Term
| composition of each monomer in the nucleic acid sequence |
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Definition
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Term
| this uniquely characterizes a nucleic acid |
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Definition
| the sequence of bases that forms linear information |
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Term
| depiction of DNA replication |
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Definition
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Term
| depiction of the polymeric structure of nucleic acids |
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Definition
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Term
| difference between ribose and deoxyribose |
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Definition
| deoxyribose lacks the O at the 2' C |
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Term
| depiction of the structure of ribose |
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Definition
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Term
| depiction of the structure of deoxyribose |
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Definition
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Term
| how monomers are linked in nucleic acids |
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Definition
the 3' OH group of the sugar component of one nucleotide binds to the phosphate attached to the 5' C on the adjacent sugar
3' --> 5' phosphodiester linkages |
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Term
| 2 ways RNA differs from DNA |
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Definition
1: RNA uses riboses instead of deoxyriboses
2: RNA uses U instead of T |
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Term
| one way DNA and RNA maintain stability |
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Definition
| they have a negative charge, which repels nucleophilic species that would otherwise hydrolyze tham |
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Term
| why DNA is more resistant to hydrolysis than RNA |
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Definition
| because DNA lacks the 2' OH croup |
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Term
| the backbone of nucleic acids |
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Definition
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Term
| depiction of the backbones of DNA and RNA |
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Definition
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Term
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Definition
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Term
| depiction of the pyrimidines |
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Definition
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Term
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Definition
| a unit consisting of a base bonded to a sugar |
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Term
| the 4 nucleoside units in DNA |
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Definition
-deoxyadenosine
-deoxyguanosine
-deoxycytidine
-thymidine (no, that's not a misprint) |
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Term
| why the prefix deoxy- is not added to thymidine |
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Definition
| because thymine-containing nucleotides are found only rarely in RNA |
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Term
| the 4 nucleoside units in RNA |
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Definition
-adenosine
-guanosine
-cytidine
-uridine |
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Term
| the C in the ribose/deoxyribose the nucleotide base is always attached to |
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Definition
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Term
| the type of linkage in a purine nucleoside |
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Definition
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Term
| depiction of the β-glycosidic linkage in a purine nucleoside |
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Definition
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Term
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Definition
| nucleoside joined to 1 or more phosphoryl groups by an ester linkage |
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Term
| the monomers that link to form DNA and RNA |
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Definition
| nucleoside triphosphates (this includes ATP!) |
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Term
| 5'nucleotide or nucleoside 5'-phosphate |
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Definition
| compound formed by the attachment of a phosphoryl group to C-5' of a nucleoside sugar |
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Term
| the most common site of phosphate esterfication |
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Definition
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Term
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Definition
adenosine 5'-triphosphate
[image] |
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Term
| the direction a sequence of DNA is written in |
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Definition
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Term
| depiction of the structure of a DNA strand |
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Definition
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Term
| replication of DNA is the basis for these cellular processes |
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Definition
-duplication
-growth
-ultimately, reproduction |
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Term
| distance between adjacent bases in nucleic acids |
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Definition
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Term
| how many bases does it take for the double helix to go 360⁰? |
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Definition
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Term
| side view of a DNA double helix |
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Definition
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Term
| end view of a DNA double helix |
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Definition
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Term
| some features of the Watson-Crick model |
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Definition
1: right-handed helix with antiparallel strands
2: the sugar-phosphate backbone is on the outside and the purine and pyrimidine bases are on the inside
3: bases nearly perpendicular to axis, 3.4 angstroms between adjacent bases, and 10.4 bases per turn of helix
4: diameter of the helix is about 20 angstroms |
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Term
| handednes of DNA 2bl helix |
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Definition
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Term
| diameter of DNA 2bl helix |
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Definition
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Term
| depiction of the structures of the base pairs proposed by Watson and Crick |
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Definition
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Term
| 2 forces that stabilize the DNA double helix |
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Definition
1: hydrophobic effect between bases on opposite strands
2: van der Waals forces between stacked bases, known as base stacking |
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Term
| depiction of semiconservative replication |
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Definition
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Term
| depiction of the detection of semiconservative replication of E. coli DNA by density-gradient centrifugation |
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Definition
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Term
| 2 ways to break the DNA double helix |
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Definition
-heating it to break the H bonds between the bases on opposite strands
-adding acid or alkali to ionize bases and disrupt base pairing |
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Term
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Definition
| the temperature at which half the helical structure is lost |
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Term
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Definition
| renaturation of the double helix below the melting temperature (Tm) |
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Term
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Definition
-B-DNA (this is the form you're already familiar with)
-A-form
-Z-form |
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Term
| depiction of B-form and A-form DNA |
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Definition
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Term
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Definition
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Term
| some things that can resemble A-DNA |
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Definition
-double-stranded regions of RNA
-at least some RNA-DNA hybrids |
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Term
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Definition
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Term
| why Z-DNA contains the letter Z |
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Definition
