Chapter 6: DNA and Biotechnology Flashcards
____________ are composed of a five-carbon sugar (pentose) bonded to a nitrogenous base.
nucleoside
How are nucleosides formed?
By covalently linking the base to the C-1’ of the sugar
carbon atoms in the sugar are labeled with a prime symbol
____________ are formed when one or more phosphate groups are attached to C-5’ of a nucleoside.
nucleotides
Nucleic acids are classified according to the ________ they contain.
pentose
If the pentose is ________, the nucleic acid is RNA; if the pentose is ____________, then it is DNA.
ribose; deoxyribose
The backbone of DNA is composed of alternating sugar and phosphate groups. It determines the directionality of the DNA and is always read from ____ to ____.
5’ to 3’
A ________ group linkes the 3’ carbon of one sugar to the 5’ ________ group of the next incoming sugar in the chain.
phosphate, phosphate
Phosphates carry a ____________ charge, thus DNA and RNA have this charge.
negative
What are the two families of nucleotides?
- purines
- pyrimidines
Purines contain ____ rings in their structure.
two
____________ contain only one ring in their structure.
pyrimidines
What are the two purines?
adenine and guanine
What are the three pyrimidines?
cytosine, thymine, uracil
What are characteristics of aromatic compounds?
- Cyclic
- Planar
- Conjugated
- 4n + 2 pi electrons
What is Huckel’s rule?
4n + 2
____________ are ring structures that contain at least two different elements in the ring.
heterocycles
The double helix of most DNA is a right-handed helix, forming what is called ________.
B-DNA
Another form of DNA is called ________ for its zigzag appearance; it is a left-handed helix. A high ____-content or a high ____ concentration may contribute to the formation of this form of DNA.
Z; GC; salt
Denatured, ssDNA can be ____________ if the denaturing condition is slowly removed.
reannealed
If a solution of heat-denatured DNA is ____________, then the 2 complementary strands can become paired again.
slowly cooled
in PCR, a well-characterized ________ DNA (DNA with known sequences) is added to a mixture of target DNA sequences.
probe
When probe DNA binds to target DNA sequences, this may provide evidence of the presence of a gene of interest. This is called ________________.
hybridization
The DNA that makes up a chromosome is wound around a group of small basic proteins called ____________, forming ____________.
histones; chromatin
2 copies each of the histone proteins form a histone core and about 200 base pairs of DNA are wrapped around this protein complex, forming a ____________.
nucleosome
What do nucleosomes accomplish?
They create a much more organized and complicated DNA.
Histones are one example of ____________ (proteins that associate with DNA). Most others are acid-soluble and stimualte processes like transcription.
nucleoproteins
A small percentage of the chromatin remains compacted during interphase and is referred to as ________________.
heterochromatin
Heterochromatin appears ________ under light microscopy and is transcriptionally ____________.
dark; silent
Heterochromatin often consists of DNA with what?
Highly repetitive sequences
Dispersed chromatin is called ____________.
euchromatin
Euchromatin appears ________ under light microscopy and contains genetically ________ DNA.
light; active
DNA replication cannot extend all the way to the end of a chromosome. What does this result in?
losing sequences and information with each round of replication
Since DNA replication cannot extent to the end of the chromosome, cells form a ____________, which is a simple repeating unit at the end of the DNA.
telomere
TTAGGG
Some of the telomere sequence is lost in each round of replication and can be replaced by the enzyme ____________.
telomerase
Telomerase is more highly expressed in which cells?
rapidly dividing cells
____________ are a region of DNA found in the center of chromosomes.
centromeres
Centromeres are composed of ____________, which is in turn composed of tandem repeat sequences that alsoc contain high ____-content.
heterochromatin; GC
During cell division, the two sister chromatids can therefore remain connected at the centromere until ____________ separate the chromatids during ____________.
microtubules; anaphase
The ____________ or ____________ ________ is a set of specialized proteins that assist the DNA polymerases.
replisome, replication complex
To begin the process of replication, DNA unwinds at points called ________ of ____________.
origins of replication
The generation of new DNA proceeds in both directions, creating ____________ ________ on both sides of the origin.
