All of those concepts describe the bulk reaction. A single mutation happens in a single molecule, one of the two strands of the DNA genome of the bacteria.
If we started with genetically identical bacteria we would observe different mutations happening in different offspring, even though their ancestors were genetically identical. We can measure the mutation rate across many generations and many populations, but the individual mutations are not predictable and can only be described stochastically.
Artificial DNA synthesis might be helpful here. I often order short DNA molecules called oligonucleotides (a few nucleotides), or oligos for short, usually in nmole amounts. These are made synthetically by adding one base at a time in a non-enzymatic process. Most of the time I want all of the oligos to be the same sequence. However, sometimes I do order what are called degenerate oligos which can be more than one base at a specific position. For example, if I order an oligo with the sequence AAATTTB, that last base can be a C,G, or T. What they do is add all three bases to that cycle of the oligo extension so we get a random attachment of the different bases to different oligos. There is no way to predict ahead of time which specific oligo molecule will get which base. The same applies to mutations.
I am considering how you would get the single bacterium - I assume it is from a bulk sample. If so, there would be a probability that you may select a phage resistant strain or one that is not, since your comments indicate the mutation(s) are linked to the reproduction rate(s) while the phage would then knock out the non-resistant ones.
You spread the bacteria out and let them grow on an agar plate. The next day you will have isolated colonies which are the descendants of a single bacterium. It’s what I described as “streaking for isolation” in one of the earlier posts.
Those single, well separated colonies towards the top of the plate come from a single bacterium.
Note: E coli live as single rod shaped bacterium, so the above description does work for E coli. However, different species of bacteria can grow as chains/groups of individual bacteria that share very recent common ancestry. In these cases we would describe the multi-cellular chain as a colony forming unit.
There is a chance of picking a colony that came from a bacterium that recently acquired phage resistance mutation. However, it’s not very probable. We are talking a few hundred phage resistant bacteria out of billions, so something like 1 in 10 million colonies will be phage resistant.
Also, if the single bacterium founder was phage resistant then it would show up in the results of the experiment. Instead of getting just ~100 phage resistant colonies at the end of the experiment you would get billions.
Then we would expect to see the same mutation happen every time in identical reactions, but that’s not what we observe. We see different mutations occurring in different bacteria, even though they were genetically identical.
It’s counting the number of mutations and dividing by the number of DNA replication cycles, usually normalized by the number of bases that are copied. Reported mutation rates for E coli are around 2E-10 per nucleotide copied in a genome of ~4.5E6 nucleotide pairs. So there will be cell divisions where there aren’t any mutations, but a few will have a mutation.
I think we are still not getting to the main point, so I will say this - is the resistant mutation triggered by introduction of the phage? In your previous response you seem to indicate that mutations were spontaneous and accumulated with reproduction rates, while the phage deselected the non-mutated ones.
In other words, they are statistical.
Unless you’re saying that chemistry is done by taking one atom of this and another of that and putting them together into single molecules.
That they are statistical is inherent in the concept of moles.
If some given mutation is the result of a cosmic ray, of course it’s random: neither the cosmic ray nor the DNA string have any input as to where the cosmic ray will strike.
The same is true of any other mutagen or mutagenic process.
A rate is a distribution across a sample, e.g. the rate of traffic past a certain point is a matter of how many cars pass regardless of their speed. That means that a rate is the result of measuring a bulk sample. The same applies to lava flows, glacier movements, etc.
Yes, an atom, or interimediate reacts with another - that is why we develop mechanisms. I have provided info for a simple kinetcs scheme for H2 and O2. The mechanism is well understood:
Step 1: Initiation The reaction starts with the breaking of the H₂ and O₂ molecules into their respective atoms. This step requires a significant amount of energy due to the strong H-H and O=O bonds.
H2→2H
O2→2O
Step 2: Propagation Once we have the hydrogen and oxygen atoms, they can combine to form intermediate species. These intermediate species are highly reactive and propagate the reaction further.
H+O2→HO2
HO2+H→2O
Step 3: Chain Branching In this step, the hydroxyl radicals (OH) formed in the propagation step react with hydrogen molecules to produce more hydrogen atoms and water. This step is crucial as it leads to a branching chain reaction, which rapidly increases the rate of reaction.
OH+H2→H2O
Step 4: Termination Finally, the reaction reaches a termination step where the reactive intermediate species are consumed, leading to the formation of stable water molecules.
H+OH→H2O
Summarizing the overall reaction mechanism:
Initiation: Breaking H₂ and O₂ into atoms.
Propagation: Formation of HO₂ and OH radicals.
Chain Branching: OH radicals react with H₂, forming water and more H atoms.
Termination: Formation of stable H₂O molecules.
This reaction mechanism shows how complex and fascinating the process of forming water from hydrogen and oxygen can be.
