Biology Chapter 17: From Gene to Protein

Chapter 17: From Gene to Protein

• DNA's information content is in specific nucleotide sequences.
• Inherited DNA dictates protein synthesis, determining traits (phenotype).
• Phenotype is the link between genotype (genetic makeup) and observable traits.
• Gene expression, the process of DNA directing protein synthesis, has two stages: transcription and translation.

Concept 17.1: Genes Specify Proteins via Transcription and Translation

• Historical discovery of the relationship between genes and proteins:
  • Archibald Garrod (1902) suggested genes dictate phenotypes through enzymes catalyzing chemical reactions. Symptoms of inherited diseases reflect an inability to synthesize specific enzymes.
  • Understanding metabolic pathways, where molecules are synthesized and degraded in cellular steps, linked genes to enzymes.
• George Beadle and Edward Tatum's work with Neurospora mold:
  • Creating mutants with X-rays unable to survive on minimal media.
  • Identifying three classes of arginine-deficient mutants, each lacking a different enzyme for arginine synthesis.
  • Developing the one gene-one enzyme hypothesis; each gene dictates the production of a specific enzyme.
  • Later revised to "one gene-one polypeptide" because some proteins aren't enzymes and are composed of multiple polypeptides, each with its own gene.

Overview: The Flow of Genetic Information

• DNA's information, encoded in nucleotide sequences, directs protein synthesis, ultimately determining traits.
• Proteins are the link between genotype and phenotype.
• Gene expression involves two stages:
  • Transcription, DNA directs RNA synthesis, produces messenger RNA (mRNA).
  • Translation, mRNA directs polypeptide synthesis, using information in mRNA to make a polypeptide chain.

Basic Principles of Transcription and Translation

• RNA is the bridge between genes and the proteins they code for.
• Transcription is the synthesis of RNA under the direction of DNA.
• Transcription creates mRNA.
• Translation is the synthesis of a polypeptide using the information in mRNA.
• Ribosomes are the sites of translation.

Concept 17.2: Transcription is the DNA-directed synthesis of RNA: a closer look

• Transcription as the first stage of gene expression.

Molecular Components of Transcription

• RNA synthesis is catalyzed by RNA polymerase.

• RNA polymerase unwinds the DNA strands, and combines RNA nucleotides complementary to the DNA template strand.

• RNA polymerase uses uracil instead of thymine in its synthesis.

• The DNA sequence where RNA polymerase attaches is the promoter; the sequence signaling transcription end is the terminator. The stretch of DNA transcribed is the transcription unit.

Synthesis of an RNA Transcript

• Three stages of transcription:
• Initiation, Elongation, Termination.

RNA Polymerase Binding and Initiation of Transcription

• Promoters signal the transcriptional start point.
• Transcription factors mediate RNA polymerase binding and initiation.
• Transcription initiation complex, the completed assembly, includes RNA polymerase II bound to a promoter. A crucial promoter is the TATA box in eukaryotes.

Elongation of the RNA Strand

• As RNA polymerase moves along the DNA, the double helix unwinds 10-20 bases at a time.
• Transcription proceeds at 40 nucleotides per second in eukaryotes.
• Several RNA polymerases can work simultaneously.
• New nucleotides are added to the 3’ end of the growing RNA molecule.

Termination of Transcription

• Mechanisms of bacterial and eukaryotic termination differ.
• In bacteria, RNA polymerase stops at the end of a terminator sequence, releasing mRNA for translation.
• Eukaryotic RNA polymerase II transcribes a polyadenylation signal sequence, releasing mRNA from the polymerase 10-35 nucleotides later.

Concept 17.3: Eukaryotic cells modify RNA after transcription

• Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm.
• Alteration of mRNA ends, 5' cap and 3' poly-A tail. These modifications help in mRNA export, protect mRNA from hydrolytic enzymes, and help ribosomes attach.
• Split Genes and RNA splicing, where introns (non-coding sequences) are removed, and exons (coding regions) are joined to form continuous mRNA molecules.
• Spliceosomes, complex of proteins and snRNPs (small nuclear ribonucleoproteins) carry out RNA splicing.

Ribosomes

• Ribosomes facilitate the coupling of tRNA anticodons with mRNA codons in protein synthesis.
• Ribosomes comprise proteins and ribosomal RNA (rRNA).
• Bacterial and eukaryotic ribosomes have similarities, which can be targeted by antibiotics.

Concept 17.4: Translation is the RNA-directed synthesis of a polypeptide: a closer look

• Genetic information goes from mRNA to protein via translation.

Molecular Components of Translation

• Cells translate mRNA to protein with the help of transfer RNA (tRNA) which brings amino acids to the ribosome during protein synthesis.
• Translation is complex biochemically and mechanistically.

