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DNA Condensed Notes.
Timeline
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1865- Mendel- traits are passed as distince
alleles (various forms fo the same trait)
• ex: trait= eye color
• alleles= blue, green, hazel, brown
• Mendel studdied patterns of train
inheritance- nothing about the mechanisms
and chemicals invovled. Not many people
read his paper.
1869- Friedrich Miescher discovered
deoxyribonucleic acid. naming nuclein -->
nuclei acid-=> deoxyribonucleic acid.
1900- deVries, Correns, Tschermak
independently rediscover Mendel's work.
• what a coincidence! none of them have
heard of Mendel before. all three wrote
their papers within three weeks of each
other. all of them turned them in to nature
magazine to be published at the same time
1908- Hardy and Weinbertg- laws of
population genetics determined a math formula
that explains how recessive traits stay constant
in a stable population.
• fathers of population genetics.
1910- Morgan- "genes" are on chromosomes.
thread things had been seen in cells doing the
mitosis thing. Morgan determined that they
contained the trait passing capcity. coined the
term "gene"
1928- Griffith- first transformation
experiments DNA could be the genetic stuff.
1941- Beadle and Tatum: " one gene codes for
one polypeptide" hypothesis. Polypeptidechain of amino acids, the fundamental building
blocks of proteins.
1944- Avery, Colin McLeod, McCarty team,
proved that dna is the genetic stuff.
1950- Chargraff's Rules
• T=A
• C=G
1952- Hershey and Chase- second team to
prove that dna is the genetic stuff.
1953- Watson, Crick, Wilkins and Franklindetermined that dna is a double helix.
Published in NATURE. Won the Nobel Prize
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1962 (except for Franklin- she died).
1958- Meselson and Stahl- proved that DNA
replicates semi conservatively.
1966- Nirenberg and Khorana: break the
genetic language code.
MACROMOLECULE 4,
NUCLEIC ACIDS
micromolecule: nucleotides
all nucleotides are made of three parts:
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phospate group
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five carbon sugar, pentose
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a nitrogen contining base
1. Phosphate group
has negative charge. if you add an H you get phosphoric
acid.
2. five carbon sugar- pentose
2 possibilties, know the numbering of carbons.
ribose: has OH on the two carbon. Used in RNA.
deoxyribise: no OH on the scond carbon, used in
DNA.
3. Nitrogen containing Bases
5 different types (see picture pages)
DNA/RNA
T/U
G/G
C/C
A/A
some are single rings: pyrimidines
some are double rings: purines
purines: adenine, DNA RNA. guanine DNA and RNA.
"puga"
pyrimidines: thymine RNA only, ctosine DNA and RNA,
uracil RNA only.
"if you sit naked on top of a pyrimid it will C.U.T. you!"
Two dehydration synthesis reactions:
phosphate: joins to the number five carbon of
sugar
base: joins to the number one carbon of sugar.
A base and a sugar is known as a nucleoside: ex: adenine
and ribose=adenosine
Other important nucleotides..
DNA Condensed Notes.
1. ATP (adenosine tri-phosphate)
3 phosphates--ribose sugar--adenine base.
The most important of all nucleotides it is the nergy
transfer molecule.
gold of the cel, energy currency, high energy bonds.
fully charged-->partially charges---> run down.
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other only has one ring. These pile designations are
important.
purines: those that are double ringed. (drink two glasses
of urine a day for good health.)
pyrimidines: those that have only one ring. (All built one
pience at a time, no double room pyramids, etch.)
see picture pages: know how ATP works, recharged in
mtchondria like a NiCad battery.
PUGA: purines: guanine and adanine.
if you sit naked on pyramids, it iwll cut you thymine,
cytosine, uracil.
Mitocchondria is a battery rechargeer--putst he Fi back
on.
The five bases are: adenine, guanine, thymine, cytosine,
uracil.
2. NADP+ a coenzyme used in photosynthses
3. FAD+ a coenzyme used in cellular respiration.
how to build a nucleotide
you have to have a pentose (deoxyribose or ribose), the
phosphate group, and the bases.
12/9/02 1:06 pm
DNA and DNA ase made up f nuclaic aids
ribonuclaic acid
deoxyribonuclaic acid.
every nucleotide is made up of a phosphate group (a
derivitive of phoshphoric acid), the phosphate groups
are negatively charged. They hydrogens donated by
DNA and RNA come from the phosphate groups. The
phosphate groups are identical in the both.
Nucleotides: made up of phosphate groups,pentose
sugar, nitrogen containing base.
the two different pentoses are ribose and deoxyribose,
respectively.
