Fritzie Claire C.

Lopez

BSChE-4

Assignment in Introduction of Biotechnology

1. Comparison chart

DNA RNA

DeoxyriboNucleicAcid RiboNucleicAcid

Definition

A nucleic acid that contains the genetic The information found in DNA determines which
instructions used in the development and traits are to be created, activated, or deactivated,
functioning of all modern living organisms. DNA's while the various forms of RNA do the work.
genes are expressed, or manifested, through the
proteins that its nucleotides produce with the
help of RNA.

Function

The blueprint of biological guidelines that a living Helps carry out DNA's blueprint guidelines.
organism must follow to exist and remain Transfers genetic code needed for the creation of
functional. Medium of long-term, stable storage proteins from the nucleus to the ribosome.
and transmission of genetic information.

Structure

Double-stranded. It has two nucleotide strands
which consist of its phosphate group, five-carbon
sugar (the stable 2-deoxyribose), and four
nitrogen-containing nucleobases: adenine,
thymine, cytosine, and guanine
Single-stranded. Like DNA, RNA is composed of its
phosphate group, five-carbon sugar (the less
stable ribose), and four nitrogen-containing
nucleobases: adenine, uracil (not thymine),
guanine, and cytosine.

Base Pairing

Adenine links to thymine (A-T) and cytosine links Adenine links to uracil (A-U) and cytosine links to
to guanine (C-G). guanine (C-G).

Location

DNA is found in the nucleus of a cell and in Depending on the type of RNA, this molecule is
mitochondria found in a cell's nucleus, its cytoplasm, and its
ribosome.

Stability

Deoxyribose sugar in DNA is less reactive Ribose sugar is more reactive because of C-OH
because of C-H bonds. Stable in alkaline (hydroxyl) bonds. Not stable in alkaline
conditions. DNA has smaller grooves, which conditions. RNA has larger grooves, which makes
makes it harder for enzymes to "attack." it easier to be "attacked" by enzymes.
Propagation

DNA is self-replicating. RNA is synthesized from DNA when needed.

2. Deoxyribonucleic acid is the biological material responsible for storing and expressing genetic
information in living things and handing down this information to offspring. A living thing's
characteristics are largely determined by its particular complement and placement of proteins. A
gene is a segment of a DNA molecule that contains the instructions for creating a protein. A DNA
molecule can contain thousands of genes. Each gene is responsible for blueprinting a full or partial
protein. When a cell reproduces, each cell contains a copy of the organisms DNA and genes. In
sexual reproduction, each offspring receives a set of genes from each parent, which is why children
look like a mix of their parents.DNA is a long strand of repeating sugar molecules linked by
phosphorus-oxygen groups. A nitrogen-containing nucleotide molecule hangs off each sugar. The
four types of nucleotide are abbreviated A, T, C, and G. The linear sequence of nucleotides spells
out the genetic code: a sequence of nucleotide maps to a sequence of amino acids, the building
blocks of protein. Each gene is a small portion of a DNA strand. At the heart of the gene are the
"coding" nucleotide sequences that translate into proteins. Spaced among the genes on the DNA
strand is the so-called inter-genetic material. This material is composed of DNA sections that help
control gene operation, as well as other sections whose purposes are either not completely
understood or are leftover junk sequences that serve no known function. Control sections,
usually but not always located near a gene, help determine whether that gene will actively
elaborate proteins or lie dormant.

3. Horizontal Gene Transfer. One fundamental of Darwins theory of natural selection is that traits
are passed from parents to offspring. The study of genetics has worked out many details of how
characteristics are inherited. Geneticists have discovered that not all genes are passed from
parents to offspring. Prokaryotic organisms in particular, can directly transfer DNA without
reproduction or pick up DNA from the environment. Gene transfer that is divorced from
reproduction is called horizontal gene transfer. Although, horizontal gene transfer is not as familiar
as vertical gene transfer it is thought to have been a very important force in the early evolution of
life on earth. It continues to be important in facilitating the evolution of modern bacteria.

