Video Notes: Nucleus and Gene Expression - Vocabulary Flashcards

The Nucleus

• Largest structure in the cell; cell's control center.
• Typically only one nucleus per cell; exceptions include:
  • Erythrocytes (red blood cells) with no nuclei
  • Skeletal muscle cells with many nuclei
• Nuclear shape generally mirrors cell shape; some cells have unique shapes.

Nuclear Envelope and Nucleolus

• Nucleolus:
  • Dark-staining, spherical body within the nucleus
  • Not membrane-bound
  • Composed of protein and RNA
  • Produces small and large ribosomal subunits
  • Not present in all cells; e.g., more than one in nerve cells due to production of many proteins
  • Absent in sperm cells because they do not produce proteins
• Nuclear envelope and pores:
  • Nuclear pores regulate traffic between nucleus and cytoplasm
  • Envelope surrounds the nucleus; contains chromatin inside

Structure of the Nucleus (overview)

• Key components include:
  • Nuclear envelope
  • Nuclear pores
  • Chromatin
  • Nucleolus
  • Ribosome (visualized in context of the nucleus)

DNA and RNA

• Nucleic acids are large organic molecules containing carbon, hydrogen, oxygen, nitrogen, and phosphorus.
• DNA (Deoxyribonucleic acid): forms the genetic code inside each cell and regulates most cellular activities over a lifetime.
• RNA (Ribonucleic acid): relays instructions from genes in the nucleus to guide amino acid assembly into proteins by ribosomes.
• Basic units: nucleotides, each consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

Nucleobases and sugars (DNA vs RNA)

• DNA bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)
• RNA bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G)
• Sugar differences:
  • DNA sugar: deoxyribose (lacks 2′-OH)
  • RNA sugar: ribose (has 2′-OH)
• Base pairing:
  • DNA: A pairs with T (two hydrogen bonds); C pairs with G (three hydrogen bonds)
  • RNA: A pairs with U; C pairs with G (in RNA-RNA pairing)
• thymine in DNA is replaced by uracil in RNA; Uracil base pairs with adenine in RNA.

DNA, Chromatin, and Chromosomes

• DNA double helix is wound around histone proteins to form nucleosomes; together these form chromatin.
• When not dividing, DNA exists as a finely filamented mass called chromatin.
• When dividing, chromatin condenses into tightly coiled chromosomes.
• Chromosome structure and organization are essential for accurate genetic inheritance during cell division.

DNA structure and organization (details)

• Levels of organization (from DNA to chromosome):
  • DNA wrapped around histones → nucleosome
  • Nucleosomes coil to form chromatin
  • Chromatin condenses into chromosomes during division
• Promoter region: the “start” signal for transcription.
• Terminator region: the “stop” signal for transcription.
• Gene: a segment of DNA that provides instructions for protein synthesis; promoter and terminator flank the coding region.

DNA and genes

• Genes are segmented units of nucleotides that provide instructions for protein synthesis.
• Functional unit: a gene.
• Terminology:
  • Promoter region: start signal
  • Terminator region: stop signal
• Transcription is directed by DNA; transcription produces RNA as a copy of a gene in the nucleus.

Function of the Nucleus and Ribosomes

• Cellular activities depend on protein synthesis, which is directed by DNA.
• Transcription: synthesis of RNA from DNA in the nucleus.
  • A copy of a gene is formed as an RNA strand (mRNA is formed later from pre-mRNA).
• Translation: RNA is used to synthesize proteins by ribosomes in the cytosol or on the endoplasmic reticulum.

Transcription: Synthesizing RNA

• Required structures:
  • DNA serves as the template for complementary RNA synthesis.
  • Ribonucleotides (ribonucleotide monomers) with ribose sugar, phosphate group, and one of four nitrogenous bases.
  • RNA polymerase enzyme: catalyzes RNA synthesis; located in the nucleoplasm within the nucleus.
• Three types of RNA produced during transcription:
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)
• Three events of transcription:
  • Initiation
  • Elongation
  • Termination

Transcription: Initiation, Elongation, Termination

• Initiation:
  • DNA is unwound by enzymes to make it accessible to RNA polymerase.
  • RNA polymerase attaches to the promoter region and locates the transcription start point.
  • The promoter serves as the start point for transcription; the template strand is used for copying; the coding strand mirrors the mRNA (not copied).
• Elongation:
  • Free ribonucleotides base-pair with exposed bases on the DNA template strand via hydrogen bonding.
  • RNA polymerase moves along the DNA, forming phosphodiester bonds between successive ribonucleotides.
  • A growing RNA strand is formed until the entire gene is transcribed.
• Termination:
  • RNA polymerase is released at the terminal region; the newly formed mRNA strand is released.
  • DNA rewinds back into a double helix.