In dna you use: guanine and adanine. and tymine and
cytosine. If you see a uracil it is a mutation and it will be
removed, you will never find it tere. In your rna you have
Guanine and adanine, and cytosine and uracil. There is
no tymine in RNA. Uracil and thymine trade places.
Within a single nucleotide: the base is always hooked to
the one primary carbon and the phsophate is always
hooked on to the five primary carbon. This will always
happen.
To construct the nucleotide togeterh you will have to do a
condensation reaction (times two).
Phosphates are always represented by a circle, sometimes
with a P in it.
It is imperitive for todays lecture that you learn the
numberingb for ribose and deoxyriose. Starting form
tghe oxygen, you number them clockwise around the
ring, witt he fifth carbon sticking out of the ring.
Now when you link nucleotides together
it's a polyumerization reaction.
The phophate of one nucleotide attaches to the three prime
carbon of the sugar in nuclotide above.
(number of linked-1)
Phosphate goins five prime carbon if it's own nucleotide.
The difference between ribose and doxyribose
moleculary is that the deoxyriose has been
deoxygenized, it is missing a hydroxyl group.
"Deoxyribose is missing a hydroxyl group off of the two
primary carbon."
The differnece between one side of the dna and the other is
that on one side the dna has the oxygens pointing up, while
on the other side the oxygens are pointing down.
Everything in dna and rna are described in the terms of
the numbering system of the sugar. You must know this.
The prime is after them because they are that important.
You must learn what the prime designations are (the
aprostaphe ' thing).
The last part of the nucleotides are the bases. The basic
shape difference is that one pile has two rings, while the
If you look at the dna like a ladder, there will always be a
phosphate group attached to it's own five carbon sugar in
a corner, it is then called the five prime corner. It is the
top left of hte ladder. The oxygens point up on that
vertical column. The bottom left corner are the three
prime corner. Opposite the three prime corner on the
other side, since it is reversed, is the five prime corner, you
then have the three prime on the top right of the ladder.
The right and left side of the dna are built upsidedown to
DNA Condensed Notes.
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each other. It's called antiparallel construction. (like
shoes in a shoebox).
Shape is a double helix (a twisted ladder). Watson, Rick,
Wilkins, and Franklin determined the shape in 1954.
The steps of a ladder are referred to as the rungs of a
ladder. The steps of a ladder are the nitrogen
containing bases. The side rails of the ladder are the
alternating phosphates and sugars.
Side rails of ladder: P-S-R-S-P-S-P-S
TA, CG. a purine and a pyrimidine are always matched
up on a single step, maintaing the 2 nm constant width
of the dna. the standard width would be around three
rings wide. .34 nanometers is the distance between the
centers of each step.
The bonds between nucleotides are called
phosphodiester bonds. The middle of each step are held
together by hydrogen bonds, not actual covalent bonds.
this is so you can unzip the dna during mytosis. Every
other bond in the dna is a covalent bond.
phosphodiester bonds: COPOC. From theh three
carbon, to the oxygen, to the phosphorus, to the oxygen,
to the five prime carbon.
The two nucleotides that make up one secition (step and
siderails) are called a base pair. They are held
together by the hydrogen bond. If you go though and
add up the weight of all the atoms, thus the base pair is
660 daltons (amu's). The average gene is 1200 base
pairs long.
12/10/02 1:20 pm
Each step (rungs) of the ladder= two bases side by side.
T with A: 2 H bonds
G with C: bound by 3 H bonds
Average gene is 1200 base pairs long.
Puring always hydrogens to a pyrimidine.
Rungs of ladder are always three rings wide.
wide and narrow groves.
complementary, fit togetherbut are not identical.
RNA: looks like half of a dna ladder a cob messenger from
dna to the ribosmes.
T bas is never used Looks like a ladder buzz sawed down
the middle. Always use the pentose ribose in its
nucleotides.
12/11/02 1:04 pm
12/16/02 1:10 pm
Donner Party
they left too late and got stuck in the Sierra Nevada
mountains. They got stuck in a snowstorm and had to
spend the winter.
5 billin nucleotide in one human genome
2 chaines of nucleotides, side by side, hydrogen bonded
together at the bases.
3/21/03 11:28 am
messleson and stahl: semiconservative replication.
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bluerint molecule of life
complete set of instructions for you.
complete set in every cell of your body
directs wthich proteins will be made in the cell on a
daily basis
the enetic material that directs what your babies will
be lilke
always in the nuclus, never ever leaves. The guard
proteins keep it in there at all costs.
always uses the pentose deoxyribose in it's
nucleotides.
