Biochemistry Assignment: PTMs, Gene Expression, Metabolism, and Cancer

This biochemistry assignment delves into the intricate world of post-translational modifications (PTMs) and their profound impact on gene expression, metabolism, and cancer development. The assignment begins by identifying writer, eraser, and reader proteins, along with their respective enzymes and substrates. It then explores various PTMs, including phosphorylation, protein glycosylation, and ubiquitination, detailing their sites of modification and providing a reaction scheme for one such PTM. Furthermore, the assignment examines two experimental methods, namely immunoprecipitation and immunofluorescence, used to characterize these PTM sites, and explains the rationale behind their suitability. The authors monitored transcription and translation. In summary, the authors' findings suggest that PTMs of biological enzymes contribute to the increase in cancerous cells and metabolism by impacting molecular and genetic processes. The authors link PTMs to metabolism and cancer by showing that these modifications affect metabolic enzymes and the binding of genetic compounds, ultimately influencing cancer metabolism. The findings support the histone code by demonstrating that the protein code does not function as an independent signal to specify the interaction with downstream regulatory proteins, but rather provides further interactions to stabilize the achievement of corepressor complexes.

Biochemistry
1. Identify the writer, eraser, and reader proteins if applicable. For each writer and
eraser in question 1 state the enzyme and its substrate.
Adeno LHPP is the writer
PGAM5 RNA is a reader protein
ARH1 and ARH3 are the erasers
PARG enzyme is primarily responsible for hydrolyzing the glyosidic linkages between
ADP-ribose units of PAR polymers to generate free ADP-ribose monomers.
2. List the post-translational modifications (PTM) found to alter gene expression and
the site of these modifications (protein, amino acid). Provide the reaction scheme for
at least one PTM.
Phosphorylation- Reversible macromolecule phosphorylation, primarily on
aminoalkanoic acid, essential amino acid or aminoalkanoic acid residues and plays
essential roles within the regulation of the many cellular processes, as well as cell
cycle, growth, apoptosis, and signal transduction pathways.
Protein glycosylation- encompasses a various choice of sugar-moiety additions to
proteins that ranges from easy saccharide modifications of nuclear transcription
factors to extremely advanced branched carbohydrate changes of cell surface
receptors.
Ubiquitination whereby Ubiquitin is Associate in Nursing 8-kDa peptide
consisting of seventy-six amino acids that are appended to the Îμ-NH2 of essential
amino acid in target proteins via the C-terminal glycine of ubiquitin.

Reaction scheme in phosphorylation
3. Describe two methods/experiments (discussed in class) use to characterize these
PTM sites. In your discussion state, why you think the methods suited these
characterizations.
Immunoprecipitation primarily based techniques- a way that's utilized in many
completely different PTM detection assays. significantly, informatics permits researchers
to complement for specific, low-abundance PTM modifications on a target dish (Kohn,
2012). Enrichment is achieved through affinity-based purification technology.
Antibodies (or specific binding molecules) hooked up to a solid support matrix (such as
agarose resin) bind to the dish or PTM, whereas non-targeted proteins within the
advanced lysate don't seem to be captured and removed through wash steps. The enriched
proteins are then removed off of the support matrix victimization extraction buffers and
isolated during a focused volume. The isolated population is analyzed by downstream
ways like western blot or by mass spectroscopy to see if a dish is post-translationally
changed (Helmut L. Haas, 2012).
Immunofluorescence for world PTM- technique techniques could also be a fruitful
approach to learning global changes during a PTM profile in tissues or cells. particularly
distinguishing world, and abstraction changes in response to drug or genetic knockout is
accomplishable with this technique. The identification of target-specific PTM
modifications isn't doable by this technique. However, this approach could also be
applicable as a biological readout; so, could also be a useful gizmo as AN indicator for
development or illness progression.
4. What gene expression step (s) did the authors monitor and how?
The author monitored varied steps in organic phenomenon.
Transcription: the assembly of mRNA (mRNA) by the catalyst RNA enzyme, and
therefore the process of the ensuing RNA molecule.

Translation: the utilization of RNA to direct super molecule synthesis, and therefore the
consequent post-translational process of the molecule (Fiammetta Alagna, 2017).
Some genes are answerable for the assembly of alternative kinds of ribonucleic acid that
play a job in translation, as well as tRNA (tRNA) and ribosomal RNA (rRNA).
5. In a few sentences summarize the authors finding. Address the following questions
in your summary
a. How did the authors link PTM to metabolism or cancer?
b. How do their findings support the histone code?
In relation to the research paper it can be deduced that PTMs of various biological
enzymes contribute to some extent to increase in cancerous cells and metabolism. This is
because the PTMs impact molecular and genetic processes that in turn directly affect
cancer metabolism. Taking into account various figures and diagrams and processes
shown in the research paper, various PTMs control behaviors and properties of metabolic
enzymes and binding of genetic compounds, and substrates
The findings show that during this case, the simple protein code concerned doesn't appear
to function AN freelance signal in a very communication cascade to specify the
interaction with a downstream restrictive protein(s) (Zhou, 2015). Rather, it functions in a
very feed-forward mode to supply further interactions to stabilize the achievement of the
corepressor complexes.

References
Fiammetta Alagna, M. B. (2017). Plastid Proteostasis: Relevance of Transcription, Translation
and Post-Translational Modifications. Lausanne : Frontiers Media SA.
Helmut L. Haas, G. B. (2012). Synaptic Plasticity in the Hippocampus. New York: Springer
Science & Business Media.
Kohn, A. (2012). Control of Gene Expression. London: Springer Science & Business Media.
Zhou, M.-M. (2015). Histone Recognition. London: Springer.