Chapter four

DNA is a linear polymer of four nucleotides: $A),\;G,\;C,\;T$ . Each nucleotide contains a 5-carbon sugar (deoxyribose), a phosphate group, and a base.
Backbone and polarity: sugars and phosphates form the backbone; bases extend from the sugar. Each strand has 5′ and 3′ ends; nucleotides are linked by phosphodiester bonds between the 3′-OH of one sugar and the 5′-phosphate of the next.
Double helix features: two strands run antiparallel; 10 base pairs per turn; diameter $\approx 2\ \text{nm}$ . Bases pair inward; backbones wind on the outside.
Base pairing and complementarity: $A$ pairs with $T$ via $2$ hydrogen bonds; $G$ pairs with $C$ via $3$ hydrogen bonds. Complementary strands allow exact copying.
Chargaff’s rules: in natural DNAs, $[A] = [T]$ and $[G] = [C]$ across strands; amounts vary between organisms but complementary pairing is maintained.
Stability and structure: base stacking (nonpolar bases) stabilizes the helix; hydrogen bonding provides base-pair specificity.
Nucleotides vs nucleosides: a nucleoside = sugar + base; a nucleotide = nucleoside + phosphate(s).
Evidence for DNA as genetic material (brief): Griffith (1928) transformation; Avery, MacLeod, McCarty (1944) showed DNA, not protein or RNA, carries genetic information.
DNA replication hint: the double-stranded, complementary nature suggests a copying mechanism (template-based) that preserves sequence.

Information storage: genetic information is encoded in the linear base sequence; the sequence has high information-carrying capacity.
Replication: faithful copying via base pairing; parental strands serve as templates for daughter strands; DNA polymerase synthesizes new strands and has proofreading to minimize errors (mutations).
Relationship to function: structure enables storage, replication, and directing synthesis of other macromolecules.
Central dogma (concept): usually DNA -> RNA -> Protein; RNA acts as intermediary; some RNAs can catalyze reactions (ribozymes) or regulate gene expression.
DNA as genetic material also guides development and heredity across generations.

RNA vs DNA: RNA uses ribose (not deoxyribose), contains uracil (not thymine), is typically single-stranded, and often shorter than DNA.
RNA polymerase: synthesizes RNA in the 5′ to 3′ direction by adding ribonucleoside triphosphates to the 3′ end, using a DNA template.
Transcription basics: begins at a promoter, proceeds through elongation, and ends at a terminator. The DNA template is read 3′ to 5′ while the RNA grows 5′ to 3′.
Prokaryotes vs. Eukaryotes:
- Prokaryotes: transcription and translation are coupled; promoter recognition involves sigma factors; often polycistronic mRNA.
- Eukaryotes: transcription involves general transcription factors and enhancers; Pol II transcribes protein-coding genes; promoters can be distant (involving looping and mediator complex).
Exceptions to flow: RNA can direct some information flows (e.g., RNA to DNA in HIV replication, RNA to RNA in some viral replication);
the usual pathway is DNA -> RNA -> Protein.
Gene expression: transcription is regulated; housekeeping genes are continually transcribed; others are condition- or tissue-specific.

Primary transcript vs mature mRNA: in prokaryotes, primary transcript often serves directly as mRNA; in eukaryotes, processing converts the primary transcript into mature mRNA.
5′ cap: addition of a 7-methylguanosine cap to the 5′ end; essential for translation initiation by ribosomes.
3′ poly(A) tail: addition of ~250 adenine residues; promotes mRNA export and stability.
Splicing: removal of introns and joining of exons by the spliceosome; exons encode protein-coding sequences.
Alternative splicing: same primary transcript can be spliced in different ways to yield multiple mRNA variants and proteins; over 80% of human genes are alternatively spliced.
Noncoding RNAs: many transcripts do not code for proteins but have regulatory or structural roles (examples include rRNA, tRNA, snRNA, miRNA, siRNA).
Abundance: in mammalian cells, ribosomal RNA (~80%) and tRNA are highly abundant among RNAs.

DNA is a polymer of nucleotides forming a double helix with a backbone of sugars and phosphates and a base-paired interior.
Nucleotide bases: $A-G-C-T$ ; base pairing: $A\cdot T$ (2 H-bonds), $G\cdot C$ (3 H-bonds); complementary strands enable replication.
Evidence for DNA as genetic material: Griffith; Avery–MacLeod–McCarty; Hershey–Chase.
Information storage and replication: sequence encodes genes; replication uses base pairing; high-fidelity via proofreading; mutations introduce variation.
Central dogma: DNA -> RNA -> Protein; RNA can be catalytic or regulatory; RNA world hypothesis discusses RNA’s early roles.
RNA structure and function: RNA sugar is ribose; uracil replaces thymine; often single-stranded but can fold; some RNAs catalyze reactions.
Transcription: DNA template → RNA; promoter and terminator define transcription start/stop; RNA polymerase synthesizes in the 5′ to 3′ direction; transcription bubble forms.
RNA processing in eukaryotes: 5′ cap, 3′ poly(A) tail, and splicing; alternative splicing expands proteome diversity; many RNAs are noncoding.
Prokaryotes vs. Eukaryotes transcription/translation: coupling vs. separation; promoter recognition and regulation differ (sigma factors vs. general transcription factors and enhancers).