Key numbers in Biochemistry
Key numbers in Biochemistry für die Vorlesung Grundlagen der Biologie II: Molekularbiologie und Biochemie, Dozent Rudi Glockshuber
Key numbers in Biochemistry für die Vorlesung Grundlagen der Biologie II: Molekularbiologie und Biochemie, Dozent Rudi Glockshuber
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Avogadro number
\(N_A = 6.0\cdot 10^{23}\ mol^{-1}\)
Proton concentration
\(\mathrm{[H^+]=10^{-pH}\ M\\pH=-\log[H^+]}\)
What does a two-state equilibrium (\(A\leftrightarrow B\)) at 25 °C with an equilibrium constant Keq of \(\frac{[A]}{[B]}=\frac{10}{1}\) indicate?
It indicates that A is 5.7 kJ/mol more stable than B; every order of magnitude of Keq translates into 5.7 kJ/mol \(\mathrm{(\Delta G=-RT\ln K_{eq}) \rightarrow if\ K_{eq}=1000:1, \Delta G =3\cdot 5.7\ kJ/mol=17.1\ kJ/mol}\)
The same applies to enzymes: if the activation energy of a reaction is lowered by 5.7 kJ/mol by an enzyme, the reaction becomes 10 times faster.
Time for an average protein to traverse an E. coli cell by free diffusion
\(\sim 10\ \mathrm{ms}\)
Time for an average protein to traverse a HELA cell (Menschliche Epithel Zelle) by free diffusion
\(\sim10\) s
Size and volume of an E. coli cell
~3 x 0.5 \(\mu\)m / 1 \({\mu m}^3\)
size and volume of a yeast cell (S. cerevisiae)
5 - 10 \(\mu m\ 40\ {\mu m}^3\)
Size and volume of mitochondria
\(1\ \mu m;\ 1{\mu m}^3\)
Size of animal cells
\(10-100\ \mu m\)
Diameter of the cell nucleus
\(2-10\ \mu m\)
Genome size / number of protein-encoding genes: Mycoplasma mycodes
0.57 Mb / 473 (smallest known genome)
Genome size / number of protein-encoding genes: E. coli
4.6 Mb / 4300
Genome size / number of protein-encoding genes: S. cerevisiae (yeast)
12.5 Mb / 6000
Genome size / number of protein-encoding genes: H. sapiens
3000 Mb / ~20'000 - 25'000
Length of a C-C bond
1.54 A = 0.154 nm
Distance between the heavy atoms (donor and acceptor) of a hydrogen bond in proteins and nucleic acids
2.8 A
Length of the \(\alpha\)-helix
1.5 A per amino acid
Amino acids per \(\alpha\)-helix turn
3.4
Length of a \(\beta\)-strand (extended polypeptide chain)
3.3 - 3.5 A per amino acid
Average mass of an amino acid in a protein
110 Da
Average length of cellular proteins
~300 - 350 amino acids (~35 kDa)
Diameter of a folded protein with 100 amino acids
~30 A
Distance between superposed base pairs in the DNA double helix (B-DNA)
3.3 A
Diameter of the DNA double helix (B-DNA)
20 A
Number of base pairs per turn of the double helix (B-DNA)
10.5
Average mass of a DNA base pair
~650 Da
Total hypothetical extended length of human genomic DNA
~1 m
Total intracellular protein concentration
~200 - 300 mg/mL, 2 - 4 million proteins per \({\mu m}^3\)
Rule of thumb: a protein concentration of 1\(\mu M\) corresponds to 1'000 molecules per E. coli cell (volume \(\sim 10\ {\mu m}^3\))
Total and individual metabolite concentration
Der Metabolit (griechisch μεταβολίτης metabolítes, deutsch ‚der Umgewandelte‘, Plural: Metaboliten) ist ein Zwischenprodukt (Intermediat) in einem meist biochemischenStoffwechselweg.
total: ~300 mM
individual metabolites: \(0.1\ \mu M\ -\ 100\ mM\)
In E. coli, individual metabolite concentrations are generally higher than their KM values.
Equilibrium thermodynamics, energetics of ATP hydrolysis \((\Delta G^{0'})\)
\(\Delta G^{0'}=-30.5\ kJ/mol\)
Dissociation constants of natural protein-ligand interactions
\(10^{-3}-10^{-15}\ M\)
On-rates of physiological protein-ligand interactions
\(10^3-10^9\ M^{-1}s^{-1}\)
Half-lives of spontaneous dissociation of protein-ligand complexes
\(\sim 10\ ms\rightarrow 10^6\) years
Upper (diffusion) limit of second-order rate constants in water (small molecules)
\(\sim 10^10\ M^{-1}s^{-1}\)
KM values of natural enzyme/substrate pairs
\(0.1\ \mu M-100\ mM\)
kcat values of natural enzymes
\(0.01-10^6\ s^{-1}\)
Upper (diffusion) limit of catalytic efficiency (kcat/KM)
\(\sim 10^9\ M^{-1}s^{-1}\)
Acceleration factors (kcat / kuncat) of natural enzymes
\(10^3-10^17\)
