BIO 215 Exam 4

What is transcription the process of

DNA to RNA

what are the 3 main RNA products of transcription

rRNA, tRNA, and mRNA

explain this photo

rRNA’s make up the ribosome

explain this photo

tRNA’s are involved in translation

explain this photo

mRNA’s are the messages that are translated

explain the start site of prokaryotes for transcription

RNA polymerase binds to promoter through a promoter sequence at the transcription start site where transcription begins

what are the 3 steps of transcription

initiation, elongation, and termination

operons are found in

bacteria

what is an operon

multiple genes transcribed as one unit (oftentimes related genes or in same enzymatic pathway)

explain prokaryotic transcription initiation

one RNAP initiates transcription by binding to promoter (prinbow box with TATATT), sigma factors aid promoter recognition, without sigma it transcribes randomly

explain prokaryotic elongation for transcription

RNAP continues through the gene and transcribes, uses NTP’s for complementary sequences, hydrolyzes the pyrophosphate off

explain rho-dependent termination

form of prokaryotic termination, rho factor terminates transcription, rho protein is a DNA-RNA helicase, binds around a 72 base C region, uses ATP hydrolysis to move along RNA, breaks hydrogen bonds between RNA and DNA

explain rho-independent termination

internally complementary sequence near 3’ end of transcript folds to form hairpin loop structure that serves as termination signal and kicks of RNAP

what are the three RNAPs in eukaryotes

RNAPI (rRNA), RNAPII (main one, mRNA), RNAPIII (tRNA)

explain eukaryotic initiation for transcription

TATA box promoter, TBP/TFIID bind to the transcription start site, general transcription factors assemble RNAPII which forms the pre-initiation complex, TFIIH uses ATP and helicase to unwind DNA

explain chromatin and the major groove

transcription factors in eukaryotes must bind the DNA sequences obscured by chromatin, penetrates to the bases through the major groove of the DNA to read the sequence

explain elongation and termination in eukaryotes

dependent on phosphorylation of the CTD of the RNAPII, not much is known about termination

explain the promoters of RNAPIII

internal, 5S rRNA has two internal promoter sequences bound TFIIIs and RNAPIII, RNAPIII is lined up in the beginning to transcribe the whole thing

explain the promoters for RNAPI

normal, rRNAs, promoters, TFIs

what is the end product of transcription

RNA transcript

explain introns and exons

exons are expressed sequences and are retained, introns are intervening sequences and are spliced out

explain splicing using snRNPs

small nuclear ribonucleoproteins binds to pre-mRNA, 3 sites (5’, 3’, and branch sites)

explain the spliceosome

binding of snRNPs form the spliceosome, loops intron around after breaking bonds, lariat structure, joins the exons together

explain the other 2 groups of introns

Group I is mRNA and tRNA in bacteria, mitochondrial and chloroplasts, self-splicing ribozymes. Group II is also some mitochondrial and chloroplasts, some mRNA in bacteria, and encode proteins for splicing in vivo

explain capping

enzymatic addition of a methyl guanosine 5’ to 5’ cap, helps with stability, nuclear export, and ribosome binding

what happens to the 3’ end of mRNA

Poly(A) tail is added, which helps with half-life of mRNA in cytoplasm, nuclear export, and ribosome binding

explain rRNA cleavage

45S transcription units are transcribed as a precursor and processed into 3 mature rRNAs, (18S, 5.8S, and 28S), RNases and endonucleases degrade the spacer RNA

what happens after rRNAs are made

they are methylated by snoRNAs, which protects sites from cleavage

what is the first step of tRNA transcription

tRNAs are clustered together in genome,

explain tRNA processing

5’ leader removed, 3’ end replaced with CCA, modification of bases

explain ribosome export from nucleus

in nucleolus, assembles proteins and rRNAs, exports subunits out into cytoplasm

explain mRNA export from nucleus

nuclear transport factor binds mRNA, Poly(A) binding proteins and Cap binding proteins bind, exported through nuclear pore complex

what is a codon

3 base pairs and 1 amino acid

what is a degenerate

multiple codons for some amino acids

what are the important codons

AUG (start codon/methionine), UAA/UAG/UGA (stop codon, no amino acid, release factor)

explain percent coding

88% of genome coded by E.Coli, only 1.5% of genome coded in humans

explain the genetic code in prokaryotes

it is colinear which means the length of the gene in the DNA is proportional to the length of protein produced, has no introns/splicing, codon length is 4³ which means 64 codons can fit between the 20 amino acids

explain triplet codons

64 codons, must be non-overlapping, to test they took single/double/triple mutants to determine if base deletion caused protein or no protein