BI 559 Lecture 2: how big is a bacterial cell?
BI 559 Lecture 2
Notes and announcements:
BI 559 Lecture 2: how big is a bacterial cell?
Today:�
How big is a bacterial cell?
Milo, Phillips, and Orme, Cell Biology by the Numbers
microbe length scale, ~1 µm
1 µm
our bodies
How big is a bacterial cell?
Bacteria infecting a mammalian cell (sped up x150)
Listeria monocytogenes
*CDC
*wikipedia
Long-nosed Potoroo
(food-borne pathogen)
What’s the significance of this size?
1 µm
3 µm
1 µm
Approximate cell volume:
What’s the significance of this size?
1 µm
3 µm
1 µm
Approximate cell volume:
What’s the significance of this size?
1 µm
3 µm
1 µm
Approximate cell volume:
~3 femtoliters
What’s the significance of this size?
3 µm
1 µm
3 femtoliters
If there is one of a particular kind of molecule in a bacterial cell, what is its concentration?
Rounding up, 1 molecule in 1 bacterial cell has roughly a concentration of
What’s the significance of this size?
3 µm
1 µm
3 femtoliters
# in one bacterium | concentration |
1 | 1 nM |
1,000 | 1 µM |
1,000,000 | 1 mM |
1,000,000,000 | 1 M |
What’s the significance of this size?
3 µm
1 µm
3 femtoliters
# in one bacterium | concentration |
1 | 1 nM |
1,000 | 1 µM |
1,000,000 | 1 mM |
1,000,000,000 | 1 M |
molecule | # in one bacterium | concentration | citation(s) |
inorganic ions | ~108 | ~100-500 mM | |
H+ | 100 (!) | 10-7 M (~pH 7) | |
DNA basepairs | 5×106 | 5 mM | |
protein | 2-3×106 | 2-3 mM | Neidhardt and Umbarger Vol. 1, Ch. 3 |
ribosomes | 2×104 | 20 µM | Neidhardt and Umbarger Vol. 1, Ch. 3 |
mRNA | 2×103 | 2 µM | Neidhardt and Umbarger Vol. 1, Ch. 3 |
ATP | 1×107 | 10 mM |
*these values are mostly from E. coli under lab conditions!
What’s the significance of this size?
3 µm
1 µm
3 femtoliters
# in one bacterium | concentration |
1 | 1 nM |
1,000 | 1 µM |
1,000,000 | 1 mM |
1,000,000,000 | 1 M |
molecule | # in one bacterium | concentration | citation(s) |
Highly expressed protein (TufB, ribosome component, in exponential E. coli) | 58,000 | 58 µM | |
Low expressed protein (EnvZ, osmoregulation, in exponential E. coli) | 100 | 100 nM | |
Highly expressed mRNA (ompT, outer membrane protein, in exponential E. coli) | 100 | 100 nM | |
Low expressed mRNA (yhiJ, unknown maybe inositol metabolism, in exponentialE. coli) | 0.1 | 100 pM |
What’s the significance of this size?
3 µm
1 µm
3 femtoliters
# in one bacterium | concentration |
1 | 1 nM |
1,000 | 1 µM |
1,000,000 | 1 mM |
1,000,000,000 | 1 M |
How do people measure these values?
mRNA
RNA sequencing
RNA:
Field of “transcriptomics”
How do people measure these values?
Mass spectrometry
Proteins:
Proteins
+
+
+
+
+
+
+
Field of “proteomics”
How do people measure these values?
Common method: MALDI-TOF
Proteins:
Proteins
Matrix-assisted laser desorption/ionization:
method of ionizing and evaporating proteins
Time of flight:
method of determining mass
protein sample and gel matrix
detector
laser
-
+
high voltage
+
+
+
MALDI-TOF system
(much $$$)
Each circular spot contains one sample
What makes a cell?
3 µm
1 µm
nucleic acids
cell envelope
storage & misc
protein
Great resources for these kind of numbers
Note: the point of these things is not strictly the numbers themselves, but that comparing numbers and thinking about how they relate to biological processes forces you to think differently about biology!
How do bacterial cells transport things in their cytoplasm?
DNA
gene
RNA polymerase
?
10 µm
Mikael Häggström/wikimedia
Short answer: diffusion—stuff constantly bumps into each other.
We’ll see quantitatively why bacteria don’t have the transport systems like you see on the left.
Brownian motion
(these are large beads—not molecules—but it’s the same principle)
Diffusion is a means of molecular transport!
Ballistic motion vs. Brownian motion
Ballistic
Brownian/diffusive
Can we quantitatively predict this average? What does that tell us about transport within microbes?
We ask: in a given amount of time, how far do you go by diffusion?
If you are randomly bouncing around, there are many possible trajectories you can take.
So there are many distances you could travel. We can only talk about the average distance after a certain amount of time!
Let’s take a look then.
How far do you go on average after N steps? Let’s actually compute the average for different values of N in one dimension
N = 1
What are all the possibilities?
Series of steps
Displacement, r
{+1}
{-1}
1
-1
Hmmmm . . .
Squared displacement, r2
1
1
How far do you go on average after N steps? Let’s actually compute the average for different values of N in one dimension
N = 2
Series of steps
Displacement, r
{+1, +1}
{+1, -1}
2
0
Squared displacement, r2
4
0
{-1, +1}
{-1, -1}
0
-2
0
4
How far do you go on average after N steps? Let’s actually compute the average for different values of N in one dimension
N = 3
Series of steps
Displacement, r
{+1, +1, +1}
{+1, +1, -1}
3
1
Squared displacement, r2
9
1
{+1, -1, +1}
{+1, -1, -1}
1
-1
1
1
{-1, +1, +1}
{-1, -1, +1}
1
-1
1
1
{-1, -1, +1}
{-1, -1, -1}
-1
-3
1
9
How far do you go on average after N steps? Let’s actually compute the average for different values of N in one dimension
N (number of steps) | | |
1 | 0 | 1 |
2 | 0 | 2 |
3 | 0 | 3 |
Very physics/math derivation
Very physics/math derivation
(mean of sums is sum of means)
Diffusion constant: inversely proportional to molecule size
Why am I making such a big deal about this?�
What does transport in the cytoplasm look like?
Well maybe it looks like this?
We’ve never actually observed this, but why do we believe it?
How does this compare to ballistic transport?
How does this compare to ballistic transport?
Motor proteins in eukaryotes (e.g. dynein)
How does this compare to ballistic transport?
It’s proportional to the square root of time. This is highly unintuitive. Let’s see how it impacts how microbes transport things in their cytoplasm.
What do these equations mean for our bacteria?
The question I’m going to ask is: for a given distance, how long does diffusive vs. ballistic transport take to transport something that distance?
Driving an average of 20 miles/hour on Rt 9, how long does it take to drive the ~20 miles from Symphony Hall to Framingham, MA?
Let’s examine this in the context of a bacterium vs. a neuron.
What do these equations mean for our bacteria?
We’ll compare the transport times for:
*image from wikipedia
Bacterial cell
Neuron
What do these equations mean for our bacteria?
You can transport things way faster with these motor proteins. Why are bacteria not using these?!
Let’s zoom in on our relevant microbial length scale . . .
What do these equations mean for our bacteria?
Laws of physics and the size of microbes has revealed something quite deep across the entire living kingdom!
Microbes
Small size enables rapid transport across the cell for 0 cost with diffusion
Large cells
Must spend large protein and energy resources on elaborate transport machinery