LABS 9 AND 10
DNA STRUCTURE
OBJECTIVE
OBJECTIVE
OBJECTIVE
OBJECTIVE
EXERCISE
1.
2.
3.
4.
AND REPLICATION;
SYNTHESIS
Describe the structure of DNA.
Explain how DNA replicates.
Understand the structure ofRNA and the process of transcription.
Explain the process of translation and the role of codon-anticodon
protein synthesis.
1. DIAGRAM A POLYNUCLEOTIDE
MATERIALS
RNA AND PROTEIN
pairing in
CHAIN
NEEDED:
Biology textbook
Lead pencil and colored pencils
DNA, deoxyribonucleic acid, is the carrier of genetic information in most living organisms. This
nucleic acid is composed of four kinds of subunits, called nucIeotides, bonded together in a long
interconnecting chain. Each nucleotide building block of DNA consists of (1) a S-carbon sugar
molecule, (2) a phosphate group and (3) a nitrogenous (nitrogen- containing) base.
The sugar molecule is deoxyribose and has the molecular formula CSH 1004. Use your textbook
to examine the structural formula of deoxyribose. All DNA nucleotides contain the phospate group and
the sugar deoxyribose. However, there are four different types of bases in DNA- thymine (abbreviated
T), cytosine (C), adenine (A) and guanine (G). Thus, DNA is composed of A containing nucleotides,
T containing nucleotides, C containing nucleotides, and G containing nucleotides. Again, use your
textbook to examine the structural formulas of these four nitrogenous bases. Also, examine a diagram
of the structure of a nucleotide, and note how the three parts of the nucleotide are joined.
PROCEDURE:
In the area marked Exercise I on the answer sheet, diagram with a lead pencil a single stranded
polynucleotide chain that has the following base sequence: If you are using a computer to generate this,
use black font.
TACCCAAAATCC
In your diagram, you may use the following symbols (these symbols should be used in Exercises II
and ill as well) or generate your own. If you generate your own symbols, be sure to include a key for
your symbols.
Phosphate group
®
Deoxyribose
Labs 9 and 10 - 1
0
Thymine
Adenine
D
Guanine
EXERCISE
n. FORMATION
Cytosine
OF A DOUBLE-STRANDED
DNA MOLECULE
DNA is made up of two complementary strands of nucleotides twisted to form a double helix,
something resembling a spiraled rope ladder. The sides of the ladder are formed by the sugar and
phosphate molecules. The rungs are formed by nitrogenous bases joined together by hydrogen bonds.
Before you start this exercise, read about the structure of DNA in your textbook. Be sure to study the
diagrams in your text.
PROCEDURE:
In the area marked Exercise Il on the answer sheet, diagram (again, with the lead pencil or black
font) a double-stranded DNA molecule, using the strand you drew in Exercise I as the template, i.e. a
complementary, single strand of DNA nucleotides must now be constructed to bond with the initial
strand. Remember, the nucleotides should be diagrammed so that cytosine of the initial strand always
pairs with guanine on the new strand and vice versa. The thymine containing nucleotides on the initial
strand should always pair with adenine containing nucleotides on the new strand and vice versa.
Connect the base pairs with dotted lines to represent the hydrogen bonds. Do not worry about twisting
the stand into the double helix! Your drawing obviously represents a tiny portion of a DNA molecule.
EXERCISE
ill.DNA REPLICATION
As mentioned earlier, DNA carries the inherited genetic information found in the coded sequence .
of its bases. It is essential that DNA be duplicated exactly from one cell division to the next. A mutation
results if there is a change in the base sequence. The process of duplication is termed DNA replication.
For replication to begin, the double helix must be unwound and separated into two single strands of
DNA called templates. An enzyme called DNA polymerase binds to each of the unwound strands. It
then moves along each strand linking nucleotides with complementary bases to the exposed bases on
the templates with hydrogen bonds. The result of this replication is the synthesis of two identical
double- stranded DNA molecules. Read about DNA replication in your textbook. Be sure to pay careful
attention to the diagrams.
PROCEDURE:
In the area marked Exercise ill on the answer sheet, replicate the DNA molecule that you drew in
Exercise II. Use the LEAD pencil to diagram the ORIGINAL strands in the replicated molecules, and
a COLORED pencil to diagram the NEWLY SYNTHESIZED strands. Thus, by looking at your
drawings, one can see that the replication is semi-conservative; that is, each new double stranded
molecule consists of one original strand and one newly synthesized strand.
Answer the quiz questions on DNA structure
and replication on the answer sheets at the end
Labs 9 and 10 - 2
of this lab. Each question counts one point toward the 25 points for Lab 9.
