Last updated:
08/18/98
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Read the DISCLAIMER
before proceeding.
The Last BioNotes of the YEAR!!!
Typed by PINOY (name change
no more H.H. Sorry yall
J )
(TEST NOTICE: 8am class has the test on WEDNESDAY, December 16, 1998 @ 8am!!!
The 9am class has the test on FRIDAY, December 18, 1998 @ 8am!!!
Oh yeah
BTW, Dr. Benjamin said that there were going to be at least 3copies
of the test for EACH CLASS. Hes not stupid, so dont
expect us 8 am people to be able to tell you everything you want to know (not like I
am
). So STUDY already
chances are that youll have this document for a
full 2 days more than the rest of us in 8am class. See ya!!!)
Notes: This is IT!!! The last BioNotes of the SEMESTER and the 1998
year
FINALLY!!! As always, theres the standard disclaimer: If you read this and
fail, you cant blame me! J Duhh
The information
in this study sheet I try to make as accurate as possible, but since no one else out there
EVER helps me on this, you cant possibly expect me to make this PERFECT
people
make mistakes, ya know?
God helps those who help themselves
-- the Bible
(Quote Explication: If you havent already started studying for this exam
and think that these notes are your ticket out, you are SORELY MISTAKEN. You dont
deserve these notes
SO GET AWAY!!!! NO EXCUSES!!! (and DONT
blame the controller that you lost your match in StreetFighter II - maybe YOURE
the one who really doesnt know how to do a FIREBALL
) In any case,
good luck, and have fun over Winter Break YOU DESERVE IT!!!
OK
here we go! Turn the page for some serious fun. And trust me - itll be a
BLAST
no kidding J
BIONOTES!!! - Exam #3!!!
Chapter 16
Genes and Heredity
Garrod - This dude identified the first genetically based human disease,
sometime in the early 1900s.
Its symptoms included black urine (uhhh
thats pretty disgusting),
which is caused when alkaptons are oxidized when exposed to air. The alkaptons got there
because who ever had the disease lacked an enzyme that was needed to break down alkaptons.
He also hypothesized that the disease was inherited. Of course, everyone thought he was
nuts.
Decades later, they figured out that he was actually right. This disease is called alkaptonuria.
Scientists traced it down to a gene that dictates the production of the specific
enzyme that breaks down alkaptons. It is an autosomal recessive disorder that followed
Mendels laws of inheritance. Descendents got the disease
Beadle and Tatum (1941)
These dudes, working again, after finding their mutants in Drosophila started
looking for mold in bread. (Pretty fun job, eh?) Just like the white eyed male mutant
flies before, they looked in Neurospora, hoping to find other mutants that
would back up their work.
Normal "wild-type" Neurospora survives only when its got enough
food to eat
without these essential nutrients, itll die. So, they tried to
grow the stuff on MINIMAL medium, stuff that had the absolute minimum of stuff,
hypothesizing that any mutants wouldnt be able to survive because they wouldnt
have certain key enzymes to live off of such small stuff. SO, any mutants that didnt
survive, they took to another table and tried to give them back each nutrient that the
medium lacked from the COMPLETE medium one by one, until they found what ever it was they
could live on. (e.g. argine, tryptophane or uracil)
Any mutants, etc. were called auxotrophs (auxo means "to
increase", troph means "nutrients")
As a result, the one gene à one enzyme theory
developed. Over the years, this was revised to one gene à
one polypeptide, because not all proteins are enzymes. This tied changes in the DNA to
changes in specific enzymatic activities, which in the end, changes genotype or phenotype.
Sanger (he da MAN!)
This guy determined the amino acid sequence of proteins. (Dont have to know how
he did it
he just did
and got the Nobel Prize for it too. If you actually
wanna read about it, go to page 378)
He used this method to show that sickle cell anemia is actually caused by a
change in one amino acid. In the protein sequence (polypeptide chain), one amino had been
changed and was different than what was SUPPOSED to be there.
