Download Protein Synthesis

Cell Biology and Genetics: the Central Dogma
Transcription and Translation
DNA directs the synthesis of proteins by indirectly specifying the exact sequence of
amino acids in each protein. This is accomplished through a series of chemical coding
and decoding steps. Each sequence of three nucleotides in a strand of the DNA helix is
called a triplet code word. The DNA is used as a template to make complementary
RNA. In this way, the sequence of nucleotides in DNA is transcribed into RNA. The
complementary nucleotide triplets in the RNA are called codons. The RNA (actually
messenger RNA or mRNA) then carries the message to ribosomes in the cytoplasm,
where protein synthesis occurs. Meanwhile, another type of RNA, transfer RNA, picks
up amino acids and transfers them to the site of protein synthesis. There are many
different tRNAs, each specific for a particular amino acid. Each tRNA also contains a
specific triplet of nucleotides (an anti-codon) that is complementary to the mRNA
codon. For protein synthesis to occur, each anticodon pairs with the appropriate codon,
which aligns a particular amino acid and gets it ready to become part of a growing protein
chain. The amino acids can then be linked together in the specified order.
Although proteins are three-dimensional molecules, the principle of encoding and making
proteins can be illustrated on paper.
1. Your instructor will assign you a sequence of 63 nucleotides forming 21 DNA code
words. Beginning at the left and proceeding to the right, transcribe (by writing
the sequence on paper) the DNA code words into mRNA codons using the following key
to transcription:
 A (adenine) in DNA transcribes to U (uracil) in mRNA
 G (guanine) in DNA transcribes to C (cytosine) in mRNA
 T (thymine) in DNA transcribes to A in mRNA
 C in DNA transcribes to G in mRNA
As a matter of convenience, bracket each mRNA triplet (codon).
For example, the DNA code word of ATT would transcribe to a mRNA codon of
UAA. When all of the code words have been transcribed you have, in effect,
synthesized a strand of mRNA.
2. Each codon specifies a particular amino acid, as shown in the Standard Genetic Code
Table on page 3 of this handout. Using this table, determine the specific type of amino
acid that is coded for by each mRNA codon. As you proceed with this translation step,
you are setting up the primary structure of a polypeptide molecule. An examination of the
table will reveal several features of the genetic code:
a. The code is degenerate - that is, there is more than one codon for most of the
amino acids. For example, serine is specified by six different codons. Only two
amino acids are represented by a single codon. What are they?
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b. The codon AUG not only encodes Methionine but also functions as a “start”
signal for ribosomes to begin translating the mRNA at that point. Thus, AUG is
also called a start codon.
c. The three codons UAA, UAG, and UGA are frequently called nonsense
codons because they do not specify any amino acid at all. Rather, they serve as
punctuation marks: they are “stop” signals or termination codons, marking the
end of translation.
Amino Acids and Their Abbreviations
Amino Acid
alanine
arginine
asparagine
aspartic acid
cysteine
glutamic acid
glutamine
glycine
histidine
isoleucine
Abbreviation
ala
arg
asn
asp
cys
glu
gln
gly
his
ile
Amino Acid
leucine
lysine
methionine
phenylalanine
proline
serine
threonine
tryptophan
tyrosine
valine
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Abbreviation
leu
lys
met
phe
pro
ser
thr
trp
tyr
val
Standard Genetic Code Table:
Codons and the Amino Acids They Specify:
d. Once you have determined the sequence of amino acids, get twenty labels or
post-its from your instructor. These labels may need to have their edges trimmed
to reduce their overall size. Your instructor will give directions for doing this if it
is necessary. Number each label by placing a small numeral (1 through 20) in its
lower left hand corner. Then print the abbreviation of the first amino acid on the
first label and so on until you have done this for all twenty amino acids. Place the
first label near the middle of the bottom of a blank page of paper. (Don't glue it or
any other label until you get them all properly positioned on the page.) As you
position each succeeding amino acid adjacent to the one before, obey the
following rules to determine the two dimensional conformation of your protein.
Position each additional amino acid to the right of its predecessor, observing the
following :
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
A proline makes a left turn, i.e., place the proline label at right angles
to the previous amino acid. (See Fig. 1.)
PRO
MET
THR
Reading Direction 
Figure 1

A serine amino acid makes a right turn, i.e., place the serine at right
angles to the previous amino acid. (See Fig. 2.)
SER
PRO
MET
THR
Reading Direction 
Figure 2
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4.
Note that each polypeptide configuration will fit in its entirety on an 8 1/2 x II"
piece of paper. After you have worked out the arrangement of your 20 amino acid
polypeptide, ask your lab instructor to check it before you stick the labels onto the
paper.
5.
The peptide bonds that form between the adjacent amino acids are somewhat
flexible. Further stabilization of a particular protein conformation occurs by
joining two parts of the chain together by a disulfide bond (-S-S-). These bonds
form between cysteine amino acids. Therefore, whenever two cysteines are within
two label lengths apart, indicate a disulfide bond (see Fig. 3).
SER
CYS
PRO
LEU
S
MET
PRO
S
CYS
LEU
Reading Direction 
Figure 3
Can you ascertain, from your polypeptide model, if there are any regions which
seem to have a very specific and unusual conformation; unusual in the sense that a
particular shaped substrate molecule might fit into the area like a key into a lock?
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6.
Mutations can be of several types. One type is a "reading frame
mutation" in which a single nucleotide within a sequence is missing or added.
This then changes all the succeeding (or “downstream”) triplets to completely
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different code words, some of which may be "nonsense" and therefore completely
prevent that protein from being synthesized. Shift the reading frame on your DNA
sequence of nucleotides at any point and estimate the length of the polypeptide
that can be synthesized before a break in the chain occurs, due to the lack of an
appropriate codon and amino acid. Another kind of mutation which can occur is
one in which one nucleotide is replaced by a different nucleotide (base
substitution mutation). It is known that in some cases a single substitution can
cause rather drastic changes in the biological properties of a given protein, while
in other cases nucleotide substitutions can occur without apparent changes. Can
you reason why this might be predicted from what you have learned during this
exercise?
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Nucleotide Sequences:
1. TACCCAGGTGAATGAGGGGGAACAAGAGTAAGCACGAGTGGCGGACAAAGGATAAGTCTTACT
2. TACGGGGGGACGTCGGACTCGACAGGGGGGTGGTTTTAAGGGCATCAGGGGTCAAAAGGGATT
3. TACCTGGGTGGTAGTAGTGGTGAGGGTCCGGGTACAAGTGGTAGTAGTTGAACATATTCGATC
4. TACGGGACCGGCACGTCATCGGGTACAGGAGTTCGAGGCACGGGATCATCGGGGACGGGTACT
5. TACGCAGTGGGAGGCAGGAGTGGATTAGGGGGTAGTGTGAGAACGAGGGGAGGGACAGGTATC
Questions: Answer the following questions in your laboratory notebook.
1. Both nucleic acids and protein molecules are examples of polymers. What does this
mean?
2. What is the effect of a reading frame mutation.
3. What is the effect of a base substitution.
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Circular Genetic Code Table
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