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The next two questions are what I call a procedural question.

If I want to know if you


understand a procedure or a biochemical pathway I could ask you to draw the pathway.
But what about in the multiple choice format? To do this in a multiple choice format I as
you to put a procedure/list/recipe in the correct order. On an exam, it might be a bit
shorter because of time constraints.
When you are faced with one of these on an exam, it would behoove you to quickly rule
of certain choices. Look for things that are absolutely wrong. Then mark out all answer
choices that contain that particular entry. This should give you a smaller list of possible
answers to choose from.
1.

From the list below, I want you to tell how translation initiation occurs in
PROKARYOTES. You will finish with the formation of a dipeptide.
You should use as many of the choices as possible. But you should NOT use all of
them.
If you can draw the process then you should be able to put this list in the correct order.
1.
A charged fmet-tRNA binds the start codon.
2.
A charged met-tRNA binds the start codon.
3.
A charged tRNA that decodes the second codon enters the A site of the ribosome.
4.
A charged tRNA that decodes the second codon enters the E site of the ribosome.
5.
An uncharged tRNA enters the A site and is charged by peptidyl transferase.
6.
First, transcription of the mRNA must finish before translation can begin.
7.
Peptidyl transferase catalyzes the formation of a peptide bond between the amino
acid in the P site and the A site of the ribosome.
8.
Peptidyl transferase charges the tRNA in P site. This makes it chemically reactive
and a peptide bond quickly forms between the amino acid in the P site and the A
site of the ribosome.
9.
Second, the mRNA must be transported from the nucleus to the cytoplasm
10. The large subunit assembles in such a way that the initiator tRNA is in the
completed P site.
11. The ribosome translocates three nucleotides down the mRNA.
12. The small riboosomal subunit scans the mRNA from the 5' methylated Cap until it
locates the start codon. The start codon is almost always the first AUG in the
mRNA.
13. The small ribosomal subunit positions itself correctly by interacting with (binding)
the Shine-Delgarno sequence within the mRNA.
14. The uncharged tRNA is now in the E site, the tRNA carrying a dipeptide is in the P
site and the A site is empty awaiting another charged tRNA.
15. This places the start codon in the P site of the small subunit.

The correct order of this list is:

A)
B)
C)
D)
E)

12, 15, 1, 10, 3, 7,


13, 15, 1, 10, 3, 7,
13, 15, 1, 10, 4, 7,
13, 15, 2, 10, 3, 7,
6, 9, 13, 15, 1, 10,

14, 11
11, 14 *
11, 14
14, 11
5, 8, 11, 14

**ANSWER EXPLANATION**
The correct order is:
13, 15, 1, 10, 3, 7, 11, 14
13. The small ribosomal subunit positions itself correctly by interacting with (binding)
the Shine-Delgarno sequence within the mRNA. *1*
15. This places the start codon in the P site of the small subunit. *2*
1.
A charged fmet-tRNA binds the start codon. *3*
10. The large subunit assembles in such a way that the initiator tRNA is in the
completed P site. *4*
3.
A charged tRNA that decodes the second codon enters the A site of the ribosome.
*5*
7.
Peptidyl transferase catalyzes the formation of a peptide bond between the amino
acid in the P site and the A site of the ribosome. *6*
11. The ribosome translocates three nucleotides down the mRNA. *7*
14. The uncharged tRNA is now in the E site, the tRNA carrying a dipeptide is in the P
site and the A site is empty awaiting another charged tRNA. *8*
These should NOT be used for either prokaryotic or eukaryotic translation.
4.
A charged tRNA that decodes the second codon enters the E site of the ribosome.
5.
An uncharged tRNA enters the A site.
8.
Peptidyl transferase charges the tRNA in P site. This makes it chemically reactive
and a peptide bond quickly forms between the amino acid in the P site and the A
site of the ribosome.
These entries are eukaryotic specific.
2.
A charged met-tRNA binds the start codon.
6.
First, transcription of the mRNA must finishes before translation can begin.
9.
Second, the mRNA must be transported from the nucleus to the cytoplasm
12. The small riboosomal subunit scans the mRNA from the 5' methylated Cap until it
locates the start codon. The start codon is almost always the first AUG in the
mRNA.

2.

From the list below, I want you to tell how translation initiation occurs in
EUKARYOTES. You will finish with the formation of a dipeptide.
You should use as many of the choices as possible. But you should NOT use all of
them.
If you can draw the process then you should be able to put this list in the correct order.
1.
2.
3.
4.
5.
6.
7.
8.

