Download AP Exam 5 Study Guide

AP Exam #5 Study Guide
DNA History







Scientists very unsure of what molecule contained genetic information.
Initially thought it was proteins.
Transforming Factor (Frederick Griffith). Trying to find a cure for pneumonia mixed
harmless live bacteria with heat-killed infectious bacteria. Found that harmless became
virulent. Called this transformation.
Avery, McCarty & MacLeod wanted to know which molecule was the transforming
factor. Injected protein into bacteria (No effect). Injected DNA into bacteria (Bacteria
were transformed into virulent). Conclusion= DNA is transforming factor.
Hershey and Chase- Confirmation of DNA as genetic material. Conducted blender
experiment with bacteriophages. 2 separate media used 35S was used in their proteins,
and 32P was used in their DNA. Infected bacteria with the labeled phages. Once the
blender was used on the broth, they noticed that the radioactive proteins were in the
supernatant (Not the pellet where the bacteria were). In the other group, they noticed
that the radioactive material was in the pellet. They concluded that the 32P was
transferred from the phages into the bacteria which were located in the pellet.
Erwin Chargaff- Came up with the base pairing rules. A and T, C and G pair up in DNA. In
humans: A= 30.9%, T=29.4%, G=19.9%, and C=19.8%
Watson & Crick- Developed the double helix model.
Structure of DNA





DNA is a double helix (Two strands). It is looks like a spiral staircase.
The two strands run anti-parallel or complimentary (mirror image).
In DNA a purine (A or G) will always pair with a specific pyrimindine (T or C). A:T and C:G
is the specific pairing. Held together with hydrogen bonds.
Phosphodiester bonds= Phosphate to sugar bonds (The outsides of the ladder), are
bonded at the 5’ and 3’ ends.
Strands run in a 5’ to 3’ prime direction on one side of the ladder, and from 3’ to 5’ on
the other side.
Replication (Copying) of DNA


Occurs during S phase of the cell cycle.
Semi-conservative replication is the widely accepted model. 1 strand becomes 2 with
each new DNA molecule receiving one original, and one new strand of DNA.











Meselson & Stahl- labled nucleotides of parent DNA strands. Confirmed semiconservative replication theory.
Replication occurs in a series of coordinated steps. Enzymes drive the process.
Step 1- DNA is unwound with an enzyme called helicase. This causes a replication fork to
form. The replication fork is stabilized with single-stranded binding proteins. There are
multiple replication forks in a DNA molecule at one time.
Step 2- New nucleotides are brought in to match up to the template strands. The new
strand is built from 5’ to 3’. It is read from 3’ to 5’, but grows from 5’ to 3’. DNA
polymerase III adds nucleotides, but it can only extend an existing molecule. In order to
place the first base, a short RNA primer is built by an enzyme primase. Once primer is
added, DNA polymerase III can start adding bases. Energy for all of this is provided by
nucleosides. These nucleosides are converted to the nucleotides that are attached to
the strand.
Since DNA can only be read from 3’ to 5’, this creates an issue due to the
complementary arrangement of the strands. The issue is that one strand replicates
faster than the other creating a leading strand, and a lagging strand. The leading strand
is replicated in a continuous manner. The lagging strand must be pieced together using
Okazaki fragments, and a spot welding enzyme called ligase.
Finally an enzyme called DNA polymerase I comes through and removes the RNA
primers, and basically acts as a proofreader checking for any errors that may have
occurred during replication.
Every time that a copy of DNA is made, the DNA strand shortens by some bases
(Telomeres)
PCR (Polymerase Chain Reaction) allows scientists to make many copies of specific
segments of DNA. Need just 1 molecule to make many copies. Making copies of DNA in
a test tube.
Items needed- Template DNA strand, DNA polymerase enzyme, nucleotides, and primer.
Primers are crucial because they bracket the specific sequence you are looking for.
Primers define the section to be cloned.
Pretty simple process- take DNA and denature it with heat (900C), then cool it and build
the DNA. Problem is that DNA polymerase is destroyed at (90 0C). Have to find another
molecule that does the same thing, but can withstand heat (Taq Polymerase). Taq
polymerase is found in hot springs bacteria.
Transcription


Transcribed DNA strand= template strand. Un-transcribed DNA strand= coding strand.
Transcription bubble is formed. RNA polymerase in charge of transcription.









