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MICROBIOLOGY LAB MANUAL

Lab Exercise 9 – The Anatomy and Function of
DNA
Exercise 9 - Objectives:
1. describe the molecular composition and bonding in DNA.
2. draw a DNA molecule from memory with no references – labeling
phosphate, deoxyribose sugar, nucleotide bases (A, T, G, and C),
covalent and hydrogen bonds.
3. construct a molecule of DNA with a specific nucleotide sequence.
4. simulate the replication of DNA before cell division.
5. construct a molecule of messenger RNA from the DNA template.
6. construct an amino acid sequence (polypeptide) from the mRNA.
7. evaluate the effect of a change in the base sequence due to a variety of mutations.

DNA, deoxyribonucleic acid, is the basis of life, as we know it. It is the same in every
living organism, from bacteria and flies to humans. Located in the nucleus of eukaryotic cells, it
determines the structure and function of the cell and carries the information code, or
inheritance, for each organism. It is structured like a spiral staircase. The outer rails are
composed of phosphate and a sugar called deoxyribose. The inner rungs are composed of for 4
nucleotide bases; adenine, guanine (called purines), thymine and cytosine (called pyrimidines).
Each rung is composed of only 2 bases, one pyrimidine and one purine, and each base bonds
exclusively with only one other base; adenine with thymine, and cytosine with quanine. The
monomer (individual unit) of a nucleic acid is called a nucleotide; this is composed of a
phosphate, sugar and one base. The nucleotides are referred to by the base – A, G, T, or C.
DNA must accomplish two very important functions: 1) duplication for reproducing the
organisms, and 2) the manufacturing of proteins for cell structures and metabolism. It is
essential that DNA replicate itself identically for each daughter cell during cell division. This
occurs through a process called semi-conservative replication. In order to copy the DNA in
preparation for producing a new daughter cell, the DNA unzips and new nucleotide bases,
floating in the cytoplasm, line up along the parent strands. One half of each new strand of DNA
is new and one half is the original. This is called semiconservative replication and helps to
guarantee that the code is duplicated exactly. In addition enzymes monitor the shape and
composition of the DNA repairing errors. When something disrupts this careful replication, a
mutation has occurred.
The second function of DNA is the direction of protein synthesis. DNA represents a
recipe or blueprint for producing proteins essential to the cell. The anabolism or synthesis of a
protein is determined by the sequence of nucleotide bases. Each set of three bases represents a
code for a single amino acid (see the table below). In other words if the bases are letters in an
alphabet, the sets of three represent a word, and the length of the gene represents the
complete sentence. For instance, CAGAGAGGG spells out three amino acids, glutamine-
arginine-glycine, part of a protein. The entire gene, which may be several hundred or thousand
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bases long, will make an entire sentence or a protein.
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Dr Janet Fulks Bakersfield College August 2010
MICROBIOLOGY LAB MANUAL

RNA acts as the interpreter of the DNA blueprint and manufacturer of the protein. The
actual process involves mRNA transcribing the DNA triplets. mRNA is a single stranded molecule
made of nucleotide bases similar to those found in DNA. Adenine, cytosine and guanine are all
found in RNA. The fourth RNA nucleotide base is uracil (there is no thymine in RNA). Three
sequential RNA bases are called a codon, and will code for a specific amino acid. A series of
these codons in a row
represent a chain of
amino acids which,
when bound together
in the ribosome of a
cell, become a
protein. Here are a
few sample RNA
codons and the
amino acids that they
represent. Note that
some amino acids are
represented by more
than one codon.
Image credit: U.S.
Department of Energy
Human Genome
Program,
http://www.ornl.gov/h
gmis
Middle Letter
First U C A G Last
Letter 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ Letter
U UUU phenylalanine UCU serine UAU tyrosine UGU cysteine U
UUC phenylalanine UCC serine UAC tyrosine UGC cysteine C
UUA leucine UCA serine UAA (stop) UGA (stop) A
UUG leucine UCG serine UAG (stop) UGG tryptophan G
C CUU leucine CCU proline CAU histidine CGU arginine U
CUC leucine CCC proline CAC histidine CGC arginine C
CUA leucine CCA proline CAA glutamine CGA arginine A
CUG leucine CCG proline CAG glutamine CGG arginine G
A AUU isoleucine ACU threonine AAU asparagine AGU serine U
AUC isoleucine ACC threonine AAC asparagine AGC serine C
AUA isoleucine ACA threonine AAA lysine AGA arginine A
AUG methionine ACG threonine AAG lysine AGG arginine G
(start)
G GUU valine GCU alanine GAU aspartate GGU glycine U
GUC valine GCC alanine GAC aspartate GGC glycine C
GUA valine GCA alanine GAA glutamate GGA glycine A
2