Later, it was shown to be one change in the DNAs nucleotide sequence (as
predicted by the genetic code)
Central Dogma of Molecular Biology (KNOW THIS!!!)
DNA à RNA à protein
The whole point is that the DNA controls ALL! It makes the RNA that in the end
makes the proteins that control what and who YOU are.
now DNA ß RNA also known (reverse transcription
by viral transcriptase)
Note that there are also RETROVIRUSES that are RNA that can actually RE-ENGINEER your
DNA via a viral "reverse transcriptase". This is how HIV works, and it really
fucks everything up!!!
RNA Molecules
differences between DNA and RNA
The big difference between deoxyribose and ribose is the deoxy- part of it. DEOXYRIBOSE
is missing an oxygen atom from on part of the pentose, so its just a lone H instead
of a complete OH group.
Another difference is that Uracil replaces Thymine in RNA. These two
nitrogenous bases are also very similar in structure, except that one carbon on Thymine
has a methyl (CH3) group and Uracil has a single hydrogen.
types of RNAs
mRNA - messenger RNA, has coding sequence for protein(s) (for example: UUGCTAA)
tRNA - transfer RNA, carry activated amino acids to ribosome (The tRNA carries
specific amino acids on one end and an anti-codon that latches on to the corresponding
codon on the mRNA)
rRNA - ribosomal RNA, part of the ribosome (Remember this from Masaracchia?
These come out of the nucleus, etc. Right? These sites are where the mRNA and tRNA stick
together)
snRNA - small nuclear RNA, involved in splicing out introns (more on the intron
/ exon thing later
dont u know?)
Transcription (RNA Synthesis)
RNA polymerase, transcription bubble
A big thingy type of enzyme called RNA polymerase swoops in and starts to open up the
dual stranded DNA. Its a lot like DNA replication, and uses the rNTPs
(remember? UTP, CTP, ATP, and GTP). Theres an ori (or transcription bubble) that
opens up, and the RNA polymerase comes in and starts chuggin.
Whats cool is that the mRNA just kind of peels of as its made. In the wake
of it, the DNA winds back together automatically
Whats even COOLER is that multiple mRNA polymerases can work at the same
time on the same strand of DNA (I think
)
promoter (where the mRNA binds to DNA and start transcription)
Certain sequences of DNA act as promoters, where the RNA polymerase can hook up with
the DNA and start making all that fun RNA. TRANSCRIPTION occurs (thats when
the message is just kinda copied
just a different handwriting
see?)
5 à 3 direction of synthesis à (This is the way we make RNA
make RNA
make
RNA
all through the morning
)
uses ribonucleotide triphosphates, does not proofread, no primer required
Thats right. CTP, ATP, GTP, and UTP (these are the rNTPs like I said before!)
It doesnt proofread (the polymerase doesnt give jack if it screws up
)
Plus, you dont need a primer. (its in the 5 to 3 anyway
no OKAZAKI frags
)
complementary pairing with DNA template (anti-parallel)
In other words, the DNA is the RNAs template and they are ANTIPARALLEL
(RNA is made in the OPPOSITE direction. The RNA is 3 à
5)
primary RNA transcript (generally processed later; exception - bacterial mRNAs not
processed)
OK
so youve got an ugly little pre-mRNA type thing after transcription. You
still gotta process it! Its got a lot of blank stuff that doesnt even code for
anything. You want to take out unneeded material called INTRONS and keep the EXONS.
So, the genes are spliced, and you get the REAL mRNA. COOL, huh?
Translation (protein synthesis) (kinda like translating English to a foreign
language
lets say, Filipino! J )
ribosomes are RAD
rRNAs and proteins
ribosomal RNA or rRNA is actually 60% RNA and 40% protein (believe it or not)
small and large subunits
made up of large and small, they come together as soon as they see mRNA and tRNA on the
way
mRNA (the messenger RNA)
codon - dont ya know? Its an mRNA base triplet. Each triplet codes
for one particular amino acid. The sequences of these determine the sequence of the
polypeptide chain.
