DNA and Gene Expression
Name
Objectives
Basic DNA Units

Deoxyribonucleic acid is the
biological molecule that stores hereditary
information. A single molecule of DNA can
contain many thousands of informational
units called genes. A gene is a segment of
DNA that carries the instructions for a single
protein.
To understand how a DNA molecule
carries instructions, one must first
understand the structure of DNA.
Deoxyribonucleic acid is built of four
different deoxyribonucleotides linked
together in two chains. There are four
deoxyribonucleotides: Guanosine, Cytosine,
Thymidine, and Adenosine.
A deoxyribonucleotide is made of three
components: a phosphate group, a
deoxyribose sugar, and one of four different
nitrogenous bases (Guanine, Cytidine,
Thymine and Adenine). See Figure 1.
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Name the three parts of a nucleotide and
show how the components are bonded
together
Describe the difference between a DNA
and an RNA nucleotide
Draw the structure of a DNA molecule,
showing the 5' and 3' ends, covalent
bonds between nucleotides, and
hydrogen bonds between the bases.
Write the nucleotide sequence of an
mRNA that has been transcribed from a
DNA gene, and name the enzyme
performing this process.
Write the amino acid sequence that was
translated from an mRNA, given a
Codon Dictionary.
Define mutation and name one type of
protein mutation resulting from a point
mutation and an insertion.
Figure 1. The three parts of a deoxyribonucleotide
phosphate
group
nitrogenous
base
sugar
(deoxyribose)
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pg. 1
DNA is made in the cell by linking the
DNA-type nucleotides together. The
linkage occurs between the "3' OH" of the
sugar part of one nucleotide and the "5' OH"
of the phosphate group on another.
1. In Figure 2 below, draw a line
between the "O" of the "3' OH" on the
upper nucleotide down to the black ball
just under the "OH" of the lower
nucleotide. This line represents the
covalent bond that forms during the
linking reaction of
deoxyribonucleotides. In making DNA,
two chains of deoxyribonucleotides are
formed and then linked together.
The nucleotide Adenine forms
hydrogen bonds with Thymine, and
Cytosine bonds with Guanine. The two
chains of DNA run in opposite directions,
and so are called antiparallel.
1. Working with a partner, get a set of
DNA nucleotides and build a single
strand of nucleotides. You should
begin with the 5' end of the first
nucleotide turned sideways to your
left and build on new nucleotides to
the right. The nucleotides should be
built using the following sequence:
CGATGTACTCGTGAC and should
look something like this on the
desktop (but with different
nucleotides):
Figure 2. Two deoxyribonucleotides
2. Double check that you’ve laid down
the DNA nucleotides so that the
dashed lines (hydrogen bonds) are
facing upwards and the 5’ P groups
have lines that connect fully with the
3’ carbon of the adjacent
nucleotide’s sugar. Put the 5’ end at
your left.
The DNA Molecule
A full DNA molecule is composed of
two chains of deoxyribonucleotides held
together by hydrogen bonds between the
nitrogenous bases.
3. Next, build the opposite strand of
DNA, using the correct nucleotides
to make pairs with the nucleotides in
the first strand. Remember, Adenine
bonds with Thymine (A-T) and
Guanine bonds with Cytosine (G-C)
Build the second strand over the top
of the existing strand, in a right to
left direction. This means you
begin adding nucleotides opposite
the end of the existing strand that
Bios 140 Biology Lab Manual
pg. 2
reads CAGTG etc. The two strands
should show connections like this
(note the dashed hydrogen bonds
holding the nucleotides together in
the middle):
4. The ends of each of the two strands
can be labeled 5' or 3' based on
which part of the nucleotide is left
hanging out. Label the ends of the
DNA molecule below to reflect how
your DNA is built as it lays in front
of you. Do the two strands have
different labels at the same end?
They should.
build a specific protein, the gene sequence
must first be transcribed (copied).
