3/4 Structure of Nucleic Acids and synthesis of DNA Flashcards
What is the quaternary structure for proteins vs Nucleic acids?
for proteins it is a complex, for nucleic acids it is an association with histones
which tautomer form is used for base pairing of pyrimidines and purines?
keto form is used
what bases are purines and what are pyrimidines?
GA are purines, CUT are pyrimidines
What types of bond is between the base and sugar in nucleic acids?
glycosidic bond
what type of bond is between the sugar and phosphate backbone in genetic material?
phosphodiester bonds
reduction of which carbon on ribose will convert to deoxyribose?
2’ C
which carbons of deoxy/ribose takes part in creating the backbone for genetic material?
3’ and 5’
which carbon of the sugar is the base added to in nucleic acid?
1’
which conformation is the base in relation to the sugar for nucleic acids usually and why?
anti due to steric hinderance
what is the difference between nucleotides and nucleosides?
nucleosides are only base and sugar while nucleotides are base, sugar and any number of phosphate groups
what ratio does chargaffs rule outline?
ratio is [A=T x G=C] = 100% of bases
what is different about GC bonds vs AT bonds?
GC bonds are triple and thus closer harder to break while AT bonds are double
Describe the double helix structure of DNA
It is a helix with two antiparallel strands that form helixes that result in a major groove and minor groove
What are the forms that the double helix can be in and how are they named
Standard is B form with a clockwise(right) direction, A form is usually a DNA-RNA hybrid which is wider and is right handed, Z form is transient left handed form with extremely tight turns with almost no differences in groove size
what is the differences in purpose between RNA and DNA
RNA expresses information while DNA retains and passes on information to future generations
What two factors make RNA more unstable than DNA and why
2’ OH on ribose and Uracil instead of T, these features can be fixed as in DNA but requires energy so is only done for DNA since its accuracy is more important
How does RNA instability in pH compare to DNA?
DNA will only denature by strands but RNA will denature into individual bases in the presence of high pH
How does the subunits of ribosomes between prokaryotes and eukaryotes compare?
prokaryotes= 50S + 30S = 70S eukaryotes= 60S + 40S = 80S
what ribosomes are the same in both euks and proks
5S
What extra ribosome does eukaryotes have that has different genetic information than the nuclear DNA?
mitoRNA 55S
What are tRNA?
they are small RNA forms with a cloverleaf pattern with a CCA sequence that attaches to amino acids and have an anticodon for recognizing translated sequences on mRNA
what is the “melting temperature” and how is it calculated?
Tm= 69.3+0.41(%G+C)
Why does RNA denature into bases while DNA does not for high pH?
2’ ribose OH loses an -H in high pH and the oxidized O- breaks the phosphodiester bonds of the backbone
what is reannealing
AKA hybridizing, is when temp are taken back down below melting and strands of DNA and sometimes RNA can come together and bind at their complementary sequences.
How are DNA organized
that coil around a core of 8 histones from H2-4 and is linked from histone to another by H1 histone. These strands of chromatin can coil into a larger chromatid which then is paired with a centrosome to form a chromosome
how many chromosomes do we have?
normal is 23 pairs including a possible mismatched a pair of sex chromosomes
How does AZT/cipro work?
azt is a antibiotic that binds to bacterial 50S and inhibs protein synth (warning mito DNA is similar), cipro target DNA gyrase
how does chemo agents work?
ie 5FU are analogues that interferes with the cell replication process and thus slows down tumors more than healthy cells (although high amt of side fx)
what are the constituent components of prok DNA replication?
DNA pol I-III, helicase, gyrase(topoII), topoisomerase, SSRB, RNAse H, Ligase, RNA primase
What are the characteristics of DNA replication?
semiconservative and read 3-5 but synthed 5-3, leading and lagging strands with different mechanisms, higher fidelity vs transcription, lagging strands fragments are joined by exonuclease, polymerase and ligase
what shape is prok DNA? euk DNA? implications?
prok are circular, euks are linear. linear DNA leads to 3’ overhang which requires noncoding telomeres to support them
what is DNA pol alpha?
primase
what is DNA pol beta
repair, primer excision
What is DNA pol gamma
mito DNA synth
what is DNA pol delta
replication, 3-5 exonuclease, proofreading
what is DNA pol epsilon
replication, 3-5 exonuclease, proofreading, DNA repair
What is DNA pol I
replication, repair, primer excision
What is DNA pol II
DNA repair
What is DNA pol III
major replicative poly, 3-5 exonuclease for proofreading
Which polymerase in euks are responsible for leading and lagging strands?
leading strand: pol epsilon
lagging strand: pol gamma
What is the significance of the degree of DNA methylation
biological marker of strand age
What are the two important sources of DNA dmg
UV light causing thymine dimers
benz[a]pyrene from smoking causing guanine adducts
both fixed by nucleotide excision repair
what enzyme removes the initial base in base excision repair?
glycosylase removes the glycosidic bond
how do the pol nucleases differ in BER from NER
BER- APexo/endo NER-Endo
how is the correct template chosen for mismatch repair?
mechanism chooses higher methylated strand as correct
What are the three genetic recombinations?
homologous recombination, nonhomologous translocation (balanced or not), random transposition
why is DNA have T and RNA have U when T requires more energy to create?
T is more stable than U against deamination
why is primase necessary in DNA repair?
3’OH is already present