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How do proteins perform their function


I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here.


Let's, for example, take a ribosome. It is an enzyme that is in turn just a molecule that must follow the laws of physics.

Correct me if I'm wrong, but it can be looked upon as a molecular machine made up of several pieces. What exactly makes those pieces work together?

Why does the ribosome bind to a strand of RNA? Is it just the shape and electric charge or is it something more? Once the ribosome is bound to a piece of RNA, how does it move?

In a way, I'm looking for the "ghost in the machine". I'm interested in molecules in general, not just ribosomes. What is it that, on a level of single atoms, makes molecules "alive" - move, assemble a protein, etc. ?


PS. I'm having trouble phrasing my question, so if anything is not clear, please leave a comment and I will address it.


Edit 1: This is most definitely a physics question. I'm looking at the scale of several atoms.

Let me give a hypothetical example:

Imagine a strand of carbons. Also imagine that there exists a molecule that can move along this strand. How would it do it? What forces would move it along this strand? Is it electromagnetism? Would gravity be involved to a significant degree? What effect would shape have?

Does this make the question clearer?


This question is waaaay too broad, but I'll give some short and simplified answers to the hypothetical you asked at the end. First, let's reformulate your example a little bit:

How does the ribosome move along a strand of RNA?

  • How would it do it?
    • By hydrolyzing GTP and somehow coupling the free energy associated with that reaction to forward motion. Keep in mind that both ribosome and RNA are constantly undergoing random-walk Brownian motion (ie jiggling), so it's more a matter of biasing the ribosome's motion in a particular direction than it is of moving the ribosome in the first place.
  • What forces would move it along this strand?
    • The current understanding of molecular biophysics, which is by no means complete, says that the primary driver of this sort of protein activity is electrostatic forces.
  • Is it electromagnetism?
    • There are no electric currents, per se, so magnetism does not play a role.
  • Would gravity be involved to a significant degree?
    • At these scales gravity does not have a significant effect.
  • What effect would shape have?
    • Shape has an enormous effect. One of the fundamental axioms of molecular biophysics is that function follows form. The 3D configuration of those electrostatic forces I mentioned is determined in turn by the 3D configuration of the involved macromolecules.

If you want to know (a lot) more about this specific question, and if you have access to journals, check out this review: How Should We Think About the Ribosome?


Transport Protein

Transport proteins are proteins that transport substances across biological membranes. Transport proteins are found within the membrane itself, where they form a channel, or a carrying mechanism, to allow their substrate to pass from one side to the other.

The substances transported by these proteins can include ions such as sodium and potassium sugars such as glucose proteins and messenger molecules and many more.

Transport proteins generally perform two types of transport: “facilitated diffusion,” where a transport protein simply creates an opening for a substance to diffuse down its concentration gradient and “active transport,” where the cell expends energy in order to move a substance against its concentration gradient.


Volume 2

Kelsey N. Retting , Karen M. Lyons , in Handbook of Cell Signaling (Second Edition) , 2010

BMPs and Bone Development

BMP function in development is well characterized in the skeletal system. BMPs were originally discovered by Marshall Urist in 1965, who found that subcutaneously implanted decalcified bone could induce ectopic cartilage and bone formation [97] . Subsequent purification of osteoconductive factors led to the discovery of BMPs [98, 99] . The majority of the vertebrate skeleton is composed of endochondral bone. Endochondral ossification occurs when mesenchymal cells differentiate into chondrocytes, which form a highly organized template known as the growth plate [100] . This structure, in which cells are stratified in layers based on their stage of differentiation, permits assessments of the roles of BMP signaling pathways in specific aspects of cell commitment, survival, proliferation, withdrawal from the cell cycle, differentiation, and apoptosis. Several studies have demonstrated that BMP signaling is required for multiple aspects of endochondral bone formation (reviewed in [101, 102] ). BMP signaling promotes the formation of early prechondrogenic condensations by sustaining the expression of Sox9, a transcription factor required for commitment of mesenchymal cells to the chondrogenic lineage, adhesion molecules such as N-cadherin, and matrix production [103–105] . BMPs can also induce proliferation and differentiation of chondrocytes by induction of target genes including type II and type X collagen [104, 106, 107] . In addition, promoter activity of type X collagen can be induced in prehypertrophic chondrocytes by overexpressing Smads1 or 5 [108, 109] . In the growth plate, chondrocytes align into distinct zones of small rounded resting, flattened disk-like proliferating, and large hypertrophic chondrocytes. Many BMP ligands are expressed within the growth plate and in the surrounding perichondrium and periosteum, while BMP antagonists are expressed in opposing patterns [12, 110] . Furthermore, the level of nuclear phosphorylated Smads1, 5, and 8 increases in chondrocytes as they progress from the resting to the prehypertrophic zone [10] . These studies raise the possibility that BMPs may act as a gradient within the growth plate to regulate the balance between proliferation and differentiation.

