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What Proteins Are Universal To All Life Forms?

What Proteins Are Universal To All Life Forms?


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According to National Geographic, there are 23 proteins that are common to all life forms:

All species in all three domains share 23 universal proteins, though the proteins' DNA sequences-instructions written in the As, Cs, Gs, and Ts of DNA bases-differ slightly among the three domains

According to NCBI there are 324 proteins common to all life forms.

How many proteins are common to all life forms, and what are their names?


This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement:

All species in all three domains share 23 universal proteins, though the proteins' DNA sequences-instructions written in the As, Cs, Gs, and Ts of DNA bases-differ slightly among the three domains (quick genetics overview). The 23 universal proteins perform fundamental cellular activities, such as DNA replication and the translation of DNA into proteins, and are crucial to the survival of all known life-forms-from the smallest microbes to blue whales.

The article is referring to a paper published in Nature in 2010.

http://www.ncbi.nlm.nih.gov/pubmed/20463738

This paper uses a set of 23 proteins to test the idea that certain genes arose only once.

The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution27. The conserved proteins in this data set were identified based on significant sequence similarity using BLAST searches, and they have consequently been postulated to be orthologues.

There is no suggestion that there are only 23 such proteins, it's just that the author chose this subset to test his ideas.

And here they are:

alanyl-tRNA synthetase, aspartyl-tRNA synthetase, glutamyl-tRNA synthetase, histidyl-tRNA synthetase, isoleucyl-tRNA synthetase, leucyl-tRNA synthetase, methionyl-tRNA synthetase, phenylalanyl-tRNA synthetase β subunit, threonyl-tRNA synthetase, valyl-tRNA synthetase, initiation factor 2, elongation factor G, elongation factor Tu, ribosomal protein L2, ribosomal protein S5, ribosomal protein S8, ribosomal protein S11, aminopeptidase P, DNA-directed RNA polymerase β chain, DNA topoisomerase I, DNA polymerase III γ subunit, signal recognition particle protein and rRNA dimethylase


Must the Molecules of Life Always be Left-Handed or Right-Handed?

One of the strangest aspects of life on Earth—and possibly of life elsewhere in the cosmos—is a feature that puzzles chemists, biologists and theoretical physicists alike. Each of life’s molecular building blocks (amino acids and sugars) has a twin—not an identical one, but a mirror image. Just like your right hand mirrors your left but will never fit comfortably into a left-handed glove, amino acids and sugars come in both right and left versions. This phenomenon of biological shape selection is called “chirality”—from the Greek for handedness.

On Earth, the amino acids characteristic of life are all “left-handed” in shape, and cannot be exchanged for their right-handed doppelgänger. Meanwhile, all sugars characteristic of life on Earth are “right-handed.” The opposite hands for both amino acids and sugars exist in the universe, but they just aren’t utilized by any known biological life form. (Some bacteria can actually convert right-handed amino acids into the left-handed version, but they can’t use the right-handed ones as is.) In other words, both sugars and amino acids on Earth are homochiral: one-handed.

More than 4 billion years ago, when our home planet was in its fiery and temperamental youth, both the biological building blocks and their mirror reflections were present. In fact, both still coexist on Earth today—just not in life as we know it. Certainly, if you cook up a batch of amino acids, sugars or their precursor molecules in a laboratory, you’ll always get a 50-50 mixture of left and right. But somehow, as life emerged in the countless millennia that followed the Earth’s formation, only the left-handed amino acids and the right-handed sugars were selected.   

Chiral molecules have even been found in interstellar space. In a landmark discovery announced by the National Radio Astronomy Observatory this June, scientists identified molecules at the center of the galaxy that could be used to construct either the right- and left-handed sugars. While they still have no clue whether there are more of one hand than the other, the finding sets the stage for further experiments that could illuminate more about the origins of handedness.

The big questions still remain: How and why did life choose only one of two mirror reflections to construct every single creature in her menagerie? Does life require homochirality to get its start, or could life forms exist that use both the earthly building blocks and their alter egos? Did the seeds of homochirality originate in the depths of interstellar space, or did they evolve here on Earth?

