Scaling and Scales in Biology�Limits to Bacterial Growth

MCB137L/237L

Spring 2025

Developing Intuition: What Sets the Scale of X?

The Incredible Diversity of Time Scales in Biological Processes

What Sets the Scale for Bacterial Growth?

• Your turn: Estimate the division time in this movie
• What sets the time scale for bacterial division?
• Let’s answer this question by developing a feeling for the organism!

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Your turn: What sets the limit on how fast one cell can become two cells?

10 μm

What is in a cell? Everything needs to be duplicated in order for a cell to divide

Everything is transported or synthesized

Everything is transported or synthesized

The Molecular Census of E. coli and the Importance of Reproducibility

Taking the �E. coli census using mass spectrometry

Reproducibility in the E. coli cell census

The building blocks of proteins

Importing Carbon Skeletons

• How many copies do you need?
• Can you fit more on the membrane without crowding?

Everything is transported or synthesized

Paying the workers:�The energetic cost of making proteins

• 4 ATPs worth of energy per amino acid incorporated

Stouthamer’s analysis of ATP usage in bacteria

Synthesizing ATP: Your turn

ATP Synthase

Rotating at the speed of a jet engine

Everything is transported or synthesized

Lipids in E. coli

Lipid Synthesis

Everything is transported or synthesized

Peptidoglycan Synthesis

Everything is transported or synthesized

The molecular machines that link the “two great polymer languages”

The Central Dogma in Action

Miller et al., 1970, Science 169:392

The Machines of the Central Dogma

• DNA polymerase
• 500-1000 nt/s (for E. coli, probably 600 nt/s)
• RNA polymerase
• 30-90 nt/s
• Ribosome
• 10-20 aa/s

How fast can a cell replicate all of its DNA?

E. coli? Fastest cell division time ~20 minutes

Drosophila? Fastest cell division time ~ 8 minutes (!)

Fastest bacterial division times:

Vibrio natriegens - 9.8 minutes

Clostridium perfringens ~6.3 min

DNA replication

Your turn: Estimate the rate of DNA replication

• As replication complex moves along, it replaces dsDNA on tether with ssDNA. This shortens the tether and hence by examining tether shortening (as reported by bead motion) one can measure kinetics of the replication complex.

Van Oijen et al., Nature

Bacteria Have One Origin of Replication

E. coli DNA replication: Making your daughter and granddaughter simultaneously

Cell Biology by the Numbers

E. coli DNA replication: Making your daughter and granddaughter simultaneously

Everything is transported or synthesized

How Long Does It Take to Make All Proteins?

• How many proteins are there in the cell?
• How many ribosomes are there?
• How long does it take for these ribosomes to make all proteins?

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How Many Ribosomes Are There in a Single Cell?

• What are some approaches for making this estimate?
• Overall protein synthesis rate
• Volume and volume fraction
• Others?

Estimating the number of Ribosomes in�E. coli Using EM

Baumeister lab, MPI

Cryo Electron Microscopy image of Spiroplasma melliferum

Number of Ribosomes in E. coli Using Super-Resolution Microscopy

Weisshaar lab, University of Wisconsin

What is larger, a fast growing or a slow growing E. coli?

Faster Growing Cells Have More Ribosomes

• How long does it take for one ribosome to make another ribosome?

E. coli and Salmonella handbook

Faster Growing Cells Have More Ribosomes

Scott, et al., Science (2010)

Everything is transported or synthesized

Ribosomal RNA

How Long Does It Take to Make Ribosomal RNA?

• What’s the maximum transcription rate?
• How long does it take to make all rRNA molecules?

Even at maximum speed, RNAP cannot transcribe a single RNA to make all ribosomes!

Cell’s solution: Parallelize again!�Have multiple copies of the rRNA genes

Everything is transported or synthesized

Ribosomal composition

Ribosome Production Cannot Be Parallelized

Limits to Bacterial Growth