Molecular Mass
-
Unit: 1 u or Da is defined as$$\frac{1}{12}$$ of the mass of
$${}^{12}C$$ isotope -
Mole: Amount of Substance, which contains as many elementary entites as atoms in
$$0,012 kg\ of\ {}^{12}C$$ isotope -
Avogadro Constant:
$$N_A$$ or$$L$$ , entities per mole and is defined as$$6,022 * 10^{23}\ mol^{ -1}$$
Spatial dimensions:
-
Ångström: 1 Å is equivalent to
$$0,1\ nm$$ or$$100\ pm$$ - Radius of atoms:
$$0,3 - 3$$ Å - Distance of different chemical bonds:
-
C-C:
$$154\ pm$$ -
C=C:
$$134\ pm$$ -
C-H:
$$109\ pm$$ -
C-O:
$$143\ pm$$ -
C=O:
$$120\ pm$$ -
C-N:
$$147\ pm$$ -
N-H:
$$101\ pm$$
-
C-C:
- Average weight of amino acid:
$$100 - 110\ Da$$ - Typical length for soluble proteins:
$$3 - 6\ nm$$ - ~ 300 amino acids for prokaryotic proteins
- ~ 400 amino acids for eukaryotic proteins
Terms:
- Cell Membrane: A selective barrier separating the inside of a cell / organelle from the outside, consisting of a phospholipid bilayer.
- Cytoplasm: semi-liquid medium inside the cytoplasm membrane
- Cytoplasmatic Membrane: the membrane around the cell
- Cell Compartment: a region within the cell mostly enclosed by a membrane
- Cell Organelle: a special type of compartment that has a certain function within the cell
- Nucleus: a membrane enclosed volume of the cell, which contains most of the genomic material
- Cell Wall: Some cells have an extra cellular rigid layer
Cell Organelles: Ribosome, Mitochondrium, Chloroplasts
Prokaryotic vs Eukaryotic Cells:
| Eukaryotic Cell | Prokaryotic Cell |
|---|---|
| membrane enclosed compartments | No membrane enclosed compartments |
| genomic material in nucleus | Genomic Material located in nucleoid region |
| organelles: mitochondria, chloroplasts | No organelles |
| compartments: endoplasmatic reticulum, Golgi-apparatus |
Hydrophilic: likes to interact with water because of partial electrical charges (mostly polar)
Hydrophobic: avoids interaction with water, because of distinct charging points (mostly non-polar)
Lipophilic: likes to interact with fatty / unpolar molecules (-> hydrophobic)
Lipophobic: avoids interaction with fatty / unpolar molecules (-> hydrophilic)
Biomolecules
- typically polymers (= constructed from many identical or similar residues)
- can form complexes
- can contain both hydrophilic and lipophilic parts
Carbohydrates: (sugars)
- molecule consisting of **C, H, O **atom
-
$$C_m(H_2O)_n$$ - usually hydrogen-oxygen ratio of 2:1 - hydrophilic
- purpose: fuel, energy storage, structural components, ...
Lipids:
- loosely defined as being soluble in non-polar solvents
- fats, waxes, vitamins, ...
- purpose: energy storage, signaling, structural components
**Glycerolipids: ** (Phospholipids)
- Glycerol with 3 docking slots (hydrophobic)
- 3 fatty acids: triglycerids (energy storage)
- 2 fatty acids + 1 phosphate group: Phospholipid, major building block of membranes
Nucleic Acids:
- Store and transmit genetic information
- A polymer built out of Nucelotides (base+sugar+phosphate)
- hydrophobic nucleobases on the inside
- hydrophilic backbone (phosphate + sugar)
- RNA: single stranded, but can adopt complex secondary structure with itself or other RNA
- DNA: typically double stranded (double helix) formed by a reverse-compliment strand
- Has a 5' end and a 3' end.
- always annotated from 5' to 3'
- Bonds: non-covalent hydrogen bonds (rather weak)
Proteins:
- polymerized amino acids
- work horse or machinery of life
- functions
- catalysis of chemical reactions (enzymes)
- structural elements (collagen fibers)
- sensing
- immune system
- etc ...
Gene: Any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression
= every subsequence of DNA that encodes a functional protein
Central Dogma of Molecular Biology: (!!!) Describes the flow of information from DNA to RNA to Protein
1) Replication: Duplication of DNA
- highly controlled, carried out by multi-protein complex
- for each strand in the double helix, a complementary strand is synthesized
- in 5' -> 3' direction
2) Transcription: Creation of working copy of genes
- synthesis of a single stranded RNA from a template sequence in the DNA (after a promoter region)
- carried out by a multi protein complex
- the resulting mRNA undergoes several maturing steps before Translation
- mRNA: translated into protein
- xRNA: function
- rRNA: component of the Ribosome
- tRNA: amino acid carrier for translation
3) Translation: Conversion of mRNA into protein
- carried out by ribosomen
- starts with AUG codon
- by default: Sequence of RNA and Protein are noted in the same direction
Inheritance / Mutation: Copy errors lead to rise of evolution
- Mutation Types
- (longe range) rearrangements
- point mutations
- Rearrangements
- rearrangements of DNA segments due to error in recombination process
- induced by
- DNA damage (chemical, radiation)
- virus infections
- consequences: loss of gene functions or loss of controls
- Point Mutations
- change of a single DNA residue
- Frame-Shift (loss / gain of a single residue), effect rather unpredictable
- **Substitution **
- Transition: A <--> G or C <--> T
- Transversion: A,G <--> C, T
- Consequences:
- silent
- missense (= amino acid change)
- nonsense (= stop codon introduced)
- affects splicing site
- Induced by: replication errors
Gene Regulation: Takes place on several layers
- transcription rate
- stability of mRNA
- translation
Anabolism: Reactions that aim to the synthesis of a new substance
Catabolism: Reactions that aim to the degradation of a substance (energy generation, removal of damaged structures)
steady state / equilibrium: degradation and synthesis rate are balance (System is dynamically stable)
More about proteins in future lectures.
∅