(no subject)

Nucleoside: pentose (5-carbon sugar) attached to purine or pyrimidine.
Nucleotide: nucleoside attached to a phosphate group.

ATP and ADP are also nucleotides.

The double helix of DNA runs in two anti-parallel strands. One terminates in a phosphate group attached to a carbon 5'. The other terminates in a carbon 3' with a hydroxyl group attached to it.

The base pairs are connected through hydrogen bonds. A:T has 2 bonds, and G:C has 3.

The base pairs are stacked, so that the middle of the double helix is solid.

These stacking interactions are a form of van der Waals interaction.

The stacking interactions between G:C are stronger than the stacking interactions between A:T.

You can denature DNA by heating it gently so the bonds break.

If you don't cool it too quickly, it will renature as the complementary strands find each other. The double helix will therefore reform.

Short strands anneal faster than long strands.

Chromosomes are super long. They have to be condensed into very compact structures for metaphase.

Chromatin normally consists of beads joined together on a string.

In the middle of the beads are 8 histone proteins. The DNA wraps around it. Holding the bead together on the outside is a histone protein. Joining the beads is a string of linker DNA.

We don't know how the DNA gets joined into the familiar metaphase chromosome shape. If you remove all the histone proteins, the DNA gets spread out like a cloud, but at the center is a scaffold of non-histone proteins in the metaphase chromosome shape.

(no subject)

DNA replicates semiconservatively. This means the parent double helix splits into two strands, and each strand has a new strand joined to it. Therefore the two daughter double helixes contain one parental strand and one new strand.

We know more about smaller chromosomes, like bacterial ones that have the shape of a circle.

We know that unwinding begins at a single point of origin and proceeds bidirectionally around the circle. Eventually, two circles are formed.

We know that the much longer chromosomes of eukaryotes have many points of origin.

Supercoiling of chromosomes helps them take up much less space.

In order to separate the strands, a topoisomerase comes along, nicks the strand, winds it around, and rejoins it. This decreases the supercoiling and helps ease the separation process (through some topological voodoo I can't quite visualize). At any rate, I agree that it would be easier than pulling the whole chromosome taut and then manipulating the whole thing.

Some topoisomerases can increase supercoiling.

Some topoisomerases nick one strand and rejoin it. Others nick two strands and twist the whole helix around. Two-strand nicking requires outside energy in the form of ATP.

At the origin, proteins bind to the DNA and melt it open in an ATP-dependent manner. Then new strands are synthesized.

Helicases, dependent on ATP, separate the DNA into two separate strands.

Then DNA polymerase synthesizes a new strand.

DNA polymerase can only extend a new strand, it can't get started. So RNA polymerase comes along and starts up a primer, which DNA polymerase then extends. The enzyme that produces the primer is known as primase.

DNA polymerase can only go in one direction. The polymerase makes the C3' OH group attach to the phosphate group of a free nucleotide that can then base pair with the parental strand.

So it can only go in the 5' -> 3' direction.