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Do all cells produce the same proteins?

Do all cells produce the same proteins?


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If DNA is more or less the same in all cells, and DNA is used to produce proteins from aminoacids, then do all cells produce the same proteins or are they specialised/controlled by something?


Each cell will indeed have the same DNA sequences and ability to produce any given protein. However, there are certain factors (transcription factors) and cellular conditions within a cell that dictate which proteins are produced. If the conditions are right then only certain proteins will be produced depending on what type of cell it is. This process by which a cell continues to express selected proteins and becomes specialized for a specific function, is called differentiation. Expression of proteins that are not required can be prevented by transcriptional repressors (or by epigenetic mechanisms such as methylation of DNA sequences). So to answer your question, while cells contain the instructions (DNA sequences) to produce potentially any protein, not every type of protein will always be produced.

Keep in mind that my answer is very basic; the answer isn't as simplistic as I'm making it out to be.


Protein expression in cells is majorly governed by a concept called RNA splicing. This also forms the basis of different types of cells which has different proteins expressed at different levels, but from the same nuclear material: DNA, which can be visually seen here. Differential splicing leads to various isoforms of the mRNAs, which are precursors of protein expression in cell. So, based on how the splicing occurs in different types of cells, different proteins are expressed at different levels, which constitute to the different phenotypes. This is just a brief introduction to these concepts following the previous comments, but I thought it would be a good time to mention these as these are pertinent.

I am new to this site, so may be not giving the best and most comprehensice answers, but I hope this is useful.


if you sequence deep enough and add single-cell sequencing you will also find cell to cell differences in the DNA which will add an other layer of heterogeneity in protein expression between cells.


In a simplistic sense DNA can be viewed as more or less the same amongst species, but with a variability of say 0.2% between humans and chimps that might not seem like much, but it really is. A human genome is over 3 billion bases long, which means that 10s of millions of bases are different between humans and chimps and every three bases encodes an amino acid that then become one piece of a protein.

As such there is a high degree of variability in the proteins expressed in a given cell. There are many homologous proteins between cells/species, which are proteins translated/transcribed from variable DNA/mRNA sequences, but ultimately serve the same function. Additonally, even though all human cells have the same genome (within the same individual), specialized control and compartmentalization of the genetic code (DNA) is why we have different organs and tissues such as the heart, skin, and lungs.


There are millions of protein factories in every cell. Surprise, they’re not all the same

The plant that built your computer isn't churning out cars and toys as well. But many researchers think cells' crucial protein factories, organelles known as ribosomes, are interchangeable, each one able to make any of the body's proteins. Now, a provocative study suggests that some ribosomes, like modern factories, specialize to manufacture only certain products. Such tailored ribosomes could provide a cell with another way to control which proteins it generates. They could also help explain the puzzling symptoms of certain diseases, which might arise when particular ribosomes are defective.

Biologists have long debated whether ribosomes specialize, and some remain unconvinced by the new work. But other researchers say they are sold on the finding, which relied on sophisticated analytical techniques. "This is really an important step in redefining how we think about this central player in molecular biology," says Jonathan Dinman, a molecular biologist at the University of Maryland in College Park.

A mammalian cell may harbor as many as 10 million ribosomes, and it can devote up to 60% of its energy to constructing them from RNA and 80 different types of proteins. Although ribosomes are costly, they are essential for translating the genetic code, carried in messenger RNA (mRNA) molecules, into all the proteins the cell needs. "Life evolved around the ribosome," Dinman says.

The standard view has been that a ribosome doesn't play favorites with mRNAs—and therefore can synthesize every protein variety. But for decades, some researchers have reported hints of customized ribosomes. For example, molecular and developmental biologist Maria Barna of Stanford University in Palo Alto, California, and colleagues reported in 2011 that mice with too little of one ribosome protein have short tails, sprout extra ribs, and display other anatomical defects. That pattern of abnormalities suggested that the protein shortage had crippled ribosomes specialized for manufacturing proteins key to embryonic development.

Definitive evidence for such differences has been elusive, however. "It's been a really hard field to make progress in," says structural and systems biologist Jamie Cate of the University of California (UC), Berkeley. For one thing, he says, measuring the concentrations of proteins in naturally occurring ribosomes has been difficult.

In their latest study, published online last week in Molecular Cell, Barna and her team determined the abundances of various ribosome proteins with a method known as selected reaction monitoring, which depends on a type of mass spectrometry, a technique for sorting molecules by their weight. When the researchers analyzed 15 ribosomal proteins in mouse embryonic stem cells, they found that nine of the proteins were equally common in all ribosomes. However, four were absent from 30% to 40% of the organelles, suggesting that those ribosomes were distinctive. Among 76 ribosome proteins the scientists measured with another mass spectrometry-based method, seven varied enough to indicate ribosome specialization.

