USMLE/COMLEX 1 - DNA Compaction

Primary structure is the sequence of nucleotides. Gives DNA polarity. Nucleotides:

• Pyrimidines are cytosine and thymine
• Purines are guanine and adenine

Secondary structure is the double helix stabilized by H-bonds Double helix details:

• 10 base pairs per full (360 degree turn)
• Adenine and thymine form TWO hydrogen bonds
• Guanine and cytosine form THREE hydrogen bonds
• 10 base pairs per full (360 degree) helical turn

Tertiary structure is "relaxed" or "supercoiled". Nucleosomes & Chromatin Nucleosome: The packaging unit of chromatin. Comprises histone (the histone octamer) and nonhistone protines (the DNA wrapped around it) - think: beads on a string (a 10nm chromatin fiber).

• Note that H1 binds to "linker" DNA and to the nucleosome to stabilize them into a solenoid-like structure (a 30 m fiber, see the corkscrew figure in the drawing)).
• Histone octamer is formed from 2 copies of H2A, H2B, H3, and H4

Chromatin: DNA and associated proteins. DNA fits into the condensed chromatin formation in order to fit into the nucleus. As mentioned above, it wraps around a histone octamer to form a nucleosome.

• Phosphate give DNA a NEGATIVE charge.
• Histones are rich in lysine and arginine, which provide POSITIVE charge on the proteins.
• During mitosis, DNA compacts to form chromosomes. During the S phase, DNA and histone synthesis occurs. Note that mitochondria have their own DNA (it does not use histones and it has a circular shape).

Heterochromatin (Inactive) and Euchromatin (Active) Heterochromatin: DNA is in its heterochromatin state when it is highly condensed in "higher order packaging". In this state DNA is sterically inaccessible, so it is transcriptionally INACTIVE. This is a High Methylation state. Think: Methylation = Mute. Barr body is inactive X chromosome - it is an example of highly condensed, inactive heterochromatin. Euchromatin: DNA exists as euchromatin in numerous states (double helix, nucleosome, solenoid, etc...). During these states it is NOT highly condensed and it is regularly transcribed. Think: "Eu" is "true", so euchromatin is "truly transcribed". This is a High Acetylation state. Think: Acetylation = Active. From most active (most open) to most inactive (most closed): free DNA - 10 nm chromatin (nucleosome) - 30 nm chromatin (nucelofilament (solenoid) - nuclear scaffold - higher order packing of DNA (think: heterochromatin, for example as in a Barr body). The more active, more open form of DNA, will be more sensitive to enzymatic attack. Solenoid: nucleofilament Histones are small basic proteins rich in arginine and lysine

• 5 classes of histones
• Can be acetylated or methylated: regulates local DNA compaction
• H1: binds spacer DNA (20-80 bp) and promotes tight packing of nucleosomes

Chemotherapies exert effects on DNA in many ways, including being intercalating agents and binding agents, inhibiting topoisomerase and causing structural distortion, respectively. As well, they can be cell cycle specific inhibitors (eg methotrexate is an S phase inhibitor).