A report on Cofactor (biochemistry), Protein and Enzyme kinetics

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

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).

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.

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

John Kendrew with model of myoglobin in progress

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

The redox reactions of nicotinamide adenine dinucleotide.

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.

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.

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

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

A ribosome produces a protein using mRNA as template

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.

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

Saturation curve for an enzyme reaction showing sigmoid kinetics.

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

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

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).

Kinetic scheme for reversible enzyme inhibitors.

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 energy variation as a function of reaction coordinate shows the stabilisation of the transition state by 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

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 rates at which these happen are characterized in an area of study called enzyme kinetics.

- Cofactor (biochemistry)

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

- Enzyme kinetics

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

- Protein

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.

- Enzyme kinetics

In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules.

- Protein

1 related topic with Alpha

Metabolism

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Set of life-sustaining chemical reactions in organisms.

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

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

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.

These group-transfer intermediates are called coenzymes.

The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated.