RNA polymerase is the enzyme that controls transcription by unwinding DNA, building an RNA strand based on the DNA template, and proofreading as it adds nucleotides to improve accuracy. It makes an error about once per 10,000 nucleotides. Gene expression involves two main phases - transcription of DNA into mRNA and translation of mRNA into protein by ribosomes. Regulation of gene expression modulates these processes to control when genes are expressed. Post-translational modifications further process proteins after translation through additions like phosphorylation, glycosylation and lipidation that influence protein structure and function.

2. By: Abdul-Rahman,Aamir, Sadam & Muhammad-Bux (BS III & Previous)

4. RNA polymerase functions:
RNA polymerase (RNAP or RNApol),
also known as DNA-dependent RNA
polymerase, is an enzyme that produces
primary transcript RNA. In cells, RNAP
is necessary for constructing RNA chains
using DNA genes as templates, a process
called transcription.

5. RNA polymerase is a huge factory with
many moving parts. It is composed of a
dozen different proteins. Together, they
form a machine that surrounds DNA
strands, unwinds them, and builds an
RNA strand based on the information held
inside the DNA. Once the enzyme gets
started, RNA polymerase marches
confidently along the DNA copying RNA
strands thousands of nucleotides long.

7. RNA polymerase needs to be accurate in its
copying of genetic information. To improve
its accuracy, it performs a simple proof
reading step as it builds an RNA strand.
The active site is designed to be able to
remove nucleotides as well as add them to
the growing strand. The enzyme
tends to over around mismatched
nucleotides longer than properly added
ones, giving the enzyme time to remove
them.

8. This process is some what wasteful, since
proper nucleotides are also occasionally
removed, but this is a small price to pay for
creating better RNA transcripts. Overall,
RNA polymerase makes an error about once
in 10,000 nucleotides added, or about once
per RNA strand created.

10. RNA polymerase: The enzyme that controls
transcription and is characterized by:
1. Search DNA for initiation site.
2. It unwinds a short stretch of double helical
DNA to produce a single-stranded DNA
template.
3. It selects the correct ribonucleotide and
catalyzes the formation of a phosphodiester
bond,
4. It detects termination signals where
transcript ends.

12. Modulation of RNA polymerase activity:
Folding of the trigger loop of RNA
polymerase promotes nucleotide
addition through creating a closed,
catalytically competent conformation

13. of the active center. Here, we discuss the
impact of adjacent RNA polymerase
elements, including the F loop and the jaw
domain, as well as external regulatory
factors on the trigger loop folding and
catalysis.
Termination: After translation has
been initiated the peptide chain is
extended by the addition of further amino
acid residues (elongation) until the

14. ribosome reaches a stop codon on the mRNA
and the process is interrupted (termination).
When one of the three stop codons (UAA,
UAG, or UGA) appears at the A site,
termination starts.
There are no complementary tRNAs for
the stop codons. Instead, two releasing factors
bind to the ribosome. One of these factors
(RF–1) catalyzes hydrolytic cleavage of the
ester bond between the tRNA and the C–
terminus of the peptide chain, thereby

15. Releasing the protein.
Hydrolysis of GTP by factor RF–3 supplies
the energy for the dissociation of the whole
complex into its component parts. Energy
requirements in protein synthesis are high.
Four energy-rich phosphoric acid anhydride
bonds are hydrolyzed for each amino acid
residue. Amino acid activation uses up two
energy-rich bonds per amino acid (ATP AMP
+ PP, and two GTPs are consumed per
elongation cycle. In addition, initiation and

16. Stop Codons Are:
UAA , UGA , UAG

17. termination each require one GTP per chain.
Gene Expression: The process by which a
gene's information is converted into the
structures and functions of a cell by a process
of producing a biologically functional
molecule of either protein or RNA (gene
product) is made.
Gene expression is assumed to be controlled
at various points in the sequence leading to
protein synthesis.
Gene Expression is done in two phases:

19. Transcription :
Synthesis of an RNA that is
complementary to one of the strands of DNA.
Translation :
Ribosomes read a messenger RNA and make
protein according to its instruction.

