🐾General Biology II Unit 2 – From DNA to Protein: Gene Expression

Key Concepts and Terminology

• Central dogma of molecular biology describes the flow of genetic information from DNA to RNA to proteins
• Transcription process of synthesizing RNA from a DNA template catalyzed by RNA polymerase enzymes
• Translation process of synthesizing proteins from an mRNA template facilitated by ribosomes
• Genetic code set of rules that defines how codons (triplets of nucleotides) in mRNA specify amino acids during protein synthesis
  • Consists of 64 codons, 61 of which code for amino acids and 3 serve as stop codons (UAA, UAG, UGA)
• Gene expression process by which genetic information is used to synthesize functional gene products (proteins or non-coding RNAs)
  • Tightly regulated at multiple levels (transcriptional, post-transcriptional, translational, and post-translational)
• Mutations changes in the DNA sequence that can alter gene function and potentially impact an organism's phenotype
  • Can be caused by various factors (replication errors, environmental mutagens, etc.)

DNA Structure and Function

• DNA (deoxyribonucleic acid) double-stranded helical molecule that carries genetic information in living organisms
• Composed of nucleotides, each consisting of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (adenine, thymine, guanine, or cytosine)
• Complementary base pairing (A-T and G-C) and hydrogen bonding between bases stabilize the double helix structure
• Antiparallel nature of DNA strands one strand runs 5' to 3' while the other runs 3' to 5'
• Functions as a template for its own replication and for the synthesis of RNA molecules during transcription
• Packaged into chromatin structures (nucleosomes and higher-order structures) to fit within the nucleus and regulate gene expression
• Genetic information encoded in the sequence of bases along the DNA molecule determines the amino acid sequence of proteins

Transcription: DNA to RNA

• Transcription process of synthesizing RNA from a DNA template catalyzed by RNA polymerase enzymes
• Occurs in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells
• Initiation begins with the binding of RNA polymerase to a promoter region upstream of the gene to be transcribed
  • Transcription factors help recruit RNA polymerase and regulate gene expression
• Elongation RNA polymerase moves along the DNA template, synthesizing the RNA strand in the 5' to 3' direction
  • Ribonucleotides (ATP, UTP, GTP, and CTP) are added complementary to the DNA template strand
  • RNA sugar (ribose) contains an additional hydroxyl group compared to DNA sugar (deoxyribose)
  • Uracil (U) replaces thymine (T) in RNA and base pairs with adenine (A)
• Termination occurs when RNA polymerase reaches a terminator sequence, causing the enzyme to dissociate and release the newly synthesized RNA
• Three main types of RNA produced during transcription messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA)

RNA Processing and Modifications

• Pre-mRNA initial transcript produced by RNA polymerase II in eukaryotes undergoes several processing steps to become mature mRNA
• 5' capping addition of a 7-methylguanosine cap to the 5' end of the pre-mRNA protects it from degradation and facilitates translation initiation
• 3' polyadenylation addition of a poly(A) tail (150-250 adenine residues) to the 3' end of the pre-mRNA enhances stability and translation efficiency
• Splicing removal of non-coding introns and joining of coding exons to form a continuous coding sequence
  • Carried out by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs) and other factors
  • Alternative splicing can generate multiple mRNA isoforms from a single gene, increasing protein diversity
• RNA editing post-transcriptional modification of specific nucleotides in the RNA sequence (e.g., adenosine to inosine conversion)
• tRNA and rRNA also undergo specific processing and modifications to achieve their functional forms

Translation: RNA to Protein

• Translation process of synthesizing proteins from an mRNA template facilitated by ribosomes
• Occurs in the cytoplasm of both eukaryotic and prokaryotic cells
• Ribosomes complex macromolecular machines composed of rRNA and proteins
  • Consist of a small subunit (decodes mRNA) and a large subunit (catalyzes peptide bond formation)
• tRNAs adapter molecules that link specific codons in mRNA to their corresponding amino acids
  • Contain an anticodon loop that base pairs with the mRNA codon and an amino acid attachment site
• Initiation begins with the assembly of the initiation complex (small ribosomal subunit, initiator tRNA, and initiation factors) at the start codon (AUG) of the mRNA
• Elongation ribosome moves along the mRNA, recruiting aminoacyl-tRNAs that match the codons and catalyzing peptide bond formation between adjacent amino acids
  • Amino acids are added to the growing polypeptide chain in the N-terminus to C-terminus direction
• Termination occurs when the ribosome encounters a stop codon (UAA, UAG, or UGA), leading to the release of the completed polypeptide and dissociation of the ribosomal subunits
• Post-translational modifications (e.g., folding, cleavage, addition of functional groups) often required for proteins to achieve their final functional form