Transcription of a gene involves the
opening of the DNA helix by the breaking of
hydrogen bonds between the bases. The
RNA polymerase enzyme then reads the
nucleotide sequence on one of the two
strands of DNA, called the template. The
non-template strand is not read. RNA
polymerase builds a complementary
molecule of messenger RNA as it reads the
template strand. The complementary
mRNA molecule has matching, not
identical, ribonucleotides to the DNA
sequence.
RNA, or ribonucleic acid, is different
from DNA in that it contains ribose sugar,
not deoxyribose. It also contains the
nitrogenous bases: Adenine, Uracil,
Guanine, and Cytosine. Uracil replaces
thymine in RNA, but it still pairs with
adenine using hydrogen bonds.
1. Working with a partner, open the DNA
strands of your desktop DNA molecule
by breaking the hydrogen bonds between
the bases and separating them a bit. As
you do this, you are simulating the
action of a molecule machine (enzyme)
called RNA polymerase.
Transcription
2. Using the RNA nucleotides provided
(they are a different color than DNA
nucleotides), make a complementary or
matching copy of the template strand of
the DNA. The template strand is the
one that reads from the 5' end:
GTCAC…..etc. You therefore need to
place matching RNA nucleotides next to
the template strand, "U" by a DNA "A",
"A" by a DNA "T", "G" by a DNA "C",
and "C" by a DNA "G".
A gene is a sequence of DNA
nucleotides that carry the information to
build a single protein or protein. In order to
3. You are playing the part of RNA
polymerase when you transcribe a DNA
gene into mRNA. This enzyme lays
5. How many hydrogen bonds (dashed
lines) are there between adenine and
thymine?
6. How many hydrogen bonds are there
between guanine and cytosine?
Bios 140 Biology Lab Manual
pg. 3
down new RNA in a 5’ to 3’ direction.
The mRNA made from the template
strand is antiparallel to the template
strand. Therefore, your mRNA should
read from the 5’ end: CGAU, etc. if
you are doing this correctly.
Table I. mRNA codons and the amino acids
(abbreviated) they specify
Translation
Once a gene has been transcribed into
messenger RNA, the next step is to build a
protein from these RNA instructions. In
prokaryotes like bacteria, the protein
building "machine", or ribosome, is nearby.
In eukaryotic cells, the mRNA must first
leave the nucleus and enter the cytoplasm to
encounter a ribosome.
Translation is the process whereby a
ribosome reads the mRNA nucleotide
sequence and builds a protein from these
instructions. Building a protein involves
linking specific amino acids together by
peptide bonds. Amino acids are brought to
the ribosome by transporting molecules
called transfer RNAs, or tRNAs.
A ribosome is composed of two bloblike units containing over 50 different
proteins plus two or three pieces of nucleic
acid called ribosomal RNA. Together these
proteins and RNA molecules are capable of
reading the genetic code on the mRNA,
positioning the amino acids, and forming
peptide bonds between them, one at a time.
The mRNA directs the ribosome to
place specific amino acids in a specific
ordered sequence based the three-letter
"code words" or codons . The ribosome
begins reading the mRNA at the 5' end and
only starts building a protein when it reads a
start codon, or AUG. According to Table I,
what amino acid is always used to start a
protein?
When the ribosome reads a stop codon
on the messenger RNA, translation is
complete. According to Table I, what are
the three stop codons?
,
, and
.
Transfer RNA molecules bring amino
acids to the ribosome, one by one, according
to the codon instructions. As each tRNA
enters the ribosome, the mRNA codon is
matched with a specific sequence or "sign"
found at the bottom of each tRNA. This
"sign" is called an anticodon. The
anticodon of the tRNA must be the
complementary match to the mRNA codon
before the ribosome will accept the amino
acid the tRNA is carrying.
1. Examine the transfer RNA (shaped like a
cloverleaf) in Figure 3 which is carrying
an amino acid. Locate the anticodon and
the hydrogen bonds between the
anticodon and the codon.
