3rd Quarter (Biology)

Performance Task No. 2

Answers to the following questions MUST be COMPLETE and ACCURATE (3pts each except for #5)

1. State the differences between DNA and RNA

2. Why is there a need for DNA replication to occur first before mitosis/meiosis?
Answers: DNA replication needs to occur because existing cells divide to produce new cells. In
order for genetic information to be transferred into daughter cells. Each cell needs a full
instruction manual to operate properly. So the DNA needs to be copied before cell division so
that each new cell receives a full set of instructions..
3. Why is helicase called the “unzipping enzyme”?
Answers: DNA helicase breaks down the hydrogen bonds between the purines and pyrimidines;
Helicases are enzymes involved in unzipping of the double stranded DNA molecule at beginning
of DNA replication. They do so by binding at DNA sequences called origins on DNA molecule then
they break the hydrogen bonds between complementary base pairs causing the two strands of
DNA molecule to unzip, then that is why it is called the "unzipping enzyme".

4. Why is there Okazaki Fragment?

Answers: Okazaki fragments are short strands of DNA, which are synthesized discontinuously and later
linked together by the enzyme DNA ligase to create the lagging strand during DNA replication. Okazaki
fragments are found on the lagging strand during replication. Because these fragments will not be
attached together following strand synthesis, a protein is required to combine the fragments.

5. Give all the types of enzyme involved DNA Replication and explain each function *18 pts.

Answers:
 DNA polymerase
DNA polymerases are enzymes used for the synthesis of DNA by adding nucleotide one by one to the
growing DNA chain. The enzyme incorporates complementary amino acids to the template strand.
DNA polymerase is found in both prokaryotic and eukaryotic cells. They both contain several different
DNA polymerases responsible for different functions in DNA replication and DNA repair mechanisms.
 DNA Helicase enzyme
This is the enzyme that is involved in unwinding the double-helical structure of DNA allowing DNA
replication to commence.
It uses energy that is released during ATP hydrolysis, to break the hydrogen bond between the DNA
bases and separate the strands.
This forms two replication forks on each separated strand opening up in opposite directions.
At each replication fork, the parental DNA strand must unwind exposing new sections of single-stranded
templates.
The helicase enzyme accurately unwinds the strands while maintaining the topography on the DNA
molecule.
 DNA primase enzyme
This is a type of RNA polymerase enzyme that is used to synthesize or generate RNA primers, which are
short RNA molecules that act as templates for the initiation of DNA replication.
  DNA ligase enzyme
This is the enzyme that joins DNA fragments together by forming phosphodiester bonds between
nucleotides.
 Exonuclease
These are a group of enzymes that remove nucleotide bases from the end of a DNA chain.
 Topoisomerase
This is the enzyme that solves the problem of the topological stress caused during unwinding.
They cut one or both strands of the DNA allowing the strand to move around each other to release
tension before it rejoins the ends.
And therefore, the enzyme catalysts the reversible breakage it causes by joining the broken strands.
Topoisomerase is also known as DNA gyrase in E. coli.
 Telomerase
This is an enzyme found in eukaryotic cells that adds a specific sequence of DNA to the telomeres of
chromosomes after they divide, stabilizing the chromosomes over time.

6. What is meant by 3’ (three prime) and 5’ (five prime)?

Answers: Each end of DNA molecule has a number. One end is referred to as 5' (five prime) and the other
end is referred to as 3' (three prime). The 5' and 3' designations refer to the number of carbon atom in a
deoxyribose sugar molecule to which a phosphate group bonds. The 5' and 3' mean "five prime" and
"three prime", which indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a
phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA
strand a "direction.

7.Summarize the steps in DNA Replication process.

