College Biology Study Guide: Structure of Nucleic Acids, DNA Replication, Gene Expression, and Microbial Models

Nucleotide Components: Composed of a phosphate group, a 5-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.
Nitrogenous Bases:
- Purines (double ring): Adenine ( $A$ ) and Guanine ( $G$ ) ("Pure As Gold").
- Pyrimidines (single ring): Cytosine ( $C$ ), Thymine ( $T$ in DNA), and Uracil ( $U$ in RNA).
Chargaff's Rules & Base Pairing:
- DNA: $A = T$ (held by 2 hydrogen bonds) and $G = C$ (held by 3 hydrogen bonds).
- RNA: $A \leftrightarrow U$ and $G \leftrightarrow C$ .
Backbone & Orientation:
- Phosphodiester bonds covalently link the $3'$ carbon of one sugar to the $5'$ phosphate of the next.
- Strands run antiparallel ( $5' \rightarrow 3'$ opposite $3' \rightarrow 5'$ ).

Semiconservative Model: Each replicated DNA double helix contains 1 original parental strand and 1 new strand.
Key Replication Enzymes:
- Helicase: Unwinds double helix by breaking hydrogen bonds.
- SSBP: Stabilizes single strands to prevent re-annealing.
- Topoisomerase: Relieves strain ahead of the replication fork.
- Primase: Synthesizes RNA primers providing a free $3'\text{-OH}$ group.
- DNA Polymerase: Synthesizes DNA $5' \rightarrow 3'$ and performs proofreading.
- DNA Ligase: Covalently joins Okazaki fragments via phosphodiester bonds.
Leading vs. Lagging Strand Synthesis:
- Leading Strand: Synthesized continuously toward the replication fork.
- Lagging Strand: Synthesized discontinuously away from the fork in short Okazaki fragments.

Central Dogma: $\text{DNA} \xrightarrow{\text{transcription}} \text{mRNA} \xrightarrow{\text{translation}} \text{Protein}$ .
Transcription (Eukaryotic Nucleus):
- RNA polymerase binds the promoter (containing a TATA box) and builds pre-mRNA $5' \rightarrow 3'$ .
- Processing: Introns excised via splicing (exons joined); $5'$ methyl-G cap and $3'$ poly-A tail added for stability and export.
Translation (Ribosomes):
- RNA Roles: mRNA (carries transcript), tRNA (delivers amino acids via anticodons), rRNA (catalyzes peptide bonds).
- Process: Begins at start codon AUG (Methionine), proceeds codon-by-codon, and terminates at a stop codon.
Mutations:
- Point Mutations: Silent (no amino acid change), Missense (alters amino acid, e.g., Sickle Cell Anemia), Nonsense (creates premature stop codon).
- Frameshift Mutations: Insertions or deletions not in multiples of 3 shift the mRNA reading frame.

Viruses: Non-cellular genomes (DNA or RNA) enclosed in a capsid protein shell; host specificity determined by viral-host receptor binding.
Bacteriophage Cycles:
- Lytic: Hijacks host cell, synthesizes viral particles, and lyses the host cell.
- Lysogenic: Integration of viral genome into bacterial chromosome as a prophage, replicating silently until induced.
Retroviruses: Convert RNA to DNA using reverse transcriptase (e.g., HIV, targeted by AZT).
Bacterial Gene Transfer:
- Transformation: Direct uptake of free environmental DNA.
- Transduction: Viral-mediated transfer via bacteriophage.
- Conjugation: Direct cell-to-cell transfer via a conjugation pilus.
Operon Regulation:
- Repressible (e.g., trp): Default ON; turned OFF in response to high product levels.
- Inducible (e.g., lac): Default OFF; turned ON in response to substrate presence.

Chromatin Packaging: Negatively charged DNA wraps around positively charged histone octamers to form nucleosomes, which condense into chromatin loops and chromosomes.
Gene Expression Regulation: Multilevel control (chromatin remodeling, transcription, splicing, mRNA decay, translation, post-translational) creates diverse cell types from identical genomes.
Regulatory Factors: Transcription factors, enhancers, and tissue-specific activators modulate expression rates.
X-Chromosome Inactivation: Random transcriptional silencing of one female X chromosome into a condensed Barr body balances dosage between sexes.