Term
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Definition
| DNA is longer (thousands-millions bp) than RNA (22-10,000+bp) |
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Term
| Compare the general structure of a DNA strand and an RNA strand |
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Definition
DNA: double-stranded and either circular or linear
RNA: generally single stranded and linear |
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Term
| How are nucleotides important as cofactors? |
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Definition
| Levels of ATP/AMP regulate metabolic pathways, cAMP and cGMP are second messengers, nucleotides are essential coenzymes |
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Term
| List the nucleotides by how they bind to each other |
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Definition
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Term
| What are the two pyrimidines? |
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Definition
Thymine, Cytosine
(They have a 'y' in their names) |
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Term
| What are the two purines? |
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Definition
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Term
| Describe the bond between a nucleotide and the pentose |
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Definition
| A %beta;-Glycosidic bond between the 1'C on the pentose and the nucleotide |
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Term
| Which nitrogen in a pyrimidine binds to ribose? Which on a purine? |
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Definition
Pyrimidine: the N1 binds
Purine: the N9 binds |
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Term
| What distinguishes the structures of thymine and uracil? |
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Definition
| Uracil is lacking a methyl group on its Carbon-5 |
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Term
| What differentiates a ribonucleotide and a deoxyribonucleotide? |
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Definition
| Ribonucleotides have another -OH on the 2'C, leaving it susceptible to hydroxide attack and cleavage under basic condition |
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Term
| What is the difference between a nucleotide and a nucleoside? |
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Definition
| A nucleoside lacks phosphate groups attached |
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Term
| What is on the 5' end of a DNA strand? What is on the 3' end? |
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Definition
Phosphate at 5' end
Hydroxyl at 3' end |
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Term
| What sequence is DNA read and synthesized? |
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Definition
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Term
| How does AZT work to inhibit HIV? |
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Definition
| An N3 (azide group) on the 3' carbon of AZT binds to HIV reverse transcriptase, preventing chain elongation |
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Term
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Definition
A+G= C+T
Number of As, Gs, Ts, Cs varies by species but does not vary in an individual |
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Term
What bases have two H-bonds between them?
Which have three? |
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Definition
A-T is 2 bonds
C-G is 3 bonds, therefore stronger |
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Term
| Why would alternating A and T or C and G in an RNA strand be favorable? |
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Definition
| Alternating hydrogen donor/acceptor bases enhance stability |
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Term
| Very basically describe how PCR works to break DNA |
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Definition
| Heating DNA repeatedly to break H-bonds, denaturing DNA for analysis |
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Term
| What is the two-step process to reversible melting? |
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Definition
1. Slow step: A few complimentary bases randomly collide
2. Fast step: After a few pairs form, the remaining pairs rapidly form |
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Term
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Definition
| The temperature at which DNA is 50% denatured |
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Term
| Why does the thermal stability of DNA increase with a higher percentage of G and C? |
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Definition
1. It has 3 H-bonds instead of 2
2. Its base stacking (to hide hydrophobic forces) is more sterically favorable and form a helix |
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Term
| How can you distinguish the major groove from the minor groove? |
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Definition
| The groove flanked by the glycosidic bonds is the minor groove |
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Term
Who published the structure of DNA and when did they win the Nobel prize?
(doubt he'd ask this, but just in case) |
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Definition
| Watson and Crick (with help from Franklin and Wilkins), won Nobel Prize in 1962 |
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Term
| Which groove do proteins generally bind? |
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Definition
| Proteins generally bind in the major groove |
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Term
| Why is the backbone of polynucleotides more complicated than it looks in most diagrams? |
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Definition
Because of "torsion angles"
(He says that's all we have to know) |
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Term
How do bases form their anti counterparts?
Ex. syn-Adenosine vs anti-Adenosine |
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Definition
| The base rotates around the glycosidic bond |
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Term
| Because the sugar ring cannot lie flat due to the 5-carbon structure, what happens? |
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Definition
| The rings "pucker", and the C2'-endo position is preferred due to steric hindrance |
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Term
| Which has a longer Å difference between phosphates, C'3 endo or C'2 endo |
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Definition
C'2 endo is longer, 7Å between phosphate
compared to 6Å in the C3'-endo |
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Term
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Definition
The most common helix form in cells. 10.5bp/turn. C2'-endo.