4. DNA replication is the process of producing two identical replicas from one original DNA
molecule. This biological process occurs in all living organisms and is the basis for biological
inheritance. DNA is made up of two strands and each strand of the original DNA molecule serves as
a template for the production of the complementary strand, a process referred to as
semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near
perfect fidelity for DNA replication.

In a cell, DNA replication begins at specific locations, or origins of replication, in the genome.[3]
Unwinding of DNA at the origin and synthesis of new strands results in replication forks growing
bidirectional from the origin. A number of proteins are associated with the replication fork which
helps in terms of the initiation and continuation of DNA synthesis. Most prominently, DNA
polymerase synthesizes the new DNA by adding complementary nucleotides to the template
strand.

DNA Replication, like all biological polymerization processes, proceeds in three enzymatically
catalyzed and coordinated steps: initiation, elongation and termination. It starts with the process
called Initiation .For a cell to divide, it must first replicate its DNA.[10] This process is initiated at
particular points in the DNA, known as "origins", which are targeted by initiator proteins.[3] In E.
coli this protein is DnaA; in yeast, this is the origin recognition complex.[11] Sequences used by
initiator proteins tend to be "AT-rich" (rich in adenine and thymine bases), because A-T base pairs
have two hydrogen bonds (rather than the three formed in a C-G pair) which are easier to unzip.
[12] Once the origin has been located, these initiators recruit other proteins and form the pre-
replication complex, which unzips the double-stranded DNA. Second procees is called the
Elongation .DNA polymerase has 5'-3' activity. All known DNA replication systems require a free 3'
hydroxyl group before synthesis can be initiated (Important note: the DNA template is read in 3' to
5' direction whereas a new strand is synthesized in the 5' to 3' directionthis is often confused).
Four distinct mechanisms for initiation of synthesis are recognized:

All cellular life forms and many DNA viruses, phages and plasmids use a primase to synthesize a
short RNA primer with a free 3' OH group which is subsequently elongated by a DNA polymerase.
The retroelements (including retroviruses) employ a transfer RNA that primes DNA replication by
providing a free 3 OH that is used for elongation by the reverse transcriptase. In the adenoviruses
and the 29 family of bacteriophages, the 3' OH group is provided by the side chain of an amino
acid of the genome attached protein (the terminal protein) to which nucleotides are added by the
DNA polymerase to form a new strand. In the single stranded DNA viruses a group that includes
the circoviruses, the geminiviruses, the parvoviruses and others and also the many phages and
plasmids that use the rolling circle replication (RCR) mechanism, the RCR endonuclease creates a
nick in the genome strand (single stranded viruses) or one of the DNA strands (plasmids). The 5
end of the nicked strand is transferred to a tyrosine residue on the nuclease and the free 3 OH
group is then used by the DNA polymerase to synthesize the new strand. The first is the best
known of these mechanisms and is used by the cellular organisms. In this mechanism, once the
two strands are separated, primase adds RNA primers to the template strands. The leading strand
receives one RNA primer while the lagging strand receives several. The leading strand is
continuously extended from the primer by a DNA polymerase with high processivity, while the
lagging strand is extended discontinuously from each primer forming Okazaki fragments. RNase
removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the
replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading
strand and several nicks on the lagging strand can be found. Ligase works to fill these nicks in,
thus completing the newly replicated DNA molecule. The primase used in this process differs
significantly between bacteria and archaea/eukaryotes. Bacteria use a primase belonging to the
DnaG protein superfamily which contains a catalytic domain of the TOPRIM fold type.[13] The
TOPRIM fold contains an / core with four conserved strands in a Rossmann-like topology. This
structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-
family nucleases and DNA repair proteins related to the RecR protein. The primase used by archaea
and eukaryotes in contrast contains a highly derived version of the RNA recognition motif (RRM).
This primase is structurally similar to many viral RNA dependent RNA polymerases, reverse
transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of the A/B/Y families
that are involved in DNA replication and repair. In eukaryotic replication, the primase forms a
complex with Pol . Multiple DNA polymerases take on different roles in the DNA replication
process. In E. coli, DNA Pol III is the polymerase enzyme primarily responsible for DNA replication. It
assembles into a replication complex at the replication fork that exhibits extremely high
processivity, remaining intact for the entire replication cycle. In contrast, DNA Pol I is the enzyme
responsible for replacing RNA primers with DNA. DNA Pol I has a 5' to 3' exonuclease activity in
addition to its polymerase activity, and uses its exonuclease activity to degrade the RNA primers
ahead of it as it extends the DNA strand behind it, in a process called nick translation. Pol I is much
less processive than Pol III because its primary function in DNA replication is to create many short
DNA regions rather than a few very long regions. In eukaryotes, the low-processivity enzyme, Pol ,
helps to initiate replication. The high-processivity extension enzymes are Pol and Pol . As DNA
synthesis continues, the original DNA strands continue to unwind on each side of the bubble,
forming a replication fork with two prongs. In bacteria, which have a single origin of replication on
their circular chromosome, this process creates a "theta structure" (resembling the Greek letter
theta: ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at
multiple origins within these. The replication fork is a structure that forms within the nucleus during
DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA
strands together. The resulting structure has two branching "prongs", each one made up of a single
strand of DNA. These two strands serve as the template for the leading and lagging strands, which
will be created as DNA polymerase matches complementary nucleotides to the templates; the
templates may be properly referred to as the leading strand template and the lagging strand
template. DNA is always synthesized in the 5' to 3' direction. Since the leading and lagging strand
templates are oriented in opposite directions at the replication fork, a major issue is how to achieve
synthesis of nascent (new) lagging strand DNA, whose direction of synthesis is opposite to the
direction of the growing replication fork. Leading strand. The leading strand is the strand of
nascent DNA which is being synthesized in the same direction as the growing replication fork. A
polymerase "reads" the leading strand template and adds complementary nucleotides to the
nascent leading strand on a continuous basis. The polymerase involved in leading strand synthesis
is DNA polymerase III (DNA Pol III) in prokaryotes and Pol ("delta") in eukaryotes.[16] Pol can
substitute for Pol in special circumstances. Lagging strand. The lagging strand is the strand of
nascent DNA whose direction of synthesis is opposite to the direction of the growing replication
fork. Because of its orientation, replication of the lagging strand is more complicated as compared
to that of the leading strand. The lagging strand is synthesized in short, separated segments. On
the lagging strand template, a primase "reads" the template DNA and initiates synthesis of a short
complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki
fragments. The RNA primers are then removed and replaced with DNA, and the fragments of DNA
are joined together by DNA ligase. DNA polymerase III (in prokaryotes) or Pol (in eukaryotes) is
responsible for extension of the primers added during replication of the lagging strand. Primer
removal is performed by DNA polymerase I (in prokaryotes) and Pol (in eukaryotes).[18]
Eukaryotic primase is intrinsic to Pol .[19] In eukaryotes, pol helps with repair during DNA
replication.

5. As with any of the polymerization reactions, protein synthesis can be divided into three phases:

Initiation where a functionally competent ribosome is assembled in the correct place on an mRNA
ready to commence protein synthesis. Elongation whereby the correct amino acid is brought to the
ribosome, is joined to the nascent polypeptide chain, and the entire assembly moves one position
along the mRNA. Termination which happens when a stop codon is reached, there is no amino acid
to be incorporated and the entire assembly dissociates to release the newly-synthesized
polypeptide. There are two rules about protein synthesis to keep in mind: mRNA is translated 5' ->
3'. Proteins are synthesized from the N-terminus to the C-terminus.
6. There are actually several types of ribonucleic acid or RNA, but most RNA falls into one of three
categories:

mRNA or Messenger RNA - mRNA transcribes the genetic code from DNA into a form that can be
read and used to make proteins. mRNA carries genetic information from the nucleus to the
cytoplasm of a cell.

rRNA or Ribosomal RNA - rRNA is located in the cytoplasm of a cell, where ribosomes are found.
rRNA directs the translation of mRNA into proteins.

tRNA or Transfer RNA - Like rRNA, tRNA is located in the cellular cytoplasm and is involved in
protein synthesis. Transfer RNA brings or transfers amino acids to the ribosome that correspond to
each three-nucleotide codon of rRNA. The amino acids then can be joined together and processed
to make polypeptides and proteins.