Background
Science is a process of applying and building on the findings of others, so one of the major tasks of any
scientist is to communicate their work to their colleagues. Scientific research in medicine, nutrition,
agriculture and many other related fields relies on the sharing of new discoveries and insights.
Scientific research is reported in written form in specialist journal articles, and at scientific meetings
where scientists gather to hear oral presentations on the latest developments. New ideas and new
explanations grow out of the work of many individual scientists who communicate and discuss their
work together in these ways.
This assessment task will provide you with an opportunity to develop your research and inquiry skills
and to refine your scientific writing skills.
Proteins are the most prevalent macromolecules in biological systems. They are extraordinarily
diverse in terms of size, structure and biological function, and they participate in the majority of
cellular processes including metabolism, energy production, transport, storage, cell signalling, defence
and the maintenance of cell structure.
The function of a protein invariably requires some form of interaction with another molecule, and the
molecule that interacts with and is bound by the protein is referred to by biochemists as a ‘ligand’.
Biochemists have a broad definition of the term ‘ligand’ that can include any molecule that forms a
functional complex with a protein to serve a useful biological role, a small ion or chemical, or even a
large ligand like another macromolecule (eg. a sugar/carbohydrate, a lipid, another protein, or even a
molecule of DNA or RNA).
The task
For this assignment you are asked to investigate the interaction between a particular protein and its
ligand to learn how the complex formed carries out a useful biological function. You are expected to
delve into the interaction at the molecular level, ideally to describe exactly which amino acid
residue(s) of the protein are directly involved in forming the protein-ligand complex, i.e. to explain
how the interaction occurs.
You are free to investigate a protein-ligand interaction of your own choosing and that you find
interesting. To help you, potential topics appear in the choice system on the LMS.
You will research the scientific literature to gather information about the protein, its ligand and the
interaction between them, and then use this information to write a 1200-word report on the major
features of the protein-ligand complex and its biological function.
This assessment task is to be completed individually and will contribute 40% to your overall mark for
this subject. Your written report will be assessed using the marking rubric provided.
Objectives
The objectives of this task are:
To investigate a protein-ligand interaction at the molecular level in order to improve your
understanding of the relationship between protein structure and biological function;
To develop literature research skills: to select appropriate sources of reliable and relevant
information from primary research articles and specialist texts in the scientific literature;
To develop scientific writing skills: to use vocabulary appropriate for a general scientific
audience; to write in full sentences with correct grammar and spelling; to develop a concise
story that conveys the major features of the protein-ligand interaction in a logical sequence;
To refine correct referencing and other acknowledgement skills: including in-text citations and
a reference list using a standardized format;
Format of your report
Your written report should be presented in essay form using complete grammatically-correct
sentences with correct punctuation and spelling. You should use paragraphs and/or headings to
organize and add structure to the material presented. Use of relevant figures is recommended.
The main text of your report should be about 1200 words in length +10% (excluding in-text citations,
figure legends and references).
First Section
* Describe the two components of the protein-ligand pair
* Describe where this interaction occurs (i.e. in which species, cell type or organ the protein and ligand
interact)
* Describe the primary biological function that the interaction mediates (i.e. part of immune
responses, cell signalling, metabolism, etc)
Second section
* Describe the interaction in greater molecular detail, try to include details such as:
o Which amino acids of the protein are involved?
o What triggers the interaction?
o Does the interaction change the conformation/structure of the protein and/or ligand?
o Are there cofactors required for this interaction or inhibitors that can block it?
Third section
* Other relevant or interesting information related to the interaction not covered above, such as:
o Can the interaction be artificially manipulated or utilised for another purpose? (like antibody
usage in biotechnology)
o Does this interaction vary in different cells or organisms?
o Are there mutations that affect the protein and/or cause genetic disease? (if so how?)
Conclusion
* Briefly summarise the major points covered in the report, emphasising the importance or key
features of the protein-ligand interaction
Remember, your report should be written using complete sentences and grammar (not dot points as
in the above example).
Resources
Journal articles and reviews
For advanced work on breaking research in later years of study, your first port of call will almost
certainly be primary research articles, but for this task at second year university level you may find
that review articles offer more relevant information in a condensed and concise form. . There are links
on the LMS in the assessment section to databases such as Pubmed and Google Scholar.
Textbooks
You may find useful information about many of the suggested inborn errors of metabolism in general
introductory Biochemistry and Molecular Biology textbooks, for example:
Nelson DL & Cox MM (2016) Lehninger: Principles of Biochemistry, 7“ edition, W.H.Freeman
and Co., New York [alternatively Sth edition (2008) or the 6″ edition (2012) will suffice]
Lodish H, Berk A, Kaiser CA, Krieger M, Scott MP, Bretscher A, Ploegh H and Matsudaira P
(2016) Molecular Cell Biology, 8 edition., W.H.Freeman and Co., New York [alternatively 6th
edition (2008) or 7th edition (2013) will suffice].
Websites will not be considered as acceptable references for the written part of this task
The web is an immense resource that contains both reliable and unreliable information. Apart from
sites such as those run by the publishers of scientific journals, very few web sites are peer-reviewed
or checked for accuracy. For this and other reasons, web sites will not be considered as acceptable
‘references’ for the written part of any reports.