Conceptual image of OSIRIS-REx. (NASA/Goddard / University of Arizona)

Jason Dworkin, who heads the Astrochemistry Laboratory at NASA’s Goddard Space Flight Center in Greenbelt, Maryland says that one challenge for scientists attempting to answer these questions is that “the early Earth is gone, and we have a string of very, very scant evidence of what it was like.” Four-or-so billion years of volcanic eruptions, earthquakes, meteor bombardments and, of course, the profound geological influence of life itself have so transformed the planet that it is nearly impossible to know how the Earth looked when life began. That is why Dworkin’s research group and many of his colleagues at NASA focus on meteorites—the remnants of space debris that find their way down to solid ground.

“These are time capsules from 4.5 billion years ago,” says Dworkin. “So what we collect in meteorites now is very similar to what was raining down on the Earth then.”

Dworkin is also the lead government scientist on the OSIRIS-REx mission to the near-earth asteroid, Bennu. The mission, which launches this September, will spend around a year taking measurements of the asteroid to better understand how it moves through our solar system. When the spacecraft’s time with Bennu is up, it will collect the ultimate prize: a sample from the surface of the asteroid, which it will bring it back to the Earth in the year 2023 so that scientists can study its chemical composition. “Everything we do supports getting that one sample,” says Dworkin.

The scientists chose Bennu in part because of its resemblance to a special type of meteorite that provides an intriguing (though by no means conclusive) clue to the origins of homochirality. Many meteorites contain carbon-based molecules including amino acids and sugars, which are just the right ingredients for life. Dworkin’s group analyzed the composition of these “organic” compounds in dozens of meteorites, and came to a surprising conclusion. Oftentimes both the left- and right-handed versions of, for example, an amino acid, were found in equal amounts—exactly what might be expected. But in many cases, one or more organic molecule was found with an excess of one hand, sometimes a very large excess. In each of those cases, and in every meteorite studied so far by other researchers in the field, the molecule in excess was the left-handed amino acid that is found exclusively in life on Earth.

Dworkin says that the sample from Bennu may provide even stronger evidence of this phenomenon. “Unlike meteorites, which, one, fall on the ground and then get contaminated, and, two, are separate from their parent body,” with Bennu, the scientists will know exactly where on the asteroid the sample came from. They are taking “extraordinary measures” confirm that nothing from Earth’s biology can contaminate the sample. “So when we get these (hopefully) excesses of amino acids on the Bennu sample in 2023, we can be confident that it’s not from contamination,” Dworkin says.

The evidence thus far from meteorites implies that perhaps there is a means of producing homochirality without life.  However, Dworkin says, “We don’t know if the chemistry that lead to homochirality and life came from meteorites, from processes on the earth, or perhaps from both.” There is also still the question of how and why that excess developed in the meteorite or its asteroid parent or on the early Earth in the first place.

Hypotheses abound. For example, polarized light found on our side of the galaxy can destroy the right-handed version of many amino acids by a small, but noticeable amount. The slight excess of the left-handed amino acid, would then have to be drastically amplified to get to the levels found in living organisms on Earth.

It is this amplification process that intrigues Donna Blackmond of the Scripps Research Institute in La Jolla, California. Blackmond has been studying the potential chemicalorigins of homochirality for nearly her entire career. “I think it’s going to be some combination of chemical and physical processes,” she says. Blackmond’s group is currently trying to discover how chemical reactions that could have taken place on the early Earth may have been swayed to produce only life’s building blocks. In 2006, her team showed that they could amplify only the left-handed form of an amino acid starting from a small excess. In 2011, they showed that the amplified amino acid could then be used to produce a huge excess of a precursor to RNA, which is made right-handed by a sugar that is attached to it. (RNA is thought by many scientists to be the original biological molecule.) Blackmond and many other chemists have made strides in this type of chemistry, but they are still a long way from being able to model all of the chemistries and conditions that might exist on an asteroid or a juvenile planet.

