133 notecards = 34 pages (4 cards per page)
The basic unit of nucleic acids
Nucleotides are made up of 3 parts:
1. phosphate group
The Central Dogma (3 parts)
DNA makes RNA (transcription) and RNA makes protein (translation)
a macromolecule composed of repeating units called nucleotides
The 4 nitrogenous bases that make up DNA neucleotides
How do the pairs line up to form the double stranded DNA helix?
Guanine (purine) always pairs with cytosine (pyramidine) and adenine (purine) always pairs with thymine (pyramidine).
How is the DNA helix held together?
It is covalently held with hydrogen bonds
The double helix unwinds and then complementary nucleotides are matched up to the exposed bases on both strands of the original DNA.
the original strand of DNA used to match up nucleotides
the enzyme that pulls the DNA double helix apart into two strands
Why is DNA replication called semiconservative?
Because both new double-stranded DNA molecules contain one original strand that was preexisting and one new strand. The process of DNA replication is referred to as semiconservative replication.
What happens after the DNA has replicated?
the cell divides, forming two daughter cells, each containing identical genetic information
provide the instructions for making specific proteins
The bridge between DNA and protein synthesis
How is RNA similar to DNA?
It is similar in all ways except its sugar is ribose and in place of thymine, there is uracil
the information stored in a DNA molecule is copied into RNA molecules
Depending on the gene, transcription makes one of three possible kinds of RNA:
1. messenger RNA (or mRNA)
Messenger RNA carries the coded information blueprint (the message) from the DNA to the ribosome for the making of proteins.
Ribosomal RNA forms ribosomes, the site of protein synthesis
Transfer RNA bring amino acids (specific amino acids dictated by the sequence of codons) to the ribosome where they are incorporated into proteins
decoding the language of nucleic acids and converting it into the language of proteins to make protein
The rules that govern translation
What does the order of the bases in mRNA specify?
The order of the bases in mRNA specifies the order of amino acids for a particular protein.
a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis
How are the bases on the mRNA molecule are "read" or translated?
As sequential codons. Three DNA nucleotides will be transcribed into one RNA codon. And one RNA codon will be translated into one amino acid.
The key players in the process of translation are what?
ribosomes and transfer RNA (tRNA)
a three-nucleotide sequence that will match up to a complementary codon on the mRNA to form amino acids
How is tRNA structured?
tRNA carries a specific amino acid at one end, and at the other end it has an anticodon
What is the function of the ribosome?
The function of the ribosome is to direct the orderly binding of tRNAs to codons and to assemble the amino acids into a chain, ultimately producing a protein
Translation begins when?
when the mRNA attaches to a ribosome
What are the 6 steps in translation?
1. The small subunit of the ribosome binds to the mRNA, (to that message) followed by the large subunit and gets it lined up so that it can find the start codon
a group of genes that are regulated in a coordinated fashion
operons are either ______ or ______
the genes are in the "off" mode until an inducer is present which acts to induce transcription
the genes are transcribed until they are turned off, or repressed
A change in the base sequence of DNA. A change in DNA will change the mRNA transcribed. When this altered mRNA is translated into protein, the incorrect base may cause the insertion of an incorrect amino acid in the protein
Sometimes mistakes are made during DNA replication
The chances of mutation can increase when cells are exposed to radiation or certain chemicals
What happens to DNA when exposed to UV light?
When DNA is exposed to UV light, any adjacent thymines in the DNA molecule may covalently bond together forming thymine dimers. Excessive UV exposure causes large numbers of thymine dimers to form in skin cells. Unrepaired damage may cause proteins that regulate the cell cycle to be made incorrectly, and this may eventually lead to skin cancer
3 ways genetic information is shared between two bacterial cells or between a virus and a bacterial cell
so-called naked DNA in solution is taken up by a bacterial cell
requires direct contact between two living cells. A sex pilus connects two cells allowing the transfer of DNA
bacterial DNA is transferred from a donor cell to a bacteriophage
recipient cell inside a virus that infects bacteria
In the three processes of sharing genetic info between bacteria, if the donor DNA is integrated into the recipient's DNA, the resultant cell is called a recombinant
In DNA, the synthesis happens from the _____ to the _____ end
Why do we have three phosphate groups in DNA?
because these are high energy bonds and we need energy to power this reaction
In DNA, the phosphate groups are attached to which end?
the 5 carbon end
In DNA, what is on the 3 carbon end?
an OH hydroxyl group
In a polymer of nucleotides, how are the carbons counted?
The chimney is the 5 carbon, and then you count 1 through 4 on each corner going clockwise to the right.
When we are synthesizing RNA or DNA, where do we add the nucleotide?
We always synthesize (in RNA or DNA) by adding energy charged nucleotide onto the 3 prime end of the growing chain. We start at 5 carbon end (at chimney) and add the nucleotides to the 3 carbon end (where the OH is). The chain grows this way.
