Als de pasta klaar is, doet Tom er wat kaas op.

Because als introduces a subordinate clause. In Dutch subordinate clauses, the conjugated verb usually goes to the end.

So:

• de pasta is klaar = the pasta is ready
• als de pasta klaar is = when/if the pasta is ready

This is very normal Dutch word order:

• Ik weet dat hij thuis is.
• Als het regent, blijf ik binnen.

English does not do this, so it often feels strange at first.

Because the sentence starts with the als-clause:

• Als de pasta klaar is, ...

When something other than the subject comes first in a Dutch main clause, the finite verb must still be in second position. This is the usual V2 word order rule.

So after the introductory clause, Dutch says:

• Als de pasta klaar is, doet Tom er wat kaas op.

Not:

• Als de pasta klaar is, Tom doet ...

You can compare:

• Tom doet er wat kaas op.
• Als de pasta klaar is, doet Tom er wat kaas op.

In the second sentence, the whole clause Als de pasta klaar is takes the first position, so doet must come before Tom.

Als can mean if or when, depending on context.

In this sentence, it will often be understood as when, because cooking pasta naturally leads to the next action. But grammatically, als itself can cover both ideas.

So:

• Als de pasta klaar is...
  can mean When the pasta is ready...
  or If the pasta is ready...

The exact meaning depends on the situation.

Here er is part of er ... op, which refers back to something already known: in this case, the pasta.

So:

• Tom doet wat kaas op de pasta. = Tom puts some cheese on the pasta.
• Tom doet er wat kaas op. = Tom puts some cheese on it.

In Dutch, instead of repeating op de pasta, you often use er ... op.

A useful way to think of it is:

• er + preposition = it/there + preposition
• er ... op = on it

This is very common in Dutch.

Because er ... op is split here.

Dutch often combines er with a preposition:

• erop = on it
• erin = in it
• eraf = off it
• eraan = onto it / attached to it

But when other words come in between, it can split:

• Tom doet erop kaas.
• Tom doet er wat kaas op.

In your sentence, wat kaas comes between er and op, so op ends up near the end.

This is a very common Dutch pattern.

No. Here wat means some.

So:

• wat kaas = some cheese

This wat is often used with uncountable nouns or when the amount is not specific:

• wat water = some water
• wat suiker = some sugar
• wat geld = some money

So in this sentence, wat kaas does not mean what cheese. It simply means some cheese.

Yes, absolutely.

These are both natural:

• Tom doet wat kaas op de pasta.
• Tom doet er wat kaas op.

The second version avoids repeating de pasta and sounds very natural in Dutch. It is similar to the difference between:

• Tom puts some cheese on the pasta.
• Tom puts some cheese on it.

So the version with er is not a different meaning; it is just a more compact, more idiomatic way to refer back to de pasta.

Klaar is an adjective. It means ready or finished, depending on context.

In this sentence:

• de pasta is klaar = the pasta is ready

Dutch often uses klaar in everyday speech:

• Ik ben klaar. = I’m finished / I’m ready.
• Het eten is klaar. = The food is ready.
• Ben je klaar? = Are you ready?

So klaar is a very useful common word.

Because the sentence begins with a subordinate clause, and in Dutch that clause is normally separated from the main clause with a comma.

So:

• Als de pasta klaar is, doet Tom er wat kaas op.

This is standard punctuation in Dutch and helps show where the first clause ends and the main clause begins.

Here de pasta is grammatically singular.

That is why the verb is:

• de pasta ... is klaar

not:

• de pasta ... zijn klaar

Even though pasta may consist of many pieces, Dutch usually treats pasta as a singular mass noun here, just like English often does.