Blackmond also notes that it’s far from clear that life needed total homochirality in order to get its start. “One real extreme would be to say that nothing could ever happen until we have a completely homochiral pool of building blocks, and I think that’s probably too extreme,” she says. “We could start making information type polymers”—like DNA and RNA—“possibly before we had homochirality.” For now, all scientists can do is keep asking questions about molecules here on Earth and on the celestial bodies that surround us. In the hopes of unlocking one more piece of this puzzle, researchers are now developing new technologies to determine if there are excesses of one hand in interstellar space. 

In the meantime, life on Earth will continue, mysterious and asymmetric as ever.


Genetic Code: Degeneracy and Universality | Protein

The information stored in DNA is in the form of code. DNA contains 4 bases, A, T, G and C, whereas, proteins are made of 20 different amino acids. Therefore, the genetic code must contain more than one bases so as to specify the 20 different kinds of amino acids.

By the work of a number of scientists, the code and the relationship of amino acids with different codes was determined. It has been established that the code consists of 3 letters (3 bases), i.e., the code is
a “triplet” code. The number of triplet codes constituted from the 4 bases is 4 3 = 64.

The sequence of bases in DNA specifying an amino acid is called “code”, while its completely base sequence in mRNA is called “codon”. In tRNA, the sequence of bases specifying an amino acid is called “anticodon”. Thus, if one reads in 5′-»3’direction, the code for methionine is 5′ CAT3′-, the codon is 5′ AUG3′ and the anticodon is 5′ CAU3′.

Since the mRNA is directly involved in protein synthesis, “codons” are in common usage instead of “code” (DNA) to specify the amino acids. All the 64 codons with their meanings constitute the “coding dictionary” (Table 4.3). Of them, 61 codons specify amino acids, so they are called “sense” “codons” or “sense words”.

The rest 3 condons, UAA, UAG and UGA do not specify some amino acid and they are called “nonsense codons” or “nonsense words” (in terms of amino acid). But they are very important and necessary codons because they are used to stop or terminate the growing polypeptide chain.

Therefore, these codons are called “stop codons” or “chain termination codons.” The amino acids methionine and trytophane are specified by single codons AUG and UGG, respectively.

The codon AUG is an ambiguous codon because it specifies N-formylmethionine and methionine, both amino acids. Others are “degenerate” or synonymous” codons, i.e., the same amino acid is specified by more than one codons, (Table 4.3).

Degeneracy of Genetic Code:

There are two methods by which the same amino acid is specified by two or more codons:

1. The tRNAs accepting the same amino acid are different for different synonymous codons. Such tRNAs are called “isoacceptortRNAs” and they differ in anticodons. For example, one of the tRNAs carrying leucine is tRNA1 leu with anticodon 3′ GAC5′, while the other is tRNA2 leu with anticodon 3′ GAG5′.

2. A single type of tRNA pairs with two or more synonymous codons. For example, tRNA. accepting the amino acid alanine in yeast (tRNA aIa ) bears the anticodon 3′ CGI5′ that can pair with the codons 5′ GCU3′, 5′ GCC3 and 5′ GCA3′ on mRNA Crick in 1966 proposed the “wobble hypothesis” to explain the pairing of a single type anticodon with synonymous codons.

According to the Wobble hypothesis, the base position at the 5′-end of anticodon is the “wobble position”. Two bases of anticodon from 3′-end are complementary to the two bases of the codon (in mRNA). The base at the wobble position can pair with different bases. For example, a single type of tRNA gly with the anticodon 3′ CCI5′ can pair with the codons 5’GGU3′, 5’GGC3′ and 5’GGA3′ specifying the amino acid glycine.

Thus inosine (I) at the wobble position can pair, with U, C and A in the codon. Similarly, U can pair with A and G, while G at the wobble position can pair with C and/U.

Universality of the Genetic Code:

The meaning of the universality of genetic code is that the same genetic code is utilized by all the organisms. For example, the lac + gene producing the enzyme P-galactosidase in E. coli functions to produce the same enzyme in human fibroblast tissue culture cells deficient in this enzyme.

