DNA to Protein Notes
Overview
DNA acts as a comprehensive code, providing detailed instructions for protein production, essential for cellular functions and organismal development.
The code is the specific sequence of nitrogenous bases (adenine, guanine, cytosine, and thymine) in the DNA molecule, dictating the order of amino acids in proteins.
A gene is a distinct DNA sequence that codes for a specific polypeptide, representing a functional unit of heredity.
A polypeptide is a chain of amino acids linked by peptide bonds, which folds into a specific three-dimensional structure to form a protein.
The conversion of DNA sequence to amino acid sequence involves two major steps: transcription and translation.
Transcription: The process by which DNA is used as a template to synthesize RNA molecules, specifically messenger RNA (mRNA).
Translation: The process by which the information encoded in mRNA is used to assemble a polypeptide chain of amino acids.
These processes are carried out by complex molecular machines composed of proteins and RNA molecules, ensuring accurate and efficient protein synthesis.
Types of RNA
Ribosomal RNA (rRNA)
Integral component of ribosomes, providing structural support and enzymatic activity for protein synthesis.
Messenger RNA (mRNA)
RNA copy of a DNA sequence, carrying the genetic information from the nucleus to the ribosomes for translation.
Transfer RNA (tRNA)
Brings specific amino acids to the ribosome for polypeptide synthesis, matching the mRNA codon with the appropriate amino acid.
Additional types of RNA exist, including small nuclear RNA (snRNA) and microRNA (miRNA), which play regulatory roles in gene expression.
Transcription
Occurs when a specific protein is needed in response to environmental or physiological cues, allowing the cell to adapt to changing conditions.
Requirements:
Precursors: Ribonucleotide triphosphates (ATP, CTP, GTP, UTP), which serve as the building blocks for RNA synthesis.
Energy: Provided by the precursors themselves, as the hydrolysis of their phosphate bonds drives the polymerization reaction.
Enzymes: RNA polymerase, the enzyme responsible for catalyzing the synthesis of RNA from a DNA template.
Template: DNA, the sequence of which determines the sequence of the newly synthesized RNA molecule.
Transcription converts DNA into pre-mRNA, an initial RNA transcript that undergoes processing to become mature mRNA.
Major Steps:
Initiation
Begins at the promoter region of the DNA, a specific sequence that signals the start of a gene.
Involves the formation of a transcription bubble, where the DNA double helix is unwound to allow access for RNA polymerase.
Elongation
RNA polymerase synthesizes RNA along the DNA template, adding nucleotides to the growing RNA strand in a complementary manner.
RNA nucleotides are added to the growing RNA strand according to the base pairing rules (A with U, G with C).
DNA is re-annealed and rewound after RNA synthesis, restoring the double helix structure.
Termination
Occurs when RNA polymerase reaches a specific DNA sequence called the terminator, signaling the end of the gene.
RNA polymerase is released from the DNA template, and the newly synthesized mRNA molecule is freed.
Post-transcriptional Processing of mRNA
The initial mRNA transcript is called pre-mRNA and undergoes several processing steps to become mature mRNA before it can be translated.
5' Cap
Addition of 7-methyl guanine to the 5' end of pre-mRNA, protecting the mRNA from degradation and enhancing translation efficiency.
Helps stabilize mRNA by preventing its degradation by cellular enzymes.
Assists with ribosome loading, facilitating the initiation of translation.
Helps with nuclear export, ensuring that the mRNA can exit the nucleus and enter the cytoplasm for translation.
Poly-A Tail
Addition of hundreds of adenine nucleotides to the 3' end of mRNA, enhancing mRNA stability and promoting translation.
Helps stabilize mRNA by preventing its degradation by cellular enzymes.
Splicing (Intron Removal)
Removal of introns (non-coding segments) from pre-mRNA, allowing only the coding sequences (exons) to be translated.
Remaining segments (exons) are joined together to form a continuous coding sequence.
Spliceosome is a large RNA-protein complex that carries out splicing, ensuring accurate and efficient removal of introns.
snRNPs (small nuclear ribonucleic particles) are components of the spliceosome, recognizing specific sequences at the intron-exon boundaries.
