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MMBIO 240 Ch 4 EVANS
Chapter 4
56
Microbiology
Undergraduate 1
01/26/2011

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Term
A-DNA
Definition
- 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.
Term
Palindrom
Definition
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'
Term
Plasmid
Definition
- 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.
Term
Base-stacking
Definition
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.
Term
How many conformations does DNA have?
Definition
Three: A-DNA, B-DNA, and Z-DNA
Term
The melting temperature of DNA is dependent on the ______ content.
Definition
G+C content
Term
What are the differences between the three types of DNA conformation
Definition
A, B-DNA have right handed conformation, Z-DNA is a left handed helix
Term
What influences DNA conformation and structure
Definition
Its base sequence
Term
DNA renaturation is a (speed) _____ process. Why
Definition
slow. Because it requires precise collisions between complementary strands at the correct positions
Term
Why can we measure DNA denaturation?
Definition
Single-stranded and double-stranded DNA have typical absorbances, allowing the melting temp, for DNA denaturation to be measured.
Term
Double stranded DNA is stabilized by...
Definition
hydrogen bonds, base staking, and ionic strength
Term
DNA helicases do what?
Definition
they unwind the DNA helix to form single-stranded intermediates.
Term
True or False? Circular DNA's can form supercoils due to under- or over-winding.
Definition
True
Term
Topoisomerases do what?
Definition
They transiently break DNA to change the supercoiling.
Term
What is the difference between type I topoisomerase and type II topoisomerase?
Definition
Type one branke a sinslge strand of dsDNA, whereas type II break both strands and require ATP
Term
What is the average weight of a nucleotide in DNA?
Definition
310 Daltons
Term
By convention DNA is written how?
Definition
From the 5' to 3' direction
Term
B-DNA
Definition
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
Term
Relaxed circle
Definition
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.
Term
Renaturation
Definition
Or reannealling - this is when denatured DNA is treated in such a way that native DNA re-forms.
Term
Denaturation
Definition
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.
Term
Single-stranded DNA binding protein (SSB)
Definition
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.
Term
DNA gyrase
Definition
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.
Term
Stem-loop structure
Definition
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.
Term
Hairpin
Definition
When a polynucleotide chain folds back on itself, forming intra strand hydrogen bonds to produce a double stranded segment
Term
Supercoil
Definition
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.
Term
Helicase
Definition
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.
Term
Topoisomer
Definition
are molecules with the same chemical formula and stereochemical bond connectivities but different topologies.
Term
Inverted repeat
Definition
is a sequence of nucleotides that is the reversed complement of another sequence further downstream. For example, 5’ GACTGC….GCAGTC 3’
Term
Topoisomerase
Definition
these are enzymes that unwind and wind DNA, in order for DNA to control the synthesis of proteins and to facilitate DNA replications.
Term
Melting temperature
Definition
the temperature at which a DNA double helix dissociates into single strands.
Term
Nicked circular DNA
Definition
This is when in a circular DNA one of the strands is broken in one or both strands. Called RFII (replicating form II)
Term
Z-DNA
Definition
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.)
Term
Antiparallel
Definition
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.
Term
Topology
Definition
Term
Autoradiography
Definition
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.
Term
Histone
Definition
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.
Term
Nucleosomes
Definition
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.
Term
Nucleosomes
Definition
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.
Term
Nucleosides are...
Definition
a sugar group (ribose) and a base
Term
Nucleotides are different from nucleosides in that....
Definition
phosphorylation of nucleosides in the sugar's primary alcohol group produces nucleotides.
Term
nucleosides are...
nucleotides are...
Definition
nucleoside= sugar+base
nucleotide= sugar+base+phosphate
Term
What is type of bond links nucleotides in a strand of DNA
Definition
phosphodiester bonds
Term
The term dyad can often be used instead of
Definition
palindrome
Term
What technique shows that regions of animal DNA are in the Z-conformation
Definition
Fluorescent antibody
Term
DNA Tm increases with ______ content
Definition
% G+C
Term
Tm stands for
Definition
melting temperature
Term
True of False Base stacking stabilizes double stranded DNA
Definition
True
Term
Base Stacking is an example of _____ interaction
Definition
cooperative
Term
True or False- Ionic strength does not influence DNA structure
Definition
False
Term
True or False- DNA is in a static state.
Definition
False
Term
Helicases are...
Definition
motor proteins that use the energy of nucleoside triphosphates to unwind DNA
Term
What type of chemicals denature DNA without breaking phosphodiester bonds?
Definition
Alkali such as sodium hydroxide
Term
Topoisomerases do what?
Definition
catalyze the conversion of one topoisomer into another
Term
Type II topoisomerases need what in order to convert one topoisomer into another
Definition
ATP
Term
Bacteria use what to introduce negative supercoils into covalently closed circular DNA
Definition
DNA gyrase
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