9.
10.
11.
12.

13.
14.
15.

A charged fmet-tRNA binds the start codon.


A charged met-tRNA binds the start codon.
A charged tRNA that decodes the second codon enters the A site of the ribosome.
A charged tRNA that decodes the second codon enters the E site of the ribosome.
An uncharged tRNA enters the A site and is charged by peptidyl transferase.
First, transcription of the mRNA must finish before translation can begin.
Peptidyl transferase catalyzes the formation of a peptide bond between the amino
acid in the P site and the A site of the ribosome.
Peptidyl transferase charges the tRNA in P site. This makes it chemically reactive
and a peptide bond quickly forms between the amino acid in the P site and the A
site of the ribosome.
Second, the mRNA must be transported from the nucleus to the cytoplasm
The large subunit assembles in such a way that the initiator tRNA is in the
completed P site.
The ribosome translocates three nucleotides down the mRNA.
The small riboosomal subunit scans the mRNA from the 5' methylated Cap until it
locates the start codon. The start codon is almost always the first AUG in the
mRNA.
The small ribosomal subunit positions itself correctly by interacting with (binding)
the Shine-Delgarno sequence within the mRNA.
The uncharged tRNA is now in the E site, the tRNA carrying a dipeptide is in the P
site and the A site is empty awaiting another charged tRNA.
This places the start codon in the P site of the small subunit.

The correct order of this list is:

A)
B)
C)
D)
E)

12, 15, 1, 10, 3, 7,


13, 15, 1, 10, 3, 7,
13, 15, 1, 10, 5, 7,
6, 13, 15, 1, 10, 3,
6, 9, 12, 15, 2, 10,

14, 11
11, 14
14, 11
7, 11, 14
3, 7, 11, 14

**ANSWER EXPLANATION**
The correct order is:
6, 9, 12, 15, 2, 10, 3, 7, 11, 14
6.
First, transcription of the mRNA must finishes before translation can begin.
9.
Second, the mRNA must be transported from the nucleus to the cytoplasm.
12. The small riboosomal subunit scans the mRNA from the 5' methylated Cap until it
locates the start codon. The start codon is almost always the first AUG in the
mRNA.
15. This places the start codon in the P site of the small subunit.
2.
A charged met-tRNA binds the start codon.
10. The large subunit assembles in such a way that the initiator tRNA is in the
completed P site.
3.
A charged tRNA that decodes the second codon enters the A site of the ribosome.
7.
Peptidyl transferase catalyzes the formation of a peptide bond between the amino
acid in the P site and the A site of the ribosome.
11. The ribosome translocates three nucleotides down the mRNA.
14. The uncharged tRNA is now in the E site, the tRNA carrying a dipeptide is in the P
site and the A site is empty awaiting another charged tRNA.
These should NOT be used for either prokaryotic or eukaryotic translation.
4.
A charged tRNA that decodes the second codon enters the E site of the ribosome.
5.
An uncharged tRNA enters the A site.
8.
Peptidyl transferase charges the tRNA in P site. This makes it chemically reactive
and a peptide bond quickly forms between the amino acid in the P site and the A
site of the ribosome.
These should not be used because they are prokaryotic specific events.
13. The small ribosomal subunit positions itself correctly by interacting with (binding)
the Shine-Delgarno sequence within the mRNA.
1.
A charged fmet-tRNA binds the start codon.

3.

Which of the following clearly prove that, in prokaryotes, the translation


initiation codon (start codon) is not necessarily the first methionine codon in
a mRNA?
A) monocistronic mRNAs
B) polycistronic mRNAs *
C) The existence of an special tRNA that is used to initiate translation.
D) the fact that methionine codons are found internally in the mRNA

4.

During translation the term charged tRNA means that


A) the tRNA has a reactive hydroxygroup.

B)
C)
5.

the tRNA has an amino acid covalently attached to its 3' end. *
the tRNA has an amino acid covalently attached to its 5' end.

What are the minimum number of anticodons necessary to decode the six
different codons for leucine?
A) 1
B) 3*
C) 6

Explanation
321
3' AAU 5' anticodon
5' UUA 3' codon
123
321
3' AAU 5' anticodon
5' UUG 3' codon
123
321
3' GAI 5' anticodon
5' CUU 3' codon
wobble base-pairing
3' GAI 5' anticodon
5' CUC 3' codon
wobble base-pairing

wobble base-pairing
U can bp with A or G

3' GAI 5' anticodon or GAU anticodon


5' CUA 3' codon
wobble base-pairing

3' GAC 5' or GAU anticodon


5' CUG 3' codon
wobble base-pairing
6.

