Jib 223 assignment 2

DEBBRA MARCEL JP/8544/13 ASSIGNMENT 2

JIB 223 CELL BIOLOGY AND GENETICS

THE ROLE OF ENZYMES INVOLVED IN REPLICATION, TRANSCRIPTION AND

TRANSLATION

Overview

Genetics is a field of biology that study about genes, heredity and genetic variation in

living organisms. It is generally linked with the study of information systems that intersects with

many of life sciences including genetic information and processes; and the way it is translated

into systems that control the physiology, development and metabolism, which determine the

reappearance of parental characters among progeny of organism. Watson and Crick (1953) are

among the pioneer biologists that DNA as genetic material by working out the gene structure so

that their function can be understood to the molecular level. This assignment will

explain how different enzymes involved in process of replication of DNA to transcription of

DNA until the polypeptide chains of proteins produced by translation.

Introduction

Deoxyribonucleic acid (DNA) provides a mechanism for replication and the main

substance of inheritance making it as most important molecule in each living organism. This is

because DNA contains nucleic acids that can uniquely direct its own replication from monomers

The information of hereditary encoded chemically by DNA and reproduced in all the cells of

living organisms, be it prokaryotes or eukaryotes. That is why it is often to see offspring

resemble their parents, as the anatomical, physiological, biochemical, and to some extent,

behavioral traits were transmitted from one generation to the next. In each living organism, the

sequential process called "central dogma of biology" is the process of survival that begins from

combination of coded genetic information into DNA, followed by transcription of individual

transportable cassettes which composed of messenger RNA (mRNA) and finally each cassette

will synthesis a particular protein according to their specific functions. However, each of these

processes cannot be done without the presence of specific enzymes to carry out their respective

functions. Generally, the synthesis of any biological macromolecule can be divided into three

main stages, namely initiation, elongation and termination. This is not true for DNA replication,

but also for the transcription as well as the translation.



Discussion: The roles of enzymes for each stage

INITIATION

There are at least 20 different enzymes involved in DNA replication process. The

initiation stage started when enzyme called helicase promotes the unwinding of the DNA double

helix. Helicase enzyme separates two strands of DNA double helix molecules forming an

opening called "bubble", which is also known as "origin of replication". In the presence of

energy (ATP), it also promotes repair by binding to the single-stranded DNA and travels 5'to 3'to

separate the strand and to move the fork forward. Then, single-stranded binding proteins keep the

parental strands to open and act as templates at the replication fork. These proteins coats the

single strands formed by melting and unwinding to stabilize the unwound parental strands.

Additionally, topoisomerase (or gyrase) enzyme alters the superhelix density in supercoiled

DNA by breaking, swiveling, and rejoining the parental DNA as well as relieving the strain

caused by unwinding additional coiling ahead of the replication fork.

In transcription process, RNA polymerase in a bacterial cell can simply recognizes the

gene's promoter and binds to it but transcription factors required in a eukaryotic cell as mediate

the binding of RNA polymerase to the promoter. Among the several eukaryotic transcription

factors (promoter), the most recognized is the TATA box, which must attach to the DNA before

RNA polymerase II allowed bind with the correct position and orientation. Along with RNA

polymerase, there are also other transcription factors called sigma factor attach to the DNA

enabling the transcription initiation complex to form. When the polymerase II unwind the DNA

double helix, the synthesis of RNA synthesis will then initiated at the start point of the template

strand.

Unlike replication and transcription, the initiation stage of translation occurs only when a

complex molecules comprising mRNA, a ribosome, and tRNA is formed. The translation

(protein synthesis) in eukaryotes occurs in ribosomes within the cytoplasm, but not in nucleus

region as occur in replication and transcription. Ribosomes are the proteins which consist of

RNA molecules and subunits numerous associated proteins such as ribosomal RNA, rRNA.

There are a number of initiation factors required for the conversion codons into a sequence of

amino acids such as tRNA . Aminoacyl-tRNA synthetases which is made of the nucleotide bases



in mRNA joins the amino acids in the sequence by a further class of RNA, transfer RNA

(tRNA). Anticodon is a region of tRNA in each amino acid that is complementary for its codon

of the mRNA.

