Molecular Biology: Protein Synthesis and Regulation

PHBC522 Biochemistry I, Winter 2024, Lecture 6: Gene Expression & Protein Synthesis

• Learning Objectives: By the end of the lecture, students should be able to identify all RNA types and structures, understand gene transcription regulation by chromatin remodeling, describe promoter regions and roles of enhancers/inhibitors in transcription, illustrate post-transcriptional mRNA modification, recognize the role of RNA interference in gene expression regulation, describe epigenetic regulation and RNA editing, identify the genetic code, and discuss protein synthesis steps.

RNA Structure and Synthesis

• Genetic Code: An organism's genetic key is encoded in the deoxyribonucleotide sequence in DNA.
• Transcription to RNA: DNA information is transferred to RNA. Transcription is the copying process where one DNA strand acts as a template for mRNA synthesis.
• mRNA Types: There are three types of RNA: ribosomal RNA (rRNA), messenger RNA (mRNA), and transfer RNA (tRNA).
• RNA vs. DNA Differences: RNA uses ribose sugar instead of deoxyribose, uracil instead of thymine, and is usually single-stranded while DNA is double-stranded.

Ribosomal RNA (rRNA)

• Composition: rRNA comprises about 80% of RNA in cells and is a large complex of proteins and rRNA.
• Location and Function: Ribosomes act as protein synthesis factories, located in the cytosol or attached to the endoplasmic reticulum.
• Svedberg Values: rRNA exists as sedimentation coefficients (S values) representing particle movement in a centrifuge, related to molecular mass and shape.
• Ribosome Structure: Complete ribosomes have three binding sites (A, P, and E sites) extending over both subunits for amino acid attachment and polypeptide chain formation.

Messenger RNA (mRNA)

• Function: mRNA carries genetic information from the DNA in the nucleus to the cytoplasm for protein synthesis.
• Structure: mRNA is often monocistronic in eukaryotes andpolycistronic in prokaryotes, meaning it carries information from one or multiple genes respectively. It includes a 3′ poly A tail and a 5′ cap.
• Exons and Introns: In eukaryotic mRNA, protein-coding regions (exons) alternate with non-coding regions (introns) which need to be removed.

Transfer RNA (tRNA)

• Function: tRNA molecules, each with a specific amino acid attachment site, are adapter molecules that recognize specific mRNA codons and translate them into amino acids.
• Structure: Each tRNA molecule has an anticodon loop that pairs with mRNA codons and an amino acid attachment site, and unique structural folds (e.g., D loop, T-loop). The structure is unique to each specific amino acid.

RNA Transcription

• Transcription Process: Transcription is the copying process using one DNA strand (antisense) as a template to synthesize mRNA. The DNA strand that is not being transcribed is the Coding strand (sense).
• Example Transcript: The sample transcript demonstrates how DNA is transcribed to mRNA using complementary base pairs (A-U, T-A, C-G).

Questions and Solutions

• Example Question/Solution: If a coding strand has the sequence 5'-TACGTA-3', the transcribed mRNA sequence is 5'-AUGCAU-3'.

RNA Polymerase and Gene Expression

• RNA Polymerase Classes: Eukaryotic cells have three main types of RNA polymerase (I, II, and III) in the nucleus that synthesize different kinds of RNA each.
• RNA Polymerase I: Synthesizes rRNA.
• RNA Polymerase II: Synthesizes mRNA and some small nuclear RNAs (snRNAs).
• RNA Polymerase III: Synthesizes tRNA and some small ribosomal RNAs (rRNAs).
• RNA Polymerase Function: RNA polymerase needs to recognize the promoter region of the gene and initiate RNA synthesis; it reads from 3′ to 5′ and synthesizes from 5′ to 3′ on the DNA template strand.

Pre-transcriptional Regulation

• Chromatin Remodeling: Chromatin remodeling involves the interconversion of active chromatin (euchromatin) and inactive chromatin (hetero chromatin). influenced by DNA methylation and histone acetylation.
• DNA Methylation: Methylation of cytosines permanently inactivates certain genes by preventing transcription factor binding.
• Histone Acetylation: Histone acetylation relaxes chromatin structure, enhancing accessibility to transcription and gene activation. Histone deacetylase (HDAC) does the opposite, condensing chromatin and suppressing transcription.

