Biology Chapter 17

Gene Expression: From Gene to Protein

• Gene expression is the process by which DNA directs protein synthesis.
• Proteins are the link between genotype and phenotype.
• The process includes two key stages: transcription and translation.
• In 1902, Archibald Garrod suggested genes dictate phenotypes through enzymes (catalyzing specific chemical reactions).
• He also thought that inherited diseases result from an inability to synthesize a specific enzyme due to a metabolic pathway of cells.
• Cells synthesize and degrade molecules sequentially.
• George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that could not survive on minimal media.
• Beadle and Tatum's colleagues, Adrian Srb and Norman Horowitz, identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for arginine synthesis.
• Experiments demonstrated that the function of a gene is to dictate the production of a specific enzyme.

Transcription: DNA to RNA

• RNA is the bridge between genes and protein synthesis.
• Transcription is the synthesis of RNA using information from DNA.
• Transcription produces messenger RNA (mRNA).
• Translation is the synthesis of a polypeptide (a chain of amino acids) from an mRNA molecule.
• mRNA is translated into a chain of amino acids.
• Ribosomes are the sites of translation.
• In prokaryotes, translation of mRNA can begin before transcription is finished.
• In eukaryotes, the nuclear envelope separates transcription from translation.
• Eukaryotic RNA transcripts are modified through RNA processing before leaving the nucleus.
• A primary transcript is the initial RNA transcript from any gene prior to processing.
• The central dogma is the concept that cells are governed by a cellular chain of command. DNA → RNA → protein.
• Transcription is the first stage of gene expression.
• RNA synthesis is catalyzed by RNA polymerase.
• The RNA polymerase pries the DNA strands apart. It then joins together RNA nucleotides.
• The RNA is complementary to the DNA template strand).
• RNA polymerase does not need any primer.

Codons: Triplets of Nucleotides

• The flow of information from gene to protein is based on a triplet code consisting of non-overlapping, three-nucleotide words.
• The words of a gene are transcribed into complementary non-overlapping three-nucleotide words of mRNA.
• These mRNA words are translated into a chain of amino acids.
• One of the two DNA strands acts as a template for the sequence of complementary nucleotides in the RNA transcript.
• The template strand is always the same for a given gene.
• The nontemplate strand is called the coding strand; it is identical to the mRNA sequence, except that T takes the place of U in the mRNA.
• The mRNA molecule is complementary to the template strand.
• During translation, the mRNA base triplets (codons) are read in the 5' → 3' direction.
• Each codon specifies a particular amino acid.

Cracking the Code

• All 64 codons were deciphered by the mid-1960s.
• Of the 64 triplets, 61 code for amino acids; 3 triplets are "stop" signals to end translation.
• The genetic code is redundant (more than one codon may specify a particular amino acid), but not ambiguous (no codon specifies more than one amino acid).
• Codons must be read in the correct reading frame (correct groupings) for the specified polypeptide to be produced.

Transcription Initiation, Elongation, and Termination

• The three main stages of transcription are initiation, elongation, and termination.
• Promoters signal the transcription start point.
• Transcription factors help the binding of RNA polymerase and initiate transcription.
• The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex.
• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes.
• As RNA polymerase moves along the DNA, it untwists the DNA double helix, 10–20 nucleotides at a time.
• Nucleotides are added to the 3' of the growing RNA molecule.
• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes.
• A gene can be transcribed simultaneously by several RNA polymerases.
• The termination mechanisms vary in bacteria and eukaryotes.
• In bacteria, the polymerase stops transcription at the end of the terminator.
• In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence.

RNA Processing

• Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic message is dispatched to the cytoplasm
• During RNA processing, both ends of the primary transcript are altered.
• In most cases, certain interior sections of the molecule are cut out and the remaining parts are spliced together.

Alternative RNA Splicing

• Some introns contain sequences that regulate gene expression and many affect gene products.
• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.
• This is called alternative RNA splicing.
• Consequently, the number of different proteins an organism can produce is much greater than its number of genes.

Protein Folding

• During synthesis, a polypeptide chain begins to coil and fold spontaneously into a specific shape (three-dimensional molecule with secondary and tertiary structure).
• A gene determines the primary structure, and the primary structure in turn determines shape.
• Post-translational modifications may be required before the protein can begin doing its function in the cell.

Targeting Polypeptides to Specific Locations

• Two populations of ribosomes exist in cells: free ribosomes in the cytosol and bound ribosomes attached to the ER.
• Free ribosomes mostly synthesize proteins that function in the cytosol.
• Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell.
• Ribosomes are identical and can switch from free to bound.
• Polypeptide synthesis always begins in the cytosol.
• Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER.
• Polypeptides destined for the ER or for secretion are marked by a signal peptide.
• The signal peptide is a sequence of about 20 amino acids at or near the leading end of the polypeptide.
• A signal-recognition particle (SRP) binds to the signal peptide.
• The SRP escorts the ribosome to a receptor protein built into the ER membrane.
• The signal peptide is removed by an enzyme.
• Other kinds of signal peptides target polypeptides to other organelles.

Making Multiple Polypeptides

• Multiple ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome).
• Polyribosomes enable a cell to make many copies of a polypeptide very quickly.
• A bacterial cell ensures a streamlined process by coupling transcription and translation.

Mutations

• Mutations are changes in the genetic information of a cell.
• Point mutations are changes in just one nucleotide pair of a gene.
• The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein.
• If a mutation has an adverse effect, the condition is referred to as a genetic disorder or hereditary disease.
• Point mutations can be classified as:
  • Substitutions (silent, missense, nonsense) and
  • Insertions/Deletions (frameshift).

New Mutations and Mutagens

• Spontaneous mutations can occur during DNA replication or recombination.
• Mutagens are physical or chemical agents that cause mutations.
• Chemical mutagens fall into a variety of categories.
• Most carcinogens (cancer-causing chemicals) are mutagens.

Gene Editing Using CRISPR

• Biologists who study disease-causing mutations have sought techniques for gene editing.
• The powerful technique called CRISPR-Cas9 is transforming the field of genetic engineering.
• In bacteria, the protein Cas9 acts together with a guide RNA to help defend bacteria from viral infection.
• The Cas9 protein cuts any sequence to which it is targeted.
• Scientists can introduce a Cas9-guide RNA complex into a cell that they wish to alter (the guide RNA is engineered to target a gene).
• Cas9 cuts both strands of the targeted gene.
• The broken ends trigger a DNA repair system in which repair enzymes remove or add some random nucleotides while joining the broken ends.

Gene Therapy

• To treat genetic disease, researchers have modified this technique.
• They can introduce a template with a normal, functional copy of the gene to correct the defective gene.

Test your knowledge on protein synthesis and the molecular mechanisms involved in it. This quiz covers topics such as ribosomes, RNA processing, and the roles of various molecules like tRNA and SRP. Challenge yourself and deepen your understanding of these critical biological processes!