DNA Replication

Initiation:
- Helicase unwinds double helix and breaks the hydrogen bonds
- Single strand bonding pairs keep the DNA separated and stabilized
- Gyrase relives tension between the two strands of DNA by cutting them
- RNA Primase signals polymerase II by putting primers to begin replication

Elongation:
- DNA opens up as replication forks
- DNA polymerase II adds nucleotide to 3' end
- 2 strands: lagging/leading
- Leading strand: RNA primes starts replication and DNA polymerase III replicates 5 to 3 towards the opening
- Lagging strand replicates the 5 to 3 template strand so it is replicating 3 to 5. Since DNA polymerase III only replicates 5 to 3 in segments okazaki fragments. RNA primes starts each segment with primer and DNA polymerase III continues until the end of the segment.

Termination:
- DNA Ligase joins okazaki fragments together
- DNA polymerase I proofreads the bases then replaces the RNA with DNA
- The two DNA molecules separate

DNA Translation

Initiation:
- Initiator factors assemble small tRNA initiator and mRNA
-mRNA is transferred to the ribosome on the endoplasmic reticulum once it is moved out of the nucleus
- Ribosomes are made up of two units: large and small subunits
- Large subunits join together to form an active ribosome
- The large subunit contains three sites: E, P, and A
- P site has tRNA with polypeptides attached to it, A site has tRNA with amino acid to be added to the polypeptide, and E site has uncharged tRNA with no amino acid attached
- tRNA moves in the A site and reads the mRNA sequence in threes (codon) starting with AUG as the first codon

Elongation:
- Polypeptides become longer, one amino acid at a time
- tRNA contains anticodon that binds with these codons
- Each tRNA carries a peptide that when binded with the codon, it moves to the P site and picks up all of the other peptides from the previous tRNA in the P site. The previous tRNA moves to the E site and exits the ribosome.
- This creates a chain of peptides called polypeptide
- There are 64 combination of 3 pairs for base sequences but only 20 amino acids. This is due to the wobble effect making every amino acid responsible for 2-3 different base sequences and  decreasing the chance of mutation

Termination:
- Stop codon on mRNA is reached
- There are 3 base sequences that signal a stop codon for the polypeptide chain
- tRNA that carry the anticodons move into the A site and are the last tRNA to move in before translation stops
- Once translation stops, the ribosome breaks up and everything attached to it breaks off with the end result of a polypeptide chain and later on protein

DNA Transcription

Initiation:
- Transcription machine is assembled
- Transcription Factors spot out the promoter (TATA box)  and termination (AAUAA) region on either strand and begin copying the base sequences to make pre-mRNA.
- For each gene only one strand of double strand DNA is transcribed
- The strand being used to make the pre-mRNA is called the template (antisense) strand and the other strand is the coding (sense) strand
- RNA polymerase II crates an initiation complex
- DNA unwinds and RNA polymerase II starts transcription

Elongation:
- The coding strand and the RNA strand are very similar with Thymine being replaced with Uracil
- Nucleotides are added to the 3' end (OH)
- The m-RNA strand stars from the promoter and copies until the AAUAA
- The pre-mRNA is anti-parallel with the template strand and transcribes downstream

Termination:
- Once the RNA polymerase reaches the AAUAA sequence, transcription stops
- Pre-mRNA cuts off and  the DNA strands get winded back together
- Pre-mRNA is then guarded by a G-Cap on the 5' side and Poly-A-Tail on the 3' side due to enzymes in the cytoplasm that try to break down the mRNA
-Pre-mRNA contains useless sequence parts called introns that are not needed. They are taken out of the mRNA by spliceosome and the eons are connected.