When the hemoglobin mRNA molecules are injected into the Xenopus eggs, protein synthesis occurs and the α and β polypeptide chains are produced. However, variation in the genetic code has been observed in mitochondria where some of the condons are differently translated.

UGA (termination codon in universal code) specifies tryptophane, while AUA (for isoleucine in universal code) specifies methionine in mitochondria. To some extent, the mitochondria of different organisms also differ in genetic code. For example, CUA is a codon for threonine in yeast mitochondria, while it specifies leucine in Drosophila and mammalian mitochondria.


Protein Stability

  • Proteins are very sensitive molecules. The term ‘native state’ is used to describe the protein in its most stable natural conformation, in situ. This native state can be disrupted by a number of external stress factors, including temperature, pH, removal of water, the presence of hydrophobic surfaces, the presence of metal ions and high shear.
  • The loss of a secondary, tertiary or quaternary structure due to exposure to stress is called denaturation. Denaturation results in the unfolding of the protein into a random or misfolded shape.
  • A denatured protein can have quite a different activity profile than the protein in its native form, and it usually loses its biological function. In addition to becoming denatured, proteins can also form aggregates under certain stress conditions. Aggregates are often produced during the manufacturing process and are typically undesirable, largely due to the possibility of them causing adverse immune responses when administered.

The eleven nonessential amino acids are primarily produced in the body. In humans, these are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, ornithine, proline, serine and tyrosine. Some of these depend upon the availability of essential amino acids in the diet which act as precursors to non-essential forms.

Conditionally essential amino acids are grouped to define a potential lack in the cellular environment either due to an unhealthy diet or a physical state in which increased amounts of these usually nonessential amino acids are necessary, such as during childhood, pregnancy, and illness. This group includes arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine arginine is essential for the young, but no longer necessary after the development period has ended. It is therefore considered ‘conditionally’ essential.

Selenocysteine and Pyrrolysine

All amino acids have a central alpha carbon atom upon which is bound a carboxyl group (COOH), a hydrogen atom (H), an amine group (NH2), and a functional and variable radical side chain which defines which amino acid it is. The most basic form of amino acid is glycine (C2H5NO2), which has a side chain consisting of a single hydrogen atom, as pictured below.

Alternatively, tryptophan (C11H12N2O2) is the largest amino acid. This complex molecule can be seen below.


Why does all life use the same 20 amino acids?

The way in which fragments of proteins formed on the prebiotic Earth has shed light on why all living organisms use the same set of 20 amino acids. Researchers in the US found that proteinogenic amino acids – those used to make natural proteins – more readily link into small peptide chains known as oligomers than those that are similar in structure but that life doesn’t make use of. These chemical properties may have made them more likely to be incorporated into proteins during the evolution of the earliest life forms.

‘Before life on prebiotic Earth, there would have been a larger set of available amino acids than the 20 that were eventually selected by biology,’ says Luke Leman from the Scripps Research Institute in La Jolla, who led the work together with Loren Williams at the Georgia Institute of Technology. ‘We know this because of experiments simulating the early Earth, and because non-proteinogenic amino acids have been found in meteorites, sometimes in much higher abundance than the amino acids used in proteins.’

Origin-of-life scientists have long been drawn to intriguing questions surrounding the evolution of proteins. ‘Why does biology use 20 amino acids – why not 12 or 40? And why did nature choose these particular 20 amino acids?’ says Leman. ‘We discovered that there are purely chemical factors, based on higher polymerisation reactivity and fewer side reactions, that might have contributed to this selection process.’

He explains the group is particularly interested in the three proteinogenic amino acids that have positively-charged side chains – lysine, arginine and histidine – because they are involved in a broader research programme studying co-evolution between early proteins and early nucleic acids. ‘Based on prior work, we knew that peptides and depsipeptides could be generated by simply drying down mixtures of amino acids and hydroxy acids, both of which are produced in prebiotic simulation reactions and found on meteorites,’ says Leman. ‘We decided to try a set of several positively charged amino acids in [these] prebiotic polymerisation reactions.’

