Understanding the Genetic Code

• Genetic information is stored in the form of bases (ATCG).
• Nucleotide triplets of DNA and RNA molecules carry genetic information in living cells which is the GENETIC CODE.
• Genetic code is made up of 3 bases.
• Genetic code can be expressed as either RNA codons or DNA codons.
• The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells.
• Instructions for protein construction is written in DNA using the genetic code.

Important Points for Genetic Code:

• The genetic code consists of 64 triplets of nucleotides called codons.
• UUU (Phenylalanine), UUA (Leucine), and AUG (Methionine) exemplify codons.
• With three exceptions (3 stop codons), each codon encodes for one of the 20 amino acids used in protein synthesis.
• Most amino acids are encoded by more than one codon.
• RNA codons, present in messenger RNA (mRNA), are "read" during polypeptide synthesis, a process called translation.
• mRNA molecules acquire their nucleotide sequence through transcription from the corresponding gene (DNA).

RNA Codons

• There are 64 Condons and 20 amino acids
• UAA, UGA and UAG are stop codons
• AUG (Methionine) is a start codon

DNA Codons

• These are read on the sense (5' to 3') strand of DNA.
• Thymidine (T) replaces uridine (U) in DNA codons, but code the same as RNA codons.
• mRNA is synthesized using the antisense strand of DNA (3' to 5') as the template.

Protein Synthesis

• Protein synthesis also known as translation
• Genetic language is translated into protein language during this process
• This involves 2 steps:
  • Transcription
  • Translation
• Proteins are produced by ribosomes within a cell
• Protein structures have 4 levels: primary, secondary, tertiary, and quaternary.
• The primary structure is non-functional
• There are 3 types of RNA involved: mRNA, rRNA, and tRNA
• There are 2 main steps: transcription (making mRNA) and translation (mRNA to Protein)
• Transcription occurs within the nucleus that contains the DNA
• Translation occurs within the cytoplasm with the Ribosome

RNA Components:

• Ribose sugar
• Bases: Adenine (A), Cytosine (C), Guanine (G), Uracil (U)
• Phosphate
• Single strand

Types of RNA and Functions:

• The three types of RNA: mRNA, rRNA, and tRNA.
• Each has unique size, shape, and function in protein synthesis.

Messenger RNA (mRNA):

• mRNA mediates the transfer of genetic information from the cell nucleus to ribosomes in the cytoplasm.
• It serves as a template for protein synthesis.
• It's synthesized from a DNA template during transcription by RNA polymerase enzymes.
• mRNA is transcribed in the nucleus, processed, and then transported to the cytoplasm.
• There, the genetic language is translated by the ribosome into a protein.
• mRNA is eventually degraded.

Ribosomal RNA (rRNA):

• rRNA is an essential RNA component of the ribosome for protein synthesis.
• It's the predominant material within the ribosome.
• Ribosomes have ~60% rRNA and ~40% protein by weight and contain two major rRNAs and 50+ proteins.
• The LSU and SSU rRNAs exist within the large and small ribosomal subunits, respectively.
• Protein synthesis occurs in the ribosome.
• The small subunit forms for the initiation complex, decodes genetic information, and controls codon-anticodon interactions.
• The large subunit catalyzes peptide bond formation and guides the nascent polypeptide chain.

Transfer RNA (tRNA):

• Transfer RNA (tRNA) is an essential component of the protein synthesis
• There are at least twenty different kinds of tRNA in the cell
• Each tRNA serves as the carrier of a specific amino acid to the site of translation.
• Amino acids bind to the 3' end, with the opposite end containing three anticodon nucleotides.
• The anticodon pairs with a codon in messenger RNA (mRNA) to ensure that the correct amino acid is incorporated into the growing polypeptide chain.
• Aminoacyl-tRNA synthetase, allows the correct amino acids to become attached to the correct tRNAs

Transfer RNA (tRNA) function:

• There are 3 sites in ribosome for tRNA
  • A = amino acid
  • P = Peptide
  • E = Exit of tRNA

Protein Synthesis Details

• There are two steps in protein synthesis details
• Transcription
• Translation
• Transcription
  • Initiation
  • Elongation
  • Termination
• Translation
• Initiation
• Elongation -Termination

Transcription

• Process: The synthesis of messenger RNA from a DNA molecule is transcribed
• Template Strand: The strand of DNA that synthesizes mRNA during transcription
• Enzyme: RNA polymerase facilitates transcription
• Initiation: Transcription starts when RNA polymerase recognizes and binds to a PROMOTOR region of a double-strand DNA
• Promoter: Also known as Initiator region
• Subunits: RNA polymerase has 4 subunits, the Sigma Factor helps to recognize the Promoter region of DNA

mRNA Transcription- Initiation

• Shortly after transcription begins, the SIGMA FACTOR dissociates from RNA polymerase, starting the elongation process.

mRNA Transcription - Elongation

• RNA Polymerase moves along the template strand of DNA
• synthesizes a complementary single strand of mRNA molecule
• (ELONGATION)
• mRNA synthesis occurs in the 5' to 3' direction, adding nucleotides to the growing mRNA strand.

mRNA Transcription - Termination

• When RNA Polymerase reaches a specific nucleotide sequence on the DNA, a transcription terminator
• STOP SEQUENCE/ TERMINATOR REGION/ the newly synthesizing mRNA forms a HAIRPIN LOOP structure.
• The hairpin loop helps to dissociate the RNA Polymerase and the mRNA molecule from the template strand of the DNA, completing THERMINATION .

Protein synthesis-Translation - Initiation

• There are 3 binding site for tRNA
  • P-site= Peptide
  • E-site= Exit
  • A-site= Amino acid
• The mRNA attaches itself to a ribosome on the small subunit, and six bases of the mRNA are exposed
• A complementary tRNA molecule with it's attached amino acid (methionine) base pairs via its anticodon UAC with the AUG on the mRNA in the first position, which is INIATION.

Translation - Elongation

• Another tRNA (with amino acids) attaches to the ribosome with the three mRNA bases at position A.
• The peptidyl transferase enzyme forms a peptide bond between the two amino acids.
• The first tRNA (without its amino acid) then leaves the ribosome.
• This process repeats until the ribosome reaches a stop codon, marking the end of Elongation.

Translation - Termination

• the end of translation occurs when the ribosome moves to a stop codon on the mRNA.
• the ribosome is then signaled to be released from the that specific mRNA
• The termination factor (a protein) binds to the stop codon and cleaves the polypeptide from the tRNA.
• A completely synthetised protein is released.

RNA Polymerase Subunits:

• Protein size is approximately 480 kd
• Made of four subunits: alpha, beta, beta', and sigma
• Only the first three subunits needed for polymerase activity, the core enzyme
• The sigma factor is required for RNA polymerase to bind to the promoter
• The enzyme has a loose affinity for DNA, which when the sigma factor is present, will bind only at the promoter