What catalyzes DNA or RNA synthesis?
DNA polymerase catalyzes this
Where does DNA polymerase get its energy to catalyze synthesis?
Gets energy from breaking off phosphates
Helicase unwinds DNA and forms a _________
in DNA replication, at the origin of replication, the two strands of DNA separate, serving as templates for making new strands. This separation forms a replication bubble
the replication bubble grows in two directions (above and below), forming to replication forks (one to the left and one to the right)
one new strand in the replication fork that is built continuously
the other new strand in the replication fork that is on the bottom that lags behind and is built in pieces
relieves the strength of the twisting forces once helicase has separated the DNA strands
one piece of replicated DNA on the lagging strand
builds a new strand of DNA on either the leading or lagging strand by adding DNA nucleotides one at a time
What does DNA polymerase need before it can begin building a new strand of DNA?
A primer to tell it where to start. DNA adds a primer made out of RNA synthesized by RNA primase. Just one on leading strand. Many on lagging strand that are removed by another form of DNA polymerase after copying and replaced with DNA.
joins the Okazaki fragments on the lagging strand together
portion of the genome that contains an origin and is replicated as a unit
nucleoside triphosphate (NTP)
A molecule containing a nucleoside bound to three phosphates. Nucleotide derivatives are necessary for life, as they are building blocks of nucleic acids and have thousands of other roles in cell metabolism and regulation. NTPs generally provide energy and phosphate group for phosphorylations.
deoxynucleoside triphosphate (dNTP)
The nucleoside triphosphates containing deoxyribose. They're the building blocks for DNA (they lose two of the phosphate groups in the process of incorporation)
What is a key thing to remember about transcription?
The chemistry of this, the key thing to remember about transcription is that we don’t need to synthesize a copy of all of our DNA. We only need one small region.
Tells pRNA polymerase where in the DNA to use to start transcription.
a protein needed for initiation of RNA synthesis. tells it where to start and what direction to point in
sense strand or template strand
in transcription, only one strand of DNA acts as a template
nonsense strand or non template strand
The strand not transcribed
Once it attaches to the promotor via the sigma factor, where does RNA polymerase start copying from?
Everyone before the +1, all the promoter sequence is still part of the gene. We consider this to be upstream (all those in negative numbers).
tells RNA polymerase where to stop transcribing
the transcribing of DNA to RNA from the 5 to 3 prime direction, with a small transcription bubble
What happens when polymerase encounters the terminator?
When polymerase encounters the Terminator code it dissociates from DNA and releases mRNA
Ribosomes are made up of what two parts?
1. small subunit
Codons are what three things?
1. unambiguous - each codon = amino acid
UAA, UAG, UGA
Polymerase Chain Reaction (PCR)
is used to make multiple copies of a desired piece of DNA enzymatically
How do we get our primer to run a PCR?
From sequences on the outer edges of the gene
4 steps of PCR
1. Start with solution containing template DNA, synthesized primers, and an abundant supply of the 4 dNTPs
Why doesn't heat denature our Polymerase enzyme?
Thermus aquaticus bacteria (Taq Polymerase)
Why do we use PCR testing? Name 5 possible reasons.
Identify presence of:
How did we get to the three domain system?
Carl Woese wanted to find evolutionary relationships and find a gene that was common to everyone but wouldn’t change too quickly. He decided to look at RRNA genes that form ribosomal RNA involved in Parkinson's. Ribosomes are different in bacteria and in euk cells and that difference is conveyed in the genes.
What does a change in gene do to the bacteria?
It alters its genotype. This can have a profound impact on bacteria because they are haploid. Because of this, a change in genotype can easily alter the observable characteristics of an organism, its phenotype.
How do we generate diversity and variety in bacteria who are all haploid?
changes in as little as one nucleotide (one base in the DNA). Those point mutations will change the sequence of bases we see in MRNA when we transcribe the gene and may or may not result in a change in the end product in the primary sequence of our protein.
Universal code is made up of ________
What do codons do?
each codon codes for an amino acid
What is the advantage of having multiple condons that code for an amino acid?
We can accommodate changes in certain spots without changing end product of amino acids.
Change in genotype (genetic sequence) results in change in protein primary structure
most common type. GCT to GCA which changes RNA synthesis which still gives us ARG because the universal code is redundant. We have a change in the gene sequence but the end product is exactly the same. Doesn’t change phenotype.
Change in Genotype results in termination of protein synthesis
Change in Genotype results in change in protein primary structure
if it randomly happens
radiation or exposing it to something to mutate
Bacteria that can repair the problem if they are exposed to radiation. If they are able to repair then they are a revertant through the process of reversion. They had a mutation and then they fixed it and went back to what they had before
kill off the bacteria
Some bacteria can change what they look like on the plate
you only notice mutation under certain environmental conditions
All mutations are rare. Why?
because all cells have repair mechanisms. We can assess our genetic sequence and see if we have mismatched when synthesizing.