The researchers chose the three positively charged proteinogenic amino acids, as well as three structurally similar positively charged amino acids that are believed to have been abundant on prebiotic Earth but are not found in proteins. They heated each amino acid together with a hydroxy acid – glycolic or lactic acid – at 85°C for a week, before analysing the residue to see what had been produced.

‘We thought that, in general, all of these amino acids would react similarly because they are structurally similar,’ says Leman. But while almost all the experiments did produce oligomers, the three proteinogenic amino acids reacted more efficiently and produced fewer side products compared with their non-proteinogenic counterparts. ‘That came as a real surprise. We thought “Is this for real?”,’ Leman says.

The team set up additional reactions to verify the result, each containing two types of amino acid – one proteinogenic and one that wasn’t – that could compete in the reaction. They found that, consistent with their initial results, the proteinogenic amino acids out-competed the non-proteinogenic amino acids.

‘This … underscores that there are still hidden chemical and physical factors that played important roles in the transition from a prebiotic soup to life,’ Leman says, adding that now the group are investigating interactions between RNA and the positively-charged oligomers that were produced in these reactions.

‘This is an interesting piece of work showing some of the nuances of polymerisation chemistry, and how they may have affected protein evolution,’ comments Jim Cleaves, who researches origin-of-life geochemistry at the Tokyo Institute of Technology in Japan. He adds that there is more to the story of protein evolution, however, as previous work has suggested the amino acids lysine and histidine were later additions to the set used by primitive cells to make proteins. ‘That said, there is an awful lot we don’t know about early biological evolution, and this very nice work helps fill in some gaps in this highly speculative research area,’ he says.

References

M Frenkel-Pinter et al, Proc. Natl. Acad. Sci. USA, 2019, DOI: 10.1073/pnas.k1904849116


Criterion for the classification of proteins:

Ø Proteins are classified based on the following THREE criterion:
(I). Classification based on STRUCTURE of Protein
(II). Classification based on COMPOSITION of Protein
(III). Classification based on FUNCTIONS of Proteins

(I). Classification of Proteins based on the Structure of Proteins

Ø Based on the structure, proteins are classified into 3 groups.
(A). Fibrous Proteins
(B). Globular Proteins

(C). Intermediate Proteins

(A). Fibrous Proteins

Ø They are linear (long fibrous) in shape.

Ø Secondary structure is the most important functional structure of fibrous proteins.

Ø Usually, these proteins do not have tertiary structures.

Ø Physically fibrous proteins are very tough and strong.

Ø They are insoluble in the water.

Ø Long parallel polypeptide chains cross linked at regular intervals.

Ø Fibrous proteins form long fibres or sheaths.

Ø Functions of fibrous proteins: perform the structural functions in the cells.

Ø Examples of fibrous proteins: Collagen, Myosin, Silk and Keratin.

(B). Globular Proteins

Ø Globular proteins are spherical or globular in shape.

Ø The polypeptide chain is tightly folded into spherical shapes.

Ø Tertiary structure is the most important functional structure in globular proteins.

Ø Physically they are soft than fibrous proteins.

Ø They are readily soluble in water.

Ø Most of the proteins in the cells belong to the category of globular proteins.

Ø Functions: Form enzymes, antibodies and some hormones.

Ø Example: Insulin, Haemoglobin, DNA Polymerase and RNA Polymerase

(C). Intermediate Proteins

Ø Their structure is intermediate to linear and globular structures.

Ø They are short and more or less linear shaped proteins

Ø Unlike fibrous proteins, they are soluble in water.

Ø Function: blood clotting proteins

(II). Classification of Proteins based on Composition:

Ø Two broad categories of proteins according to its composition, they are:

(A). Simple Proteins

(B). Conjugated Proteins

(A). Simple Proteins

Ø Simple proteins composed of ONLY amino acids.

Ø Proteins may be fibrous or globular.

Ø They possess relatively simple structural organization.

Ø Example: Collagen, Myosin, Insulin, Keratin

(B). Conjugated Proteins

Ø Conjugated proteins are complex proteins.

Ø They contain one or more non-amino acid components.

Ø Here the protein part is tightly or loosely bound to one or more non-protein part(s).

Ø The non-protein parts of these proteins are called prosthetic groups.