20. Transcription

21. Translation

22. Regulation of gene expression :
It includes a wide range of mechanisms that
are used by cells to increase or decrease the
production of specific gene products (protein
or RNA), and is informally termed gene
regulation. Sophisticated programs of gene
expression are widely observed in biology, for
example to trigger developmental pathways,
respond to environmental stimuli, or adapt to
new food sources. Virtually any step of gene
expression can be modulated, from -

23. transcriptional initiation, to RNA processing,
and to the post-translational modification of a
protein. Gene regulation is essential for
viruses, prokaryotes and eukaryotes as it
increases the versatility and adaptability of an
organism by allowing the cell to express
protein when needed. Although as early as
1951, Barbara McClintock showed
interaction between two genetic loci,
Activator (Ac) and Dissociator (Ds), in the
color formation of maize seeds, the first

24. discovery of a gene regulation system is
widely considered to be the identification in
1961 of the lac operon, discovered by Jacques
Monod, in which some enzymes involved in
lactose metabolism are expressed by E. coli
only in the presence of lactose and absence of
glucose. Furthermore, in multicellular
organisms, gene regulation drives the
processes of cellular differentiation and
morphogenesis, leading to the creation of
different cell types that possess different gene

25. expression profiles, and hence produce
different proteins/have different
ultrastructures that suit them to their
functions (though they all possess the
genotype, which follows the same genome
sequence).
Post translational modifications (PTM):
It refers to the covalent and generally
enzymatic modification of proteins during or
after protein biosynthesis. Proteins are
synthesized by ribosomes translating mRNA

26. into polypeptide chains, which may then
undergo PTM to form the mature protein
product. PTMs are important components in
cell signaling.
Post-translational modifications can occur on
the amino acid side chains or at the protein's
C- or N- termini. They can extend the
chemical repertoire of the 20 standard amino
acids by introducing new functional groups
such as phosphate, acetate, amide groups, or
methyl groups.

27. Phosphorylation is a very common
mechanism for regulating the activity of
enzymes and is the most common post-
translational modification. Many eukaryotic
proteins also have carbohydrate molecules
attached to them in a process called
glycosylation, which can promote protein
foldings and improve stability as well as
serving regulatory functions. Attachment of
lipid molecules, known as lipidation, often
targets a protein or part of a protein to the cell
membrane.

28. Other forms of post-translational modification
consist of cleaving peptide bonds, as in
processing a propeptide to a mature form or
removing the initiator methionine residue.
The formation of disulfide bonds from
cysteine residues may also be referred to as a
post-translational modification. For instance,
the peptide hormone insulin is cut twice after
disulfide bonds are formed, and a propeptide
is removed from the middle of the chain; the
resulting protein consists of two

29. polypeptide chains connected by disulfide
bonds. Some types of post-translational
modification are consequences of oxidative
stress. Carbonylation is one example that
targets the modified protein for degradation
and can result in the formation of protein
aggregates. Specific amino acid modifications
can be used as biomarkers indicating
oxidative damage. Sites that often undergo
post-translational modifications are those that
have a functional group that can serve as a

30. nucleophile in the reaction: the hydroxyl
groups of serine, threonine, and tyrosine; the
amine forms of lysine, arginine, and histidine;
the thiolate anion of cysteine; the
carboxylates of aspartate and glutamate; and
the N- and C-termini. In addition, although
the amides of aspargine and glutamine are
weak nucleophiles, both can serve as
attachment points for glycans. Rarer
modifications can occur at oxidized
methionines and at some methylenes in side
chains.

31. Post-translational modification of proteins can
be experimentally detected by a variety of
techniques, including mass spectrometry,
Eastern blotting, and Western blotting.