6.1 DNA and RNA Structure

DNA and RNA are both nucleic acids made of nucleotides (sugar + phosphate + base) that store and transfer genetic information, but they differ in structure and roles. DNA is a double helix with two antiparallel strands (deoxyribose sugar) and bases A, G (purines) and C, T (pyrimidines); A pairs with T and G with C via hydrogen bonds. In cells, DNA usually forms chromosomes (prokaryotes: circular; eukaryotes: multiple linear chromosomes condensed with histones) and can exist as plasmids (circular extra-chromosomal DNA). RNA is usually single-stranded (ribose sugar), uses uracil (U) instead of thymine so A pairs with U, and exists in several forms (mRNA, tRNA, rRNA) that help express DNA’s information. These structural differences (sugar, bases, strand number, location/function) explain why DNA is the stable hereditary material and RNA is more versatile for gene expression. For a quick AP-aligned review, see the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and extra practice (https://library.fiveable.me/practice/ap-biology).

Purines (adenine, guanine) always pair with pyrimidines (thymine/uracil, cytosine) because of shape and hydrogen-bonding rules that keep the DNA double helix stable and uniform. Purines are double-ringed and pyrimidines single-ringed, so pairing one of each preserves a constant 2 nm width of the helix; two purines would be too wide and two pyrimidines too narrow. Hydrogen bonds provide specificity: A–T (or A–U in RNA) forms two H-bonds, G–C forms three—those specific donors/acceptors on the bases match only when a purine pairs with the correct pyrimidine. This complementary pairing plus antiparallel strands and base stacking gives DNA its stable, predictable structure used to store hereditary information (CED EK 6.1.B.1–3). For a quick CED-aligned refresher, see the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice more at (https://library.fiveable.me/practice/ap-biology).

Prokaryotes typically have one circular chromosome (plus possible plasmids) that’s compacted without histones and replicated from a single origin—the circular shape means no ends to worry about and supercoiling/topoisomerases manage tension during replication (EK 6.1.A.1.i; keywords: circular chromosome, plasmid). Eukaryotes have multiple linear chromosomes packaged with histones into chromatin; each chromosome has ends (telomeres) and needs telomerase to solve the end-replication problem, and chromosomes condense for mitosis/meiosis (EK 6.1.A.1.ii; keywords: linear chromosome, histone, chromatin condensation, telomere). For the AP exam, know the structural differences and consequences (replication origins, telomeres, packaging) because LO 6.1.A asks you to describe structures that pass heredity. Want a quick review? Check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice questions (https://library.fiveable.me/practice/ap-biology).

Histones are small, positively charged proteins that help package eukaryotic DNA into compact chromatin (EK 6.1.A.ii). DNA wraps ~1.7 turns around a histone octamer (two each of H2A, H2B, H3, H4) to form a nucleosome "bead"—the basic unit of chromatin. Nucleosomes fold into higher-order fibers (often described as a 10-nm “beads-on-a-string” to more condensed 30-nm structures) and loop on scaffold proteins to make chromosomes compact enough to fit in the nucleus and to be segregated during cell division. Besides compaction, histones control accessibility: chemical modifications (acetylation, methylation) change how tightly DNA is bound, regulating transcription and other processes—a key link to gene expression regulation on the AP exam (LO 6.1.A, chromatin condensation keyword). For a quick refresher, check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and try practice problems (https://library.fiveable.me/practice/ap-biology).

Think of base pairing as a precise “fit” rule that keeps DNA stable and readable. DNA’s four bases are two purines (adenine, guanine—double rings) and two pyrimidines (cytosine, thymine—single rings). Purines always pair with pyrimidines so the helix width stays constant: A pairs with T (in DNA) via 2 hydrogen bonds, and G pairs with C via 3 hydrogen bonds. More H-bonds = stronger local bonding, so G–C regions are slightly more stable. In RNA, uracil (U) replaces thymine, so A pairs with U. Base pairing also follows strand antiparallel orientation, letting complementary sequences encode the same genetic info on opposite strands. This is exactly what EK 6.1.B.1 describes—conserved nucleotide base pairing. If you want quick review or practice Qs that match AP wording and visuals, check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and the practice problem bank (https://library.fiveable.me/practice/ap-biology).

