Microbiology Questions

ILikeBananas

I'm doing an applied maths masters and my disertation is on modelling the dynamics of phenotypic diversity in isogenic populations of bacteria.

I don't come from a biological background so I've had to teach myself a lot of the basics in order that I could understand the academic papers out there. Now I'm writing the segment of my dissertation on the background theory and I keep running into what seem like fundamental questions that not only do I not know but I cannot seem to find the answers to easily. So in no particular order:

1. Is the process of Gene expression responsible for creating every part of every new bacteria cell?

2. I've read that 50% of a bacteria cell's mass is made up of protein what is the rest made up of?

(The two questions above are related really in that if the answer to question 1 is no then I know that the other 50% is made up of other things beside DNA and RNA in 2)

3. I keep reading about phenotypic variation occurring when different cells exist with the same genotype but different phenotypes due to different expression levels of proteins. Does this mean that one of these cells actually has more proteins in total than the other or is it that it just has more proteins of a particular type?

4. Lastly, I have this image in my head of the cell using gene expression as a means of providing it with the RNA and protein that it needs to pretty much do everything it needs to function (especially growing and thus subsequently reproducing by binary fission). Is this accurate or am I missing out on something?

Tree

ILikeBananas wrote: »

I'm doing an applied maths masters and my disertation is on modelling the dynamics of phenotypic diversity in isogenic populations of bacteria.

I don't come from a biological background so I've had to teach myself a lot of the basics in order that I could understand the academic papers out there. Now I'm writing the segment of my dissertation on the background theory and I keep running into what seem like fundamental questions that not only do I not know but I cannot seem to find the answers to easily. So in no particular order:

1. Is the process of Gene expression responsible for creating every part of every new bacteria cell?

2. I've read that 50% of a bacteria cell's mass is made up of protein what is the rest made up of?

(The two questions above are related really in that if the answer to question 1 is no then I know that the other 50% is made up of other things beside DNA and RNA in 2)

3. I keep reading about phenotypic variation occurring when different cells exist with the same genotype but different phenotypes due to different expression levels of proteins. Does this mean that one of these cells actually has more proteins in total than the other or is it that it just has more proteins of a particular type?

4. Lastly, I have this image in my head of the cell using gene expression as a means of providing it with the RNA and protein that it needs to pretty much do everything it needs to function (especially growing and thus subsequently reproducing by binary fission). Is this accurate or am I missing out on something?

1. Gene expression is responsible for the generation of protein.
2. Lipids, water, carbohydrates? 50% of a cell being DNA is a lot, (also, is that dry weight) but that will depend on teh cell in quesiton.

3. Consider that all the cells in your body pretty much have the same genotype (there's some small exceptoins like VDJ recomb in lymphocytes, but that's a special case). The protein content and type will depend on the specific cell (some might be different in size), the expression of protein is controlled by genes and other proteins, by switching off one set and on another, you can get a totally different phenotuype.

4. Gene expression is pretty important for life alright.

I like Lodish's Cell and molecular biology, if you wanna get a textbook from the library and get in nice and deep into the genetics stuff, it's a great book.

Not sure if this is the level/sort of answer you're after

ILikeBananas

Tree wrote: »

1. Gene expression is responsible for the generation of protein.
2. Lipids, water, carbohydrates? 50% of a cell being DNA is a lot, (also, is that dry weight) but that will depend on teh cell in quesiton.

3. Consider that all the cells in your body pretty much have the same genotype (there's some small exceptoins like VDJ recomb in lymphocytes, but that's a special case). The protein content and type will depend on the specific cell (some might be different in size), the expression of protein is controlled by genes and other proteins, by switching off one set and on another, you can get a totally different phenotuype.

4. Gene expression is pretty important for life alright.

I like Lodish's Cell and molecular biology, if you wanna get a textbook from the library and get in nice and deep into the genetics stuff, it's a great book.

Not sure if this is the level/sort of answer you're after

Thanks for the reply. Yes that was a dry weight figure for the protein content.

So where do the lipids and carbohydrates come from? Like I understand that the proteins and RNA are synthesised through the process of gene expression but I'm just wondering how everything else gets in there?

Your answer to question 3 is very interesting. I've not thought of it like that before. Can we use the term phenotype to describe a subset of a larger organism though? Like, we can refer to the phenotype of the human as a whole but can we also then refer to the phenotype of their skin cells for example?

darjeeling

ILikeBananas wrote: »

So where do the lipids and carbohydrates come from? Like I understand that the proteins and RNA are synthesised through the process of gene expression but I'm just wondering how everything else gets in there?

Some proteins are nano-machines that assemble things from precursors. Many of the lipids and carbohydrates in the cell (those that aren't taken in directly from the surroundings) are produced by these proteins (or 'enzymes').

For example, the major biochemical cellular pathways involved in fatty acid and carbohydrate metabolism in animals are summarised on this site. The site shows how the pathways interact, and outlines the key enzymes involved.

mk1600

1/ DNA is the code or all proteins in the cell, proteins control what is happening inside the cell (complex if you look deeper (look at lodish)). Gene expression is very complicated. One line cannot explain it accurate.

2/carbohydrates, lipids,...... + inorganic compounds

3/epigentics, it is a regulation of how genes are expressed. It is too complicated to explain on an ad hoc basis, Lodish will be your friend.

4/DNA is the control of the cell, however it is not a case of this is the code this is what should be done. External stimulus, Internal stimulus and anything else controls gene expression.

It is not a mathematical system the cell. The complexity will only become apparent as you understand biology. I like the idea but....... not enough is understud about biology to put forward a solid scientific argument which results in x formula. Science is great and so is ethanol.

ILikeBananas

mk1600 wrote: »

It is not a mathematical system the cell. The complexity will only become apparent as you understand biology. I like the idea but....... not enough is understud about biology to put forward a solid scientific argument which results in x formula. Science is great and so is ethanol.

It certainly isn't a mathematical system but from a qualitative perspective it does generally follow basic rules. When anything follows rules it can be modeled to some extent. The sophistication of the model is of course limited in that it does not tackle the complex reasons behind these rules.

Apparently there is a lot of money being spent on the general area of biological modelling at the present, so in the coming years we should see these models increase in their sophistication which will hopefully help us learn more about the cell.

ILikeBananas

ILikeBananas wrote: »

So where do the lipids and carbohydrates come from? Like I understand that the proteins and RNA are synthesised through the process of gene expression but I'm just wondering how everything else gets in there?

Everything gets in there through nourishment. When new cells are made, either in single-celled or complex organisms, you can't just keep splitting a cell in two and have two daughter cells exactly equal to the parent. The DNA might be equal, but the actual amount of matter in the cell is halved. More matter needs to be assimilated, either before the splitting or afterwards, usually both. Which is why organisms eat/digest/absorb/assimilate molecules from outside the cell.

So all the components get in there through taking in matter from the outside, and then they get re-jigged by enzymes and processes to form the molecules needed. This is also related to your question 1 in your first post, in that while gene expression governs what proteins are created, the cell needs the right materials to assimilate into proteins, and also the right materials for the proteins (particularly enzymes) to work on/with. This is clearly seen in humans in that while you might have a genetic tendency to be muscly (I'm not actually sure if that exists, but you get me) but if you don't eat enough protein, you wont have the amino acids to undergo anabolic processes. To put it less confusingly (I ramble), gene expression is like any other kind of expression, it depends on a medium, like a writer can't express without paper or a singer can't express without air to breathe.

Thinking of gene expression as creating every part of a new cell is totally fine, but I personally wouldn't include a statement such as that in writing, as it's not strictly true.