Notes on Gene to Protein and Molecular Biology Processes

The Flow of Genetic Information

• Genes are sequences of nucleotides that contain information for synthesizing proteins.

• The relationship between genotype (genetic makeup) and phenotype (observable traits) is mediated by proteins.

• Gene expression is the process of converting DNA into RNA and then into proteins, consisting of two stages: transcription and translation.

Basic Principles of Transcription and Translation

• RNA ( Ribo nucleic acid) serves as a bridge between genes in DNA and proteins.

• RNA is single-stranded and contains ribose sugar and uracil (instead of thymine).

Transcription

• Translation is the synthesis of RNA from a DNA template.

  • During translation you are translating a nucleotide to an amino acid sequence

  • Ribosome are the sites of translation

• The RNA synthesized during transcription of protein-coding genes is called messenger RNA (mRNA). (Not straight away)0

  • Prior to the modification - pre messenger RNA

  • Messenger RNA make a protein , if it is a primary transcript it doesn’t make protein

• Prokaryotic translation can start even before transcription finishes, whereas in eukaryotes, mRNA is modified in the nucleus before being transported to the cytoplasm for translation.

Process of Gene Expression

Gene Expression Stages:

1. Transcription: Where mRNA is synthesized from a DNA template.

   • Involves the RNA polymerase enzyme.

2. Translation: Where ribosomes synthesize proteins based on the mRNA sequence.

   • Takes place in the cytoplasm.

The Central Dogma

• Describes the flow of genetic information as: DNA → RNA → Protein.

The Genetic Code

• The genetic code consists of 20 amino acids coded by combinations of 4 nucleotide bases (A, U, C, G).

• The code is read in triplets, known as codons, where each codon corresponds to a specific amino acid.

• There are 64 possible codons (43) but only 20 amino acids, indicating redundancy in the code.

• Specific codons signal 'start' (AUG) and 'stop' (UAA, UAG, UGA) during translation.

Transcription Mechanism

Stages of Transcription: Copy of strand is made > mRNA

First three of the strand is “codon” and every three from then have own name that call for specific amino acids.

Trip phe giv se

½ strands called template strands , provides a template for ordering the sequence of complementary nucleotide in an RNA transcript

You need 3 nucleotides codes for amino acids, messenger RNA is 3 times the size of the protein

1. Initiation: RNA polymerase binds to the promoter region on DNA. (Called terminator in baceteria)

2. Elongation: RNA polymerase synthesizes RNA in the 5' to 3' direction.

3. Termination: RNA polymerase encounters a terminator sequence and releases the RNA transcript.

   1. Stretch of DNA that is transcribes is called a transcription unit

   Inc

RNA Processing in Eukaryotes

• Modifications occur on the pre-mRNA transcript including:

  • Addition of a 5' cap and a poly-A tail at the 3' end.

  • Splicing out of introns (non-coding regions) and joining exons (coding sequences).

  • The processed mRNA is then transported out of the nucleus into the cytoplasm for translation.

  • Messenger RNA ha a 5’ cap at the start and a Poly A tail at the end

  • Large structures called spliceosoms made of proteins, (snRNPs) splices RNA, cut messenger RNA

Ribozymes

Catalytic RNa molecules that function as enzymes and can splice RNA .

• Alternative splicing: one gene can form more than one kind of protein

• Not just waiting , transfer RNA is bringing it there and there is a anticodon telling it where to bond it to

• 20 different enzymes, 1 for each amino acid

• A match between tRNA and an amino acid if done by the nzyme aminooacly-tRNA-synthesate . Must have the correct match between tRNA anticodon and an mRNA codon

Ribosomes

• Two ribosomal subunit (large and small) and made of proteins and ribosomal RNA (rRNA)

  • Three bonding sites :

    • P site - holds the tRNA that has the peptide chain attached

    • A site - holds the tRNA that carries the next amino acid to be added to the chain

    • E chain - is he exit site, where discharges tRNA leave the ribsome

Translation Mechanism

• Translation converts the mRNA sequence into a polypeptide chain.

• tRNA brings specific amino acids to the ribosome, where they are matched to the codons on the mRNA.

• Ribosomes facilitate the coupling between tRNA and mRNA.

Stages of Translation:

1. Initiation: mRNA, tRNA, and ribosome components assemble at the start codon.

2. Elongation: Amino acids are added to the growing polypeptide chain.

   1. Amino acids are added one by one to the C-terminus of the growing chain .

      1. Each addition involves proteins called elongation factors and occurs in 3 steps : codon recognition, peptide bond formation, nd translocation.

3. Termination: When a stop codon is reached, the process ends and the polypeptide is released. Called “release factor”

4. Release factor causes the addition of water molecule instead of an amino acid

   1. Codons must be read in the correct reading frame

   2. Completely different protein formed when a nucleotide is missed , since the rest will skip

Post-Translational Modifications

• Newly synthesized proteins may undergo further modifications that are essential for their final functional state and activity.

• These modifications include folding, cleavage, or the addition of chemical groups.

• Targeting mechanisms direct proteins to their functional locations within cells.

Multiple ribosome can translate a single mRNA a the same time , forming a POLYRIBOSOME or POLYSOME

• Bacteria’s stream line this process with transcription and translation bc there is no nucleus and they cam do it all in the cell

Mutations and Their Effects

• Mutations are changes in the nucleotide sequence of DNA that can impact the RNA and resulting protein.

• Point mutations: Changes involving a single nucleotide leading to silent, missense, or nonsense mutations.

  • Silent: No change in the amino acid.

  • Missense: A different amino acid is produced.

  • Nonsense: A stop codon is introduced prematurely.

• Insertions and Deletions: Can cause frameshift mutations that alter the protein drastically.

• Substitutions

  • Nucleotide -pair replaces one and its partner with another pair

  • Silent have no effect on the amino acid produces by a codon because of redundancy in the genetic code

  • Misssense still code for an amino acid but not the correct amino acid

  • Nonsense mutation change an amino acide codon into a stop codon, always leading to a nonfunctional protein