**One gene codes for one polypeptide chain. The
ribosomes will then go out and make that polypeptide
chain as specified.
DNA REPLICATION
DNA replication takes place during the S (synthesis) part
of the cell cycle.
1.
Helicase: opens hydrogen bonds of DNA ladder
to form a replicating bubble at the origin of replication.
Spends two ATP/per bond to open. breaks the double
helix, pulls apart the hydrogen bonds. often end up with
two forks, (replication forks). the place where helicase
started is the origin of replication. the entire open area is
the replication bubble. Spends two atp per bond to open.
2.
There is one replicating bubble in prokaryotesmultiple replicating bubbles in Eukaryotes. you have
DNA Condensed Notes.
many origins of replication, sequences with lots of T
and A.
3.
Eukaryotes build new complimentary DNA- 50
nucleotides/second.
4.
Prokaryotes build new complimentary DNA500 nucleotides /second.
Why the difference in rates???
they do it alot faster than eukaryotes. they are much
faster because they don't' live as long as eukaryotic
cells and because prokaryotic cells do not have as many
error checking mechanisms as eukaryotes.
One out of every ten million base pairs in eukaryotes is
incorrect. in prokaryotes it is one ouut of every
thousand/ten thousand.
5.
Like kite string being pulled apart in the middle
of a strand, DNA would bend and kink while being
unwound if the topoisomerase did not work ahead
(upstream) of the helicase relieving the stress. prevents
the tension of the dna molecule by allowing it to spin.
6.
Movement is bi-directional the bubble grows in
both directions.
7.
the points on the ladder where the hydrogen
bonds between the bases are being opened are called
Replicating forks.
8.
DNA nucleotides must join on to a 3' OH above
it. First nucleotide has a problem. there is not 3'OH to
join on to. DNA strands must always build 5' to 3'.
9.
So… RNA nucleotides must be put in place
first to supply the 3' OH for the DNA nucleotides to
hook onto Look at your detail picture. About 10-12
RNA nucleotides start the new strand. these are called
an RNA Primer.
The RNA nucleotides cannot stay there forever and
must later be cut out and replaced with DNA
nucleotides.
10.
RNA primase is the enzyme which places the
RNA primer in position.
11.
excisions endonuclease "cuts" out the RNA
nucleotides and
12.
DNA Polymerase puts the correct DNA
nucleotides in place and...
13.
DNA Ligase will "patch" the strand back
together (fixes phosphodiester bonds!) the Elmer's glue
of enzymes.
14.
One new side is easy to build. ONe RNA
primer and then the process continues to build 5'-3'.
The strand is called the leading strand.
easy side: leading strand
hard strand: lagging strand
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15.
The other side is tougher. It must keep putting in
RNA primers as the helix opens up and makes sites
available. The primers must keep being removed and
DNA patched in to fill the spaces. This is called the
Lagging Strand. the short little segments of DNA that
can be fabricated and eventually patched together are
called Okazaki Fragments.
16.
The Okazaki fragments in prokaryotes are
typically 1000-2000 nucleotides long. In eukaryotes they
are 100-200 nucleotides long.
17.
Additional point. As the DNA helix is opened by
the helicase enzyme, it would quickly close back up before
the new complimentary nucleotides could be placed if they
weren't held open. Single Stranded Binding Proteins do
this job.
18.
Proofreading: DNA polymerasae also checks to be
sure the correct nucleotide was placed in the growing
chain. It is the number one proofreading enzyme in DNA
replication.
19.
The new DNA nucleotides that are going to be
placed in the growing strand float in as tri-phosphate
nucleotides. The extra two phosphates (P~P) are removed
by DNA polymerase and supply the energy for their
condensation into the strand.
DNA Replication in Prokaryotes
Special Points
As you know, bacteria usually replicate by binary fission.
• The ring of DNA is attached at one point to the cell
membrane.
• An origin of replicating starts opening up into a
replicating bubble and the ring is duplicated as
described above.
• This method is called "theta" replication because it
kinda looks like the Greek letter theta while it is
happening.
News Flash!!! Bacteria sometimes have sex!
It's called conjugation. and that long ting between them is
called a pilus. The shorter spikes are usually called
fimbrae.
there is a certain gene that allows the bacteria to make the
spikes.. the long one is the pilus, the short ones are
fimbrae.
the bacteria that can give bacteria are the males.
Other news: besides the regular ring chromosome of DNA
in a bacteria, they usually ahve smaller circles of extra
DNA called plasmids.
DNA Condensed Notes.
Plasmids• carry anywhere from 2 to 10 genes on them.
