# AP Biology/Genes and How They Work

This article has only one contributor. Therefore, it may suck (at looking good), be totally off-track (and be in a trainwreck), or be one-sided (how does this apply to Biology articles?). So jump in and prevent the potential kitten death toll.

## The Basics

Of course, let's start off simple. A gene is a piece of DNA which codes for one specific protein. A human has tens of thousands of genes! For example, the TP53 gene codes for the p53 protein. Special enzymes go in to the nucleus and "read" genes. They make a copy out of RNA. RNA is exactly the same thing as DNA, but is different because:
* RNA is not stuck inside the nucleus like DNA is,
* RNA is single-stranded, and
* RNA uses the base uracil instead of thymine.
The RNA is given to ribosomes, which read the RNA strand and uses the information on the RNA to make polypeptide chains, which then fold and - voila! - you have yourself a ready-to-go protein. Polypeptide chains are a giant strand of linked amino acids. There are twenty essential amino acids necessary to make protein.
This whole process is called expression, which basically means that whatever the particular gene codes for is being put into action.

## The Tougher Stuff

Now we're getting into details. Don't read this part until you understand the fundamentals. You might get confused and then have an incorrect perception of what we're going to say here!
This whole big thing is split up into two processes: transcription and translation. Transcription, process that comes first, is when DNA is copied into an RNA strand. Translation, on the other hand, is the reading of the information on that RNA strand, and making a protein based on that RNA strand.

### About RNA

Before we go too far into the deep ocean of information, we need to know some more about RNA.
There are actually three kinds of RNA:
* Messenger RNA, also called mRNA, is the copy of the DNA which the ribosomes read.
* Ribosomal RNA, or rRNA, makes up the ribosomes. This RNA has no genetic information in it whatsoever.
* Transfer RNA, or tRNA, bring amino acids to the ribosome during translation. (Don't worry too much about this - yet - we'll go over it in more depth in the translation section.)

### Transcription

When a gene is ready to be expressed, transcription initiation factors go in, along with RNA Polymerase, and bind to the DNA in a place called the promoter. (The RNA Polymerase is the big cheese here - it actually copies the DNA into the mRNA strand. Transcription Initiation Factors are only there to help the RNA Polymerase bind to the DNA.) RNA Polymerase then unwinds and splits apart a segment of the DNA to make a transcription bubble (otherwise RNA Polymerase cannot read the nucleotide sequence, as the nucleotides on both sides of the DNA are stuck together by hydrogen bonds). The transcription initiation factors leave. Then, by the rules of complimentarity, RNA polymerase starts transcribing the DNA from the template strand. Here's how it would work (the coding sequence is entirely fictional):
Here's the DNA segment RNA polymerase wants to transcribe:
| T | A | C | G | A | A |
RNA Polymerase reads the first nucleotide, and as, by the rules of complementarity, thymine pairs up with adenine (^ indicates the current position of RNA polymerase):
| T | A | C | G | A | A |
| A | | | | | |
Because RNA uses uracil instead of thymine, RNA polymerase would assign a uracil nucleotide for position 2:
| T | A | C | G | A | A |
| A | U | | | | |
Cytosine pairs up with guanine:
| T | A | C | G | A | A |
| A | U | G | | | |
| T | A | C | G | A | A |
| A | U | G | C | | |
And we already know the last two:
| T | A | C | G | A | A |
| A | U | G | C | U | |
| T | A | C | G | A | A |
| A | U | G | C | U | U |
Once RNA Polymerase is done making the mRNA strand, the mRNA strand is released along with RNA Polymerase, and the DNA reforms into a double helix.
However, our little friend, mRNA, isn't done here. The mRNA strand, the primary mRNA strand, is given a 5' cap (a modified guanine nucleotide) and a poly-A tail (just a series of adenine nucleotides). Then spliceosomes go in and cut off parts of the mRNA. This isn't random; what the spliceosomes are cutting off are the intron segments of the RNA, and leaving only the exons. Exons are the part of the genetic information which code for the protein (the parts that get EXpressed). Introns don't code for a protein. Then why are they there? They used to be called garbage, but now scientists think that introns might have some function. We used to think that humans have about 100,000 genes, but now it turns out we might only have about 30,000! How are we supposed to be alive with just 30,000? Well, there are different hypotheses. One hypothesis is that these introns might have an enzymatic function. Another is that introns allow the exons to be rearranged so that instead of just one protein you can make hundreds. Or the introns are some kind of molecular signals which tell the cells what to do.
Well, back to Earth. Once the cap and the poly-A tail are added, and the introns are spliced, we have a mature mRNA. It is important to note that prokaryotes do not have spliceosomes, and therefore do not have introns.

### Translation
#### tRNAs

Before we get too deep into translation, you'll need to learn more about tRNAs.
As you read in the basics, you learned that tRNAs bring amino acids to the ribosomes. But how?
Here's how. tRNAs are a chunk of RNA which have two important things: the amino acid itself, and the anticodon. The sequence of the three-nucleotide anticodon (ribosomes read by three - three nucleotides together are a codon) determines which amino acid is attached. For instance, if a tRNA molecule has the anticodon CCA, CCG, CCU, or CCC, the tRNA molecule will have the amino acid glycine.

#### Ribosomes

Ribosomes are made up of rRNA. They actually make the polypeptide chain which folds to become a protein. But how?
Ribosomes right off the shelf require some assembly, as they come in two halves, or ribosomal subunits. You really can't call them halves, though, as one "half" is bigger than the other.

#### The process

The first step is when the large and small ribosomal subunits snap onto a strand of mRNA. Now this is where the transfer RNA comes in. A transfer RNA comes in (the first codon, which is 3 nucleotides together, always dictates for methionine [AUG]) and latches on to the first codon by its anticodon. Now the second tRNA comes in and bonds to the second codon. The ribosome then *snap!* takes off the amino acid off the first tRNA and bonds it to the amino acid of the second tRNA. Then the first tRNA runs off to get another amino acid, while the ribosome moves along the mRNA, allowing another tRNA to bond to the third codon. This process repeats over and over until the ribosome gets to the stop codon on the mRNA, at which point a release factor binds to the stop codon (as the stop codon has no corresponding anticodon) and initiates the disassemblage of the two ribosomal subunits. The resulting polypeptide chain is also released to fold and become a fully functional protein.