DNA/RNA Flashcards
3 main classes of RNA species in human cells
- structural
- information carrying
- regulatory
structural RNA
- ribosomal RNA (rRNA)
- transfer RNA (tRNA)
- small nuclear RNA (snRNA)
- small nucleolar RNA (snoRNA)
regulatory RNA
- micro RNA (miRNA)
2. small interfering RNA (siRNA)
information containing RNA
messenger RNA (mRNA)
purine
adenine
guanine
double ring
pyrimidine
cytosine
thymine
uracil
single ring
central dogma
DNA–> replication–>DNA
DNA–> transcription–>RNA
RNA–>translation–> protein
building blocks of nucleic acids
ribonucleiotide and 2’deoxy-nucleotide residues
universal energy currency is
ATP
building block of RNA
ATP
Nucleotides are NOT in
DNA and RNA
ribose is a
5 carbon sugar thats the primary building block of ribonucleic acids
it is a deoxyribose that has been de-hydroxylated at the 2’ position
nucleosides are
the central ribose sugr and bas attached to it at the 1’ position
a nucleoside with one phosphate group attached tot eh 5’ position of the ribose is called
nucleotide or nucleoside monophosphate
if there is a chain of two phosphates tagged on 5’ position, it is a
nucleoside diphosphate
tri if it’s 3…
phosphates are fairly hydro_____, while bases are
hydrophillic
hydrophobic
diseases that can result from accumulation of excess purine derivatives in tissue
gout: build up of uric acid in joints as precipitant of purines
Lesch-Nyhan Disease: causes severe neuro symptoms
3’ end
open hydroxyl group at that ribose position
5’ end
phosphate end
phosphodiester link is between
the phosphate and hydroxyl group of 3’ to 5’ end
which is more soluble, a purine or pyrimidine?
a purine is less soluble
solubility:
nucleoside, base, nucleotide
nucleotide> nucleoside> base
conventional way of writing DNA
5’ –> 3’
DDL and AZT drugs work by
inhibiting DNA synthesis by the reverse of transcriptase (RNA–>DNA), hence inhibiting HIV replication
Avery, McCloud, McCarty discovered
DNA is genetic material
the mouse thing
Franklin and Wilkins
x ray diffraction of moist DNA fibers showed helical structure with 10 layer line and major repeat of 3.4 nm
watson and crick
double helical structure with major and minor groove
chargaff’s rule
- molar ratios of total purine and total pyrimidines are roughly equal (G+A= C+T)
- the molar rations of adenine to thymine and guanine to cytosine are equal
(G=C, A=T)
why is DNA so much more stable than RNA?
2’ hydroxyl group on ribose makes it much less stable
why does DNA grow 3’ to 5’?
the 3’ OH group of the 5” end attacks the next 5’ a-phosphate
G-C have ___ H- bonds
3
A-T have ____ H bonds
2
What factors affect the melting point of DNA?
Factors affecting the Tm or DNA:
• Salt concentration: high salt concentrations will increase the Tm
o When salt concentration decreases, the negatively charged phosphate groups on the phosphodiester backbone are no longer stabilized by positively charged ions.
o The negative charge of the backbone tends to force the strands apart
o Thus, higher salt concentrations neutralized this repulsion and increase DNA stability
• Extremes of pH will alter the ionization states of the groups on the bases which provide/accept H-bonds
• Increase in DNA chain length will increase Tm
• Increase in G=C base pairs will increase Tm
o G=C has 3 H-bonds, while A-T has only 2 H-bonds.
Covalent methylation of human DNA:
Covalent methylation of human DNA: addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring
o Major covalent modification of human DNA in which a methyl group is attached to a Cytosine
o CpG sites: regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. “CpG” is shorthand for “—C—phosphate—G”
o Aka cytosine and guanine separated by a phosphate
o “CpG” notation is used to distinguish this linear sequence from the base-pairing of cytosine and guanine
o CpG islands: regions of DNA with higher concentrations of CpG sites, often associated with the “start” site of a gene (promoter or promoter proximal element)
o Basis of “epigenetics”
o Also important for cancers: hypermethylation in silencing tumor suppressor genes, hypomethylation in aberrant transcription of oncogenes
Deamination of bases is a cause of
of mutations
o Removal of an amine group
o Deamination of cytosine converts it to uracil
o Easily recognized and repaired because Uracil is so obviously not supposed to be a part of DNA
o Deamination of 5-methyl cytosine converts it to thymine
o Most common mutation, not recognized by the repair machinery so often persists
o Cause of rarity of CpG sites in eukaryotic cells
o Deamination of Guanine results in the formation of xanthine
o Selectively base pairs with thymine instead of cytosine
o Results in a post-replicative transition mutation, where the original G-C base pair transforms into an A-T base pair
o Correction of this mutation involves the use of alkyladenine glycosylase during base excision repair
o Deamination of Adenine results in the formation of hypoxanthine
o Selectively base pairs with cytosine instead of thymine
o Results in a post-replicative transition mutation, where the original A-T base pair transforms into a G-C base pair
Depurination
. Depurination also results in mutations
o The purine base (adenine or guanine) is removed from the deoxyribose sugar by hydrolysis of the beta-N-glycosidic link between them
o After depurination, the sugar phosphate backbone remains and the sugar ring has a hydroxyl (-OH) group in the place of the purine – apurinic site
o Depurinated bases in double-stranded DNA are efficiently repaired by portions of the base excision repair pathway
o Depurinated bases in single-stranded DNA undergoing replication can lead to mutations, because in the absence of information from the complementary strand, BER can add an incorrect base at the apurinic site, resulting in either a transition or transversion mutation
Ultraviolet light covalently links
. Ultraviolet light covalently links thymines: pyrimidine dimmers
o Creates a kink in the DNA
o Dimers may be repaired by photoreactivation or nucleotide excision repair, but unrepaired dimers are mutagenic
o In humans they are the primary cause of melanomas
. Alkylating agents are carcinogenic
. Alkylating agents are carcinogenic
• Alkylation = transfer of an alkyl group from one molecule to another
• Nucleophilic groups are reactive to alkylating agents
Explain the chemistry of DNA polymerization and how nucleoside analogues are used as drugs.
In DNA polymerization, new bases are added to the growing strand via the nucleophilic attack of the 3’ Hydroxyl of the 5’end on the alpha phosphate on the 5’ carbon of the new base.
Nucleoside analogues are engineered to be antiviral drugs that halt viral DNA replication.
Instead of a free hydroxyl group on the 3’ carbon, they have an Azide (N=N=N) or a hydrogen atom. When incorporated into the growing DNA strand, there is no longer a free 3’ hydroxyl to act as a nucleophile and add bases to the growing chain. As a result, replication stops.
