DNA Flashcards
4 deoxyribonucleotides of DNA
deoxyadenylate, deoxyguanylate, deoxycytidylate, thymidylate
the 4 deoxyribonucleotides are combined through
3’ to 5’ phosphodiester bonds
composition of nucleotide
base + sugar + phosphoric acid
the 3’ hydroxyl of 1 sugar is combined with the _____ through a phosphate group
5’ hydroxyl of another sugar
thymidine is attached to _____ then _____ is attached to ______ through ______
cytidine, cytidine, adenosine, phosphodiester bonds
in DNA, the ______ is of paramount importance
base sequence
the deoxyribose and phosphodiester linkages are the _____ in all repeating nucleotides
same
polarity of DNA molecule
the base sequence is always written from the 5’ to 3’ end
(A, B, or Z DNA) right-handed helix
A & B DNA
(A, B, or Z DNA) left-handed heliz
Z DNA
(A, B, or Z DNA) base pairs per turn of 11
A DNA
(A, B, or Z DNA) base pairs per turn of 10.5
B DNA
(A, B, or Z DNA) base pairs per turn of 12
Z DNA
(A, B, or Z DNA) 2.6 nm helical diameter
A DNA
(A, B, or Z DNA) 2.0 nm helical diameter
B DNA
(A, B, or Z DNA) 1.8 nm helical diameter
Z DNA
(A, B, or Z DNA) 2.6 nm helical length
B DNA
(A, B, or Z DNA) 3.4 nm helical length
B DNA
(A, B, or Z DNA) 3.7 nm helical length
Z DNA
(A, B, or Z DNA) Broadest and shortest in shape
A DNA
(A, B, or Z DNA) Intermediate shape
B DNA
(A, B, or Z DNA) narrowest and longest shape
Z DNA
(A, B, or Z DNA) major grove is wide, deep
A DNA
(A, B, or Z DNA) major grove is narrow, deep
B DNA
(A, B, or Z DNA) major grove is flat
Z DNA
(A, B, or Z DNA) minor grove is narrow, shallow
A DNA
(A, B, or Z DNA) minor grove is broad, shallow
B DNA
(A, B, or Z DNA) minor grove is narrow, deep
Z DNA
the watson crick structure is referred to as the
B-form DNA
the most stable structure for a random-sequence DNA molecule under physiological conditions
B DNA
in the Watson-Crick model, right-handed double helix DNA consists of _____ chains twisted around another in a right-handed double -helix similar to a spiral staircase
2 polydeoxyribonucleotide chains
in the Watson-Crick model, what is the base-pairing rule
the 2 strands are complementary to each other
in the Watson-Crick model, what is the Chargaff’s rule
the no. of purines id equal to the number of pyrimidines
in the Watson-Crick model, the 2 strands in a DNA molecule run in a ________
antiparallel manner
alkali or heat causes strands of DNA to separate but does not break phosphodiester bonds
denaturation
this is also called as the melting of DNA
denaturation
this is when strands of DNA are separated by heat and then the temperature is slowly decreased under the appropriate conditions, base pair re-for, and a complementary strands of DNA come back together
renaturation/annealing
a single strand of DNA pairs with complementary base sequences on another strand of DNA or RNA
hybridization
in higher organisms, DNA is organized inside the
nucleus
double-stranded DNA is 1st wound over histones, and this is now called
nucleosomes
this is a loose term employed for a long stretch of DNA in association with histones
chromatin
chromatin is then further and further condensed to form
chromosomes
these are proteins containing unusually high concentrations of basic amino acids
histones
the 5 classes of histones
H1, H2A, H2B, H3, H4
the ___ histone is loosely attached to the DNA
H1
the other histones other than H1 are called
core histones
core histones form the
nucleosome
amino-terminal 1/3 region of ____ and _____ are lysine rich
H2A, H2B
H3, H4 histones are
arginine histones
[cell cycle of eukaryotic cells] synthesis at DNA (replication) occurs
S1 (synthesis phase)
[cell cycle of eukaryotic cells] cells prepare to duplicate their chromosomes
G1/first gap
[cell cycle of eukaryotic cells] cells prepare to divide
G2/2nd gap
[cell cycle of eukaryotic cells] cell division occurs
mitosis
[cell cycle of eukaryotic cells] can _____ the cell cycle many times
traverse
[cell cycle of eukaryotic cells] cells can also leave the cycle ____ to divide again
never
[cell cycle of eukaryotic cells] phase that cells enter in which they remain for extended periods
G0
[cell cycle of eukaryotic cells] in response to _____, cells reenter the cell cycle and divide again
appropriate stimulus
During cell division, each daughter cell gets
an exact copy of the genetic information of
the mother cell. This process of copying the
DNA is known as
DNA replication
what model of DNA replication is characterized by the two parental strands separate and each makes a
copy of itself. After one round of replication, the two daughter molecules each comprise one old and one new strand. Note that after two rounds, two of the DNA molecules consist only of new material, while the other two contain one old and one new strand.
