conserved
How do genes evolve
New genes are generated from pre-existing genes
- Intragenic mutation
- Duplication: give rise to new families
- DNA segment shuffling
- Horizontal transfer
Gene homology
- Ortholog: homologous genes with same function in two
species
- Paralog: homologous genes with different functions in
same species
Minimal amount of genes for a living cell
Smallest living organisms: 530 genes – Mycoplasma genitalium
Minimal amount of genes which are necessary for life is estimated at ~300
Increased complexity: from prokaryote to eukaryote
The biochemistry of all organisms has a common origin that was fixed during early
evolution
3
Table of Contents
Molecular Biology
Lecture 1: Cell and genomes ................................................................................. 2
Lecture 2: Cell chemistry and proteins .................................................................... 5
Lecture 3: DNA, chromosomes ............................................................................. 10
Lecture 4: DNA replication and repair (part 1) ....................................................... 14
Lecture 5: DNA replication and repair (part 2) ....................................................... 18
Lecture 6: How cells read the genome: transcription ............................................ 24
Lecture 7: How cells read the genome: translation ............................................... 29
Lecture 8: Analyzing molecules: DNA ................................................................... 34
Cell Biology
Lecture 1
Lecture 1A: Microscopy ..................................................................................... 37
Lecture 1B: Membranes .................................................................................... 39
Lecture 2: Intracellular compartments and membrane sorting .............................. 42
Lecture 3: Intracellular membrane traffic .............................................................. 47
1
, Molecular biology
Lecture 1 Cells and genomes (3 pages)
Understanding cell biology
- Components
- Processes
Why cell biology
- Smallest form of life is a cell
- Most organisms are single cells
- Once in their life multicellular organisms were single cells
Comparing cells of all organisms
Common:
- Storage of information in DNA
How DNA is built up, double stranded DNA, DNA double helix
- Replication, transcription and translation
DNA > RNA > protein
- Each protein encoded by specific gene
DNA: genes encode information for molecules with a functionality
Gene: region of DNA that is transcribed as a single unit and carries
information for a discrete hereditary characteristic:
1) Single protein (or set of related proteins)
2) Single RNA (or set of single RNA’s)
- Proteins are catalysts
RNA and proteins fold into structures that can perform specific tasks
Lysozyme (protein) is a catalyst for polysaccharide digestion
- Enclosed by a membrane: internal and external environment
2
, Comparing cells of all organisms
Different:
- Source of energy
Lithotrophic: energy from (energy-rich) inorganic chemicals
Phototrophic: energy from sunlight
Organotrophic: energy from other cells and organic cell-products
- Diversity in shape and size
- Prokaryote or eukaryote
Prokaryote: one compartment
Eukaryote: many membrane-bound compartments (organelles)
Diversity in life forms: three domains of life
• Bacteria
• Archaea
• Eukaryotes
Archaea are phylogenetically more similar to eukaryotes than bacteria are
to either archaea or eukaryotes
- Number of genes (500 to 31.000)
Essential genes for basic life functions (such as rRNA genes) from archaea,
bacteria and eukaryotes are very similar
Many specialised genes are more variable in sequence
➢ Thus, some genes evolve rapidly; others are highly conserved
How do genes evolve
New genes are generated from pre-existing genes
- Intragenic mutation
- Duplication: give rise to new families
- DNA segment shuffling
- Horizontal transfer
Gene homology
- Ortholog: homologous genes with same function in two
species
- Paralog: homologous genes with different functions in
same species
Minimal amount of genes for a living cell
Smallest living organisms: 530 genes – Mycoplasma genitalium
Minimal amount of genes which are necessary for life is estimated at ~300
Increased complexity: from prokaryote to eukaryote
The biochemistry of all organisms has a common origin that was fixed during early
evolution
3
