It's not like a force on an individual ion because there's a lower concentration on the other side. It doesn't know or care about that. It's just thermodynamically favorable if there's an equal concentration. That can be exploited to do work, though, like when the proton gradient across the inner mitochondrial membrane makes the ATP synthase spin and generate ATP.

>Ions are able to pass the membrane freely because of their size and chemical properties your teacher discussed.

Oh no. Apart from a small amount of leakage, ions definitely do not freely cross the membrane. Having control over when and how ions cross membranes is critical to life, not just by enabling neuronal signaling in animals but in being harnessed for ATP synthesis across all domains of life.

Your teacher/professor is correct in that both the concentration gradient and the electric field contribute. The Gibbs free energy change of moving an ion across the membrane follows this equation:

ΔG = RTln(c_inside/c_outside) + zFV_membrane

So the first part would be the energy involved in moving with/against the concentration gradient, the second the energy involved in moving with/against the electric field.

Influenza is caused by RNA viruses with a segmented genome, so they can mutate and escape immunity very quickly. Tetanus is caused by certain soil bacteria that don't mutate nearly so rapidly (and aren't under as much selection pressure to escape human immunity, as they mainly live in soil).

> You might find you can consciously choose which eye is acting as the master; ambidextrous people (me) find this easier than most, or so I understand; we use both sides of our brain more readily.

Well, it's different with vision. Both eyes use both sides of the brain. More specifically, each side of the brain is responsible for one side of the visual field in each eye.

No, it's just a little less common than having same side dominance for eye and hand.

https://pubmed.ncbi.nlm.nih.gov/15513026/

>in a population with 9.25% left-handedness and 36.53% left-eyedness, 34.43% of right-handers and 57.14% of left-handers are left-eyed.

So 5.29% are left eye + left hand dominant and 59.50% are right eye + right eye dominant, meaning there's concordance in 64.79% of people. The remaining 35.21% have different dominant sides for eye and hand (31.25% left eye + right hand, 3.96% right eye + left hand).

> > > > > Nerves cannot be naturally regrown by the body,

Not entirely true, but in the CNS the regeneration capacity is extremely limited. Peripheral neurons can regenerate to a reasonable degree, typically guided along the existing path of supporting Schwann cells.

If there's a sequence of AUG in an RNA, then an RNA-dependent RNA polymerase can copy that to UAC in a newly synthesized RNA, because those bases "fit" in base pairs. Then the UAC in that RNA can be copied into AUG in a new RNA that's identical to the original one.

A ribosome can read the exact same AUG sequence and insert a methionine into a protein.

One method is essentially just straight copying while staying in the same language, while the other is translating to a different language. That's why the process of making proteins is called translation.

>If one bit of the RNA the virus injects, when read by the cell's machinery and assembled into a protein, builds one bit of the copy virus' RNA, then the copies can't have both a full copy of the RNA and a capsule and other proteins.

Why not? Are you assuming the RNA is consumed when it's read? It's not. Or are you thinking it can only be read in one way? There are two different kinds of systems for reading genetic information and making something based on the sequence. The ribosome reads three RNA bases at a time, dictating a protein sequence. Polymerases read one base at a time by matching up base pairs before insertion.

> > > > > Contrast that to AAV. AAV doesn’t really integrate into a genome (well isn’t supposed to in theory) - they work by creating what’s known as an episome (i.e a circular piece of dna that persists in cells and gets translated into the desired protein). AAVs can only shutoff a mutant gene if they carry a payload like siRNA/microRNA or something. AAVs never really fix the mutant gene, the episome just expresses the protein that’s not working. I suppose over the long run AAVs might not really ‘cure’ a genetic disease, because the episome will likely dilute out over time with cell divisions. You can only really administer an AAV once too because of immunogenicity issues.

That's often how they are used in practice, but unmodified AAVs are capable of insertion, in humans mostly at the AAVS1 locus.

In actual use, AAVs often cannot integrate into the cellular genome. It's just used to temporarily deliver something else. In fact it's a commonly used vector for CRISPR/Cas systems.

But it's true that unmodified AAVs are capable of integration. It's a lot more specific about that than lentiviral vectors, because AAVs mostly just integrate into the human genome at the AAVS1 site.

Lentiviral vectors can insert at many, many sites throughout the genome. The same applies for transposon systems such as Sleeping Beauty and PiggyBac.

As for CRISPR/Cas, that's a whole range of systems that is mainly distinguished by the ability to easily program targeting of a specific sequence (in almost any context). That can be used to insert something at a specific genomic site, but it can also be used for all sorts of other things. Some Cas enzymes don't even target DNA but instead target RNA.

