Transcription

Question 1

Central dogma

Answer 1

Normal flow of information in the cell- DNA holds information, transmits it between generations of cells, RNA is copied from DNA, proteins are made from RNA

Question 2

RNA

Answer 2

Singled-stranded nucleic acid, transcribed from DNA, has uracil instead of thymine, ribose instead of deoxyribose

Question 3

Similarities between RNA and DNA

Answer 3

Composed of nucleotides, synthesized in 5’-3’ direction, sequence is complementary to DNA template, 5’ phosphate, 3’ OH, internal phosphodiester bonds

Question 4

RNA polymerase

Answer 4

Synthesized RNA from DNA template, adds new base at 3’ end, uses NTPs as source, needs 3’ OH to add another base

Question 5

Function of RNA polymerase

Answer 5

Synthesis in 5’-3’ direction, reads DNA template in 3’-5’ direction, polymerase can correct errors

Question 6

Prokaryotic RNA polymerase

Answer 6

4 subunits, sigma factors scan DNA for promotors, polymerase binds to sigma, sigma separates, scans again, apoenzyme produces RNA, transcription in cytoplasm, allows simultaneous translation

Question 7

Holoenzyme

Answer 7

RNA polymerase bound to sigma factor

Question 8

Apoenzyme

Answer 8

RNA polymerase without sigma factor

Question 9

Eukaryotic RNA polymerase

Answer 9

Transcription in nucleus, different polymerases produce various types of RNA- RNA polymerase I, II, and III

Question 10

RNA polymerase I

Answer 10

Produces rRNA except 5S- structural and functional part of ribosomes

Question 11

RNA polymerase II

Answer 11

Produces mRNA- carries protein coding sequence

Question 12

RNA polymerase III

Answer 12

Produces tRNA, small RNAs (5S rRNA)- protein synthesis, splicing, gene regulation

Question 13

Action of polymerase

Answer 13

Reads template strand in 3’-5’ direction, adds ribonucleotides in 5’-3’ direction, RNA strand is displaced from 5’ end before synthesis is complete

Question 14

Template strand

Answer 14

DNA strand used by RNA polymerase

Question 15

Coding strand

Answer 15

DNA strand resembling the RNA produced, but it is not a substrate for RNA polymerase

Question 16

Polycistronic genes

Answer 16

Some prokaryotic genes, one RNA codes for more than one protein, all proteins part of the same metabolic pathway, can regulate whole pathway at once (ex- lac operon)

Question 17

Eukaryotic genes

Answer 17

Genes have several regions that are not important, promotor is at the 5’ end, not transcribed into RNA

Question 18

Prokaryotic promoter elements

Answer 18

Pribnow box at -10 TATAAT, recognized by sigma70 factor, TTGACA sequence at -35, recognized by sigma factors

Question 19

Eukaryotic promoter elements

Answer 19

Hogness or TATA box at -25, recognized by TFIID, CAAT boxes and GC rich regions between -40 and -100, specific transcription factor binding regions

Question 20

Eukaryotic transcription complex

Answer 20

In addition to RNA polymerase, TATA binding protein (TBP) and other transcription factors (TFII) are necessary for initiation, co-activators are promoter specific

Question 21

Cis element

Answer 21

DNA sequence that can potentially bind to a protein factor

Question 22

Trans factor

Answer 22

Protein that can potentially bind to a DNA sequence

Question 23

Enhancer element

Answer 23

Cis element that binds transcriptional activators and increases transcription rate

Question 24

Repressor

Answer 24

Proteins that bind to silencer elements and lower transcription rate

Question 25

Silencer element

Answer 25

Cis element that binds to repressors and lowers transcription rate

Question 26

Eukaryotic mRNA processing

Answer 26

Transcribed as hnRNA, 5’ cap added early during synthesis, poly A tail added, introns spliced out, transported out of the nucleus to the cytoplasm and ribosomes

Question 27

5’ cap structure

Answer 27

Cap is methylated GTP, triphosphate linkage, not cleaved by RNase, reverse insertion 5’ to 5’ linkage

Question 28

Polyadenylation

Answer 28

Poly A tail is not added at the end of the primary transcript, specific site indicates where to add poly A, RNA is cleaved and many A’s added by specific enzyme, not encoded in DNA, binding site for proteins that stabilize mRNA

Question 29

Splicing of mRNA

Answer 29

Introns must be removed before mRNA is mature, bases at each end of intron are signals, series of snRNPs perform splicing, forms a lariat structure and rejoins exons

Question 30

Thalassemias

Answer 30

A mutation found in patients with beta+-thalassemia is a point mutation near the 3’ end of the beta-globin gene (AATAAA to AACAAA) changes the sequence in hnRNA at the polyadenylation site

Question 31

Prokaryotic rRNA precursor

Answer 31

Large precursor to ribosomal RNA, also includes some tRNA, after folding into secondary structure, excess material is lost by cleavage of the backbone

Question 32

Maturation of rRNA

Answer 32

Transcribed as 45S precursor, several cleavage steps, 5.8S RNA pairs with 28S

Question 33

RIbosome assembly

Answer 33

Ribosomes are built in the nucleus (nucleolus), rRNA precursor cleaved in nucleolus, 5S is from separate gene, proteins are added to rRNAs, each subunit exported separately to the cytoplasm

Question 34

Structure of tRNA

Answer 34

Cloverleaf pattern, several bases altered after synthesis, includes thymine and pseudouracil

Question 35

Processing of tRNA

Answer 35

Introns and exons are present in prescursor, cleavage and splicing are necessary, bases altered, 3’ CCA added enzymatically

Question 36

Inhibitors of RNA synthesis

Answer 36

Drugs that bind to DNA and sterically hinder replication and transcription- actinomycin D

Question 37

Drugs that inhibit bacterial RNA synthesis

Answer 37

Drugs that bind to bacterial RNA polymerase- rifampicin/rifamycin- prevents transcription initiation, streptolydigin- prevents message elongation

Question 38

Rifampicin/Rifamycin

Answer 38

Prevents transcription initiation, not elongation, used to treat tuberculosis, meningitis, inhibits prokaryotic transcription initiation, binds to beta-subunit of bacterial RNA polymerase interferes with formation of initial phosphodiester bond in mRNA

Question 39

Streptolydigin

Answer 39

Prevents message elongation