Lecture 3:
Building a Living Cell
The Bacterial Standard Ruler:
E. coli
➔ prokaryotic cell (no
compartments)
➔ minimal requirements for life:
- DNA based genome
- DNA → RNA transcription
- ribosomes (convert RNA
into protein sequences)
A) AMF image
B) electron micrograph
C) schematic picture
D) A head of a pin
Molecular census on E. coli (has 4 lipid layers):
➔ volume: 1 fL = 10-15 L; mass: 1pg = 10-12 g; density: 1g/mL (H2O)
➔ dry weight of the cell: ~30% of its total (0.30 pg);
half of dry weight is protein (0.15 pg)
➔ half of dry mass comes from the carbon content of E. coli, so there
is ~1010 carbon atoms in a cell
➔ number of proteins: assume each protein ~300 amino acids and
each amino acid 100 Da (30 kDa; 1 Da = 1.6 x 10-24 g), thus:
3 x 106 proteins (1/3 of these within the membrane, 2/3 inside)
➔ number of ribosomes: the mass of each ribosome 2.5 MDa; each
ribosome consists 1/3 of protein and 2/3 of RNA; 20% of all
proteins in the cell resides in ribosomes: 20,000 ribosomes
(Total ribosomal protein mass / protein mass inside on ribosome)
➔ the diameter of ribosome is 20 nm: 10% cell volume
Figure 2.12: Physical interpretation
of concentration.
(A) Concentration in E. coli units: number
of copies of a given molecule in a volume
the size of an E. coli cell as a function of
the concentration.
(B) Concentration expressed in units of
typical distance d between neighboring
molecules measured in nanometers.
Molecular census on a yeast cell:
➔ E. coli volume: VE. Coli = 1.0 m3 (1 x 2 m)
Yeast cell size distribution. Distribution of cell volumes
measured for wild-type yeast cells. (Adapted from P.
Jorgensen et al., Science 297:395, 2002.)
➔ Yeast: a sphere of d = 5 m: Vyeast = 65 m3 ~ 60 VE. Coli ;
surface area Ayeast ~ 80 m2 ; yeast nucleus - a sphere of d = 2 m and Vn ~ 4
m3 with 1.2 x 107 base pairs (bp) of yeast genome divided in
16 chromosomes
➔ DNA packed into nucleosomes (histone-DNA complexes): each 150 bp
wrapped around a cylindrical core, histone octamer (radius 3.5 nm, height 6
nm, volume 230 nm3), with 50 bp spacers in between:
Nnucleosomes ~ 60,000
(Exp.: 80,000 nucleosomes with a mean spacing of ~170 bp)
➔ volume of one bp ~ 1 nm3 & volume of all histones: 14 x 106 nm3
➔ the genomic DNA packing fraction (Vgen / Vn), pack ~ 3 x 10-3
Figure 2.13: Experimental techniques that have revealed the structure of both cells and their organelles.
Figure 2.15: Powers-of-10 representation of biological length scales.
(A) the protist
Giardia lamblia
(B) a plant cell
(C) yeast cell
(with a bud)
(D) red blood cell
(E) a fibroblast cell
(F) a nerve cell
(G) retinal rod cell
Figure 2.26: The macromolecular
assemblies of the cell.
(A) The nucleosome is a complex of
eight protein units and DNA.
(B) The nuclear pore complex
mediates the transport of material
in and out of the nucleus.
(C) The replisome is a complex of
proteins that mediate the copying
of the genetic material.
(D) The ribosome reads mRNA and
synthesizes the corresponding
polypeptide chain.
(E) The proteasome degrades
proteins.
(F) ATP synthase is a large complex
that synthesizes new ATP
molecules.
Figure 2.27: Helical motifs of molecular assemblies.
Macromolecular assemblies have a variety of different helical
structures, some formed from individual monomeric units (such as
(A)–(C)), others resulting from coils of proteins (D), and yet others
made up of paired nucleotides (E).