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70 Cards in this Set

  • Front
  • Back
DNA is a unit of ____.
Inheritance.
DNA is a polymer of:
Nucleotides.
Where would you find circular DNA in a person?
Mitochondria.
How long has DNA been around?
4.6 billion years.
What are the four nitrogenous bases in DNA?
Adenine, Thymine, Guanine, Cytosine.
Which DNA bases are purines?
A/G
Which DNA bases are pyrimidines?
T/C
What's a nucleoside?
A N base with a pentose sugar.
What's a phosphodiester bond?
A bond between nucleotides. A phosphate attaches the 3' carbon of one sugar to the 5' carbon of the next sugar.
Which end of DNA is the 5'?
The end with a free phosphate group.
Which end of DNA is the 3'?
The end with a free hydroxyl group.
When we read the genetic code, we read from __ to __.
5' to 3'.
What's a nucleoside analog and what is it good for?
It's when a nucleoside lacks a free 3' hydroxyl. A phosphodiester bond can't be made and the strand can't be elongated. Useful in restricting the replication of cancer and viruses.
How many H bonds form between C and G?
Three.
How many H bonds form between A and T?
Two.
What is Chargaff's rule?
# of Pyrimidines=# of Purines
A+G=C+T since A=T and G=C.
What function do major and minor grooves serve?
They are loading docks for DNA-binding regulatory proteins. Drugs can also bind there.
How does dactinomycin work and what is it used for?
It intercalates into the minor groove in DNA and treats cancer.
What four factors make DNA quite stable?
H-bonding, hydrophobic nature of nucleotides, base stacking, and the negative charge of phosphates.
How many structural forms of DNA are there? What are they?
Three--A, B, and Z.
When do you see the A form of DNA? How many nucleotides per twist?
Under high salt conditions. 11 nucleotides.
When do you see the B form of DNA?
It's the common, normal form. Most condensed--10 nucleotides.
When do you see the Z form of DNA?
It's rare.12 nucleotides and a left-handed helix.
How long would DNA be if it weren't condensed?
A meter.
What are the DNA binding proteins and what do they do?
Histones (H1, H2A, H2B, H3, H4). Multi-class, small, positive proteins that bind DNA.
What is a nucleosome?
A complex of histones.
How many times is DNA wrapped around a nucleosome?
Twice.
What is a nuclear scaffold?
A collection of nucleosomes.
What's a centromere?
The region of DNA near the center of a chromosome.
Telomeres and centromeres have important roles in ____ and ____.
Cell division and DNA replication.
What are polymerases?
Enzymes involved in DNA synthesis.
Do polymerases make an exact copy or a complementary copy of each strand?
Complementary. Always complementary.
What's the origin of replication?
The starting point of DNA synthesis. It's made up of specific and unique nucleotide sequences.
What does DnaA protein do?
It recognizes A-T rich nucleotide sequences and separates the strands there to begin DNA replication.
What do single-stranded DNA-binding (SSB) proteins do?
They keep the ssDNA from re-forming dsDNA. They also protect the ssDNA from ssDNA-cleaving nuclease.
What good is ssDNA-cleaving nuclease?
It attacks viral DNA, which is single-stranded.
Where does DNA helicase bind? What does DNA helicase do?
It binds to ssDNA near the replication fork. It unzips the neighboring dsDNA.
What's the difference between Type I and II Topoisomerase?
Type I cuts one strand of the double helix to remove supercoils. Type II cuts both strands.
How do quinolone antibiotics work? What's an example of one?
They target topoisomerases. Ciprofloxicin is an example.
Does the replication fork go one way or both? Where does it start?
The fork goes both ways, and it usually starts in the middle of the DNA helix.
Which way does DNA Polymerase "read"? Which way does it "write"?
It reads the template stand from 3' to 5' and writes the new strand from 5' to 3'.
In relation to the ____, the lagging strand is synthesized in the ____ direction.
Replication fork; opposite.
What puts all the Okazaki fragments together?
DNA Ligase.
What does DNA Primase do?
It synthesizes the RNA primer to begin DNA replication.
How long is the RNA primer?
~10 nucleotides.
Is the RNA primer used in DNA replication, RNA transcription, both, or neither?
It's only used in DNA Replication.
What is the primosome and what does it do?