Plasmids are extra-chromosomal, typically circular DNA molecules that replicate independently of the main chromosome (EK 6.1.A.2). They’re common in prokaryotes (bacteria) and also found in some eukaryotes (e.g., yeast) or used as vectors in lab eukaryotic cells. Plasmids often carry nonessential but beneficial genes—like antibiotic resistance, toxin production, or metabolic pathways—that can increase fitness in certain environments. Because they replicate independently and can be transferred between cells (horizontal gene transfer, e.g., conjugation), they spread adaptive traits fast through populations. For the AP Bio CED, plasmids fit LO 6.1.A (structures passing hereditary info) and help explain variation and rapid adaptation. Want to review this topic more? Check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice questions at (https://library.fiveable.me/practice/ap-biology).

Good question—short answer: RNA uses uracil (U) because RNA’s role and chemistry let it get away with the simpler pyrimidine, while DNA benefits from the extra stability and repair advantages of thymine (T). Details: both T and U are pyrimidines and pair with adenine via hydrogen bonds, so base-pairing rules in EK 6.1.B.1 still hold. Chemically, thymine is just uracil with a methyl group at carbon-5 (5-methyluracil). That methyl group makes DNA more chemically stable and helps repair systems spot and fix C→U (deamination) mistakes—if DNA used U, repair enzymes couldn’t easily tell whether a U came from damage or was the correct base. RNA is short-lived and used transiently (messenger, structural, catalytic), so it’s cheaper to make and doesn’t need that extra stability, so U is fine. For the AP exam, know the purine/pyrimidine classification and that adenine pairs with thymine in DNA or uracil in RNA (CED EK 6.1.B.1). For a quick refresher, check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD)—and practice problems at (https://library.fiveable.me/practice/ap-biology).

Purines and pyrimidines differ in ring structure and size. Purines (adenine and guanine) are double-ringed molecules: a six-membered ring fused to a five-membered ring. Pyrimidines (cytosine, thymine in DNA, and uracil in RNA) have a single six-membered ring. Because purines are larger, DNA/RNA pairs always match a purine with a pyrimidine (A with T in DNA or A with U in RNA; G with C) so the helix has a uniform width. That pairing is stabilized by hydrogen bonds (A–T/A–U = 2 H-bonds; G–C = 3 H-bonds). This is exactly what the CED lists in EK 6.1.B.1 (purines double ring, pyrimidines single ring; purine–pyrimidine pairing). For a quick review tied to Topic 6.1, see the Fiveable study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice problems (https://library.fiveable.me/practice/ap-biology).

The double helix is perfect for storing hereditary info because its structure combines stability, precise coding, and easy copying. Two antiparallel sugar-phosphate backbones form a sturdy exterior while the nitrogenous bases face inward and pair specifically (A–T, G–C) via hydrogen bonds—that base pairing is what preserves sequence information and lets one strand act as a template for exact replication and repair. The helical shape compacts long DNA molecules so many base pairs fit into chromosomes (eukaryotes further package DNA with histones), protecting the code. Complementary pairing also provides redundancy: if one strand is damaged, the other guides accurate repair. These are the same features the AP CED emphasizes (EK 6.1.A, EK 6.1.B). For a quick Topic 6.1 review, see the study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD). Want extra practice? Try the AP question bank (https://library.fiveable.me/practice/ap-biology).

DNA is called hereditary material because its chemical structure reliably stores and passes information across generations. The sequence of nucleotides (A, T, G, C) encodes genes; complementary base pairing (A–T, G–C) and hydrogen bonds let DNA be copied precisely during replication, so offspring inherit the same instructions (LO 6.1.A, LO 6.1.B). The double helix (antiparallel strands) and the stability of the sugar-phosphate backbone protect the code. In eukaryotes DNA is organized into linear chromosomes wrapped around histones (chromatin condensation), and in prokaryotes it’s often a circular chromosome; both chromosomal DNA and extra-chromosomal plasmids can carry heritable traits. Sometimes RNA stores genetic info (e.g., some viruses). On the AP exam you’ll be asked to describe these structures and explain how base pairing and replication enable heredity—review Topic 6.1 in the Fiveable study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice questions (https://library.fiveable.me/practice/ap-biology).

