Description
Pre-Lab Report SheetLab Section: .
Modeling DNA Structure, Replication, & Protein Synthesis Exercise
Name: .
Before coming to labs carefully read the previous pages on DNA Structure, DNA Replication, DNA Transcription, and RNA Translation then answer these pre-lab questions.Be prepared to hand in your responses to the pre-lab questions at the start of lab.
- Explain how it is possible for you to have so many different kinds of cells in your body (e.g.
- Explain in your own words your understanding of the central dogma of biology.
- Answer each of the following questions.
- What is the primary structure of a protein?
- Of what importance is the primary structure of a protein?
- What ultimately determines the primary structure of a protein?
- What is a mutation?During what process are mutations most likely to occur?
- Why do mutations affect the primary structure of a protein?
- Describe in your own words the structure of DNA.
- Describe in your own words how DNA makes copies of itself. (I.e. Describe DNA
- Protein synthesis involves two processes, transcription and translation. Describe in your
- Transcription
- Translation
muscle cells, skin cells, liver cells, etc.) when nearly all of the cells contain the same 46 molecules of DNA (chromosomes).
replication.).
own words how each process occurs.
Unformatted Attachment Preview
Laboratory 8: Modeling DNA Structure, Replication,
& Protein Synthesis
Pre-lab Assignment
Before coming to lab carefully read the pages on Modeling DNA Structure, Replication & Protein
Synthesis, then answer the pre-lab questions (pages 117 and 118). Be prepared to discuss and hand in
your responses to the pre-lab questions at the start of lab.
Perspectives
This investigation differs from those you have completed up to this point. You will use models to
learn how DNA controls the activities of cells. Many scientists use models to understand biological
processes. Watson and Crick used models to figure out the structure of DNA and scientists use models
today to study biological problems, from the structure of proteins to making predictions concerning how
environmental factors may influence entire ecosystems.
In this investigation, you will work collaboratively with your partners to propose a structure for
DNA, show how DNA is replicated, show how DNA acts as a template to make RNA, and show how RNA
is used as a template to make protein. To accomplish these tasks you will use models of the building
blocks of DNA, RNA, and protein to represent DNA replication and protein synthesis.
Though it comes as no surprise that the composition of DNA between different organisms is
different, it is not immediately obvious why the muscle cells, blood cells, and brain cells of any one
particular vertebrate are so different in their structure and composition when the DNA of every one of
their cells is identical. This is the key to one of the most exciting areas of modern cell biology. In
different cell types, different sets of the total number of genes (genome) are expressed. In other words,
different regions of the DNA are "active" in the muscle cells, blood cells, and brain cells, while other
regions remain inactive or inaccessible to the cell.
To understand how this difference in DNA activity can lead to differences in cell structure and
composition, it is necessary to consider what is often known as the central dogma of molecular biology
(Figure 1): "DNA copied into RNA and RNA is read into protein”. In molecular terms, a gene is that
portion of DNA that encodes for a single protein. The dictum "one gene makes one protein" has
required some modification with the discovery that some proteins are composed of several different
polypeptide chains, but the "one gene makes one polypeptide" rule does hold.
Central Dogma of Biology: DNA→ RNA → Protein (Product) → Phenotype
Figure 1 Central Dogma The central dogma of biology states that DNA contains a genetic code that allows it to
make copies of itself that can be read into a protein to define a phenotype..
An essential group of proteins, called enzymes, act as biological catalysts and regulate all aspects of
cell metabolism and conspire to complete the steps of DNA replication and protein synthesis or
essentially they regulate you. Their role in DNA replication and protein synthesis are vital in maintaining
the integrity of these molecules to ensure continued functioning of the cell. In fact the structure of the
enzyme is encoded into the DNA molecule.
