A report on Enzyme and Cofactor (biochemistry)

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow.
The succinate dehydrogenase complex showing several cofactors, including flavin, iron–sulfur centers, and heme.
Eduard Buchner
A simple [Fe2S2] cluster containing two iron atoms and two sulfur atoms, coordinated by four protein cysteine residues.
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.
The redox reactions of nicotinamide adenine dinucleotide.
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.

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)

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

- Enzyme
The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow.

7 related topics with Alpha

Overall

The redox reactions of nicotinamide adenine dinucleotide.

Nicotinamide adenine dinucleotide

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The redox reactions of nicotinamide adenine dinucleotide.
UV absorption spectra of NAD and NADH.
Some metabolic pathways that synthesize and consume NAD in vertebrates. The abbreviations are defined in the text.
Salvage pathways use three precursors for NAD+.
Rossmann fold in part of the lactate dehydrogenase of Cryptosporidium parvum, showing NAD in red, beta sheets in yellow, and alpha helices in purple.
In this diagram, the hydride acceptor C4 carbon is shown at the top. When the nicotinamide ring lies in the plane of the page with the carboxy-amide to the right, as shown, the hydride donor lies either "above" or "below" the plane of the page. If "above" hydride transfer is class A, if "below" hydride transfer is class B.
A simplified outline of redox metabolism, showing how NAD and NADH link the citric acid cycle and oxidative phosphorylation.
The structure of cyclic ADP-ribose.
Arthur Harden, co-discoverer of NAD

Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism.

However, it is also used in other cellular processes, most notably as a substrate of enzymes in adding or removing

Simplified view of the cellular metabolism

Metabolism

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Set of life-sustaining chemical reactions in organisms.

Set of life-sustaining chemical reactions in organisms.

Simplified view of the cellular metabolism
Structure of adenosine triphosphate (ATP), a central intermediate in energy metabolism
Structure of a triacylglycerol lipid
This is a diagram depicting a large set of human metabolic pathways.
Glucose can exist in both a straight-chain and ring form.
Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the extreme left.
The structure of iron-containing hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in green. From.
A simplified outline of the catabolism of proteins, carbohydrates and fats
Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black.
Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis
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.
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).
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

These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.

These group-transfer intermediates are called coenzymes.

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).

Protein

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Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

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).
John Kendrew with model of myoglobin in progress
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.
Resonance structures of the peptide bond that links individual amino acids to form a protein polymer
A ribosome produces a protein using mRNA as template
The DNA sequence of a gene encodes the amino acid sequence of a protein
The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.
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).
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).
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.
Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

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

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

Yeast

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

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
A block of compressed fresh yeast
Active dried yeast, a granulated form in which yeast is commercially sold
Diagram showing a yeast cell
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

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.

Many proteins important in human biology were first discovered by studying their homologues in yeast; these proteins include cell cycle proteins, signaling proteins, and protein-processing enzymes.

Summary of aerobic respiration

Glycolysis

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Metabolic pathway that converts glucose , into pyruvic acid (CH3COCO2H).

Metabolic pathway that converts glucose , into pyruvic acid (CH3COCO2H).

Summary of aerobic respiration
Summary of the 10 reactions of the glycolysis pathway
Glycolysis pathway overview.
Eduard Buchner. Discovered cell-free fermentation.
Otto Meyerhof. One of the main scientists involved in completing the puzzle of glycolysis
Yeast hexokinase B
Bacillus stearothermophilus phosphofructokinase
Yeast pyruvate kinase

Glycolysis is a sequence of ten reactions catalyzed by enzymes.

Arthur Harden and William Young along with Nick Sheppard determined, in a second experiment, that a heat-sensitive high-molecular-weight subcellular fraction (the enzymes) and a heat-insensitive low-molecular-weight cytoplasm fraction (ADP, ATP and NAD+ and other cofactors) are required together for fermentation to proceed.

Sodium and fluorine bonding ionically to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions are then attracted to each other. The sodium is oxidized; and the fluorine is reduced.

Redox

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Type of chemical reaction in which the oxidation states of substrate change.

Type of chemical reaction in which the oxidation states of substrate change.

Sodium and fluorine bonding ionically to form sodium fluoride. Sodium loses its outer electron to give it a stable electron configuration, and this electron enters the fluorine atom exothermically. The oppositely charged ions are then attracted to each other. The sodium is oxidized; and the fluorine is reduced.
The international pictogram for oxidizing chemicals
Illustration of a redox reaction
A redox reaction is the force behind an electrochemical cell like the Galvanic cell pictured. The battery is made out of a zinc electrode in a ZnSO4 solution connected with a wire and a porous disk to a copper electrode in a CuSO4 solution.
Oxides, such as iron(III) oxide or rust, which consists of hydrated iron(III) oxides Fe2O3·nH2O and iron(III) oxide-hydroxide (FeO(OH), Fe(OH)3), form when oxygen combines with other elements
Iron rusting in pyrite cubes
Enzymatic browning is an example of a redox reaction that takes place in most fruits and vegetables.
Blast furnaces of Třinec Iron and Steel Works, Czech Republic

Wide varieties of aromatic compounds are enzymatically reduced to form free radicals that contain one more electron than their parent compounds.

In general, the electron donor is any of a wide variety of flavoenzymes and their coenzymes.

3D structure of a hammerhead ribozyme

Ribozyme

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3D structure of a hammerhead ribozyme
Schematic showing ribozyme cleavage of RNA
Image showing the diversity of ribozyme structures. From left to right: leadzyme, hammerhead ribozyme, twister ribozyme
A ribosome is a biological machine that utilizes a ribozyme to translate RNA into proteins

Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes.

For example, the functional part of the ribosome, the biological machine that translates RNA into proteins, is fundamentally a ribozyme, composed of RNA tertiary structural motifs that are often coordinated to metal ions such as Mg2+ as cofactors.