STUDENT NAME:

This assignment is worth 60 points.

https://www.dnalc.org/resources/3d/
and watch ALL of the animations on the bottom of this page
YES, every single one of them.
Questions:
1.What is a nucleotide? What are the three basic parts of a nucleotide?
a. Nucleotides are a compound consisting of a nucleoside linked to a phosphate
group. The three basic parts of a nucleotide are a sugar, called deoxyribose, a
phosphate, and one of the four bases, adenine, guanine, cytosine, and thymine.
2.List 3 specific structural differences between RNA and DNA.
a. One structural difference between RNA and DNA are that DNA has a deoxyribose
and phosphate backbone while RNA has a ribose and phosphate backbone. The
second structure differences is that DNA is double stranded and RNA is single
stranded. The third structural differences between the two are that DNA have
the base pairings of adenine to thymine and cytosine to guanine. However, in
RNA Adenine links to uracil and cytosine links to guanine.
3.Specifically, where can RNA be found inside cells? Specifically, where can DNA be found
inside cells?
a. RNA is usually found in the cytoplasm of a cell but it is usually synthesized in the
nucleus. DNA is found in the nucleus of the cell.
4. What is rRNA and why is it important in cells?
a. rRNA, is ribosomal RNA. RRNA is a molecule in cells that forms part of the
protein-synthesizing organelle know as a ribosome. RRNA are important in cells
because rRNA physically move along an mRNA molecule which catalyze the
assembly of amino acids into protein chains. They also bind tRNAs and various
accessory molecules necessary for protein synthesis.
5. What is tRNA and why is it important in cells?
a. TRNA is transfer ribonucleic acid. It is a type of molecule that helps decode a
messenger RNA sequence into a protein. TRNA is important because it is a
required component of protein translation.
6. Describe the process of transcription.
a. Transcription is the process by which DNA serves as a template to produce
single stranded mRNA. RNA polymerase slides down the DNA template and
catalyzes the polymerization of the RNA molecule. The code of the resulting
mRNA is a direct result of the sequence of DNA because adenine and thymine
matchup and so do guanine and cytosine.
7. Describe the process of translation.
a. Translation is the process where your mRNA floats out the nucleus, slides into
the ribosomal complex in the cytoplasm and translates the nucleotide code
within mRNA to the amino acid code. Every three nucleotides in this mRNA code
for a specific amino acid, at which point a peptide bond is joined between amino
acids to produce a polypeptide or protein. Translation is therefore the process by
which mRNA codes for protein.
8. What is an intron? What is an exon?

a. An intron is a segment of a DNA or RNA molecule that does not code for proteins
and interrupts the sequence of genes. An exon is a segment of DNA or RNA
molecule containing information coding for a protein or peptide sequence.
9. What is junk DNA? Is it really junk
a. Junk DNA is genomic DNA that does not encode protein, and whose function, if
it has one, is not well understood. Junk DNA is really junk.
10. What is RNA splicing?
a. Splicing is the editing of the nascent pre-messenger RNA transcript.
11. Specifically, what gene are we using for DNA Barcoding to identify the various fish
species? Why this gene and not another one?
a. The gene used for DNA barcoding to identify various fish species is cytochrome
oxidase subunit I (COI). Why this gene is being used for DNA Barcoding is
because many studies have shown that infraspecific variations of COI barcodes
is generally small and clearly discriminable.
12. Explain how and why DNA Barcoding can be used to identify a specific species.
a. How DNA Barcoding can be used to identify a specific species is by first getting
DNA Barcoding of identified species. Once certain species are barcoded, then
unidentified species DNA Barcoding can be compared to known DNA barcoding.
13. What does the abbreviation PCR stand for?
a. PCR stands for polymerase chain reaction.
14. Regarding PCR, what are primers and why are they important?
a. In PCR, primers are used to determine the DNA fragment to be amplified by the
PCR process. They are important because the primers are used to start the
chain reaction.
15. Why is the Taq Polymerase used during PCR and not the DNA polymerase from a
different species? (what can this specific polymerase tolerate that other polymerases
cannot?)
a. Taq Polymerase is used during PCR and not the DNA polymerase from a
different species because it is stable at high temperatures.
16. Chemically, what is agarose? Why is it used to make gels for DNA separation?
a. Agarose is a substance that is the main constituent of agar and is used
especially in gels for electrophoresis. Chemically, agarose is a linear polymer
made up of the repeating unit of agarobiose, which is a disaccharide made up of
D-galactose and 3,6-anhydro-L-galactopyranose. It is used to make gels for DNA
separation because the agarose polysaccharide matrix helps catch the molecules
as they are transported by the electric current.
17. Explain why DNA moves through an agarose gel. Which fragments move farther,
smaller or larger DNA fragments?
a. Why DNA moves through an agarose gel is because the phosphate molecules
that make up the backbone of DNA molecules have a high negative charge.
When the DNA is placed on a field with an electric current, these negatively
charged DNA molecules migrate towards the positive end of the field. The DNA
molecules are pulled to the positive end by the current, but they encounter
resistance from this agarose mesh. The smaller molecules are able to navigate
the mesh faster than the larger ones, so they make it further does the gel than
the larger molecules.
18. Why is it important to add the fluorescent stain to the agarose gel?

