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62 Cards in this Set
- Front
- Back
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What molecules make up a DNA strand?
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A phosphate backbone, Deoxyribose sugar, and Nitrogenous bases- Adenine, Cytosine, Guanine, Thymine
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How do the nucleotides pair?
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DNA:
adenine-thymine Guanine-cytosine RNA: Adenine-uracil Guanine-cytosine |
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How man rings do pyrimidines have?
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They are single ringed.
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Which base pairs are Pyrimidines?
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Cytosine, Uracil, and thymine
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Which base pairs are Purines?
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Adenine and Guanine
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How many rings do Purines have?
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2 rings
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What's the difference between a nucleotide and a nuceloside?
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Nucleosides lack a phosphate group. They are composed of a sugar and a base.
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Which carbon does DNA lack a carbon?
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It lacks the 2' OH group which RNA has, which makes it less stable.
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What is Chargoff's rule?
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*A=T and A=U
*C(triple bond) G in both *Example: in DNA, you have 20% Adenine. How much Guanine is there? You have A=T, so 20=20 = 40. 100-40= 60 60/ 2 = 30% Guanine |
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Are the 2 DNA strands anti-parallel and complimentary?
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Yes
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What is the most prevalent form of DNA in cells? and is most prevalent in biological systems?
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B-form DNA
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What handed helix does B-form DNA have?
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Right handed helix
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Is A-form DNA more compact than B-form DNA?
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Yes
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What handed helix is A-form DNA?
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Right handed helix
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What handed helix is Z-form DNA?
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Left-handed helix
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Which base pairs is the Z-form rich in?
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Rich in G-C regions which mean it's more stable and harder to break the bonds because G-C has 3 hydrogen bonds. It has a higher Tm.
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What type of bond is found in the phosphate backbone? What type of bonds are found between base-pairs?
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Covalent bonds are found between phosphate backbone and hydrogen bonds are found between base-pairs
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What is Tm?
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The temperature at which half the DNA is unwound/ denatured.
1. More GC base pairs = high Tm 2. More AT base pairs= lower Tm |
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DNA electrophoresis: Why does it run towards the red +?
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Because the phosphate is negative and DNA will migrate towards the positive electrode.
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What does RTR stand for?
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Run towards red
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What are the steps in DNA replication in prokaryotes?
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1. Helicase: unwinds DNA
2. SSBP 3. Gyrase/ Topoisomerase: stabilizes DNA, holding for spin control--now helix is open 4. Primase: takes away (put down) the RNA primer 5. DNA Pol III: add bases 5' to 3' 6. DNA Pol I: Removes the RNA primer 7. Ligase: links Okazaki fragments |
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What are topoisomerases? (such as Gyrase)
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-Enzyme that helps relieve tension from DNA that occurs when it is unwound.
-10.5 BPs per turn is relaxed. Most DNA in cells is NOT relaxed. |
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What is positive supercoiling?
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overwound
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What is Negative supercoiling?
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underwound
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What is Heterochromatin?
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+Highly coiled
+Usually inactive +Located at centromeres and telomeres +Not transcribed |
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What is Euchromatin?
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+Non-coiled, active
+Euchromatin is a lightly packed form of chromatin (DNA, RNA and protein) that is rich in gene concentration, and is often (but not always) under active transcription. Euchromatin comprises the most active portion of the genome within the cell nucleus. 92% of the human genome is euchromatic. |
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What is a Nucleosome?
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A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores.This structure is often compared to thread wrapped around a spool.
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What is a histone?
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Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA).
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What does Methylation do to a gene sequence?
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+deactivates/ silences genes
+decrease in gene activity |
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Chromosomal puff:
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+active area on a chromosome that is being transcribed
+usually in euchromatin +highly repetitive short sequences repeated thousands to millions of times +Polytene chromosomes are over-sized chromosomes which have developed from standard chromosomes and are commonly found in the salivary glands of Drosophila melanogaster. Specialized cells undergo repeated rounds of DNA replication without cell division (endomitosis), to increase cell volume, forming a giant polytene chromosome. Polytene chromosomes form when multiple rounds of replication produce many sister chromatids that remain synapsed together. |
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epigenetics:
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+DNA and environment interacting and how they have effects on one another
+epigenetics is the study of heritable changes in gene activity that are not caused by changes in the DNA sequence; it also can be used to describe the study of stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable. |
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DNA polymerase I
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removes primer & needs free 3’ OH
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DNA polymerase II
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main proof reading & repair
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DNA polymerase III
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main synthesis, elongation
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Polymerase do not initiate chain synthesis, only Poly I does 5’ to 3’ exonuclease activity
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True
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What does DNA polymerase alpha do?