replication forks
The bacterial chromosome is a closed, double-stranded circular DNA molecule with a ________ origin of replication. Thus there are ____ replication forks that move away from each other inopposite directions around the circle, until they meet and produce two identical circular molecules of DNA.
single; two
As the replication forks move toward each other and ________ ____________ are created, the chromatids will remain connected at the ____________.
sister chromatids; centromere
____________ is the enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase.
Helicase
Unpaired DNA strands are very sticky and the free purines/pyrimidines try to seek each other out. Thus, proteins are therefore required to hold the strands apart: ________-____________ ____-________ proteins will bind to the unraveled strand, preventing both the reassociation of the DNA strands and degradation of DNA by ____________.
single-stranded DNA-binding; nucleases
As the helicase unwinds the DNA, it causes positive ____________ that strains the DNA helix.
supercoiling
Supercoiling is a wrapping of DNA on ________ as its helical structure is pushed ever further toward the telomeres during replication.
itself
like a telephone cord becoming tangled on itself
To alleviate this torsional stress and reduce the risk of strand breakage, ____ ________________ introduce negative supercoils.
DNA topoisomerases
How do DNA topoisomerases work?
They work ahead of helicase, nicking one or both strands, allowing relaxation of the torsional pressure, and then resealing the cut strands
DNA ____________ are responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand.
polymerase
The ________ strand in each replication fork is the strand that is copied in a continuous fashion. It is read ____ to ____ and synthesized in a ____ to ____ manner.
leading; 3’ to 5’; 5’ to 3’
The ____________ strand is the strand that is copied in a direction opposite the direction of the replication fork.
lagging
Because DNA polymerase can only synthesize in the 5’ to 3’ direction from a 3’ to 5’ template, small strands called ____________ ____________ are protduced from the lagging strand.
Okazaki fragments
Each time DNA polymerase completes an Okazaki fragment, what happens?
It turns around to find another gap that needs to be filled in
DNA cannot be synthesized de novo, it needs another molecule to “hook onto.” Thus, ________ synthesizes a short ____ ________ (roughly 10 nucleotides) in the 5’ to 3’ direction to start replication on each strand.
primase; RNA primer
Primers are constantly being added to the lagging strand, why?
each Okazaki fragment must start with a new primer
DNA ____________ ____ (prokaryotes) or DNA ____________ ____, ____, ____ (eukaryotes) then synthesize the daughter strands of DNA in the 5’ to 3’ manner.
polymerase III, polymerases alpha, delta, and epsilon
What are the incoming nucleotides for DNA synthesis?
5’ deoxyribonucleotide triphosphates
As each new phosphodiester bond is made, what is released?
A free pyrophosphate is released
RNA primers must eventually be removed to maintain the genome’s integrity. This is accomplished by DNA ____________ ____ (prokaryotes) or ________ ____ (eukaryotes).
polymerase I; RNase H
After the RNA primer is removed, DNA ____________ ____ (prokaryotes) or DNA ____________ ____ (eukaryotes) adds DNA nucleotides where the RNA primer had been.
polymerase I, polymerase delta
DNA ________ seals the ends of the DNA molecules togehter to create one continuous strand of DNA, e.g. closes gaps between Okazaki fragments
ligase
Mutated genes that cause cancer are termed ________.
oncogenes
Before oncogenes are mutated, they are often referred to as ________-____________.
proto-oncogenes
________ ________ genes, like p53 or Rb, encode proteins that inhibit the cell cycle or participate in DNA repair processes.
tumor suppressor
They normally function to stop tumor progression, and are sometimes called ____________.
antioncogenes
How does DNA polymerase discriminate between parent and daughter strands?
Looks at the level of methylation - template strand has existed in cell for a longer period of time, and is thus more heavily methylated
DNA ligase lacks proofreading ability, thus what?
Likelihood of mutations is considerably higher than the leading strand
UV light induces the formation of ____________ between adjacent ________ residues in DNA.
dimers; thymine
Thymine dimers are eliminated from DNA by a ____________ ________ ________ (NER) mechanism, which is a cut-and-patch process.
nucleotide excision repair
An ____________ ____________ then makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide.
excision endonuclease
The nick made by excision endonuclease is sealed by DNA ____________.
ligase
Uracil should not be found in DNA molecules; if it is, ________ ____________ repair occurs.
base excision
Once the incorrect base is recognized, it is removed by a ____________ enzyme.
glycosylase
Once a base is removed by a glycosylase enzyme, it leaves behind an ________/____________ site, also called an ________ site.
apurinic/apyridiminic, abasic
The abasic site is recognized by an ____ ____________ that removes the damaged sequence from the DNA.
