MMT: Nucleic Acids II Flashcards
Compare and contrast the molecular structures of DNA and RNA in terms of base composition, ribose, phosphodiester bonds, base pairings, and polarity.
both have polarity, even with RNA being single stranded unlinke DNA. It has the same 3’ to 5’ phosphodiester bonds. DNA and RNA are both very flexible, due to the bonds/molecule being able to rotate.
their main differences are that DNA is double stranded while RNA is single stranded, and DNA uses bases ATGC while RNA uses AUGC
Explain why RNA is hydrolyzed under alkaline conditions, but DNA is not
Under alkaline conditions, the OH group in RNA can become reactive by the loss of its proton. This results in non-enzymatic hydrolysis of the phosphodiester bonds to generate free nucleotides. DNA, in comparison, denature under alkaline conditions due to the disruption of hydrogen bonds between base pairs. However, the phosphodiester bonds stay in tact so the strands stay intact.
name and briefly describe the main features that characterize the secondary structure of RNA
complementary base-pairing: Double stranded regions form by G-C and A-U base pairing
unmatched bases: buldges in double stranded regions
mismatched base pairing: GU base pairings (2 H bonds) can occur in double stranded regions
stem-loops: stem of double-stranded RNA with single stranded loop forms a “hairpin”
Distinguish between the coding strand and template strand of DNA. Specify the strand that is complementary to RNA and the strand that is identical to RNA (except U replaces T).
Template Strand: DNA strand that is transcribed in the 5´ to 3´ direction to synthesize RNA. RNA sequence is complementary to its template strand of DNA
Coding Strand: DNA strand that is not transcribed. RNA sequence (5´ to 3´) is identical to the coding strand of DNA except U replaces T
what types of RNA are common among prokaryotes and eukaryotes
rRNA, tRNA, mRNA
describe the classes of RNA found in prokaryotes
rRNA: around 80% of total RNA in bacteria is rRNA. They have a 30s and 50s subunit.
tRNA: about 15% of total tRNA in bacteria. There’s at least 20 different rRNAs. 4s with average length of 80 nucleotides. They fold into the classic clover shape.
mRNA: 5% of total RNA in bacteria. They’re heterogenous as they code for many proteins. They have start and stop codons. They are also polycistronic, meaning there are multiple protein coding sequences per mRNA.
describe the three main classes of RNA found in eukaryotes
rRNA: small unit is 40s assembled from 18s, large unit is 60s assembled from 28s, 5s, and 5.8s.
tRNA: same as prokaryote
mRNA: They’re heterogenous as they code for many proteins. Composed of a region not coded for, a start codon, and a single protein coding sequence (monocystronic). They then have a stop codon, followed by another sequence of non-coding.
what is miRNA?
a type of RNA found in eukaryotes; small, noncoding RNA’s that have a sequence complementary to a sequence in the mRNA (typically the 3’ UTR region). This can bind to the mRNA and stop it from being translated or degrade it.
what is siRNA?
a type of RNA found in eukaryotes;: very similar to miRNA, but form intracellularly or are taken up from a virus
what is lncRNA?
a type of RNA found in eukaryotes; noncoding RNA that is variable in length and function. It can find a specific sequence on RNA or DNA and bind via complementary base pairing. Can recruit other proteins or RNAs to work on the gene.
Describe the basic components of ribosomes in prokaryotes and eukaryotes.
Prokaryotes: small (30s) unit has a 16s rRNA, large has 23s and 5s assembled into a 50s subunit
eukaryotes: small unit is 40s assembled from 18s rRNA, large unit is 60s assembled from 28s, 5s, and 5.8s rRNA.
Identify the following components of a eukaryotic mRNA molecule : 7-methylguanosine cap, 5´-UTR, coding sequence, 3´-UTR, polyA tail.
Describe the structural and functional differences between prokaryotic and eukaryotic mRNAs.
Prokaryotic mRNA is polycistonic, while eukaryotic is monocystonic, this means the prokaryotic mRNA can code for many proteins with one strand, where the eukaryotic has one protein coding sequence in a strand.
Describe DNA and RNA in alkaline conditions
Under alkaline conditions, the OH group in RNA can become reactive by the loss of its proton. This results in non-enzymatic hydrolysis of the phosphodiester bonds to generate free nucleotides. DNA, in comparison, denature under alkaline conditions due to the disruption of hydrogen bonds between base pairs. However, the phosphodiester bonds stay int act so the strands stay intact.
Describe RNA hybridization to DNA
RNA can anneal to a single stranded DNA via complementary base pairing. This happens in processes such as priming of DNA synthesis. It is also very important in terms of experimental methods!