AUG - called the "start" codon, it ALWAYS begins mRNA
molecules and codes for a methionine to come in and start everything up.
ribosome binding site (RBS) - the ribosome actually has TWO sites where tRNA
(the ones that bring in the amino acids) come in and match up with the mRNA (the sequence
from the DNA with codons)
Theres the P Site or Peptidyl-tRNA binding site, which is where the
current tRNA is letting go of its protein for the protein to hook up to the ever growing
polypeptide chain.
Then theres the A Site, or Aminoacyl-tRNA binding site, where the next
tRNA, amino acid, and anti-codon, is just itching to go get em.
UAA, UAG, UGA à stop translation
-- These three codons dont actually code for a tRNA and amino acid as others
normally do, but instead, they code for a protein release factor. This comes in and tells
the growing to stop, so theres no more stuff to add on, etc. SO STOP THAT ALREADY!!!
read mRNA 5 à 3 --- uhhh
yeah
mRNA is read in the 5 to 3 direction. OK?
reading frame (significance, how set, what if changed accidentally)
Oh yeah
this is a REALLY big deal
Lets say you had the sentence:
"The Red, mad Filipino killed the BOOM-BAY". If you jumbled all the
letters together, youd get "theredmadfilipinokilledtheBOOM-BAY". You might
think that the first word was THERE, but its NOT! Thats what happens when you
have a FRAMESHIFT. Normally, codons are read in "3 lettered words", like UGA,
TTT, or CAC. If something happens to alter the reading frame, the sequence UUU-GGG-AAA
could be read UUG-GGA-AA? (missing the first U) Now that would screw EVERYTHING up,
wouldnt it?
tRNAs or transfer RNAs
JUST WHAT ARE THEY? Theyre adapters,
"converting the nucleotide sequence of codons to amino acid sequences"
Everyone knows this concept by now, right? These tRNA molecules play a key role in
creating the polypeptide sequence.
Theyre actually made of real RNA sequences with the loop type things that keep
the whole structure together in the 3 dimensional form
The lowest loop has three nucleotide bases that are collectively the ANTICODON
that pairs up with the CODON on mRNA.
The amino acid hooks up on the 3 end, while the 5 end
well...is just
kinda there I guess
(theres a picture on page 307
go stare at it if
youre bored - the simplified structure (letter "c" on the diagram)
actually looks like a stick of dynamite. GO LOOK if you dont believe me!!!)
Each tRNA brings in a different amino acid (kinda
if you dont
understand what Im talking about, dont worry about it)
The tRNA picks up amino acids from the cytosol (the cell is just jam packed FULL of
them!!!). But they just dont instantly latch on. Thats what
"Aminoacyl-tRNA Synthetases are for!!!
activating or tRNA charging enzymes, Aminoacyl-tRNA Synthetases (20 different, 1
for each amino acid, use ATP for NRG)
Well, this is actually a whole phreakin FAMILY of enzymes - 20 different ones
(one for each amino acid hookin up to a tRNA)
FIVE STEP PROCESS:
1. The active site of the enzyme binds the amino acid and an ATP molecule (it needs
NRG!!!)
The ATP loses two phosphate groups and joins to the amino acid as AMP (adenosine
MONOphosphate)
The appropriate tRNA covalently bonds to the amino,
Displacing the AMP from the enzymes active site.
The enzyme the releases the Aminoacyl-tRNA, the "activated" amino
acid.
2. anticodon (tRNA region which pairs w/ codon)
Yeah
whatever. You know this, right? The tRNA anticodon pairs with the mRNA
codon, bringing in the amino acid that its supposed to have
OK?