semi-conservative model
what model of DNA replication is characterized by the parental molecule directs the synthesis of an entirely new double-stranded molecule, such that after one round of replication, one molecule is conserved as two old strands. This is repeated in the second round
conservative model
This model is only theoretical, this does not actually take place
conservative
[Stages of DNA replication] 3 stages of DNA replication
initiation, elongation, termination
[Stages of DNA replication] in initiation, DNA synthesis is initiated at particular points within the DNA strand known as
origins
[Stages of DNA replication] these are specific coding regions
origins
[Stages of DNA replication] the specific coding regions are targeted by
initiator proteins
[Stages of DNA replication] initiator proteins go on to recruit more proteins that help aid the replication process, forming a ________ around the DNA origin
replication complex
[Stages of DNA replication] There are multiple origin sites, and when replication of DNA begins, these sites are referred to as
replication forks
[Stages of DNA replication] Within the replication complex is the enzyme
DNA Helicase
[Stages of DNA replication] the action of DNA helicase is
unwinding the double helix to expose each of the 2 strands so that they can be used as template for replication
[Stages of DNA replication] the DNA helicase used to ______ that form the bonds between the nucleobases, therefore breaking the bond holding the two strands together
hydrolyzes ATP
[Stages of DNA replication] this synthesizes a small RNA primer, which acts as a ‘kick-starter’ for DNA
Polymerase
DNA primase
[Stages of DNA replication] this is the enzyme that is ultimately responsible for the creation and expansion of new strands of DNA
DNA polymerase
[Stages of DNA replication] DNA polymerase is only able to extend the primer by adding free nucleotides to the
3’ end
[Stages of DNA replication] Polymerization of the new strand of DNA is taking place from
5’ to 3’ direction
[Stages of DNA replication] the template is read in the
3’ to 5’ direction
[Stages of DNA replication] in elongation, the 3rd hydroxyl of the last deoxynucleotide is joined with the _______, Thus, the 3’ end of the last nucleotide is free
5th phosphate of the newly
entering nucleotide
[Stages of DNA replication] One newly formed strand is referred to as the
leading strand
[Stages of DNA replication] along the leading strand, DNA Primase only needs to synthesize an _____ once,
at the beginning, to initiate DNA Polymerase
RNA primase
[Stages of DNA replication] fragments in the lagging strand are called
Okazaki fragments
[Stages of DNA replication] the stage where 2 replication forks meet or no more DNA template is left to replicate
termination
[Stages of DNA replication] The meeting of two replication forks is not _______ along the course of the chromosome
regulated and happens randomly
[Stages of DNA replication] Once DNA synthesis has finished, it is important that the newly synthesized strands are
bound and stabilized
[Stages of DNA replication] in the lagging strand in the termination phase, ______ removes the RNA primer that is at the beginning of each Okazaki
fragment
RNAase H
[Stages of DNA replication] in the lagging strand in the termination phase, _______ joins fragments together to create one complete strand
DNA ligase
[mechanism of replication] replication is
bidirectional and semiconservative
[mechanism of replication] this means that replication begins at a site of origin and simultaneously moves out in both directions from this point
bidirectional
[mechanism of replication] Prokaryotes have ____ site of origin on each chromosome
1
[mechanism of replication] ______ have multiple sites of origin on each chromosome
eukaryotes
[mechanism of replication] this means , following replication, each daughter molecule of DNA contains one intact parental strand and one newly synthesized strand joined by base pairs
semiconservative
[mechanism of replication] __________ are the sites at which DNA synthesis is occurring
replication forks
[mechanism of replication] Helicases unwind the helix, and _______ hold it in a single-stranded conformation.
