science

Proteome

Proteome is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Proteome rather than just read about it. In short: A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

Key takeaways

Proteome belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Proteome to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Proteome from memory before moving on to harder problems.

Reference excerpt

A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.

Types of proteomes While proteome generally refers to the proteome of an organism, multicellular organisms may have very different proteomes in different cells, hence it is important to distinguish proteomes in cells and organisms. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term proteome has also been used to refer to the collection of proteins in certain sub-cellular systems, such as organelles. For instance, the mitochondrial proteome may consist of more than 3000 distinct proteins. The proteins in a virus can be called a viral proteome. Usually viral proteomes are predicted from the viral genome but some attempts have been made to determine all the proteins expressed from a virus genome, i.e. the viral proteome. More often, however, virus proteomics analyzes the changes of host proteins upon virus infection, so that in effect two proteomes (of virus and its host) are studied.

Importance in cancer

The proteome can be used in order to comparatively analyze different cancer cell lines. Proteomic studies have been used in order to identify the likelihood of metastasis in bladder cancer cell lines KK47 and YTS1 and were found to have 36 unregulated and 74 down regulated proteins. The differences in protein expression can help identify novel cancer signaling mechanisms. Biomarkers of cancer have been found by mass spectrometry based proteomic analyses. The use of proteomics or the study of the proteome is a step forward in personalized medicine to tailor drug cocktails to the patient's specific proteomic and genomic profile. The analysis of ovarian cancer cell lines showed that putative biomarkers for ovarian cancer include "α-enolase (ENOA), elongation factor Tu, mitochondrial (EFTU), glyceraldehyde-3-phosphate dehydrogenase (G3P), stress-70 protein, mitochondrial (GRP75), apolipoprotein A-1 (APOA1), peroxiredoxin (PRDX2) and annexin A (ANXA)". Comparative proteomic analyses of 11 cell lines demonstrated the similarity between the metabolic processes of each cell line; 11,731 proteins were completely identified from this study. Housekeeping proteins tend to show greater variability between cell lines. Resistance to certain cancer drugs is still not well understood. Proteomic analysis has been used in order to identify proteins that may have anti-cancer drug properties, specifically for the colon cancer drug irinotecan. Studies of adenocarcinoma cell line LoVo demonstrated that 8 proteins were unregulated and 7 proteins were down-regulated. Proteins that showed a differential expression were involved in processes such as transcription, apoptosis and cell proliferation/differentiation among others.

The proteome in bacterial systems Proteomic analyses have been performed in different kinds of bacteria to assess their metabolic reactions to different conditions. For example, in bacteria such as Clostridium and Bacillus, proteomic analyses were used in order to investigate how different proteins help each of these bacteria spores germinate after a prolonged period of dormancy. In order to better understand how to properly eliminate spores, proteomic analysis must be performed.

History Marc Wilkins coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. It appeared in print in 1995, with the publication of part of his PhD thesis. Wilkins used the term to describe the entire complement of proteins expressed by a genome, cell, tissue or organism.

… excerpt ends here. Continue reading the full article.

Illustrations

Worked examples

Example 1 — a first encounter with Proteome

Start with the simplest possible case. Write down what Proteome claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Proteome before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Proteome ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Proteome

In research: Proteome appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Proteome in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Proteome is common in secondary-school and first-year university syllabi. It links to neighbouring topics Proteomics, so understanding it makes those chapters shorter.
In everyday life: Look for Proteome outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Proteome in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Proteome means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Proteome out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Proteome in simple terms?

Why does Proteome matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Proteome?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Proteome.