Term
| During which phase of the cell cycle is the genome replicated? |
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Definition
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Term
| How much DNA do cells in G2 stage of their cycle have compared to cells in G1 phase? |
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Definition
|
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Term
| How can you sort out cells in G1 phase from cells in G2 phase? |
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Definition
| Use a fluorescence activated sorter and dye that binds to DNA quantitatively. Since cells in stage G2 have twice as much DNA they will glow twice as bright. |
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Term
| What chemical reaction does DNA polymerase catalyze? |
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Definition
| A nucleophilic attach by the 3' OH group of the growing chain on the alpha phosphate of the incoming dNTP. |
|
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Term
| What do DNA polymerases need in order to polymerize? |
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Definition
| all 4 dNTPs, Mg 2+, a template strand, and a primer with a free OH. |
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Term
| What special ability does the enzyme "terminal transferase" have? |
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Definition
| The ability to add random junk to the 3' end of DNA without a template. |
|
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Term
| What special ability does the enzyme "terminal transferase" have? |
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Definition
| The ability to add random junk to the 3' end of DNA without a template. |
|
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Term
| What does DNA polymerase kinda look like? |
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Definition
| A hand with fingers, a thumb, and a palm. |
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Term
| What type of activity does DNA polymerase alpha have? |
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Definition
|
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Term
| Does polymerase alpha have high or low processivity and fidelity? |
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Definition
|
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Term
| What tasks does polymerase alpha do? |
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Definition
| Lagging strand synthesis and possibly repair. |
|
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Term
| What type of activity does polymerase beta have? |
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Definition
|
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Term
| What task does polymerase beta do? |
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Definition
|
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Term
| What activity does polymerase gamma have? |
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Definition
| polymerase and 3' to 5' exonuclease activity. |
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Term
| What tasks does polymerase gamma do? |
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Definition
| It lives in the mitochondria and replicates mtDNA. |
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Term
| What type of activity does polymerase delta have? |
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Definition
| polymerase and 3' to 5' exonuclease activity. |
|
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Term
| Does polymerase delta have high or low processivity and fidelity? |
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Definition
|
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Term
| What tasks does polymerase delta do? |
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Definition
| Leading strand synthesis and repair. New evidence suggests it also works on the lagging strand. |
|
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Term
| What activity does polymerase epsilon have? |
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Definition
| polymerase, and exonuclease in both directions. |
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Term
| What tasks does polymerase epsilon do? |
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Definition
| Lagging strand synthesis and possibly repair. |
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Term
| How many known DNA polymerases do humans have? |
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Definition
|
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Term
| xerodoma pigmentosum can result from defects in which DNA polymerase? |
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Definition
| eta, which can synthesize new DNA from a damaged strand. |
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Term
| What is the sliding clamp made of? |
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Definition
| 3 units of PCNA (proliferating cell nuclear antigen) that form a ring around the DNA. |
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Term
| How can a sliding clamp be modified |
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Definition
| ubiquitination or phosphorylation may attract different polymerases, |
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Term
|
Definition
| Replication protein A: single strand binding protein. |
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Term
| 2 reasons that DNA polymerase manages to usually add the correct nucleotide: |
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Definition
-It requires less energy of activation than adding the wrong one.
-Its active site comfortable accomodates a purine and a pyramidine. |
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Term
|
Definition
| They are units of replication controlled by an origin of replication. |
|
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Term
| What does telomerase use as a template for DNA? |
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Definition
| A small guide RNA that is part of the enzyme. |
|
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Term
| How does methylation protect DNA? |
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Definition
| It is protected from endonucleases that are designed to destroy foreign DNA such as bacterial DNA which has a different methylation pattern. |
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Term
| Define epigenetics and give an example. |
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Definition
| Any heritable influence on gene activity that does not change the DNA sequence. eg. methylation |
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Term
| Where does Eukaryotic DNA tend to get methylated? |
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Definition
| Cytosines that are upstream from guanines. Sometimes there is a region of CpG's 5' to a gene and the methylation of these is related to genetic activity. |
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Term
| What can be the consequence of improper methylation of CpG islands? |
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Definition
| Tumors can occur if the tumor suppressor gets suppressed or the wrong gene gets overexpressed. |
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Term
| How much similarity does site-specific recombination require? |
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Definition
| Not much; just a limited stretch of it. |
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Term
| Name 3 biological roles of recombination. |
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Definition
