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41 Cards in this Set
- Front
- Back
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what are the three componets of a nucleotide?
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a nucleobase, pentose sugar in the beta conformation, and a phosphate group.
phosphates groups can vary from one to three |
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what is a nucleoside?
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a nucleobase attached to a sugar without the phosphate
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What are the 2 linkages that link the components of the nucleic acid together? What breaks them down?
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between the base and the sugar - N-glycosidic linkage
broken by Glycosylases between the phosphate and the sugar phosphoester linkage broken by nucleases |
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what is the structure of the polynucleotide chain?
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-it has alternating phosphate and carbohydrate backbone
-it is polar -nucleotides are linked by phosphodiester linkages -written 5' to 3' |
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what is Chargaff's rule?
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in double stranded DNA, # of A = # of
T; # of C = # of G |
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how do 2 polynucleotide chains pair?
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-they are antiparallel to each other
-held together by complementary base-pairing -A pairs with T/U -G pairs with C -bases are interior; phosphate sugar backbone to the exterior |
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how many hydrogen bonds are there between G and C?
How many hydrogen bonds are there between A and T/U? which is stronger? higher melting point? |
G and C -> 3
A and T/U -> 2 therefore G and C are stronger |
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why is the molecule in a helical structure?
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because successive base pairs are rotated by a definite angle - forming a sprial staircase or double helix. ;
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what is speical about the major groove? how is it formed?
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the major groove contains rich chemcial inforamtion that allows sequence specific interactions of proteins with DNA
it is formed because N-Glycosidic bonds in base pairs are not diametrically opposite giving rise to major and minor droves in the paired structure |
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What are 2 main factors that stablize the paired structure?
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Stacking interactions‐ combination of hydrophobic forces and van der Waals int
Provides stability to the double helix Hydrogen bonds between bases from opposite strands, determines specificity |
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what is the hyperchromic shift?
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when nucleic acids are denatured, there is increased absorbance at 260 nm.
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what is the transition temperature?
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this is the temperature at which 50 percent of the helix is denatured, this depends on the base composition.
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what is the helix rotation for the following forms of the DNA:
B, A and Z? |
B - right
A - right Z - left |
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in the B form of DNA what is the BP/turn?
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10
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in the B form of DNA what is the rotation/BP?
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36 degrees
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in the B form of DNA what is the helix lenght and diameter?
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helix length - 3.4 nm
helix diameter - aprox 2.0 nm |
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describe the minor and major grove for the B form of DNA?
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the minor grove is narrow and intermediate depth, the major grobve is wide and intermediate depth
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what are plasmids?
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plasmids are found in prokaryotes, circular, they do not encode for essential genes, but encode special functions such as resistance to antibiotics
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the winding of DNA around its own axis can form three dimensional structures called topoisomers, what 2 kinds of structures can be created?
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plectonemic
solenoidal note: only covalently closed DNA or linear DNA with constrained ends have supercoiling; breaks in one or both strands will result in loss of the supercoil - relaxed DNA |
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What are the properties of negative supercoils?
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negative supercoils twist the DNA about its axis in the opposite direction from the right - handed double helix.
-the DNA is underwound which favors further unwinding of the duplex DNA |
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what are the properties of positive supercoils?
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positive supercoils twist the DNA in the same direction as the turns of the right handed double helix;
-the DNA is overwound (helix is wound more tightly) |
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what is the structure of Bacterial DNA ?
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bacterial DNA is negatively supercoiled, covalently closed circular DNA, no structural proteins (histones)
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what does the enyzme Gyrase do?
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it introduces negative supercoils in closed circular DNA, thus relaxing positively coiled DNA
-it is ATP dependent -Aids in DNA packing, replication, and transcription -target of antibacterial drugs - ciprofloxacin and novobiocin |
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what form is eukaryotic DNA found in?
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it is negatively supercoiled forming solenodial supercoils, linear DNA constrained by structural proteins called histones
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what are the 5 histones? what are they made of? what is the DNA histone complex called?
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the 5 histones are H1, H2A, H2B, H3, H4.
they are basic proteins rich in Lys and Arg; the DNA histone complex is called chromatin; under the EM looks like beads on a string |
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what is the definition of Nucleosome?
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DNA wrapped around histone cores is the fundamental organizational unit of chromatin
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what makes up the chromatin core?
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(H2A, H2B, H3, H4 ) x 2 to form an octamer
150 bp wrap around each core in aprox 2 turns |
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what does H1 histone do?
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there is a space between nucleosomes 30 to 50 bp long,
nucleosomes are complexed together with H1 histone |
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what effect does chromatin have on the organism?
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it is a dynamic structure; the histones have N-terminal tails which can be modified by phosphorylation, methylation, or acetylation; these modifications alter chromatin accessibility and function resulting in chromatin remodeling and gene expression
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what is the structure of RNA?
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it is unbranched polymeric molecules composed of riobonucleotides joined by phosphodiester bonds
the sugar is a ribose, bases are A, G, C, U the helical structure is in the A form -it is mostly single stranded, strands loop back to form intra-strand base pairing which defines structure -paired regions are anti-parallel with respect to each other |
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does chargaff's rule apply to RNA?
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no, except with double stranded RNA virus where A pairs with U and G pairs with C
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is RNA considered stable?
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no, inherently unstable, undergoes base catalyzed cyclization forming 2' and 3' cyclic phosphodiester
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which bases does tRNA have?
how long is it? |
is has pseudouridine, dihydrouridine and thymine
it is 75 to 85 bases long making up 10 to 15% of total cellular RNA |
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what is the purpose of tRNA?
what does it look like? |
it serves as an adaptor molecule carrying specific amino acids to the site of protein synthesis; there is one tRNA per AA;
it forms a 2d cloverleaf, with extensive intra-strand base-pairing forming stems and loops. |
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how does the AA attach to the tRNA?
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the 3' end of all tRNAs end with the sequence CCA;
the AA is attached to the 2' C or 3' C of the sugar of the last nucleotide -an AA attached to tRNA is aminoacyl-tRNA in the charged state |
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what is the form of rRNA in prokaryotes? in Eukaryotes?
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in prokaryotes - 23S, 16S and 5S
in euk. 28S, 18S, 5.8S, and 5S |
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what does rRNA do?
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rRNA are associated with proteins to form ribosomes. most abundant in the cell;
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what is one main difference between pro and euk mRNA?
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pro. mRNA is polycistronic (single transcript codes for more than one protein) while euk mRNA are monocystronic
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how is euk. mRNA capped?
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euk - mRNA is capped at the 5' end by 7 methylguanosine triphospate attached to the C5' of the first nucleotide and has a poly(A) tail at the 3' end
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what is the general structure and function of mRNA?
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least abudant- variable size with a short half life - very little intra strand base pairing; primary sequence directs the sequence of AAs in proteins
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what is miRNA?
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this micro RNA found only in eukaryotes; regulatory RNA; non coding; ~250 identified in
humans; serve widespread functions in post‐transcriptional gene silencing by inducing target RNA degradation or translational inhibition. Recent research has demonstrated that miRNAs are crucial regulators of gene expression, affecting a wide variety of cellular functions including development, proliferation, differentiation, and apoptosis. May find application in gene therapy in the future. |