Answers: The first step in DNA replication is to unwind the double helix structure of the DNA
molecule via helicases. The separation of the strands forms a Y-like shape structure called a
replication fork. The two separated strands serve as templates for making the new copies of
DNA. One of the strands is oriented in the 3’ to 5’ direction (the leading strand). The other strand
is oriented in the 5’ to 3’ direction (the lagging strand). At the leading strand, a short piece of
RNA (primer) is made by the enzyme primase. The primer acts as the starting point for DNA
synthesis. The enzyme DNA polymerase binds to the leading strand and moves along the DNA
strand starting from the primer. It attaches a new complementary nucleotide to the growing
strand of DNA in the 5’ to 3’ direction. At the lagging strand, numerous RNA primers are made
by the primase while DNA polymerase provides the elongation of these primers. These short DNA
fragments, called Okazaki fragments, are then added to the lagging strand also in the 5’ to 3’
direction. Next, exonuclease strips away the rimers while the gaps between them are filled with
complementary nucleotides via DNA polymerases. Finally, DNA ligase joins DNA fragments
together. As a result, the DNA replication process results in the formation of two DNA molecules.

8. What will happen if DNA Polymerase caught error in matching the wrong DNA bases?

Answers: DNA replication is a highly accurate process, but mistakes can occasionally occur as when a
DNA polymerase inserts a wrong base. Uncorrected mistakes may sometimes lead to serious
consequences, such as cancer. Repair mechanisms can correct the mistakes, but in rare cases mistakes
are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or
defective.
9. How can you compare the DNA molecule into a zipper?

Answers: DNA molecule is a double stranded molecule, that is, there are two legs or chains of
this molecule. The strands are complementary to each other and are connected together by
interlinking. The interlinking is provided by base pairing (adenosine (A) with thymine (T) and
cytosine (C) with guanine (G)). The two sides have to fit well with each other (through base
pairing) for the molecule to work. Similarly, the zipper (on our bags, trousers, clothing, sleeping
bags, etc.) has two strands or two legs. These two strands are complementary to each other and
are interlinked to close the zip. The 'teeth' on one side of the zipper fits well into the open space
between tooth on the
other side of the zipper. The zipper is closed by moving the slider. The zipper's utility is because
we can close it. Hence, DNA and zipper are similar to each other in a number of ways.

10. What is meant by being “semi-conservative” of DNA?

Answers: Semiconservative replication describes the mechanism of DNA replication in all known
cells. DNA replication occurs on multiple origins of replication along the DNA template strand. As
the DNA double helix is unwound by helicase, replication occurs separately on each template
strand in antiparallel directions. This process is known as semi-conservative replication because
two copies of the original DNA molecule are produced.

11. Why is DNA Replication important in Protein Synthesis?

Answers: DNA makes RNA makes proteins. DNA is the nucleic acid that stores genetic
information. RNA is the nucleic acid responsible for using the genetic information in DNA to
produce proteins.

12. Both DNA Replication and Transcription use DNA as template in the process. How is it used for each
process?

Answers:

DNA replication is the process of duplication of the DNA, where each strand serves itself as a template
strand to synthesize a new DNA strand. From DNA molecules, three types of RNA molecules including
mRNA are produced via the transcription process. In transcription, an RNA polymerase uses the
template DNA strand of a gene to catalyze synthesis of a complementary, antiparallel RNA strand. RNA
polymerases use ribose nucleotide triphosphate (NTP) precursors, in contrast to DNA polymerases,
which use deoxyribose nucleotide (dNTP) precursors.

17. What is intron splicing? And why is there a need for that process before an mRNA can proceed with
Translation?

Answers:

RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor
messenger RNA transcript is transformed into a mature messenger RNA. During splicing, introns are
removed and exons are joined together. For those eukaryotic genes that contain introns, splicing is
usually required in order to create an mRNA molecule that can be translated into protein... Not only do
the introns not carry information to build a protein, they actually have to be removed in order for the
mRNA to encode a protein with the right sequence. If the spliceosome fails to remove an intron, an
mRNA with extra "junk" in it will be made, and a wrong protein will get produced during translation.

18. After the Termination stage in Transcription, does the mRNA leaves directly the nucleus and goes to
the cytoplasm? Yes or No? Justify your answer.