single-strand binding proteins
[mechanism of replication] _______ act to prevent the extreme supercoiling of the parental helix that would result as a consequence of unwinding at a replication fork
Topoisomerases
[mechanism of replication] _____ a topoisomerase inhibited by the quinolone family of antibiotics, is found only in
prokaryotes
DNA gyrase
[mechanism of replication] _______ catalyze the synthesis of DNA
DNA polymerases
[mechanism of replication] Prokaryotes have _____ DNA polymerases
3
[mechanism of replication] the polymerases of prokaryotes
pol I, pol II, pol III
[mechanism of replication] the polymerase of prokaryotes that is the replicative enzyme
pol III
[mechanism of replication] the polymerase of prokaryotes that is involved in repair and synthesis on the lagging strand
pol I
[mechanism of replication] eukaryotic polymerase for replication (in a complex with primase and aids in starting the primer, and is also for DNA repair
pol alpha
[mechanism of replication] eukaryotic polymerase for DNA repair exclusively
pol beta
[mechanism of replication] eukaryotic polymerase for DNA replication in mitochondria
pol gamma
[mechanism of replication] eukaryotic polymerase for replication on lagging strand, and for DNA repair
pol delta
[mechanism of replication] eukaryotic polymerase for replication on leading strand, and for DNA repair
pol epsilon
[mechanism of replication] DNA polymerases can only copy a DNA template in the ______ direction and produce the newly synthesized
strand in the ______
3’ to 5’; 5’ to 3’ direction
[mechanism of replication] Deoxyribonucleoside triphosphates which include _______ are the precursors for DNA synthesis
dATP, dGTP, dTTP, and dCTP
this refers to injuries to DNA that introduce deviations from its normal, intact structure and which may if left unrepaired, results in a mutation or a block of NDA replication
DNA damage
this refers to permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements
mutation
a structural change in DNA
DNA damage
an alteration of the nucleotide sequence in DNA
mutation
most damages are repaired by cellular mechanisms
DNA damage
permanent changes in DNA
mutation
unrepaired DNA damages become ____ in replication cells
mutations
this is caused by compounds released during metabolism and environmental factors
DNA damage
caused by errors in DNA replication and recombination
mutation
3 types of DNA damage
changes of nitrogenous bases, missing bases, breaks in DNA strands
three types of mutations
substitutions, deletions, insertions
prevents the proceeding of DNA replication
DNA damage
change the genetic information encoded by DNA
mutation
this can be passed over generations
mutation
2 types of DNA damage
endogenous, exogenous
type of DNA damage such as attack by reactive oxygen species produced from normal metabolic byproducts
endogenous damage
type of DNA damage caused by external agents such as UV (200-400), other radiation frequencies, certain plant toxins, and viruses
exogenous damage
3 types of mutations
base substitutions, deletions, insertions
2 types of base substitutions
transition, transversion
[types of mutations] Single base substitutions are called
point mutations
[types of mutations] the most common type of mutation
point mutations/single base substitutions
[types of mutations] example of single base mutations
sickle cell anemia
[types of mutations] type of point mutation that occurs when a purine is substituted with another purine or when a pyrimidine is substituted with another pyrimidine
transition
[types of mutations] type of point mutation occurs when a purine is substituted for a pyrimidine or a pyrimidine replaces a purine
transversion
[types of mutations] results when one or more base pairs are lost from the DNA that further leads to a frameshift
deletion
[types of mutations] an example of deletion mutation
cystic fibrosis
[types of mutations] additional base pairs may lead to frameshifts
insertion
[types of mutations] Diseases caused by insertional mutations include
Fragile X Syndrome. Huntington’s Disease. Myotonic dystrophy
involves the removal of the segment of DNA that contains a damaged region or mismatched bases
DNA repair
[DNA repair] filling in the gap by action of a ________ that uses the ______ strand as a template, and _______ of the newly synthesized segment to the remainder of the chain
DNA polymerase, undamaged sister, ligation
[DNA repair] types of single strand repair
nucleotide excision repair (NER), base excision repair (BER), DNA mismatch repair (MMR)
[DNA repair] type of single strand repair which is a particularly important excision mechanism that removes DNA damage
induced by ultraviolet light (UV)
nucleotide excision repair
[DNA repair] UV DNA damage results in
bulky DNA adducts
[DNA repair] bulky DNA adducts are usually
pyrimidine dimers
[DNA repair] in NER, Recognition of the damage leads to removal of a ______ that contains the lesion
short single-stranded DNA segment
[DNA repair] type of single strand repair that is a cellular mechanism for removing damaged bases that could otherwise
cause mutations by mispairing or lead to breaks in DNA during replication
base excision repair (BER)
