1.6 Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotide monomers—each nucleotide has a 5-carbon sugar (deoxyribose in DNA, ribose in RNA), a phosphate, and a nitrogenous base (A, T, C, G in DNA; U replaces T in RNA). Biological information is encoded in the linear sequence of those nucleotides; strands have distinct 5' phosphate and 3' hydroxyl ends and grow by adding nucleotides to the 3' end (phosphodiester bonds). DNA is an antiparallel double helix (A pairs with T, C with G via hydrogen bonds); RNA is usually single-stranded and pairs A–U. Nucleic acids are essential because they store and transmit genetic information (replication, heredity) and guide protein synthesis (gene expression), which underlies all cell structure and function—a core AP Bio concept tied to information storage and transmission. For a focused Topic 1.6 review, check the Fiveable study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and more unit practice at (https://library.fiveable.me/practice/ap-biology).

Short answer: DNA and RNA are both polymers of nucleotides (sugar + phosphate + base), but they differ in sugar, bases, strand number, and overall shape. DNA uses deoxyribose (no 2' OH) and the base thymine; it’s usually an antiparallel double helix with two strands running opposite 5' → 3' directions and A–T and C–G hydrogen bonding. RNA uses ribose (has a 2' OH) and uracil instead of thymine; it’s usually single-stranded and can fold into complex 3D shapes where A pairs with U. Both have linear 3' and 5' ends and grow by adding nucleotides to the 3' end (phosphodiester bonds). These differences matter on the AP exam for LO 1.6.A (recognize deoxyribose vs ribose, thymine vs uracil, double vs single strand, antiparallel orientation, base pairing and 3'/5' ends). For a quick topic review, see the Fiveable study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU). For more practice, try the unit practice set (https://library.fiveable.me/practice/ap-biology).

Think of each nucleotide like a Lego with two special connectors on the sugar: a 5' end (the carbon #5 attached to a phosphate) and a 3' end (the carbon #3 with an -OH). The strand has direction because those sugar carbons are numbered—so one end is called 5' and the other 3'. During synthesis, new nucleotides are joined by a phosphodiester bond between the 5' phosphate of the incoming nucleotide and the 3' hydroxyl of the growing strand—so nucleic acids grow 5' → 3' (nucleotides are added to the 3' end) (CED 1.6.A.2). In double-stranded DNA the two strands run antiparallel: one runs 5'→3' and the other 3'→5' (CED 1.6.A.3). Practically, when you read or draw sequences, always note the orientation (e.g., 5'-ATG-3'). Want a quick review and practice problems on nucleic acids? Check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU), the unit overview (https://library.fiveable.me/ap-biology/unit-1), or practice questions (https://library.fiveable.me/practice/ap-biology).

Nucleotides connect by forming a sugar–phosphate backbone through covalent phosphodiester bonds: the phosphate on the 5′ carbon of one nucleotide links to the 3′ hydroxyl (3′ OH) of the next nucleotide. During synthesis, DNA polymerase adds new deoxyribonucleotide triphosphates (dNTPs) to the free 3′ end of the growing strand (so growth is 5′ → 3′), releasing pyrophosphate and making that phosphodiester bond (CED 1.6.A.2). Two strands run antiparallel (one 5′→3′, the other 3′→5′) and are held together by hydrogen bonds between bases (A–T, C–G) to form the double helix (CED 1.6.A.3). If you want a short AP-aligned review of these ideas, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU). For extra practice, try problems at (https://library.fiveable.me/practice/ap-biology).

Short answer: DNA uses thymine (5-methyluracil) while RNA uses uracil because of stability and repair needs tied to DNA’s role as long-term information storage. Both are nucleotide bases that pair via hydrogen bonds (A–T in DNA, A–U in RNA). The methyl group on thymine makes DNA chemically more stable and helps cells detect and repair spontaneous deamination of cytosine (which creates uracil). If DNA normally had uracil, repair systems couldn't easily tell whether a U came from a real base or from a damaged C → U change, so mutations would persist. RNA is short-lived and made from ribose (not deoxyribose), so using uracil is “cheaper” and fine for transient messages (mRNA, tRNA). These points map to CED essentials: nucleotide structure, sugar difference (deoxyribose vs ribose), and base pairing (A–T vs A–U). For a quick review, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and Unit 1 overview (https://library.fiveable.me/ap-biology/unit-1). Practice more with questions at (https://library.fiveable.me/practice/ap-biology).

