Biology Lecture Notes: Macromolecules, DNA Replication, Transcription, and Translation

Hydrolysis and Dehydration Synthesis

• Dehydration synthesis (condensation) and hydrolysis are opposite covalent-bond forming/breaking processes.
  • Dehydration synthesis removes a molecule of water to form a covalent bond between monomers.
  • Hydrolysis adds water to break a covalent bond.
• Example with amino acids (peptide bond formation):
  • Two amino acids join to form a dipeptide via a peptide bond with the loss of a water molecule.
  • General reaction: AA1{-}COOH + AA2{-}NH2 ightarrow AA1{-}CO{-}NH{-}AA2 + H2O
  • This is the same kind of condensation process that forms polypeptides during protein synthesis.
• Hydrolysis examples from the transcript:
  • Hydrolysis can break down carbohydrates (polysaccharides), proteins, DNA, and RNA.
  • In digestion, proteins are broken down into amino acids via hydrolysis.
• Key takeaway:
  • Dehydration synthesis forms covalent bonds by removing water; hydrolysis breaks covalent bonds by adding water.

Translation and Dehydration Synthesis in Context

• The forward direction (dehydration synthesis) is exemplified by amino acids forming a dipeptide with a peptide bond.
• The reverse direction (hydrolysis) occurs during digestion, breaking the peptide bond and releasing amino acids.
• Simple link to metabolism: bond formation requires energy input; bond cleavage via hydrolysis releases energy used in metabolic pathways.

Prokaryotes vs Eukaryotes: Cell Organization and Gene Expression

• Prokaryotes:
  • Simple, no nucleus; transcription and translation occur in the cytoplasm, often simultaneously.
  • No membrane-bound organelles (e.g., no nucleus or mitochondria).
  • RNA polymerase synthesizes RNA while a ribosome can begin translating the mRNA as it is being transcribed.
  • Spatial and temporal coupling: transcription and translation occur concurrently.
• Eukaryotes:
  • Have a nucleus; transcription occurs in the nucleus, translation in the cytoplasm.
  • Transcription produces a pre-mRNA that is processed before export to the cytoplasm for translation.
• Question posed in class:
  • How does compartmentalization affect where and how transcription and translation occur?
  • Answer given: In prokaryotes, transcription and translation occur in the cytoplasm and can be coupled; in eukaryotes, transcription is nuclear and translation is cytoplasmic.

DNA Directionality During Replication

• Replication fork and origins of replication set up: 5' to 3' ends on the parental strands.
• Leading vs lagging strands (example scenario from the transcript):
  • The strand template orientation dictates which strand is synthesized continuously (leading strand) vs in fragments (lagging strand).
  • In the discussed example, the top strand serves as the leading-strand template because its orientation allows continuous synthesis in the 5'→3' direction by DNA polymerase moving along the template 3'→5'.
  • The bottom strand becomes the lagging-strand template, synthesized in short Okazaki fragments moving away from the fork.
• Primers:
  • Leading strand: typically one RNA primer near the start of synthesis.
  • Lagging strand: multiple RNA primers, one at the start of each Okazaki fragment.
• Important concept: every nucleotide has a 5' end and a 3' end; DNA polymerase synthesizes in the 5'→3' direction; lagging-strand synthesis occurs discontinuously to maintain this directionality.

DNA Structure: Base Pairing and Base Stacking

• Base pairing and hydrogen bonding:
  • Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds.
  • Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.
• Base stacking and DNA stability:
  • Hydrophobic interactions and Van der Waals forces between stacked bases stabilize the double helix.
  • Bases are hydrophobic and tend to stack, reducing exposure to water.
• Double helix features:
  • Two antiparallel strands form a right-handed helix stabilized by hydrogen bonds and base stacking.
• Note: Text references Achieve ebook section 4.1/4.2 for hydrogen bonding, base directions, and base pairing details.