You may, however, use web sites to source diagrams to include in your report if you wish. Keep in
mind that this task is primarily an exercise in scientific writing, so including a diagram drawn by
someone else will only earn you marks if it is relevant to your topic and you specifically refer to and
elaborate on it in the text of your report. If you include a web-sourced diagram, remember that it
must be acknowledged (just as you would credit a diagram from a printed journal article).
You should present at least four independent published sources of information, such as primary
journal articles, reviews or textbooks (but excluding websites) for the written part of your report.
If you source any diagrams from the web, they should be given a citation and included in your
reference list (to give due acknowledgement), but they will not be counted towards your minimum of
four information sources.
Despite not being able to use a web site as a direct reference in this assignment, be aware that the
web can be an excellent starting point to find information about your topic. For example, although
Wikipedia obviously cannot be used directly as areference, it can lead you to primary research articles
which can be cited directly in your assignment.
Marking Rubric
The marking rubric below shows the criteria that will be used to allocate marks for your report –
content (50%), presentation (30%) and referencing (20%).
Criterion Fail Pass (D) Good (C to B) Excellent (A)
(less than 50%) | (50 – 60%) (60-80%) (80 – 100%)
‘Scientific Content (50%) Does not meet Covered bare ‘Covered Covered
oo minimum minimum minimum with — | minimum with
Protein & ligand names, standard, some further further
details of their interaction, Descriptions . . :
a explanations in | explanations in
biological function as Inadequate barely
cone area most areas and
described, with greatest content adequate
hasi: ft i (i ial (lacking depth Interacti t excellent
emphasis on focussing on especial lacking de raction a
P ” e pecially dept explanations in at
the interaction at 2 inadequate ‘or clarity) molecular level
least one area.
molecular level coverage of described
= Scientific
interaction at adequately Excellent
Plus at least 1 other feature content not
molecular level) description of
presented fully Good description | i traction st
Scientific content | understood or and
molecular level
misunderstood or | interpreted understanding of
misinterpreted correctly scientific content | Excellent
understanding
and description
of all aspects of
scientific content
Presentation quality (30%)
(Clear, concise and coherent
presentation style
Complete grammatically-
‘correct sentences with
correct punctuation and
spelling
Appropriate use of
paragraphs and/or
headings to organize the
material
Logical layout and
sequencing/chronology
{clear and coherent flow of
information)
Diagrams — appropriate use
of images where
appropriate; diagrams
specifically referred to and
discussed in the text
Does not meet
minimum
standard.
Poor structure
and organization
of material
Poor grammar,
punctuation,
spelling
‘Organized into
paragraphs.
Full sentences –
grammar,
punctuation
and spelling
substantially
correct.
Figures
included, but
not referenced
or directly
addressed in
‘text.
Organized into
paragraphs and
with headings
Full sentences,
with good
grammar,
punctuation and
spelling.
Scientific
vocabulary used
appropriately.
Logical flow
Figures included,
with adequate
discussion in the
text
Organized into
paragraphs and
with headings
Full
grammatically
correct sentences
with excellent
punctuation and
spelling
Excellent use of
scientific
vocabulary –
concepts used
correctly and
with
understanding.
Logical flow of
information, with
conclusion.
Figures included,
with explanatory
Interesting and engaging
Assessor to analyse Turnitin
Originality Report (view
overall % match but also
look at text matches in
context]
titles and
legends, and
excellent
discussion
seamlessly
blended into the
text, referenced
fully and correctly
Showed thorough
understanding of
whole topic.
Referencing (20%)
Gathered at least four
independent references /
sources (no web sites
except for diagrams)
Correct use and format of
in-text citations
Full references provided
appropriately in reference
list, in correct alphabetical
order
Does not meet
minimum
standard.
‘Only websites
were cited (no
primary sources)
Insufficient
references cited,
In-text citations
missing or
incomplete
Reference list
either missing,
incomplete or
includes
references that
are not cited in
text
Four references
cited, but only
from textbooks
(no primary
references or
reviews, for
example).
No web sites
(“except for
diagrams only}
References
linked to text
with in-text
citations.
Reference list
complete and
formatting
substantially
correct and
consistent.
Four references
including journal
review or article,
for example.
No web sites (*
except for
diagrams only).
References
linked to text
with in-text
citations.
Reference list
complete with
consistent
formatting in
almost all
entries.
More than four
references,
including journal
reviews or
articles.
No web sites
(*except for
diagrams only).
References linked
to text with in-
text citations and
figure legends.
Reference list
complete with
perfectly carrect
and consistent
formatting
<p>The post For this assignment you are asked to investigate the interaction between a particular protein and its ligand to learn how the complex formed carries out a useful biological function. You are expected to delve into the interaction at the molecular level, ideally to describe exactly which amino acid residue(s) of the protein are directly involved in forming the protein-ligand complex, i.e. to explain how the interaction occurs. You are free to investigate a protein-ligand interaction of your own choosing and that you find interesting. To help you, potential topics appear in the choice system on the LMS. You will research the scientific literature to gather information about the protein, its ligand and the interaction between them, and then use this information to write a 1200-word report on the major features of the protein-ligand complex and its biological function. first appeared on For academic Help.</p>