4 causes of mutations caused by environmental conditions
What does UV do that causes mutations?
Causes covalent bonding between adjacent thymine bases forming thymine dimers which distorts DNA
Name 3 reactive oxygen species and how do they cause mutations?
How do the alkylating agents cause mutations?
Largest group of chemical mutagens
How do intercalating agents cause mutations? What is an example?
They are planar molecules that are flat and bind to DNA and inserts itself in between the bases. Is an intercalating agent. When it does this, it distorts how the bases all stack up on themselves and it makes it look like there is a space where a base should go. So DNA polymerase adds a base where you did not have one before in the middle of your strand. They are carcinogens because you start making all these changes to the DNA and you can have cells growing out of control.
The Ames Test
Based on observation that most carcinogens are also mutagens
3 methods of repair for mutations
1. photoreactivation (light repair)
Enzyme uses visible light to break covalent bonds between bases
Endonuclease excises damaged section
How does DNA polymerase execute mutation repair?
DNA polymerase is able to spot check as it adds one base at a time to make sure the new base fits in the proper orientation. If we add the wrong base, a G instead of a T, they don’t form the proper hydrogen bonds and it distorts the nice smooth two strands winding up perfectly in terms of sized and that is what DNA polymerase is able to sense that we are able to line up these bases so that the width is the same. If not lined up properly it wont be the same length. DNA polymerase can cut out a wrong area and try again and this reduces the rate of mutation by like 1000 fold. Doesn’t catch the environmental exposures where thiamine dimers form due to UV radiation where DNA is not able to tell what it is supposed to match up against. It solves some problems but not all problems.
series of enzymes that add methyl groups to the backbone all the time in the cell. So over time we accumulate a number of methyl group tabs along the length of the DNA.
How does DNA methylation help with excision repair?
Excision repair doesn’t know which is the wrong base and which is the right base but it does know which is the old strand and the newly synthesized one based on methylation. So the default is that the old strand is the one that is right. So we replace bands on the new side when we have to with the ones that we have on the old as opposed to the ones on the new.
What catalyzes DNA methylation
separate thymine dimers using energy from visible light
Last ditch effort to bypass damage
Vertical gene transfer
Clonal process of vertical reproduction. When we go from one parent cell to two daughter cells, those two daughter cells are directly identical. No shuffling of genes. No swapping parts. One copy of everything and we are not interacting with another cell in reproduction they divide themselves in half.
Horizontal gene transfer
Bacteria can transfer genes between each other as adults. If you could go and swap genes with other people in a room that would be horizontal gene transfer.
Three Methods of Gene Transfer
1. Transduction (not covered this exam)
taking up free floating DNA from environment.
direct contact between two living cells.
Two events always occur in gene exchange
1. Donor DNA is transferred and accepted by the recipient cell
Process of integrating DNA where your new DNA and old DNA (free standing chromosome) have sequences that are really the same in terms of the series of bases and when they are the same, there is a protein the RecA Recombinase that takes these two sequences, lines them up, and swaps those sequences. Sometimes swaps them so that they are bigger. If we are able to line up some of the ends in a chromosome then we can have the chromosome with a new DNA insert and the chromosome becomes bigger. Tied up the ends and make it a part of the giant circle.
Some bacteria, not all, that have the aility to take free floating DNA from other dead cells and incorporate them into their genome.
establishes a physical bridge in between two cells through which we can transfer genetic information
F Plasmid Transfer
We start with a cell that makes a pili and one that does not. The one that has the pili and has F plasmid as an F + cell. That is our donor cell and the recipient one is F- cell. Pili forms a physical bridge in between these two cells that penetrates the cell wall. We transfer DNA from along pili from cytoplasm of one cell into the other cytoplasm of other cell. We make copy of F plasmid and transfer copy to other end and at the end of the day when the pili breaks apart we end up with donor cell and recipient cell that now has extra genetic F plasmid info and can make a pili itself so it can go and contact another cell and transfer itself. A copying method.
Rolling Circle Replication
Cut one of the strands of DNA and unwinds DNA from double helix and as they unwind DNA polymerase fills in the gap behind it and as we unwind and pull off the single stranded length of DNA that can then be fed down the pili. Like a roll of paper towels. A new roll, that one part glued on is nicking and then we pull the strand off the roll but we use the cardboard roll as a template to make new copies.
is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. Most commonly found as small circular, double-stranded DNA molecules in bacteria
high frequency recombination
Briefly explain the differences between F+, F-, Hfr, and F' cells.
An F+ cell will contain a circular plasmid seperate from the chromosome. the Hfr cell has the f factor integrated into its chromosome. in F' strains the f factor exists as a seperate circular plasmid but the plasmid carries bacterial genes that were originally part of the bacterial chromosome. The F- strain does not contain the f factor and can recieve DNA from cells that contain the F factor. (F+, Hfr, and F' )