test 3: nucleic acid Flashcards
what are the nitrogenous bases
cytosine, thymine, uracil , adenine and guanine
what are the pyramidine bases
cytosine, thymine, uracil
what are the purine bases
adenine, guanine
what absorbance do all of the bases have
260 nm
what is a common tautomeric form
lactam(keto)
what is a rare tautomeric form
lacti (enol)
what is a nucleoside
base+ sugar
what is sugar
D ribose or 2-deoxy-D ribose
what connects nucleosides to the base
B-N-glycosidic bond
how is a nucleoside numbered
1st number goes to where the base is attatched to the sugar and then 5 is HOCH2
what is a nucleotide
nucleoside + phosphate
- phosphoric acid is extrified with an -OH of the monosacc either the 3’ or the 5’OH
what does esterified mean
an acid reactions with an alcohol to make an ester
what is 3-5 cyclic adenosine monosphosphate (cyclic adenosinde monophosphate, cAMP)
- derived from ATP
- used in intracellular signal transduction( signalingn) as a second messenger
wht does the 2nd messenger do in signal transduction
amplifies the signal
wht are the bases for DNA and RNA
dna: ATGC
RNA; AUGC
what are the nucleoside names based off of the base
- adenine= adenosine
- guanine= guanosine
- cytosine= cytidine
- Uracil = uridine
- thymine = deoxythymidine
what is an example of a nucleoside/ tide in medicine
- antivirals
- zidovudine = nucleoside analog reverse transcriptase inhibitor
what does NRTI do
used to treat HIv
zidovudine is what analog
uracil
what is emtricitabine
- used for the treatment of HIV in adults
what analog is emtricitabine
cytosine analaog
what contains minor bases in RNA
tRNA
what does a methylated form of a major base mean in DNA
- role of regulating and protecting genetic info
what are the names of the xanthines
hypoxanthine, inosine, xanthine
where is inosine found
in tRNA for wobble base pairs
what structure is this
hypoxanthine
what structure is this
inosine
insoine = Hypoxanthine + ribose
what structue is this
xanthine
what are polynucleotides
- nucleic acids
- joined by phosphodiester linkage
what is the primary structure of dna and rna
- sequence read from 5’ to 3’ end
- RNA: 5’-AUCG-3’ or AUGC
what bond is this showing
phosphodiester bond
what structure is this
phosphoester
what is RNA’s problem
stability
what is RNA susecptible to
base catalyzed hydrolysis
what makes RNA unstable
- 2 OH group
who examined base rations from bacteria and plants and founded chargaffs rules
erwin chargaff
what was chargaffs rules
A = T
G= C
who discovered complementary base paiting
watson and crick
who did X ray fiber diffraction
rosalind franklin
who knew it was a helix
francis crick
what is the central dogma of biology by francis crick
framework that dscribes the flow of genetic information
- dna to rna = trancription
-rna to protein = protein translation
what are some characteristics of B DNA structure
- right hand helix
- bases perpen to the helix axis
- wide and deep major; narrow and deep minor
- phosphate backbones on outside
- pitch = 10 bases per turn = 34 angstroms
- helix rise per basepair = 3.4
what grooves does B DNA have
- wide and deep major, narrow and deep minor
what is the pitch of B DNA
- 10 bases per turn = 34 angstroms
what is the helix rise for B DNA
- 3.4 angstroms
is B DNA antiparallel
yes
what is anti conformation in base
the base is rotated away from the sugar
what is syn conformaiton
the base is rotated towards the sugar
which one is syn which one is anti
syn is on the left and anti is on the righ
what structure is this
a dna
what dna is this
b dna
What type of groove does Z have
major flat
minor: narrow and deep
what tyeo of groove does A have
major groove: narrow and deep
minor: wide and shallow
what structure is the one on the far left
Z dna
what structure does RNA-RNA/ RNA DNA hybrids assume
A dna like structure
which occurs in alternating purine -
z dna
pyramidine tracts and is favored in high salt conc
what are telomeres
the end of chromosomes
what tyoe of dna does the telomers have
tetraplex or quadruplex dna
what does tetraplex or quadruplex dna have a role in
- transcription, telomere maintenence, dna recom
what is the structure of rna
- single stranded
- double helical regions that assume tupe A helix
what structure is this
rna
describe the tertiary structure of tRNA
- cloverleaf secondary structure’- L or banana tertiary structure
dna supercoling topology: what are the different super coiling
positive and negative
what is positive supercoiling
- dna DH is twisted in the same direction as the natural right handed helical twist
- makes it tightly wound
what is negative supercoiling
- dna is twisted in the opposite direction
- easier to seprate strands for transcription and replication
what supercpil do most natrual dna in cells use
negative supercoil
how does supercoiling occur in linear dna
both strands are anchored
what are the enzymes that affect dna superstructures
- topoisomerases
-type 1 and type 2
what does topoisomerase do
- relax or make supercoils in dna by causing a transient nick that is resealed
what does type 1 do
relax supercoils by breaking 1 strand( ssDNA) break
what does type 2 do
relax or make supercoil by breaking two strands
where are topoisomerase inhibitors uesed
in anticancer and antibacterial agents like quinolones
what is the size of a human dna molecule
3,200,000 Kb
describe the dna in prok
- supercoiled circular dna that is bound to basic proteins = bacterial chromosomes in the nucleoid
what is a separate small circular molecules that carries genes for their own replicaton adnd code for benefical enzymes like antibiotic degredation
bacterial plasmids
euk. package dna as what
chromatin at normal stage of cell cycle; chromosomes when cells are ready to divide
what is dna coiled around
histone octamer called a nucleosome
what are the types of histones
H2A, H2B, H3, and H4 (2x)
how many turns of dna arouund the nucleosome
1.8
what amino acids are histones rich in
lysine and argine whose sides chains have a +Ve charge
what charge is dna
negative (-ve)
what is the last histone
H1
what is the role of H1 histone
- linker histone
- stabilizes the chromatin fiber
- regulation of genes and chromatin
which structure does not have jistones
mitochondrial (mtDNA) and chloroplast DNA(ct DNA)
what is mito and chloroplast dna used for
forensic analysis when nuclear dna is too degraded
what can damage dna
UV irridation
thymine dimers(cyclobutyl dimers)
alkylation
HNO2
what is alkylation
causes dna mismatch mutations that can lad to cancer
what are some alkylating agents
- mustard gas
nitrogen mustard
what does HNO2 do
causes dna mismatch mutations
- food cured with NaNO2
