Class 1/2 - The Genetic Code and Replication

Comprehensive vocabulary flashcards covering the history of DNA discovery, key experiments (Griffith, Hershey-Chase, Meselson-Stahl), and the detailed molecular mechanism of DNA replication.

Antony van Leeuwenhoeck

The 18th-century researcher who first described the nucleus when looking at amphibian cells.

What was the first structure discovered in cells?

Nucleus

Robert Brown

The scientist who named the nucleus in the early 19th century. **structure was reported but function mostly unknown at the time

3 Key Observations when nucleus and chromosomes could be stained and visualized

1. Chromosomes migrate to the daughter cell when a new cell is formed

2. Nuclei fuse during fertilization

3. some information within the nucleus is extremely important

Nucleus Composition

The structure is composed of DNA ($15\%-20\%$), RNA ($5\%-10\%$), proteins ($15\%-30\%$), and water and salts ($40\%-60\%$).

Virulence

The ability of a virus or a bacterium to cause damage to its host.

Staphylococcus pneumoniae

The bacterium used in Griffith’s experiment to determine the information-carrying molecule; includes a virulent S-strain and a nonvirulent R-strain.

Symptoms of s. pneumoniae

fever, chills, shortness of breath

Griffith’s Experiment Conclusion

Information-carrying material can be transferred from the virulent S cells to the nonvirulent R cells, making them virulent.

Avery, McLeod, McCarthy Experiment

An experiment that used RNase, Protease, and DNase to identify DNA as the molecule that carries the information making bacteria virulent. RNase + Protease had no effect on outcome, DNase stopped transformation of R cells.

Conclusions so far from Griffith + Avery

genetic material can be transferred between bacterial cells, the genetic material of s.pneumoniae is DNA

Bacteriophages

Viruses that specifically infect bacteria, consisting mostly of proteins (labeled with radioactive sulfur) and DNA (labeled with radioactive phosphorus).

Setup of the Hershey-Chase experiment

Blender is key - “ghosts: stay attached to bacterium, to determine which substance has been injected ghosts have to be removed by blender. Because ghosts are lighter, they can be separated from the rest of the bacteria using centrifugation.

Hershey-Chase Experiment Conclusion + Result

DNA is the molecule that carries information. Determined that DNA, not protein, is injected into host cells and passed on to progeny phages.

Nucleotide

A single subunit of DNA comprised of a deoxyribose sugar, a phosphate group, and a nitrogenous base.

Nitrogenous Bases

Subunits of nucleotides including double-ring purines [adenine (A) or guanine (G)] and single-ring pyrimidines [cytosine (C) or thymine (T)].

Phosphodiester bonds

Covalent linkages where the phosphate on the $5'$ carbon of an incoming nucleotide is linked to the hydroxyl group on the $3'$ carbon of the last nucleotide.

Antiparallel

The opposing orientation of the two strands in double-stranded DNA, where one strand runs $5'$ to $3'$ and the other runs $3'$ to $5'$.

Complementary base pairing

The formation of hydrogen bonds between specific bases (A:T and G:C) on opposite DNA strands.

B-form DNA

The most common DNA shape, forming a right-handed helix with a smooth backbone.

Z-form DNA

A DNA shape that forms a left-handed helix and has an irregular backbone.

Hydrogen bonds between the bases

Stabilize the DNA helix, 3 H-bonds between C and G, 2 H-bonds between A and T

Semiconservative replication

The Watson-Crick model where each old DNA strand serves as a template, resulting in new DNA molecules with one old and one new strand.

Conservative replication

Parental double helix remains intact, both strands of daughter helices are newly synthesized

Dispersive replication

both strands of both daughter helices contain original and newly synthesized DNA

Meselson-Stahl Experiment

An experiment using ${}^{15}N$ (heavy) and ${}^{14}N$ (light) isotopes and density gradients to prove that DNA replication is semiconservative.

Replication Fork

A Y-shaped area where two unwound DNA strands are used as templates for replication. Origins of replication are 40,000bp apart, complete replication of the entire nuclear genome in eukaryotes usually takes from 5-10 hours.

Helicase

The enzyme that unwinds DNA at the replication fork to separate parental strands.

Single-strand binding protein (SSB)

stabilizes single strands of DNA at replication fork

Gyrase (topoisomerase II)

The enzyme that introduces a double-stranded break ahead of the replication fork to relieve the stress of helix unwinding.

DNA Polymerase III

The enzyme that synthesizes new DNA by adding nucleotides to the $3'-OH$ group of a growing strand in the $5'$ to $3'$ direction. forms the phosphodiester bond between adjacent nucleotides.

Problem of DNA Polymerase

Needs a free 3’OH group

RNA primer (Primosome)

A short stretch of RNA synthesized by primase that provides the free $3'-OH$ group needed for DNA polymerase to start synthesis.

Leading strand

The DNA strand synthesized continuously in the $5'$-to-$3'$ direction toward the replication fork.

Lagging strand

The DNA strand synthesized discontinuously in small precursor fragments called Okazaki fragments.

Okazaki fragments

Small DNA fragments ($1000$-$2000$ bp in prokaryotes, $100$-$200$ bp in eukaryotes) that make up the lagging strand.

DNA ligase

The enzyme that stitches Okazaki fragments together by forming phosphodiester bonds.