As you already know, DNA (deoxyribonucleic acid) is the carrier of genetic information in living
organisms. The sequence of nucleotides found in DNA codes for the sequence of amino acids in
proteins. This encoded information is carried by RNA into the cytoplasm where protein synthesis
occurs. It is the responsibility of ribonucleic acid (RNA) to express this genetic information. Messenger
RNA carries the information from the DNA in the nucleus to the ribosomes in the cytoplasm and
transfer RNA takes specific amino acids to the mRNA transcript..
RNA is similar to DNA but it differs in three aspects: 1) RNA is single-stranded,
not
double-stranded, 2) RNA has a ribose sugar rather than deoxyribose in its backbone, 3) RNA contains
the pyrimidine base uracil (U) which replaces the thymine (T) found in DNA.
In Exercises IV, V, and VI use the following symbols or one that you devise for ribose and uracil.
Uracil
Ribose
EXERCISE
IV. TRANSCRIPTION
The first step in protein synthesis is transcription. In this process, RNA is synthesized using DNA
as a template. The enzyme RNA polymerase binds to one strand (the sense strand) of the DNA
molecule. While causing the DNA to unwind, the RNA polymerase moves along the sense strand,
making an RNA chain of nucleotides which are complementary to the chain of nucleotides in DNA.
The complementary RNA strand does not remain paired with the DNA template. Rather, the growing
RNA strand is released while the two strands of DNA reattach and wind back together. RNA
polymerase does not copy all the DNA of an entire chromosome. Instead, the RNA transcript thus
formed has the information for making a polypeptide (a gene is transcibed). A short sequence of DNA
nucleotides called the promoter marks the origin of a gene. The enzyme recognizes this sequence as the
starting place and transcribes the DNA until it reaches a different DNA sequence that signals it to stop.
Read about the formation of mRNA from DNA in your textbook. Again, be sure to carefully study the
diagrams of transcription in your textbook before you start this exercise.
PROCEDURE:
In the area marked Exercise IV on the answer sheet, use a colored pencil to diagram a mRNA
strand transcribed from the DNA strand that begins with the base sequence TAC used in the previous
exercises. Remember, mRNA contains the base uracil and the sugar ribose.
EXERCISE
V. TRANSLATION
Once the mRNA has been synthesized, it leaves the nucleus and travels to a ribosome in the
cytoplasm. Each ribosome is composed of two subunits. The small subunit recognizes and binds
mRNA. The large subunit contains an enzymatic unit that catalyzes the addition of amino acids to the
growing polypeptide chain and two sites (designated A and P) that bind molecules to the tRNA. As the
Labs 9 and 10 - 3
-
mRNA travels to the ribosome, enzymes in the cytoplasm recognize each specific tRNA molecule and
attach the correct amino acid to it. There are over sixty different kinds of tRNA, usually two to four for
each kind of amino acid. The tRNA has two important attachment sites. One, known as the anticodon,
binds to the codon on the mRNA. The other attachment site carries a specific amino acid. Look at the
diagram of the structure of tRNA in the text.
Your text contains a mRNA codon chart (labeled Dictionary of the Genetic Code). You will need
to use this chart to complete exercise V. A codon codes for a specific amino acid. Note that it is the
codons of mRNA (not tRNA anticodons) that are used to specify the amino acids. For example, if a
mRNA codon is AAG, the amino acid that it would code for would be lysine (abbreviated lys). Thus,
the amino acid lysine would be delivered to the mRNA strand by a molecule of tRNA with the anticodon VUC. Study the diagrams of translation in your textbook before you make your diagram.
In the area marked Exercise V on the answer sheet, illustrate the bonding of the anticodons of
tRNA to the codons of mRNA for the mRNA strand that you diagrammed in Exercise IV. In other
words, draw the mRNA strand again and then draw the specific tRNA molecules carrying their specific
amino acids that would bind to the mRNA. Use the following symbol to stand for tRNA. Be sure to
show the anticodon for each tRNA used and the amino acid that it carries.
Specific amino acid (3 letter abbreviation)
Base sequence of tRNA antocodon
EXERCISE
VI. TRANSLATION
COMPLETED
In the area marked Exercise VI on the answer sheet, write the order of the amino acids (using the
3 letter abbreviation) in the polypeptide fragment that has been translated.
Answer the quiz questions on RNA Structure and Protein Synthesis on the answer sheet.
Each question counts 2 points toward the 25 points for Lab 10.