Step 1 Initiation- RNA polymerase binds to a promoter sequence. Promoter is a starting
point, tells which strand to read, and the direction in which it is read. DNA is always
read from 3’ to 5’.
Step 2 Elongation- RNA polymerase unwinds DNA ~20 base pairs at a time. There is no
proofreading going on because many RNA copies are made, and there is a short shelf
life.
Step 3 Termination- RNA polymerase stops at the termination sequence. mRNA then
leaves the nucleus through the nuclear pores.
3 RNA polymerase enzymes. RNA poly 1- only transcribes rRNA, RNA poly II- only
transcribes genes into mRNA, and RNA poly III- only transcribes rRNA genes.
Once mRNA is created, there needs to be some additional work to the mRNA strand.
Cell must protect mRNA from enzymes that might break it down. It does this by adding a
5’ G cap, and a poly A tail to the 3’ end.
In eukaryotic cells, there is a lot of junk in the strand of RNA. This non-coding junk is
called an intron. Introns must be cut out, so that an RNA strand that is information only
can be formed. Information is called an exon. Introns are cut out by molecules called
spliceosomes. Introns are cut out, and then the exons are pasted back together. RNA
can also act as an enzyme (ribozyme)
Remember splicing has to be exactly accurate. No mistakes can be made in the changing
of DNA to RNA.
Frameshift Mutation- Occurs when there is an addition or deletion. Remember the
frame is read in three letter chunks called codons. One additional, or one less throws
the frame off and leads to the complete protein not being made.
Point Mutation- Happens at a point in the DNA strand where one or a few letters get
changed. Not as bad due to having the same number of letters. Protein will still get
made, it may be different from original.
Translation






Codons- blocks of 3 nucleotides that “code” for an amino acid.
This is the strongest support for a common ancestor. (All organism have a common
code).
Code is redundant- several codons code for each amino acid. (This prevents point
mutations from being overly harmful)
Start Codon- AUG (School starts in August). Ribosomes need an “on” switch to initiate
translation.
Stop Codons- UAA, UAG, UGA. Off switch for ribosomes.
mRNA- strand that gets read













rRNA- RNA that is in charge of reading mRNA
tRNA- RNA that is in charge of bringing the amino acid. tRNA is shaped like a clover leaf.
Amino acids attach at the 3’ end of the clover.
tRNA must have amino acid loaded onto it. This is done using the enzyme Aminoacyl
tRNA synthase. It is an endergonic reaction that is unstable. It needs to be unstable so
that the amino acid can easily be removed from tRNA.
Ribosomes- Site where translation occurs. It is made up of rRNA and proteins. It is
composed of 2 subunits a large and a small.
There are three sites inside the ribosome that are used for building the protein. E, P, and
A.
P Site- where the polypeptide chain grows. Amino acid is added to the chain
A Site- holds the tRNA that is next in line to drop off amino acid (On deck circle)
E Site- site where empty tRNA is released back into the cell.
Translation happens in three steps. Initiation, Elongation, and Termination
Initiation- mRNA is brought to ribosome and begins to slide through (Dollar bill in
vending machine)
Elongation- As mRNA is being read, the polypeptide chain grows.
Termination- Release factor is used (Protein) to bond to A site. Usually a water molecule
to polypeptide chain. Protein is made and translation is done.
What happens to protein once made?? It is used for any number of things depending on
the protein. Secretion, mitochondria may need it, golgi apparatus might take it and
modify it, could be a used structurally.
Viruses






Basically a package of genes in transit from one host cell to another.
A virus is considered to be emerging if it jumps host species. Ex- Ebola, SARS, bird flu,
hantavirus.
A virus is composed of DNA or RNA enclosed in a protein coat. Viruses are not cells.
They are extremely tiny needing an electron microscope to be seen.
Viruses lack enzymes for metabolism, ribosomes for protein synthesis, and need host
machinery to replicate and function.
Viral genomes can vary significantly depending on the family of virus one belongs to.
You can have double-stranded or single-stranded DNA. There are viruses that have
double or single-stranded RNA. DNA can be linear or circular depending on the virus.
Protein coat for viruses is called a capsid. It is a crystal like shell.





Some viruses have another outer covering called a viral envelope. It is a lipid bilayer that
is used to hide the virus. Viral envelope is used to provide camouflage to virus in order
to help it attack.
Two different lifecycles: Lytic and Lysogenic
Lytic- reproduce in host cell, and then spread to other parts of body by causing cell lysis
(breaking).
Lysogenic- integrates DNA into host and reproduces with cell. Most of the time, will
enter a lytic stage at some point.
RNA viruses- Called retroviruses. Contain an enzyme called reverse transcriptase. Can
change RNA into DNA. By doing this, the cell now produces viral mRNA. This in turn
causes host to produce viral proteins.
Biotechnology








DNA sequencing developed by Fred Sanger. Idea is to synthesize DNA in vitro. Creates
sequences to study genes.
Human Genome Project- US government project. Designed to map out the entire
human genome. Arms race established between government group, and private group.
All genes for humans are mapped and available online free of charge.
There are roughly 30,000 human genes.
Transposons- a piece of DNA that can move from one location to another. These genes
allow for mutations to occur within an organism’s genome.
Gene manipulation is not a new science per say. We have been controlling outcomes in
plants and animals for years. Artificial selection- choosing traits we like best, and
breeding those traits in organisms.
New science is found in genetic engineering. Instead of breeding, we manipulate the
DNA directly. In order to manipulate genes, we need a set of tools that we can use.
Basic idea is, we can cut DNA up (restriction enzymes), then paste it (ligase). Once we
have the template we want, we can copy it using plasmids, and finally we can find the
gene we are looking for through PCR (Creating multiple copies).
This stuff is used when we are talking about finding cures for diseases, producing certain
proteins that may benefit our population, and any other private uses that may be
necessary.