Decrypting the GENETIC CODE
triplet (43 or 64 possible codons), non-overlapping code -
since there are 20 amino acids and 4 different bases, there had to be 64 possible
codons (4 to the third). Why? 4 2 is not enough to cover it all
Plus,
none of them overlap meaning that one codon codes for only ONE amino acid (not
multiple amino acids per codon)
degeneracy (define/explain), more than one codon / amino acid
Degeneracy or "wobble" as the book calls it (funny name there,
eh?) is the fact that youve got extra codes that you can use up (You only needed 20,
and youve got 64!!!) So, multiple codons can stand for one amino acid. That way, if
theres any accidental mutation, etc. most of the time it wont do jack, because
itll still code for the same amino acid (check the chart on page 303 of you still
dont get it
)
61 codons call for amino acids, but the AUG codon is used for methionine and a
"Start" signal - so proteins start with methionine as first amino acid
There are 3 stop or "nonsense" codons for stops (there
are no tRNAs for these, just a protein release factor). They are UAA, UAG, UGA
universal code - Whats pretty cool is that all this codon stuff is actually more
or less universal for all organisms - they use nearly identical codons for the same amino
acids. THAT ROX!!!! (kinda
I guess
well
maybe not
)
mitochondrial / chloroplast changes in genetic code usage (also, note prokaryotic
nature of organelle gene expression and theory to explain), antibiotics can harm organelle
gene expression why?
This ones a little tough, so listen up. Its theorized that mitochondria (as
well as chloroplasts, were actually bacteria from like along time ago that got trapped
within our own cells (can you say SYMBIOSIS?) Well, theyve got their very own DNA
and do a lot of stuff on their own.
reading frame - like I said before, know the meaning of the term , and that its
just set by the start AUG codon
mechanism of protein synthesis (dont YOU feel like making proteins TOO?)
Initiation (ribosome, mRNA, initiator met-tRNA, protein factors, AUG, ribosome
binding site identifies start AUG codon and interacts with small sub-unit rRNA)
Ok.. this is where it all begins. You first have to get everything together à the mRNA comes in and binds with a small ribosomal sub-unit and
a special tRNA initiator. Everything starts at the 5 end of the mRNA sequence,
at a particular sequence of mRNA.
Down stream, theres the awaiting AUG codon that says, "Come on!!! Lets
make some proteins already!!!" So, when the timings right, the special tRNA
initiator brings in the methionine amino acid. The large ribosomal sub-unit then hooks up
and youve got a functional ribosome. Some tRNAs are constantly being fed into the
whole thing. GTP provides NRG for the initiation process.
Elongation - basically, the polypeptide sequence gets longer as more stuff is
processed.
Codon Recognition - The mRNA codon waiting in the A site of the ribosome forms
H-bonds with the incoming tRNAs anti-codon, carrying the appropriate amino acid. An
elongation factor (a protein) pushes the tRNA into the A site. This also requires the
hydrolysis of a phosphate bond from GTP.
Peptide Bond Formation - A little thing in the big ribosomal sub-unit rushes the
two amino acids along and says, "Hey
I dont got all day! MAKE A PEPTIDE
BOND ALREADY!!!" So, they do. The POLYPEPTIDE SEQUENCE that is on the tRNA in the P
site moves itself to hook up with the one amino acid on the tRNA in the A site. So, it
just got longer.
Translocation - The tRNA in the P site just kinda floats away. It doesnt
have any business in there any more. The tRNA in the A site is translocated to the P site
where the other one WAS. As the tRNA moves around, it is still hydrogen bonded to the
mRNA, so they two move forward as a unit. This movement is fueled by yet another GTP
molecule. The movement is in the 5 to 3 direction. Then, it starts all over
again.
Termination - "Its all over
THEY IN TROUBLE
"
By now, its all over. Elongation goes on until it hits a stop (UAA, UAG, or UGA).
