Pregnancy-associated plasma protein-A (PAPP-A) largest of the pregnancy associated proteins produced by both embryo and placenta ( syncytiocytotrophoblasts) during pregnancy (Placenta Notes). This protein is thought to have several different functions, including preventing recognition of the fetus by the maternal immune system, matrix mineralization and angiogenesis. Levels of PAPP-A rise from first detection in the first trimester until term.

Maternal serum concentrations are related to subsequent fetal growth and this relationship has suggested that it can be used as a diagnostic test for adverse pregnancy outcomes (intrauterine growth restriction, premature birth, preeclampsia, and stillbirth).

(taken from the University NSW Embrology website)

Human chorionic gonadotropin (hCG) is a hormone produced in pregnancy that is made by the embryo soon after conception and later by the syncytiotrophoblast (part of the placenta). Its role is to prevent the disintegration of the corpus luteum of the ovary and thereby maintain progesterone production that is critical for a pregnancy in humans. hCG may have additional functions; for instance, it is thought that hCG affects the immune tolerance of the pregnancy. Early pregnancy testing, in general, is based on the detection or measurement of hCG. Because hCG is produced also by some kinds of tumor, hCG is an important tumor marker, but it is not known whether this production is a contributing cause or an effect of tumorigenesis.

(taken from Wikopedia)

Both proteins have 'normal' function during the pregnancy. I don't think they have fully worked out why the altered levels occur more often in pregnancies when the bub has down syndrome. Or why the levels can be altered when the bub does not have down syndrome.

They have just worked out that by combining the results of all these different screening tests (serum/NT scan/age) they can more accurately calculate the probability so that parents have more info and they can then consider whether they want to have more invasive tests to give a definitive answer to whether the bub has a chromosomal variation.

I think it is great that you are asking the questions.