2. The RNA nucleotides that make up the
mRNA codon are missing. Fill in the
missing complementary/matching bases
on the mRNA that would match pair
with the nucleotides of the anticodon.
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3. Looking at the Codon Dictionary in
Table I, determine which amino acid the
tRNA pictured in Figure 3 is carrying.
The amino acid is:
Figure 3. The anticodon of a transfer RNA molecule
can form hydrogen bonds with a codon on the
messenger RNA.
read the names of the nucleotides
sequentially until you discover the
sequence AUG. These three bases
together are known as a Start Codon,
and they instruct the ribosome to place
the amino acid Methionine first in all
proteins. Get a Methionine amino acid
card and place it next to the AUG codon.
3. Next, read the series of three nucleotides
(the next codon) immediate following
the AUG. Use the RNA Codon
Dictionary (Table I) to determine what
amino acid is specified by this codon.
Get this amino acid card and place it
(link it) next to the methionine amino
acid card.
4. Continue building your protein chain by
reading the subsequent codons and
laying down the appropriate amino
acids.
5. At some point you will arrive at a codon
whose instruction is "Stop". This type of
codon (there are three) is called a Stop
Codon. When this codon is read by the
ribosome, the protein is finished. No
further amino acids are added, even if
there are more unread nucleotides in the
mRNA.
Translation
1. With the available collection of all 20
amino acids, translate the messenger
RNA you made earlier into a protein.
The ribosome translates mRNA from the
5’ to the 3’ end. Be sure you build your
protein by reading the mRNA in the
correct direction!
6. Write the sequence of all the amino
acids chained together in your protein,
using the three-letter abbreviations for
each. Begin with Met (methionine).
2. Begin by starting at the 5' end of your
messenger RNA. Don't clear away your
DNA molecule yet because you will still
need it later. Beginning at the 5' end,
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pg. 5
Mutation
A mutation is a permanent, heritable
change in the DNA. Mutation occurs
naturally, but rarely, whenever DNA is
being made. Mutation also occurs when
mutagenic agents such as ultraviolet light,
cigarette smoke, X-rays, or formaldehyde
cause alterations in the DNA.
When the nucleotide sequence in a
gene is altered, the messenger RNA made
from this gene has an altered sequence. The
resultant effect on the amino acid sequence
of the protein can be disastrous or neutral.
A point mutation is a change in a
single nucleotide in a DNA gene; the
substitution of a different nucleotide. A
point mutation in a gene can cause the
resultant protein chain to have a single
amino acid change (missense mutation), a
truncated or shortened sequence (nonsense
mutation), an extra long sequence (run-on
mutation), or no change whatsoever (silent
mutation). In another type of DNA
mutation, the insertion or deletion of
nucleotides alters a DNA gene. This nearly
always results in a greatly altered amino
acid sequence in the protein (a frameshift
mutation).
Point Mutation
1. Introduce a point mutation into your
DNA. First, remove a nucleotide
(anywhere) and replace it with another
one from the cup of DNA nucleotides.
Then replace the nucleotide on the other
strand so that it is complementary to
(matches) the new nucleotide.
2. Transcribe this new gene sequence in the
same way you did before, laying down
RNA nucleotides using the template
strand. Use the same strand you did
before as the template strand.
3. Translate the mRNA into a protein and
write down the amino acid sequence
here using the three-letter abbreviations:
4. What type of protein mutation resulted
from the DNA point mutation?
5. How different is the amino acid
sequence from the original sequence?
Insertion Mutation
1. Introduce an insertion mutation into your
DNA gene. Randomly select a DNA
nucleotide from the box and insert it into
your gene by pushing the other
nucleotides aside to make room. Then
fill in the space on the other strand with
the complementary nucleotide.
2. Transcribe this new gene sequence in the
same way you did before. Use the same
strand you did before as the template
strand.