AP endonuclease
____________ DNA technology allows a DNA fragments from any source to be multiplied by either gene cloning or PCR.
recombinant
DNA ____________ is a technique that can produce large amounts of a desired sequence.
cloning
Cloning requires that the investigator ligate the DNA of interest into a piece of nuclei acid referred to as a ____________, forming a ________________ ____________.
vector; recombinant vector
Vectors are usually what? What can they be transferred to?
Bacterial or viral plasmid; a host bacterium after insertion of the DNA of interest
During cloning, bacteria re then grown in colonies, and then what? How?
A colony containing the recombinant vector is isolated; conferring antibiotic resitance to the vector so that you can kill off all the other ones without antibiotic resistance
After cloning, the bacteria can be used for what?
- express the gene of interest
- lysed to reisolate the replicated recombinant vectors
____________ enzymes are enzymes that recognize specific dsDNA sequences.
restriction
Restriction enzymes are ____________, meaning that the 5’ to 3’ sequence of one strand is identical to the 5’ to 3’ sequence of the other strand.
palindromic
Restriction enzymes are isolated from ____________, which are their natural source.
bacteria
In bacteria, what do restriction enzymes do?
They selective cleave foreign DNA
Some restriction enzymes produce ________ ________, yielding sticky ends on the fragments. The vector of choice can be cut with the same restriction enzyme, allowing what to happen?
sticky ends; allowing the fragments to be inserted directly into the vector
DNA cloning can be used to produce DNA ____________ are large collections of known DNA sequences; in sum, these sequence could equate to the ____________ of an organism.
libraries; genome
How are DNA libraries made?
DNA fragments are digested randomly and cloned into vectors
Genomic libraries contain what?
Large fragments of DNA and include both coding and noncoding regions of the genome
________ (complementary )libraries are constructed by reverse-transcribing processed mRNA.
cDNA
cDNA lacks ____________ regions and only includes genes that are expressed in the tissue from which mRNA was isolated.
noncoding
____________ is the joining of complementary base pair sequences.
hybridization
PCR requires ________ that are complementary to the DNA that flanks the region of interest.
primers
In addition to specific primers, what else does PCR need?
- nucleotides (dATP, dTTP, dCTP, dGTP)
- DNA polymerase
Primers have high ____ content, as the additional hydrogen bonds in this region would confer stability.
GC
PCR also needs ____ to melt DNA part.
heat
The prferred gel for DNA electrophoresis is ____________ gel; the ____________ the DNA strand, the slower it will migrate.
agarose; longer
Gel electrophoresis is often used while performing a ____________ blot, which is used to detect the presence and quantity of various DNA strands.
southern
In a Southern blot, DNA is first cut by ____________ enzymes and then separated by gel electrophoresis.
restriction
southern blot
After cutting by restriction enzymes, DNA fragments are transferred to a ____________ and their separation is retained.
membrane
southern blot
Once DNA fragments are transferred to a membrane, the membrane is probed with many copies of a ________ sequence
ssDNA
southern blot
The ________ binds to its complementary sequence and form ________.
probe; dsDNA
Probes are labeled with ____________ or ____________ proteins, both of which can be used to indicate the presence of a desired sequence.
radioisotopes; indicator
Gene ________ now offers potential cures for individuals with inherited diseases. BY transferring a ________ copy of the gene into the affected tissues, the pathology can be fixed.
therapy; normal
________ mice are altered at their ________ line by introducing a cloned gene into fertilized ova or into embryonic stem cells.
transgenic; germ
The cloned gene that is introduced to a fertilized ova / embryonic stem cell is referred to as a ____________.
transgene
____________ mice have a gene that has been initially deleted.
knockout
The resulting offspring is a ____________, meaning that it has patches of cells, including germ cells, derived from each of the 2 lineages.
chimera