Transcription: Modifications of mRNA

• Initial RNA product is pre-mRNA.
• Pre-mRNA undergoes processing to form mature mRNA before leaving the nucleus.
• Mature mRNA is used as a template for protein synthesis in translation.

The Central Dogma

• Concept: DNA encodes RNA, which encodes protein.
• Representation: DNA --transcription--> mRNA --translation--> Protein.
• This flow underpins gene expression in cells.

RNA: Types and Roles

• mRNA: carries genetic information from DNA to the cytoplasm, where proteins are made.
• tRNA: delivers amino acids to the ribosome during translation; has an anticodon that pairs with mRNA codon.
• rRNA: forms the core of ribosome structure and catalyzes protein synthesis; most RNA is rRNA.
• Nucleobases in RNA: A, C, G, U (Uracil replaces Thymine).

Translation: Synthesizing Protein

• Translation occurs at ribosomes in the cytoplasm (and on the rough ER in eukaryotes).
• Process converts the nucleotide sequence of mRNA into a polypeptide chain of amino acids.
• Core players:
  • mRNA template
  • Ribosome (large and small subunits)
  • tRNA (carrying specific amino acids with anticodons)
  • Enzymatic factors required for initiation, elongation, and termination
• Ribosome structure: two subunits (large and small) with A, P, and E sites for tRNA binding.
• Start/Stop signals:
  • Start codon: AUG (codes for Methionine in eukaryotes; formyl-Methionine (fMet) is used in prokaryotes during initiation)
  • Stop codons: UAA, UAG, UGA (do not code for amino acids)
• Types of RNA involved in translation: mRNA, tRNA, rRNA (tRNA structure often depicted as a cloverleaf with anticodon and amino acid attachment site).
• Protein synthesis requires the ribosome, mRNA template, tRNA, and various enzymatic factors.

Translation: Mechanism

• Initiation:
  • Small and large ribosomal subunits assemble with a charged tRNA (with the anticodon complementary to the start codon) at the P site.
  • The first amino acid incorporated is typically methionine (Met).
• Elongation:
  • Anticodon of a charged tRNA pairs with the codon of the mRNA in the A site.
  • A peptide bond forms between the amino acids in the P and A sites.
  • The ribosome shifts by one codon; the growing polypeptide chain remains attached to the tRNA in the P site.
  • Additional amino acids are provided by tRNAs as the ribosome moves along the mRNA until a stop codon is reached.
• Termination:
  • When a stop codon enters the A site, a release factor binds and terminates translation.
  • The completed polypeptide is released and the translation complex dissociates.
• Visualized steps include the initiator tRNA in the P site, codon-anticodon pairing in the A site, peptide bond formation, and ribosome translocation.
• In many diagrams, the process is shown with the first amino acid as fMet in prokaryotes; in eukaryotes, the initiating amino acid is Met.

The Genetic Code

• Codon concept:
  • The genetic code is based on triplets of nucleotides in mRNA called codons.
  • Each codon specifies one amino acid or a stop signal.
• Properties:
  • mRNA alphabet: A, C, G, U
  • Protein sequences use 20 standard amino acids.
  • The code is universal across most organisms (with notable exceptions in mitochondria).
• Key codons:
  • Start codon: AUG → Met (start signal)
  • Stop codons: UAA, UAG, UGA → Stop
  • Example codons: UUU/UUC → Phe; UCU/UCC/UCA/UCG → Ser; GCU/GCC/GCA/GCG → Ala; UGG → Trp; etc.
• Redundancy (degeneracy): multiple codons can code for the same amino acid, providing a buffer against mutations.
• Universality and exceptions:
  • The genetic code is universal in most organisms and is strong evidence for a common evolutionary origin.
  • Mitochondrial code exceptions exist (e.g., AUA codes for Met in mitochondria instead of Isoleucine; UGA may code for Trp instead of Stop; some mitochondria encode Arg as a stop codon in certain contexts).
• Reading frames:
  • Only one reading frame in a gene yields a meaningful protein; shifting the reading frame produces nonfunctional sequences.
  • Analogy: reading a sentence in triplets; only the correct frame yields recognizable words.
• Numerical perspective:
  • With 4 nucleotides and triplet codons, there are 4^3 = 64 possible codons, enough to code for the 20 standard amino acids plus stop signals.
  • Third-base wobble and redundancy allow multiple codons to encode the same amino acid.

Translation: Summary of Mechanism and Energetics

• The translation machinery converts the mRNA message into a growing polypeptide chain.
• It requires:
  • mRNA template
  • Ribosome (large and small subunits)
  • Charged tRNA molecules
  • Energetic input (GTP hydrolysis) and supporting factors
• Summary steps:
  1) Initiation: ribosome assembles on mRNA with the initiator tRNA at the start codon.
  2) Elongation: successive tRNAs enter at the A site, peptide bonds form, and the ribosome moves along the mRNA.
  3) Termination: release factor recognizes stop codon; polypeptide released; ribosomal subunits dissociate.

