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DNA & Protein Synthesis

LEARNING OBJECTIVES

1. Describe and distinguish between the structure of DNA and RNA.

2. Describe DNA replication.
3. Explain the role of mRNA, rRNA, and tRNA in the building of polypeptides.
4. Describe how mutations effects amino acid sequence of proteins
5. Define: nucleotide, semi-conservative replication, gene, polypeptide,
transcription, translation, triplet, codon, anti-codon, double helix.

BACKGROUND

Deoxyribonucleic acid (DNA) is the molecule found within a nucleus that contains the
instructions for making a multitude of proteins necessary for the structure and function of
every organism. A gene is a section of DNA that contains the code for a single
polypeptide (protein). Genes are expressed as proteins. Proteins play a role in nearly
every aspect of life including chemical reactions/metabolism (enzymes), motility (muscle
fibers and flagella), cellular communication (receptors and signaling proteins), structures
(bacteria cell wall, hair, and exoskeletons), and defense (antibodies, capsasin, and
lymphocytes).

DNA Structure and Replication

DNA is a double-stranded polymer made up of repeating units (monomers) called

nucleotides. Each nucleotide consists of a five-carbon sugar (deoxyribose), a phosphate
molecule, and one of four different nitrogen bases (adenine, thymine, guanine, and
cytosine). The phosphate molecule links with the deoxyribose (sugar) to form the
backbone of each strand. The two strands are linked together by paired nitrogen bases.
There are two kinds of nitrogen bases: purines and pyrimidines. A purine will always
pair with a pyrimidine. They are held together by hydrogen bonds. The purine adenine
always pairs with the pyrimidine thymine, and guanine with cytosine. The number of
hydrogen bonds that can be formed between the bases determines base pairing. Adenine
and thymine form two hydrogen bonds, while cytosine and guanine form three. The
resulting structure is a double helix that resembles a twisted ladder. Replication of DNA
is accomplished when the hydrogen bonds between the nitrogen bases break, and the
molecule “unzips.” The unzipped portion of the DNA is called a replication fork. New
nucleotides from within the nucleus bond to the exposed bases and covalent bonds form
between the sugar and phosphate molecules creating a new side to each original strand.
©2015, 2008, 2006 Department of Biological Sciences, Arkansas Tech University
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DNA replication is said to be semi-conservative because each new DNA molecule

consists of one side of the “old” strand of DNA and a new strand.

Exercise 1: Modeling DNA and Its Replication

1. Using the DNA Modeling kits, assemble the nucleotides of DNA

2. Use your newly constructed nucleotides to construct a DNA Molecule. Your
instructor will direct you on the base pair sequence.
3. Replicate your DNA molecule.

Protein Synthesis

To understand how information found in the DNA is translated into proteins, one must
first be familiar with another nucleic acid called RNA (ribonucleic acid). RNA, like
DNA, is made of nucleotides. RNA differs from DNA in that it is a single-stranded
molecule that contains the five-carbon sugar ribose, instead of deoxyribose. It uses the
pyrimidine uracil, instead of thymine, and comes in three forms: messenger RNA
(mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). DNA comes in only one
form. Each type of RNA has a specific job in protein synthesis.

Transcription: Transcription is the synthesis of mRNA in the nucleus. The DNA

molecule unwinds and “unzips” at a gene. One strand of the DNA is the sense or master
strand and is used as the template for making mRNA. The ribonucleotides assemble on
one of the DNA strands in much the same way that DNA is replicated. When the mRNA
is complete, it detaches from the DNA, undergoes some editing in the nucleus, and leaves
the nucleus via a pore in the nuclear envelope. In the meantime, the DNA molecule
rezips and rewinds.

Translation: Translation is the conversion of the message encoded in the mRNA to a

polypeptide (protein) composed of amino acids. Translation occurs in the cytoplasm.
Outside the nucleus, a ribosome (made up of rRNA) attaches to the mRNA at the area of
the “start” codon (a series of bases “AUG” that signals begin). Next, a tRNA with an
attached amino acid moves to the site. The arrival and positioning of the tRNA is
controlled by the complementary pairing of three bases on the tRNA (the anti-codon) to
the codon on the mRNA. The ribosome moves down the mRNA, and the tRNA
continues to bring in amino acids in the order dictated by the mRNA. During this time,
the amino acids are being linked together with peptide bonds, forming a new polypeptide.
When a stop codon is reached by the ribosome, the process halts, and the polypeptide
(protein) is released.