Ø The prosthetic group may be metal ions, carbohydrates, lipids, phosphoric acids, nucleic acids and FAD.

Ø The prosthetic group is essential for the biological functions of these proteins.

Ø Conjugated proteins are usually globular in shape and are soluble in water.

Ø Most of the enzymes are conjugated proteins.

Ø Based on the nature of prosthetic groups, the conjugated proteins are further classified as follows:

$ Phosphoprotein: Prosthetic group is phosphoric acid, Example- Casein of milk, Vitellin of egg yolk.

$ Glycoproteins: Prosthetic group is carbohydrates, Example – Most of the membrane proteins, Mucin (component of saliva).

$ Nucleoprotein: Prosthetic group is nucleic acid, Example – proteins in chromosomes, structural proteins of ribosome.

$ Chromoproteins: Prosthetic group is pigment or chrome, Example: Haemoglobin, Phytochrome and Cytochrome.

$ Lipoproteins: Prosthetic group is Lipids, Example: Membrane proteins

$ Flavoproteins: Prosthetic group is FAD (Flavin Adenine Dinucleotide), Example: Proteins of Electron Transport System (ETS).

$ Metalloproteins: Prosthetic group is Metal ions, Example: Nitrate Reductase.


What Proteins Are Universal To All Life Forms? - Biology

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective they may serve in transport, storage, or membranes or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

Proteins have different shapes and molecular weights some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids otherwise, the amino acids are identical.

Figure 1. Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.

The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology, or similarity, among different species — in other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.


Overview of Cell Lysis and Protein Extraction

All cells have a plasma membrane, a protein-lipid bilayer that forms a barrier separating cell contents from the extracellular environment. Lipids comprising the plasma membrane are amphipathic, having hydrophilic and hydrophobic moieties that associate spontaneously to form a closed bimolecular sheet. Membrane proteins are embedded in the lipid bilayer, held in place by one or more domains spanning the hydrophobic core. In addition, peripheral proteins bind the inner or outer surface of the bilayer through interactions with integral membrane proteins or with polar lipid head groups. The nature of the lipid and protein content varies with cell type and species of organism.

Cell membrane structure. Illustration of a lipid bilayer comprising outer plasma membrane of a cell.

In animal cells, the plasma membrane is the only barrier separating cell contents from the environment, but in plants and bacteria the plasma membrane is also surrounded by a rigid cell wall. Bacterial cell walls are composed of peptidoglycan. Yeast cell walls are composed of two layers of ß-glucan, the inner layer being insoluble to alkaline conditions. Both of these are surrounded by an outer glycoprotein layer rich in the carbohydrate mannan. Plant cell walls consist of multiple layers of cellulose. These types of extracellular barriers confer shape and rigidity to the cells. Plant cell walls are particularly strong, making them very difficult to disrupt mechanically or chemically. Until recently, efficient lysis of yeast cells required mechanical disruption using glass beads, whereas bacterial cell walls are the easiest to break compared to these other cell types. The lack of an extracellular wall in animal cells makes them relatively easy to lyse.

There is no universal protocol for protein sample preparation. Sample preparation protocols must take into account several factors, such as the source of the specimen or sample type, chemical and structural heterogeneity of proteins, the cellular or subcellular location of the protein of interest, the required protein yield (which is dependent on the downstream applications), and the proposed downstream applications. For instance, bodily fluids such as urine or plasma are already more or less homogeneous protein solutions with low enzymatic activity, and only minor manipulation is required to obtain proteins from these samples. Tissue samples, however, require extensive manipulation to break up tissue architecture, control enzymatic activity, and solubilize proteins.

The quality or physical form of the isolated protein is also an important consideration when extracting proteins for certain downstream applications. For instance, applications such as functional enzyme-linked immunosorbent assay (ELISA) or crystallography require not only intact proteins but also proteins that are functionally active or retain their 3D structure.

Examples of protein sources for sample collection. Proteins can come from many sources, including the following: native sources such as mammalian cell cultures, tissues or bodily fluids overexpression in a model system such as bacteria, yeast, insect or mammalian cells monoclonal antibodies from hybridoma cells or plant cells used in agricultural biotechnology.


