DNA structure Flashcards
what is the central dogma
dna (transcription) rna (translation) protein
what are the differences between the DNA and RNA primary structure
the DNA structure has deoxyribose & uses T as a base
the RNA has ribose (so every C accompanied by O unlike DNA) & uses U as a base
what is indicative of the 5’ end vs 3’
5’ has unreacted phosphate
3’ has unreacted hydroxyl
what are the 2 characteristics of primary structures
- each strand has direction & enzymes recognize that direction
- the sequences of bases determine the info
what are the complementary base pairs in DNA and how would it be different in RNA
DNA: A=T G=C
RNA: A=U G=C
what forms can adenine and cytosine exist in
amino or imino forms
what forms can thymine and guanine exist in
keto or enol forms
bases primarily exist in what forms
amino and keto
what are the purines and what are the pyrimidines
purine: adenine, Hypoxanthine, Guanine, Xanthine
pyrimidine: cytosine, uracil, thymine
what does the major groove allow
it allows proteins to gain access to the bases
during transcription which form (B, A, or Z) predominates
A form bc of DNA/RNA associations
-A form is also the structure for double stranded RNA and RNA-DNA hybrids
Why is there no B form RNA
because there’s an extra hydroxyl group on RNA
which form of DNA is left handed (B, A, or Z)
Z form
which form of DNA has a zigzag path due to alternating purine and pyrimidine sequences
Z form
which form of DNA has major and minor grooves
B form
which form of DNA has the bases tilted WITH respect to the helical axis
A form
-while B form is perpendicular to helical axis
a GC repeating sequence is characteristic of what form of DNA
Z form
-GC makes it very stable
which form is wet and which is low humidity
B = wet A = low humidity
what is the least stable form of DNA and why
P form bc it puts the negatives in the middle so they repel a lot
which base pair is more stable A=T or G=C? why?
G=C bc it has more hydrogen bonds
and adjacent GC pairs have stronger van der waals intxn than AT
what are the three stabilizing factors of secondary dna
hydrogen bonds
van der waals interactions
ions in cells (K, Na, Mg)
which has the largest melting poitn, A=T or G=C?
G=C
what is the destabilizing factor of secondary dna
electrostatic repulsion aka if there was a negative charge on a phosphate group at pH=7 bc the negative charges would repel
which absorbs more light? single stranded or double stranded
single stranded bc the bases absorb UV light and SS bases are more exposed
hybridization is when
complementary nucleic acids are combined
the more percent of GC you have then the higher the…
melting point at which it can be denatured is
nucleotides and nucleic acids absorb light at how many nm
260
what is the problem with the HIV virus in relation to the central dogma
it causes reverse transcriptase so from RNA –> DNA
-the reverse has poor proof reading abilities
what inhibitor is used to treat HIV and how does it do so
NRTIs (nucleoside reverse transcriptase inhibitors)
they block HIV RNA from being reverse transcribed into DNA
what molc is an example of an NRTI and what structures is it made of
AZT
-Nucleoside and Thymine
how does the AZT work to block HIV (hint has to do w it’s structure)
the thymidine is incorporated into the growing DNA strand
the lack of an unreacted hydroxyl group in its 3’ position prevents addition of the next nucleotide
how does acyclovir help treat HIV
acyclovir converted into dGTP (a nucleoside analog)
it inhibits viral DNA polymerase by acting as an analog to dGTP
dGTP–> DNA results in chain termination bc of the absence of a 3’ hydroxyl group to attach more nucleosides
what type of drug is ciprofloxacin
topoisomerase inhibitor
denaturing is also called…
melting bc heat is usually used to separate the double stranded DNA into single stranded
hyperchromicity
increased absorption as the strands of the double helix separate
the Tm or melting point is the temperature where
half the DNA has denatured
T/F
once dna is denatured it can never return to it’s last state
false
dna can renature or reanneal under specific conditions
enxymes that break one or both strands of DNA
topoisomerase
increasing or decreasing the number of helical turns in the DNA causes it to be
strained
to reduce the strain, the DNA
forms supercoils
why is DNA negatively supercoiled in nature
causes opennes to the structure while is needed for it to be utilized
if it were positively supercoiled, the dna would be less accessible for info retrieval
T/F
type 1 topoisomerase found in prokaryotes while type 2 is found in eukaryotes
false
both types are present in both pro and eu
type 1 topoisomerase acts on DNA that is strained. so when it cuts the DNA..
