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Cell biology by the numbers
The Path to Biological Numeracy
Preface
Why We Should Care About the
Numbers
How to make
back-of-the-envelope calculations
Order-of-Magnitude
Biology Toolkit
Rigorous Rules for
Sloppy Calculations
The
Geography
of the Cell
I: Size and Geometry
Cells
Size and Geometry Introduction
How big are
viruses
?
How big is an
E. coli
cell and what is its mass?
How big is a
budding yeast
cell?
How big is a
human
cell?
How big is a
photoreceptor
?
What is the range of cell
sizes and shapes
?
Organelles
How big are
nuclei
?
How big is the
endoplasmic reticulum
of cells?
How big are
mitochondria
?
How big are
chloroplasts
?
How big is a
synapse
?
Cellular Building Blocks
How big are
biochemical nuts and bolts
?
Which is bigger,
mRNA
or the
protein
it codes for?
How big is the
“average” protein
?
How big are the
molecular machines
of the central dogma?
What is the thickness of the
cell membrane
?
How big are the
cell’s filaments
?
II: Concentrations and Absolute Numbers
Making a cell
Concentrations and Absolute Numbers – Introduction
What is the
elemental composition
of a cell?
What is the
density
of cells?
What are environmental
O2
and
CO2
concentrations?
What quantities of nutrients need to be supplied in
growth media
?
What is the
concentration of bacterial cells
in a saturated culture?
Cell census
What is the
pH
of a cell?
What are the concentrations of different
ions
in cells?
What are the concentrations of free
metabolites
in cells?
What
lipids
are most abundant in membranes?
How many
proteins
are in a cell?
What are the
most abundant
proteins in a cell?
How much
cell-to-cell variability
exists in protein expression?
What are the concentrations of
cytoskeletal
molecules?
How many
mRNAs
are in a cell?
What is the
protein to mRNA
ratio?
What is the
macromolecular composition
of the cell?
Machines and signals
What are the copy numbers of
transcription factors
?
What are the absolute numbers of
signaling proteins
?
How many
rhodopsin
molecules are in a rod cell?
How many
ribosomes
are in a cell?
III: Energies and Forces
Biology meets physics
Energies and Forces – Introduction
What is the
thermal energy
scale and how is it relevant to biology?
What is the energy of a
hydrogen bond
?
What is the energy scale associated with the
hydrophobic effect
?
How much energy is carried by photons used in
photosynthesis
?
What is the
entropy
cost when two molecules form a complex?
How much
force
is applied by
cytoskeletal filaments
?
What are the physical limits for
detection
by cells?
Energy currencies and budgets
How much energy is released in
ATP hydrolysis
?
What is the energy in transfer of a
phosphate group
?
What is the free energy released upon
combustion of sugar
?
What is the
redox potential
of a cell?
What is the
electric potential
difference across membranes?
What is the
power consumption
of a cell?
How does
metabolic rate
scale with size?
IV: Rates and Duration
Time scales for small molecules
Rates and Durations – Introduction
What are the time scales for
diffusion
in cells?
How many
reactions
do enzymes carry out each second?
How does temperature affect
rates and affinities
?
What are the rates of
membrane transporters
?
How many ions pass through an
ion channel
per second?
What is the
turnover time
of metabolites?
Central dogma
What is faster,
transcription or translation
?
What is the
maturation time
for fluorescent proteins?
How fast do
proteasomes degrade
proteins?
How fast do
RNAs and proteins
degrade?
Cellular dynamics
How fast are
electrical signals
propagated in cells?
What is the frequency of
rotary molecular motors
?
What are the rates of
cytoskeleton assembly
and disassembly?
How fast do
molecular motors
move on cytoskeletal filaments?
How fast do
cells move
?
Cell life cycle
How long does it take cells to
copy
their genomes?
How long do the different stages of the
cell cycle
take?
How quickly do different cells in the body
replace
themselves?
V: Information & Errors
Genome
Information & Errors – Introduction
How big are
genomes
?
How many
chromosomes
are found in different organisms?
How many
genes
are in a genome?
How
genetically similar
are two random people?
Mutations
What is the
mutation rate
during genome replication?
What is the
error rate
in transcription and translation?
What is the rate of
recombination
?
VI: A Quantitative Miscellany
A Quantitative Miscellany – Introduction
How many
cells
are there in an
organism
?
How many
chromosome replications
occur per generation?
How many
ribosomal RNA
gene copies are in the genome?
What is the
permeability
of the cell membrane?
How many
photons
does it take to make a
cyanobacterium
?
How many
virions
result from a single viral infection?
Epilogue
whet your appetite
>
How does metabolic rate scale with size?
>
How many reactions do enzymes carry out each second?
>
What is the turnover time of metabolites?
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