Download The Genetic Code for Certain Amino Acids

Lab Exercise 9 – The Anatomy and Function of DNA
1
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 bases long, will make an entire sentence or a
protein.
Lab Exercise 9 – The Anatomy and Function of DNA
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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/hgmis
First
U
Letter 5’ 3’
UUU phenylalanine
U
C
A
G
C
5’ 3’
Middle Letter
A
5’ 3’
G
5’ 3’
UUC phenylalanine
UCU serine
UCC serine
UAU tyrosine
UAC tyrosine
UGU cysteine
UGC cysteine
UUA leucine
UUG leucine
UCA serine
UCG serine
UAA (stop)
UAG (stop)
UGA (stop)
UGG tryptophan
CUU leucine
CUC leucine
CCU proline
CCC proline
CAU histidine
CAC histidine
CGU arginine
CGC arginine
CUA leucine
CUG leucine
CCA proline
CCG proline
CAA glutamine
CAG glutamine
CGA arginine
CGG arginine
AUU isoleucine
AUC isoleucine
ACU threonine
ACC threonine
AAU asparagine
AAC asparagine
AGU serine
AGC serine
AUA isoleucine
AUG methionine
(start)
GUU valine
GUC valine
ACA threonine
ACG threonine
AAA lysine
AAG lysine
AGA arginine
AGG arginine
GCU alanine
GCC alanine
GAU aspartate
GAC aspartate
GGU glycine
GGC glycine
GUA valine
GUG valine
GCA alanine
GCG alanine
GAA glutamate
GAG glutamate
GGA glycine
GGG gylcine
Last
Letter
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Lab Exercise 9 – The Anatomy and Function of DNA
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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=15
4880&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
source
Location/Qualifiers
1..105
/organism="Escherichia coli"
/mol_type="genomic DNA"
/strain="JE5519"
/db_xref="taxon:562"
/clone="pMB8::Tn3"
39 a
17 c
14 g
35 t
BASE COUNT
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
Nucleotid A_______ Nucleotid A_______ Nucleotide A_______
e bases
T_______ e bases
U______ bases
U______
G______
G______
G_______
_
_
C_______
C_______
C_______
3. Collect the proper components and cut them out with a pair of scissors
(bring scissors from home please)
Lab Exercise 9 – The Anatomy and Function of DNA
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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.
Lab Exercise 9 – The Anatomy and Function of DNA
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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?
Date last updated 5/1/2017
©Janet Fulks