Barna and colleagues then asked whether they could identify the proteins that the seemingly distinctive ribosomes made. A technique called ribosome profiling enabled them to pinpoint which mRNAs the organelles were reading—and thus determine their end products. The specialized ribosomes often concentrated on proteins that worked together to perform particular tasks. One type of ribosome built several proteins that control growth, for example. A second type churned out all the proteins that allow cells to use vitamin B12, an essential molecule for metabolism. That each ribosome focused on proteins crucial for a certain function took the team by surprise, Barna says. "I don't think any of us would have expected this."

Ribosome specialization could explain the symptoms of several rare diseases, known as ribosomopathies, in which the organelles are defective. In Diamond-Blackfan anemia, for instance, the bone marrow that generates new blood cells is faulty, but patients also often have birth defects such as a small head and misshapen or missing thumbs. These seemingly unconnected abnormalities might have a single cause, the researchers suggest, if the cells that spawn these different parts of the body during embryonic development carry the same specialized ribosomes.

Normal cells might be able to dial protein production up or down by adjusting the numbers of these specialized factories, providing "a new layer of control of gene expression," Barna says. Why cells need another mechanism for controlling gene activity isn't clear, says Cate, but it could help keep cells stable if their environment changes.

He and Dinman say the use of "state-of-the-art tools" makes the results from Barna's team compelling. However, molecular biologist Harry Noller of UC Santa Cruz doubts that cells would evolve to reshuffle the array of proteins in the organelles. "The ribosome is very expensive to synthesize for the cell," he says. If cells are going to tailor their ribosomes, "the cheaper way to do it" would entail modifying a universal ribosome structure rather than building custom ones.


Where does transcription occur and where does translation occur in the cell?

Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm.

Explanation:

Terms transcription and translation in biology are generally related to the DNA and its properties. Human cells replicate. In order to do that, they have to produce the same constituents for the new cell that is to be made. The only way to do that is by producing proteins.

The proteins are produced in the process that is called protein synthesis. The first step is in the nucleus where a particular gene is being expressed so it enables all protein factors to come and to replicate that part of a chromosome. This is finished when mRNA, the same single-stranded genetic code of a particular gene, is formed. This is transcription.

Right after that, the mRNA enters the cytoplasm through nuclear pores. There, it could be translated into proteins by ribosomes. This process is called translation.


How Are Proteins Produced in a Cell?

Proteins are produced by stringing amino acids together in the order specified by messenger RNA strands that were transcribed from DNA in the cell nucleus. The process of synthesizing a protein is called translation, and it occurs on ribosomes in the cytoplasm of a cell.

During protein production, ribosomes serve as the site where synthesis takes place, and transfer RNAs serve as the tools that build the growing protein strand. Transfer RNA can attach to both RNA and amino acids. As a ribosome slides down the strand of messenger RNA and exposes each codon one by one, individual molecules of transfer RNA attach the corresponding amino acid to the growing protein chain. Once the entire messenger RNA strand has been read, the completed polypeptide chain is released from the ribosome.

A newly made polypeptide chain is not yet a functional protein. The polypeptide chain must be folded properly into a specific conformation to become a protein. In some cases, multiple polypeptide chains must assemble into a cohesive protein structure before they can function. In some cases, proteins self-assemble, folding into the proper configuration completely on their own. More complex proteins sometimes require molecular chaperones, molecules that assist or stabilize the folding process. During and after the folding process, some proteins are also altered by enzymes or modified by the addition of lipids or carbohydrates to the protein surface.


ATP vs. GTP/CTP - Why does nature use ATP for energy coupling? (Apr/03/2006 )

I am preparing my final exam and just asked myself a simple question which turned out to be not so simple.

Why does nature use (in most cases) ATP to couple energy into reactions? Why not GTP or CTP?
(Actually, GTP is used for some processes, but I don't know any reactions that use CTP)
The amount of energy they provide upon hydrolysis into ADP/GDP/CDP and Pyrophosphate is the same.
So there should be some evolutionary advantage, which is the reason to favor ATP.

hi
i don't have a strick answer, but i realized once that GTP gives some energy in reactions and also serves as cofactor for G proteins.
And A and G are purines. So probably purines are better holded than pyrimidines.
But why A vs G .