Uses energy (ATP) to remove introns and link exons, ensuring the precise joining of exons.
Introns are chopped up and recycled, conserving cellular resources.
Translation
Translation converts mRNA into a polypeptide, using the genetic code to specify the order of amino acids.
Major Steps:
Initiation
Elongation
Termination
Ribosome
Complex of many proteins and rRNA, serving as the site of protein synthesis.
Reads mRNA sequence three nucleotides at a time to form a polypeptide, translating the genetic code into an amino acid sequence.
Small subunit (~30 proteins + rRNA) binds to mRNA and recruits the large subunit.
Large subunit (~50 proteins + rRNA) catalyzes the formation of peptide bonds between amino acids.
Codon: A 3-base sequence in mRNA that codes for a specific amino acid or a termination signal, providing the instructions for protein synthesis.
tRNA (transfer RNA)
RNA molecule that brings specific amino acids to the ribosome, ensuring that the correct amino acid is added to the growing polypeptide chain.
Has an anticodon that complements the mRNA codon, allowing the tRNA to recognize and bind to the appropriate codon.
Charged tRNA: A tRNA molecule carrying its specific amino acid, ready to be used in translation.
Uncharged tRNA: A tRNA molecule that has released its amino acid and is no longer carrying an amino acid.
Initiation
Small subunit binds to mRNA, initiating the formation of the translation complex.
Initiator tRNA (Met) binds to start codon (AUG), marking the beginning of the protein coding sequence.
Large subunit joins the complex, forming the functional ribosome that can carry out translation.
Elongation
tRNA brings amino acid to the A site of the ribosome, adding amino acids to the growing polypeptide chain.
Peptide bond forms between amino acids in the A and P sites, linking the amino acids together.
tRNA in the P site moves to the E site and exits, freeing up the P site for the next tRNA.
Ribosome advances one codon along the mRNA, allowing the next codon to be read.
Termination
Occurs when a stop codon is reached in the mRNA, signaling the end of the protein coding sequence.
Release factor binds to the stop codon, causing the ribosome to disassemble and release the polypeptide.
Sites of Protein Production
Free Ribosomes
Occurs in the cytosol, producing proteins that are used within the cell.
Polyribosomes: Multiple ribosomes translating the same mRNA simultaneously, allowing for more rapid protein production.
Rough Endoplasmic Reticulum (ER)
Network of interconnected fluid-filled tubes and parallel membranes, extending throughout the cytoplasm.
Has ribosomes attached to its surface, giving it a rough appearance under the microscope.
Proteins synthesized here are typically destined for secretion or insertion into membranes, playing critical roles in cell signaling and communication.
Golgi Apparatus
Stacks of membrane-bound sacs, which collects, modifies, packages, and distributes proteins and lipids to their final destinations.
Proteins are shipped from the rough ER to the Golgi apparatus via transport vesicles, ensuring efficient and targeted delivery.
Glycosylation: Sugar chains are attached to proteins in the Golgi apparatus, modifying their structure and function.
Vacuole
Vesicle within the cell, serving as a storage and recycling compartment in plant and fungal cells.
Secretory vesicles: Transport vesicles that carry proteins to the plasma membrane for exocytosis, releasing proteins outside the cell.
Post-translational Processing
Proteins undergo modifications after translation, ensuring they are properly folded, targeted, and functional.
Types of modifications:
Targeting to an organelle (e.g., digestive enzyme to lysosome), directing the protein to its correct location within the cell.
Exocytosis (e.g., collagen), secreting the protein outside the cell to perform its function.
Formation of secretory vesicles (e.g., neurotransmitters), packaging the protein into vesicles for controlled release.
Chaperones: Proteins that help other proteins/polypeptides to fold properly, preventing misfolding and aggregation.
Disulfide bonds: Form early, no more than 5-8 per polypeptide; followed by secondary and tertiary structure formations, stabilizing the protein structure.
Proteolysis: Protein/peptide cutting for proper structure/function, activating or inactivating the protein.
