"He thinks you know his brother."
Translation:Он думает, ты знаешь его брата.
This masculine noun is animate and ends in a consonant (брат), so in the accusative form, you add “а” in the end.
As hinted at by apveay, animate masculine nouns have an accusative form that is identical to the genitive form. However, any adjectives that describe them still have their normal accusative form.
What is the difference between animate noun and inanimate noun? Could you please provide some examples here?
Animate nouns are things that are alive and can move by themselves, e.g. people, animals. Everything else is an inanimate noun, e.g. concepts, plants, cars.
It's a general rule of grammar, according to https://en.wikibooks.org/wiki/Russian/Grammar/Accusative_case1
Masculine nouns in the accusative case take nominative endings if they are inanimate and genitive endings if they are animate. In simple terms, for Masculine Accusative nouns, inanimate objects do not change their default ending, while such animated nouns either add -а or replace -й and -ь with -я.
why was a comma placed here? In english it wouldn't make sense to separate it because it splits the continuation of a thought.
In Russian, parts of a compound or complex sentence are typically separated by a comma.
This sentence is the equivalent of "Он думает, (что) ты знаешь его брата."
The conjunction что (that) which introduces a new dependent clause, must be preceded by a comma.
"Он думает ты готовишь его брата" Duolingo can get really dark at times