Hi,
ATP: Adenosine is the all-purpose nucleotide, assuming several roles in almost every pathway in the cell. Adenosine can be used as a source of energy, acting alone as ATP or combined with other nucleotides, like niacin in NAD or riboflavin in FAD. Enzymes which directly hydrolyse ATP into ADP and phosphate are called ATPases. ATPases are found throughout the cell performing a wide variety of functions from pumping ions across the membrane to running all of the cytoplasmic motors that shuttle material around the cell and drive cilia, flagella, and muscles. Adenosine is also used extensively by the cell as a source of phosphates for modifying proteins - several proteins require phosphorylation to be activated or inactivated, and this is used by the cell to control which enzymes are on or off. The enzymes which phosphorylate other proteins are called kinases and all require ATP to function. There are several other functions of Adenosine that I won't go into here to save space.

GTP
: Guanosine is used similarly to Adenosine, but in fewer roles. There are a very few instances in which GTP is used as a phosphate donor or an energy source, most notable of which is Tubulin, which must hydrolyze GTP to GDP to form the microtubules of the cytoskeleton. There are several other GTPase enzymes in the cell, however most of these enzymes are not used for their enzymatic properties, but rather are used to transmit signals throughout the cell. G-proteins are a specific class of GTPases which use their binding to GTP to interact with other enzymes to activate the cell. Many hormones and neurotransmitters have receptors that use G-proteins to transmit their signals to the rest of the cell. There are several other GTPases, including the Ras and Rab families of small GTPases, that are all also used to transmit signals and to control other intercellular traffic through their binding to GTP.

UTP
: Uridine is used for a different purpose from the purine nucleotides. The most common example of this is in glycogen synthesis. Many cells in the body (especially in the liver) store glucose (sugar) in the form of glycogen, a complex starch composed of long, branching chains of glucose molecules. To enhance this reaction, free glucose molecules prepared for addition by reacting them with UTP to produce UDP-glucose and free phosphate. This makes the glucose molecules more reactive, since the glucose-phosphate bond in UDP-glucose is a high energy bond. As the UDP-glucose is added to glycogen, the UDP is released, and the energy is used to attach the glucose to the glycogen molecule. In fact, Uridine is used for UDP-glucose, UDP-galactose, UDP-mannose, etc., the building blocks of numerous carbohydrates that are essential for many cellular functions.

CTP
: Cytidine is used very similarly to Uridine, however instead of sugars, CTP is used with fats. CDP-diacylglycerol, CDP-ethanolamine, and CDP-choline are the building blocks of the phospholipids that make up the cell membrane. Since all cells require intact membranes to survive, this is an exceedingly important cellular function.

The purine nucleotides have a wide range of uses, while the pyrimidines act more as handles than anything else. This is probably due to the more reactive nature of the purine rings, which makes ATP especially an ideal co-enzyme.

I doubt there's an energy reason -- as you noted, there's an equal amount of energy in the phospate bonds of other nucleotides.

It's likely that this is an evolutionary preference -- an early enzyme worked with ATP, and through evolution, other orthologous genes arose through gene duplication and genetic drift. Nature doesn't waste time reinventing the wheel, so since the early ancestor used ATP, so do the bulk of its orthologs.

As the cell became more complex, the ability to separate energy-producing enzymatic reactions on the basis of the nucleotide providing the bonds becomes beneficial, and thus orthologs which preferencially use GTP, for example, were selected for.

The inter-related nature of these genes can not only be seen at the sequence level, but also in their catalytic abilities -- most of these enzymes show a strong preference for "their" NTP, but will also catalyse other nucleotide triphosphates as well, at a greatly reduced rate.

A similar example can be found regarding the isocitrate dehydrogenases -- some of which reduce NAD (to make ATP, BTW) and others of which reduce NADP (in the synthesis of certain amino acids).

BTW, I suppose it is equally likely that ATP is the most wide-spread energy-providing NTP used by the cell because it was the first one that could be synthesized by the cell, or that it is the one most easily synthesized, or some other reasons (likely a combination of reasons).


Proteins

Proteins are the "workhorse" molecules of life, taking part in essentially every structure and activity of life. They are building materials for living cells, appearing in the structures inside the cell and within the cell membrane. They carry oxygen, they build tissue, they copy DNA for the next generation - they do all the work in any organism. While many of the proteins are structural proteins, many are regulatory proteins called enzymes.

They contain carbon, hydrogen, and oxygen like the carbohydrates and lipids, but they also contain nitrogen and often sulfur and phosphorus.

Protein molecules are often very large and are made up of hundreds to thousands of amino acid units. Though large, the protein typically has a small working region, such as a pocket located on the three-dimensional surface of the folded protein chain which acts as a binding site. The 20 amino acids are combined in different ways to make up the 100,000 or so different proteins in the human body. Some of these proteins are in solution in the blood and other fluids of the body, and some are in solid form as the framework of tissue, bone and hair. Shipman, et al. suggests that they make up about 75% of the dry weight of our bodies.

