Coquus aquam addit, ut panis mollis sit.

Because aquam is the direct object of addit: it is the thing the cook is adding.

• aqua = water as a nominative subject form
• aquam = water as an accusative object form

In this sentence:

• Coquus = the cook, the one doing the action
• aquam = the water, the thing being added
• addit = adds

So Latin uses the accusative for aquam.

Because panis is the subject of sit, not the object of addit.

In the clause ut panis mollis sit:

• panis = the bread
• mollis = soft
• sit = may be / is to be

So the bread is the thing that is soft. That makes panis the subject of the verb sit, so it stays in the nominative case.

If it were panem, that would be accusative, which would suggest bread was an object instead.

Because after ut in a purpose clause, Latin normally uses the subjunctive, not the indicative.

So:

• est = is (indicative)
• sit = may be / might be / be (subjunctive)

Here ut panis mollis sit means something like:

• so that the bread may be soft
• in order that the bread be soft

This is one of the most common uses of the subjunctive in Latin.

Here ut means so that or in order that.

It introduces the reason or goal behind the action:

• Coquus aquam addit = the cook adds water
• ut panis mollis sit = so that the bread may be soft

So the whole sentence shows purpose.

Important: ut can mean different things in different sentences, but here it is specifically a purpose word.

Because mollis is an adjective agreeing with panis.

In Latin, adjectives must agree with the nouns they describe in:

• number
• case
• gender

Here:

• panis is singular nominative
• so mollis is also singular nominative

Also, mollis is a third-declension adjective, so its nominative singular masculine/feminine form is mollis.

So panis mollis means soft bread or, in this sentence, the bread is soft.

It is agreeing with panis, which is masculine in Latin.

Even though mollis has the same form for masculine and feminine in the nominative singular, its gender here is understood from the noun it describes:

• panis = masculine
• mollis = masculine because it agrees with panis

So grammatically it is masculine, even though the form itself does not change between masculine and feminine.

They are present for slightly different reasons.

• addit is present indicative: he adds
• sit is present subjunctive: may be / be

The main verb addit simply states what the cook does.
The subordinate verb sit is present subjunctive because the sentence expresses a present-purpose idea: the cook adds water so that the bread may be soft.

So although both are present forms, they are not the same mood:

• addit = indicative
• sit = subjunctive

Yes. Ut panis mollis sit is a classic purpose clause.

A purpose clause usually has:

• ut
• a subjunctive verb

and it answers the question why?

Why does the cook add water?

• ut panis mollis sit
• so that the bread may be soft

That is exactly what a purpose clause does.

Yes. Latin word order is much freer than English word order because the endings show the grammatical relationships.

This sentence could be rearranged in several ways and still mean basically the same thing, for example:

• Aquam coquus addit, ut panis mollis sit.
• Coquus addit aquam, ut panis mollis sit.

However, the original order is natural and clear. Word order in Latin often affects emphasis more than basic meaning.

That comma is a feature of modern punctuation, used to separate the main clause from the subordinate clause.

• Main clause: Coquus aquam addit
• Subordinate clause: ut panis mollis sit

Ancient Latin manuscripts did not use punctuation in the same way modern editions do. So the comma is helpful for readers, but it is not part of the grammar itself.

A very literal translation would be:

• The cook adds water so that the bread may be soft.

But in more natural English, you might say:

• The cook adds water so that the bread is soft.
• The cook adds water to make the bread soft.

Latin often uses a structure with ut + subjunctive where English may prefer a smoother expression like to make or so that.