The Structure of DNA: Nucleotide strands
DNA is a double helix shaped molecule, with about 10 nucleotide pairs per helical turn (Figures 2
and 3) in an anti-parallel arrangement (5’ to 3’ and 3’ to 5’). Each spiral strand consists of nucleotide
molecules composed of a phosphate group (P), a sugar (deoxyribose) (S), and an attached base (B) or
P-S-B, that is connected to a complementary strand by hydrogen bonding between paired bases,
adenine (A) with thymine (T) and guanine (G) with cytosine (C). Two hydrogen bonds (weak noncovalent bonds) connect adenine and thymine, while guanine and cytosine are connected by three.
James Watson and Francis Crick first described this structure in 1953.
Figure 2 DNA Structure DNA is a double stranded molecule, each strand consisting of a chain of nucleotides.
Each nucleotide consists of a phosphate group, a deoxyribose sugar, and a nitrogen containing base (Guanine
Cytosine, Adenine, or Thymine). Weak hydrogen bonds between the bases of each strand hold the two strands
together.
Figure 3 DNA Structure An illustration of the double helical structure of the DNA molecule.
Nucleic acids are long, chain-like molecules formed by the linking together of smaller molecules
called nucleotides. The nucleic acid DNA or deoxyribonucleic acid is the material from which genes are
made. Watson and Crick used information gathered by other researchers to make models of DNA in
1953. Their models led them to make one of the greatest scientific discoveries of the last century, the
determination of the structure of DNA.
Chemical analyses of DNA prior to the 1950’s had shown that DNA is constructed from building
blocks called nucleotides. Chemists found that a nucleotide is composed of the following covalently
linked together: a sugar (deoxyribose), one phosphate group, and a nitrogen base (P-S-B).
Notice the polarity of DNA and RNA. There is always a 3’ and 5’ prime end of each strand (Figure 4)
due to the number sequence of the carbons in the nucleotide sugar (Figure 5). The phosphate is always
attached to the 5’C of the nucleotide sugar (either deoxyribose or ribose) and the nucleotide base is
always attached to the 1’C of the sugar. This orientation leaves the 3’C available to attach to the next
nucleotide (P-S-B) at its phosphate end (5’C). Why is this specific orientation required in both DNA and
RNA?
Figure 4 Representation of DNA Replication The two strands of the original DNA molecule separate, and then
each serves as a template in the formation of two new DNA molecules that will have the identical base sequence
as the one original DNA molecule.
Figure 5 Sugar Carbon Ring Numbering Each carbon in a sugar ring or either deoxyribose or ribose sugar is
numbered starting with the carbon to the right of the oxygen in the ring.
http://www.nicerweb.com/doc/class/bio1152/Locked/media/lab/molymod/index.html
DNA Replication: Semi-conservative replication
To reproduce a cell must first copy and transmit its genetic information (DNA) to all of its progeny.
To do so, DNA is replicated, following the process of semi-conservative replication (Figure 4) by laying
down the new bases in a 5’ to 3’ direction by reading the original strand in a 3’ to 5’ direction. Because
of this orientation the replication process follows one template strand in a straight forward
direction(leading strand) while the opposite template strand is read in short sequences (called Okasaki
fragments) in the opposite direction from the leading strand but in the correct direction in terms of 5’
to 3’ (lagging strand). Each strand of the original molecule acts as a template for the synthesis of a new
complementary DNA molecule.
In the last section of their paper, Watson and Crick added this statement: “It has not escaped our
notice that the specific base pairing we have postulated immediately suggests a possible copying
mechanism for the genetic material”. The process they were thinking of involved the separation of the
two strands of DNA by an enzyme known as DNA Helicase. Once open another enzyme called RNA
Primase lays down a short sequence using RNA bases as a primer against the strand to be copied to
direct the enzyme called DNA polymerase III to read the original strand and lay down the appropriate
base in the opposite position to build a new strand of DNA. Another enzyme called DNA polymerase I
comes along and reads the primers as RNA and subsequently removes this portion and adds the
appropriate DNA bases to complete the new strand and finally DNA Ligase ties all the loose ends
together such that two single-stranded sections of DNA are formed from one double-stranded molecule
or from replication. The key is the consistency to hopefully avoid copying issues or mutations.
