DNA Structure and Packaging Flashcards
What are the 4 bases in DNA? Which ones are purines and which ones are pyrimidines?
Adenine and guanine - purines
Cytosine and thymine - pyrimidines
What type of bond links nucleotides together?
Phosphodiester bonds
What creates the 5’ to 3’ polarity of nucleic acid strands?
The position of the phosphodiester bonds. One end has a free 5’ phosphate and the other has a free 3’ OH
What is a genome?
The complete set of genetic information in a single cell in an organism
What is a chromosome?
A molecule made of nucleic acids that contains the genetic information of an organism
What is a gene?
A segment on a chromosome that encodes a functional product
What two methods do prokaryotes use to package DNA?
Looping and supercoiling
How do DNA binding proteins help with looping DNA in prokaryotes?
They bend the DNA and make it form a floret structure that has stable loops
What is supercoiling?
When the DNA double helix is coiled up and twisted onto itself
How is supercoiling induced in prokaryotic cells?
The linear DNA is unwound by one turn then sealed into circular DNA. This creates a strained circle at 11.67 base pairs per turn, and the DNA undergoes supercoiling to revert back to the stable 10.5 base pairs
What is the general mechanism of how topoisomerases work?
They make a nick in the strand, untwist the DNA by one turn, then seal the strands back together
What types 1 and 2 topoisomerases do?
Type 1 makes a temporary single strand nick, type 2 makes a temporary double strand break
What kinds of topoisomerases do prokaryotes have? Eukaryotes?
Prokaryotes have topoisomerases that induce supercoiling and others that remove it. Eukaryotes only have topoisomerases to remove supercoiling
How is supercoiling maintained?
DNA binding proteins
What is the smallest level of DNA packaging in eukaryotes?
The nucleosomes
What is chromatin?
A complex of DNA and all packaging proteins
What was the experiment that determined how much DNA was bound to proteins vs not bound to proteins in a nucleosome?
They added micrococcal nuclease that cleaves any unbound DNA, and saw only one band on the gel for 147 bp. That indicated how much DNA was bound to a protein. They then added less micrococcal nuclease to get incomplete cleavage, and the nuclease on average cut at the halfway point between proteins to determine that there are 50 base pairs in between each nucleosome
How much DNA is wrapped around the protein in a nucleosome and how much DNA is in between nucleosomes?
147 base pairs are wrapped around the protein, 50 base pairs in between as linker DNA
What is the structure of the histone in a nucleosome?
An octamer, made of 8 subunits of 4 types with 2 of each
What are the 4 types of subunits in the histone octamer?
H3, H4, H2A and H2B
What is the charge on the histone proteins?
Positive, it binds to the negatively charged DNA
What is the purpose of the histone protein tails?
They are flexible and about 19-39 amino acids long. They are believed to interact with neighbours and help form the 30 nm fibre and higher levels of packaging
What are the two types of linker histones? What do they do?
H1 and H5. They stabilize DNA entering and leaving the nucleosome
What is the next level of packaging after the nucleosome?
The 30 nm fibre. The beads on a string structure of the nucleosomes get condensed into a fibre that is 30 nm wide
What is the next level of packaging after the 30nm fibre?
30nm fibre is packaged into loops with scaffold proteins
What is the highest level of packaging in eukaryotes?
Chromosomes
What is euchromatin?
Packaged DNA that is relatively loose, which makes it easier for transcription to occur
What is heterochromatin?
Packaged DNA that is much tighter. It squishes the nucleosomes together and stops transcription from occurring
What is constitutive heterochromatin? Where is this seen?
DNA that is always in the tightly packed state. Found in structural components of the chromosome that don’t contain genes, so they don’t need to be unwound anyways, aka telomeres and centromeres
What is facultative heterochromatin?
DNA that is sometimes euchromatin and sometimes heterochromatin, this only happens in a few situations
What are protamines?
An alternative method of DNA packaging. They are positively charged proteins that bind to the major groove of DNA
How do protamines allow DNA to be packaged more tightly than in nucleosomes?
They neutralize the negative charge on DNA, so it stops repelling itself
What structure does DNA packaged with protamines form?
Toroid structures. They are planar and donut shaped so they can be stacked very closely together
What type of cell is DNA packaged with protamines found in?
Mammalian sperm
If protamines can pack DNA tighter than nucleosomes, why isn’t it used everywhere?
It ends up packed up even tighter than heterochromatin, so it is impossible for transcription to occur. This is not a problem for sperm, but will be for anything else