the strain in the supercoiled DNA forces it towards a more relaxed state
if the DNA is negatively supercoiled when cutting w a type 1 topoisomerase
it removes one negative supercoil –> more relaxed state
if the dna is positively supercoiled when cutting with a type one topoisomerase will
remove one positive supercoil
T/F
no ATP is involved in the topoisomerase type 1 process
true
describe the steps of topoisomerase type 1A
cuts one strand of the double helix
enzyme bridges the break by covalent attachment to one end and noncovalent binding to the other
the unbroken strand is passed through the break
then rejoined
describe the steps of topoisomerase type 1B
binds to the dna
cuts one strand
stays covalently attached to one cut strand
other end of cut strand free to rotate about the intact strand
cut ends then rejoin
type 2 topoisomerases introduce negative supercoils into newly synthesized dna in… (pro or eu)
prokaryotes
in eukaryotes
which topoisomerases relax negatively supercoiled DNA and which relax positively supercoiled
Type 1A relaxes negative
type 1B and type 2 relax positive or negative
how do eukaryotes relax their supercoils
by dna wrapping around histones in the formation of nucleosomes
how do topoisomerase inhibitors (used on rapidly dividing cells like cancer and bacterial cells) work
they introduce breaks into the DNA by inhibiting the rejoining step
this blocks DNA replication
compacted form of the tertiary structure of the bacterial chromosone that is associated with a RNA-protein scaffold is known as
nucleoid
T/F
all prokaryotic dna is linear
falso
all eukaryotic
tight wrapping of DNA around the nucleosome pore causes
the removal of 1 helical –> creates negative supercoil
what is linker dna
area bn nucleosomes thats not packed as tightly
H1 histone is positively charged at both ends and does what
binds to linker regions to keep nucleosomes tightly associated
*H5 replaces H1 in some vertebrae
what does nucleosome packing do to DNA
shortens the DNA length by 6-7 fold
what does the solenoid folding do to DNA
shortens it by 35-40 fold
which is the most dispersed form of chromatin the cell
euchromatin
which chromatin is more condensed
heterochromatin
ehich chromatin results in higher order folding of the solenoid structure
heterochromatin
what is the most compact chromatin structure and how much does it shorten by
mitotic chromosomes - shorten by 10,000 fold
loops of solenoid may be held together by what
H1 which bind to linker DNA in two adjacent loops of the solenoid
what are the three advantages to nucleosome folding
- pack large amounts of DNA into small nucleus
- negative supercoiling opens DNA for utilization
- chromatin structure brings sequences closer together so regulatory proteins can bind to sequences that aren’t next to each other
In prokaryotes
DNA/protein sequences are
colinear
the size of the genome corresponds to the number of genes in pro or eu
PROKARYOTES
dna is not unique in pro or eu
eukaryotes
in eukaryotes, what does 10% of the genome code for
proteins
tandem repears are usually short and rich in
AT
in highly repetitive eukaryotes, each repeat is present how many times
> 300,000
tandem repeats make up how much of genome
10% or less
what is the difference (using values) between unique, moderately repetitive, and highly repetitive sequences
1= unique
2-300,000= moderately repetitive
>300,000=highly repetitive
what are transposons & which type of sequence is derived from them
segments of DNA that can move from one location to another
moderately repetitive sequences are derived from transposons
in a prokaryote, what is the relationship bn the DNA and the mRNA
sequence identical besides U in RNA and T in DNA
which frequency of sequences is interspersed with single copy DNA (LINES and SINES)
moderately repetitive sequences