A release factor protein binds directly to the termination codon in the A site. This
causes the ribosome to add a water molecule to the growing polypeptide chain. This
reaction hydrolyzes the completed polypeptide chain from the tRNA in the P site, freeing
everything up, and letting everything go. THE END!
poly(ribo)somes - This just means that you can have multiple ribosomes on a
single mRNA. This occurs in both eukaryotes and prokaryotes. This allows proteins to be
made faster.
coupled transcription / translation - This occurs in prokaryotes only.
Their DNA doesnt have all the intron / exon crap that we eukaryotes do.
(Theres no room for it in them anyway!) Since there is nothing to splice out, you
can go straight from transcription to translation. The mRNA peeling off of the DNA in
prokaryotes can go immediately hook up with their ribosome friends (polyribosomes, if you
want to!)
Diphtheria toxin inactivates translocase in eukaryotes
DO WHAT???
RNA processing in eukaryotes - now THIS is complicated
stuff
introns and exons - when pre-mRNA peels off of the DNA, theres a bunch of
extra crap in there that doesnt really code for anything. So, you gotta take them
out. You WANT to keep IN the EXONS, but take OUT the INTRONS. (introns removed to make
mRNA from primary transcript)
capping of eukaryotic mRNA on the 5 end - when mRNA is first formed, a
modified version of a guanine (G) nucleotide is attached. This seems to serve two
important functions:
It helps protect the mRNA from hydrolytic enzymes that will destroy it instantly.
It is the signal sequence I was talking about earlier when I was talking about the
small ribosomal sub-unit "attach-to-me" sign.
poly A tail on 3 ends of eukaryotic mRNAs - On the OTHER end, when
its all done, anywhere from 30 to 200 adenine nucleotides are added on, again to
protect the mRNA and (scientists are still trying to figure out) maybe regulate protein
synthesis in facilitating the export of mRNA from the nucleus to the cytoplasm.
snRNPs - pronounced "snurps"! - taking out them INTRONZ during RNA
splicing
snRNPs are short for small nuclear ribonucleoproteins.
They play a key role in taking out the introns out of the pre-mRNA just after it is
transcribed from the DNA. (the pre-mRNA is technically called hnRNA, which stands for
heterogeneous nuclear RNA, because the it is a mix of intron and exons kept within the
nucleus. (REMEMBER: IT TAKES PLACE IN THE NUCLEUS)
snRNPs contain snRNA, small nuclear RNA. A bunch of these snRNPs join together
to help form a spliceosome. It cuts at specific points in introns and immediately joins
the surrounding exons. A clearer picture can be found on figure 16.21 on page 316.
Ribozymes - these are RNA molecules that function as catalysts to help splice
other types of RNA transcripts like tRNA and rRNA.
Differences between eukaryotic and prokaryotic gene expression
|
Prokaryotic
Gene Expression |
Eukaryotic
Gene Expression |
Antibiotics and their
tactics / effects |
|
|
Transcription / Translation
Process |
In prokaryotes, mRNA
transcribed from the DNA can be directly used with out further processing |
In Eukaryotes, the
pre-mRNA (hnRNA) must first be processed to take out the introns and splice together the
exons. |
Regulatory proteins |
|
|
Transcription Units |
|
|
How to Translates |
|
|
|
|
|
antibiotics and their tactics / effects
coupled transcription / translation?
processing of mRNAs before translation
eukaryotic genes tend to have many binding sites for regulatory proteins at each
promoter (complex)
operons vs. single genes per transcription unit
polycistronic (prokaryotes) vs. monocistronic (eukaryotes) mRNAs
Chapter 17 (p. 344 and onward)
Regulating gene expression
negative (repressor protein) vs. positive (activator protein) regulation
Negative Gene Regulation - In this, there is a molecule, or combination of
molecules, that will inhibit the transcription of a certain portion of a DNA molecule,
thus producing more of the enzymes/proteins coded by the mRNA. Its basically turning
the gene on and off with a little switch. (ex. The trp operon and the lac
operon)
Positive Gene Expression - In this case, the molecule added will INCREASE the
transcription of a segment of a DNA molecule, so in the end, there will be shit loads more
of the stuff. This can also be thought of as the volume control of the DNA. (ex. CAP)
constitutive (constant) vs. inducible/repressible
All this is basically pointing out is that some genes are constitutive, meaning
that they are in the ON position and being transcribed ALL THE TIME. In the other case,
certain molecules regulate the gene expression, so it may or may not be on, depending on
the production of repressor or activator proteins. (examples of this coming right up!)