• a rare few have been found with thirty genes in
them.
• cells can have anywhere from a couple to fifty or
more plasmids in them.
• some pop into the bacterial chromosome =
episomes.
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Drug resistance is also passed from bacteria to bacteria this
way. Serious medical implications.
concatemer: a piece of the replicated dna that is one
entire revolution (genome). plasmids end up getting alto
of genes that are on the genome. they jump in and out as
episomes. there is alot of genetic variation.
when the bacteria replicates the plasmids sometimes
replicate as well.
because plasmids are sent over so easily it is easy to have
antibiotic resistance.
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The dna comes out like a two ply sheet of toilet paper as
opposed to a replication bubble.
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some plasmids only replicate when the ring
chromosome replicates.
Other plasmids replicate on their own schedule.
Important genes they might carry:
Drug resistance
fertility factor (F+) if you have f+, you are a male, if
you are F-, you are a female. during conjugation
plasmids can be transferred from one bacteria to
another. F+ has gene to make a pilus.
helicase starts at the point of origin!
single stranded binding proteins keep the helix from
reforming. they actually cover over the half strand and
thus cover where the hydrogen bonds would be and it
keeps the strand from re helixing.
the primer is about ten to twelve units in length!
3/31/03 11:52 am
How to fold a strip of DNA
into a chromosome
Before mitosis and meiosis, all the linear strips of DNA in
the cell must fold up into the chromosomes. During most
of the cell cycle, DNA is loose and unwound so the bases
can be reacehd. Tangled mess if you tried to separate them
like that during mitosis. Two meters of DNA in each
human cell.
The folding process is called condensation.
it takes about ten to twelve nucleotides to cause the
electrostatic interactions to cause rna primase to fall
away from the chain.
Histone protein spools are the key component around
which the DNA wraps itself. Histones have large amounts
of positively charged amino acids (lysine and arginine).
bacteria are not conservative with their genes.
1/2 of the weight of a chromosome is protein.
3/26/03 12:58 pm
During the interphase, much of the DNA stays wound up
partially with these proteins.
If a bacteria has fertility factor (F+), it has the genes for
growing a pilus. (And is known as the male partner).
When bacteria conjugate, they do not use theta
replication Instead, they use the rolling circle method.
This allows multiple copies of the chromosome or
plasmid to be made at once in one long strip an then
injected through the pilus to the mating cell. Fast quick
method of dispersing resistance.
Histones come in five flavors:
• H1
• H2a
• H2b
• H3
• H4
3/31/03 11:35 am
If an F- cell (female partner) receives the fertility factor
plasmid from conjugation it then becomes a F+ cell.
Sobering thought: maleness is contagious
A histone core (histone spool) is made up of eight of these
proteins:
• H2a
H2a
• H2b
H2b
• H3
H3
• H4
H4
DNA Condensed Notes.
it looks like a double layered cheese cake cut into four
pieces. each layer is exactly the same. each one of the
four pieces is one of the histone proteins.
The H1 proteins are not in the histone core.
Histone genes are highly conserved sequences in all
eukaryotes.
ex: H4 from cow varies from the H4 for peas by
only 2/102 amino acids.
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tortoise-shell cat (calico)
males extremely rare.
KNOW:
different levels of coiling
replication proteins
NOTES TAKEN FROM:
LEVELS OF
CONDENSATION
1.
Beads on a String
The dna double helix winds twice around the histone
core forming a nucleosome bead. A short strip of DNA
(about sixty base pairs long) acts like a linking chain
(hence linker DNA between adjacent nucleosomes.
This step reduces the length of DNA by six times.
2. Further condenses into the solenoid: hollow center
held together by H1/H1 interactions.
4/1/03 11:37 am
3. solenoids then condense into radial loops. the radial
loops are tacked on to the scaffold protein. the tubes
on the protein then condense further into a coil.
4. coiling
5. super coiling keeps coiling until it is in the shape of a
chromosome (the final level of DNA condensation.
During interphase DNA may stay in radial loops
attached to the nuclear lamina. RNA polymerase works
around the histone proteins. Called euchromatin.
Gene rich- used genes that is! (Light bands on
karyotype). the dark bands are tightly coiled because
those genes are not actively producing proteins.
Some stretches stay highly condensed...
heterochromatin. Stain very dark (NOT often used
genes)
Barr bodies: the second X chromosome in females that
is turned off. stains differently.
Random which one is turned off except in
kangaroos, koala, and wombats.
Olympics test.
bio10-genetics
bio10-protein synthesis
chem10- dna & rna
chem10- dna replication