Energetics

Thermal energy at T=298K: kBT=4.1 pNnm=4.110-21 J

Energy hydrogen bond: 5-15kBT 10kBT
Energy of covalent bond: 80-250kBT 102 kBT
DNA: 4 nucleotides (GTCA) bound covalently to a backbone of sugar-phosphate
G-C: 3 hydrogen bonds; A-T: 2 hydrogen bonds
Free energy of the reaction ATP ADP + Pi
under standard conditions: G0-12kBT
for the concentrations in the cell: G -20kBT
Catabolic reactions:
Close to equilibrium when G0 >-5kBT
Far from equilibrium when G0 <-5kBT

Concentrations:

Avogadro number: NA=61023 mol-1

Atomic mass unit: 1Da=1g/NA
Cell volume: 1m3 (E. coli), 100m3 (human red blood cell)
Molar concentration of water: cH2O=55 mol/l
Hydronium ion (H3O+) molar concentration in pure water: cH+=10-7 mol/l
Concentrations of ATP, ADP, Pi in the cell ~ 1-5 mM

Central dogma:

Cell cycle time: 1000s (E.coli), several hours (most human cells)
Number of amino acids encoded by the genetic code: 20
N. of amino acids with peptide link (R-CONH-R-CONH-R) in proteins: 100-1000 (typical 350)
Weight of a protein: 0.1 kDa per amino acid
Number of proteins in the cell: 106 proteins/m
Number of different proteins in the cell: 5000 (E. coli), 20000 (human)
Relation between nucleic acids and proteins: 1codon(=3 nucleotides) encodes 1 amino acid
Genome size: 5106 bp (E.coli); 3109 bp (human)
Number of chromosomes in human: 46 (22 chromosome pairs + 2 sex chromosomes)
Rate of replication by DNA polymerase: 500-1000 bp/s (E.coli); 40 bp/s (human)
Rate of transcription by RNA polymerase: 30-80 bp/s (human)
Rate of translation by the ribosome: 10-20 amino acids/s
Polymer elasticity:

Persistence length of dsDNA: lp 50 nm

Diffusion and molecular motors:

Typical diffusion constant in the cell: D 0.1-1 m2/ms

Step size of kinesin-1: 8 nm
Speed of kinesin-1: ~ 800 nm/s
Stall force of kinesin-1: ~ 6 pN
Processivity of kinesin-1: ~ 100 steps

Cell membrane electrical properties:

Membrane capacity: ~1 F/cm2

Typical resting membrane potential (eukaryotes): -40 to -95 mV