E. coli lactose (lac) operon
What an OPERON? - It is the sum of the structural genes, operator, promoter, and
the entire stretch of DNA sequence that is regulated, etc. (If you dont understand
this, read page 344 until you do
)
promoter - sequence of the DNA where the RNA polymerase can bind to in order to
begin transcription of the DNA
operator - The "switch" segment of the DNA. If an active
repressor is present in the cell, it will then bind to this operator. The operator and
promoter of the DNA are right next to each other. If the active repressor binds, then the
RNA polymerase can not bind and therefore, the DNA is not transcribed.
structural genes (Z, Y, and A)
lac Z - This gene sequence codes for the enzyme b
-Galactosidase, which is the primary enzyme responsible for catalyzing the reaction which
breaks down the disaccharide lactose (milk sugar) into glucose and galactose (remember all
the sugar stuff the Dr. Massarachia taught? Well, here it is again!)
lac Y - This gene sequence codes for the enzyme permease, which helps to
bring in the lactose into the cell. (More stuff from Massarachia! Remember the cell
membrane? Its really hydrophobic while the lactose molecule is really hydrophilic.
So, it wont go in unless you do endocytosis and all that jazz
, right?)
lac A - To tell you the truth, scientists have absolutely no idea what
the hell this is for, but Ill keep ya posted on it, so dont worry.
The CAP site and the CAP protein
Well, theres a small tiny site that is part of the promoter called the CAP
binding site. When an activated CAP protein binds here, then the DNA is transcribed
TONS after, so more of the enzymes needed for the processing of lactose is made.
When are activated CAP proteins made? CAP protein are all over the cell, but they need
to be activated by "cyclic adenine mono-phosphate", otherwise known as cAMP.
These are cousins of the well-known ATP. Well, if the E. Coli bacteria is starving,
it will have low ATP levels (IT NEED NRG) and high cAMP levels (thats just the way
it is!) These cAMPs activate the CAP proteins and the process is sped up.
In the same way, if there is a lot of ATP being made because of the break down of
lactose,, the cAMP levels fall, and not so much of the lac stuff is made
(youre not hungry any more - go do something else)
The lac repressor
Of course, I already talked about this. This is just more nifty info. Part of the DNA
in front of the promoter is responsible for coding for the protein that acts at the
repressor for this operon. This gene is the lacI gene.
Note that the enzyme product of the lacI gene is initially ACTIVE (unlike the trp
operon). So, this operon, under normal conditions, is repressed. It is rendered
inactive when its inducer (Allolactose, an isomer of lactose) binds with the protein. So,
since lactose IS there, why not start making the stuff that helps to break it down?
catabolic operon, inducible
As a result, this is said to be a catabolic operon, because when it is on, it
promotes the break down of a lactose molecule. This is also said to be inducible,
because the gene is always turned off and must be induced to turn back on
through the presence of another molecule (Allolactose).
The E. coli trp operon
This is basically very similar to the lac operon except for a couple of very
significant differences.
anabolic operon, repressible
Unlike the lac operon, an inducible operon that broke down stuff, the trp
operon is responsible for making the polypeptides that make up the enzymes for tryptophan
synthesis.
Heres the situation: E. Coli needs tryptophan to survive, REGARDLESS. It
usually takes it up from the outside world, but if there isnt any, it has a way to
produce tryptophan from stuff that it finds around the place. (Just like making an MTV
logo from household items)
Normally, tryptophan that is present acts as the co-repressor, latching itself into the
repressor that keeps the operon in the off position.