DNA → RNA: Transcription
RNA is produced using DNA as a pattern. During this process, called transcription, the genetic code
is transferred from DNA to RNA. During transcription the two strands of a DNA molecule become
separated by a group of enzymes known as transcriptions factors along part of the molecule’s length by
binding to a region known as a promoter region. One strand, the non-coding strand, remains inactive
(maybe used at another time), but the other, the coding strand, is used as a template to synthesize RNA,
a single stranded molecule.
The enzyme responsible for transcription, RNA polymerase, like DNA polymerase, can only build
RNA in the 5’ to 3’ direction (Why?). Therefore, begin transcription at the 3’ (sugar) end of the DNA
molecule strand that is going to be read by pairing each DNA nucleotide with its RNA complement. The
base pairing rules are the same as in DNA, except Uracil pairs with Adenine since RNA does not contain
Thymine. The process is completed when the transcription factors read a terminator region on the DNA.
Before the synthesis of a protein begins, the corresponding RNA molecules messenger (mRNA),
transfer (tRNA), and ribosomal (rRNA) are produced by RNA transcription (Figures 5 and 6) by reading
the DNA strand in a 3’ to 5’ direction and laying RNA bases down in 5’ to 3’ direction. One strand of the
DNA double helix is used as a template (coding strand) by the enzyme RNA polymerase to synthesize
RNA, while the other strand (non-coding strand) could be read at a later as a coding strand to build a
different product. Before the RNA’s migrate from the nucleus to the cytoplasm they go through a
maturation process. During these steps of maturation non coding sequences are removed (called
introns (these regions do not code for product as far as we know) from coding sequences (called exons
(both sides of the DNA code for product in these regions)) are spliced together. Finally a GTP cap (not
shown) is added to the 3’ end and a poly A tail (not shown) is added to the 5’ end of the molecule. The
coding sequence of the mRNA can be described as units of three nucleotides called codons.
Figure 5 DNA Transcription RNA polymerase faithfully copies DNA to produce RNA molecules.
Figure 6 DNA Transcription During transcription the two strands of a DNA molecule become separated along
part of the molecule’s length. Only one of the two strands of DNA, the coding strand (the bottom strand in this
case) acts as a template during transcription. The enzyme RNA polymerase reads the coding strand to produce a
single stranded RNA molecule by following the base pairing rules used in DNA, with one exception—since thymine
is not found in RNA, uracil pairs with adenine.
Take Note... Transcription produces three major types of RNA which all get transported from the
nucleus through a nuclear pore to the cytoplasm of the cell.
• Ribosomal RNA (rRNA): Combines with proteins in the cytoplasm to form ribosomes, the
protein making factories of the cell.
• Messenger RNA (mRNA): Brings the instructions for product synthesis (the genetic code)
from DNA in the nucleus to the ribosomes.
• Transfer RNA (tRNA): Combine with amino acids in the cytoplasm and transport them to
the ribosome where tRNA interacts with ribosomes and mRNA to link the amino acids together to form
proteins.
There is a different tRNA molecule for each of the 20 amino acids. Each tRNA molecule consists of
about 75 nucleotides. At one end of each tRNA molecule is a three base sequence called the anticodon,
which are complementary to one of the codons in mRNA. An activating enzyme called aminoacyl-tRNA
synthetase can attach a specific amino acid to the opposite end (3’) of the tRNA molecule. This enzyme
is specific for a particular amino acid and a particular tRNA: each tRNA can carry only one kind of the 20
naturally occurring amino acids.
