trait
particular characteristic
Which elements make up the macromolecule of DNA?
carbon, nitrogen, oxygen, phosphorous, and hydrogen
What
... [Show More] is the structure of DNA?
phosphorylated ribose sugar (deoxy ribose) backbone with a nitrogenous base (guanine, adenine, cytosine, thymine) two strands joined together through hydrogen bonds form a double helix
What type of bond joins two nucleotides?
phosphodiester bond
nucleotide
a nucleic acid with a phosphorylated ribose sugar and a nitrogen base, triphosphate
nuclein
viscous substance isolated from nuclei, discovered by Miescher and later found to be DNA
nitrogen base
a carbon-nitrogen ring structure that is part of a nucleoside
deoxyribose
ribose without a hydroxyl group on the carbon in position 2 on the sugar ring, with a hydroxyl group on the third carbon which is important for phosphodester bond formation
The. sequence is the ________ of nucleotides.
order
nucleoside
ribose sugar (unphosphorylated sugar) + nitrogenous base, adenosine, guanosine, cytidine, thymidine
purine
adenine, guanine (think Ag gold is pure, still has ring formation) double ring structure
pyrimidine
cytosine, uracil, thymine (think CUT, ring structure has been "cut") single-ring
Does adenine thymine pairing or cytosine guanine pairing have three hydrogen bonds?
cytosine + guanine (think c&g closer in alphabet, closer in space)
Which carbon on the deoxy ribose sugar forms a phosphodiester bond? Which catbon is the phosphate group attached to? What is this process called?
the third carbon, the fifth carbon, DNA polymerization
What is the difference between B-form, A-form, and Z-form DNA?
B- hydrated, 10.5 steps, right handed
A- dehydrated, 11 steps, right handed
Z- torsional stress, 12 steps, left handed
What is the directionality of DNA? What is the directionality of the complementary strand? What is the orientation of DNA?
5' to 3', 3' to 5', antiparallel
hybridization
formation of hydrogen bonds between two strands of DNA
Will single strands of DNA with identical sequences hybridize?
No, due to antiparallel orientation of DNA
denaturing agents
formamide, urea, mercaptoethanol, displace hydrogen bonds and separate two DNA strands
major groove and minor groove
two phosphate sugar backbones arranged as specific distances from each other, site of interaction with proteins or recognition sites
DNA synthesis occurs in which direction?
5'-->3'
DNA polymerase reads the template strand in which direction?
3' to 5'
What replication model describes the key to maintaining the sequence of nucleotides in DNA through new generations?
semi-conservative model of DNA replication
Does the leading strand or lagging strand have Okazaki fragments?
lagging strand because DNA polymerase reads in the 3'-->5' direction and the template strand is in the 5'-->3' orientation leaving jumps between sections of DNA replication
What is the orientation of the leading strand?
3' to 5'
DNA synthesis cannot proceed if a deoxyribose 3'hydroxyl oxygen is not available. Which enzyme provides the preceding base?
primase
What is the function of helicase?
unwinds the DNA double helix for replication
holoenzyme
polymerase II functions with a larger assembly of proteins to perform priming, initiation, regulation, and termination
replisome
complex of multiple proteins involved in replication
RNase H
the enzyme that helps to remove the RNA primer during DNA replication
DNA polymerase III
In charge of synthesizing nucleotides onto the leading end in the classic 5' to 3' direction.
DNA pol I
Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides
pyrophosphorolysis
The reverse of a nucleotide polymerization reaction, in which pyrophosphate reacts with the 3'-nucleotide monophosphate of an oligonucleotide, releasing the corresponding nucleotide triphosphate.
Klenow fragment
large protein fragment of DNA pol I with 5' --> 3' polymerase activity, loses exonuclease activity
mutations
copying error in DNA replication that results in base changes
nick translation
the phenomenon in which DNA polymerase uses its 5' to 3' exonuclease activity to remove a region of DNA and at the same time replaces it with new DNA in the 3' to 5' direction. Occurs when there are errors in base pairing or can be used for labeling DNA products in experiments for hybridization analysis
DNA ligase
enzyme that chemically links DNA fragments together in DNA replication, Okazaki fragments, or nick translation
Pyrimidine dimers are caused by
ultraviolet light
Terminal transferase
a template independent polymerase that catalyzes the addition of deoxynucleotides to the 3' hydroxyl terminus of DNA molecules
hybrid vigor
the characteristic of offspring that are stronger than their parents - produced through crossbreeding
Gametes
a mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote.
endonuclease vs exonuclease
Endonuclease cleaves Phosphodiester bonds within the polymer, exonuclease cleaves phosphodiester bonds at the ends of the polymer
restriction enzymes
an enzyme produced chiefly by certain bacteria as a basic immune system, having the property of cleaving DNA molecules at or near a specific sequence of bases.
Type II restriction enzymes
used most frequently in the laboratory - do not have inherent methylation activity in the same molecule as the nuclease activity. Can leave sticky ends or blunt ends.
Are type II restriction enzymes found on eukaryotes?
No, prokaryotes only
Which restriction enzymes have methylation activity?
Type I, II, IV, IIG
What is the basis for paternity testing and specimen identity?
restriction enzyme fragment analysis
What is the advantage of blunt ends over sticky ends?
blunt ends can be joined together and do not have to match while sticky ends must match exactly in order to hybridize or converted to blunt ends through exonuclease activity or polymerase activity
CRISPR
an adaptive immune system for bacteria and archaea, clustered interspaced short palindromic repeats and case protein which recognizes foreign DNA and keeps record of previous infections
PAM
Protospacer Adjacent Motif, necessary sequence found adjacent to the protospacer in the target DNA, discriminates target from self
Oligonucleotides
segments of nucleic acid that are 50 nucleotides or less in length
Why is it important in DNA isolation techniques to eliminate or inactivate exonuclease and endonuclease activity?
because these enzymes degrade DNA
DNase I
enzyme that digests DNA
Why is DNA stored in TE buffer?
TE buffer chelates ions which are needed for nuclease activity, to stabilize DNA
topoisomerase
corrects "overwinding" ahead of replication forks by interconverting isomers or relax supertwised DNA
Gyrase
untangles DNA through ds breaks; separates linked rings of DNA (type II topoisomerases)
Methyltransferase
enzyme that methylates newly synthesized DNA strands and are involved in mismatched repair
What is the difference in methylation between prokaryotes and eukaryotes?
prokaryotes use methylation to distinguish between self and non-self, nearly all sites are methylated or hemimethyalted. Eukaryotes use methylation in specific regions to promote or prevent gene transcription
Recombination
the genetic process by which one chromosome breaks off and attaches to another chromosome during reproductive cell division (crossing over)
Conjugation
genetic recombination in bacteria F+ (fertility factor)-->F- bacteria which then becomes F+ through a filamentous bridge
Transduction
bacteriophage serves as a carrier of DNA from a donor cell to a recipient cell by infecting bacterial cells
Transformation
(genetics) modification of a cell or bacterium by the uptake and incorporation of exogenous DNA, Griffith experiment, basis for recombination in labs
Protease
enzyme that digests protein
Ribonuclease
digests RNA [Show Less]