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A-DNA

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- is one of the many possible double helical structures of DNA. It is a right handed double helix fairly similar to the more common and well known B-DNA form, but with shorter more compact helical structure.

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Palindrom

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restriction enzymes recognize a specific sequence of nucleotides and produce a double stranded cut in the DNA. While recognition sequences vary widely, with lengths between 4 and 8 nucleotides, many of them are palindromic, which correspond to nitrogenous base sequences between complementary strands, which, when read from the 5’ to 3’ direction are identical sequences. An example of this 5' GAATTC 3'

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Plasmid

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- is a DNA molecule that is separate from and can replicate independently of the chromosomal DNA. They are double stranded and in many cases circular. They usually occur naturally in bacteria but are sometimes found in eukaryotic organisms.

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Base-stacking

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these interactions in DNA and RNA are due to dispersion attraction, short- ranged exchange repulsion, and electrostatic interactions which also contribute to stability. Again GC stacking interactions with adjacent bases tend to be more favorable. Base stacking effects are especially important in the secondary structure and tertiary structure of RNA.

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How many conformations does DNA have?

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Three: A-DNA, B-DNA, and Z-DNA

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The melting temperature of DNA is dependent on the ______ content.

answer

G+C content

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What are the differences between the three types of DNA conformation

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A, B-DNA have right handed conformation, Z-DNA is a left handed helix

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What influences DNA conformation and structure

answer

Its base sequence

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DNA renaturation is a (speed) _____ process. Why

answer

slow. Because it requires precise collisions between complementary strands at the correct positions

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Why can we measure DNA denaturation?

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Single-stranded and double-stranded DNA have typical absorbances, allowing the melting temp, for DNA denaturation to be measured.

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Double stranded DNA is stabilized by...

answer

hydrogen bonds, base staking, and ionic strength

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DNA helicases do what?

answer

they unwind the DNA helix to form single-stranded intermediates.

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True or False? Circular DNA's can form supercoils due to under- or over-winding.

answer

True

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Topoisomerases do what?

answer

They transiently break DNA to change the supercoiling.

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What is the difference between type I topoisomerase and type II topoisomerase?

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Type one branke a sinslge strand of dsDNA, whereas type II break both strands and require ATP

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What is the average weight of a nucleotide in DNA?

answer

310 Daltons

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By convention DNA is written how?

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From the 5' to 3' direction

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B-DNA

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In B-DNA the major and minor grooves are about the same depth whereas in A-DNA it has a deep major groove and a shallow minor groove

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Relaxed circle

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When supercoiled DNA molecules are treated with small quantities of DNase to introduce a single nick into one of their strands, the molecules uncoil to form these ( rings that have no superhelical turns and are unconstrained when they lie flat on a surface.

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Renaturation

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Or reannealling - this is when denatured DNA is treated in such a way that native DNA re-forms.

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Denaturation

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is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent or heat.

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Single-stranded DNA binding protein (SSB)

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Proteins that bind to single stranded DNA stabilize the transient single stranded regions that are formed by the action of helicases on double stranded DNA.

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DNA gyrase

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is an enzyme that relieves strain while double stranded DNA is being unwound by helicase. This causes supercoiling of the DNA. Many antibiotics work by attacking bacterial DNA gyrase.

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Stem-loop structure

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intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting lollipop-shaped structure is a key building block of many RNA secondary structures.

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Hairpin

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When a polynucleotide chain folds back on itself, forming intra strand hydrogen bonds to produce a double stranded segment

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Supercoil

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in a “relaxed” double helical segment of B-DNA, the two strands twist around the helical axix once every10.4-10.5 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were to be closed into a circle by joining the ends the circular DNA would contort into a figure eight called a super coil.

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Helicase

answer

are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.

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Topoisomer

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are molecules with the same chemical formula and stereochemical bond connectivities but different topologies.

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Inverted repeat

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is a sequence of nucleotides that is the reversed complement of another sequence further downstream. For example, 5’ GACTGC….GCAGTC 3’

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Topoisomerase

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these are enzymes that unwind and wind DNA, in order for DNA to control the synthesis of proteins and to facilitate DNA replications.

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Melting temperature

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the temperature at which a DNA double helix dissociates into single strands.

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Nicked circular DNA

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This is when in a circular DNA one of the strands is broken in one or both strands. Called RFII (replicating form II)

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Z-DNA

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is one of the many possible double helical structures of DNA. It is a left handed double helical stucutre in which the double helix winds to the left in a zig-zag pattern (instead of to the right, like the more common B-DNA form.)

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Antiparallel

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two molecules are antiparallel if they run side-by side in opposite directions. In DNA the 5’ carbon is located at the top of the leading strand, and the 3’ carbon is located at the lower section of the lagging strand. The nucleotides are similar and parallel, but they go in opposite directions.

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Topology

answer

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Autoradiography

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this is the study of images on an x-ray film or nuclear emulsion produced by the pattern of decay emissions from a distribution of a radioactive substance.

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Histone

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these are highly alkaline proteins found in eukaryotic cell nuclei, which package and order DNA into structural units, called nucleosomes. They are the chief protein components of chromatin, act as spools around which DNA winds, and play a role in gene regulation.

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Nucleosomes

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are the basic unit of DNA packaging in eukaryotes (cells with a nucleus), consisting of a segment of DNA wound around a histone protein core.

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Nucleosomes

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are the basic unit of DNA packaging in eukaryotes (cells with a nucleus), consisting of a segment of DNA wound around a histone protein core.

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Nucleosides are...

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a sugar group (ribose) and a base

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Nucleotides are different from nucleosides in that....

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phosphorylation of nucleosides in the sugar's primary alcohol group produces nucleotides.

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nucleosides are...
nucleotides are...

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nucleoside= sugar+base
nucleotide= sugar+base+phosphate

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What is type of bond links nucleotides in a strand of DNA

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phosphodiester bonds

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The term dyad can often be used instead of

answer

palindrome

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What technique shows that regions of animal DNA are in the Z-conformation

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Fluorescent antibody

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DNA Tm increases with ______ content

answer

% G+C

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Tm stands for

answer

melting temperature

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True of False Base stacking stabilizes double stranded DNA

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True

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Base Stacking is an example of _____ interaction

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cooperative

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True or False- Ionic strength does not influence DNA structure

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False

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True or False- DNA is in a static state.

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False

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Helicases are...

answer

motor proteins that use the energy of nucleoside triphosphates to unwind DNA

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What type of chemicals denature DNA without breaking phosphodiester bonds?

answer

Alkali such as sodium hydroxide

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Topoisomerases do what?

answer

catalyze the conversion of one topoisomer into another

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Type II topoisomerases need what in order to convert one topoisomer into another

answer

ATP

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Bacteria use what to introduce negative supercoils into covalently closed circular DNA

answer

DNA gyrase

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