Lecture 5 - Gene to Protein

Overview of Gene Function

• Genes (DNA) play crucial roles in cellular processes.

• Central dogma: DNA → RNA → Protein.

• Key concepts: transcription, RNA processing, translation, post-translational modification.

• The principle of 1 gene = 1 protein.

• Not all genes are expressed at all times; gene expression is fundamental.

Key Concepts in Transcription and Translation

• Genes: Specific sequences of nucleotides that determine the amino acid sequence of proteins.

• Triplet Genetic Code: Three nucleotides specify each amino acid (AA).

• Transcription: DNA-directed synthesis of mRNA; involves promoter regions and transcription factors.

• RNA Processing: Eukaryotic cells undergo modifications to RNA after transcription but before translation.

• Translation: RNA-directed synthesis of polypeptides occurs on ribosomes with the aid of tRNA.

• Post-Translational Processing: Further modifications occur in the ER.

• Mutations: Changes in nucleotides can significantly affect protein structure and function.

mRNA as the Intermediary

• Function of mRNA: Carries information from DNA to ribosomes in the cytoplasm for protein synthesis.

• Structure of RNA: Single-stranded, contains ribose sugar, uses uracil instead of thymine.

• Central Dogma Revisited: Genes encode proteins; many genes code for non-translated RNAs with varied functions.

Coding for Amino Acids

• Four nucleotide bases code for 20 amino acids; three nucleotides (codons) specify each amino acid.

• Codons: More combinations (64 total) exist than needed, providing redundancy.

• Stop and Start Codons: AUG (start), UAA/UAG/UGA (stop).

Transcription Overview

Synthesis of mRNA

• Process: mRNA is synthesized from a DNA template; RNA polymerase creates a complimentary RNA transcript from DNA.

• RNA Polymerase: The enzyme responsible for synthesizing mRNA.

Mechanism of Transcription

1. Initiation: RNA polymerase binds to the promoter; the DNA unwinds to begin synthesis.

2. Elongation: RNA polymerase synthesizes the RNA transcript as DNA reforms into a double helix.

3. Termination: mRNA is released upon reaching a terminator sequence; RNA polymerase detaches from DNA.

Promoter Regions and Initiation of Transcription

• Role of Promoters: Specific sequences in DNA where transcription begins, recognized by transcription factors.

• Eukaryotic Promoters: Include the TATA box (20-30 nucleotides upstream), recognized by transcription factors prior to polymerase binding.

Processing mRNA in Eukaryotes

• Steps Before Translation:

  1. RNA splicing (removal of introns).

  2. Addition of a 5' cap.

  3. Addition of a 3' poly(A) tail.

• Purpose of Modifications: Protect mRNA from degradation and enhance translational efficiency.

Alternative RNA Splicing

• Function: Allows for the removal of selected exons along with introns, leading to protein diversity.

• Gene Count vs. Protein Diversity: ~25,000 genes can encode for ~100,000 proteins due to splicing.

Translation Process

• Definition: Synthesis of proteins (polypeptides) directed by mRNA and involving tRNA and ribosomes.

• Ribosomes: Sites of protein synthesis comprising rRNA and proteins, categorized into small and large subunits.

Steps in Translation Elongation

1. tRNA binds to the A site, matching anticodon with mRNA codon.

2. Peptide bond forms between the new amino acid and the polypeptide chain in the P site.

3. Ribosome advances along mRNA and tRNA molecules shift along with it.

Post-Translational Modifications of Proteins

• Types of Modifications: Chemical changes such as glycosylation.

• Final Product: Polypeptides are folded into functional forms and transported in vesicles for storage or export.

Effects of Mutations

• Impact of Single Nucleotide Changes: Can dramatically alter protein function and phenotype.

• Genetic Flow: DNA → RNA → Protein; differences in genotype lead to variations in phenotype as observed in different mouse coat colors.

SIMPLIFIED

Overview of Gene Function

• Genes are pieces of DNA that help control how our bodies work.

