DNA and the Cell Cycle › DNA Structure

DNA Compaction

Notes

DNA Compaction

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Summary & USMLE Board Highlights

DNA STRUCTURE

Primary Structure

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

Secondary Structure

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

Tertiary structure is "relaxed" or "supercoiled".

LEVELS OF COMPACTION

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

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

CLINICAL CORRELATION (CHEMOTHERAPIES)

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).

Full-Length Text

DNA Structure and Compaction

Here we will learn about DNA structure and compaction. We will learn the levels of DNA structure, and how DNA is compacted within the nucleus of a eukaryotic cell.

To begin, start a table to let's learn the key components of DNA structure.

Denote that like proteins, DNA maintains the following levels of structure:

  • Primary structure, which is the sequence of nucleotides.
  • Secondary structure, which is a double helix stabilized by hydrogen bonds.
  • Tertiary structure, which can be one of two possible states: relaxed or supercoiled.

We will illustrate secondary and tertiary structure. We learn primary structure elsewhere, but we will summarize some key points about it here.

  • Draw a series of nucleotides as follows:
  • Draw a sugar phosphate backbone as a series of pentagons bound to phosphate groups.

Now, add the nitrogenous bases as follows:

  • Draw the pyrimidines, cytosine and thymine, each as a hexagon.
  • Represent the purines, guanine and adenine, each as a hexagon connected to a pentagon.
  • Now, label 5-prime for the nucleotide with a free phosphate group.
  • And add a hydroxyl group to the nucleotide at the opposite end.
    • Label it 3-prime.
  • Finally, indicate that the 5-prime to 3-prime structure gives DNA polarity.

Next, let's illustrate secondary structure.

  • Draw two simplified strands of DNA in a double-helix structure.
  • Label the 5-prime and 3-prime ends of one strand.
  • Then, indicate that the second strand is antiparallel to the first.
  • Demarcate the following bases on the 5-prime to 3-prime strand: thymine, guanine, guanine, thymine.
  • Indicate that there are actually ten base pairs per helical turn; we draw two four per turn for simplicity.
  • Now, fill in the complementary purine or pyrimidine base on the opposite strand: adenine, cytosine, cytosine, and adenine.
    • Write that because of purine-pyrimidine base pairing, DNA contains an equal amount of purines and pyrimidines.
  • Finally, let's draw a single line for each hydrogen bond that forms between each purine-pyrimidine pair.
    • Show that thymine and adenine form two hydrogen bonds.
    • Show that guanine and cytosine form three hydrogen bonds. These hydrogen bonds maintain DNA's secondary structure.
  • As a clinical correlation, denote that many anti-cancer drugs bind to a groove in the DNA double-helix to prevent DNA replication and transcription in cancerous cells.

Finally, let's illustrate tertiary structure.

  • Indicate that eukaryotic DNA can either be relaxed or supercoiled.
  • Continue our linear DNA helix structure and indicate that it is relaxed.

To illustrate super-coiled DNA, let's use the analogy of a telephone cord.

  • Draw a telephone cord and show that its structure resembles a double helix.
  • Now, extend it to illustrate that the helical cord can coil on itself to form a "supercoil."
  • Note that many viruses and prokaryotes have circular DNA that can also be relaxed or supercoiled. We discuss them elsewhere.
  • In eukaryotes, tertiary structure is integral to DNA compaction in the nucleus.
  • Return to our table to learn the key levels of DNA compaction.
  • Denote that they are:
    • Nucleosome
    • Chromatin
    • Solenoid (nucleofilament)

Let's illustrate them, now.

  • To begin, draw a cluster of eight histone proteins.
  • Write that histone proteins are small basic proteins that are rich in arginine and lysine.
    • And that there are five classes of histone proteins.
  • This octamer contains two copies of four different histones.
  • Show that our double helix wraps around the histone proteins in what is equivalent to approximately one and three quarters of a supercoil in length.
  • Now indicate that a nucleosome comprises a histone octamer and the DNA that supercoils around it.
  • Write that histones can be acetylated or methylated, which regulates the local compaction of DNA.
  • Now, draw another histone octamer.
  • Extend our DNA to wrap around it.
  • Next, label the DNA between the nucleosomes as a DNA spacer.
  • Indicate that it's about 20-80 base pairs in length.
  • All nucleosomes are separated by DNA spacers and resemble beads on a string.
  • Show that H1 (a histone protein) binds the DNA spacer.
  • Write that it facilitates the tight packing of nucleosomes.
  • Now, represent our nucleosome as a square with DNA wound around it.
  • Next, draw a series of vertical stacks of four nucleosomes each.
  • Label this entire structure chromatin, a term for DNA and its associated proteins.
    • Chromatin also includes non-histone proteins, but we will not draw them here.
  • Write that chromatin can further divide into:
    • Heterochromatin, which is DNA that is highly condensed and not transcribed.
    • Euchromatin, DNA that is not highly condensed and regularly transcribed.
  • Finally, draw a thick, helical tube and label it solenoid (aka nucleofilament).
  • Illustrate that the close packing of nucleosomes allows chromatin to wind into a solenoid.

Finally, let's illustrate how DNA is compacted in preparation for cell division.

  • Draw a circular nuclear scaffold protein, which is found in the nucleus as its name suggests.
  • Show that nucleofilaments coil and form loops that anchor at the scaffold protein and radiate from its center.
  • Illustrate that the resulting structure is a condensed chromosome, which comprises two sister chromatids that join at a centromere.
    • This structure is visible under a microscope and is indicative of a dividing cell.