ELONGATION

During the DNA replication, the elongation stage involves an enzyme called primase

which synthesize complementary RNA chain (primer) from a single RNA nucleotide and adding

each RNA nucleotides at a time by using a template from the parental DNA strand. DNA

polymerases is the primary enzymes in DNA replication due its multiple functions. By adding

nucleotides to a chain, the enzymes catalyze the synthesis of new DNA strand. Polymerase also

covalently links to the complementary nucleotides to deoxynucleotide triphosphates. After RNA

primer is made, the synthesis of leading strain done by DNA polymerase III, which is then

continuously in the 5'to 3' direction as the fork progresses. On the other hand, the lagging strand

is synthesized when primase joins RNA into a primer. This allows DNA polymerase III adds

DNA nucleotides to the primer, forming the first fragmented strand (Okazaki fragment). The

DNA polymerase III will be detached after the next RNA reached to the right once the second

Okazaki fragment from the first fragment primer. Then DNA polymerase I allowed the DAN to

be replaced with the RNA by adding to the 3' end of fragment. In elongation, DNA ligase (DNA

repair enzyme) will join all the Okazaki fragments by restoring the broken phosphodiester bonds

in DNA until the lagging strand completed.

In gene transcription, the elongation stage in occurs of when RNA polymerase moves

along the DNA and the double helix continues to be untwisted for the pairing with the

nucleotides by exposing about 10-20 DNA nucleotides at a time. The RNA polymerase adding

nucleotides to the 3' end of the growing RNA molecules and it continues along the double helix.

As the reaction cause as the new RNA peels away from its DNA template, the double helix form

of DNA re-forms . In bacteria for example, sigma factor (proteins) binds to RNA polymerase to

aid the elongation process in transcription. Several molecules of RNA polymerase can also

transcribe a single gene and adds the amount of mRNA transcribed. This reaction allows the cell

to make larger amount of encoded proteins.



On the other hand, the elongation of translation process is subdivided by a three phase

namely codon recognition, peptide bond formation and translocation. During the recognition

step, base pairs formed by the reaction of anticodon of an incoming aminoacyl tRNA with the

complementary mRNA codon in the A (aminoacyl) site. The hydrolysis of GTP plays a

significant role in the elongation process as it increases the efficiency and accuracy of this step.

Second elongation step called peptide bond is the formation of peptide binding which occur

when the large ribosomal subunit containing rRNA molecule catalyzes the peptide bond

formation of the amino group of the new amino acid by. Translocation which is the last step of

translation happens when the A site translocated to the P (peptidyl) site by ribosome. The

movement of mRNA along its bound with tRNAs, leading the translation of the next codon into

the A site. Eventually, P site containing the empty tRNA is moved to the E site, where the

polypeptide chains finally released.

TERMINATION

In DNA replication, termination occurs in a zone where the

forks meet. In the termination stage, prokaryotes does not have specific enzyme for the process,

but rather use Tus protein for the action. contrast, eukaryotes have the termination enzyme called

telomerase attaches many copies of DNA repeat sequence to the ends of chromosomes. It is

series of short nucleotide sequences repeated at the ends of eukaryotic chromosomes. The

presence of telomeres postpones the erosion of genes by causing a repetitive sequence at the ends

linear DNA molecules. In eukaryotes, telomerase enzyme catalyzes the lengthening of telomeres

in germ cells. DNA polymerases then proofread the DNA by replacing incorrect nucleotides (for

example: mutation) in mismatch repair, while other DNA repair enzymes also correct errors that

persist by cutting out and replace damaged stretches of DNA, these both process significantly

reduce the result of genetic disease or cancer, and also may lead to evolution by natural selection.

Meanwhile, the mechanism of termination in transcription between bacteria and

eukaryotes is not same. This is because in bacteria, transcription can be preceded through a

terminator sequence in the DNA. When the termination signal transcribed terminator, the

polymerase enzyme detached from the DNA and causing the transcript RNA sequence to be

released. This requires no further modification before the translation process occur. For



example, a DNA sequence called the polyadenylation sequence in eukaryotes which transcribed

by RNA polymerase II, which coded for a polyadenylation signal (AAUAAA) in the pre-mRNA.

However, changes are very rapid sincetranscription and translation are tightly coupled in

prokaryotes but such changes are slower in eukaryotes. Enhancers are the proteins that the

activity of eukaryotic transcription factors, which may exert their influence over distances of

several thousand base pairs, which may also be tissue specific. Spliceosome (composed of

several subunits of snRNPs) is responsible for the removal of instrons from eukaryotic pre-

mRNA by splicing to excise the introns from the primary transcript.