RNA/DNA Transcription and Translation: Key Concepts

• Transcription:
  • Enzyme: RNA polymerase.
  • Requires transcription factors and a promoter region to initiate.
  • Reads the DNA antisense (template) strand 3'→5' and builds an RNA transcript 5'→3'.
  • No primer is required for transcription.
  • Result: messenger RNA (mRNA) transcript that will be translated.
  • In eukaryotes, transcription occurs in the nucleus; in prokaryotes, it occurs in the cytoplasm.
• Translation:
  • Occurs in the cytoplasm (ribosomes).
  • Three steps: initiation, elongation, termination.
  • Initiation: initiator tRNA bound to methionine, small ribosomal subunit binds the mRNA and scans for the start codon; large subunit joins.
  • Elongation: an aminoacyl-tRNA enters the A site; a peptide bond forms between the growing chain in the P site and the amino acid in the A site (peptide bond formed via dehydration synthesis); ribosome translocates, moving the tRNA from A to P site and freeing the previous tRNA to leave via the E site.
  • Termination: stop codon is reached; release factor promotes dissociation of ribosomal subunits and release of the polypeptide.
• tRNA charging concept:
  • The term “charge” for tRNA refers to the tRNA being loaded with its amino acid, not an electrical charge.
• tRNA and codon recognition:
  • tRNA carries an amino acid; anticodon pairs with a codon on mRNA during translation.
• Translation and energy:
  • GTP provides energy during initiation and elongation steps, particularly in peptide-bond formation and translocation (not expanded in detail in the transcript).
• Structure-function note:
  • The polypeptide’s eventual folding into secondary (e.g., helices and sheets), tertiary, and sometimes quaternary structures depends on amino acid sequence and interactions like hydrogen bonds and hydrophobic effects.

Proteins: Amino Acids, R Groups, and Structure

• Primary structure:
  • Linear sequence of amino acids linked by peptide (amide) bonds.
• Secondary structure:
  • Localized folding stabilized by hydrogen bonds between backbone amide and carbonyl groups (e.g., α-helix, β-pleated sheet).
• Tertiary structure:
  • Three-dimensional folded conformation of a single polypeptide chain driven by interactions among R groups (hydrogen bonds, ionic interactions, hydrophobic effects, disulfide bridges).
• Quaternary structure:
  • Association of multiple polypeptide subunits into a functional protein.
• Structure dictates function: “structure follows function.”
• Amino acid R groups determine properties:
  • R groups can be acidic/basic/neutral, polar/nonpolar, and influence solubility and charge.
• How to infer R-group properties from functional groups:
  • Look for: acidic groups (carboxyl) or basic groups (amino) at the end of the side chain to infer charge tendencies.
  • Polar covalent bonds or functional groups indicate polar side chains.
  • Nonpolar, hydrophobic side chains often lack strongly polar functional groups.
• Practical tip for identifying R groups:
  • Do not memorize all 20 R groups; instead, identify the presence of acidic (carboxyl) or basic (amino) groups to classify polarity/charge tendencies.
• Special functional groups (brief overview):
  • Phosphate: polar, hydrophilic, can be charged; can act as a proton donor.
  • Sulfhydryl (–SH): polar; forms disulfide bridges.
  • Methyl (–CH3): nonpolar, neutral.
  • Hydroxyl (–OH): polar, not an acid/base.
  • Carboxyl (–COOH): acidic, can lose H+; charged at physiological pH.
• General rule for functional groups:
  • Presence of oxygen or nitrogen atoms usually indicates higher electronegativity and polarity.
• Practical note:
  • The transcript emphasizes not needing to memorize all 20 R groups for basic understanding; focus is on polar vs nonpolar, acidic vs basic functional groups.

Lipids: Types and Roles

• Lipids are nonpolymers; they do not form long covalent chains like proteins or nucleic acids.
• The three main lipid classes:
  • Neutral lipids (neutral fats): predominantly hydrophobic hydrocarbon chains; examples include triacylglycerols (triglycerides), fats, oils, waxes.
  • Phospholipids: phosphate-containing head (polar) and fatty acid tails (nonpolar); form bilayers for cellular membranes due to amphipathic nature.
  • Sterols: four-ring structure; cholesterol is a key sterol component of membranes and a precursor for steroid hormones.
• Membrane relevance:
  • Phospholipid bilayers create barriers and compartmentalization in cells.
• Important conceptual point:
  • Lipids are essential for energy storage, membrane structure, and signaling, but they do not form polymers like carbohydrates, nucleic acids, or proteins.