In vivo, overexpression of BMPs leads to enlarged, misshapen, and fused skeletal elements as a result of increased matrix production and chondrocyte proliferation [94, 111, 112] . In contrast, low levels of BMPs induced by exposure to noggin prevent mesenchymal cell aggregation and differentiation, and at later stages lead to osteopenia and reduced bone formation [113–115] . Likewise, at the Smad level, transgenic mice overexpressing the inhibitory Smad6 exhibit delayed chondrocyte hypertrophy, postnatal dwarfism, and osteopenia [116] . Chondrogenic differentiation is severely impaired in transgenic mice lacking both Bmpr1a and Bmpr1b in cartilage, leading to a virtual lack of endochondral skeletal formation [14] . It remains to be determined whether the loss of intracellular R-Smads can mimic the effects of the BMP receptor knockout on endochondral bone formation in vivo.


Kate's A-level Biology

All known proteins are long, chain sequences of amino acids, there are only twenty different amino acids and they’re able to make up millions of different proteins, all with different structures and functions. Amino acid molecules are joined together by a peptide bond, this is a condensation reaction, and therefore water is produced as a waste product. Two amino acids with a peptide bond make the primary structure, they’re known as peptides.

The secondary structure is the first 3D structure, it’s held together by hydrogen bonds. At this stage either an alpha helix or a beta pleated sheet is formed, which is formed is dependent on the hydrogen bond between –NH, which is positively charged and –C=H, which is negatively charged. The hydrogen which is used to form the hydrogen bond will make the structure either alpha or beta, this will majorly effect the physical structure of the protein, even though the same elements are present.

The tertiary structure is the polypeptide 3D structure coiling up, these form specific structures. The structure is maintained by different bonds, which are once again are dependent on the primary structure of the protein. These bonds include disulphide bridges which are relatively strong ionic bonds which are weaker and can be broken by changes in pH and finally hydrogen bonds which are plentiful in the structure and are very easily broken.

The quaternary structure is achieved when two or more polypeptides are bonded into a large and complex molecule. Additionally they contain groups that aren’t proteins, for example iron—containing haem can be found in the complex molecule haemoglobin.

Structural proteins provide an internal structure to the cell and are sometimes involved in cell movement. Structural proteins provide vital support for larger molecules so that they don’t collapse in on themselves, making them essential in larger molecules.

For example, collagen is a structural protein and accounts for around a quarter of all proteins in our bodies. They provide strength for a variety of cells, they keep our skin plump and provide structure for blood vessels, ligaments and tendons. When under a microscope they look like long fibres that are woven together to create extra strength.

Transport proteins are essential to the function of living beings, and very few molecules are able to cross between membranes without the aid of a protein. Active transport moves molecules from regions of low concentration to areas of higher concentration, this is used in plant roots for the absorption of nutrients and minerals from soil.

Enzymes are globular proteins, meaning they have a complex quaternary structures, they act as biological catalysts. This means that enzymes allow reactions to happen more easily at a lower activation energy, their function is to breakdown or build up molecules in reactions.