The Structure and Function of Transfer RNA

• tRNA molecules aren't identical.
• Each carries a specific amino acid, and an anticodon to match with the mRNA codon.
• tRNA is a single RNA strand roughly L-shaped.

Wobble

• Flexible base-pairing at the third base of the codon allows some tRNAs to bind to more than one codon.
• Accurate translation requires correct matching between tRNA and amino acid through aminoacyl-tRNA synthetase, and tRNA anticodon and mRNA codon.

Ribosomes

• Ribosomes are the sites of translation.
• Have three binding sites for tRNA : P, A, and E sites. P holds the growing polypeptide, A the next amino acid, and E the exit site.

Building A Polypeptide

• Three stages of Translation:
• Initiation, Elongation, Termination

Ribosome Association and Initiation of Translation

• The initiation stage brings together mRNA, the first amino acid-tRNA, and the ribosomal subunits.
• A small ribosomal subunit and initiator-tRNA attach to mRNA; the small subunit moves along the mRNA until reaching the start codon (AUG).
• Initiation factors bring the large subunit into the complex.

Elongation of the Polypeptide Chain

• Amino acids are added one by one to the C-terminus of the growing polypeptide chain.
• Each addition happens in three steps:
  • Codon recognition
  • Peptide bond formation
  • Translocation

Termination of Translation

• Termination occurs when a stop codon in mRNA reaches the A site of the ribosome.
• A release factor enters the A site, adding a water molecule to the polypeptide.
• This reaction releases the polypeptide, and the translation complex dissociates.

Polyribosomes

• Multiple ribosomes can translate the same mRNA simultaneously.
• Polyribosomes allow efficient production of many polypeptide copies very quickly.

Completing and Targeting the Functional Protein

• Translation often needs post-translational modifications to make a functional protein.
  • Modifications can include activation through cleavage, or assembly into subunits.

Protein Folding and Post-Translational Modifications

• Polypeptide chains fold spontaneously into their 3-D structure, and may require further modifications before becoming functional.
• Some polypeptides are activated by enzymes that cleave them.
• Other polypeptides come together to form protein subunits.

Targeting Polypeptides to Specific Locations

• Ribosomes are either free in the cytosol, or bound to the endoplasmic reticulum (ER).
• Free ribosomes synthesize proteins that function in the cytosol.
• Bound ribosomes synthesize proteins destined for the endomembrane system or proteins for secretion.
• Proteins targeted for the ER or secretion are marked by a signal peptide.

Signal-Recognition Particle (SRP)

• The signal-recognition particle (SRP) binds to the signal peptide, bringing it and the ribosome to the ER.

Concept 17.5: Mutations of one or a few nucleotides can affect protein structure and function

• Mutations are changes in genetic material (DNA).
  • Point mutations are chemical changes in one base pair of a gene.
  • A single nucleotide change in the DNA template can lead to an abnormal protein.

Types of Small-Scale Mutations

• Point mutations are grouped into: nucleotide-pair substitutions and one or more nucleotide-pair insertions or deletions.

Substitutions: silent, missense, nonsense mutations

• Silent mutations have no effect on amino acid sequence. A different codon codes for the same amino acid.
• Missense mutations lead to a different amino acid.
• Nonsense mutations change an amino acid codon to a stop codon, often resulting in truncated and nonfunctional protein

Insertions and Deletions: frameshift mutations

• Insertions/deletions alter the reading frame of the mRNA, leading to significant changes in amino acid sequence.
• These mutations often have more disastrous consequences for the protein structure and function.

Mutagens

• Spontaneously occurring mutations can happen during DNA replication or repair.
• A mutagen is a physical or chemical agent that causes mutations.

Concept 17.6: While gene expression differs among the domains of life, the concept of a gene is universal.

• Archaea, although prokaryotes, sometimes share aspects of gene expression with eukaryotes.

Comparing Gene Expression in Bacteria, Archaea, and Eukarya

• Bacteria, archaea, and eukaryotes differ in their RNA polymerases, transcription termination, and ribosomes.

• Bacteria can simultaneously transcribe and translate the same gene.

• Transcription and translation in eukaryotes are separated by the nuclear envelope.

• In archaea, transcription and translation are likely coupled.

• A gene can be defined as a region of DNA that can be expressed to produce a functional polypeptide or RNA molecule.

Explore the intricate relationship between DNA, genes, and proteins in this quiz on Chapter 17. Delve into the processes of transcription and translation and their roles in determining phenotypes. Understand the historical discoveries that connect genes to enzymes and metabolic pathways.