CPSC 536A: Bioinformatics - Class 2 (2001/01/09)
DNA involved in organization of the chromosome:
scaffold attachment regions
telomer (capping structure at the end of chromosome)
Introns : normally no coding function
genes (product needed in high quantities at certain times)
in Mitochondria (mt DNA ), Chloroplasts (cp DNA) and bacterial cells (as Plasmids)
1. Genome Structure and Organisation
Genomes vary in complexity :
simple: Virus (have "borrowed life" - they are dependent on host)
unicellular organisms: bacteria, yeast
most complex: mammals, birds and plants (plants have the biggest genomes)
1.1.Organization of Genomes (s. overhead #1)
- 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
2. DNA Functions
protein coding DNA
3. Molecular organization of the cell (s. overhead #2)
Inorganic precursor: water, nitrogen etc.
Metabolites: Sugar, bases etc.
Building blocks: aminoacids, nucleotides
Macromolecules: proteins, nucleic acid
Supramolecular complexes: ribosomes, cytoskeleton
Organelles: Nucleus, Mitochondria
4. Prokaryotes vs. Eukaryotes
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
5. Gene Regulation in Prokaryotes (s. overhead#4)
1. Promoter recognition: appropriate sigma factor necessary
2. Operator: blocking of transcription by binding of a repressor
3. Activator: Enhancement by binding of an activator
4. Control of translation initiation: ribosome initiated translation e.g. structure of mRNA
5. Attenuation of translation: termination of mRNA synthesis
6. Control of transcription stability:
7. Methylation of DNA
8. Degree of supercoiling of the DNA
6. Signal Transduction
6.1. Example: Ion Channels (s. overhead#5)
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
6.2. Signal Integration (overhead#6)
- 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.
e.g. Amplification of the signal triggered by a photon in the retina of nocturnal animals.
6.4.Signal Network (overhead #8)
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)
7. Replication and Reproduction (overhead#9)
Is a semiconservative process: both strands are replicated such that each mother strand is basepaired with one daughter strand.
- 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)
8. Mutations (s. overhead #10)
Heritable changes in the genome (cause: depurination, deamination, oxidative damage etc.)
Constant proofreading and repair systems keeping the mutations in a cells DNA low
- 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
Note: The probability of mutations is not uniformly distributed over the genome and the distribution i variable. Some regions (hot spots) are more effected then others. e.g. immune system (overhead#11)