There are two theories of how the shape of enzymes effects their functions, this first being lock and key method, in which hydrogen bonds join the substrate to the perfectly shaped active site, forming an enzyme-substrate complex. The substrate is converted into products and released from the enzyme, then the enzyme is ready to break down the next substrate. This method is criticised as the product leave the active site for no reason and the substrate has to be an exact fit to the rigid active site.

Another method is the induced fit model, in this method the substrate bonds to the active site with an induced fit, meaning the shapes aren’t perfectly complimentary but they change shape to fit. Finally the products are released, after the products are no longer complimentary to the active site. This theory is supported by many scientists because the active site is flexible and will change shape so that the enzyme-substrate complex can be achieved.

It is known that protein structures directly affect their functions because when an enzyme, which is a type of protein, denatures due to a change in heat or pH they change shape and can no longer carry out their specific function. The shape of all proteins is determined by its primary structure, once the primary structure has been changed a whole new protein is formed that will have a new function.


Proteins act as receptors on cell membranes

Proteins are essential components of all the cell membranes and membranes of the organelles. One of the functions of these membrane proteins is that they act as receptors. Hormones, neurotransmitters, and other signalling molecules bind to these receptors and convey signals to cells. In this way, proteins play a role in cell signalling that is essential for the coordinated function of all the cells present in our body. Take the following example to understand the role of proteins as receptors.

  • Insulin is a hormone that controls the glucose levels in our blood. It performs its function by binding to its receptor that is a protein. Insulin binds to its receptor that sends signals for the opening of glucose channels so that glucose can be taken up from the blood into the liver and muscle cells. If the insulin receptors are not present, the blood glucose levels cannot be regulated.

This and various other examples in our body prove why proteins are necessary for cell signalling and coordination of cellular functions.


Proteins as Workhorses of the Body

Proteins are large and fairly complex molecules that are responsible for doing most of the work that occurs in cells. They also are needed to maintain the structure of cells and are critical for the function and regulation of all of the body's tissues. The body uses the information stored in DNA to create proteins, which are made up of subunits called amino acids. Enzymes, which help speed chemical reactions in cells, are a specialized type of protein. Protein also plays a crucial role in maintaining muscle tissue, since muscle tissue has large amounts of protein. For muscles to increase in size and strength, more protein must be made to expand the muscle fibers.


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How do enzymes work & speed up chemical reactions?

The ability of the enzyme to perform its function depends on its active site. The active site is formed by the residues of amino acids in such a way that it can bind to a molecule of a particular composition and shape. This mode of action is called the lock-and-key model.

  • At present, there is another model that is called “induced fit model“. According to that idea, the enzyme reacts to the nearness of the correct molecule (called a substrate) and shapes its active site so the substrate would fit fully into it.
  • The active site may have one or more “landing points” for molecules. This way, the enzyme can bring two molecules together so that they can react with each other.

If those molecules were just placed in the solution, they would react much slower. It happens for several reasons:

  1. First of all, each reaction requires a certain amount of energy. When the enzyme binds to the molecules participating in the reaction, it also lowers the amount of energy that would be required.
  2. During each reaction, the potential result product has to go through the so-called transition state. It is very unstable. However, when the molecules are bound to the enzyme, this transitional product is much more stable so that the reaction can go faster.
  3. The enzyme also weakens the bonds between the components of the molecule, so that it can be broken up or new parts can be attached to it.

When the reaction is finished, the products no longer fit into the active site of the enzyme, so they are released. Another molecule can take its place, and the whole process can begin again.

Inhibitors that can block the enzymes have similar shapes to the “correct” molecules, but they bind to the active site in the slightly wrong way so that the specific activity of this particular protein (for example, ability to attach chemical groups) is blocked.


What are three functions of proteins?

Proteins perform a vast array of functions within organisms.

Explanation:

catalysing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another.
1.Building blocks
Proteins make up the hair, nails, muscles etc

hormones
Many hormones are protein in nature hormones control growth and metabolic activities of the body.

catalytic activities
Enzymes are globular protein. Enzymes speed up the biochemical reactions and help in digestion.

Transport of oxygen
A protein called haemoglobin contain iron atom which temporarily links with oxygen and releases it throughout the body.

