AP Biology 6.1-6.2: DNA and RNA Structure

DNA replication

The process by which a cell produces an accurate copy of its DNA before cell division. It is essential for inheritance, cell division, and tissue repair.

DNA nucleotide

A DNA nucleotide contains a deoxyribose sugar, a phosphate group, and one nitrogenous base: adenine, cytosine, guanine, or thymine.

Distinguish a nucleoside from a nucleotide.

A nucleoside consists of a sugar and nitrogenous base. A nucleotide is a nucleoside with one or more phosphate groups attached.

Which nitrogenous bases are purines and which are pyrimidines in DNA?

Adenine and guanine are purines, while cytosine and thymine are pyrimidines.

What bonds connect nucleotides within a DNA strand, and what bonds connect complementary bases between strands?

Phosphodiester bonds connect adjacent nucleotides within each strand. Hydrogen bonds connect complementary bases between strands; A–T pairs have two, whereas G–C pairs have three.

Antiparallel DNA strands

The two DNA strands run in opposite directions: one is oriented $5' \to 3'$ and the other $3' \to 5'$.

What structural feature allows each DNA strand to serve as a replication template?

Complementary base pairing makes the sequence of one strand determine the sequence of the other: adenine pairs with thymine, and guanine pairs with cytosine.

Why can DNA strands be separated even though the DNA backbone is covalently bonded?

The phosphodiester bonds within each strand are stronger than the hydrogen bonds between complementary strands. Breaking the interstrand hydrogen bonds therefore separates the templates without breaking the backbones.

What does semiconservative replication mean?

Each daughter DNA double helix contains one strand from the original molecule and one newly synthesized complementary strand.

DNA polymerase

An enzyme that extends a DNA strand by adding complementary nucleotides to its $3'$ end, forming phosphodiester bonds. Many DNA polymerases also participate in proofreading or primer replacement.

What is the role of DNA polymerase proofreading?

If an incorrect nucleotide is incorporated, the polymerase can remove the mismatch from the growing strand and then resume extension with the correct nucleotide.

How do proofreading and mismatch repair together improve replication fidelity?

Polymerase selectivity and proofreading remove many errors during synthesis, while post-replication mismatch repair detects and corrects remaining mismatches. Together, these mechanisms reduce the final error frequency to roughly fewer than one error per $10^9$ nucleotides added.

What are the three broad stages of DNA replication?

Initiation begins synthesis at replication origins, elongation extends the new strands, and termination completes replication and resolves the resulting DNA molecules.

Replication origin

A specific DNA sequence where replication begins. Initiation at an origin produces replication forks that generally move bidirectionally.

Why are many replication origins relatively rich in adenine and thymine?

A–T base pairs contain two hydrogen bonds, compared with three in G–C pairs, so AT-rich regions are easier to separate during initiation.

During which part of the eukaryotic cell cycle does DNA replication occur?

DNA replication occurs during the S, or synthesis, phase of interphase.

What is the function of the eukaryotic origin recognition complex?

The origin recognition complex binds replication origins and recruits additional initiation proteins, including proteins that load the MCM helicase.

Pre-replication complex

A protein assembly formed at replication origins before S phase. It licenses an origin by loading the replicative helicase, helping ensure that each region of DNA initiates replication only once per cell cycle.

Why must DNA replication be tightly regulated so that each origin fires only once per cell cycle?

Repeated initiation could cause some DNA regions to be copied multiple times while others are copied once, producing abnormal DNA content and genomic instability.

Preinitiation complex

A protein complex assembled at an activated replication origin during early S phase. It activates the MCM helicase and recruits primase and other DNA polymerases to begin DNA synthesis.

DNA helicase

An enzyme that separates the two DNA strands at a replication fork by disrupting the hydrogen bonds between complementary bases.

Replication fork

The Y-shaped region where parental DNA is unwound and new DNA strands are synthesized. Each exposed parental strand serves as a template.

Why does helicase activity create a need for topoisomerase?

Unwinding the helix causes the DNA ahead of the replication fork to become increasingly twisted. Topoisomerase relieves this torsional strain so the fork can continue moving.

Topoisomerase

An enzyme that temporarily breaks and rejoins DNA strands to relieve torsional stress caused by DNA unwinding. DNA gyrase is a specialized type of topoisomerase.