Epigenetic Regulation

• Inheritance of Gene Expression: The pattern of gene expression inherited through cell division without changes in the DNA sequence.
• Maintenance Methylase: An enzyme that recognizes hemimethylated DNA during DNA replication and adds methyl groups to the complementary strand to maintain the methylation pattern.

RNA Regulation Elements

• Core Promoter: Regions immediately adjacent to transcription start sites (TSS), having short sequences like TATA box, and serving as docking sites for the transcriptional machinery.
• Proximal Promoters: DNA sequences located near the core promoter associated with initiation of transcription.
• Cis-acting elements: Short sequences that work locally.

Transcription Factors

• Function: Proteins that recognize specific DNA motifs to bind to regulatory regions and affect transcription rate.
• Mechanism: Transcription factors bind to DNA and either inhibit or enhance the binding of RNA polymerase.
• Location: Synthesized in cytoplasm and diffuse into nucleus.

Enhancers

• Function: Distal regulatory DNA elements that can enhance gene expression.
• Mechanism: Enhancers can be located far from the regulated gene but can still influence gene expression by attracting transcription factors and stimulating transcription from the start.
• Properties: Enhancers work independently of their location.

Silencers

• Function: Distal regulatory DNA elements that repress gene expression.
• Mechanism: Silencers can counteract enhancers.
• Properties: Similar to enhancers, silencers can be located far from the regulated gene.

Post-transcriptional Modifications

• 5' Capping: A modified guanine nucleotide added to the 5' end of mRNA to facilitate mRNA processing and stability.
• 3′ Polyadenylation: Addition of a poly(A) tail of adenine nucleotides to the 3′ end of mRNA, aiding in mRNA stability, nuclear export and translation.
• Splicing: Removing introns and joining exons to generate mature mRNA and form a single molecule.

RNA Editing

• mRNA Editing: Post-transcriptional alterations in mRNA sequence that can affect the protein's amino acid sequence.
• Types of Editing: Deamination and insertions/deletions of nucleotides, sometimes involving specific tissues, cells or stages in the organism.
• Examples: Apo B gene editing changes the protein's amino acid sequence, hence its function, in tissue-dependent ways.

Micro RNA (miRNA)

• Mechanism: Small non-coding RNAs that regulate gene expression by either binding to specific mRNA sequences (often leading to degradation or hindering translation) to suppress gene expression.
• Formation: Produced from larger precursor transcripts. miRNA production involves several nuclear processes and export.
• Function: miRNA contributes to controlling gene expression at a post-transcriptional level. It plays many roles in controlling gene expression.

Small Interfering RNA (siRNA)

• Mechanism of action: Short double stranded RNA molecules that target and cleave specific mRNA molecules. siRNA-mediated degradation of mRNA prevents translation of certain proteins
• Function: siRNA can be used to knock down or silence gene expression.

Genetic Code

• Sequence: The sequence of nucleotides in mRNA specify the amino acid sequence of the protein to be synthesized.
• Characteristics: The genetic code features redundancy, or more than one codon for many amino acids. Non-overlapping and commaless; the code is read continuously and without a punctuation system. Its universality, and the correspondence of specific codons to specific amino acids.

Translation: Initiation

• Initiation Factors: Initiator tRNA and IF required for proper translation start.
• Formyl-methionine (fMet): Start codon in prokaryotes is methionine, formylated by transformylase.
• Mechanism: Ribosome binding to the 5' mRNA end; recognition of start codon (AUG) by initiator tRNA and initiation factors.

Translation: Elongation

• Transfer RNA with Amino Acid: Charged tRNA with amino acids binds the mRNA codons in the A site.
• Peptide Bond Formation: A new peptide bond is formed between the amino acids on the tRNA in the A site and the polypeptide chain already on the tRNA in the P site by peptidyl transferase.
• Translocation: GTP-powered ribosome and tRNA movement, shifting mRNA over one codon to expose the next codon at the A site.

Translation: Termination

• Termination Codons: Stop codons (UAA, UAG, UGA) signal the end of protein synthesis by triggering release factors to detach the polypeptide from the ribosome.
• Release Factors (RF): Proteins that recognize stop codons to terminate protein synthesis.