Proteins can be characterized as extremely long-chain polyamides. The amides contain nitrogen, and nitrogen composes about 16% of the protein atomic content. These proteins are created in the body by condensation of amino acids under the influence of enzyme catalysts, using patterns or direction from the nucleic acids in the cells.

The amino acid units in a protein molecule are held together by peptide bonds, and form chains called polypeptide chains. The sequencing of the 20 amino acids forms a kind of alphabet for expression of the type of protein, leading to a very large number of types of proteins.

In the cell, the DNA directs or provides the master blueprint for creating proteins, using transcription of information to mRNA and then translation to actually create proteins.

A comment from Miller "Living things, after all are constructed by the execution of a series of genetic messages encoded in DNA. Genes, the functional units of that genetic program, generally encode proteins, which are the workhorses of the cell. As our exploration of the genomes of humans and other organisms expands, it becomes clear that those proteins can do just about everything required to produce an organism . "


Why the S Phase Is Important

DNA synthesis must occur rapidly, as the unpaired base pairs of the DNA strand during replication are vulnerable to harmful mutagens, which can lead to genetic abnormalities, cell disease or even cell death. This phase is highly regulated, due to its importance in the conservation of genetic material. If there is any damage to the DNA in a cell, it can be identified and fixed in the S phase.

Besides DNA replication, the numerous controls involved in ensuring the smooth running of the show are crucial in ensuring that the cell does not spend more time than is necessary in this phase. Any delays can have a cascade effect on growth rates, cell replacement, and this would have adverse implications to the organism as a whole.


Plant Cell Organelles

A Labeled Plant Cell

Amyloplasts

A major component of plants that are starchy in nature, the amyloplasts are organelles that store starch. They are classified as plastids, and are also known as starch grains. They are responsible for the conversion of starch into sugar, that gives energy to the starchy plants and tubers.

Function: S ynthesizes and stores starch granules.

Cell Membrane or Plasma Membrane

The cell membrane is a thin layer made up of proteins, lipids, and fats. It forms a protective wall around the organelles contained within the cell. It is selectively permeable and thus, regulates the transportation of materials needed for the survival of the organelles of the cell.

Function: Protects the cell from its surroundings.

Cell Wall

Unique to plant cells, the cell wall is a fairly rigid, protective wall that resists the strain of physical forces. The cell wall is mainly made up of cellulose fiber and it helps maintain the shape of the cell.

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Function: Maintains cell pressure and prevents over-expansion of the cell.

Centrosome

The centrosome is located close to the nucleus and is a small body made up of radiating tubules. It is responsible for producing and organizing the microtubules. In plant cells, the centrosome is a ‘centriole-free’ organelle. It is also called the Microtubule-organizing center (MTOC).

Function: Regulates cell-cycle progression.

Chloroplast

Found only in plants, chloroplasts are organelles that resemble the structure of the mitochondria. It is a plastid that traps energy from sunlight. It contains chlorophyll molecules, that carry on the process of photosynthesis as well as, give the plants a lush green color.

Function: Conducts photosynthesis.

Cytoplasm

The cytoplasm forms the gel-like substance that holds the organelles in the cell. It is a colorless substance that is made up of mainly water, salts and organic molecules. It also contains proteins, that make up the cytoskeleton. We can refer to it as, the stage where all the action in the cell takes place, or as the home of all the organelles of the cell.

Function: Serves as the site of multiple cell processes including cell metabolism.

Golgi Body

Known as the ‘golgi complex’ or the ‘golgi apparatus’, it is located near the nucleus. It is a stack of membrane-bound structures that, is involved in the transportation of lipids and modification of proteins. It is crucial in segregating and transporting material within the cell.
.
Function: Sorts, processes and modifies proteins.

Mitochondrion

Known to be the ‘power house’ or the ‘storehouse of energy’ of the cell, the mitochondria plays an important role in a cell. They are made up of cristae or finger-like structures, which convert the sugar into Adenosine Triphosphate or ATP. ATP stores and releases energy required for the cell to function. It is responsible for regulating membrane potential, programming the death of the cell and regulating cellular metabolism.

Function: Produces energy and converts it, regulates cell metabolism.

Nucleus

This is a spherical body that contains various organelles like the nucleolus (where ribosomal RNA is produced) and is surrounded by a nuclear membrane. The nucleus is known to be the ‘control room’ of the cell. It regulates various cell functions by controlling the protein synthesis of the plant cell. The nucleus contains DNA within the chromosomes. It is a membrane-bound structure that contains the cells hereditary information.

