Biochem - Molecular (Transcription & Translation Part 1)

Question 1

In what direction is DNA synthesized? What about RNA?

Answer 1

DNA and RNA are both synthesized 5’ => 3’

Question 2

What is the energy source for bonding of DNA/RNA, and where on the DNA/RNA is it located?

Answer 2

The 5’ end of the incoming nucleotide bears the triphosphate (energy source for bond).

Question 3

In what direction does protein synthesis occur?

Answer 3

Protein synthesis is N-terminus to C-terminus

Question 4

In what direction is mRNA read?

Answer 4

mRNA is read 5’ to 3’

Question 5

Explain 3’ hydroxyl attack, particularly by drugs.

Answer 5

The triphosphate bond is the target of the 3’ hydroxyl attack. Drugs blocking DNA replication often have modified 3’ OH, preventing addition of the next nucleotide (“chain termination”).

Question 6

What are the mRNA start codons?

Answer 6

AUG (or rarely GUG); Think: “AUG inAUGurates protein synthesis”

Question 7

What amino acids do mRNA start codons code in eukaryotes versus prokaryotes? What may be the fate of this amino acid in eukaryotes?

Answer 7

EUKARYOTES - Codes for methionine, which may be removed before translation is completed; PROKARYOTES - Codes for formylmethionine (f-met).

Question 8

What are the mRNA stop codons?

Answer 8

UGA, UAA, UAG; Think: “UGA = U Go Away, UAA = U Are Away, UAG = U Are Gone”

Question 9

Draw the functional organization of a eukaryotic gene, including and labeling the following: (1) Enhancer (2) Exon (3) Promoter (4) 5’ ends (5) 3’ ends (6) Intron (7) Sense/Coding strand (8) Template strand (9) Start of transcription (+1) (10) TATA box (11) Transcribed region (12) Termination signals.

Answer 9

See p. 73 in First aid 2014 for visual

Question 10

What characterizes the promoter, and what function does it serve?

Answer 10

Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT boxes)

Question 11

What commonly results from promoter mutation?

Answer 11

Promoter mutation commonly results in dramatic decrease in level of gene transcription

Question 12

What is an Enhancer, and what is its function?

Answer 12

Stretch of DNA that alters gene expression by binding transcription factors

Question 13

What defines a Silencer?

Answer 13

Site where negative regulators (repressors) bind

Question 14

Where are Enhancers/Silencers located in relation to the gene whose expression they regulate?

Answer 14

Enhancers and Silencers may be located close to, far from, or even within (in an intron) the gene whose expression it regulates

Question 15

Name the types of RNA polymerases in eukaryotes and the type of RNA made by each.

Answer 15

(1) RNA polymerase I makes rRNA (Think: “most numerous RNA, Rampant” (2) RNA polymerase II makes mRNA (Think: “largest RNA, Massive”) (3) RNA polymerase III makes tRNA (Think: “smallest RNA, Tiny”); Think: “I, II, and II are numbered as their products are used in protein synthesis”

Question 16

Besides making the different types of RNA, what functions do eukaryotic RNA polymerases serve?

Answer 16

No proofreading function, but can initiate chains. RNA polymerase II opens DNA at promoter site.

Question 17

What kind of RNA polymerase do prokaryotes make, and what does it do?

Answer 17

1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA

Question 18

What is the initial transcript (i.e., made from transcription ) called? In general, what happens to it?

Answer 18

Initial transcript is called heterogeneous nuclear RNA (hnRNA). hnRNA is then modified and becomes mRNA.

Question 19

What are the 3 major processes that occur following transcription, and where? What product results from them?

Answer 19

The following processes occur in the nucleus following transcription: (1) Capping of 5’ end (addition of 7-methylguanosine cap) (2) Polyadenylation of 3’ end (~ 200 A’s) (3) Splicing out of introns; Capped, tailed, and spliced transcript is called mRNA

Question 20

What occurs following RNA processing in eukaryotes?

Answer 20

mRNA is transported out of the nucleus into the cytosol, where it is translated

Question 21

Where is alpha-amantin found, and what is its mechanism? What clinical finding does it cause, and in what context?

Answer 21

Alpha-amantin, found in Amanita phalloides (death cap mushrooms), inhibits RNA polymerase II. Causes severe hepatotoxicity if ingested.

Question 22

Where are P-bodies found, and what is their purpose?

Answer 22

mRNA quality control occurs at cytoplasmic P-bodies, which contain exonucleases, decapping enzymes, and microRNAs; mRNAs may be stored here for future translation

Question 23

Does Poly-A polymerase require a template? What is the polyadenylation signal?

Answer 23

Poly-A polymerase does not require a template; AAUAAA = polyadenylation signal

Question 24

What are the 3 major steps in splicing of pre-mRNA?

Answer 24

(1) Primary transcript combines with small nuclear ribonucleoproteins (snRNPs) and other proteins to form spliceosome (2) Lariat-shaped (looped) intermediate is generated (3) Lariat is released to precisely remove intron and join 2 exons

Question 25

For which condition are antibodies to spliceosomal snRNPs (anti-Smith antibodies) highly specific?

Answer 25

Antibodies to spliceosomal snRNPs (anti-Smith antibodies) are highly specific for SLE

Question 26

With what disease are Anti-U1 RNP antibodies highly associated?

Answer 26

Anti-U1 RNP antibodies are highly associated with mixed connective tissue disease