a. It is important to add the fluorescent stain to the agarose gel because it

increases the viscosity of the sample and so the migration of the DNA through
the gel can be seen.
19. Why did you run your cell lysate sample over a column during our DNA Barcoding labs?
a. Why I ran my cell lysate sample over a column during our DNA Barcoding labs
was because we wanted to purify the DNA.
20. Briefly explain the specific function of each of the following important enzymes involved
in DNA synthesis/replication, transcription and translation:

helicase
o Helicase is an enzyme that unwinds DNA strands.
DNA Polymerase I
o DNA Polymerase I possesses a 3 to 5 proofreading funciton, which
lowers the error rate during DNA replication.
DNA Polymerase III
o DNA Polymerase I possesses the proofreading function, but DNA
Polymrases III is the enzyme that performs the 5 to 3 polymerase
function
topoisomerase
o Topoisomerase corrects overwinding ahead of relocation forks by
breaking, swiveling, and rejoining DNA strands
integrase
o Integrase is a multi domain enzyme that is required for the integration of
viral DNA into the host genome. Integrates is one of the three enzymes of
HIV.
RNA Polymerase
o During the process of transcription, RNA polymerase is an enzyme that is
responsilbe for copying a DNA sequence into an RNA sequence.
40 S Eukaryotic Ribosome Subunit
o 40 S Eukaryotic Ribosome Subunits are decoding centers that monitors
the complentarity of rRNA and mRNA in protein translation
60 S Eukaryotic Ribosome Subunit
o 60 S Eukaryotic Ribosome Subunit are what catalyze peptide bond
formation, which join amino acids into polypeptide chains.

21. List two differences in the specific molecular structure of prokaryotic ribosomes versus
eukaryotic ribosomes. Based on their molecular structure, are the ribosomes in
mitochondria more closely related to eukaryotic or prokaryotic ribosomes.
a. One difference in the structure of prokaryotic ribosomes versus eukaryotic
ribosomes are that prokaryotic ribosomes are smaller (70S) than eukaryotic
ribosomes (80S). Another difference is, in eukaryotes, rRNA in ribosomes has
four strands whereas, in prokaryotes, rRNA is organized into three strands in
ribosomes. Based on their molecular structure, mitochondria are more closely
related to prokaryotic ribosomes.
22. Regarding DNA structure, explain what is meant by the 5 end and the 3 end of a DNA
molecule. Which direction does DNA polymerase operate to copy DNA? Why cant DNA
polymerase go the other direction?
a. 5 end and 3 end indicate the carbon numbers in the DNAs sugar backbone.
However, the 5 carbon has a phosphate group attached and the 3 carbo has a
hydroxyl group. DNA polymerase can only operate to copy DNA 5 to 3 direction.
This is because it can only catalyze the growth of the DNA chain in one
direction, it can only add new subunits to the 3 end of the chain.
23. What is an Okazaki fragment? During DNA synthesis, why are they made? What
enzyme produces them and what kind of primers are required? Can the Okazaki
fragments be made without these primers? Why or why not?

a. Okazaki fragments are short newly synthesized DNA fragments that are formed
on the lagging temple strand during DNA replication. During DNA synthesis
Okazaki fragments are made because the DNA polymerase is designed only to
synthesize the DNA from 5 to 3. Therefore, only one end can be synthesized
continuously while the other end has to be synthesized in pieces, Okazaki
fragments, then put together. The enzymes the produce an Okazaki fragment are
DNA Polymerase I and DNA Ligase. RNA primers are required because each
Okazaki fragment begins with a RNA primer. Okazaki fragments are eventually
joined to produce a continuous strand of DNA. A step in the reaction is the
removal of the RNA primer, which makes in required to have primers in this
process.
24. At a basic level, explain how the production of proteins relates to genetic characteristics
in animals.
a. The production of proteins relate to genetic characteristics in animal because
through the process of transcription and translation, the genes DNA is being
transformed into proteins to be able to express certain genetic expression. The
certain characteristics that animals possess contain different protein make up,
in other words different gene expression.
25. What is the Modern Synthesis (in terms of Biology)?
a. The Modern Synthesis in terms of Biology is a consolidation of the results of
various lines of research from the 1920s through the 1950s that supported the
theory of evolution and the laws of inheritance in terms of natural selection
acting on genetic variation.