Blood Clotting
Fibrinogen is a glycoprotein which helps in healing of wounds. Thus it prevents the blood loss and inhibits the passage of germs

Immunity
Antibodies are proteins that bind to the pathogens and inhibit their activities.

Muscles contractility
Some proteins are responsible for muscles contractility and movement.


Animal Cell Parts And Their Functions

Animal cells contain a wide variety of parts, each of which plays a vital role in the survival of the cell.

The Nucleus

The nucleus is the control center of the cell and houses all of the cell’s genetic information. Usually, a cell has a single nucleus that contains all of its DNA molecules, but some (such as skeletal muscle cells) have more than one nucleus.

The nucleus protects the cell’s DNA while controlling all other cellular activities, such as cell division, growth, protein production, and cell death.

Ribosomes

The DNA molecules housed in the nucleus also contain blueprints for all of the proteins produced by a cell. These blueprints are ‘read’ and interpreted by ribosomes, which are the site of protein production in plant and animal cells. Ribosomes produce proteins by assembling amino acid sequences according to the instructions contained in the genetic code. The resulting polypeptide chains are then folded into specific primary, tertiary, or quaternary 3D structures by other cell organelles.

Mitochondria

Endoplasmic Reticulum (ER)

The endoplasmic reticulum is a network of membranes inside a cell, and its main functions are to process and transport new materials. There are two types of endoplasmic reticulum the rough ER, and the smooth ER.

The rough ER is studded with ribosomes, giving it a bumpy or ‘rough’ appearance. It folds and tags newly-synthesized proteins before transporting them to wherever they are needed in the body. The smooth ER does not have ribosomes attached to it and is instead involved in hormone and lipid synthesis.

Golgi Apparatus

Once newly-synthesized substances have left the ER, they are sent to the Golgi apparatus. This is a series of flatted, membrane-bound sacs that packages and distributes substances to the outer cell membrane, where they either become part of the lipid bilayer or leave the cell.

Lysosomes

Lysosomes are small, spherical organelles that are packed full of digestive enzymes. Their key function is to break down and recycle unwanted material for the cell, such as old cell parts or invading bacteria and viruses. Lysosomes also play an important role in apoptosis (AKA programmed cell death ).

Cytoplasm

The cytoplasm is a jelly-like substance that fills the interior space of cells. It is mainly composed of water, but also contains salts, enzymes, and other organic molecules. The cytoplasm surrounds and protects the organelles of the cell and is where many cellular processes (such as protein synthesis and glycolysis) take place.

The Cell Membrane (AKA The Plasma Membrane)

All cells are surrounded by a cell membrane, which consists of a semipermeable phospholipid bilayer. The cell membrane controls which substances enter and leave the cell, and also separates the interior of the cell from its external environment.


Industrial Biotechnology and Commodity Products

3.48.1 Introduction

Enzymes are specialized (globular) proteins with catalytic features, which occur in all living organisms and accelerate biochemical reactions necessary to support life. Enzymes are also ubiquitous in fresh and processed foods, even though they are often deactivated as it happens with other dietary proteins, enzymes are degraded by hydrolysis after ingestion and eventually metabolized. Enzymes present in traditional human diets have not been associated with relevant forms of toxicity, so they are considered as intrinsically safe [1] .

A major fraction of industrial enzymes available at present are used in the food industry, where they have found a wide variety of applications [2] this, in particular, is the case of hydrolases, a large family that includes carbohydrases, proteases, and lipases, usually employed as food additives – which amount to at least 75% of all enzymes on the market. Proteases dominate, in turn, the industrial enzyme market, with a market share of ∼60% – owing chiefly to their application in detergents. Enzymes have been successfully used in food processing to replace steps that encompass harsh chemical or physical conditions (eg, temperature, pressure, or presence of chemicals) hence, they contribute to sustainable industrial production, besides guaranteeing a safer and more nutritious food supply.