RNA → Protein: Translation
The process of translation begins with the binding of a ribosome to the mRNA at the start (or
initiation) codon, AUG (Figure 9) which means put he amino acicd methionine in the first postion.. The
ribosome then proceeds to slide down the mRNA molecule reading its message three bases (i.e. one
codon) at a time (Figure 7). During this stage, complexes, composed of an amino acid linked to tRNA,
sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the
anticodon (Figure 8) of the transfer RNA (tRNA). The ribosome (containing a short strand of rRNA)
moves from codon to codon along the mRNA as amino acids are added one by one and the message is
being translated into a polypeptide sequence dictated by DNA and represented by mRNA (Figure 7). At
the end, a release factor binds to the stop codon within the ribosome, terminating translation and
releasing the complete polypeptide (protein) from the ribosome. Since one specific amino acid can
correspond to more than one codon, the genetic code is said to be redundant.
Figure 7 RNA Translation or Protein Synthesis During protein synthesis, ribosomes move along the mRNA
molecule and "read" its sequence three nucleotides at a time (codon) from the 5' end to the 3' end. Each amino
acid is specified by the mRNA's codons. Each codon pairs with a specific anticodon, a sequence of three
complementary nucleotides at one end of a tRNA molecule. Since each tRNA molecule carries a specific amino
acid at one end, the order of codons on the mRNA molecule determines the order of amino acids to be linked
together during protein synthesis.
Proteins then are long chains of amino acids constructed by varied arrangements of the 20
different amino acids. As the proteins are released from the ribosome, they fold into unique shapes
(conformation) that depend on the particular sequence of amino acids in the chain. Hence, it is the
protein’s primary structure (i.e. the order of the amino acids in the protein), which is encoded in the
gene and faithfully transcribed to produce mRNA, which in turn is translated by ribosome’s into an
amino acid chain, that determines the three-dimensional structure of a protein, and thus its particular
function. The human body possesses some 30,000 different kinds of proteins and several million copies
of many of these. Each plays a specific role. For example, hemoglobin carries oxygen in the blood; actin
and myosin interact to generate muscle movement, and acetylcholine receptor molecules mediate
chemical transmission between certain nerve and muscle cells.
The versatility of proteins, the workhorse molecules of the cell, stems from the immense variety of
molecular shapes that can be created by linking amino acids together in different sequences. The
smaller proteins consist of only a few dozen amino acids, whereas the larger ones may contain in excess
of 200 amino acids, all linked together in a linear chain by peptide bonds. There exact sequence
dictated by DNA and represented by mRNA is constructed through the joint processes of transcription
and translation.
Translation of the mRNA molecule involves each type of RNA. The ribosome (40S and 60S
template) is attached to the mRNA by reading a start codon. The shape of the ribosome allows for only
two tRNA’s to match their individual anti-codons to respective codons within the ribosome at one time.
These matching sites are called the ribosome P and A sites, respectively. Enzymes found outside the
ribosome detach the amino acid bonded to the first amino acid and attach it the second tRNA’s amino
acid. The ribosome is then shifted to open the next codon and the steps repeat to lengthen the building
protein one amino acid at a time, until a stop codon (no tRNA matches the codon of the three stop
codons) is read at the end of the mRNA. Once the stop codon is read the resulting protein is released
(What happens to it to become functional?) from the last tRNA, the ribosome is removed, and the
message is recycled. Figure 9 and Table 1 are based on the three codon bases of mRNA.
The Genetic Code: Three Base Sequences
The process of identifying the sequence of amino acids in a protein, then reading them back into
mRNA codons, and then to DNA base sequences began in the 1930’s by work done by Tatum and
Beadle. In 1961 Nirenberg proved that by repeatedly linking uracil (UUUUUUU) into an mRNA the
resulting protein contained only one amino acid (phenylalanine). From this beginning molecular
biologists have identified the amino acid that is associated with each of the mRNA codons. The
following figures (Figure 8 and 9 plus Table 1) show this relationship and also identifies the special start
and stop codons.