(No discovered B-RNA) |
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Term
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Definition
"Dehydrated" form, coiled tightly due to C3'-endo. 11bp/turn.
dsRNA is mostly A-form, but DNA is not usually |
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Term
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Definition
Left handed (zig-zag) DNA with 12/bp turn, alternating 2'endo and 3'endo.
Function unknown. |
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Term
| What are Hoogsteen Base Pairs? |
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Definition
| Weird bindings of multiple bases to form 3 and 4 stranded structures. Allows for a triple helix. |
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Term
| Define guanosine tetraplex |
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Definition
| Binding of four guanosine in a tetromere, may be at the ends of chromosomes |
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Term
| Since RNA is single stranded, it can fold into structures. What kind of complex arrangements can form as a result? |
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Definition
| 1. Complementary segments
2. Bulges of a few uncomplementary bases
3. Internal loops with unconventional binding
4. Hairpin loops of folding-back
5. Single strand areas (about 50%) |
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Term
| What is a G•U wobble base pair? |
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Definition
| An unconventional binding between a Guanine and Uracil that often happens in complex RNA structures |
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Term
| Give some examples where secondary-structure of RNA allows the RNA to function? |
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Definition
| tRNA, Hammerhead riboxyme, and Tetrahymena Intron ribozyme are all single strands of RNA that fold unusually to create a function |
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Term
| Define the concept of semi-conservative DNA replication |
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Definition
| Newly replicated DNA molecule contains one old strand from the template DNA molecule and one newly synthesized strand |
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Term
| What reaction is catalyzed by DNA polymerase? |
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Definition
| (dNMP)n + dNTP → (dNMP)n+1 + PPi
In other words, phosphorylating an NTP for energy to add the resulting NMP to the strand of NMPs |
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Term
| How many kJ in a P-P bond? |
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Definition
| 30kJ/mol if anhydride, 14kJ/mol if ester |
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Term
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Definition
| A segment of DNA that contains the information required for the synthesis of a functional biological product (protein or RNA) |
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Term
| What is the central dogma of molecular biology? |
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Definition
| Colinearity of DNA → RNA → Protein |
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Term
| How many mRNA code for 1 peptide? |
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Definition
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Term
| What is on the inside of a nucleosome for stability? |
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Definition
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Term
| What is the difference between monocistrionic mRNA and polycistrionic mRNA? |
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Definition
| Monocistrionic mRNA has one gene → one protein, polycistrionic has multiple genes → multiple proteins |
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Term
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Definition
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Term
| What segments of RNA code for genes? |
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Definition
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Term
Describe genes in eukaryotes
(mono/polycistrionic?) |
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Definition
| Almost always monocistrionic but often segmented with introns |
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Term
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Definition
A single large DNA molecule, containing many genes
Allows for organization and ensures equal replication |
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Term
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Definition
Chromasomal DNA + RNA + proteins
The RNA and proteins allow packaging into the nucleus |
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Term
| Describe chromosome structure in the average bacteria |
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Definition
| Circular, with circular extrachromosomal plasmids independently replicating DNA molecules |
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Term
| Describe the mitochondrial chromosome |
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Definition
| Circular, encoding mitochondrial proteins and RNA. About 20,000bp, replicated each time the cell divides. |
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Term
| Are eukaryotic chromosome circular or linear? |
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Definition
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Term
| How are the locations of genes in a circular bacterial chromosome described? |
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Definition
As if the circle was a clock with 100 seconds
Each "minute" is around 40,000bp |
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Term
| Out of the entire human genome, what percent are coding exons? |
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Definition
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Term
| Describe a yeast chromosome |
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Definition
Unique gene sequences, dispersed repeats, and multiple replication origins
Also seem to have a lot of G (which form tetrads) |
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Term
| Why do humans have 700 times as much DNA as E. coli but only 10 times as much genes? |
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Definition
| Humans have a lot more introns |
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Term
| Why is DNA so tightly wound into chromatids? |
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Definition
| If you stretched out all of the DNA, it would be a mess! There is 2 meters of DNA per human cell. |
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Term
| How many chromosomes are in every normal human cell? |
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Definition
| 46 (and mitrochondrial DNA) |
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Term
| Describe the "hand" analogy used to illustrate the structure of polymerase |
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Definition
| Fingers on left, palm, and thumb on right. Palm is where the DNA passes through. |
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Term
| How many origins of replication do bacteria have? How many do humans? |
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Definition
| 1 origin in bacteria, many in humans |
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Term
| What is the "lagging strand"? |
