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BIO 240 notes.doc

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BIO 240 Lecture 4 14/10/2010 06:09:00
X-ray crystallography supports a zigzag model for the stacking of
nucleosomes in the 30-nm fiber
Cryoelectron microscopy of longer strings of nucleosome supports a
solenoidal structure with intercalated nucleosomes in the 30-nm fiber.
The causes of nucleosomes to stack so tightly on each other in a 30-nm
The nucleosome to nucleosome linkages formed by histone tails,
most notably the H4 tail constitute one important factor
Additional histone (1 to 1 ratio with nucleosome cores), known as
histone H1.
A change in the exit path in DNA is crucial for compacting
nucleosomal DNA so that it interlocks to form the 30-nm fiber.
In eukaryotes protein-coding genes are usually composed of a string of
alternating introns and exons associated with regulartory regions of DNA.
Cells contain dozens of different ATP-dependent chromatin remodeling
complexes which are specialized for different roles.
ATP-dependent chromatin remodeling complexes- due to presence of
these, arrangement of nucleosomes on DNA can be highly dynamic,
changing with needs of the cell.
As genes are turned on/off – chromatin remodeling complex brought to
specific regions of DNA to influence chromatin structure.
Most important influence on nucleosome positioning: presence of other
tightly bound proteins on DNA.
Exact position of nucleosomes along stretch of DNA depends mainly
on presence and nature of other proteins bound to the DNA.
The DNA in eucaryotes is tightly bound to an equal mass of histones, which
form repeated arrays of DNA-protein particles called nucleosomes. The nucleosome is
com-posed of an octameric core of histone proteins around which the DNA double
helix is wrapped. Nucleosomes are spaced at interuals of about 200 nucleotide pairs,
and they are usually packed together (with the aid of histone Hl molecules) into
quasi-regular arrays to form a 30-nm chromatin fiber. Despite the high degree

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of compaction in chromatin, its structure must be highly dynamic to allow
access to the DNA. There is some spontaneous DNA unwrapping and rewrapping in
the nucleosome itself; how' euer, the general strategy for reuersibly changing local
chromatin structure features ATP-driuen chromatin remodeling complexes. Cells
contain a large set of such com-plexes, which are targeted to speciflc regions of
chromatin at appropriate times. The remodeling complexes collaborate with histone
chaperones to allow nucleosome cores to be repositioned, reconstituted with dffirent
histones, or completely remoued to expose the underlying DNA.

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Lecture 5 14/10/2010 06:09:00
The structure of different members of a protein family has been more
highly conserved than has the amino acid sequence.
Some a.a sequences have diverged so far as to the only way of
identifying family relationship between the two proteins is by
determining their three-dimensional structures.
- there are limited # of ways in which protein domains fold up in nature
– maybe as few as 2000.
- proteins whose genes have evolved from a common ancestral gene
can be identified by the discover of similarities in amino acid sequences
- Generally speaking, one requires a 30% identity in sequence to
consider that two proteins match.
- many short signature sequences “fingerprints” are widely used to find
more distant relationships.
- Protein comparisons are important b/c: related structure often =
related function
- Proteins that work closely with one another in the cell often have their
genes located on different chromosomes, and adjacent genes typically encode
proteins that have little to do with the other cell. This makes decoding the
genome extremely difficult.
- the most common way for a cell to regulate the expression of each of
its genes to the needs of the moment, is by controlling the production of its
- for RNA transcription, like replication; the hydrolysis of high-energy
bonds provides the energy needed to drive the reaction forward.
- RNA polymerase catalyzes the linkage of ribonucleotides, while DNA
polymerase catalyzes deoxyribonucleotides.
- RNA poly. can start an RNA without a primer vs. DNA poly. which does
need it. This may be due to transcription need not be as accurate as DNA
- RNA poly. one mistake every 10^4 vs DNA poly. one mistake every
- RNA polymerases have a modest proofreading mechanism. If an
incorrect ribonucleotide is added to the growing RNA chain, the polymerase
can back up, and the active site of the enzyme can perform an excision
reaction that resembles the reverse of the polymerization reaction,
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