DNA & RNA Flashcards
What are the monomeric units of DNA and RNA?
nucleotides
What are the 3 components of nucleotides?
nitrogenous base, 5-carbon sugar (ribose), phosphate group(s)
What are the two classes of nitrogenous bases?
purines (2 ring), pyrimidine (1 ring)
What carbon determines whether its ribose or deoxyribose?
2’ carbon (if OH then ribose, RNA, if H group than deoxyribose, DNA)
How are ribose/deoxyribose linked to nitrogenous bases?
1’ carbon and N1 in pyrimidines or N9 in purines
The sugar ribose cyclizes into what if it’s in RNA?
beta-D-furanose
The sugar ribose cyclizes into what if it’s in DNA?
beta-2’-deoxy-D-furanose
What are the two puckers of furanose? Where are they found?
C-2’ endo (B-form DNA), C-3’ endo (RNA)
What is a nucleoside vs nucleotide?
nucleosides don’t have the phosphate rgoup
How many phosphate groups can a nucleotide have?
1, 2, or 3
Where are the phosphate groups attached on a nucleotide?
5’ carbon
What are the names for the phosphates attached to a nucleotide?
alpha (closest to ribose), beta (middle), gamma (furthest from ribose)
What does the 5’ end and 3’ end have?
phosphates
hydroxyl
WHat end are polynucleotides synthesized from?
3’ end
Are G-C bonds or A-T bonds more stable?
G-C b/c 3 hydrogen bonds instead of 2
WHat parts of dna are hydrophillic/phobic?
phosphate backbone is hydrophillic, nitrogenous bases are hydrophobic
What is the helix stabilized by?
stacking (van der waals forces) and hydrogen bond interactions
How can the faces of the base pairs be accesed?
major/minor groove
What is the watson-crick face?
between the H-bond strands
Why is RNA normally in A form and DNA in B?
the presence of the 2’ OH in RNA and its absence in DNA forces them into these conformations
What did the Hershey-Chase experiment prove?
that DNA was the genetic material, phages only injected their DNA into the thing they were infecting
Why does heating DNA strands cause the DNA to denature?
hydrogen bonds between the bases break
Can DNA be renatured? How?
yes, it can be by slow cooling
What makes RNA more flexible than DNA?
presence of the 2’ OH
WHat are some possible single stranded RNA structures?
bends, loops, bulges, hairpins, and folding back on itself to make helices
What are the smallest types of RNA?
tRNA
What do nucleases do?
catalyze the hydrolysis of phosphodiester bonds
What do exonucleases do?
degrade DNA from the ends of the nucleic acid
What do endonucleases do?
make an internal cleavage
What do restriction endonucleases look for?
they recognize palindromic sequences
What does a palindromic sequence look like?
read the same from 5’ direction and 3’
How is DNA in bacteria cell organized?
into chromatin via interactions with proteins
What is the smallest unit of chromatin called?
nucleosome
What is a nucleosome made up of?
8 histone protein (2 of 4 types)
What are the four types of histone proteins in a nucleosome?
(H2A, H2B, H3, H4) x2
What were the three potential models of DNA replication?
conservative, semi-conservative, dispersive
Where does DNA replication start?
origins of replication (makes replication bubbles)
What direction does DNA replication happen?
5’ to 3’
What polymerase is involved in dna replication in prokaryotes?
DNA pol III
What does the exonuclease activity of DNA pol mean?
DNA polymerase travels in the 3’ to 5’ direction correcting mistakes
In bacteria which dna polymerases proof read?
all three (I, II, III)
What is the difference between the leading and the lagging strand?
leading strand is made in one continuous strand
lagging strand is made in fragments called okazaki fragments (discontinuous)
What does DNA Pol III start synthesizing from? Why is it needed?
primer (made by primase)
needs a free 3’ hydroxyl end
Does RNA need a primer?
no
How are the RNA primers removed and replaced with DNA?
5’ to 3’ exonuclease and DNA Pol I
What seals the gaps in phosphodiester backbone?
ligase
What are spontaneous mutations?
caused during replication or normal cellular processes
What are induced mutations?
caused by a mutagen
What is a purine-purine or pyrimidine-pyrimidine swap called?
transition
What is a purine-pyrimidine swap called?
transversion
What are insertions vs deletions?
1 nucleotide is added vs removed (cause change in reading frame)
What do silent mutations do?
no change in amino acid
What do missense mutations do?
change the coded amino acid
What do nonsense mutations do?
change amino acid to a stop codon
How is a mismatch repaired in E coli?
MutL and MutS recognize deformations, make a complex that loops up the dna til it finds a methyl group, makes a nick and then endonucleases degrade it after its filled in by DNA pol III
In gel electrophoresis where does DNA migrate? Why?
to the anode
b/c negative charge
How can you estimate size usin gel electrophoresis?
small pieces move faster, can also buy a tube of dna with known sizes to compare
Why is RNA gel electrophoresis more complicated?
rna can take different shapes which can impact how fast it moves
What is the central dogma?
dna is transcribed into rna and then translated into protein
What is the coding strand?