Since RNA is constructed from four types of nucleotides, there are 43 or 64 possible triplet
sequences or codons. One of these codons plays a dual role in mRNA. If AUG is read in the mRNA
sequence it signifies placing a methionine in that position, but when the AUG is placed at the beginning
of the mRNA it also indicates where the rRNA is attached to begin the process of translation or the start
codon. Three other codons (UAA, UAG, or UGA) specify the termination of the polypeptide chain and
are called the "stop codons" (What happens to each of the RNA’s when translation is completed?).
The remaining 61 codons are used to specify the other 19 different amino acids. Therefore, most of the
amino acids are represented by more than one codon and the genetic code is said to be redundant,
except for UGG (codes for tryptophan) (Why?).
Figure 8 Translation The Pairing of a Codon in mRNA with an Anticodon of the tRNA inside a ribosome with rRNA
(not shown).
Figure 9 The Genetic Code The three bases of an mRNA codon are designated here as the first, second, and third
bases, reading in the 5' to 3' direction along the mRNA. Note that UGG is the only codon for the amino acid
tryptophan, but most amino acids are specified by two or more codons. For example, both UUU and UUC code for
the amino acid Phenylalanine. When either of these codons is read by a ribosome moving along an mRNA
molecule, Phenylalanine will be incorporated into the growing protein molecule. Think of UUU and UUC as
synonyms in the genetic code. Note that AUG codes for the amino acid methionine but also functions as a “START”
signal for ribosomes to begin translating the mRNA at that location. Three of the 64 codons function as "STOP"
signals. Any one of these termination codons marks the end of the genetic message.
Ala: Alanine
Cys: Cysteine
Arg: Arginine
Asn: Asparagine
Asp: Aspartic acid
Gln: Glutamine
Glu: Glutamic acid
Gly: Glycine
His: Histidine
Ile: Isoleucine
Leu: Leucine
Lys: Lysine
Met: Methionine
Phe: Phenylalanine
Pro: Proline
Ser: Serine
Thr: Threonine
Val: Valine
Trp: Tryptophan
Tyr: Tyrosine
Table 1 Amino Acid Abbreviations This table shows the abbreviations for each of the twenty different amino
acids that are used to build proteins coded for in the DNA
Exercise: Modeling DNA Structure, Replication, & Protein
Synthesis
Goals of this Lab Exercise
• Describe the components of DNA and RNA nucleotides
• Explain how DNA is replicated within a cell and use models to model the process
• Explain how DNA is transcribed to produce RNA and use models to model the process
• Explain how mRNA is translated into protein and describe the role of each of the following in
the process: mRNA, tRNA molecules, amino acids, and ribosomes
• Determine the amino acid sequence of a protein when given the base order of the coding or
non-coding strand of a gene
• Compare and contrast the possible effects each of the following point mutations have on the
amino acid sequence of a protein: a single base substitution, a single base deletion, and a single base
addition
Introduction
This lab is actually divided into four activities that are reliant on each other. For you to complete
each of the activities a clear understanding of the perspectives section is imperative. Discuss the answer
to the pre-lab questions with your classmates to ensure that you have a grip on the ideas supporting this
lab before proceeding.
You will be working with a group and a puzzle kit to demonstrate the structure of DNA and the
processes of DNA replication and protein synthesis. Ask questions to clarify these concepts. Sometimes
it is relatively easy to take puzzle tiles and organize them into the resulting puzzle without ever
appreciating the under lying process or the picture.
Materials
DNA Replication and Protein Synthesis modeling kit with directions
Clear desk space to build models
Procedure
Activity A.
Modeling DNA Structure
1. Follow the instructions provided by your instructor and answer the appropriate questions
on your Report Sheet to understand DNA Structure.
2. Once all group members understand the structure of DNA, call your instructor, demonstrate
the model, and have them sign Table 2 (page 114) on the Report Sheet.
Activity B.
Modeling DNA Replication
1. Follow the instructions provided by your instructor and answer the appropriate questions
on the Report Sheet to understand DNA Replication.
2. Once all group members understand the replication process of DNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 114) on the Report Sheet.