The Shine-Delgarno sequence is used in


A)
B)

7.

Amino acids are covalently added to the _________ end of a tRNA. Once
added, the tRNA is said to be _________.
A)
B)
C)
D)
E)

8.

3' , activated
3' , charged*
3' , formylated
5' , activated
5' , charged

The 3' end of mRNA encodes the _________ terminus of the encoded
protein.
A)
B)

9.

eukaryotes
prokaryotes*

amino
carboxy*

Refers to a series of nucleotides that are being read (conceptually or by a


tRNAs and ribosomes), as codons. These are being read consecutively three at
a nucleotides at a time. The nucleotide that you begin at will determine which
codons you read as you proceed. Each gene encodes three different sets of
codons. If I begin reading at a nucleotide called #1 then I will read one pattern of
codons and if I begin at the next nucleotide (#2), then I will read a different sent of
codons. Finally, if I begin at nucleotide #3 I will read still again another set of
codons. If you advance one more nucleotide and start at nucleotide #4 then you
will be reading from the same set of codons as when we began at #1.

What term most closely describes or matches what I am talking about?


A) codon degeneracy
B) codon redundancy
C) exonic region
D) reading frame *
E) triplet frame
10. The Shine-Dalgarno sequence
A)
B)
C)
D)
E)

is used by prokaryotic polymerase to recognize the transcription start site (+1).


interacts with RNA polymerase during transcription termination.
is used by prokaryotic ribosomes to recognize the AUG translation start codon in a
mRNA.*
is used by eukaryotic ribosomes to recognize the AUG translation start codon in a
mRNA.
is used by the spliceosome to recognize the 3' acceptor site of an intron.

11.

A mutation that removes a Shine-Dalgarno sequence from a gene will

A)
B)
C)
D)
E)

cause RNA polymerase to be unable to determine the correct transcription start site.
prevent the mRNA from being transported out of the nucleus.
stop the ribosome from recognizing the AUG translation start codon.*
interfere with mRNA polyadenylation
A and C

12. Which types of RNA are translated?


A) rRNA
B) tRNA
C) mRNA *
D) snRNA
E) microRNA
13. Transcription occurs in the ________ and translation occurs in the
__________ of eukaryotic cells.
A)
B)
C)
D)

nucleus, cytoplasm *
cytoplasm, nucleus
nucleus, nucleus
cytoplasm, cytoplasm

14. The genetic code is said to be degenerate. This means that


A) Some amino acids are specified by more than one codon. *
B) Some codons specify more than one amino acid.
C) Some codons specify non standard amino acids such as selenocysteine.

D)

There are more codons than there are amino acids.

15. Which nucleotide of the codon is involved in wobble base pairing?


A) 1st
B) 2nd
C) 3rd *
D) 4th
16. Which nucleotide of the anticodon is involved in wobble base pairing?
A) 1st *
B) 2nd
C) 3rd
D) 4th
17. The anticodon is a part of what molecule?
A) mRNA
B) ribosome
C) rRNA
D) tRNA *
18. In wobble base pairing which nucleotide can base pair with C, A, or U?
A) deoxysine
B) dideoxy guanosine
C) guanosine
D) inosine *

19. What is a charged tRNA?


A) A tRNA that has been inserted into the A site of the ribosome.
B) A tRNA that is carrying an activated anticodon
C) A tRNA that is occupying the P site of a ribosome
D) A tRNA with an amino acid covalently attached to its 3' end. *
20. The ribosome is composed of what?
A) protein
B) protein and tRNA
C) RNA
D) RNA and protein *
21. There are ________ codons in the genetic code.
A) 1
B) 20

C)
D)
E)

3
61
64 *

22. How many codons do not specify an amino acid?


A) 1
B) 20
C) 3 *
D) 61
E) 64
23. How many stop codons are there?
A) 1
B) 20
C) 3 *
D) 61
E) 64
24. A mutation that alters a codon so that it specifies a different amino acid is
called a _________ mutation.:
A) frameshift
B) missense *
C) silent
D) nonsense
E) none of the above
25. A nonsense mutation:
A) causes an amino acid substitution
B) reverts a silent mutation
C) causes the production of a truncated protein*
D) a & b
E) c & a
26. A nonsense mutation does what?
A) It alters a protein coding gene so that it becomes an RNA encoding gene.
B) It changes a codon into a nonsense (stop) codon. This causes the protein
synthesis to terminate prematurely. *
C) It changes a codon so that it specifies a different amino acid. The term
nonsense is derived from the idea that the new amino acid does not make
"sense" at its current position.
27. A mutation that is characterized by a change in the DNA sequence, but no

change in the resulting protein sequence, is called a


A.
B.
C.
D.

frameshift mutation.
missense mutation.
silent mutation. *
nonsense mutation.