Gene Regulation and Control

• Gene regulation control of gene expression to ensure that the right genes are expressed at the right time, in the right place, and in the appropriate amount
• Transcriptional regulation control of gene expression at the level of transcription initiation
  • Promoters and enhancers DNA sequences that recruit transcription factors and RNA polymerase to initiate transcription
  • Transcription factors proteins that bind to specific DNA sequences and regulate the activity of RNA polymerase
  • Chromatin modifications (e.g., histone acetylation, DNA methylation) can alter the accessibility of DNA to transcription factors and RNA polymerase
• Post-transcriptional regulation control of gene expression after transcription but before translation
  • Includes mRNA processing (splicing, capping, polyadenylation), mRNA stability, and mRNA localization
  • microRNAs (miRNAs) small non-coding RNAs that can repress translation or promote degradation of target mRNAs
• Translational regulation control of gene expression at the level of translation initiation or elongation
  • Involves factors that affect ribosome recruitment, start codon recognition, or the rate of polypeptide chain elongation
• Post-translational regulation control of protein activity, stability, or localization after translation
  • Includes protein modifications (phosphorylation, glycosylation, ubiquitination), protein-protein interactions, and protein degradation

Mutations and Their Effects

• Mutations changes in the DNA sequence that can alter gene function and potentially impact an organism's phenotype
• Types of mutations
  • Point mutations single nucleotide changes (substitutions, insertions, or deletions)
    • Silent mutations do not change the amino acid sequence due to the redundancy of the genetic code
    • Missense mutations change a single amino acid in the protein sequence
    • Nonsense mutations introduce a premature stop codon, leading to a truncated protein
  • Frameshift mutations insertions or deletions that alter the reading frame, often resulting in a completely different amino acid sequence and a premature stop codon
  • Chromosomal mutations large-scale changes affecting entire chromosomes or chromosome segments (deletions, duplications, inversions, translocations)
• Effects of mutations can range from neutral to beneficial to deleterious, depending on the location and nature of the mutation
  • Loss-of-function mutations reduce or eliminate the function of a gene product
  • Gain-of-function mutations enhance or alter the function of a gene product
• Mutations can be inherited (germline mutations) or acquired during an organism's lifetime (somatic mutations)
  • Germline mutations can be passed on to offspring and may contribute to genetic disorders
  • Somatic mutations can accumulate over time and may lead to diseases such as cancer

Applications and Real-World Relevance

• Genetic engineering techniques that allow the manipulation of DNA sequences for various purposes
  • Recombinant DNA technology insertion of foreign DNA into a host organism to produce desired proteins (e.g., insulin production in bacteria)
  • Gene therapy introduction of functional genes into cells to replace or correct defective genes causing genetic disorders
  • CRISPR-Cas9 a powerful genome editing tool that enables precise modification of DNA sequences in living cells
• Personalized medicine tailoring medical treatments to an individual's genetic profile to optimize efficacy and minimize side effects
  • Pharmacogenomics study of how genetic variations influence drug response and toxicity
  • Targeted cancer therapies drugs designed to specifically target the molecular alterations driving cancer growth in individual patients
• Forensic science application of DNA analysis techniques to identify individuals or establish familial relationships in legal cases
  • DNA fingerprinting comparison of DNA profiles to match suspects to crime scene samples or establish paternity
• Evolutionary studies analysis of DNA sequences to understand the evolutionary relationships between species and track genetic changes over time
  • Comparative genomics comparison of genomes across different species to identify conserved and divergent regions
  • Phylogenetics construction of evolutionary trees based on DNA sequence similarities to infer common ancestry and divergence times
• Biotechnology industry sector that applies biological processes and organisms to develop products and services
  • Biopharmaceuticals drugs produced using living organisms or their components (e.g., monoclonal antibodies, vaccines)
  • Agricultural biotechnology development of genetically modified crops with improved traits (e.g., pest resistance, drought tolerance)
  • Industrial biotechnology use of enzymes and microorganisms to produce chemicals, materials, and fuels from renewable resources