Reynheart Joy I.

Redondo BSED – Biology

1. Is it possible for the same segment of DNA to encode two different proteins?
Though specific segment of DNA encode specific protein, there is another not yet well
understood and appreciated mechanism and that is through cryptic translation wherein there will
be a change at the transcription start site. However, this transcription is unstable. There is also a
non-universal but still observable means that can encode a gene multiple protein sequences
called alternative translation.

2. What distinguishes various DNA molecules from each other?

A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build
up the nucleic acids like DNA and RNA. The sequence of nitrogenous bases in a DNA molecule
makes one DNA molecule different from another. These bases are crucially important because
the sequencing of them in DNA and RNA is the way information is stored.
3. What distinguishes various RNA molecules from each other?
There are 3 types of RNA molecules and they are distinguished by their functions since each
one plays a different and vital role. The mRNA carries instructions from nucleus to the
cytoplasm. The rRNA brings amino acids to ribosomes during translation. While rRNA makes
up the ribosomes, the organelles that translate the mRNA and tRNA.
4. Describe the DNA double helix in terms of:
a. General shape
The DNA molecule is shaped like a ladder that is twisted into a coiled
configuration called a double helix. It is also described as like a spiral staircase.
b. What is on the outside of the helix and what is in within the interior of the helix?
DNA has a double-helix structure, with sugar and phosphate on the outside of the
helix, forming the sugar-phosphate backbone of the DNA. The nitrogenous bases are
stacked in the interior in pairs, like the steps of a staircase; the pairs are bound to each
other by hydrogen bonds.

The sugar and phosphate make up the backbone, while the nitrogen bases are found in
the center and hold the two strands together.
c. The directionality of the two polynucleotide chains present
Adjacent nucleotides in a single strand of DNA (polynucleotide) are joined by a
phosphodiester bond between their 3' and 5' carbons. This means that the respective 5'
and 3' carbons are exposed at either end of the polynucleotide, which are therefore
called the 5' end and the 3' end. These are also called the phosphoryl and hydroxyl
ends, respectively, because of the chemical groups typically found at those ends.
d. A comparison of the total number of nitrogen-containing nitrogenous base in
polynucleotide sequence
 The nitrogenous base can be a purine such as adenine (A) and guanine (G),
characterized by double-ring structures, or a pyrimidine such as cytosine (C) and
thymine (T), characterized by single-ring structures.

5. What is the function of the enzyme DNA helicase and DNA polymerase in the DNA
replication process?
DNA Helicase are enzymes that bind and may even remodel nucleic acid or nucleic acid
protein complexes. DNA helicases are essential in DNA replication because they separate
double-stranded DNA into single strands allowing each strand to be copied. DNA Polymerase
enzymes typically work in a pairwise fashion: each enzyme replicates one of two strands that
compromise the DNA double helix. They catalyze the addition of nucleotides onto existing DNA
strands.
6. Write the steps in DNA replication
1st Step: ‘Unzip’ the double helix structure of the DNA molecule.
2: This is carried out by an enzyme called helicase which breaks the
hydrogen bonds holding the complementary bases of DNA together (A with T, C
with G).
3: The separation of the two single strands of DNA creates a
‘Y’ shape called a replication ‘Fork’. The two separated strands will act as
templates for making the new strands of DNA.
4: One of the strands is oriented in the 3’ to 5’ direction (towards the
replication fork), this is the leading strand. The other strand is oriented in the 5’ to
3’ direction (away from the replication fork), this is the lagging strand. As a result
of their different orientations, the two strands are replicated differently.

LEADING STRAND:
5: A short piece of RNA called primer (produced by an enzyme called
primase) comes along and binds to the end of the leading strand. The primer acts
as the starting point for DNA synthesis.
6: DNA polymerase binds to the leading strand and then ‘walks’ along it,
adding new complementary nucleotide bases (A, C, G, and T) to the strand of
DNA in the 5’ to 3’ direction.
7: This sort of replication is called continuous.

LAGGING STRAND:
5: Numerous RNA primers are made by the primase enzyme and bind at
various points along the lagging strand.
6: Chunks of DNA, called Okazaki fragments, are then added to the
lagging strand also in the 5’ to 3’ direction.
7: This type of replication is called discontinuous as the Okazaki
fragments will need to be joined up later.
 8: Once all of the bases are matched up (A with T, C with G), an enzyme
called exonuclease strips away the primer(s). The gaps where the primer(s) were
are then filled by yet more complementary nucleotides.
9: The new strand is proofread to make sure there are no mistakes in the
new DNA sequence.
10: Finally, an enzyme called DNA ligase seals up the sequence of DNA
into two continuous double strands.
11: The result of DNA replication is two DNA molecules consisting of one
new and one old chain of nucleotides. This is why DNA replication is described
as semi-conservative, half of the chain is part of the original DNA molecule, half
is brand new.
12: Following replication the new DNA automatically winds up into a
double helix.

7. Write the steps in protein synthesis

1st Step: The first step in protein synthesis is the transcription of mRNA from a
DNA gene in the nucleus. At some other prior time, the various other types of
RNA have been synthesized using the appropriate DNA. The RNAs migrate from
the nucleus into the cytoplasm.
2: (Initiation) In the cytoplasm, protein synthesis is actually initiated by
the AUG codon on mRNA. The AUG codon signals both the interaction of the
ribosome with m-RNA and also the tRNA with the anticodons (UAC). The tRNA
which initiates the protein synthesis has N-formyl-methionine attached. The
formyl group is really formic acid converted to an amide using the -NH2 group on
methionine (left most graphic). The next step is for a second tRNA to approach
the mRNA (codon - CCG). This is the code for proline. The anticodon of the
proline tRNA which reads this is GGC. The final process is to start growing
peptide chain by having amine of proline to bond to the carboxyl acid group of
methinone (met) in order to elongate the peptide.
3: (Elongation) Elongation of the peptide begins as various tRNA's read
the next codon. In the example on the left the next tRNA to read the mRNA is
tyrosine. When the correct match with the anticodons of a tRNA has been found,
the tyrosine forms a peptide bond with the growing peptide chain. The proline is
now hydrolyzed from the tRNA. The proline tRNA now moves away from the
ribosome and back into the cytoplasm to reattach another proline amino acid.
4: (Termination) When the stop signal on mRNA is reached, the protein
synthesis is terminated. The last amino acid is hydrolyzed from its t-RNA. The
peptide chain leaves the ribosome. The N-formyl-methionine that was used to
initiate the protein synthesis is also hydrolyzed from the completed peptide at this
time. The ribosome is now ready to repeat the synthesis several more times.
 8. Possible causes of mutation and how the body can repair it.
One of the possible causes of mutation is when DNA fails to copy accurately. Most of the
mutations that we think matter to evolution are “naturally-occurring.” For example, when a cell
divides, it makes a copy of its DNA and sometimes the copy is not quite perfect. That small
difference from the original DNA sequence is a mutation. External influences can also create
mutations. It can be caused by exposure to specific chemicals or radiation. These agents cause
the DNA to break down and when the cell repairs the DNA, It might not do a perfect job of the
repair. So the cell would end up with DNA slightly different than the original DNA and hence,
mutation.