Chapter 16: DNA on a Molecular Basis

DNA Double Helix Bonds

Hydrogen bonds between pairs of nitrogenous bases hold the two strands together.

Enzyme Effect in Chemical Reactions

An enzyme is unchanged by the reactants or products after participating in a chemical reaction.

Interphase

The part of the cell cycle during which the cell grows and replicates both its organelles and its chromosomes; divided into G1, S (where DNA replication occurs), and G2 phases.

Anaphase

The phase of mitosis during which centromeres separate and sister chromatids become individual chromosomes.

Transformation

A change in genotype and phenotype due to the assimilation of external DNA by a cell (results in horizontal gene transfer if from another species).

Bacteriophages

A virus that infects bacteria; also referred to simply as a phage.

Virus

An infectious particle incapable of replicating outside of a host cell, consisting of a DNA or RNA genome surrounded by a protein coat (capsid) and sometimes a membranous envelope.

Double Helix

The native form of DNA, referring to its two adjacent, antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape.

Antiparallel

Referring to the opposite 5' to 3' directional arrangement of the sugar-phosphate backbones in a DNA double helix.

DNA Replication

The process by which a DNA molecule is copied (also called DNA synthesis).

Semiconservative Model

Type of DNA replication in which each replicated double helix consists of one parental (old) strand and one newly synthesized strand.

Origins of Replication

Specific nucleotide sequences on a DNA molecule where replication begins. Required by both prokaryotes and eukaryotes along with double-stranded DNA, dNTPs, and primers.

Replication Fork

A Y-shaped region on a replicating DNA molecule where parental strands are unwound and new strands are synthesized.

Helicases

Enzymes that untwist the double helix at replication forks (encoded by genes such as dnaB in E. coli; mutation leads to no replication fork forming).

Single-Strand Binding Proteins

Proteins that bind to unpaired DNA strands during replication, stabilizing them and holding them apart.

Topoisomerase

A protein that breaks, swivels, and rejoins DNA strands ahead of the replication fork to relieve strain caused by unwinding.

Primer

A short RNA polynucleotide segment with a free 3′ end, bound to the template strand and elongated by DNA polymerase.

Primase

An enzyme that synthesizes an RNA primer using parental DNA as a template.

DNA Polymerases

Enzymes that synthesize new DNA by adding nucleotides to the free 3' end of an existing chain in the mandatory 5' to 3' direction.

Leading Strand

The new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the 5' to 3' direction.

Lagging Strand

A discontinuously synthesized DNA strand that elongates away from the replication fork in the 5' to 3' direction using Okazaki fragments.

Okazaki Fragments

Short segments of DNA synthesized away from the replication fork, arranged as 5' RNA nucleotides followed by DNA nucleotides extending to 3', later joined by DNA ligase.

Mismatch Repair

The cellular process using specific enzymes to remove and replace incorrectly paired nucleotides that evaded proofreading.

Nuclease

An enzyme that cuts DNA or RNA by hydrolyzing bonds between nucleotides, removing damaged bases or segments.

Nucleotide Excision Repair

A DNA repair system that removes and correctly replaces a damaged segment of DNA using the undamaged strand as a template.

Telomeres

Tandemly repetitive, noncoding DNA sequences at the ends of eukaryotic chromosomes that protect genes from erosion during successive rounds of replication.

Chromatin

The complex of DNA and histone proteins that makes up eukaryotic chromosomes.

Euchromatin

The less condensed form of eukaryotic chromatin that is accessible for transcription.

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

Nucleosomes

The basic bead-like units of chromatin packing, consisting of DNA wound around a protein core of eight histones (two of each of four main types).

Histones

Small, positively charged proteins that bind tightly to negatively charged DNA to play a key role in chromatin structure and organization.

Meselson-Stahl Experiment Round 1 Result

After one round of replication in 14N medium (starting from 15N), a single hybrid (14N-15N) band appears (Tube D), which disproves/rules out the conservative model of replication.

Storage of Genetic Information

The vast amount of hereditary information in DNA is carried within the specific linear sequence of nitrogenous bases (not the sugar-phosphate backbone or base pairing rules).

DNA Ligase Function

An enzyme that joins Okazaki fragments together on the lagging strand by sealing the sugar-phosphate backbone.

Chargaff's Base Ratio Rule

In DNA, total purines equal total pyrimidines (%A = %T and %G = %C), meaning that A + C = G + T.

Hershey-Chase Experiment Basis

Distinguished DNA from protein using radioactive isotopes because DNA contains phosphorus (32P) but no sulfur, while protein contains sulfur (35S) but no phosphorus.

Directional Constraint of DNA Polymerase

DNA polymerase can only add nucleotides to the free 3' end of a growing strand, which is the fundamental reason why the leading and lagging strands are synthesized differently.

Requirements for DNA Replication in All Organisms

Double-stranded template DNA, all four dNTPs (dATP, dTTP, dCTP, dGTP), primers, and origins of replication.