Just like the replication and transcription, the final stage of translation is termination. The

termination of translation happens when one of the nucleotide (mRNA) base triplets (UAA,

UGA, or UAG) or also known as release factor transported out of nucleus, into the cytoplasm to

the ribosome. Here transfer RNA (tRNA) involved in direct protein synthesis for each codon as

molecule of mRNA moved through ribosome. Enzyme-like RNA molecules called ribozyme

cleaves the covalent bonds at the intron-exon boundary and connect the exons together. A release

factor binds directly to the anticodon in the site hydrolyzes the bond between the polypeptide and

the tRNA in the, causing polypeptide to expell through the tunnel of the ribosome's large subunit.

In short, below are the main enzymes/proteins involved in the discussed processes:

Process Replication Transcription Translation

Init

iati

on

Helicase

Single stranded binding (SSB)

proteins

DNA topoisomerase or gyrase

Promoter: TATA box

tRNA molecules

(contains metionine, the

initial amino acid)

Elo

ng

ati

on

DNA polymerase I, II and III

(in prokaryotes), or DNA

polymerase alpha and delta

(in eukaryotes)

DNA ligase

Sigma factor

(bacteria) +

polymerase

aminoacyl tRNA

synthetases

GTP (hydrolysis

Ter

min

ati

on

Tus protein (in prokaryotes),

or telomerase (in eukaryotes)

Spliceosome

Release factor (UAA,

UAG and UGA)

Ribozyme



As can be seen in the three macromolecules process, DNA polymerase and RNA

polymerase are the most distinctive enzymes. Both type of polymerase enzymes are forms of

nucleic acid chains determined by complementary base pairing to a template strand and

synthesize to 3' direction, antiparallel to the template. However, DNA polymerase requires a

primer for the function, while RNA polymerase can simply start a nucleotide chain scratch.

Meanwhile, DNA polymerase uses nucleotides with the thymine (base) and deoxyribose (sugar),

whereas RNA polymerase uses nucleotides with the uracil (base) and ribose (sugar).

As overall comparison, all the enzymes/proteins involved in the replication process are

for the preparation of cell division, while the enzymes/proteins involved in the transcription are

for the preparation of protein translation, and both processes occur within the nucleus region of a

cell. Meanwhile the enzymes/proteins involved in translation process are for the purpose protein

synthesis, which occur outside of the nucleus within the cytoplasm region, specifically in

ribosome.

Figure 1: A summary DNA of replication in bacteria (Source: 2009, Pearson Education, Benjamin Cummings)



Figure 2: A summary of transcription in bacteria

(Source: 2006, Discover Biology, W. W. Norton & Company, Inc)

Figure 3: The basic concept of translation (Source: 2009, Pearson Education, Benjamin Cummings)

E site P site

A site



Conclusion

In a nutshell, molecular chain of command governs the cells with a directional flow of

genetic information started from DNA to RNA to protein, the concept known as central dogma

of biology. As each biological cell has about a thousand different types of enzymes, each of

these proteins act as biological regulator or mediator for all aspects of the cell metabolism by

enabling breakdown complex molecules as well as many other essential functions of cell.

Ultimately, each of the enzyme in the replication, transcription and translation processes has

their specific role to speed up and aid the chemical reactions within the cell, making sure the

continuous regenerations of genetic make-up and continuous production of functional proteins

for the survival of organism.

References:

1. Campbell, N. A., and Reece, J. B. (2008). Biology. Sixth Edition. San Francisco (CA):

Benjamin Cummings. p. 1247.

2. Brooker, R. J., Widmaier, E. P., Graham, L. E., and Stiling, P.D. (2014). Biology. Third

Edition. McGraw Hill International Education. p. 1263.

3. J. D. Watson and F. H. C. Crick. (1953). A Structure for Deoxyribose Nucleic Acid.

April 25, 1953 (2), Nature (3), 171, 737-738.

4. Watson J.D. et al.: Molecular Biology of the Gene. 3rd ed. Benjamin/Cummings

Publishing Co., Menlo Park, California, 1987.

5. Pray, L. (2008) Major molecular events of DNA replication. Nature Education 1(1):99

Jib 223 assignment 2

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