Labs 9 and 10 - 4
..•
LABS 9 and 10 ANSWER SHEET, PAGE 1
EXERCISE
I. One Strand of a Small Portion of a DNA Molecule
EXERCISE
ll. Small Portion of a Double Stranded DNA Molecule
EXERCISE
m. lllustration
of DNA Replication
Labs 9 and 10 - 5
LABS 9 and 10 ANSWER SHEET, PAGE 2
EXERCISE IV. Transcription
EXERCISE V. Translation
EXERCISE VI. Polypeptide Chain Translated in V
Labs 9 and 10 - 6
LABS 9 and 10 ANSWER SHEET, PAGE 3
Quiz for Lab 9
You may use your textbook and study guide to aid you in answering the questions.
1.
Which of the following base pairs is correct?
a. A-T
c.
G-A
b. C-A
d.
T-C
2.
The genetic code is carried in the
a. DNA backbone.
b. sequence of bases.
c. arrangement of sugar and phosphate subunits
d. Okazaki fragments.
3.
In
a.
b.
c.
d.
e.
4.
Nucleotides found in DNA are composed of the five-carbon sugar
. Attached to its 5'
carbon is a
group. Attached to its l' carbon is one of four
bases. The bases
adenine and guanine are called
; the bases thymine and cytosine are referred to as
5.
Because each base
a. cytosine equals
b. cytosine equals
c. cytosine equals
d. each nucleotide
6.
The two chains of DNA are held together by base pairing between the complementary
____
and
and the complementary bases
and
one molecule of DNA one would expect the composition of the two strands to be
both either old or new.
both all new.
both partly new fragments and partly old parental fragments.
one old, one new.
unpredictable.
pairs with a complementary base, in every DNA molecule the amount of
that of guanine.
that of thymine.
that of adenine.
is equal to that of all others.
7.
The process of copying a DNA molecule is termed DNA
8.
If the base pairing rules are followed, then in a double helix of DNA the amount of
a. A=G, C=T.
b. A + T/G + C = 1.
c. A+T=G+C.
d. A+G=C+T.
Labs 9 and 10 - 7
bases
_
_
LABS 9 and 10 ANSWER SHEET, PAGE 4
9.
a.
b.
c.
d.
bonds join the two strands of DNA together to form the double helix.
Hydrogen
Covalent
Ionic
Polar covalent
10. Consider the DNA sequence: 5' - C C GAT G - 3'. The complementary strand made after
replication is
a. 3' -C C GAT G-5'.
b.3'-GGCTAC-5'.
c.5'-GGCTAC-3'.
d.3'-TTAGCA-5'.
11. Which of the following events occurs first in the replication of DNA?
a. breaking of covalent bonds between the nitrogenous bases
b. unwinding of the helix
c. breaking of the hydrogen bonds between the sugar and the phosphate
d. addition of complementary nucleotides to 5' end of the DNA strand
12. An actively dividing culture ofE. coli is grown in a medium containing radioactive thymine (*T).
After all the thymine in the DNA is labeled, the culture is transferred to a medium containing
nonradioactive thymine (T). Samples are removed after one round of DNA replication. Which of
the following sequences represents the DNA after one round of replication in the medium containing
nonradioactive T?
a. *T *T A A G *T A
AATTCAT
b. *T T A A G *T A
A A *T*T CAT
c. *T *T A A G *T A
A A *T *T C A *T
d. T l' A A G T A
AATTCAT
Labs 9 and 10 - 8
LABS 9 and 10 ANSWER SHEET, PAGE 5
Quiz for Lab 10
You may use your textbook and study guide to aid you in answering the questions.
1.
Translation is the process in which
a. DNA, RNA
b.
b. a polypeptide, mRNA
d.
2.
For each amino acid there
a. is only one codon and tRNA.
b. can be more than one codon and tRNA.
c. are two co dons, but only one tRNA.
d. are two tRNA molecules, but one codon.
3.
DNA contains
a.
b.
c.
d.
sugar and
is synthesized from
mRNA, the nucleolus
tRNA, DNA
while RNA contains
_
sugar and
ribose, uracil, deoxyribose, adenine
deoxyribose, adenine, ribose, thymine
ribose, guanine, ribose, guanine
deoxyribose, thymine, ribose, uracil
4.
The termination of protein synthesis normally occurs
a. when the cell runs out of ATP.
b. upon recognition of a stop or termination codon.
c. upon recognition of an exon.
d. when more than 10 ribosomes attach to the mRNA.
5.
All of the following are directly required for protein synthesis except
a. mRNA.
b.
ribosomes.
c. tRNA.
d.
DNA
6-7. Which of the following sequences of amino acids would be encodedin the given DNA sequence'
TAC-GCG-AAT-CGC
a. met - arg - leu - ala
b. met - cys - gly - ser
c. ser - ala - leu - ala - val
d. ala - gly - ser - arg - val
Labs 9 and 10 - 9
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