Basic Molecular Genetic Mechanisms 1 (L1) Flashcards
basic nucleotide structure
phosphate + pentose sugar + N base
- phosphate on 5’ C
- N base on 1’ C
nucleoside structure
pentose sugar + N base only (no phosphate)
difference b/w RNA and DNA
RNA: ribose (OH on 2’ C)
DNA: deoxyribose (H on 2’ C)
bases for RNA vs. DNA
RNA: AUGC
DNA: ATGC
what are the purines and how many rings do they have?
adenine, guanine - 2 rings
what are the pyrimidines and how many rings do they have?
uracil, thymine, cytosine - 1 ring
bond made in the polymerization of nucleotides?
phosphodiester bone b/w 3’ -OH of the first nt and the 5’ phosphate of the next
what type of reaction is phosphodiester bond formation?
condensation rxn - one H2O removed
why does DNA use deoxyribose?
presence of the 2’ OH (like RNA) makes it susceptible to nucleophilic attack, breaking the phosphodiester bond and forming a 2’,3’-cyclic monophosphate derivative
what other nucleotide does each bind with?
A-T/U and G-C
what complementary nucleotides form 2 H-bonds?
A and T
what complementary nucleotides form 3 H-bonds?
G and C
what is the significance of the major and minor grooves on the DNA double helix?
different exposures of bases -> important for regulation
what type of DNA absorbs UV light better?
ssDNA
how can you denature dsDNA?
increase in temperature
what is the melting temp, Tm?
temp when 1/2 of the DNA is denatured - this is a fxn of the G-C content (more energy to break the 3 H-bonds)
how does G-C content affect melting temp of DNA?
more G-C, higher temperature to denature
what other structures can RNA have?
secondary and tertiary
what is the orientation of the strands during transcription?
template/ antisense strand of DNA is read 3’ to 5’ to produce mRNA 5’ to 3’
what does the mRNA have the same sequence as?
non-template/ sense strand
what are the three major stages of transcription?
initiation, elongation, termination
what occurs during the initiation stage of transcription?
RNA pol binds promoter, unwinds dsDNA
what occurs during the elongation stage of transcription?
building of mRNA
what occurs during the termination stage of transcription?
RNA pol reaches stop signal -> dissociation of the transcription unit
how does prokaryotic gene organization differ from that of eukaryotes?
prokaryote: operons - multiple genes transcribed together
eukaryote: individual genes - transcribed separately
what are the three modifications that transform pre-mRNA into mRNA?
- 5’ cap on mRNA
- splicing
- poly A tail
what is special about the 5’ cap on mRNA?
contains atypical nucleotide (7-methylguanylate) and has atypical linkage (5’-5’)
what is splicing?
excising out unnecessary introns to put together the exons containing information for the coding sequence
alternative splicing and implications?
putting together exons differently - can get different phenotypes: example w/ pax6 and aniridia (no iris)
what is the function of the poly A tail?
binds the PABP1 protein, which brings the end of mRNA to the front, creating a loop of mRNA -> allows efficient restart of translation once first round is done
what are the 3 major kinds of RNA?
mRNA, tRNA, rRNA
what is a codon?
3 nucleotides that code for a specific amino acid
degenerative nature of DNA
more than 1 codon per amino acid - difference is often at the wobble position (position 3 of the codon; 1 of the anticodon)
what is the start codon?
AUG/ATG (Met)
what are the stop codons?
UAA/TAA
UAG/TAG
UGA/TGA
which type of RNA contains the anticodon and amino acid?
tRNA
what is the significance of the reading frame?
changes in the reading frame often result in mutation
can a tRNA recognize multiple anticodons?
yes - wobble position
what is the purpose of rRNA?
composes the large and small ribosomal subunits that together comprise the ribosome
initiation of translation?
IF’s (IF-4) recognize 5’ cap, recruit small subunit that has other IFs - small subunit slides from cap and anchors on 5’ part of exon
which site in the ribosome does the new tRNA with the next amino acid bind to?
A site
what site in the ribosome contains the growing polypeptide chain?
P site
what is necessary for elongation in translation?
EF’s 1 and 2
function of EF-1?
binds GTP linked tRNA and bring it into A site
function of EF-2?
hydrolyzes GTP to provide energy for ribosome translocation
what is necessary for termination of translation?
once stop codon is recognized, need RF to dissociate the translation complex
what does PABP1 bind?
poly A tail and IF-4: involved in looping of mRNA to keep translation efficient
