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Intro to Cellular & Molecular Biology 
Chapter 16​: DNA, Chromosomes, and the Nucleus 
 
● Bacteriophages/phages  

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​WEEK 3  

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Phages that infect bacteria often destroy them in the process
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■ An example of these are retroviruses
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It must be this way because the diameter of a DNA double
helix is too big for two pyrimidines and too small for two purines
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Moreover, the hydrogen bonds holding the DNA
structure together only fit when A = T and G = C, not when T = G or anything like
that
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Using Chargaff’s Rules, Watson and Crick were able to deduce their
theories about the helical structure of DNA (which they totally stole from
Rosalind Franklin but that’s fine)
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This allows enzymes to bind to the
grooves and recognize sequences of DNA
without having to snip up the double helix
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How is DNA/RNA characterized by size?
■ DNA is measured in base-pairs (bp) or
kilobase pairs (kbp)
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DNA can be found in supercoiled form, like in circular loops or in mitochondria
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■ DNA can be either positively supercoiled or negatively supercoiled
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■ Supercoiling is very useful in cell division, but it can not be useful when
the DNA tries to interact
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■ Topoisomerases are enzymes that regulate this kind of
supercoiled/relaxed form thing with DNA… they can be found in ​type 1​ or
type 2 f​ orm​
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When a DNA strand is experimentally unwound, it is called DNA denaturation, or
melting
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■ When DNA is melted, it is melted in a solution and absorbs the solution as
it separates
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This
value indicates how tightly the DNA is wound
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GC pairs have more (one more in
fact) hydrogen bonds that are more resistive to separating
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However, it is now realized that the main
bacterial genome is condensed into a bacterial chromosome, like in eukaryotic cells
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This loop is bound
to small proteins and condensed in an area known as a nucleoid
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These are small, circular loops of DNA that
contain their own instructions for replication and mostly nonessential bacteria
processes
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■ DNA is wrapped around simple proteins called histones
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This structure is called
chromatin
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■ These little core structures are called nucleosomes altogether, and they’re a little
more complex:
● Histones come in octamers, which is a set of eight
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H3 and H4
like each other, and H2A and H2B like each other
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● Each histone has a “tail” that protrudes from it and contains amino acids
that affect how tightly the chromatin is packed
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○ What about H1? Well DNA actually goes on for 146bp like this
and then has linker DNA that is about 50bp long
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■ Chromatin packed together has a diameter of 30nm
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These two forms can be interchanged by
changing the salt concentration
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■ Next, the DNA must be packaged into loops 50000-100000 bp in length
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The extent to which DNA can be packaged can be determined by the DNA
packing ratio
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● Typical euchromatin has a ratio of 750, but DNA in division and stuff can
have a high ratio
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Each
histone has a tail that can be “tagged” by something else to attract activity
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● Example? Methylation of lysine via histone methyltransferase
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○ Histone deacetylase (HDAC) removes acetyl groups
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○ Which one is the key for gene silencing? Lysine 9!
○ Small numbers = N-terminus, big numbers= C-terminus
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More packing tidbits: heterochromatin is very densely packed DNA that is seen
as just a little dot when observed
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● A lot of heterochromatin can be turned into euchromatin and vice versa
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It is which regions of DNA are
facultative heterochromatin that gives us hints about what kind of cell it
is
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○ 90% of nuclear DNA is euchromatin and facultative DNA
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There are two types: telomeres and centromeres
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They
keep them together and they contain lots of repeating DNA
strands known as CEN sequences
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■ Repeating DNA can be classified into some categories
● Tandemly-repeated DNA is when multiple
copies are arranged next to each other in a row
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The
length of a tandemly-repeated DNA segment
can vary from 1-2000bp
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Remember mitochondria and chloroplasts have DNA too! This DNA is usually circular
and is void of histones, which makes it look a lot like bacterial DNA (revisit the
endosymbiont theory)
■ The size of mitochondrial DNA varies among organisms, but a larger size doesn’t
mean more proteins to synthesize
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■ Epigenetics-- cannot express the gene because other proteins have methylated
the histones or DNA to cause it to condense
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But it
also creates the problem of transport
between the cytosol and the nucleus
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■ The outer nuclear membrane is
consistent with the endoplasmic
reticulum
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● A typical nucleus has
3000-4000 pores
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The nucleoplasm refers to the space outside of the nucleolus and inside the nuclear
envelope
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● The rate of particle diffusion through a pore is inversely related to its
diameter
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■ Active transport of large particles
● Proteins are equipped with nuclear localization signals (NLS)
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● Maximum diameter for active transport is 26nm
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A cytosolic protein (a protein in the cytoplasm that wants to
get into the nucleus) is recognized by an importin on the nucleus
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This complex is is transported into the nucleus, where it goes
to visit a GTP-binding protein called Ran
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○ 3
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● What about going out of the nucleus?
○ Export is mainly used for mRNA that functions in the cytosol
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These proteins contain
nuclear export signals (NESs), which are NLSs but for RNA
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Lol
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● Also, the nuclear lamina is a thick network of fibers that lines the inner
membrane of the inner nucleus
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The nucleolus aids in the synthesis of ribosomes

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