>Actually, when you're at the scale of these molecular interactions, the concepts of rigidity hold up pretty nicely. (BTW, the broadest term for these kinds of interactions can be called "ligand-receptor binding", and the "lock-and-key" model works well for describing it.

That is not true. The lock and key model is known to be less correct than models such as induced fit or conformational selection.

> > > > > Water is a actually a very good coolant because it has a very high specific heat capacity of 4.2 J/(K g). This is typically twice as large as organic solvents and at least 4-5 times, sometimes more than 10 times larger than most solids (relative to mass). Since the thermal energy or heat is conserved during the transfer, this means that water can reduce the temperature of the material to be cooled by a certain degree, while its own temperature is increasing only by a fraction of that (considering somewhat similar mass).

Alternatively, you can rely on the very high enthalpy of vaporization of water, by using some form of evaporative cooling. Some animals rely on sweating for thermoregulation, while a lot of computer hardware relies on evaporative cooling in the form of heatpipes or vapor chambers.

Those descriptions are way too simplistic. Parkinson's is caused by a loss of dopaminergic neurons, but has little to do with reward signaling, it's a degeneration of the motor system.

Astrocyte processes may also help structurally stabilize (CNS) synapses.

Riboflavin, AKA vitamin B2, is intensely yellow and water-soluble, so whatever your body doesn't need just colors your urine.

It's even used as food coloring sometimes.

No, it's normal for the pigment to end up in the urine. There's just some variation in how fast it gets there, and on top of that the variation in urination pattern and how much red beet you tend to eat. That can all affect how much you see it coloring your urine.

https://www.sciencedirect.com/science/article/pii/S104366180500099X?via%3Dihub

I'd chuck it in the MinION sequencer in the lab and start getting some data on methylation, as well as telomere length. Problem is the association between age and methylation pattern and telomere length is somewhat weak in individuals, so you wouldn't be able to get more than a hint at their age.

Amino acids have a carboxylic acid and an amino group, so it's both an acid and a base. In any case, once you dissolve it in water you can just add other acids or bases to change the pH.

Our DNA and RNA are also acidic, the A literally stands for acid. But again it's just buffered by other stuff.

Well, Rapamycin mainly inhibits mTORC1, while this seems to target RICTOR for degradation and thus preventing assembly of mTORC2. So they would have complementary roles if you wanted inhibition of both complexes.

> > > > > What animals have a thyroid?

Vertebrates. Invertebrate chordates have an organ called the endostyle, which has some functional similarity and is very likely the evolutionary predecessor to the thyroid gland.

> Is iodine chemistry localized in a different organ in the ones that don’t?

Well... many aquatic invertebrates may rely mainly on exogenous thyroid hormones, so they don't need an organ for it. Other invertebrates may have their own endogenous production of thyroid hormones, but without a dedicated organ. Yet other invertebrates, particularly outside the bilaterians, may be less reliant on thyroid hormones in the first place, since they seem to lack an ortholog of the thyroid hormone receptor.

Here is an interesting review article about thyroid hormone signaling in invertebrates.

>Insulin is made by bacteria now

Or yeast. Bacteria usually give higher crude yields of protein, while yeast is better at making eukaryotic proteins correctly (or closer to it, at least).

There are thin cells called pericytes wrapped around the small blood vessels, and around that you have extensions of astrocyte cells. The barrier is too small to see with the naked eye.

Neurons, especially in the CNS (brain/spinal cord), are quite sensitive, and are usually kept in a sheltered environment separated from the blood by the blood-brain barrier. Astrocytes and other glial cells provide a controlled environment for the neurons. They do take nutrients from the blood, but they act as a filter to only let through the right things and in the concentrations that neurons prefer.

Even in other tissues, blood isn't usually supposed to leave the blood vessels, and can cause trouble if it does. Perhaps the easiest to understand is coagulation - if everything's clotted up, that will disrupt whatever else is supposed to be happening in that tissue. There are also immune molecules which tend to get activated and cause inflammation when outside blood vessels. Inflammation generally interferes with regular tissue function, and CNS neurons are particularly sensitive to it.

Blood also contains higher concentrations of stuff like iron that would damage neurons.

>Re “dosage compensation”, is it generally true that more copies of a gene means more gene expression?

Yes, it is true to varying extents.

Cancer cells often have genetic errors adding extra copies of oncogenes, which helps boost their growth etc. That wouldn't work if everything just got compensated back to baseline.

>Aren’t most genes regulated by homeostatic feedback systems?

There is a fair bit of that, but it wouldn't necessarily compensate fully. It also wouldn't be uniform, so some genes would have relatively more expression compared to others, which itself could have problematic effects.

>And what about the many, many plant species that get along just fine with duplicates or triplicates of their entire genome?

Well, at least those don't skew the relative dosage of different genes. It's still usually lethal in animals though, so it's an interesting question.