About the position of "are"

Question

1. You definitely know what are ventricles and the atria (or atriums), so just as a reminder... (it seems grammatically wrong)

2. You definitely know what the atria (atriums) and ventricles are, so just as a reminder...

3. "What are ventricles and the atria (or atriums)?" You definitely know the answer to this question, so just as a reminder...

Are these three sentences grammatically correct? Then what is the difference between them, if any?

Let me give you another example (& another question, simultaneously) :

A: Which do you think the best choice is?

( B: "which one do you think is the best choice?"

C:"which choice do you think is the best?" )

between these options in the parentheses & also between #2 & #3

This is one of those BrE & AmE issues, I suppose.

I've heard these kinds of sentences a lot (with this structure I mean):

"You know/X explains/Y describes/etc + what + {plural noun} + actually/really/etc + are."

e.g. If you look at this how-to book, it explains what these cleverly designed gadgets actually are.

Does this structure always work?

I wonder whether the usage of the adverbs like really/actually/certainly/etc after {plural noun} makes any difference in meaning or not.

For example:

You figure out what these beautiful jungles are.

(I think this example sounds a little weird)

Answer 1

You definitely know what are ventricles and the atria (or atriums), so just as a reminder... (it seems grammatically wrong)

You are correct, this one is grammatically wrong. When we report a question, use a relative clause, or similar forms like this, the object often moves to the beginning of the clause. Let's consider a simple example, first:

I like this cat.

As a relative clause:

This is the cat that I like.

What happened here, is that "this cat" became the relative pronoun "that", and moved to the front of the clause. As such, "like" should be at the end.

For your sentence: "ventricles are this thing" becomes "what ventricles are" in the same way. As such, numbers 2 and 3 for your first example are entirely correct.

For your second case, the difference is a little harder, but simply put, they're all correct. The difference is between subject questions and object questions. Let's look at the first example again. First we have the object question (where the object is unknown):

He likes this cat. What does he like?

Next is the subject question, where the subject is unknown:

He likes this cat. Who likes this cat?

In the subject question, the word order does not change.

In your question, "Which is the best choice?", could be one of two statements:

A is the best choice.

The best choice is A.

From this, we can see that replacing "A" can result in either a subject or object question, so both (all) word orders are correct.