28. Nonsense codons are:


A) codons that code for multiple amino acids
B) codons that code for no amino acids
C) codons that cause translation to stop
D) b & c *
E) none of the above
29. Genes are transcribed in the ______________ direction.
A) 3' to 5'
B) 5' to 3' *
C) amino to carboxy
D) carboxy to amino
30. mRNA is translated in the _____________ direction
A) 3' to 5'
B) 5' to 3' *
C) amino to carboxy
D) carboxy to amino
31. Proteins are synthesized in the _____________ direction.
A) 3' to 5'
B) 5' to 3'
C) amino to carboxy *
D) carboxy to amino
32. Which of these is NOT a character of the genetic code?
A)
B)
C)
D)

There are the same number of codons as there are amino acids. *
The code is used by nearly every living organism.
Some amino acids have multiple codons.
The code is degenerate.

33. An anticodon is a physical component of a/an _______ molecule.

A)
B)
C)
D)

DNA
mRNA
rRNA
tRNA *

34. This figure below is probably a


A)
*B)
C)
D)

FIGURE QUESTION

monocistronic mRNA from yeast


polycistronic mRNA from bacteria
monocistronic mRNA from bacteria
polycistronic mRNA from yeast

Legend
= ribosome
= these are proteins

Obviously you will not answer these questions on the homework. Use them to
help yourself prepare for the exam.
35. Short answer, Essay 2. What is wobble-base pairing? Please describe
exactly how it works and what it allows the cell to accomplish.
Answer it on your own. I will hand out an answer with the key.
This one is not graded.
Answer: Wobble base-pairing is a non-standard type of base pairing that occurs
between the THIRD nucleotide in a codon and the FIRST nucleotide in an anticodon. It
enables a single tRNA to recognize more than one codon for a particular amino acid.
Wobble base pairing allows the cell to decode 61 codons with fewer than 61 tRNAs.
That is; some tRNAs decode multiple synonymous codons.
36. Describe how the "wobble" theory applies to protein synthesis.
Answer it on your own. I will hand out an answer with the key.
This one is not graded.

Answer:
In the genetic code, all but two amino acids have multiple codons that code for their
placement into proteins through translation. Though there are 61 possible coding
codons, organisms will not have 61 tRNA molecules. Some tRNA molecules will
effectively bind to codons even though their anticodon is not a perfect match. This
"wobble effect" usually happens at the 3' position of a codon. An example is the
insertion of phenylalanine into a polypeptide. Both codons UUU and UUC code for
phenylalanine. If a single tRNA is able to bind to the codon UUPyrimidine, only one
tRNA would be needed to bind for inserting phenylalanine into a growing polypeptide.
--------------------------------------------------------------------------------------------------------------------37. This figure shows an mRNA being translated. Please label the following items
on the figure. An understanding of how genes are organized will enable you to
sensibly arrange the labels.
Gene 1,
Gene 2,
5' end of the mRNA,
nonsense codon(s),
Methionine-encoding start codon(s),
Shine-Dalgarno sequence
Answer it on your own. I will hand out an answer with the key.
This one is not graded.

Answer:

5' end of the mRNA

Gene 1

Gene 2

Methionine-encoding!
start codon(s)
Shine-Dalgarno sequence

nonsense codon(s)!
located about here

nonsense codon(s)!
located about here
Methionine-encoding start
codon(s)
Shine-Dalgarno sequence

Codon Usage by amino acid.


F
L
S
Y
TTT
TTA
TCT TAT
TTC
TTG
TCC
TAC
CTT
TCA
CTC
TCG
CTA AGT
CTG
AGC
I
ATT
ATC
ATA

M
ATG

T
ACT
ACC
ACA
ACG

N
AAT
AAC

C
TGT
TGC

W
TGG

P
CCT
CCC
CCA
CCG

H
CAT
CAC

Q
CAA
CAG

R
CGT
CGC
CGA
CGG
AGA
AGG

K
AAA
AAG

V
GTT
GTC
GTA
GTG

A
GCT
GCC
GCA
GCG

D
GAT
GAC

E
GAA
GAG

G
GGT
GGC
GGA
GGG