A report on Protein, Cofactor (biochemistry) and Metabolism

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).

The succinate dehydrogenase complex showing several cofactors, including flavin, iron–sulfur centers, and heme.

Simplified view of the cellular metabolism

John Kendrew with model of myoglobin in progress

A simple [Fe2S2] cluster containing two iron atoms and two sulfur atoms, coordinated by four protein cysteine residues.

Structure of adenosine triphosphate (ATP), a central intermediate in energy metabolism

Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.

The redox reactions of nicotinamide adenine dinucleotide.

Resonance structures of the peptide bond that links individual amino acids to form a protein polymer

This is a diagram depicting a large set of human metabolic pathways.

A ribosome produces a protein using mRNA as template

Glucose can exist in both a straight-chain and ring form.

The DNA sequence of a gene encodes the amino acid sequence of a protein

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the extreme left.

The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.

The structure of iron-containing hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in green. From.

Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).

A simplified outline of the catabolism of proteins, carbohydrates and fats

Molecular surface of several proteins showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black.

The enzyme hexokinase is shown as a conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP) and squalene shown. Some intermediates are omitted for clarity.

Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma membrane and influx of glucose (3), glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6).

Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of some of the phyla included are shown around the tree.

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.

Aristotle's metabolism as an open flow model

Santorio Santorio in his steelyard balance, from Ars de statica medicina, first published 1614

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction).

- Cofactor (biochemistry)

The three main purposes of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes.

- Metabolism

Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors.

- Protein

Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism.

- Protein

These group-transfer intermediates are called coenzymes.

- Metabolism

Therefore, these cofactors are continuously recycled as part of metabolism.

- Cofactor (biochemistry)

4 related topics with Alpha

Enzyme

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Enzyme activity initially increases with temperature (Q10 coefficient) until the enzyme's structure unfolds (denaturation), leading to an optimal rate of reaction at an intermediate temperature.

Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black.

Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow.

Chemical structure for thiamine pyrophosphate and protein structure of transketolase. Thiamine pyrophosphate cofactor in yellow and xylulose 5-phosphate substrate in black.

The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES‡) to reduce the activation energy required to produce products (EP) which are finally released.

The metabolic pathway of glycolysis releases energy by converting glucose to pyruvate via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.

In phenylalanine hydroxylase over 300 different mutations throughout the structure cause phenylketonuria. Phenylalanine substrate and tetrahydrobiopterin coenzyme in black, and Fe2+ cofactor in yellow.

Hereditary defects in enzymes are generally inherited in an autosomal fashion because there are more non-X chromosomes than X-chromosomes, and a recessive fashion because the enzymes from the unaffected genes are generally sufficient to prevent symptoms in carriers.

Enzymes are proteins that act as biological catalysts (biocatalysts).

Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life.

In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors.

Yeast

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Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom.

Yeast ring used by Swedish farmhouse brewers in the 19th century to preserve yeast between brewing sessions.

Bubbles of carbon dioxide forming during beer-brewing

Yeast in a bottle during sparkling wine production at Schramsberg Vineyards, Napa

Active dried yeast, a granulated form in which yeast is commercially sold

Gram stain of Candida albicans from a vaginal swab. The small oval chlamydospores are 2–4 µm in diameter.

A photomicrograph of Candida albicans showing hyphal outgrowth and other morphological characteristics

This ethanol is almost always produced by fermentation – the metabolism of carbohydrates by certain species of yeasts under anaerobic or low-oxygen conditions.

Nutritional yeast in particular is naturally low in fat and sodium and a source of protein and vitamins as well as other minerals and cofactors required for growth.

Yeast extract, made from the intracellular contents of yeast and used as food additives or flavours. The general method for making yeast extract for food products such as Vegemite and Marmite on a commercial scale is heat autolysis, i.e. to add salt to a suspension of yeast, making the solution hypertonic, which leads to the cells' shrivelling up. This triggers autolysis, wherein the yeast's digestive enzymes break their own proteins down into simpler compounds, a process of self-destruction. The dying yeast cells are then heated to complete their breakdown, after which the husks (yeast with thick cell walls that would give poor texture) are removed. Yeast autolysates are used in Vegemite and Promite (Australia); Marmite (the United Kingdom); the unrelated Marmite (New Zealand); Vitam-R (Germany); and Cenovis (Switzerland).

Nucleotide

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Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of nucleic acid, shown at upper left.

Structural elements of three nucleo tides —where one-, two- or three-phosphates are attached to the nucleo side (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside mono phosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside di phosphate; 3rd, adding a third phosphate results in a nucleoside tri phosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).

The synthesis of UMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(128,0,0);">inorganic molecules

The synthesis of IMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(227,13,196);">metal ions , <span style="color: rgb(128,0,0);">inorganic molecules

Nucleotides also play a central role in metabolism at a fundamental, cellular level.

They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane synthesis, moving the cell and cell parts (both internally and intercellularly), cell division, etc. In addition, nucleotides participate in cell signaling (cyclic guanosine monophosphate or cGMP and cyclic adenosine monophosphate or cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+).

Dihydrofolate reductase from E. coli with its two substrates dihydrofolate (right) and NADPH (left), bound in the active site. The protein is shown as a ribbon diagram, with alpha helices in red, beta sheathes in yellow and loops in blue. Generated from 7DFR.

Enzyme kinetics

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Study of the rates of enzyme-catalysed chemical reactions.

$As larger amounts of substrate are added to a reaction, the available enzyme binding sites become filled to the limit of V_\max. Beyond this limit the enzyme is saturated with substrate and the reaction rate ceases to increase.$

Progress curve for an enzyme reaction. The slope in the initial rate period is the initial rate of reaction v. The Michaelis–Menten equation describes how this slope varies with the concentration of substrate.

Lineweaver–Burk or double-reciprocal plot of kinetic data, showing the significance of the axis intercepts and gradient.

Random-order ternary-complex mechanism for an enzyme reaction. The reaction path is shown as a line and enzyme intermediates containing substrates A and B or products P and Q are written below the line.

Saturation curve for an enzyme reaction showing sigmoid kinetics.

Pre-steady state progress curve, showing the burst phase of an enzyme reaction.

Kinetic scheme for reversible enzyme inhibitors.

The energy variation as a function of reaction coordinate shows the stabilisation of the transition state by an enzyme.

Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or a modifier (inhibitor or activator) might affect the rate.

An enzyme (E) is typically a protein molecule that promotes a reaction of another molecule, its substrate (S).

These measurements either use changes in the fluorescence of cofactors during an enzyme's reaction mechanism, or of fluorescent dyes added onto specific sites of the protein to report movements that occur during catalysis.