[DNA repair] BER is initiated by
DNA glycosylases
[DNA repair] DNA glycosylases recognize and remove specific damaged or inappropriate bases, forming
AP (apurinic/apyrimidic) sites
[DNA repair] AP sites are cleaved by
AP endonuclease
[DNA repair] The resulting single-strand break can then be processed by either:
short patch or long patch BER
[DNA repair] short patch BER is where a
single nucleotide is replaced
[DNA repair] long patch BER is where
2–10 new nucleotides are synthesized
[DNA repair] is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA
DNA mismatch repair (MMR)
[DNA repair] During DNA
synthesis the _______________. In order
to begin repair, the mismatch repair
machinery distinguishes the newly
synthesized strand from the template
(parental)
newly synthesized (daughter)
strand will commonly include errors
[DNA repair] In gram-negative bacteria,
____________ distinguishes the strands
transient hemi-methylation
[DNA repair] in gram-negative bacteria, (the parental is ______ and daughter is not)
methylated
[DNA repair] in eukaryotes, the damage is repaired by _____, _____ and excising the wrongly incorporated base and replacing it with the correct nucleotide
recognition of the deformity caused by the mismatch, determining the template and non-template strand
[DNA repair] types of double strand repair
Non-homologous end joining (NHEJ), Homology directed repair (HDR), Microhomology-mediated end joining (MMEJ)
[DNA repair] type of double strand repair where it is a pathway that repairs double-strand breaks (DSB) in DNA
Non-homologous end joining (NHEJ)
[DNA repair] in Non-homologous end joining (NHEJ), break ends are directly ligated without the need for a
homologous template
[DNA repair] type of double strand repair where it requires s a homologous sequence to guide repair
Homology directed repair (HDR)
[DNA repair] HDR is highly accurate and uses
the _______ as a template for accurate repair of the DSB
sister chromatid
[DNA repair] type of double strand repair where . DSB breaks are sealed by microhomology (MH)-mediated base-pairing of DNA single strands
Microhomology-mediated end joining (MMEJ)
[DNA repair] in Microhomology-mediated end joining (MMEJ), when the DSB breaks are sealed, this is followed by _____, _____ , and _____
nucleolytic trimming of DNA flaps, DNA gap filling, and DNA ligation
[effects of DNA damage] _____ is the process in which a cell decides to kill itself
apoptosis
[effects of DNA damage] is an irreversible arrest of cell proliferation while the cell maintains metabolic function (often
associated with cellular aging). State of dormancy. Cell does not divide anymore
senescence
[effects of DNA damage] can cause cancer
unregulated cell division
[clinical corelates] Cancer is a group of diseases in which cells are not responsive to the
normal restraints of growth
[clinical corelates] The major causes of cancer are
radiation, chemicals, and viruses
[clinical correlates] Radiation and chemicals cause damage to DNA, which, if not repaired rapidly, produces
mutations that can result in cancer
[clinical correlates] Burning organic material (e.g., cigarettes) produces chemicals such as
benzopyrene
[clinical correlates] benzopyrene that _____bind to the bases in DNA, producing mutations that lead to lung cancer
covalently
[clinical correlates] Ultraviolet (UV) light, including that from the sun, produces _____ in DNA that lead to skin cancer.
pyrimidine dimers
[clinical correlates] UV light leading to skin cancer, is a condition is particularly pronounced in people with _______ because their DNA repair system does not function normally
xeroderma pigmentosum (XP)
[examples of mutations in other DNA repair systems] mismatch repair is defective in this disease
Hereditary nonpolyposis colorectal cancer (HNPCC)
[examples of mutations in other DNA repair systems] a defect in a helicase necessary to unwind the DNA strands during replication
Bloom syndrome
[examples of mutations in other DNA repair systems] a defect in repairing single- and double-strand breaks in DNA
Breast cancer
[treatment of cancer] ____ prevents the conversion of dUMP to dTMP, reducing the level of thymine nucleotides required for DNA synthesis
5-fluorouracil (5-FU)
[treatment of cancer] ____ prevents tile formation of tetrahydrofolate from its more oxidized precursors. As a result, the formation of both thymine for DNA synthesis and the purines for DNA and RNA syntheses is inhibited
Methotrexate
[treatment of cancer] 5-fluorouracil (5-FU) prevents the conversion of _____, reducing the level of thymine nucleotides required for DNA synthesis.
dUMP to dTMP
[treatment of cancer] 5-fluorouracil (5-FU) prevents the conversion of dUMP to dTMP, reducing the level of ______ required for DNA synthesis
thymine nucleotides
[treatment of cancer] Methotrexate prevents tile formation of ______ from its more oxidized precursors. As a result, the formation of both thymine for DNA synthesis and the purines for DNA and RNA syntheses is
inhibited
tetrahydrofolate
[treatment of cancer] Methotrexate prevents tile formation of tetrahydrofolate from its more oxidized precursors. What formations are inhibited?
thymine, purines