Most enzymes have been produced at the commercial scale via submerged cultures and have found relevant uses in the beverage and bakery industries, the production of specialty dairy products, and the processing of starch – besides their role as antimicrobial agents in the preservation of several foods. There is, however, a growing trend to manufacture enzymes via solid-state fermentation techniques – not only because enzyme titers can be higher than in submerged cultures, but also because of the major public concerns with the upgrade of agricultural wastes, which can thus serve as suitable (and low-cost) substrates for the host microorganisms. On the other hand, solid and liquid fermentation affect biomass formation and enzyme biosynthesis in different modes for example, molds grown on solid-state substrates produce more spores and fruiting bodies, which, in turn, have a physiological influence upon enzyme production therein.

The industrial production of enzymes for use in food processing dates back to 1874, when the Danish scientist Christian Hansen extracted rennin (also known as chymosin) from calf stomachs, for later use to clot milk in cheese manufacturing. Chymosin is nowadays produced by several transformed microorganisms, containing the bovine prochymosin gene introduced through recombinant deoxyribonucleic acid (rDNA) techniques. Bovine chymosin expressed in Escherichia coli K-12 became, in fact, the first recombinant enzyme approved for use in food by the Food and Drug Administration (FDA) in the United States [1] . The major industrial association dealing with enzymes worldwide, Association of Manufacturers and Formulators of Enzyme Products (AMFEP), currently lists ∼160 enzymes manufactured for use specifically in the food industry, at least 36 of which are produced via genetically modified microorganisms (GMOs). Note that the application of purified enzymes from microbial origin is a rather recent development, which dates back to the late first half of the 20th century [2] .

Improvements in bioprocessing and biocatalyst development – especially with the advent of genetic engineering, have greatly increased the availability of food enzymes and have also permitted tailoring of their properties to meet the (sometimes very) distinct requirements of food matrices and food process. By judicious selection of host microorganisms as recombinant strains containing the DNA sequences that code for a specific enzyme amino acid sequences, more efficient synthesis of said enzymes will be possible, often in the absence of undesirable enzymes or other microbial metabolites. In addition, it also became possible to engineer enzymes with increased heat stability and improved compatibility to other medium components – at the expense of introducing deliberate changes in the original enzyme amino acid sequences, targeted at specific base pairs of the complementary DNA.

Enzyme preparations, commercialized for food protection, typically contain not only the enzymes of interest, but also several other compounds, namely diluents, preservatives, and stabilizers. These extra materials are usually well-known substances that have been previously cleared for use in foods and which perform useful specific functions. Enzyme preparations may also contain other enzymes and metabolites synthesized by the production organisms, as well as residues of the raw materials used in the fermentation broth and of the solvents used in the isolation and purification of the enzyme of interest. All these materials are expected to be of a purity that is consistent with good manufacturing practices (GMPs) [1] .

The expansion of the portfolio of application of food enzymes as food-processing aids, and as part of the formulation of processed foods, has obviously captured the attention of regulators in the most developed countries. Hence, new food enzymes require a prior market authorization by FDA in the United States, or the European Food Safety Authority (EFSA) in Europe furthermore, several European Union (EU) member states have national legislations focusing on food enzymes and all serve the main purpose of ensuring the safety of enzyme preparations for the final consumers, so they often include specifications for purity and activity, and are enforced by national regulatory boards. In certain cases, occupational health issues that may arise during manufacturing and handling of food-grade enzymes are also part of the underlying legislation [1] .

In principle, identical safety measures should be considered with regard to food-grade enzymes derived from either native microorganisms or GMOs. The key issue is the safety assessment of the production organism – in particular, whether it holds any pathogenic or toxigenic potential. Although, no formally known pathogenic or toxigenic organisms have intentionally been used to produce enzymes intended to contact foods, certain fungi that have traditionally been used as sources of specific enzymes have meanwhile been found to also produce low levels of toxic secondary metabolites under the fermentation conditions employed for optimized synthesis of the desired enzymes hence, special care has to be exercised in these cases, especially with the purification steps downstream [1] .

This chapter provides an overview of the food-grade enzymes of highest relevance – to either aid in processing or be included in the final product. Hence, all steps from manufacture to safety and legislation are tackled, covering production, transformation, and utilization in foods.