Quiz #10

Question 1

What are codons and the triplet code?

Answer 1

DNA (and mRNA) are read as a series of non-overlapping three-letter words (a triplet code)

3 letter words = codons

in order to interpret the triplet code, the code must be read in the correct reading frame

codons are read in the 5’ –> 3’ direction along the mRNA, so codons are usually written in the 5’ –> 3’ direction

Question 2

What is the genetic code?

Answer 2

a table that shows which codons form which amino acids

there is redundancy in the genetic code

each codon has a specific meaning except for AUG, which has a dual function (codes for both methionine and signals to start translation)

three codons: UAA, UGA, and UAG, do not specify an amino acid, but are used as signals to stop translation

Question 3

What is the RNA polymerase (RNA pol)?

Answer 3

adds RNA nucleotides (5’ –> 3’)

does not require a primer (3’ OH)

has its own helicase activity

catalyzes phosphodiester bonds

reactants are ATP, GTP, CTP, and UTP

Question 4

How many RNA pol do bacteria, archaea, and eukaryotes have?

Answer 4

bacteria and archaea have one RNA pol for all transcription

eukaryotes have 3 classes of RNA pol for transcription

Question 5

What are the three classes of RNA pol used for transcription in eukaryotes?

Answer 5

RNA pol I: synthesizes rRNA

RNA pol II: synthesizes mRNA

RNA pol III: synthesizes tRNA

Question 6

What are promotors in transcription?

Answer 6

RNA pol initially binds to a specific DNA sequence called a promoter

said to “upstream” of the genetic information to be transcribed

provide a “target” for other proteins to bind to, which then recruit RNA pol in the correct orientation

direct the timing and frequency of initiation

Question 7

What is required for initiation of transcription?

Answer 7

the recruitment of a RNA pol, unwinding DNA helix, and beginning transcription

RNA pols do not require a primer to start synthesizing RNA, so initiation is usually the rate-limiting step in gene expression

Question 8

What does the promoter sequence look like in bacteria?

Answer 8

a typical bacterial promoter contains two consensus sequences, the Pribnow box (also called the -10 element) on coding strand and the -35 element

Question 9

What does the promoter sequence look like in eukaryotes and archaea?

Answer 9

many eukaryotic promoters contain a TATA box located 25-35 base pairs upstream of transcription start site

Question 10

What helps the RNA pol bind to the promoter in bacteria?

Answer 10

a protein called sigma binds directly to the -10 and -3 elements

RNA pol associates with sigma protein on the promoter

once transcription begins, sigma dissociates

Question 11

What helps RNA pol bind to the promoter sequence in eukaryotes?

Answer 11

none of the 3 classes of RNA pols can bind promoters of their own

several proteins called general transcription factors (GTFs) bind to promoter regions, and help recruit RNA pol to promoter

RNA pol I, II, and III each have their own set of GTFs

as transcription begins, some GTFs dissociate and are replaced by proteins required for elongation

Question 12

What are the three stages of transcription?

Answer 12

Initiation, Elongation, and Termination

Question 13

What happens in the initiation step of transcription?

Answer 13

DNA strands unwind, polymerase initiates RNA synthesis at the start point

Question 14

What happens at the elongation phase of transcription?

Answer 14

RNA pol catalyzes formation of phosphodiester bonds to synthesize the RNA polymer

the transcription “bubble” closes as the RNA pol moves forward

RNA pol moves downstream, making RNA transcript (5’ –> 3’ direction)

Question 15

What happens in the termination phase of transcription?

Answer 15

RNA transcript is released

Question 16

What does the termination of transcription look like in bacteria?

Answer 16

requires a sequence in the newly transcribed RNA that signals the end (called a terminator sequence)

Intrinsic: stem-loop forms because of GC-rich inverted repeat, this displaces RNA from template

Extrinsic: uses a nonstem-loop terminator sequence, and requires a protein with helicase activity, called rho (p) which binds to the transcript, and travelling faster than RNA pol, reaches the DNA/RNA duplex and unwinds it, RNA pol falls off

Question 17

What does the termination of transcription look like in eukaryotes?

Answer 17

RNA pol II transcribes a sequence in DNA called the polyadenylation signal sequence, in the pre-mRNA, this signal (AAUAAA) causes cleavage of the transcript and further processing, RNA pol keeps going, an RNA exonuclease eventually removes the trailing RNA and helps knock the polymerase off

RNA pol I is terminated when a protein binds to DNA downstream of coding region, and simply blocks it from proceeding further until it falls off

RNA pol III mechanism is not well understood

Question 18

Why can a single gene be transcribed simultaneously by several molecules of RNA pol?

Answer 18

happens in both eukaryotes and prokaryotes

allows a cell to produce a lot of RNA molecules in a short amount of time

the ability of a promoter to recruit RNA pol (initiation) can determine how much RNA is made in a given amount of time

Question 19

What post-transcriptional modifications occur to pre-mRNAs (in the nucleus)?

