Conjunctions

Czech sentences can get very long and complicated. They often contain many embedded clauses (sentences in a sentence) that are further develop the main clause.

The structure of compound sentences and the relationships between the clauses determine the use of commas. The Czech language has strict rules on how to use commas. The place of a comma can determine the meaning of the whole sentence.
Czech compound sentences are full of commas - Luckily, this doesn't affect the spoken language.

simple sentence:
Učím se český jazyk. (I am learning the Czech language.)

compound sentence (of 8 clauses):
Učím se český jazyk a musím přiznat, že je to velice obtížné, protože čeština je velice těžká, jelikož obsahuje hodně gramatických pravidel a způsob tvorby a odvozování slov sou neskutečně náročné, ale to nevadí, i přesto jsem odhodlaný se tu zatracenou češtinu naučit.
(I am learning the Czech language, and I have to admit that it is very difficult, because the Czech language is very difficult, as it contains a lot of grammatical rules and the way of creating and deriving words are incredibly difficult, but it does not matter, despite everything, I am determined to learn that bloody Czech language.

Examples of conjunctions:
Conjunctions are little words that are connecting clauses within the main sentence.

a (and)
Never preceded by a comma (unless it is required by the sentence structure or when it is part of composite conjunction, such as "a proto.")
Petr čte knížku a Marie peče dort. (Peter is reading a book and Maria is baking a cake)

i (and)
Never preceded by a coma. It usually connects words rather than sentences ("both... and...")
Pes i kočka jsou na posteli. (Both a dog and a cat are on the bed.)

abych/aby/abychom/abyste (to, in order to so that)
Aways preceded by a comma.
Petr se učí česky, aby rozuměl své manželce. (Petr is learning Czech in order to understand his wife.)

ale (but)
Always preceded by a comma.
Venku je pěkně, ale na výlet nepojedeme. (It's nice outside, but we're not going on a trip.)

že (that)
Always preceded by a comma.
Honza říká, že jeho pes moc štěká. (Honza says that his dog barks a lot.)

který/která/které/kteří/které/která (who, which, that)
Aways preceded by a comma.
The suffix depends on the subject of the sentence.
Je to to auto, které stojí před obchodem. (It's that car that's in front of the shop.)

protože (because)
Always preceded by a comma.
Mám tě rád, protože jsi hodný. (I like you because you are kind.)

když (when)
Always preceded by a comma.
Petr se nudí, když je ve škole. (Petr is bored when he is at school.)

až (as late as, not before, when - in the future)
Always preceded by a comma when connecting two sentences.
Petr půjde spát, až se umyje. (Peter will go to sleep when he washes himself.)

jestli/jestliže/pokud (if, whether)
Aways preceded by a comma.
Marie tam půjde, jestli tam půjde Petr. (Marie will go there if Peter goes there.)

kdyby (if, in case)
Always preceded by a comma.
Petr by šel ven, kdyby přestalo pršet. (Petr would go out if it stopped raining.)

nebo/anebo/či (or)
It may or may not be preceded by a comma (complex rules).
Chci jít k řece nebo chci jít jezdit na kole. (I want to go to the river or I want to go cycling.)

a Nebo (either... or...)
Never preceded by a comma.
Koupím hrušky a nebo koupím jablka. (I will buy either pears or I will buy apples.)

buď..., nebo.../ anbo... (either... or...)
A comma always separates it.
*Buď pojedeme v úterý, nebo budeme doma. (We will either go on Tuesday or we will be at home.)

(a) proto - (and) that is why, (and) so, (and) for that reason
Always preceded by a comma.
Neumím fotbal, a proto musím víc trénovat. (I can't play football, so/(and) that's why I have to train more.)

i když/přestože (although, in spite of)
Always preceded by a comma.
Petr odpočívá, i když ještě má práci. (Petr is resting, even though he still has work to do.)

ani,... ani... (neither..., nor)
Always separated by a comma.
Ani já, ani ty neumíme česky. (Neither you nor I speak Czech.)

aniž (without)
Always preceded by a comma.
Petr šel ven, aniž by se najedl. (Peter went out without eating.)

než (than)
Always preceded by a comma when connecting sentences. Not preceded by a comma when connecting words.
Honza byl rychlejší, než jsme čekali. (Honza was faster than we expected.)
Petr je větší než Honza (Peter is taller than Honza.)