Transcription, Translation, and DNA Repair

how does RNA polymerase know where to start transcribing?

it attaches to a sequenceof the DNA called the promoter, every gene has a promoter associated with it

other names for the template and nontemplate strand

template - nonsense strand, anticoding strand, antisense strand, transcribed strand
nontemplate - sense strand, coding strand

reasons for the 5’ cap

protects it from exonucleases (degrading), promotes ribosome binding, regulates nuclear export

reason for poly-A tail other than the ones for the 5’ cap

helps with transcription termination for RNA polymerase

how does miRNA silence mRNA

prevented from translating or sent on a pathway to degradation

rRNA’s role in translation and transcription

catalyzes the peptide bond formation in the polypeptide chain, splice out its own introns in the nucleus

function of small RNA

help form the signal recognition particle (binds onto the protein, that synthesized polypeptide chain and brings it to its final destination)

function of small interfering RNA

bind to mRNA and stimulate the break down of the mRNA

why is DNA polymerase III’s exonuclease activity specifically 3’ - 5’

when DNA polymerase III has to make that correction, it has to move backwards in the 3’ to 5’ direction

compare DNA polymerase III and DNA polymerase I exonuclease activity

DNA polymerase III is 3’ to 5’ and DNA polymerase I is 5’ to 3’

how does the protein in mismatch repair mechanism know where the incorrect base is?

there is distortion in the sugar backbone due to mismatched bases

a) nitrogen and oxygen
b) carbon and carbon
c) carbon and oxygen
d) carbon and nitrogen

d) carbon and nitrogen

a) increased rates of RNA splicing
b) increased rates of mRNA degradation
c) decreased rates of RNA splicing
d) decreased rates of mRNA degradation

b) increased rates of mRNA degradation

what happens to a cancer cell?

proliferates excessively because they can divide without stimulation from other cells and aren’t subject to normal controls on cell proliferation. can migrate by metastasis (to distant tissues by bloodstream or lymphatic system)

what are oncogenes? proto-oncogenes?

mutated genes that cause cancer; primarily encode cell cycle-related proteins
proto-oncogenes are oncogenes before mutation

how do oncogenes cause cancer?

the mutated alleles encode proteins that are more active than normal proteins, promoting rapid cell cycle advancement

compare proto-oncogenes and antioncogenes

proto-oncogenes, encode cell cycle-related proteins. mutation promotes tumour growth, one copy is enough to do so
antioncogenes, tumour suppressor genes; encode proteins that inhibit the cell cycle. mutation results in loss of tumour suppression, promoting cancer, both alleles need to be mutated (one functional copy is enough to inihibit tumour formation)

how is the DNA proofread during synthesis? what does it detect?

the two double-stranded DNA molecules will pass through a part of the DNA polymerase. unstable HB due to incorrectly paired bases

how does the enzyme discriminate which is the template strand and which is the incorrect daughter strand?

it looks at the level of methylation, the template strand would be more heavily methylated due to being in the cell for longer

what genes code for the machinery in the G2 phase for mismatch repair in eukaryotes? prokaryotes?

MSH2 and MLH1
MutS and MutL

what happens after an AP site is left behind?

AP site is recognized by enzyme AP endonuclease removes the damaged sequence from the DNA

how can prokaryotes be polycistronic?

translation of the mRNA can occur at different locationd resulting in different proteins

how is tRNA activated/charged with an amino acid?

each amino acid is activated by a diff aminoacyl-tRNA synthetase requiring two high energy bonds from ATP. aminoacyl-tRNA synthetase transfers the activated AA to the 3’ end (CCA sequence) of the correct tRNA

where does the energy come from to form peptide bonds during translation?

the high-energy aminoacyl-tRNA bond is used

where is rRNA synthesized?

in the nucleolus

what are ribozymes made of?

rRNA

T or F, the genetic code of codons is only unique to humans

false, this code is universal across species

how is the genetic code degenerate?

more than one codon can specify one AA, all AA’s but Met and Try have multiple codons

what is the wobble position?

AA’s with multiple codons often have the third base be variable, which is referred to as the wobble position

reason for the wobble position?

designed evolutionarily to protect against mutations in the coding regions, as mutations in the wobble position tend to be silent

what is a point mutation?

a mutation that affects one nucleotide in a codon. those that affect the primary AA sequence of the protein are called expressed mutations

what is the reading frame?

the three nucleotides of a codon

why is DNA transcribed to RNA?