-Generating new gene/allele combinations via crossover during meiosis
-generating new genes (eg. immunoglobulin rearrangement)
-DNA repair |
|
|
Term
| How does distance between 2 genetic markers influence recombination frequency? |
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Definition
| Further apart=more frequent recombination. |
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|
Term
| When is the most common time for recombination to occur in eukaryotes? |
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Definition
|
|
Term
| What is non-reciprocal recombination? |
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Definition
| It's where the end result of a homologous recombination event is that the gene on one chromosome gets changed and the other gets repaired back to its original state. The result is that the 2 copies of the gene are now the same. |
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Term
| What type of recombination deletes large portion of immunoglobulin during the B cell differentiation process? |
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Definition
| Site specific recombination |
|
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Term
| During intrachromosomal recombination, how are things rearranged if the recombination sites are in opposite orientations? |
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Definition
| The segment in between gets reversed. |
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Term
| During intrachromosomal recombination, how are things rearranged if the recombination sites are in the same orientation? |
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Definition
| A piece gets looped out. It may or may not re-integrate later. |
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Term
|
Definition
| A site where a DNA base is missing, but the backbone is still there. |
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Term
| What happens if you damage a phosphate group in the DNA backbone? |
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Definition
|
|
Term
| What happens to cytosine if it gets deaminated? |
|
Definition
| It gets turned into uracil. |
|
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Term
| What can happen to a DNA molecule if a sugar in its backbone is damaged? |
|
Definition
| Its shape can get messed up. |
|
|
Term
| How many abasic sites get generated in a normal cell per day? |
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Definition
|
|
Term
| What type of damage can UV light cause to DNA? |
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Definition
| Two side by side nucleotides, TT or TC, can form links between their bases. TT seems to be the most discussed. |
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Term
| If a base substitution is a transition, what has been substituted for what? |
|
Definition
| A purine for a purine or a pyrimidine for a pyrimidine. |
|
|
Term
| If a base substitution is a transversion, what has been substituted for what? |
|
Definition
| A purine for a pyrimidine or vice versa. |
|
|
Term
| How does a frame shift mutation occur? |
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Definition
|
|
Term
| Name 2 base analogs that can cause mutations. |
|
Definition
| Aminopurine or bromouracil |
|
|
Term
| What does methyl methane-sulfonate do to DNA? |
|
Definition
|
|
Term
| Name 2 intercalating agents. |
|
Definition
| acridine orange and ethidium bromide |
|
|
Term
| What is an intercalating agent? |
|
Definition
| It's something that wedges between the bases of double stranded DNA. |
|
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Term
| What types of radiation can cause double stranded breaks in DNA? |
|
Definition
| X-ray or Gamma are common kinds of ionizing radiation that will do that. |
|
|
Term
| What does UVA light do that's dangerous? |
|
Definition
| Generates oxygen free radicals. |
|
|
Term
| What does UVB light do that's bad? |
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Definition
|
|
Term
| When do cells pause in the cell cycle and check for DNA damage? |
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Definition
|
|
Term
| What bad things can happen if damaged DNA is replicated without repair? |
|
Definition
| Mutations leading to cancers, heritable disease, or cell death. |
|
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Term
|
Definition
| It performs direct repair on DNA. It can recognize DNA damage, bind, and convert it back to the correct base. |
|
|
Term
| What does 06-alkyl-guanine-DNA alkyltransferase do? |
|
Definition
| Direct DNA repair. It removes alkylation from DNA. |
|
|
Term
| What is base excision repair? |
|
Definition
| It's where long or short patches of damaged bases are removed, leaving abasic sites. These are then removed and replaced with proper nucleotides using the other strand as a template. |
|
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Term
| Which type of DNA repair is used for bulky lesions such as TT dimers caused by UV? |
|
Definition
| Nucleotide excision repair.(NER) |
|
|
Term
| Which enzyme recognizes damage requiring base excision repairs? |
|
Definition
| Xerodoma Pigmentosum C (XPC) |
|
|
Term
| How big a piece of DNA gets cut out during base excision repair? |
|
Definition
|
|
Term
| Which polymerase fills in the gap during mismatch repair after the mismatched base has been removed? |
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Definition
|
|
Term
| What are two mechanisms of fixing double strand breaks? |
|
Definition
| Homologous recombination and non-homologous end joining. |
|
|
Term
| What are the 2 options if a cell can't fix DNA damage? |
|
Definition
-Cell death
-Lesion bypass repair |
|
|
Term
| What is polymerase eta particularly good at fixing? |
|
Definition
|
|
Term
| What does polymerase zeta do? |
|
Definition
| It does lesion bypass repair by adding pretty much random nucleotides. On the bright side, it can fix just about anything. |
|
|
Term
| How long is an average unwound human chromosome? |
|
Definition
|
|
Term
| What is the diameter of DNA? |
|
Definition
|
|
Term
|
Definition
| A histone with DNA wrapped around it. |
|
|
Term
| Are histones basic or acidic? |
|
Definition
|
|
Term
| How much DNA wraps around a histone? |
|
Definition
|
|
Term
| A histone octamer consists of which bits? |
|
Definition
2 of each of the following:
H2A
H2B
H3
H4 |
|
|
Term
| What are possible histone modifications? |
|
Definition
| N terminal tail may be methylated, phosphorylated, acylated or ADP ribosylated. |
|
|
Term
| What does an octomer of histones look like? |
|
Definition
|
|
Term
| What are the minimum features of a chromosome? |
|
Definition
-Telomeres
-origin of replication
-centromere |
|
|
Term
|
Definition
| It's where the spindle fibres attach and separate the duplicated chromosomes during meiosis. The DNA in this area has a highly repetitive sequence element. |
|
|
Term
| What is special about histones in the centromere region? |
|
Definition
| They have a special H3 substitute called CENP-A that can bind kinetochore proteins to which the mitotic spindles attach. |
|
|
Term
| What happens to the attraction between histones and DNA if the histone gets acetylated? |
|
Definition
|
|
Term
| What enzyme removes acetyl groups from histones? |
|
Definition
| HDAC (histone deacetylase) |
|
|
Term
| What functions do telomeres serve? |
|
Definition
-allow the cell to tell ends of chromosomes from broken DNA.
-provide cells with a way to 'count' cell divisions because they shorten each s phase |
|
|
Term
| What is expressed in replicatively immortal cells that is not expressed in regular somatic human cells? |
|
Definition
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