DNA/RNA LO Flashcards
What are the purines?
adenine, guanine (PURe As Gold)
what are the pyrimidines?
cytosine, thymine, and uracil
what is ribose?
5 carbon sugar that is the primary building block of ribonucleic acids
how is deoxyribose different than ribose?
deoxyribose has been dehydroxylated at the 2’ position
what is a nucleoside?
central ribose sugar and a base attached to it at the 1’ position
what is a nucleotide?
a nucleoside with at least one phosphate group attached to the 5’ position of the ribose
what is the universal energy currency in the body?
ATP
what is the solubility relationship between pyrimidines and purines?
pyrimidine > purine
in regards to solubility
what is the solubility relationship between nucleosides, bases, and nucleotides?
nucleotide > nucleoside > bases
in regards to solubility
between bases and nucleosides, which is less soluble?
base is less soluble than nucleoside
Gout is caused by the build up of ________ which is a precipitant of _______
uric acid, purines
The low solubility of purines and their accumulation leads to which 2 diseases covered in lecture?
Lesch-Nyhan disease and gout
in regards to the deoxyribose, why is the direction 5’ to 3’ polarity?
5’ end has phosphate and 3’ end has hydroxyl group. phosphate at the 5’ end will bind with the hydroxyl group at the 3’ end
What did the Avery, McCloud, and McCarty experiment find?
established DNA as the genetic material with their pneumococcus experiments. (smooth strain killed mice, rough strain did not. DNA from heat killed S cultured with R then killed mice BAM!)
what did the Franklin and Wilkins find and how?
helical structure of DNA through x-ray diffraction
what are Watson and Crick known for?
definitive double-helical structure
What are Chargaff’s rules?
- Molar ratios of total purines and total pyrimidines are roughly equal (G+A = C+T)
- the molar ratios of adenine to thymine, and guanine to cytosine are roughly equal (G=C, A=T)
- G+C / A+T ratio is different for different organisms
Describe the Watson-Crick model for DNA structure
2 strands in right handed helix
sugar/phosphate groups on the outside of helix (hydrophilic)
bases paired and stacked on the inside (hydrophobic)
major groove and minor groove
10 bp per turn of helix
horizontal distance covered by A-T is almost identical to G-C
what 3 factors within the double helix help stabilize the electrostatic repulsion of the phosphate groups?
- neutralized by positively charged species in cell (magnesium)
- base pair linkages provide stability
- base pairs stack on top of one another which allows for delocalization of electrons
what does increasing the salt concentration do to the stability of the DNA?
increases the stability of DNA
what do extreme pH do to the stability of the DNA?
decreases the stability through altering the ionization of the bases which form H-bonds
what does increasing the length of the DNA strand do to the stability?
increases stability
what does a higher GC content do to the stability of the DNA?
increases stability
where is circular DNA found?
prokaryotes and mitochondra
What occurs during methylation of base pairs?
methyl group is added to cytosine or adenine DNA nucleotides
what are the consequences of DNA methylation?
decreases gene activity and there is abnormal gene regulation
what is the major covalent modifcation of human DNA?
methylation of C at CpG sequences
when does methylation of cytosine mostly occur?
when cytosine is adjacent to a guanine
what does deamination of methylcytosine yield?
thymine
why is deamination of methylcytosine a serious problem?
because turns into thymine, then on replication, an adenine will be added instead of a guanine
what compound can increase the speed of deamination and where is it mostly found?
nitrous acid, cigarette smoke
what becomes sensitive to breakage after depurination?
phosphate backbone
what happens during depurination?
breaking off purine base from ribose and leaving a hydroxyl group
what can happen if you have a few depurinations right next to each other on DNA?
breakage of the phosphate backbone
what is usually created as a result of UV radiation in DNA?
thymine dimers
how are thymine dimers usually repaired?
nucleotide excision repair
what type of agents are considered carcinogens?
alkylating agents (mustard gas, dimethylsulfate, dimethylnitrosamine, CISPLATIN (cancer drug))
through what process does actinomycin D work?
intercalation. Molecule intercalates into the DNA and then replication cannot continue
why can intercalation cause cancer cells to enter apoptosis?
causes kink in DNA and replication cannot occur, therefore cell recognizes that it is not functioning properly
what does topoisomerase do?
removes knots of DNA by removing supercoils
what is underwound DNA?
produces negative supercoils and decreased twist
what is overwound DNA?
produces positive supercoils and increased twist
what are the 4 methods of attacking DNA metabolism?
- syntehsis of precursors (dNTP)
- intercalation (getting in the middle)
- covalently binding bps
- disrupting topoisomerases
what are the 3 main types of RNA in a human cell?
- structural
- regulatory
- information-containing
what is the function of rRNA?
(ribosomal RNA) make up functional units of ribosomes and translate mRNA
what is the function of tRNA?
(transfer RNA) brings amino acid specified by codon to ribosome
what is the function of snRNA and siRNA?
(small nuclear RNA and small interfering RNA) function with in-cell modifications such as splicing
what is the function of miRNA and siRNA?
(micro RNA and small interfering RNA) downregulate gene expression
which is more easily hydrolyzed when comparing RNA and DNA?
RNA
why is RNA more easily hydrolyzed than DNA?
there can be a nucleophilic attack by 2’ OH on the phosphodiester bond
what is the ease of hydrolyzing RNA important for?
changes in gene expression
what is the usually the final form of RNA in humans after it is produced?
single strand RNA
why can RNA produce many different conformations?
there is rotation around the bonds, not hindered by hydrogen bonds from another strand like in DNA
How does puromycin work?
nucleotide analogue that mimics tRNA acceptor region. therefore allows peptide transfer and termination of translation
where do most bacteria get their antibiotic resistance from?
environmental DNA such as plasmids
how does RNA form hairpin loops?
AU, GC, and GU base pairs
what does E site of ribosomes hold?
holds RNA that will exit
what does the P site of ribosomes hold?
holds tRNA with growing polypeptide attached
what does the A site of ribosomes hold?
holds the aminoacyl tRNA
what happens at the active site of a ribosome?
location where polypeptide chain is formed
what are the 4 types of structural RNA?
- rRNA
- tRNA
- snRNA
- snoRNA
what are the 2 types of regulatory RNA’s?
- miRNA
2. siRNA
which RNA is information containing?
mRNA
how is nucleic acid melting and annealing used to detect one specific DNA sequence in total cellular DNA?
you break the hydrogen bonds between the 2 strands of DNA thus pulling the 2 strands apart. After the DNA is in single strand form it wants to re-anneal with it’s complement. If you have a primer in the solution, you can measure if a certain patient has DNA specific to the primer or specific target that you are interested in.