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Definition
| The 3'→5' side of mRNA that needs to be synthesized 5'→3' in discontinuous Okazaki fragments |
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Term
| Define processivity, as it applies to polymerase |
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Definition
The number of nucleotides polymerase can add before it dissociates
Not sure if need to know-(polC is most efficient in E. coli) |
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Term
| What does DNA polymerase require? |
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Definition
| A template strand and a primer with a free 3' end to attack the α-phosphate of the next molecule |
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Term
| What is the difference between what an RNA polymerase needs and what a DNA polymerase needs? |
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Definition
| RNA polymerase doesn't need a primer |
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Term
| Describe the active site of DNA polymerase |
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Definition
| Two Mg2+ (stabilized by 3 Aspartate) that promote phosphate cleavage |
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Term
| Is DNA replication bidirectional or unidirectional? |
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Definition
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Term
| How accurate is DNA replication? |
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Definition
| VERY accurate. DNA polymerase only makes one mistake per million or 100 mil bases, plus there's repair systems. |
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Term
| What enzyme fixes errors in DNA replication while the polymerase is acting? |
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Definition
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Term
| What enzyme does "nick translation"? |
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Definition
5'→3' Exonuclease removes the RNA primers
(Ligase seals the nick) |
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Term
| What enzyme separates the two DNA strands to allow replication? |
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Definition
DNA B Helicase
(Best pick up line ever- "If I were an enzyme, I'd be DNA helicase, so I can unzip your genes.") |
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Term
| What is the function of DNA gyrase (aka Topoisomerase II)? |
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Definition
| To relieve the topological stress caused by supercoiling during replication (keeps ahead of the fork) |
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Term
| What is the function of primase? |
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Definition
| It is an RNA polymerase that synthesizes short RNA primers to initiate DNA replication |
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Term
| What are the steps of DNA replication? |
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Definition
1. Initiation (at oriC, origin)
2. Elongation
3. Termination |
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Term
| Define the DUE accessory protein |
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Definition
| DUE= DNA unwinding element, helps unravel DNA for replication |
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Term
| Define the DnaA-ATP accessory protein |
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Definition
| Uses ATP to wrap DNA into a supercoil, stress results in "melting" of DNA strand around the DUE region |
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Term
| Define the DnaB accessory protein |
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Definition
| It holds the fork open, loaded by DnaC-ATP |
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Term
| Define the DnaC-ATP accessory protein |
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Definition
| Uses ATP to load DnaB to keep the two forks open during DNA replication |
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Term
| Define the SSB accessory protein |
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Definition
| SSB= single strand binding, helps in lagging strand synthesis |
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Term
| Describe the DNA Polymerase III Complex |
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Definition
Pulls mRNA of both the leading and lagging strand in the 5'→3' direction.
Its β Clamp-loading complex has to be undone and moved to make another Okazaki
Ensures same rate and same direction |
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Term
| How does DNA ligase seal the gap between two DNA molecules? |
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Definition
1. Adenylation of DNA ligase
2. Activation of 5' phosphate in nick via phosphate attack
3. Displacement of AMP to seal the phosphate in |
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Term
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Definition
| Sequences in E. coli replication that "trap" the replication fork either clockwise or counterclockwise |
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Term
| For the last few 100 base pairs, the new chromosomes are catenated together but need to seperate. What enzyme separates them? |
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Definition
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Term
| In bacterial DNA replication, does the polymerase move down the DNA? |
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Definition
| No, it's more like the circle of DNA is pulled through the two polymerase complexes, one on either side |
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Term
| How many origins of replication per chromosome do humans have? |
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Definition
| Multiple- spaced 30,000 to 300,000 bp apart |
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Term
| Where does termination of replication occur in humans? |
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Definition
| Telomeres (with unique sequences that let the polymerase know to stop) |
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Term
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Definition
| An antifungal drug that interferes with nucleotide synthesis |
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Term
| Define adenosine arabinoside |
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Definition
| An antiviral agent that interferes with nucleotide synthesis |
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Term
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Definition
| An anti-HIV drug that interferes with nucleotide synthesis by inhibitng reverse transcriptase |
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Term
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Definition
| An antibiotic that inhibits DNA-directed DNA polymerase |
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Term
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Definition
| An antibiotic that interferes with DNA gyrase |
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Term
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Definition
A drug that inhibits Herpes simplex. Its structure is like guanine, but missing the ribose.
An infected cell will phosphorylate it, then it is preferentially added to DNA, inhibiting any further base addition |
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