It is a protein complex (including primase) that displaces any proteins that have bound to unwound ssDNA (like SSB).
What accepts the first deoxyribonucleotide? What enzyme adds it?
The 3' OH of the RNA primer accepts it. DNA Polymerase III adds it.
What functions does DNA Polymerase III have?
It adds nucleotides to the growing DNA strand, and proofreads through its 3' to 5' exonuclease activity.
What's the difference between endo and exonuclease?
Exonuclease can only remove nucleotides at the end of a DNA strand. Endonucleotides remove nucleotides from the middle of the strand.
On the lagging strand, how are the many RNA primers removed?
DNA Polymerase I removes them one ribonucleotide at a time. It then fills the gap where the primer used to be. The fragments are attached by DNA Ligase.
How often are mistakes made in DNA replication that the proofreading function doesn't catch?
Only one in about 10^8 nucleotides.
How can DNA synthesis be ended prematurely and what clinical application does this have?
Incorporation of nucleoside triphosphates lacking a 3' hydroxyl on their sugar group. This is one approach to treating viral diseases like AIDS...using AZT, which is a dideoxy analog of deoxythymidine.
After removal of the last RNA primer, DNA polymerase can't synthesize DNA at the extreme ____ end of the lagging strand.
5'
What is telomerase?
It's a reverse transcriptase that is composed of protein and an RNA template.
What does telomerase add to the DNA strand and what's the point?
Adds 5'-AGGGTT-3' DNA units onto one strand. DNA polymerase completes the other strand. The "TG" strand is longer and loops back on itself and complexes with TRF1 and TRF2 proteins to protect the telomere from nucleases. I think it's kind of like a primer for the RNA primer.
In what cells is telomere length maintained?
Germ cells and transformed (Cancerous) cells. In these cells, telomerase maintains the telomere length.
What are the five functions of the five eukaryotic DNA polymerases?
Initiate DNA synthesis, Repair, Replicate mitochondrial DNA, Elongate leading strand and Okazaki fragments, and Repair.
What are four causes of DNA damage?
Chemical, radiation, faulty proof-reading, free radicals.
What are three systems to repair damaged DNA?
DNA mismatch repair, UV endonuclease, and Base excision repair.
In mismatch repair, what is the repair system called and how does it know which strand is the correct one?
It's called Mut, and it knows the parent strand is methylated.
What are the basic steps of mismatch repair?
1) Unmethylated strand is cleaved.
2) Mismatched nucleotide is removed and replaced.
3) Strand is ligated.
What causes hereditary non-polyposis colorectal cancers?
Problems with DNA mismatch repair. Specifically, a gene called MSH2. It's an autosomal dominant mutation. MSH2 is involved in directing the assembly of the multi-protein complex that cleaves the single strand with the mismatched base.
On the cellular/DNA level, why is UV exposure bad? What does it do?
Causes dimerization of adjacent pyrimidines (C & T). These dimers interfere with gene expression and replication.
What are the four steps in UV nucleotide excision repair?
1) A UV-specific endonuclease recognizes damaged DNA and nicks the phosphodiester backbone.
2) Nucleotides several bases before and after the dimer are removed by a helicase.
3) DNA Polymerase fills in the gap.
4) DNA ligase reseals the strand.
What causes Xeroderma Pigmentosum?
A genetic (autosomal recessive) deficiency in nucleotide excision repair. Results in skin damage and many cancers. Most people with this have a defect in both alleles of one of the 7 genes that comprise the nucleotide excision repair system.
What effect can hot dogs have on your DNA?
Nitrates can cause cytosine to be deaminated into uracil. This can also happen spontaneously.
What are the steps in Base excision repair?
1) Uracil is recognized by glycosylases that remove the uracil from the phosphodiester backbone, resulting in an apyrimidinic site.
2) Apyrimidinic-endonuclease removes the phosphate backbone at the AP site.
3) DNA Pase adds the correct nucleotide.
4) Ligase seals.
What are the steps in PCR?
1) Heat separates the strands.
2) Cool, add primers: 20-35 nucleotides bind to flanking region, just outside of target DNA.
3) Add nucleotides and special heat-stable DNA Pase.
4) Heat up to denature the DNA again and repeat the process.
After 25 cycles, how many copies of DNA do you have in PCR?
Over 33 million.