• In Eukaryotes (higher organisms) DNA forms chromosomes:
• DNA double helix wraps around Nucleosomes to form "beads on a string"
• six nucleosomes are forming a Solenoid
• Loops are formed with the help of Scaffold attachment regions (SAR) that are located on DNA basis
• 18 loops are forming Minibands
• Chromosomes are stacked Minibands

The centromer is a region roughly in the middle of a chromosome that is needed for the attachment of microtubuli necessary for the separation of replicated sister chromosomes

Prokaryotes: e.g. Bacteria like E.coli (overhead #3a)

• no organelles
• no nucleus
• DNA is "loosely" attached to cell membrane

Eukaryotes: e.g. Yeast, Mammals (overhead #3b), Plants (overhead #3c)

• nucleus that contains the DNA as chromosomes
• DNA is transcribed in the nucleus and the mRNA has to be transported to the cytoplasm
• organelles: have part of their own genome, with different "code"
• mitochondria: generate the energy for the cell
• in plants: chloroplasts: location of photosynthesis
• cytoskeleton: provides structure
• endoplasmatic reticulum : membrane bound compartment for the synthesis of lipids and membrane-bound proteins
• Specific to Plant Cells: Vacuole, Cellulose Wall, Chloroplasts

• Ion Channels: channel formed by transmembrane proteins:

Ligand binding -> conformation change -> channel opens

• G- Protein: Ligend binding to outer receptor -> leads to conformation changes at the domain in the cell ->activation of G-Protein -> relays information to other enzyme or ion channel.
• Enzyme linked receptors

• An important factor in signal transduction is phosphorylation of proteins by kinases .
• Phosphorylation can lead to the activation or deactivation of a protein.
• Phosphorylation of Proteins: signals from two different receptors A and B can be integrated to a single signal, by phosphorylation of two different sites of a protein (logical "and").
• Phosphorylation of 2 subunits: two different receptors can phosphorylate two subunits that together as a complex transmit a single signal.

• A single ligand can -through amplification- influence major cell mechanisms.

• A single activated enzyme can activate several other enzymes. Several of these mechanisms can lead to a cascade of activated enzymes and the amplification of the signal.

• signals can work as activators ( positive) and as inhibitors (negative/ logical "not")
• this leads together with the signal transduction to the possibility of "computing" in the cell.
• hypothetical: information processing implemented in a neural network could also be implemented in signaling network of a living cell.
• based on the mechanisms outlined above signal processing in the cell can in principle perform any operation any conventional computer can perform.

note: The inner workings of the cell are EXTREMELY complex (overhead #8beta)

• The directionality of the involved enzymes is very important: DNA Polymerase extends in 5' to 3' direction only !
• This is easy for the leading strand: just replicated from 5' to 3' end.
• but lagging strand is replicated in smaller pieces (Okazaki Fragments)
• double strand replication progresses bi-directionally from origin of replication (ori)

• forward mutations:
• Transitions: replacement from purine by a different purin e.g. A -> G or C->T
• Transversion: replacement of a purine by a pyrimidine or vice versa

• Silent mutations: mutation that doesn't effect the aminoacid composition
• Neutral mutations: Aminoacid is replaced by similar aminoacid e.g. charged aminoacid and doesn't effect the function of the protein.
• Missense Mutation: different aminoacid is incorporated in the protein
• Nonsense Mutation: leads to chain termination (= truncated protein)
• Single nucleotide addition or deletion: a frameshift occurs
• Addition or deletion of several to many nucleotide pairs: if not a multiple of three, a frameshift also occurs
• Reverse mutation: several mutations leading again to the wildtype
• suppressor mutations: second mutation (at different site) "compensates for" / suppresses effects of original mutation