The Genetic Code is Universal

• The code's universality is a hallmark of shared ancestry among life forms.
• Mitochondrial deviations illustrate that the code is not absolutely universal across all organelles.
• Practical takeaway: understanding the code allows inference of gene expression and protein synthesis across species.

Reading, Processing, and Regulation of Gene Expression (Eukaryotes)

• Gene expression is regulated at multiple levels:
  • Epigenetic level (DNA accessibility and chromatin state): histone acetylation, DNA methylation regulate transcription availability.
  • Transcriptional level: control of RNA synthesis in the nucleus; promoter availability; transcription factors.
  • RNA processing level: intron splicing, exon joining, 5′ capping, 3′ polyadenylation, RNA transport.
  • Translational level: regulation of mRNA translation in the cytoplasm.
  • Post-translational level: modifications after protein synthesis (e.g., folding, cleavage, phosphorylation) affecting activity and destination.
• Example: Transcription and RNA processing in eukaryotes involve exon/intron organization and splicing to produce mature mRNA.
• mRNA export: mature mRNA exits the nucleus via nuclear pores and enters the cytosol for translation.

Regulation and Practical Implications

• Gene regulation enables cells to express different proteins in different tissues (e.g., brain vs skin).
• Environmental signals can turn genes on or off, enabling responses to conditions.
• Practical implications include:
  • Understanding disease mechanisms when gene regulation goes awry.
  • Biotechnological applications in which gene expression is controlled for production of proteins.
  • Antibiotic use and resistance, given how some agents interfere with bacterial protein synthesis.
• Ethical/philosophical considerations (brief): manipulation of gene expression and genomes raises questions about safety, equity, and long-term impacts on organisms and ecosystems.

Protein Structure: Levels of Organization

• Proteins have four levels of structure:
  • Primary structure: sequence of amino acids in the polypeptide chain.
  • Secondary structure: regular folding patterns formed by hydrogen bonds in the backbone; common motifs include the alpha helix and beta-pleated sheet.
  • Tertiary structure: three-dimensional folding driven by side chain interactions (hydrogen bonds, ionic interactions, hydrophobic effects, disulfide bridges).
  • Quaternary structure: more than one polypeptide chain (subunits) associating to form a functional protein.
• Example: albumin denatures with heat (unfolding affects function).
• Visual cues include representations of the alpha helix (spiral) and beta sheet (pleated sheet).

Protein Synthesis: Analogies and Visual Aids

• Common analogies to remember the process:
  • DNA as a cookbook (recipes for proteins)
  • mRNA as a recipe copied from the cookbook
  • tRNA as a kitchen hand delivering ingredients (amino acids)
  • Ribosome as the chef assembling the dish (protein)
• Diagrammatic cues often show the roles of mRNA, tRNA, ribosome, and amino acids in a cycle.

Antibiotics and Protein Synthesis Inhibitors (Overview)

• Antibiotics can interfere with bacterial protein synthesis at different steps:
  • Aminoglycosides: block initiation and cause misreading of mRNA.
  • Macrolides: prevent continuation of protein synthesis.
  • Tetracyclines: block the attachment of aminoacyl-tRNA to the ribosome (30S).
  • Chloramphenicol: prevents peptide bond formation.
  • Streptogramins: interfere with distinct steps of protein synthesis.
  • Lincosamides: prevent continuation of protein synthesis.
  • Oxazolidinones: interfere with initiation of protein synthesis.
• These mechanisms highlight how the translation apparatus is a critical target for antimicrobial therapy.

Connections to Real-World Relevance

• The nucleus and gene expression underlie all cellular functions and organismal traits.
• The universality of the genetic code supports evolutionary theory and comparative biology.
• Understanding transcription and translation informs biotechnology, medicine, and pharmacology (e.g., antibiotic design, gene therapy strategies).
• Ethical considerations arise in gene editing, regulation, and applications that alter protein expression in organisms.

Quick Concept Checks (key takeaways)

• The nucleus is the control center of the cell, housing DNA and RNA processes.
• DNA is a double helix with a sugar-phosphate backbone and base pairing (A-T, C-G).
• RNA uses ribose, Uracil instead of Thymine, and is typically single-stranded.
• Transcription converts DNA to pre-mRNA in the nucleus; RNA processing yields mature mRNA.
• Translation uses mRNA, tRNA, and ribosomes to synthesize proteins.
• The genetic code uses triplet codons; there are 64 possible codons; at least one start codon and three stop codons.
• The genetic code is largely universal; mitochondria show codon deviations.
• Protein structure has four levels: primary, secondary, tertiary, and quaternary.
• Gene expression is regulated at multiple levels, including epigenetic control, transcription, RNA processing, translation, and post-translational modifications.