©2015, 2008, 2006 Department of Biological Sciences, Arkansas Tech University

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Exercise 2: Protein Synthesis

1. Using the DNA molecule you built in exercise 1, construct a messenger RNA
molecule.
2. Translate the mRNA into a polypeptide using the tRNA and its complimentary
anti- codons.

The Genetic Code

The code of the DNA molecule is contained in the sequence of the nitrogen bases.
Remember, there are only four nitrogen bases that have to code for twenty amino acids.
Therefore, it takes three nitrogen bases to code for one amino acid. The three-nucleotide
code on the DNA molecule is called a triplet, a codon on the mRNA, and the anticodon
on the tRNA. The genetic code is degenerative, which means that more than one three-
nucleotide sequence can code for one amino acid. See page 116 in your textbook to see
the dictionary of codons and the amino acids for which they code.

Exercise 3: The Genetic Code

Fill out the nucleotide and amino acid sequences according to the directions under
“Exercise 3: The Genetic Code” on the worksheet provided.

Mutations

Mutations are any change that occurs in the base pair sequence on the DNA molecule.
Where they occur is random and when they occur is spontaneous but dividing cells are
particularly susceptible because the DNA molecule is undergoing some kind of
manipulation (DNA replication and/or chromosome separation). Mutations are a major
contributor to the genetic diversity of a species and become the facilitator for evolution of
the species by producing new alleles. Mutations can occur on two different levels; the
gene level (gene mutation) and the chromosome level (chromosomal mutations).
Mutations will only be passed to future generations if it occurs during gamete production
(meiosis).
Gene mutations affect a single gene on a chromosome but depending on which gene is
affected, it may impact the expression of other genes. Gene mutations can be the result
of mistakes during DNA replication and/or the result of exposure to environmental
mutagens. Chromosomal mutations occur when a section of a chromosome containing
several genes is either lost or at attached incorrectly. These may occur during the
crossover process in meiosis or during the separation of chromosomes in the anaphases of
mitosis or meiosis.

©2015, 2008, 2006 Department of Biological Sciences, Arkansas Tech University

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In the following exercise, the effect two gene mutations; substitution and frame shift
mutation will be demonstrated. Substitution mutations are the most common kind of
gene mutation. As implied, one base is substituted for another. These mutations will
sometimes cause a single amino acid in a polypeptide to change. Because of the
redundancy in the code, it is possible for a substitution mutation to produce no effect in
phenotype. But even a change of one amino acid in a polypeptide sequence can result in
a nonfunctioning protein. Frame shift mutations are caused by the deletion or insertions
of one or more base pairs. They are called frame shift because they cause the three
nucleotide “reading frame” (codon) to shift up or back on the mRNA

Exercise 4: Effect of Mutations

Fill out the nucleotide and amino acid sequences with mutations as indicated in the
directions on the worksheet provided under “Exercise 4: Mutations”.

REVIEW QUESTIONS
Answer the following questions in the space provided on the worksheet.
1. What is a gene?
2. What is a nucleotide?
3. Describe the structure of DNA.
4. What kind of bonds hold together the nitrogen bases in the DNA molecule? Are
they strong or weak? Why is this beneficial? How could this be problematic?
5. DNA replication is often described as semiconservative. What does this term
imply?
6. What characteristics differentiate RNA from DNA? Name at least three.
7. What are the two stages of protein synthesis?
8. What molecules bring amino acids to the site of polypeptide synthesis?
9. What is the monomer of proteins?
10. Is there a mutation that would not affect the phenotype? Explain your answer.
11. What happens to the DNA to cause a frame shift mutation?
12. How are mutations important to a species genetic diversity and therefor its long
term survival?
13. If the gene that codes for the production of spindle fibers (structures necessary
for the division of chromosomes in cellular division process) is not functioning
due to a mutation. What effect would it have on the cell involved?
14. Ricin is one of the most deadly poisons known to man. It works by deactivating
the ribosomes in the cells. Why is this substance so deadly?

©2015, 2008, 2006 Department of Biological Sciences, Arkansas Tech University