When tryptophan isnt present and the E. Coli needs to make some,
then there isnt anything to bind to the repressor protein, so it is inactive, so the
RNA polymerase can come in and start transcribing the DNA. That is why this operon is
called a repressible one: Because the gene is always off and must be repressed
(with the ABSENCE of tryptophan) to turn back on to make tryptophan
Eukaryotic gene expression (see Figure 18.5)
multiple enhancer / regulatory elements at promoter
Just know that there are specific sequences that come before the promoter (where the
RNA polymerase binds to the DNA to being transcription) where certain "transcription
factors" bind. When the RNA polymerase is ready to transcribe, it makes a DNA loop
that touch the transcription factor and the RNA polymerase together. This enhances
something, but scientists still dont know what.
There are multiple numbers of enhancers upstream from the promoter. Each with a
different factor. People are still researching.
pre-mRNA processing (splicing, capping and 3-poly A tail)
Info on these is up at the top. Read it there
Cancer and Mutagenesis (Chapters 16 & 18)
Mutation
Mutation - a change in the nucleotide sequence of DNA (it really screws
everything up because the proteins get read wrong, etc.)
The TYPES of mutations:
Point mutation - it just happens at a certain point in the DNA à chemical changes in just one nucleotide in a single gene
Insertion - an extra nucleotide is added in somewhere along the line. No big
deal, right? WRONG!!! Theres a reading frame shift that occurs, and it will
seriously mess EVERYTHING up.
Deletion - here, instead, a nucleotide is missing from the sequence. Just about
the same result as insertion.
Translocation - These are just TOTAL screwups that occur during gametogenesis
and gene regulation. Entire portions of the DNA are moved around, so not only are wrong
amino acids made due to a reading frame shift, but theyre also in the wrong order in
the polypeptide chain to begin with! AHHHH!!!!
Ames test for mutagenic compounds
The man w/ the plan. His name is Bruce Ames, and he created a test that measured the
mutagenic strength of various chemicals (ability of these chemicals to mess up your DNA
badly)
You take the suspected mutagen and put it in some Salmonella. This is special Salmonella
though, because it needs histidine to survive. Well, place it in some stuff that
DOESNT have it. Then add rat liver extract for good measure (for biological
activation and to simulate cool stuff).
If there are tons of colonies present in the end, then that means that something in
your "suspected mutagen" reengineered the DNA of the Salmonella so that
they could make histidine to survive. (Dr. Benjamin said that they tried this w/ Marcchino
cherries which were coated with Red Dye #2 à it
failed
It doesnt matter because I HATE CHERRIES ANY WAY!!!)
If there arent many / any colonies present, then its alright. (I
guess
)
Sources of mutation
X-rays
X-rays are a really high energy form of electromagnetic radiation (this is where
chemistry starts seeping back into biology
scary, isnt it?) The X-rays can
break apart DNA, cause deletions, and create translocations. It basically has enough power
to blow the DNA to smithereens! (It can take apart H-bonds REALLY easily.)
UV light
UV light attacks your pyrimidines (remember? T and C) When harmful UV light hits
them, it can rearrange the bonds in two adjacent pyrimidines so that they bond to each
other, and not to the DNAs complementary strand. These are called pyrimidine dimers,
and the fuck everything up.
Chemicals
Basically, this is what the Ames test tested for. Certain chemicals can alter your DNA
through reaction to modify bases (like add on bromo- group to every other nucleotide) or
even miss-pair bases (so now a T will fit with a G, etc.)
Spontaneous
Not much on this. (I dont think he really talked about it.) I guess its
just when things just dont go right and everything is spontaneous. (Hmm
who
knows?)
Consequences of mutations
germ line cells, genetic defects - When mutations mess up gametes, genetic
defects can be produced in the offspring. (Chances are that the offspring wont live.
Too bad
L )
somatic cells, cancer, tumors - When mutations mess up body cells that you
already have, you get cancers and tumors. It really sucks. Then you die
L .