Function: Controls expression and transcription of the gene.

Nucleolus

Known to be the heart of the cell, the nucleolus transcribes ribosomal RNA. It is composed of proteins and nucleic acid and is known to be a genetically determined element.

Function: Produces ribosomes.

Peroxisomes

Membrane-bound packets of oxidative enzymes, the peroxisomes play a vital role in converting fatty acids to sugar. They also assist the chloroplasts in photo-respiration. The glyoxylate cycle, that takes place in germinating seeds, occurs in peroxisomes. They also assist in photo-respiration in leaves.

Function: Regulates the breakdown of metabolic hydrogen peroxide.

Ribosomes

They are small packets or granules of RNA that convert amino acids into proteins. It serves as a site of protein synthesis and is therefore termed as the workhorses of protein biosynthesis.

Function: Builds and synthesizes proteins.

Rough Endoplasmic reticulum

The rough endoplasmic reticulum or rough ER, is a vast interconnected membrane system located close to the nucleus. The presence of ribosomes on its surface gives it a rough appearance and hence the name. The RER works in accord with the golgi body to send new proteins to their proper destinations. These networks transport materials through the cell and produce proteins in sacs known as cisternae.

Function: Manufactures lysosomal enzymes, facilitates translating and folding of new proteins.

Smooth Endoplasmic reticulum

Similar to the structure of the rough ER, the smooth ER is a separate interconnected network membrane structure that is free from ribosomes. The SER transports material through the cell. It is also crucial in producing and digesting lipids and proteins.

Function: Manufactures and transports lipids.

Vacuole

Vacuole is essentially a sac filled with water that helps maintain the shape of the cell. It stores nutrients and waste products. Its functions include, isolating materials harmful to the cell, maintaining turgor within the cell and exporting unwanted materials away from the cell.

Function: Regulates internal environment.

You can save and print this diagram of the plant cell. It will help you with your revision.

That’s about how the organelles in a cell function. It’s unbelievable how a tiny cell can help a full-grown plant to grow and produce energy. As they say, life originates in a single cell and it is this cell that plays an important role in the growth of the living organism.

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Fungi and Biotechnology

Nicholas P. Money , in The Fungi (Third Edition) , 2016

Single Cell Protein

The term single cell protein was introduced in the 1960s to describe protein-rich foods manufactured from yeasts that served as dietary supplements for livestock and humans. Single cell protein was viewed as a product category that might address food shortages at a time when it seemed unlikely that agricultural production could keep pace with the skyrocketing human population. Interest in food yeast declined as improvements in plant breeding and agricultural practices led to the contemporary boom in global food production. Saccharomyces cerevisiae produced in stirred fermenters on molasses is an example of single cell protein that is manufactured today. The yeast produced in this fashion is not consumed directly, but is used for baking. Marmite is a savoury spread made from yeast extract that has been popular in the United Kingdom for more than a century. Spent yeast from beer brewing is used to produce this sticky dark brown paste. Vegemite is a similar product made in Australia.

Another fungal protein product, called Quorn, is a very successful meat substitute manufactured by a single strain of a filamentous saprotrophic ascomycete, Fusarium venenatum. Because Quorn is produced from a multi-cellular, filamentous fungus, the term single cell protein is inaccurate and mycoprotein is the preferred name. The use of a filamentous fungus makes it possible to produce a meat-like consistency that cannot be replicated with a single-cell protein . The fungus is grown in pairs of 50 m tall air-lift fermenter vessels that contain 230 tonnes of broth ( Figure 12.8 ). The vessels are connected at the top and the bottom to form a continuous loop. Compressed air and ammonia are pumped into the bottom of the first vessel, called the ‘riser’, oxygenating the culture and circulating the liquid containing the fungus toward the top. Carbon dioxide from the respiring cells is released through a vent at the top of the system, and the liquid falls through the second ‘downcomer’ vessel and is infused with fresh nutrient solution (glucose plus vitamins and minerals). A heat exchanger at the bottom of the system maintains the temperature at 30 °C and the culture is harvested at a rate of 30 tonnes per hour. The dense mycelium of branched hyphae harvested from the fermenter has a very high RNA content. This is problematic for a food product because its consumption could raise uric acid levels in the blood and lead to gout and other illnesses. This is addressed by heating the mycelium at 68 °C for 20 min, which allows endogenous enzymes to destroy much of the RNA without reducing its protein content. The heated mycoprotein is then dried and bound with egg white. Further processing creates the meaty texture and adds flavourings and colourings.


Watch the video: Cellenes oppbygning (June 2022).


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