During cell division eukaryotic chromosomes change their packaging so DNA can be accurately passed to daughter cells. Interphase chromatin is relatively loose: DNA wraps around histones into nucleosomes (chromatin). As cells enter mitosis or meiosis, chromatin condenses (with condensin proteins) into visible linear chromosomes, each made of two sister chromatids joined at a centromere. Kinetochores form at centromeres and spindle microtubules (from centrosomes) attach and pull sister chromatids apart during anaphase—this ensures equal segregation. Cohesin holds sisters together until the right phase; when cohesin is removed, chromatids separate. Prokaryotes, by contrast, usually have a single circular chromosome (and sometimes plasmids) that segregates differently (EK 6.1.A, EK 6.1.A.1–2). For AP exam phrasing, be ready to use terms like histone, chromatin condensation, centromere, kinetochore, sister chromatids, and plasmid. Want a quick review? Check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and practice questions (https://library.fiveable.me/practice/ap-biology).

You need to know nucleotide base pairing because it’s a core structural fact (LO 6.1.B, EK 6.1.B.1) that explains how DNA stores and transmits information. Base pairing (A–T in DNA or A–U in RNA; G–C) follows purine–pyrimidine rules and hydrogen-bonding patterns that make the double helix stable and allow exact copying during replication and accurate transcription into RNA. On the AP exam, questions test this as concept explanation and visual-representation skills (both in multiple choice and free-response). Knowing base pairing helps you: (1) predict complementary strands, (2) explain why mutations change amino acids, and (3) interpret models/graphs in FRQs. Unit 6 is 12–16% of MCQ content, and several FRQs expect you to describe or apply base-pair rules. Review the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and drill practice questions (https://library.fiveable.me/practice/ap-biology) so you can quickly use base-pairing knowledge on both MCQs and the 6 free-response questions.

Chromosomal DNA is the cell’s main genome: in eukaryotes it’s multiple linear chromosomes packaged with histones into chromatin, in prokaryotes it’s usually a single circular chromosome (CED EK 6.1.A.1). It contains essential genes required for growth, development, and inheritance across generations. Plasmid DNA is extra-chromosomal, usually small and circular (CED EK 6.1.A.2). Plasmids carry nonessential—but often beneficial—genes (e.g., antibiotic resistance, metabolic pathways), replicate independently of the chromosome, can have high copy numbers, and can move between cells (conjugation), so they’re more mobile than chromosomal DNA. For the AP exam, know: chromosomal DNA = core hereditary information (LO 6.1.A); plasmids = accessory, extra-chromosomal elements that can affect phenotype and horizontal gene transfer. Want a quick recap and practice? Check the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and try practice questions (https://library.fiveable.me/practice/ap-biology).

Adenine (A) and guanine (G) are purines (two fused rings); cytosine (C) and thymine (T) are pyrimidines (one ring). Base pairing specificity comes from two things: size and hydrogen-bonding patterns. A purine always pairs with a pyrimidine so the helix keeps a consistent width. More importantly, each base has a unique pattern of hydrogen-bond donors and acceptors on its edges—A and T form two hydrogen bonds, while G and C form three—so only the correct partners can line up to make the right set of H-bonds. That chemical complementarity (purine+pyrimidine + matching H-bond pattern) enforces the specific A–T and G–C pairs in DNA (and A–U in RNA). These properties are why nucleic acids reliably store and transmit information (CED EK 6.1.B.1: purines/pyrimidines, EK 6.1.B.1.iii: base pairing). For a quick Topic 6.1 review check the study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD) and more practice questions (https://library.fiveable.me/practice/ap-biology).

Histones are the protein cores that DNA wraps around to form nucleosomes, which fold into chromatin—that’s how eukaryotic linear chromosomes are condensed (EK 6.1.A.2). By packaging DNA, histones control physical access to genes: tightly packed heterochromatin is transcriptionally silent, while loosely packed euchromatin is accessible and active. Chemical changes to histone tails (e.g., acetylation, methylation) alter chromatin packing and either promote or repress transcription by changing how easily RNA polymerase and transcription factors bind. On the AP exam you should link histone-based condensation to chromosome structure and to regulation of gene expression (Topic 6.1 → Unit 6). For a quick review, see the Topic 6.1 study guide (https://library.fiveable.me/ap-biology/unit-6/dna-rna-structure/study-guide/29u5wVp2a9rSDLfLGBlD); explore the whole unit (https://library.fiveable.me/ap-biology/unit-6) and practice questions (https://library.fiveable.me/practice/ap-biology) to reinforce this.