GUG valine GCG alanine GAG glutamate GGG gylcine G
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Dr Janet Fulks Bakersfield College August 2010
MICROBIOLOGY LAB MANUAL

The information about specific genes is being uncovered and uploaded to the web every
day. Below is the sequence for a plasmid gene in E.coli that results in the production of beta
lactamase – an enzyme that destroys penicillin and related antibiotics, rendering the organism
resistant. The information is found at
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=1
54880&dopt=GenBank
LOCUS TRN3TNPA2 105 bp DNA linear BCT 19-JUN-2002
DEFINITION Escherichia coli transposon Tn3 beta lacatmase (bla) gene,
partial cds.
ACCESSION K01142 VERSION K01142.1 GI:154880
KEYWORDS ampicillin resistance; beta-lactamase; drug resistance protein;
lactamase
FEATURES Location/Qualifiers
source 1..105
/organism="Escherichia coli"
/mol_type="genomic DNA"
/strain="JE5519"
/db_xref="taxon:562"
/clone="pMB8::Tn3"
BASE COUNT 39 a 17 c 14 g 35 t
ORIGIN
1 acccctattt gtttattttt ctaaatacat tcaaatatgt atccgctcat gagacaataa
61 ccctgataaa tgcttcaata atattgaaaa aggaagagta tgagt

PROCEDURE:
1. The instructor will assign you a portion of the gene to build using the paper DNA.
Your DNA CODE is ______________.
The mRNA to transcribe this would read__________.

This would be translated by tRNA as _____________ .

This represents the following amino acid_________________.

2. How many of each of the following components will you need to construct your
assigned portion?
DNA mRNA tRNA
Deoxyribose sugars Ribose sugars Ribose sugars
Phosphates Phosphates Phosphates
Nucleotide A_______ Nucleotide A_______ Nucleotide A_______
bases T_______ bases U______ bases U______
G_______ G_______ G_______
C_______ C_______ C_______
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3. Collect the proper components and cut them out with a pair of scissors (bring
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scissors from home please)

Dr Janet Fulks Bakersfield College August 2010
MICROBIOLOGY LAB MANUAL

4. Staple them together in the correct order. The sugar is represented by a pentagon
that looks like a house with a chimney. 5’
The carbons are numbered to identify the bonds
and direction of the molecule. 4’ 1’

3’ 2’
The carbon that is represented by the portion of the deoxyribose that looks like a chimney
on a house is called the 5’ carbon. This is where the phosphate bonds to the sugar. Staple
the asterisk on the phosphate to the asterisk on the chimney. This is called the 5’ end. The
nucleotide base bonds to the 1’ carbon. Staple the area with a dot on the sugar to the dot
on the base.

5. You have now constructed a nucleic acid monomer or nucleotide. Construct the
other 2 for your assigned amino acid code. Staple the three nucleotides together,
attaching the 5’ end of each nucleotide to the 3’ end of the next nucleotide.

6. Determine which nucleotides are necessary to construct the complementary DNA
strand. Fit the pieces together to create an entire double-stranded DNA molecule
with complimentary base pairs. Construct the 3 base complementary strand but
DO NOT staple the complementary strand together with the original.

7. Now construct the mRNA and tRNA to transcribe and translate that code.

8. When each group has constructed their portion of DNA, mRNA, and t RNA we will
construct a portion of the gene and translate it into a protein.

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Dr Janet Fulks Bakersfield College August 2010
MICROBIOLOGY LAB MANUAL

Lab Exercise 9 – The Anatomy and Function of DNA
NAME _____________________________ LAB_____________________

1. What is a single unit or monomer of a nucleic acid called?

2. From memory draw a stretch of DNA that would code for the amino acid “lysine”. Be sure
you draw all the components and include the complimentary strand.

3. List 2 to 3 factors that guarantee consistent and regular coding by DNA?

4. If the sequence of base pairs on a DNA molecule are A G A T T A G T G,
what is the sequence on the complimentary strand?

5. What mRNA strand is coded for by the DNA strand above (also shown below)? What amino
acid sequence does the RNA strand code for?

DNA ----- A G A T T A G T G

mRNA ------_______________________

amino acids___________, _______________, _____________

6. Imagine that Ultraviolet radiation has affected this strand of DNA. What is the effect of UV
radiation on DNA? How would this effect the replication and coding of the DNA?

7. Look at the gene you have constructed. Imagine a single nucleotide is removed. How would
this effect the coding of the DNA?
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Dr Janet Fulks Bakersfield College August 2010