Answers:

Yes. According to the site of Encyclopaedia Britannica, because information in DNA cannot be decoded
directly into proteins, it is first transcribed, or copied, into mRNA. Each molecule of mRNA encodes the
information for one protein (or more than one protein in bacteria), with each sequence of three
nitrogen-containing bases in the mRNA specifying the incorporation of a particular amino acid within the
protein. The mRNA molecules are transported through the nuclear envelope into the cytoplasm, where
they are translated by the rRNA of ribosomes; To make RNA, DNA pairs its bases with those of the "free"
nucleotides. Messenger RNA (mRNA) then travels to the ribosomes in the cell cytoplasm, where protein
synthesis occurs. The base triplets of transfer RNA (tRNA) pair with those of mRNA and at the same time
deposit their amino acids on the growing protein chain.

20. Explain each stage in Translation process

Answers:

Initiation

Translation begins with the messenger RNA strand binding to the small ribosomal subunit upstream
of the start codon. Each amino acid is brought to the ribosome by a specific transfer RNA molecule. The
type of amino acid is determined by the anticodon sequence of the transfer RNA. After the initiator
transfer RNA molecule binds to the start codon, the large ribosomal subunit binds to form the translation
complex and initiation is complete.

Elongation

After the initiation complex has formed, but before any amino acids have been linked to make a
chain... Our first, methionine-carrying tRNA starts out in the middle slot of the ribosome, called the P
site. Next to it, a fresh codon is exposed in another slot, called the A site. The A site will be the "landing
site" for the next tRNA, one whose anticodon is a perfect (complementary) match for the exposed
codon... In the first round of elongation, a new tRNA molecule carrying an amino acid pairs with the
second mRNA codon. When the first and second amino acids are in place, an enzyme joins them by
forming a peptide bond between them. During the elongation stage, the ribosome continues to translate
each codon in turn. Each corresponding amino acid is added to the growing chain and linked via a bond
called a peptide bond. Elongation continues until all of the codons are read.

Termination

Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site. Stop codons
are recognized by proteins called release factors, which fit neatly into the P site (though they aren't
tRNAs). Release factors mess with the enzyme that normally forms peptide bonds: they make it add a
water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and
the newly made protein is released..

21. Explain how each site in rRNA functions during elongation stage in Translation

Answers:

The ribosome contains three RNA binding sites, designated A, P and E. The A-site binds an aminoacyl-
tRNA or termination release factors; the P-site binds a peptidyl-tRNA (a tRNA bound to the poly-peptide
chain); and the E-site (exit) binds a free tRNA.

22. How does tRNA molecule carrying its amino acid recognize which codon to attach?

Answers:

The tRNA molecule has a distinctive folded structure with three hairpin loops that form the shape of a
three-leafed clover. One of these hairpin loops contains a sequence called the anticodon, which can
recognize and decode an mRNA codon. Each tRNA has its corresponding amino acid attached to its end.

23. Why is it important that a stop codon be part of protein synthesis?

Answers:

It is important that a stop codon must be a part of protein synthesis because they signal to stop protein
synthesis and release the amino acid chain. If it's not present then protein synthesis will stop abruptly or
continue synthesis that results in completed defective protein. As when a ribosome reaches stop codon
then protein synthesis is terminated.

24. How does the process of Translation ends?

Answers:

Translation ends in a process called termination. Termination happens when a stop codon in the mRNA
(UAA, UAG, or UGA) enters the A site. Stop codons are recognized by proteins called release factors,
which fit neatly into the P site (though they aren't tRNAs). Release factors mess with the enzyme that
normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain.
This reaction separates the chain from the tRNA, and the newly made protein is released... After the
small and large ribosomal subunits separate from the mRNA and from each other, each element can
(and usually quickly does) take part in another round of translation.

25. A construction worker brings hollow blocks to build a wall. What do the hollow blocks and
construction worker represent in the process of Translation? Why?

26. What is the importance of Transcription and Translation in Protein Synthesis?

Answers:

Proteins are made from a sequence of amino acids rather than nucleotides. Transcription and translation
are the two processes that convert a sequence of nucleotides from DNA into a sequence of amino acids
to build the desired protein. The goal of transcription is to make a RNA copy of a gene's DNA sequence.
Translation is the process of converting or translating the RNA information into protein. This process is
carried out by an important organelle in the cell, called the ribosome.