I am so sorry that we have to start this way.
The beginning of the universe means we need to talk about the smallest, most fundamental parts of the universe, since they are the building blocks for the rest of it. So instead of easing you into our story, we have to jump into some of the deepest and most complex physics that we have discovered so far.
Good luck, and feel free to jump ahead!
We begin at, well, the beginning!
Our universe started out at a singular point that is infinitely small and infinitely dense. Nobody was around to see this point but we figured out that it existed based on evidence that our universe is expanding. If the whole universe is expanding, it must have all started from a tiny point. From that tiny point, energy erupted marking the beginning of space and time. We call this event The Big Bang.
Energy is fickle and always tends to find the most stable configuration possible. The energy condenses into a form that we call a string and we represent it as vibrations at specific frequencies, similar to a musical note. It’s easiest to understand strings with music because we can represent both with waves. Good sounding notes are waves with “harmonic resonance” meaning they are energetically stable.
Think about splashing around in a pool of water. The waves that form on the surface of the water will slosh around and interfere. The water in the pool will eventually settle into less choppy, less energetic, waves. Strings are the vibrations of energy that have calmed enough to exist. 
Depending on the exact frequency of the harmonic resonance, we give the string specific attributes with names like: mass, charge, spin, color, flavor, etc. That’s right, mass is just another attribute of energy. Strings helps Einstein’s equation E = mc2 to make way more sense: mass is just condensed energy!
Strings have the ability to interfere with each other and form composite harmonics. When the composite harmonic lowers the overall energy, we see it as an attractive force caused by destructive interference; conversely, when the composite harmonic increases the overall energy, it is seen as a repulsive force caused by constructive interference. Let’s keep with the musical allegory: when you hear two notes played at the same time, it’s called a chord.
Anybody who’s ever tinkered with a piano knows that some chords sound better than others, the good sounding chords are similar to the stable composite harmonics of strings. Musical notes interfere with each other in the same way that energy harmonics do. Some of the strings have frequencies that can pair to destructively interfere while other strings must form groups of three in order to find the lowest harmonic composite frequency.
Some strings, called quarks, have a three-way attribute called color. We’ve labeled the possible colors “red,” “green,” or “blue.” Quarks aren’t very stable on their own but find stability in groups of three. A stable group of three quarks has one of each color.
Groups of three quarks are able to trade little bits of energy, constantly playing “hot potato” with it. The energy, when absorbed or released by the quark changes the color attribute. In the process, the three slightly different strings are able to destructively interfere to a stable harmonic.
Quarks also have an two-way attribute called charge and we denote it as either “positive” or “negative”. Neutral charge means the charge attribute is nonexistent or balanced.
Because quarks exist with different amounts of charge, we give them specific names to designate what type of quark it is. The name is called the flavor and most of the quarks in the universe have a flavor of either “up” or “down.” When two up quarks and one down bunch up, we measure it’s overall charge as +1 and we call it a proton. When two downs and one up cluster, it has a neutral charge and we call it a neutron. Neutrons will not experience the force from charged particles.
Quarks aren’t the only type of strings to condense, they are actually quite large compared to some of the other condensations. Another type, that you may have heard of, is called an electron and it has a charge attribute equal but opposite to that of a proton, so we call it -1.
When a proton and an electron get near to each other, they will attract each other in order for their charges to destructively interfere and lower the overall energy. We call this proton-electron combo an atom, specifically the hydrogen atom if it only has one proton.
Remember when you thought that atoms were the smallest things in your universe?