Activity C.
Modeling Protein Synthesis = Transcription
1. Follow the instructions provided by your instructor and answer the appropriate questions
on your Report Sheet To understand DNA Transcription.
2. Once all group members understand the transcription process of DNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 114) on the Report Sheet.
Activity D.
Modeling Protein Synthesis = Translation
1. Follow the instructions provided by your instructor and answer the appropriate questions
on your Report Sheet To understand RNA Translation
2. Once all group members understand the translation process of mRNA, call your instructor,
demonstrate the model, and have them sign Table 2 (page 114) on the Report Sheet.
Activity E:
Group Report Sheet
1. As a group complete the questions on pages 113 through 116 and turn in one set at the start
of the next lab.
Pre-Lab Report Sheet
Lab Section:
Modeling DNA Structure, Replication, & Protein Synthesis Exercise
.
Name:
.
Before coming to labs carefully read the previous pages on DNA Structure, DNA Replication, DNA
Transcription, and RNA Translation then answer these pre-lab questions. Be prepared to hand in your
responses to the pre-lab questions at the start of lab.
1. Explain how it is possible for you to have so many different kinds of cells in your body (e.g.
muscle cells, skin cells, liver cells, etc.) when nearly all of the cells contain the same 46 molecules of DNA
(chromosomes).
2. Explain in your own words your understanding of the central dogma of biology.
3. Answer each of the following questions.
What is the primary structure of a protein?
Of what importance is the primary structure of a protein?
What ultimately determines the primary structure of a protein?
What is a mutation? During what process are mutations most likely to occur?
Why do mutations affect the primary structure of a protein?
4. Describe in your own words the structure of DNA.
5. Describe in your own words how DNA makes copies of itself. (I.e. Describe DNA
replication.).
6. Protein synthesis involves two processes, transcription and translation. Describe in your
own words how each process occurs.
Transcription
Translation
Purchase answer to see full attachment
Purchase answer to see full attachment
User generated content is uploaded by users for the purposes of learning and should be used following Studypool's honor code & terms of service.
Explanation & Answer
Find the attached doc
Attached.
1
Running Head: PROTEIN SYNTHESIS
Protein Synthesis
Student’s Name
Institutional Affiliation
2
Running Head: PROTEIN SYNTHESIS
Q1.
The cell is the functional, biological and structural unit of organisms. The cell theory by
schleiden and schwann states that living things are made up of one or more than one cell and that
the cells form the fundamental unit of function and structure of the lining things, that the cell
originates from preexisting cells and has the hereditary information that regulates the functions
of the cells and are transmitted to the next generations.
Q2.
The central dogma shows the linear flow of genetic materials that is unidirectional from the
DNA to MRNA t proteins. However, retroviruses use reverse transcriptase to convert RNA to
DNA like HIV virus. Central dogm...
Review
Review
Anonymous
Really great stuff, couldn't ask for more.
Studypool
4.7
Trustpilot
4.5
Sitejabber
4.4
Similar Content
climate change
research paper. I need 3 pages . all the information need to be recent. MLA format, time roman number 12, double space. lo...
10 buck help i need it 6th grade
Assignment: Mahatma Gandhi and Thurgood Marshall
Part I.
Instructions: Respond to the
questions in co...
Genetic Drift and the Founder Effect, biology homework help
Genetic Drift and the Founder EffectThere are two types of genetic drift. Describe and give an example of both the bottle ...
Consider the reaction 2CO2(g) + N2(g)2CO(g) + 2NO(g) for which H° = 746.6 kJ a
Consider the reaction2CO2(g) + N2(g)2CO(g) + 2NO(g)for which H° = 746.6 kJ and S�...
Surface area to Volume Ratio, homework help
What would the surface area: volume ratio of these 3 increments?Surface Area Volum...
University of Memphis The Core of Science Article Discussion
Please read the article and answer relative questions. Let me know if you have any further questions. Thanks ...