• The process of gene function can be summarized with the central dogma: DNA is used to make RNA, which is then used to make proteins.

• Key steps involve:

  • Transcription: Making RNA from DNA.

  • RNA processing: Preparing RNA before it’s used.

  • Translation: Turning RNA into proteins.

  • Post-translational modification: Changing proteins after they are made.

• The idea is that one gene generally corresponds to one protein, but not all genes are active all the time; regulating gene expression is important.

Key Concepts in Transcription and Translation

• What are genes? They are specific sequences in DNA that tell the cell how to produce proteins, which are crucial for various functions in the body.

• Triplet Genetic Code: Each set of three nucleotides (building blocks of DNA and RNA) corresponds to a specific amino acid, the building blocks of proteins.

• Transcription: This is when RNA is made from a DNA template. It involves special DNA sections called promoters and proteins called transcription factors.

• RNA Processing: In cells with a nucleus (eukaryotes), the RNA made from DNA is modified before it gets translated into proteins.

• Translation: This is when ribosomes (tiny machines in the cell) read the RNA to produce proteins. It involves transfer RNA (tRNA) to help build the proteins.

• Post-Translational Processing: After proteins are made, they may undergo additional changes to become fully functional.

• Mutations: These are mistakes in the DNA sequence that can change how proteins are made, which might affect their function.

mRNA as the Intermediary

• Function of mRNA: Messenger RNA (mRNA) carries instructions from DNA to ribosomes where proteins are made.

• Structure of RNA: Unlike DNA, RNA is usually single-stranded, has ribose sugar in its structure, and uses uracil instead of thymine.

• Central Dogma Revisited: Genes not only code for proteins but also for various types of non-coding RNAs that play different roles in the cell.

Coding for Amino Acids

• There are four bases in DNA and RNA, and they can combine in many ways to code for 20 different amino acids needed to build proteins.

• Codons: Each group of three bases (codon) specifies one amino acid. There are a total of 64 possible combinations of codons.

• Stop and Start Codons: AUG is the start codon for protein synthesis, while UAA, UAG, and UGA are stop codons that signal the end.

Transcription Overview

• Synthesis of mRNA: This is when mRNA is made from a DNA template by an enzyme called RNA polymerase.

How Transcription Works

1. Initiation: RNA polymerase finds a promoter and begins to unwind the DNA.

2. Elongation: The enzyme continues to build the mRNA strand while the DNA recoils back.

3. Termination: The process stops when it reaches a specific signal on the DNA, at which point the mRNA is released.

Promoter Regions and Initiation of Transcription

• Role of Promoters: Promoters are special DNA sequences where transcription starts. They are recognized by transcription factors that help initiate the process.

• Eukaryotic Promoters: In eukaryotes, promoters often have a specific element called a TATA box.

Processing mRNA in Eukaryotes

• Steps Before Translation include:

  • Removing non-coding sections (introns) from the RNA.

  • Adding a protective 'cap' on the 5' end and a 'tail' on the 3' end of the RNA.

• Purpose of Modifications: They help protect the mRNA and make it easier to read.

Alternative RNA Splicing

• This allows cells to mix and match different sections of RNA to create diverse proteins, despite having a limited number of genes.

Translation Process

• Definition: Translation is when the mRNA code is used to build proteins, with the help of tRNA and ribosomes.

• Ribosomes: They are the sites where proteins are made and consist of ribosomal RNA (rRNA) and proteins.

Steps in Translation Elongation

1. tRNA, which carries amino acids, matches its anticodon with the codon on the mRNA.

2. A bond forms between the newly added amino acid and the growing protein chain.

3. The ribosome moves along the mRNA to continue the process.

Post-Translational Modifications of Proteins

• These may include chemical changes (like adding sugar groups), and the end result is functional proteins that can be used by the cell.

Effects of Mutations

• Changes in the DNA sequence (mutations) can significantly impact how proteins work, potentially altering traits or characteristics, such as the color of a mouse's fur, reflecting a change in phenotype.