Ribosomes and protein synthesis lecture 1

BMS1025 – CELL BIOLOGYInstructor: Dr. Penny LympanyEmail: p.lympany@surrey.ac.ukSession Topics: Cellular Biology covering organelles, structure, and functionSession Content OverviewFocus Areas:

• Ribosomes

• Protein Synthesis

• Endoplasmic Reticulum

Ribosomes

Function:

• Essential in protein synthesis for all living cells, serving as the site where genetic codes are translated into functional proteins. Ribosomes' crucial role ensures that the instructions encoded in the DNA are expressed correctly.

• Comprised of two main subunits:

  • Small Subunit: Responsible for decoding the genetic information transmitted from mRNA (messenger RNA). It ensures that the correct tRNAs (transfer RNAs) are matched to the corresponding mRNA codons.

  • Large Subunit: Catalyzes peptide bond formation between amino acids, facilitating the assembly of polypeptide chains that will fold into functional proteins.

Ribosome Structure:

• Highly Ordered Organization: Ribosomes possess a highly ordered structure where ribosomal RNA (rRNA) molecules scaffold the positioning of proteins for optimum function. This architecture allows ribosomes to perform their role efficiently during protein synthesis.

• Refer to: Fig 6-65, Alberts et al. for detailed structural insights.

Functionality of Ribosomes

Role of rRNA:

• rRNA plays a direct role in guiding the protein synthesis process; it not only contributes to the structural makeup of the ribosome but is also crucial in ensuring the fidelity of translation.

Active Cells:

• Cells undergoing rapid growth or high levels of activity (such as muscle or liver cells) typically possess a significantly higher number of ribosomes to meet the demands of increased protein production.

Composition:

• Ribosomes are composed of roughly 50% rRNA and over 80 different proteins (the remaining mass), which work collaboratively to ensure effective protein synthesis.

Protein Synthesis Accuracy:

• Ribosomes maintain a high accuracy in translation, with only about 1 error occurring per every 10,000 amino acids added to a growing polypeptide chain. This low error rate is crucial for maintaining cellular function and protein integrity.

Ribosome Subunit Interaction

Binding Sites:

• Ribosomes contain four binding sites:

  • One for mRNA

  • Three for tRNA (designated A, P, and E sites)

• Process Mechanism:

  • The mRNA strand is fed through the ribosome three nucleotides (nt) at a time, where the tRNAs serve as adaptors that deliver the correct amino acids corresponding to the mRNA codons.

• Completion:

  • Translation ceases at the stop codon, resulting in the disengagement of ribosomal subunits from the mRNA.

• Speed:

  • The translation rate can reach approximately four amino acids per second, though in bacteria, this process can be even faster due to their simpler cellular machinery.

Translation Process Overview

Key Points:

• Translation occurs in the cytosol on ribosomes, and it begins with the recognition of a start codon by initiator tRNA.

• The nucleotide sequence is deciphered in groups of three, known as codons.

• Elongation factors ensure the process progresses using GTP hydrolysis for energy.

• Termination happens when a release factor binds to the ribosome upon reaching a stop codon, resulting in the release of the newly formed polypeptide chain.

• Protein folding is facilitated by molecular chaperones, which also play roles in degrading incorrectly folded proteins to maintain cellular homeostasis.

DNA Replication Overview

• The majority of genes provide instructions for the synthesis of proteins, while a minority encode RNA molecules themselves, typically facilitated by RNA polymerase I or III.

• Replication Method: Semi-conservative, ensuring each daughter cell inherits one original and one new strand of DNA.

Basics of Protein Synthesis

Stages of Synthesis:

1. Transcription: DNA is transcribed into mRNA within the nucleus.

2. Translation: The mRNA is translated to form a polypeptide chain, which ultimately folds into a functional protein.

From DNA to RNA

• Multiple identical RNA copies can be synthesized from a single gene, allowing for high levels of protein production as required.

• Variations in transcription and translation efficiency can result in differing protein expression levels among genes, impacting overall cellular function.

Key Points on Transcription and Translation

• Sequence Representation: The nucleotide sequence in DNA determines the amino acid sequence in proteins, outlining the genetic code’s significance.

• Protein Structure: The function and properties of proteins are highly contingent on their 3D structures, which arise from the specific linear sequence of amino acids. The genetic code employs a four-letter DNA alphabet to encode the twenty standard amino acids.

Transcription Details

• RNA molecules synthesized during transcription are complementary to one strand of the DNA double helix.

• In RNA, adenine pairs with uracil (U), replacing thymine (T) from the DNA template.

Process of Transcription

Steps:

1. DNA unwinds and separates due to the action of specific enzymes such as helicase.

2. Complementary base pairing allows the formation of the RNA strand, which is synthesized by RNA polymerase.

3. Three types of RNA are produced:

   • mRNA: Carries coding sequences for proteins from DNA to ribosomes.

   • rRNA: Forms the structural core of ribosomes and is integral in protein synthesis.

   • tRNA: Functions to deliver the appropriate amino acids to the ribosomes for incorporation into polypeptides.

RNA Characteristics:

• RNA is single-stranded and contains ribose sugar, differing from DNA in the replacement of uracil (U) for thymine (T).