3. Translate the mRNA into a protein and
write down the protein sequence here:
4. What type of protein mutation resulted
from the DNA insertion mutation?
5. How different is the amino acid
sequence from the original sequence?
Are all amino acids different?
Bios 140 Biology Lab Manual
pg. 6
Further Questions and Review
DNA and Gene Expression
Be sure to turn in the WHOLE
handout, not just these last few pages
1. Describe, in order, the steps the cell takes in producing a protein from a DNA gene. Name
and describe every intermediate process, including the names of any important molecules,
enzymes, or "molecular machines".
2. Given the DNA non-template strand below, write out the sequence of the template strand.
Then fill in the mRNA and the resultant protein that would come from this gene.
DNA non-template strand:
T A T G C T G C G G C G T A C C T G T T A A C G C
mRNA:
amino acid chain:
(protein)
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3. Complete the following crossword puzzle using what you have learning in this lab activity.
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pg. 8
ACROSS
1 The formal name or designation for the
RNA triplet AUG (answers is two words).
3 A permanent, heritable change in the
DNA.
4 The master table containing all the
possible RNA codons and the amino acids
that they specify, as read by the ribosome.
(Two words).
6 The formal name or designation for the
RNA triplets UGA, UAA, and UAG.
7 The molecule that links complementary
ribonucleotides together while reading a
chain of deoxyribonucleotides.
12 The addition of one or more nucleotides
to a DNA gene, causing a mutation.
14 The process whereby a DNA gene is
read in order to build a complementary RNA
copy.
15 The three letter ribonucleotide sequence
that is complementary to the codon
sequence.
16 The type of protein mutation in which
the resultant protein is much shorter than
normal.
17 The number of hydrogen bonds between
cytosine and guanine bases.
22 The type of sugar molecule in DNA
25 The ________ strand is the strand in
DNA that is actually read by the RNAmaking "copy machine".
26 The type of protein mutation in which
the amino acid sequence remains
unchanged.
28 The nitrogenous base that pairs with
cytosine. (Spell out answer fully).
29 The descriptive term for the way in
which two strands of DNA are aligned in a
DNA molecule.
31 The type of protein mutation in which all
the amino acids after a certain point in a
protein are completely different than what
they should be.
34 The basic repeating unit found linked
together in either DNA or RNA.
35 The chemical group found at the five
prime end of a nucleotide.
DOWN
2 A three letter ribonucleotide sequence
carried on mRNA that specifies a single
amino acid.
3 The working copy of a DNA gene that is
used as instructions by a ribosome to make a
protein. (Spell out answer fully).
5 The number of hydrogen bonds between
thymine and adenine bases.
8 The molecular machine that performs
translation.
9 The approximate number of nucleotides
found in an mRNA molecules that codes for
a protein that is 15 amino acids long. (Spell
out the answer).
10 The unique nitrogenous base found in
DNA but not RNA.
11 The type of protein mutation in which
only a single amino acid has changed from
the original protein sequence.
13 The process in which a messenger RNA
is used to produce a protein.
17 The number of amino acids that would
be found in a protein if the DNA gene were
900 nucleotides long. (Spell out the answer).
18 The type of sugar molecule in RNA.
19 The segment of DNA that carries the
instructions for a single protein.
20 The molecule which brings amino acids
to the ribosome. (Spell out the answer fully).
21 The type of bonds between the
nitrogenous bases in the center of a DNA
molecule.
23 The one nitrogenous base unique to
ribonucleic acid molecules; not found in
DNA.
24 The full name of the amino acid found at
the beginning of all proteins.
Bios 140 Biology Lab Manual
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27 The subtraction or removal of one or
more nucleotides from a DNA gene, causing
a mutation.
30 A type DNA mutation in which the stop
codon is obliterated, resulting in an extra
long protein during translation.
32 The chemical part of a nucleotide
(having 3 parts) which contains the three
prime end.
33 The number of strands found in an RNA
molecule
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pg. 10