RNA that has the same sequence of DNA (swapping t with u)
If you are given the noncoding strand and asked to give the transcibred sequence what would you do?
first write the coding strand (remember the primes are opposite), then transcribe (swap T for U) (remember 5’ to 3’ direction)
What is the nontemplate strand also called?
coding strand
What are the subunits of RNA polymerase?
2 alpha, 2 beta, gamma, and sigma
What does the sigma subunit of rna polymerase do?
binds and helps to recruit rna polymerase to promoters on the dna (can come on or off)
Does rna transcription need a primer?
no
What direction does rna transcription occur?
5’ to 3’
Where does the sigma subunit bind on the promoter?
-10 region, so it counts 10 nucleotides and then starts transcribing
Where does rna transcription stop?
at the terminator (not stop codon)
How does rho independent transcription termination work?
rna polyermase finds a terminator sequence, forms a hairpin at palindromic sequence (lots of UA pairs), force pulls it out of active site
How does rho dependent transcription termination work?
rho helicase binds to a rut site, this migrates along mRNA to rna polyermase, it then seperates from dna template
In prokaryotes where does transcription/translation occur? Are they coupled?
both in cytoplasm, yes
In eukaryotes where does transcription/translation occur? Are they coupled?
transcription in nucleus and translation in cytoplasm, no
What does the core promoter do?
recruit rna pol II and its general transcription factors which recuit rna polyemrase (tata box)
How does rna pol II initiate transcription?
assembles its general transcription factors, then dna is unwound and the first few nucleotdies are transcribed, the CTD of rna pol II is phosphorylated, allows it to clear the promoter and enter elongation
What does rifampycin do?
inhibits initiation of RNA synthesis
What does a-amanitin do?
binds to RNA polymerase directly
What does Actinomycin D do?
inhibits elongation
How many rna polyermases are in eukaryotes? How were they discovered?
3, have various sensitivity to a-amanitin
What is capping?
eukaryotic mRNA get a 5’ cap made up of a N7 methyl G cap linked to the first nucleotide transcribed by rn pol ii
How is the 5’ cap attached?
5’ to 5’ triphospahte linkage
Why is the 5’ cap important?
gene expression and protects from degradation
What is splicing? What is spliced?
some sequences found in dna are transcribed into mrna are not found in mature mrna, introns
How are most eukaryotic introns spliced? What are its subunits called?
spliceosomes, snRNPS
Why do snrnps have a rna and protein component?
rna component helps then bind to intron
What is the poly A tail?
a chain of A at 3’ end, they are recruited by the consenses sequence
What is teh consensus sequence?
poly A machinery is recruited by it, AAUAAA found in mrna
What does the poly A tail do?
enchances gene expression and prtects from degradation
What does the secondary/tertiary structure of tRNA look liek?
clover/elbow
What do tRNAs all end with?
CCA
What links amino acids to trna?
enzymes called aminoacyl-tRNA synthetases in a reaction called charging (ATP)
How is mrna read in translation?
5’ to 3’
What is the stop codon?
UAA, UAG, UGA
What are the three steps to the elongtion phase of translation?
decoding, peptide bond formation, translocation
Do tRNA and rRNA have a cap? Why?
no because they fold up so there 5’ end are unavaible
How many Poly A binding proteins are on a poly a tail?
many
When is the tRNA extra arm found?
serina trna
What is the shine dalgarno sequenec?
sort of like prokaryote version of cap
What do IF1 and IF3 do?
bind the small subunit and prevent the large subunit from binding until its time
What does IF2 do?
has GTP on it, recruits first trna, hydrolysis of this gtp signals that initiation is done
How does initiation happen?
30S subunit binds if1 and 3 and then binds small subunit, if2 binds and recruits fMET trna which base pairs with start codon, gtp is hydrolysed and complex dissociates
In prokaryotes what does the first trna contain?
n-formyl methionine instead of just methionine (like eukaryotes)
What does the decoding step of elongating require?
70S ribosome, elongation factors EF-Tu and Ef-Ts, EF-Tu is how decoding happens (binds to trna to bring into a site), EF-Ts is how EF-Tu is remade (both have GTP attached)
How does the peptide bond formation step of elongation happen?
happens spontaneously, amino acid from the trna in the P site binds to the new amino acid in the a site
How does the translocation step of elongation happen?
EF-G moves the tRNA from a site to p site, and from p site to e site (resets)
How does termination occur in translation?
termination factors/release factors add water (hydrolysis) instead of an amino acid to release the protein from the p site, IF3 keeps ribosome subunits apart
What steps of translation don’t use GTP?
peptide bond formation and termination
How many ribosomes can bind to a mRNA? What is this called?
more than one, polysome
What are SRPs?
signal recognition proteins, for targetting proteins to membrane/ER
What are many proteins targeted for degradation modified with?
chain of ubiquitin (Ub)
How is ubiquitin added to proteins?
activated by an E1 activating enzyme using atp hydrolysis, transfered to E2 conjugating enzyme, Ub is then targeted to lysine on protein by E3 ligase
