Comprehensive Notes on Base Pairing, DNA Replication, Transcription, and Translation

Base pairing is conserved through evolution, meaning the rules are specific between purines and pyrimidines and are consistent across organisms.
Pyrimidines (uracil, cytosine, and thymine) have a single ring structure.
Purines (adenine and guanine) have a double ring structure.
Prokaryotes typically have circular chromosomes, while eukaryotes have multiple linear chromosomes.
Prokaryotic genomes are generally smaller than eukaryotic genomes.
Both prokaryotes and eukaryotes can contain plasmids, which are small, extra-chromosomal, double-stranded, circular DNA molecules.
In prokaryotes, plasmids are found in the cytosol.
In eukaryotes, plasmids are found in the nucleus.

The purpose of DNA replication is to ensure the continuity of hereditary information.
DNA replication occurs before cell division.
Replication allows the transmission of a complete genome from one generation to the next.
DNA replication is semiconservative: each original strand serves as a template for a new strand.
The new complementary strand pairs with one of the original strands.
Directionality influences the replication process.
DNA strands have a terminal phosphate group (5' end) and a terminal hydroxyl group (3' end).
The two strands of DNA run antiparallel to each other, meaning they run in opposite directions.
New nucleotides can only be added in the 5' to 3' direction.
One strand is made continuously (leading strand), while the other is synthesized discontinuously in fragments (lagging strand).

Helicase: unwinds the DNA strands.
Topoisomerase: relaxes the supercoil at the replication fork.
DNA polymerase:
- Synthesizes the new strand of DNA.
- Requires RNA primers to initiate synthesis.
- Attaches to the 3' end of the template.
- Builds strands in the 5' to 3' direction.
Ligase: joins the fragments on the lagging strand.

Genetic information flows from DNA to RNA to protein.
RNA molecules facilitate protein synthesis using DNA information.
Ribosomes contain RNA and assemble proteins.
Transcription: an enzyme directs the formation of an mRNA molecule.
DNA strands separate during transcription.
One strand serves as a template (non-coding strand, minus strand, or antisense strand).
The other strand is the coding strand.
The template strand depends on the gene being transcribed.
RNA polymerase synthesizes messenger RNA (mRNA) in the 5' to 3' direction by reading the template in the 3' to 5' direction.
The RNA molecule is a transcribed copy of a particular gene.

Messenger RNA (mRNA):
- Carries genetic information from DNA to ribosomes.
- Directs protein synthesis at the ribosomal site.
- Contains codons (three-base sequences).
Transfer RNA (tRNA):
- Recruited by ribosomes to create a specific polypeptide.
- Carries a specific amino acid.
- Contains an anticodon (three-base sequence).
- The correct base pairing of the tRNA anticodon with the mRNA codon results in the addition of an amino acid to the growing polypeptide.
Ribosomal RNA (rRNA):
- The functional unit of the ribosome.
- Responsible for protein assembly.
- The site where codon to anticodon pairing occurs.

Poly-A tail: Addition of 100-200 adenine nucleotides to the 3' end.
- Increases stability and helps with exporting from the nucleus.
GTP cap: Addition of a modified guanine nucleotide to the 5' end.
- Helps protect the transcript and helps the ribosome attach to the mRNA.
Introns: Non-coding sequences of mRNA that are removed during RNA processing.
Exons: Coding sequences of mRNA that are retained during RNA processing and connected to make the mature mRNA transcript.
Alternative splicing: The process of splicing introns and connecting exons.
- Different mRNA transcripts can be produced from the same primary transcript by retaining different combinations of exons.

Translation: the process by which mRNA sequence is used to generate a corresponding polypeptide.
Occurs on ribosomes.
Prokaryotes have cytosolic ribosomes.
Eukaryotes have ribosomes in the cytosol and bound to the endoplasmic reticulum.
Translation involves three main steps: initiation, elongation, and termination.
In prokaryotes, translation can occur while mRNA is being transcribed.
Initiation: Starts the process.
Elongation: The polypeptide grows longer.
Termination: Stops the process.

Retroviruses introduce viral RNA into host cells.
Reverse transcriptase: An enzyme that copies viral RNA into viral DNA.
Viral DNA can then be integrated into the host genome.
Once integrated, viral DNA is transcribed and translated, resulting in the assembly of new viral progeny.
All organisms use the same genetic code, which allows retroviruses to work.
Translation mechanisms are similar in nearly all organisms, providing evidence of common ancestry.

Translation is the final process in the flow of information from DNA to RNA to protein.
The translation step involves converting RNA information into a protein.
Initiation: The rRNA of a ribosome interacts with the mRNA at the first start codon.
Codons: mRNA nucleotides grouped and read in triplets; each codon encodes a specific amino acid.
Codon chart: Used to determine which codon codes for which amino acid.
Many amino acids are encoded for by more than one codon (redundancy).
Start codon (AUG) codes for methionine.
Stop codons do not code for an amino acid and are used to terminate the process.
tRNA's job is to bring the correct amino acid to the correct place as specified by the codon of mRNA.
tRNA has an anticodon that complements the mRNA codon.
Elongation: Each tRNA brings another amino acid, which is added to the growing polypeptide chain.
Termination: Occurs when a stop codon is reached.
The newly synthesized polypeptide is released.