| because the phosphate backbone zig-zags |
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Term
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Definition
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Term
| comparison of A-, B-, and Z-DNA |
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Definition
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Term
| 2 types of grooves in B-DNA |
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Definition
-major groove
-minor groove |
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Term
| why B-DNA has major and minor grooves |
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Definition
| because the glycosidic bonds of a base pair are not diametrically opposite to each other |
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Term
| depiction of the major- and minor- groove sides of nucleotide pairs |
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Definition
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Term
| depiction of the major and minor grooves in B-DNA |
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Definition
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Term
| the importance of grooves in B-DNA |
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Definition
| exposing potential H-bond donors and acceptors to enable interactions with proteins |
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Term
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Definition
| the axis of a double helix being twisted into a superhelix |
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Term
| depiction of a negative superhelix |
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Definition
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Term
| the coiling of most naturally occurring DNA molecules |
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Definition
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Term
| negative supercoiling arises from... |
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Definition
| the unwinding or underwinding of DNA |
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Term
| what negative supercoiling does for DNA |
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Definition
| prepares it for processes requiring separation of the DNA strands, such as replication and transcription |
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Term
| why negative supercoiling is better for DNA than positive supercoiling |
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Definition
| condenses DNA as effectively, but makes strand separation more difficult |
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Term
| this has to happen to coiled DNA for it to be replicated |
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Definition
| local unwinding to allow separation of the 2 strands |
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Term
| what local unwinding of DNA causes to happen to the other DNA in the strand |
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Definition
| overwinding or supercoiling |
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Term
| what prevents the strain induced by overwinding? |
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Definition
| specialized set of enzymes introduces supercoils that favor strand separation |
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Term
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Definition
| the final DNA-protein complex |
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Term
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Definition
| small basic proteins that DNA tightly binds to |
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Term
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Definition
| the entire complex of a cell's DNA and its associated protein |
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Term
| the 5 major histones present in chromatin |
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Definition
-H1
-H2A
-H2B
-H3
-H4
H2A, H2B, H3, and H4 associate with one another |
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Term
| histones have strikingly basic properties because... |
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Definition
| a quarter of the residues in each histone are either arginine or lysine |
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Term
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Definition
| repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
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Term
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Definition
| comtains 2 copies each of H2A, H2B, H3, and H4 |
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Term
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Definition
the repeating units of chromatin
repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
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Term
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Definition
| smaller complex of the histone octamer and the 145-bp DNA fragment |
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Term
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Definition
| the DNA connecting core particles in undigested chromatin |
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Term
| what binds to linker DNA? |
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Definition
| histone H1 binds, in part, to the linker DNA |
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Term
| depiction of chromatin structure |
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Definition
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Term
| depiction of linked core particles |
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Definition
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Term
| depiction of a nucleosome core |
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Definition
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Term
| something that is done to histones to affect DNA transcription |
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Definition
| covalent modifications of their tails play an essential role in modulating the accessibility of DNA for transcription |
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Term
| the handedness of the superhelix that forms around the histone octamer |
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Definition
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Term
| how the protein core interacts with the superhelix that wraps around it |
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Definition
| forms contacts with the inner surface of it, particularly along the phosphodiester backbone and the minor groove of the DNA |
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Term
| how histone H1 interacts with the DNA wrapped around the core protein |
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Definition
| seals off the nucleosome at the location at which the linker DNA enters and leaves the nucleosome |
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Term
| how wrapping around histones contributes to the packing of DNA |
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Definition
| by decreasing its linear extent |
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Term
| wrapping around histones is just the 1st step in DNA packing. what's the next step? |
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Definition
it's thought to be nucleosomes being packed into 2 interwound helical stacks; folding of nucleosomes into loops
this is higher order chromatin structure |
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Term
| depiction of higher-order chromatin structure |
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Definition
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Term
| depiction of the compaction of DNA into a eukaryotic chromosome |
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Definition
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Term
| depiction of how cispaltin alters the structure of DNA |
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Definition
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Term
| why RNA can perform a host of functions that DNA can not |
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Definition
because RNA is single stranded, enabling it to adopt a variety of elaborate structures
this includes some functions that were once thought to be exclusively done by proteins |
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Term
| the simplest and most common structural motif in nucleic acids |
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Definition
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Term
| depiction of stem-loop structures |
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Definition
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Term
| some things that can happen to stem-loop structures |
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Definition
-many have paired bases
-some have mismatched or unpaired bases that can bulge out and destabilize local structure, but introduce deviations from the standard 2bl helix that can be important for higher order folding and for function |
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Term
| how some more complex structures in nucleic acids can form |
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Definition
| by way of interactions between more distant bases |
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Term
| depiction of the complex structure of an RNA molecule |
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Definition
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