What happens to atoms during chemical reactions?

They exchange atoms, if you are talking about electrovalent bonds. Suppose you've got two atoms. One is Sodium (#Na^11#) which has 1 electron in its outer shell because the number of electrons in its shell K is = 2 ,shell L =8 & shell M= 1 and the other one is Chlorine (#Cl^17#) which has 7 electrons in its outer shell because the number of electrons in its shell K is = 2 ,shell L =8 & shell M= 7. It's a habit of the atoms to thrive to have as many electrons as the noble gas nearest to them in the periodic table has. Most of the atoms want to have 8 electrons in their outer shell. So,you can see that if Sodium loses one electron somehow,it can have 8 electrons in its outer shell as the shell M would not exist anymore and on the other hand if Chlorine can gain one electron somehow,it'd have 8 electrons in its outer shell. So it's quite sure that these two would like to bond with each other as they can fulfill their needs perfectly. So when they'd react, Sodium would contribute one electron to Chlorine and Sodium would form a #Na^+# ion and Chlorine would form a #Cl^-# ion and they would stick together. So you've got Sodium Chloride (NaCl). All other chemical reactions sorta work like this unless they are convalent bonds. At the time of convalent bonding,the atoms do not exchange electrons,they share it. If you have got a Carbon (#C^6#) atom and four Hydrogen (#H^1#) atoms,they would form a convalent bond. Carbon would share 4 electrons in its outer shell with each Hydrogen and each Hydrogen would share 1 electron with the Carbon atom. So, Ta-da! each Hydrogen has got 2 atoms ( Hydrogen wants to be like Helium which has 2 electrons in its outer shell.) and Carbon has got 8 electrons, 4 of its own and the others from each Hydrogen. You got Methane (CH4).