Antiparallel means the two DNA strands run in opposite directions: one strand has a free 5′ (five-prime) phosphate at its end and the other has a free 3′ (three-prime) hydroxyl at that same end. In the double helix the strands are oriented 5′→3′ and 3′→5′ relative to each other. That orientation is important because nucleotides are added only to the 3′ end during synthesis, and complementary bases (A-T, C-G) form hydrogen bonds between strands. So antiparallel arrangement lets each base pair line up correctly and allows replication enzymes (which work 5′→3′ on a template) to copy DNA. This is exactly what the CED expects you to know for 1.6.A (3′/5′ ends, antiparallel double helix, base pairing). For a quick review, see the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU); for broader Unit 1 review use (https://library.fiveable.me/ap-biology/unit-1) and practice problems (https://library.fiveable.me/practice/ap-biology).

Step-by-step: 1) Know the building blocks—each nucleotide has a sugar (deoxyribose in DNA, ribose in RNA), a phosphate, and a nitrogenous base (A, T, G, C in DNA; U replaces T in RNA) (CED 1.6.A.1). 2) Read one strand 5' → 3' and remember strands are antiparallel (the other runs 3' → 5') (CED 1.6.A.2–3). 3) For each base on the template, pick the complementary base: A pairs with T (or U in RNA) by two hydrogen bonds; C pairs with G by three hydrogen bonds (CED 1.6.A.3). 4) Hydrogen bonds form between the bases—this is noncovalent and stabilizes the double helix but still allows strand separation for replication/transcription. 5) During DNA/RNA synthesis, polymerases add nucleotides to the 3' hydroxyl of the growing strand, so incoming nucleotides pair to the template before a phosphodiester bond links them (CED 1.6.A.2). For a quick review, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice problems (https://library.fiveable.me/practice/ap-biology).

A pairs with T via two hydrogen bonds; C pairs with G via three hydrogen bonds. In RNA, A pairs with U (also two H-bonds). Those bond counts come from base-pairing rules in the CED (1.6.A.3) and are why DNA regions richer in C–G are more thermally stable (higher melting/denaturation temperature) than A–T rich regions. For AP exam prep, just remember “A–T (or A–U) = 2 H-bonds, C–G = 3 H-bonds” and be able to connect C-G content to double-helix stability or melting behavior. For a quick topic review, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice related questions at (https://library.fiveable.me/practice/ap-biology).

They’re always added to the 3′ end of the growing strand. Each incoming nucleotide brings a 5′ phosphate; the free 3′ hydroxyl (3′-OH) on the last sugar of the chain attacks that phosphate to form a phosphodiester bond, so synthesis proceeds in a 5′ → 3′ direction. That’s why DNA strands are described with 5′ and 3′ ends, why polymerases work only in the 5′→3′ direction, and why the two DNA strands in the double helix are antiparallel (one runs 5′→3′, the other 3′→5′). This is exactly what the CED expects you to know for Topic 1.6 (see 1.6.A.2). For a quick review, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and try practice questions (https://library.fiveable.me/practice/ap-biology).

A nucleotide has three parts: (1) a five-carbon sugar—ribose in RNA or deoxyribose in DNA, (2) a phosphate group attached to the 5′ carbon, and (3) a nitrogenous base (A, T, C, G in DNA; U replaces T in RNA). These components form the sugar-phosphate backbone (phosphates link 5′ to 3′ via phosphodiester bonds) and the bases encode sequence information (CED 1.6.A.1–A.3 keywords: deoxyribose, ribose, phosphate backbone, A/T/U, G/C). Memory trick: picture a “SPB” sandwich—Sugar (bottom), Phosphate (top), Base (filling)—or use the phrase “Sugar-Phosphate, Base Inside.” Another: remember the 5′ phosphate and 3′ OH ends (nucleotides are added at the 3′ end)—useful for AP exam questions on strand orientation (CED 1.6.A.2–A.3). For quick review, check the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice problems (https://library.fiveable.me/practice/ap-biology).

