RNA and the Genetic Code Notes

Hepatitis C virus (HCV) leads to cirrhosis and liver failure.
HCV is commonly associated with intravenous drug use.
The virus causes ongoing damage and inflammation, leading to scar tissue formation that replaces normal liver cells.
Scar tissue buildup impairs liver function, eventually leading to liver failure.
Interferon, a peptide signal, is released by infected hepatocytes to combat the virus by interfering with viral replication.
Interferon curtails transcription and translation in virally infected cells.
Interferon induces the production of RNNase L, which cleaves RNA, further reducing viral replication.
Interferon acts as a defense mechanism against viral pathogens.
Transcription converts double-stranded DNA into single-stranded RNA.
Translation converts the nucleotide sequence into a protein.
Gene expression is controlled, leading to the differentiation of the totipotent zygote into various tissues.

Organisms must:
- Store and preserve genetic information.
- Pass information to future generations.
- Express information to carry out life processes.
DNA and RNA use nitrogenous bases for coding.
Proteins are composed of amino acids.
The genetic code translates genetic information into proteins.
Proteins are essential for organism development and function.
The central dogma of molecular biology illustrates the transfer of genetic information.
A gene is a DNA unit encoding a specific protein or RNA molecule.
Genes are expressed through transcription and translation.
DNA replication, transcription, and translation are key processes.
Messenger RNA (mRNA) is synthesized in the 5' to 3' direction.
mRNA is complementary and antiparallel to the DNA template strand.
The ribosome translates mRNA from the amino terminus (N-terminus) to the carboxy terminus (C-terminus).

mRNA carries the amino acid sequence information to the ribosome.
mRNA is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus.
mRNA undergoes post-transcriptional modifications before release from the nucleus.
mRNA contains information translated into protein.
mRNA is read in three-nucleotide segments called codons.
In eukaryotes, mRNA is monocistronic, translating into only one protein product.
In prokaryotes, mRNA may be polycistronic; translation at different locations can yield different proteins.

tRNA converts the language of nucleic acids to the language of amino acids.
Each tRNA molecule contains a folded RNA strand with a three-nucleotide anticodon.
The anticodon recognizes and pairs with the appropriate codon on mRNA in the ribosome.
There are 20 amino acids in eukaryotic proteins, each represented by at least one codon.
Amino acids are connected to specific tRNA molecules, which are then considered charged or activated.
Mature tRNA is found in the cytoplasm.
Each amino acid is activated by a different aminoacyl-tRNA synthetase, requiring two high-energy bonds from ATP.
Aminoacyl-tRNA synthetase transfers the activated amino acid to the 3' end of the correct tRNA.
Each tRNA has a CCA nucleotide sequence where the amino acid binds.
The high-energy aminoacyl-tRNA bond supplies the energy to create a peptide bond during translation.

rRNA is synthesized in the nucleolus.
rRNA functions as part of the ribosomal machinery during protein assembly in the cytoplasm.
Many rRNA molecules function as ribozymes (enzymes made of RNA molecules).
rRNA helps catalyze the formation of peptide bonds and is important in splicing out its own introns within the nucleus.

A codon is a three-letter unit that is translated into an amino acid.
Genetic code tables help determine the amino acid translated from each mRNA codon.
Each codon consists of three bases, resulting in 64 possible codons.
Codons are written in the 5' to 3' direction.
The code is unambiguous: each codon specifies only one amino acid.
61 codons code for amino acids; 3 codons encode for termination of translation.
The genetic code is universal across species.
During translation, the mRNA codon is recognized by a complementary anticodon on tRNA.
The anticodon sequence allows tRNA to pair with the codon in mRNA in an antiparallel orientation.
For example, the aminoacyl-tRNA Ile (isoleucine) has an anticodon sequence 5'-GAU-3', pairing with the isoleucine codon 5'-AUC-3'.
Every preprocessed eukaryotic protein starts with methionine, and the codon for methionine (AUG) is the start codon.
Three codons (UGA, UAA, and UAG) encode for termination of protein translation; no charged tRNA molecules recognize these codons.

The genetic code is degenerate because more than one codon can specify a single amino acid.
All amino acids except methionine and tryptophan are encoded by multiple codons.
For amino acids with multiple codons, the first two bases are usually the same, and the third base varies.
The variable third base in the codon is called the wobble position.
Wobble protects against mutations in the codon region of DNA.
Mutations in the wobble position are often silent or degenerate, with no effect on amino acid expression.
For example, glycine requires only the first two nucleotides of the codon to be GG; the third nucleotide can be A, C, G, or U without changing the amino acid.

A point mutation occurs when one nucleotide in a codon is changed.
Expressed point mutations can affect the primary amino acid sequence of the protein.
Expressed point mutations are categorized as:
- Missense mutation: where one amino acid substitutes for another.
- Nonsense mutation: where the codon encodes for a premature stop codon (truncation mutation).

The three nucleotides of a codon are referred to as the reading frame.
A frameshift mutation occurs when nucleotides are added to or deleted from the mRNA sequence.
Insertion or deletion of nucleotides shifts the reading frame, resulting in changes in the amino acid sequence or premature truncation of the protein.
The effects of frameshift mutations are typically more serious than point mutations, depending on where the mutation occurs within the DNA sequence.