DNA cannot leave the nucleus as it will quickly be degraded, so RNA is used to transmit genetic info

enzyme used to synthesize RNA

DNA-dependent RNA polymerase II

role of transcription factors

help RNA polymerase locate and bind to promoter region, help to establish where transcription will start

roles of other RNA polymerases

RNA polymerase I: kicated in nucleolus and synthesize rRNA
RNA polymerase II: located in nucleus and synthesize hnRNA (pre-processed) and some nuclear RNA (snRNA)
RNA polymerase III: located in nucleus and synthesize tRNA and some rRNA

T or F, RNA polymerase does not proofread its work like DNA polymerase

true, RNA polymerase does not proofread its work like DNA polymerase

what is used to locate important bases in the DNA strand?

a numbering system; first base transcribed is +1, to the left of it (toward 5’ end) are given - numbers and to the right (3’ end) are given + numbers

T or F, the RNA formed right after transcription is ready to be translated

false, right after transcription the RNA is termed heterogenous nuclear RNA (hnRNA) or pre-processed mRNA. it needs to go through posttranscriptional modifications before translation

how are the introns excised by the spliceosome?

exicsed in the form of a lariat (lasso-shaped structure) and then degraded

explain how the poly-A tail is like s fuse for a “time bomb”

as soon as the mRNA leaves the nucleus, it wills tart to get degraded from its 3’ end. the longer the tail, the mroe time it has to survive before being digested

T or F, the entire mRNA is always translated

false, untranslated regions of the mRNA (UTR) will still exist at the 5’ and 3’ edges because the ribosome initiates translation at the start codon (AUG) and end at a stop codon

what is the 5’ cap being added onto the mRNA?

a 7-methylguanylate triphosphate cap

T or F, the mature mRNA exits the nucleus through the nuclear pores

true, the mature mRNA exits the nucleus through the nuclear pores

T or F, the large and small ribosomal subunits are always bound together, even before protein synthesis

false, the large and small ribosomal subunits only bind together during protein synthesis

name the three ribosomal binding sites

A (aminoacyl)
P (peptidyl)
E (exit)

which rRNA strands make up the 80S ribosome in eukaryotes and where are they found

28S [60S large subunit], 18S [40S small subunit], 5.8S [60S large subunit], and 5S [60S large subunit] (diff strand sizes)

how are the rRNA strands that make up the ribosome transcribed

28S, 18S and 5.8S in the nucleolus are transcribed by RNA polymerase I as a single unit resulting in a 45S ribosomal precursor RNA
RNA polymerase III transcribes 5S outside the nucleolus

compare eukaryotic vs prokaryotic ribosome

eukaryotic: 80S → large subunit 60S contains 5S, 5.8S and 28S rRNA, small subunit 40S contains 18S rRNA
prokaryotic: 70S → large subunit 50S contains 5S and 23S rRNA, small subunit 30S contains 16S rRNA

names of the specialized factors used during translation and function

initiation factors (IF) + GTP during initiation →help large subunit bind to small subunit
elongation factors (EF) + GTP during elongation → help locate and recruit aminoacyl-tRNA and GTP while removing GDP
release factors (RF) + GTP during termination → binds to termination codon causing water molecule to be added
termination factors during termination → this + peptidyl transferase use the added water to hydrolyze the completed chain from the last tRNA

which ribosomal subunit binds to the mRNA first?

the small subunit

T or F, the first AA in prokaryotic proteins is methionine

false, the first AA in prokaryotic proteins is N-formylmethionine

what enzyme is involved in the peptide bond formation during elongation

peptidyl transferase, is part of the large subunit. GTP used for energy

what are signal sequences

found on some eukaryotic proteins, they designate where a protein should go. ie. those that’ll be secreted direct the ribosome to move to ER then sent to Golgi to be secreted from vesicle. other places include nucleus, lysosome, cell membrane

posttranslation modifications

cleavage → insulin is cleaved from a larger, inactive peptide to achieve its active form
phosphorylation → adding phosphate group by protein kinase to de/activate
carboxylation → adding carboxylic acid groups, usually serve as Ca binding site
glycosylation → adding oligosaccharides when proteins pass thru ER and Golgi to determine destination
prenylation → adding lipid groups to certain membrane-bound enzymes