Protein

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Protein, highly complex substance that is present in all living organisms. Proteins are of great nutritional value and are directly involved in the chemical processes essential for life. The importance of proteins was recognized by chemists in the early 19th century, including Swedish chemist Jöns Jacob Berzelius, who in 1838 coined the term protein, a word derived from the Greek prōteios, meaning “holding first place.” Proteins are species-specific that is, the proteins of one species differ from those of another species. They are also organ-specific for instance, within a single organism, muscle proteins differ from those of the brain and liver.

What is a protein?

A protein is a naturally occurring, extremely complex substance that consists of amino acid residues joined by peptide bonds. Proteins are present in all living organisms and include many essential biological compounds such as enzymes, hormones, and antibodies.

Where does protein synthesis take place?

Protein synthesis occurs in the ribosomes of cells. In eukaryotic cells, ribosomes are found as free-floating particles within cells and are also embedded in the rough endoplasmic reticulum, a cell organelle.

Where is protein stored?

Proteins are not stored for later use in animals. When an animal consumes excess proteins, they are converted into fats (glucose or triglycerides) and used to supply energy or build energy reserves. If an animal is not consuming sufficient protein, the body begins to break down protein-rich tissues, such as muscles, leading to muscle wasting and eventually death if the deficiency is severe.

What do proteins do?

Proteins are essential for life and are essential for a wide range of cellular activities. Protein enzymes catalyze the vast majority of chemical reactions that occur in the cell. Proteins provide many of the structural elements of a cell, and they help to bind cells together into tissues. Proteins, in the form of antibodies, protect animals from disease, and many hormones are proteins. Proteins control the activity of genes and regulate gene expression.

A protein molecule is very large compared with molecules of sugar or salt and consists of many amino acids joined together to form long chains, much as beads are arranged on a string. There are about 20 different amino acids that occur naturally in proteins. Proteins of similar function have similar amino acid composition and sequence. Although it is not yet possible to explain all of the functions of a protein from its amino acid sequence, established correlations between structure and function can be attributed to the properties of the amino acids that compose proteins.

Plants can synthesize all of the amino acids animals cannot, even though all of them are essential for life. Plants can grow in a medium containing inorganic nutrients that provide nitrogen, potassium, and other substances essential for growth. They utilize the carbon dioxide in the air during the process of photosynthesis to form organic compounds such as carbohydrates. Animals, however, must obtain organic nutrients from outside sources. Because the protein content of most plants is low, very large amounts of plant material are required by animals, such as ruminants (e.g., cows), that eat only plant material to meet their amino acid requirements. Nonruminant animals, including humans, obtain proteins principally from animals and their products—e.g., meat, milk, and eggs. The seeds of legumes are increasingly being used to prepare inexpensive protein-rich food (see human nutrition).

The protein content of animal organs is usually much higher than that of the blood plasma. Muscles, for example, contain about 30 percent protein, the liver 20 to 30 percent, and red blood cells 30 percent. Higher percentages of protein are found in hair, bones, and other organs and tissues with a low water content. The quantity of free amino acids and peptides in animals is much smaller than the amount of protein protein molecules are produced in cells by the stepwise alignment of amino acids and are released into the body fluids only after synthesis is complete.

The high protein content of some organs does not mean that the importance of proteins is related to their amount in an organism or tissue on the contrary, some of the most important proteins, such as enzymes and hormones, occur in extremely small amounts. The importance of proteins is related principally to their function. All enzymes identified thus far are proteins. Enzymes, which are the catalysts of all metabolic reactions, enable an organism to build up the chemical substances necessary for life—proteins, nucleic acids, carbohydrates, and lipids—to convert them into other substances, and to degrade them. Life without enzymes is not possible. There are several protein hormones with important regulatory functions. In all vertebrates, the respiratory protein hemoglobin acts as oxygen carrier in the blood, transporting oxygen from the lung to body organs and tissues. A large group of structural proteins maintains and protects the structure of the animal body.