Example: Insulin. Pre-proinsulin is cut to form proinsulin, then cut to form insulin, activating the hormone.
Glycosylation: Adding sugar chains for targeting and recognition, directing the protein to its correct destination and mediating interactions with other molecules. Example: lysosomal enzyme deficiency.
Covalent modification
Phosphorylation: Alters shape of protein and enzyme activity (on/off), regulating protein function in response to cellular signals. Phosphorylation group to a polypeptide.
Kinase: Enzyme that adds a phosphate group to a protein, activating or inactivating the protein.
Phosphatase: Enzyme that removes a phosphate group from a protein, reversing the effects of phosphorylation.
Control of Gene Expression
Operon Model of Gene Regulation
Genes of interest plus regulating sites, controlling gene expression in response to environmental conditions.
Inducible: Default setting is "off", where the gene is not expressed unless induced by a specific signal.
Repressor: A protein that binds to the operator and blocks RNA polymerase, preventing transcription.
Operator: A DNA sequence where the repressor binds, controlling access of RNA polymerase to the gene.
What induces repressor to come off DNA? (Ex: protein A).
As amount of A decreases, more free repressor binds operator, reducing gene expression.
Repressible: Default setting is "on", where the gene is expressed unless repressed by a specific signal.
What can repressor be? (Ex: protein D).
D can be considered 'co-repressor', which binds to the repressor and enhances its ability to bind to the operator.
Examples to consider (Inducible or Repressible??)
Glycolysis
Heat shock protein expression
mRNA Degradation
mRNA in cytosol is not stable and is degraded over time, controlling the amount of protein produced.
Turnover: balance between mRNA synthesis vs. mRNA breakdown, maintaining a steady-state level of gene expression.
Proteosome
Protein machinery that degrades unwanted or damaged proteins, maintaining cellular homeostasis.
Ubiquitin: Tag for protein degradation, marking proteins for destruction by the proteasome.
Recycle amino acids, conserving cellular resources.
Eliminate defective proteins, preventing their accumulation and potential harm to the cell. Example: neurodegenerative diseases.
Genetic Code
Redundancy: Several codons can code for the same amino acid, providing robustness to the genetic code.
No ambiguity: Each codon codes for only one amino acid, ensuring that the correct protein is produced.
Mutations
Spontaneous and random, driving evolution and contributing to genetic diversity. Can be beneficial, but usually detrimental.
Point Mutations
Substitution: One nucleotide is wrong, replacing one base with another.
Silent Mutation: Changes, but still the same amino acid, having no effect on the protein sequence.
Missense Mutation: Results in a different amino acid, potentially altering protein function.
Nonsense Mutation: Introduce a stop codon in place, truncating the protein and likely rendering it non-functional.
Deletions: Missing one or more nucleotides, altering the reading frame and potentially leading to a non-functional protein.
Insertions: Extra nucleotide(s) in the sequence; Results in frame shift, disrupting the protein sequence and often leading to a non-functional protein.
Cancer
Mutation of DNA results in abnormal protein for control mechanism of the cell cycle, leading to uncontrolled cell growth and division.
Uncontrolled cell division, resulting in the formation of tumors.
Cells produced are abnormal, interfering with normal cells/tissue, disrupting tissue structure and function.
Metastasis - cancer breaks from original site, spreading to other parts of the body and forming secondary tumors.
Benign (not cancer) - tumor cells grow only locally and cannot spread by invasion or metastasis, posing less of a threat to the organism.
Malignant (cancer) - cells invade neighboring tissues, enter blood vessels, and metastasize to different sites, posing a significant threat to the organism.
Cancer cells have high amounts of genetic variation, may initially be from same tumor, but express different genes, so develop differently, making them difficult to treat.
Target drug delivery difficult because the target has changed (usually a protein) in cancer cell, requiring personalized treatment strategies.
Any time DNA is replicated, mistakes can be made, leading to mutations and the potential for cancer development.
Ex: viral mutations allow crossing of species barriers. example: Bird Flu / H5N1 Virus mostly wild birds → → domestic birds