Answer 19

1. Addition of a 5’ cap: a modified form of guanosine is added to the 5’ end of the RNA polymer via an unusual 5’ to 5’ phosphate linkage
2. Addition of 50-250 adenine nucleotides to the 3’ end, known as the poly-A tail, the same enzymes that cut the RNA and add the poly-A tail
3. RNA splicing: large portions of pre-mRNA are removed (introns) and the remaining sections (exons) are pasted together in order, almost all eukaryote genes have introns

Question 20

What are the functions of the 5’ cap and the poly-A tail?

Answer 20

Facilitate the export of mRNA from nucleus

Protect the RNA from degradation by exonucleases

Help ribosomes attach to 5’ end of mRNA (occurs in cytoplasm)

Question 21

What are spliceosomes?

Answer 21

in some cases, RNA splicing is carried out by spliceosomes

spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize splice sites

Question 22

What are the steps of the RNA splicing reaction?

Answer 22

snRNPs and other proteins form a complex called the spliceosome

snRNA base pairs with nucleotides at specific sites along the intron

the spliceosome cuts the RNA, releasing the intron for rapid degradation, and ligates the exons together

Question 23

What are introns?

Answer 23

can vary in size (from 50 nucleotides to several thousand)

some evidence suggests that introns could have evolved from a mobile self-splicing element called a group II intron

Question 24

What are two possible reasons why introns have been retained in eukaryotic genes?

Answer 24

some introns contain sequences that help regulate the expression of genes (mechanism is not always clear)

alternative splicing allows for an increase in the diversity of proteins

Question 25

What is translation?

Answer 25

the process by which the genetic code in mRNA directs the synthesis of proteins from amino acids

Question 26

What were the steps in Marshall Nirenberg’s experiment?

Answer 26

he knew the DNA was read in a triplet code but didn’t know which codon encoded which amino acids

1. synthesized an artificial mRNA with repeating UUU codons
2. used cell extracts to translate the synthetic RNA in a test tube (in vitro translation)
3. checked the protein that he made, poly-U RNA gave rise to a polypeptide that had only phenylalanine amino acids
4. used other combinations of repeated nucleotides to determine which amino acids were specified by other codons

Question 27

What are the ingredients for translation?

Answer 27

tRNA (transfer RNA)

Aminoacyl-tRNA synthetases

Ribsosomes

Question 28

How is tRNA (transfer RNA) involved in translation?

Answer 28

tRNAs are the adaptor molecules that mediate the transfer of information from nucleic acid to protein

they are the “transfers” of the RNA code

tRNA consists of single RNA strand, about 80 nucleotides long

because of hydrogen bonds, the tRNA molecule twists and folds into a three-dimensional shape

the anticodon sequence is complementary and antiparallel to a codon in the mRNA

Question 29

How are Aminoacyl-tRNA synthetases involved in translation?

Answer 29

correct matching of tRNA and its associated amino acid is accomplsihed by aminoacyl-tRNA synthetases

there are 20 different synthetases for the 20 different amino acids

linking an amino acid to its tRNA is endergonic, the reaction is coupled to the hydrolysis of ATP

protein synthesis requires a steady supply of each of the 20 different charged tRNAs

Question 30

How are ribsomes involved in translation?

Answer 30

the enzymes of translation

facilitate the specific coupling of tRNA with mRNA codons during protein synthesis

catalyze the formation of peptide bonds

large complexes made of many proteins and rRNAs

Question 31

What is streptomycin?

Answer 31

catalyze the formation of peptide bonds

large complexes made of proteins and rRNAs

interferes with translation in bacteria, eukaryote 185 rRNA is structurally different, thus streptomycin has limited effect on translation of eukaryotic proteins

Question 32

What are the three binding sites for tRNA molecules on a ribosome large subunit?

Answer 32

1. A site: aminoacyl tRNA enters here
2. P site: holds the tRNA attached to the growing peptide chain
3. E site: discharged tRNA leave the ribsosome from this site

Question 33

What is the initiation step in translation?

Answer 33

involves the associated of four components (mRNA, tRNA, small subunit, large subunit)

ribosome mall subunit binds to Shine-Dalgarno sequence of mRNA, just upstream of the start codon, initiator tRNA hydrogen bonds to mRNA

many proteins called initiation factors are required to bring all translation components together, GTP hydrolysis provides the energy for assembly

Question 34

What is the elongation step in translation?

Answer 34

Codon recognition: anticodon of incoming aminoacyl tRNA pairs with complementary mRNA codon

Peptide bond formation: an rRNA of the large subunit catalyzes peptide bond between amino acid end of a.a. in A site and carboxyl end of the growing chain in the P site, polypeptide is removed from the tRNA in the P site and attached to the new amino acid in the A site

Translocation: ribosome translocates the tRNA in the A site to the P site (and moves in 3’ direction along mRNA by codon), empty tRNA in the P site is moved to the E site for release

Question 35

What is the termination step in translation?

Answer 35

ribosome reaches a STOP codon, a protein shaped like a tRNA (called a release factor) enters the A site

the release factor promotes hydrolysis of the bond between tRNA in the P site and the last amino acid of the polypeptide

the two ribosomal subunits and the other components, dissociate, 2 GTPs and other proteins are required

Question 36

How can bacteria simultaneously transcribe DNA and translate mRNA?

Answer 36

because they both take place in the same location

this does not happen in eukaryote, because transcription and translation are separated by nuclear envelope