1. Differences in DNA Heterochromatin vs. Euchromatin
Heterochromatin is DNA which tends to be highly compacted and dark staining.
Euchromatin is not so compacted or dark.
The number of genes in heterochromatin is generally small relative to euchromatin.
Heterochromatin lacks genes or they are inactive
Much heterochromatin is found in certain structural parts of the chromosomes: centromeres and telomeres. Also, much of Y chromosome.
Move euchromatin to an area next to heterochromatin and it becomes heterochromatin: position effect.

2. Chromosome structure Arm
medic.med.uth.tmc.edu/.../ cellbio/hist-01.htm

3. More on Differences in DNA
Base sequences are obviously different from one organism to another, but overall DNA composition can differ as well.
In most eukaryotic organisms, DNA composition is not uniform across all the DNA in the cell: patches within the same cell where DNA composition is distinct from other regions.

4. Composition of DNA: % G+C
There is always equal #s of A and T, and G and C, but the
percentage of G+C pairs and A+T pairs can be different among different organisms.

5. Basepairs held together by H-bonds
T-A base pairs are held together by 2 H-bonds
G-C base pairs are held together by 3 H-bonds.
Therefore G-C pairs require slightly more energy to separate.

6. Measuring % G+C hyperchromic shift
As DNA “melts”, becomes SS, absorbs more UV at 260 nm.
Because G-C pairs have 3 H-bonds instead of two, DNA with
more G+C is more stable, melts at higher temperature (blue).

7. Satellite DNA
In prokaryotes, the %G+C base pairs is pretty much averaged out over the entire DNA; not so with eukaryotes.
Density gradient ultracentrifugation can also be used to determine %G+C.
G+C pairs are denser than A+T, migrate to a lower location (greater density) in the gradient.
Fragmented eukaryotic DNA showed something odd…

8. Satellite DNA
When the DNA was analyzed, a portion has a lower %G+C than the rest of the DNA, producing a “satellite band”. How could a portion of DNA have a different composition than the rest?

9. Repeated sequences
If a section of DNA with a %G+C composition different from the rest of the DNA is repeated many times, DNA fragments from these regions of DNA would behave differently during the centrifugation.

10. Study of the Composition of DNA using DNA renaturation kinetics
Break DNA into random fragments.
Denature with heat (melt).
Cool, allow strands to find their complements and go from ss to ds again (anneal/renature).
Follow entire process using UV light absorption at 260 nm
as DNA goes from ss to ds, Abs decreases.

11. Renaturation kinetics
Kinetics: study of the rate of change.
Major Point #1: the more copies of the complementary strands there are, the less time they will take to
find each other
the more DNA,
the faster the process.
In this fig., 2 different amounts of DNA from the SAME organism.

12. Renaturation kinetics-2
Major Point #2:
Given equal amounts
(same mass) of DNA,
the bigger the total genome
of the organism, the slower
the renaturation.
If the genome is bigger, and the amounts of DNA used in the experiment are the same, the organism with the bigger genome will have fewer copies of the complementary fragments, so annealing will take longer (see point #1).

13. Understanding genome size
Imagine you have 20 playing cards. In one instance, you have these 5 cards, another 5 cards exactly the same, and 2 more sets of the Ace thru 10 but of diamonds. <Deck 1>
In the second instance, you have ace thru 5 of hearts and also of diamonds. <Deck 2>
In which case will you match up pairs of hearts and diamonds most quickly? The Deck 1 gets matched up quicker.

14. Cot curves: Studying renaturation of DNA
The amount of DNA affects the rate at which DNA fragments
renature. To avoid the problem of comparing samples with
different amounts of DNA, the change in ss DNA is graphed vs.the initial DNA concentration (Co) x the time (t): Cot
Y-axis is the fraction or
percent of the DNA that is
ss (experiment starts by
denaturing the DNA).
X-axis is Cot which is a
Log scale.
lect7/fig9p8c.jpg

15. Satellite DNA and Cot curves
When human DNA was analyzed this way, this was the result:
Remember the card deck experiment: when there is only one of each card in the deck, they take longer to match up. So DNA that anneals quickly must be in multiple copies…

16. Cot curves and satellite DNA
Categories variable among different organisms.
Highly repetitive DNA, many complements, find each other quickly. Single copy (unique sequence) much slower.

17. Types of DNA
Highly repetitive DNA: 5-45 % of DNA depending on species. In humans:
ALU family: contains Alu I site. 300 bp long, appears 500,000 times, dispersed. 5% of DNA.
SINEs = short interspersed elements
transposable
Alpha satellite DNA: tandem repeats of 170 bp occur 5,000-15,000 times; make up part of centromere. 6%
L1 family (in humans), example of LINEs
Long interspersed elements

18. DNA in fewer copies Moderately (middle) repetitive DNA:
Tandem or interspersed repeats
VNTRs, good for DNA fingerprinting
Variable number tandem repeats
15 – 100 bp long, between or within genes
Dinucleotide repeats (CA)N, also good for forensic work
in maize and yeasts: transposons in large numbers.
genes for rRNA, ribosomal proteins, histones
Unique, “single copy”: typically 30-75% of DNA in most eukaryotes.

19. All your DNA codes for proteins? Sorry, not close
Only 4% codes for proteins, in 30,000 genes
96% of DNA includes
Introns, “junk” DNA within and around genes.
Genes coding for rRNA and tRNA
Junk DNA called repetitive sequences
Pseudogenes; have sequences that look like genes but are never expressed, don’t work.
We are related to everything else
Our genes look like those from chimpanzees, bacteria.