DNA is double stranded mainly because its sugar (deoxyribose) and bases (A, T, G, C) favor stable, long-term complementary base pairing and an antiparallel double-helix—A pairs with T and C with G through hydrogen bonds, which stabilizes two strands running 5'→3' opposite each other. RNA has ribose (with a 2'-OH) and uracil instead of thymine; the 2'-OH makes the backbone more reactive and sterically less favorable for a long, stable helix. RNA’s roles (messenger, catalytic, structural) require shorter-lived molecules that can fold into complex single-strand secondary structures (hairpins, stems, loops) by internal base pairing rather than forming a permanent duplex. So RNA is “typically single stranded” but can form double-stranded regions locally. This distinction matches AP CED Essential Knowledge 1.6.A.3–1.6.A.4. For a concise topic review, see the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU). For extra practice, try problems at (https://library.fiveable.me/practice/ap-biology).

In real labs, scientists read DNA by first isolating DNA, then making many copies (PCR) and preparing it for a sequencer. Two common approaches: Sanger sequencing (reads single DNA fragments ~700 bp using chain-terminating nucleotides) and next-generation sequencing (NGS, like Illumina) that fragments DNA, attaches adapters, and uses “sequencing-by-synthesis” to read millions of short bases in parallel. Machines do base-calling (translate signal to A/T/C/G), then software aligns short reads to a reference or assembles them into longer sequences. All this depends on the nucleotide code (A, T, C, G), antiparallel strands, and knowing 3' vs 5' ends when building libraries—concepts in Topic 1.6. Outputs let researchers identify mutations, compare genomes, or measure gene expression. If you want a quick Topic 1.6 review, check the study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice problems (https://library.fiveable.me/practice/ap-biology) to prep for AP-style questions.

Ribose and deoxyribose are both five-carbon (pentose) sugars in nucleotides, but they differ at the 2' carbon: ribose (in RNA) has a hydroxyl group (–OH) at the 2' position, while deoxyribose (in DNA) has just a hydrogen (–H) there—i.e., “deoxy” means missing an oxygen. That small change matters: the 2' OH in RNA makes the backbone more chemically reactive and less stable (so RNA is usually single-stranded and short-lived), whereas DNA’s lack of the 2' OH makes its backbone more stable for long-term information storage and the double helix. Both sugars still provide the 3' hydroxyl and 5' phosphate used to form phosphodiester bonds (nucleic acid directionality, 3' and 5' ends), which the AP CED requires you to know (see 1.6.A.1–1.6.A.3). For a quick Topic 1.6 review, check the AP Bio nucleic acids study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU).

You were supposed to learn the basic rules and why they matter for DNA/RNA. Key points from the CED: nucleotides = sugar (deoxyribose in DNA, ribose in RNA) + phosphate + base. Base-pairing rules: in DNA A pairs with T and C pairs with G via hydrogen bonds (A–T = 2 H-bonds; C–G = 3 H-bonds); in RNA A pairs with U. DNA forms an antiparallel double helix (strands run opposite 5′ → 3′ directions) and bases pair complementary to encode information (so one strand determines the other). In the lab you’d usually observe extraction or model work that reinforces complementary base pairing, H-bonding, and the idea that nucleotides are added to the 3′ end during synthesis. These concepts are explicitly tested by LO 1.6.A (structure/function, base pairing) on the AP exam. Review the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice questions (https://library.fiveable.me/practice/ap-biology) if you want to catch up.

You need to know 5′→3′ because that direction is how nucleic acids are built, read, and paired on the exam. AP CED Essential Knowledge 1.6.A.2 says nucleotides are added to the 3′ end (phosphodiester bond forms between 3′ OH and 5′ phosphate), and 1.6.A.3 stresses DNA’s antiparallel strands (one runs 5′→3′, the other 3′→5′). Practically, this matters for understanding replication (leading vs. lagging strands), transcription, base pairing (A–T, C–G; A–U in RNA), and enzyme directionality—types of questions the exam tests in both multiple choice and free response. If you can quickly label strand orientation and predict where synthesis or primers are needed, you’ll save time and points. Review the Topic 1.6 study guide (https://library.fiveable.me/ap-biology/unit-1/nucleic-acids/study-guide/RKOM4rhL6iJsAMdbDOWU) and practice questions (https://library.fiveable.me/practice/ap-biology) to drill examples.