Cancer
Epidemiology - studying the relationship between a disease and its cause.
Epidemiologists graph and study all cancers across the US, graphing how many cases per
a given year, and then correlating that with causes that might have caused them.
For example, 20 or 30 years after the rise of smoking and looking "cool",
everyone came down with lung cancer. Before that time (when no one smoked) lung cancer
didnt even exist. There are also similar correlations between:
Meat & intestinal (colon) cancer,
Fat intake & breast cancer, and even
Cancer vs. Age (This will make a lot of sense as you keep reading - Its the whole
"Check a box" idea.)
CANCER, CANCER, CANCER (words to know: )
virus - what the hell is THIS doing here?
oncogenes - cancer causing genes (things that you DONT want - these code
for the continuous, uncontrolled growth of whatever cell its in)
tumor suppressors - genes that code for proteins that normally help prevent
uncontrolled cell growth (cancer). Anything that messes up these genes could help the
onset of cancer.
cancer - DUHHH
you should know this by now
"Uncontrolled growth
of cells
they just keep going, and going, and going
"
RSV & Peyton Rous (1910)
RSV stands for the Rous Sarcoma Virus, a retrovirus containing RNA that
actually has the ability to change the sequence of DNA in a cell. It contains oncogenes,
which will kill a chicken (injected with it) almost immediately. (It is an example of an
acute transforming virus.)
It was also found that if you injected extract from the dead chicken, with out any
cells at all in it, into another chicken, it would die to. (It was an instant killer.)
transforming retroviruses - they carry oncogenes (those cancer causing ones)
that can reengineer your DNA so that theyll have them (and eventually, youll
get cancer!)
proto-oncogenes - genes found normally in animal cells that normally regulate
cell growth, cell division, and cell adhesion. These are cousins of oncogenes, and can
readily be changed into one via gene amplification, chromosome translocation, gene
transposition, and possible point mutations. (You probably wont need to know all
that - I just put it in for the hell of it).
Regularly, the proteins coded by the proto-oncogenes directly alter the division of the
cell. If the proto-oncogene is turned into an oncogene, then it can directly alter
anything. In this way, there is no stopping an oncogene, so it acts in a dominant fashion.
oncogene products found in nucleus (DNA binding
proteins), in the cytoplasm and in / around plasma membrane
The loss of tumor suppressor genes is responsible for
the genetically inherited increased risks of cancer. In this way, since you have to take
over two of them, they are recessive?
Chapter 19
Plasmids
Plasmids are small replicons found in primarily in bacterial cells
They carry valuable, but generally non-essential genes
antibiotic resistance
some catabolic pathways
Restriction enzymes - Enzyme that recognize a specific sequence of DNA and cut it up
(remember BIOLAB? J )
It is used as bacterial defense against invading DNAs (bacteriophage) (it chews up
foreign DNA)
It can be used to cleave DNA at specific sequences (e.g. G/AATTC for Eco R 1)
It often creates "sticky ends" on cleaved DNA
Cloning
pSC101 - first chimeric DNA (cloned segment in plasmid) by Cohen and Boyer - 1973
(dont need to know names or plasmid here)
cloning procedure
cleave target DNA and plasmid vector with restriction enzyme
use DNA ligase to tie ends of plasmid to target DNA fragment (insert DNA into plasmid)
transform recombinant plasmid into E. Coli cells
screen for cells containing recombinant plasmid (antibiotic resistance, lacZ
activity screening - blue/white)
applications of recombinant DNA technology
production of pharmaceuticals (especially proteins such as insulin, interferon, human
growth factor, TPA, etc.)
herbicide resistant plants (using Ti plasmid and Agrobacterium)
virus resistant plants
"insecticidal plants"
transgenic farm animals (particularly those making pharmaceuticals)
piggyback vaccines (harmless viruses which code for surface antigens from disease
causing viruses or other organisms)
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