Enzymes Involved in DNA Replication

• Topoisomerase: relieves torsional strain in DNA by inducing transient breaks, allowing unwinding and preventing knots/tangling during replication.
• Helicase: separates the two DNA strands by breaking hydrogen bonds between base pairs.
• Primase: places RNA primers at the start of DNA segments to provide a 3'-OH for DNA polymerase to extend from.
• DNA polymerase: synthesizes new DNA by adding nucleotides to the 3' OH of the growing strand; catalyzes phosphodiester bond formation; reads template 3'→5' and synthesizes 5'→3'.
• Ligase: joins Okazaki fragments on the lagging strand by sealing nicks through phosphodiester bond formation.
• Single-stranded binding proteins (SSBPs): stabilize unwound DNA, preventing reannealing of strands; they are not enzymes but assist in replication.
• Okazaki fragments: short segments on the lagging strand synthesized discontinuously; primers mark the start of each fragment.
• Phosphodiester bond formation in DNA replication:
  • The bond forms between the 3' OH of the last nucleotide in the growing strand and the 5' phosphate of the incoming nucleotide, creating a sugar-phosphate backbone.
  • General idea: 5'{-}P{-}O{-} ext{current nucleotide}
    ightarrow 3'{-}OH ext{end of growing strand}
• Practical implication:
  • Inhibitors targeting these enzymes are used as antibiotics or anticancer agents (e.g., topoisomerase inhibitors, DNA polymerase inhibitors); understanding their roles informs therapeutic strategies.

Transcription Factors, Promoters, and the Transcription Process

• Transcription factors bind specific promoter regions and recruit RNA polymerase to initiate transcription.
• Promoter: DNA sequence where transcription starts; marks the beginning of gene transcription.
• Template (antisense) strand vs non-template (sense) strand:
  • Template/antisense strand is used as the template to generate mRNA.
  • Non-template/sense strand has the same sequence as the mRNA (except T replaced by U in RNA).
• RNA polymerase:
  • Reads the antisense strand from 3' to 5' and builds mRNA from 5' to 3', attaching nucleotides to the 3' end.
  • Does not require a primer, unlike DNA polymerase.
• Main takeaways:
  • Transcription converts DNA to RNA using RNA polymerase in the context of promoters and transcription factors.

Key Takeaways and Connections

• Dehydration synthesis and hydrolysis are fundamental for forming and breaking polymers across macromolecules:
  • Proteins: amino acids linked by peptide bonds; hydrolysis during digestion.
  • Nucleic acids: nucleotides linked by phosphodiester bonds; replication and transcription rely on polymerases and other enzymes that form or break these bonds.
  • Carbohydrates: monosaccharides linked by glycosidic bonds; hydrolyzed in digestion.
• DNA structure and replication rely on directionality (5' to 3' synthesis) and complementary base pairing, with leading and lagging strands and continuous vs discontinuous synthesis.
• RNA transcription and protein translation convert genetic information into functional proteins, with distinct cellular compartments in eukaryotes and a coupled process in prokaryotes.
• The properties of amino acids (R groups) govern protein folding and function, with functional groups informing polarity, acidity/basicity, and potential bonding (e.g., disulfide bridges from sulfhydryl groups).
• Lipids provide energy, membrane structure, and signaling roles, with distinct classes tailored to hydrophobic and amphipathic properties.
• Hydrogen bonds, Van der Waals forces, and base stacking collectively stabilize nucleic acids and macromolecular assemblies.
• The practical and ethical implications of these processes include understanding disease mechanisms, drug design (e.g., replication inhibitors), and gene-expression regulation in biotechnology and medicine.

Quick Reference: Formulas and Notation

• Dehydration synthesis (polypeptide formation):
  AA1{-}COOH + AA2{-}NH2 ightarrow AA1{-}CO{-}NH{-}AA2 + H2O
• Hydrolysis (peptide bond cleavage):
  AA1{-}CO{-}NH{-}AA2 + H2O ightarrow AA1{-}COOH + AA2{-}NH2
• Peptide bond (general): - ext{CO}- ext{NH}- linkage between amino acids.
• Transcription directionality:
  • Template strand read 3'→5'; resulting mRNA synthesized 5'→3'.
• DNA replication directionality: synthesis of both strands in the 5'→3' direction; leading strand continuous, lagging strand discontinuous (Okazaki fragments).
• Base pairing:
  • A with T: 2 hydrogen bonds.
  • G with C: 3 hydrogen bonds.
• Phosphodiester backbone formation (general): occurs between the 3' OH of the growing strand and the 5' phosphate of the incoming nucleotide, forming the sugar-phosphate backbone and releasing a small molecule (often pyrophosphate in nucleotide polymerization).
• tRNA charging:
  ext{tRNA} + ext{amino acid}
  ightarrow ext{aminoacyl-tRNA}

End of notes