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primase activity
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what does DNA Polymerase delta do?
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lagging strand synthesis
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what does DNA Polymerase Epsilon do?
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leading strand synthesis
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What does DNA polymerase beta do?
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repair
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DNA polymerase epsilon is equivalent to which DNA polymerase in prokaryotes?
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DNA polymerase 3
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What are the licensing factors of DNA synthesis?
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A licensing factor is what allows the DNA to be replicated. If there are no licensing factors on the replication fork, DNA replication will not occur.
eukaryotes=ARS (Autonomously Replicating Sequence) prokaryotes=oriC (origin of replication) |
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What is an anti-codon?
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a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA.
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What is a codon?
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a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule
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What is a Spliceosome?
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is a large and complex molecular machine found primarily within the nucleus of eukaryotes. Spliceosome is assembled from snRNPs and protein complexes. Spliceosome removes introns from a transcribed pre-mRNA, a kind of primary transcript. This process is generally referred to as splicing. [1] Only eukaryotes have spliceosomes and metazoans have a second spliceosome, the minor spliceosome.
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What is the Origin of replication?
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The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated.[1] This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
DNA replication may proceed from this point bidirectionally or unidirectionally. The specific structure of the origin of replication varies somewhat from species to species, but all share some common characteristics such as high AT content (adenine and thymine are easier to separate because they form only 2 hydrogen bonds whereas guanine and cytosine form 3). The origin of replication binds the pre-replication complex, a protein complex that recognizes, unwinds, and begins to copy DNA. |
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What does acetylation do?
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activates genes
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What does DNA-A protein bind to?
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-Several 9-mers
-DnaA is a protein that activates initiation of DNA replication in prokaryotes.[1] It is a replication initiation factor which promotes the unwinding of DNA at oriC.[1] The onset of the initiation phase of DNA replication is determined by the concentration of DnaA.[1] DnaA accumulates during growth and then triggers the initiation of replication.[1] Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of oriC. |
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Proteins bind to the ARS to flag areas to be replicated in G1?
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True
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What is Geminin?
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+involved in negative control of replication
+signals to the cell to NOT replicate it |
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What are MCM & DCT?
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+licencing factors
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What kinases?
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puts a phosphate group on an enzyme
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What is Telomerase?
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a reverse transcriptase
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Code: DNA
Codon: mRNA Anticodon: tRNA |
true
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Template strand:
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+Making RNA from DNA
+The 3’ to 5’ strand of DNA +The RNA is synthesized in the 5’ to 3’ direction |
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What is Transcription?
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+DNA to RNA
+Euk: happens in nucelus +Prok: happens in cytoplasm +RNA transcribed from coding strand/template strand/3’ to 5’ of DNA +RNA is single stranded |
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What is a TATA box?
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+In eukaryotes
+In promoter region +In prokaryotes: Pribnow box @ -10 |
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Prokaryotes transcription info:
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+Sigma subunit allows the RNA polymerase to recognize and bind specifically to promoter regions
+Or Reading Head +Sigma recognized +Beta provides the catalytic active site Look at slide 19 |
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Eukaryotes transcription info:
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+RNA polymerase II is the mRNA producer
+Introns = non coding regions of DNA +Google ISIS chrons rx |
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Translation is?
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mRNA to protein
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Initation in translation consists of?
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+Shine-Dalgarno sequence in prokaryotes
+Kozak sequence in eukaryotes |
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Slide 5 table: (Just info)
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IF1-stabalizes 30s subunit
IF2- binds fmet-tRNA to 30s-mRNA complex; binds to GTP and stimulates hydrolysis IF3-binds 30s subunit to mRNA; dissociates monosomes into subunits following termination |
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Percentage of RNA is in what form?
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mRNA=5%
rRNA=85% tRNA=1-% |
