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2. Accurate transmission
-traits
-signals: methylation pattern
*specific base pairing (A-T, G-C)
*error repair/proofreading mechanism (it’s a process that the DNA undergoes, not a feature of the DNA
itself)
3. Stability
-low mutation
rate
-flexible
(adapt to the
environment
esp. change in
its secondary
structure)
4. Mutability
-capacity for
genetic
change
-->variation--
>evolution
*pyrimidines : 1 ring
T (2,4-dioxy-5-methylpyrimidine or
5-methyluracil),
C (2-oxy-4-aminopyrimidine),
U (2,4-dioxy pyrimidine)
INFORMATION FROM
THE PRIMARY
STRUCTURE
1. Size/ length:
1Mb, 1000kb,
2. MW: 80,000
daltons
3. Configuration:
ds linear (human), ss
circular
4. Base
composition: 10% A,
50% G+C
5. Base sequence:
5' to 3' ( in letters)
In diploids
-the DNA that contains one complete set of the genes (2C)
~C value paradox
-exceptions: toad and South American lungfish > humans
b. The DNA content is also correlated with certain processes or properties of a cell.
-species with lower DNA content have faster cell division (fewer DNA to replicate faster cell cycle)
-in Asian rice species, wild species have higher DNA content than domesticated (cultivated) species
(man made the selection)
Hairpin
-formed by ss DNA or RNA
-palindromes
-
Cloverleaf
-tRNA molecule
-multiple palindromes
-3 stem and loops in one molecule (anticodon, d,tyc arms)
-acceptor arm
SUPERCOILED DNA
-axis of the helix is curved
-occur in two forms: with scaffold - occurs in nucleosome; in circular DNA
-equilibrium centrifugation in CsCl containing ethidium bromide (EtBr-a flat molecule that intercalates
DNA causing unwinding--> changes supercoiling of DNA depending on its concentration; direct
relationship)
-gel electrophoresis
~smaller or more compact molecules willsmove faster; pass through the matrix easier and
migrate farther than large molecules
~in terms of rate of migration
Supercoiled>relaxed circular
~linear DNA migrate according to size
Writhe (Wr)
-a measure of the coiling of the axis of the double helix
-the number of turns of the axis about the superhelical axis
-the measure of the degree of coiling
Lk= Tw + Wr
relaxed (+)
(-) supercoil
DNA supercoil
Lk 95 100 95
Wr -5 0 5
Tw 100 100 100
due to due to
underwiding overwinding
*e.g
extracted
DNA
Sample Problems
1. Given 3 cccDNA molecules of the same length and sequence but varying Lk. Predict their
expected configuration.
overwinding --
1000 200 5 clockwise
> (+) SC
faster than
relaxed
underwinding
1000 50 20 counterclockwise
--> (-) SC
TOPOISOMERS
DNA molecules with the same length but different Lk
Can be interconnected by connecting one or both strands and then rejoining them
o By topoisomerases
Relieve torsional strain
e.g. gyrase
1. Toposisomerase I
a. Monomeric protein; 100,000 MW
b. Break only one strand
c. Involved in the formation of “catenates”
d. E. coli Topoisomerase I relaxes (-) SC DNA without using external energy
e. Introduces a change of increments [n+1 or n-1] of 1 in Wr
Significance of Toposiomerase
1. Facilitate strand separation
Replication, transcription, recombination
2. Assist structural transition in DNA
Gene accessibility expression
E.g.
o BZ
o Cruciform formation
Principle: the DNA associated with the histone core is less susceptible to nuclease digestion
Conclusions:
1. In human chromatin, protein complexes are space along the DNA at regular intervals, one for
each 200bp
2. 146pb are closely attached to each protein complex
a. Nucleosome
i. H2A,
ii. H2B,
iii. H3,
iv. H4
b. H1: attached to the linker DNA
Chromosomal Proteins
Histones NHCP (Non-histone Chromosomal
Proteins)
a well defined class of structural proteins hundreds of different proteins
primarily for packing DNA into chromosome affect packing of DNA to control gene
expression
high in Arg and Lys [basic aa:(+) charged --> variable aa composition
binds to (-) DNA]
enormous quantity per cell variable amounts; <<< histones
highly conserved gene sequences variable
5 types: H2A, H3B, H3, H4,H1 and related very many types (RNA polymerases, regulatory
proteins (H5 may replaced H1 in some proteins, HMG 14 and HMG 17, other enzymes
organisms) and protein factors)
Histone Genes
In clusters (gene families, ~like in operons)
Gene clusters in a given species are located at specific chromosomal regions
o E.g. human: long arm of chromosome 7
Each gene is transcribed separately (unlike operons)
Vary in different species in terms of:
1. number of clusters per genome
Drosophila: 100 copies
Mammals: 20
Chicken: 10
2. Size of the spacers (not an intron, i.e., it is found in the gene itself) that separate
genes in a cluster
3. Gene order in a cluster
4. Direction and template strand for transcription
SOLENOID
A chromatin fiber: 30 nm wide
Formed from the folding and twisting further of the 10nm chromatin fiber (beads on a string) into
a supercoil
o Adjacent H1 proteins are in contact with each other
o H1 not only linked nucleosomes but also responsible for solenoid formation
A left handed helix
6 nucleosomes per turn
Nuclear Matrix
A protein scaffold
Metaphase scaffold
Filamentous structure in interphase cells found in the interior of the nuclear membrane where
chromatin often appears to be attached