• RNA can fold into complex structures that are stabilized by internal complementary base pairing, contributing to their diverse functions.

Completion and Editing of Transcription

• After transcription, the mRNA strand detaches from the DNA template.

• A 5' cap (methylated guanosine) is added, and non-coding sequences (introns) are excised. A poly-A tail is then added to the 3' end of the mRNA to mark its readiness for export from the nucleus to the cytoplasm.

mRNA Features

Functionality:

• As the most variable class of RNA, the functions of mRNA are largely determined by the rates at which specific genes are transcribed.

Lifespan variability:

• Signal proteins that are needed rapidly often degrade swiftly (within less than 10 minutes), while structural proteins, which have longer establishments, may persist for over 10 hours or more.

Transcriptome:

• Represents the total array of mRNA molecules present in a cell, showcasing variability based on cell types.

• For example, insulin genes are expressed in pancreatic cells but not in bone cells, illustrating the influence of cell type on gene expression.

Transcription Regulation

Initiation:

• RNA polymerase binds to specific promoter regions, which typically include the TATAAA box, to facilitate transcription initiation. This binding ensures that transcription begins at the correct location on the DNA.

Elongation:

• RNA polymerase moves along the DNA template, synthesizing the RNA strand in a 3' to 5' fashion—adding ribonucleotides complementary to the DNA template strand.

Termination:

• The mRNA separates from the DNA template upon reaching specific termination sequences, with termination factors aiding this process to ensure efficient release.

Translation Mechanism

• Each amino acid in a protein is encoded by a specific triplet nucleotide sequence (codon) present in the mRNA. The translation machinery ensures that the appropriate tRNAs deliver the right amino acids to the ribosome for assembly into proteins.

• Example: The codon AGC codes for the amino acid serine, while UAA functions as a stop codon, signaling the end of translation.

Translation Readability

• The reading frames of mRNA sequences can shift due to mutations, but typically, only one reading frame encodes the functional protein required for cell operations.

Transfer RNA (tRNA)

• Functions as essential adaptors connecting mRNA codons to their corresponding amino acids during protein synthesis.

• Structure: tRNA is often described using the cloverleaf model, which further folds into a compact and stable L-shape due to hydrogen bonding.

• Each tRNA molecule is approximately 80 nucleotides long and possesses an anticodon that pairs specifically with mRNA codons, ensuring accuracy in amino acid addition.

tRNA Summary

• As a key player in protein synthesis, tRNA links specific amino acids to their corresponding codons found in mRNA.

• Each tRNA has two distinct ends: one site for amino acid attachment and another for mRNA codon binding, which facilitates the sequential addition of amino acids to a growing polypeptide chain during translation.

• The lengths of protein chains can vary significantly, ranging from a few to several thousand amino acids, with the energy from GTP hydrolysis driving the assembly process.

Amino Acid-tRNA Linkage

• Specialized enzymes known as aminoacyl-tRNA synthetases exist for each of the 20 different amino acids. These enzymes are vital for correctly attaching amino acids to their respective tRNAs.

• The linkage occurs through the formation of ester bonds at the 3' end of the tRNA, ensuring that amino acids are activated and ready for incorporation during translation.

Assembly of Protein Chains

• The formation of peptide bonds between adjacent amino acids is instrumental in the assembly of protein chains, thereby forming proteins according to the genetic code specified in mRNA (Refer: Fig 6-63, Alberts et al.).

Codon-anticodon Interactions

• Some amino acids can be associated with multiple tRNAs because of wobble pairing at the third codon position. This property enhances the efficiency of protein translation under varied conditions.

• Redundancy: The redundancy within the genetic code allows for variations in codons that code for the same amino acid, a feature attributed to the flexible base-pairing capability of the tRNAs.

• Notably, humans possess nearly 500 tRNA genes that comprise approximately 48 distinct anticodons, underscoring the complexity and adaptability of the translation machinery.

Additional Resources

• For extended reading and deeper understanding, consult:

  • Alberts B et al. Molecular Biology of the Cell

  • Module discussion board

  • Email Dr. Lympany for inquiries: p.lympany@surrey.ac.uk

Glossary

• Aminoacyl-tRNA synthetase: Enzyme responsible for matching amino acids to their corresponding tRNA.

• Anticodon: tRNA sequence that is complementary to the mRNA codon, ensuring proper translation.

• Codon: A triplet sequence of nucleotides in DNA/mRNA that specifies a particular amino acid.

• Open reading frame: A continuous nucleotide sequence in DNA or mRNA without stop codons, indicating potential protein-coding regions.

• Proteasome: A cellular complex that degrades unneeded or misfolded proteins marked for destruction.

• Ribosome: The molecular machine composed of rRNA and proteins that catalyzes protein synthesis.

• Ribozyme: An RNA molecule that possesses catalytic activity and can facilitate biochemical reactions.

• Transfer RNA (tRNA): The adaptor molecule that links mRNA codons to specific amino acids during the process of protein synthesis.

• Translation: The cellular process that directs the incorporation of amino acids into proteins, occurring on ribosomes.