Single-strand DNA-binding protein

A protein that binds exposed single-stranded DNA after helicase unwinds it. It prevents the strands from reannealing and limits formation of interfering secondary structures.

In what direction is a new DNA strand synthesized?

DNA polymerase adds nucleotides to the free $3'$ hydroxyl group, so the new strand is always synthesized $5' \to 3'$ while its template is read $3' \to 5'$.

Why is an RNA primer required for cellular DNA replication?

DNA polymerases generally cannot begin a new strand from unpaired nucleotides. A primase creates a short RNA primer that provides the free $3'$-OH needed for DNA polymerase to extend the strand.

What provides the energy for adding a nucleotide to a growing DNA strand?

The incoming nucleotide is a deoxyribonucleoside triphosphate. Formation of a phosphodiester bond is driven by release of pyrophosphate, followed by pyrophosphate hydrolysis, making the overall reaction effectively irreversible.

Sliding DNA clamp

A ring-shaped protein that holds DNA polymerase on the template, increasing its processivity and reducing dissociation during strand synthesis.

What is the role of a clamp loader?

A clamp loader places the sliding clamp onto DNA at the junction between a template and a primed region, allowing DNA polymerase to begin highly processive synthesis.

Leading strand

The new strand synthesized continuously in the same general direction that the replication fork moves. It usually requires one RNA primer.

Lagging strand

The new strand synthesized discontinuously because its template orientation is opposite the direction of fork movement. It is produced as a series of Okazaki fragments.

Why is lagging-strand synthesis discontinuous even though DNA polymerase performs the same chemical reaction on both strands?

DNA polymerase can extend DNA only $5' \to 3'$, but the two templates are antiparallel. The lagging strand must therefore be built in short $5' \to 3'$ segments as more template DNA becomes available.

Okazaki fragment

A short DNA segment synthesized on the lagging strand from an RNA primer. The fragments are later joined to form a continuous strand.

How is the lagging strand converted into a continuous DNA strand?

RNA primers are removed and the resulting gaps are filled with DNA. DNA ligase then seals the remaining nicks by forming phosphodiester bonds.

DNA ligase

An enzyme that seals breaks, or nicks, in the sugar-phosphate backbone, including the gaps between adjacent Okazaki fragments.

What is the replisome?

The coordinated molecular machine at a replication fork. It includes helicase, DNA polymerases, sliding clamps, primase, single-strand DNA-binding proteins, topoisomerases, and other replication factors.

Trombone model of DNA replication

A model explaining how one replisome coordinates continuous leading-strand synthesis with discontinuous lagging-strand synthesis. The lagging-strand template forms loops so both polymerases can operate within the same replication complex.

How does eukaryotic DNA replication differ from replication of a typical bacterial chromosome in its initiation pattern?

Eukaryotes use multiple replication origins along their long linear chromosomes, whereas a typical bacterial circular chromosome is described as having a single principal origin. Replication forks proceed bidirectionally from each active origin.

Why do linear eukaryotic chromosomes face an end-replication problem?

After the final RNA primer at a chromosome end is removed, conventional DNA polymerase cannot fill the resulting gap because there is no upstream $3'$-OH group. Consequently, chromosome ends would shorten with successive rounds of replication.

Telomere

A repetitive DNA region at the end of a eukaryotic chromosome that helps protect gene-containing DNA from loss during replication and chromosome shortening.

Telomerase

An enzyme that extends telomeres by adding repetitive DNA sequences to chromosome ends. It is active in germline and some stem cells, but inappropriate activation in somatic cells can contribute to cancer.

Hayflick limit

The finite number of times many somatic cells can divide before telomere shortening and associated DNA damage prevent further division.

Why can inappropriate telomerase activity promote cancer?

By maintaining telomeres, telomerase can allow cells that would normally stop dividing to continue proliferating, supporting the extended or nearly unlimited division characteristic of many cancer cells.

How does chromatin structure complicate DNA replication in eukaryotes?

DNA is wrapped around histone proteins, so replication machinery must temporarily reorganize chromatin and then redistribute or replace histones so the daughter DNA molecules can regain appropriate chromatin structure.

What is PCR in relation to DNA replication?

Polymerase chain reaction is an in vitro method that repeatedly copies a selected DNA sequence using a DNA template, primers, and DNA polymerase. It demonstrates that DNA synthesis can be performed outside cells under controlled conditions.