DNA Replication

Initiation and Unwinding
- Helicase: This enzyme breaks the hydrogen bonds between the nitrogenous base pairs, "unzipping" the double helix to create a replication fork.
- Single-Strand Binding (SSB) Proteins: These proteins bind to the separated DNA strands to prevent them from re-annealing or forming secondary structures.
- DNA Gyrase (Topoisomerase): It reduces the torsional strain (supercoiling) created ahead of the replication fork as the DNA unwinds.
Elongation and Nucleotide Alignment
- DNA Primase: This enzyme synthesizes short RNA primers (approximately $10$ - 15 nucleotides long), providing a free $3'$ hydroxyl ( $OH$ ) group for DNA polymerase to begin synthesis.
- DNA Polymerase III: Aligns free deoxyribonucleoside triphosphates ( $dNTPs$ ) with their complementary bases on the template strand. It covalently joins them in a $5'$ to $3'$ direction.
- Covalent Bonds: Specifically, phosphodiester bonds are formed between the $5'$ phosphate group of the incoming nucleotide and the $3'$ hydroxyl group of the existing chain.

Leading and Lagging Strands

Leading Strand
- Synthesized continuously toward the replication fork because the template is oriented $3'$ to $5'$ .
Lagging Strand
- Synthesized discontinuously away from the replication fork in segments known as Okazaki fragments.
- This occurs because DNA polymerase can only add nucleotides to the $3'$ end, forcing it to re-initiate synthesis with new RNA primers as the fork opens further.

DNA Polymerase I: This enzyme removes the RNA primers from the lagging strand and replaces the ribonucleotides with deoxyribonucleotides.
DNA Ligase: Joins the Okazaki fragments by sealing the "nicks" in the sugar-phosphate backbone, catalyzing the final phosphodiester bond formation to create a continuous strand.

Semiconservative Model: The accepted model (demonstrated by Meselson and Stahl), where each daughter DNA molecule consists of one parental (original) strand and one newly synthesized strand.
Conservative Model: Postulates that the parent molecule remains intact and an entirely new double helix is formed.
Dispersive Model: Suggests that parental and daughter DNA are interspersed in segments throughout both strands.

Types and Structures of RNA

mRNA (Messenger RNA): A linear molecule containing the genetic blueprint. In eukaryotes, it undergoes processing (capping, tailing, and splicing) before leaving the nucleus.
tRNA (Transfer RNA): Has a characteristic cloverleaf secondary structure. It carries specific amino acids to the ribosome. The anticodon loop pairs with mRNA codons, while the $3'$ end carries the amino acid.
rRNA (Ribosomal RNA): Plays both a structural and catalytic role (ribozyme) within the ribosome.

Triplet Nature: Every three bases (a codon) code for one amino acid.
Degeneracy (Redundancy): There are $64$ possible codons but only $20$ amino acids, meaning multiple codons can code for the same amino acid, which helps minimize the impact of mutations.
Start Codon: $AUG$ (codes for methionine).
Stop Codons: $UAG$ , $UGA$ , and $UAA$ (do not code for amino acids but signal termination).

1. Transcription

Initiation: RNA polymerase binds to a specific DNA sequence called the promoter.
Elongation: RNA polymerase moves along the antisense (template) strand. $3'$ to $5'$ ) to synthesize a complementary mRNA strand in the $5'$ to $3'$ direction.
Termination: RNA polymerase reaches a terminator sequence and detaches.

2. Translation

Ribosomal Sites:
- A site (aminoacyl): where the incoming tRNA carrying an amino acid binds.
- P site (Peptidyl): Where the tRNA holding the growing polypeptide chain resides.
- E site (Exit): Where the empty tRNA is discharged.
Peptide Bond Formation: The ribosome catalyzes a peptide bond between the amino acid in the $A$ site and the polypeptide in the $P$ site.
Translocation: The ribosome moves one codon along the mRNA, shifting tRNAs from $A$ to $P$ and $P$ to $$E$