Tag Archives: Metabolism

Proteins

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Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ᵻnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acidresidues. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactions, DNA replication,responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.

Once formed, proteins only exist for a certain period of time and are then degraded and recycled by the cell’s machinery through the process of protein turnover. A protein’s lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important incell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals’ diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.

Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function includeimmunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry.

In chemistry, hydrophobicity is the physical property of a molecule (known as a hydrophobe) that is seemingly repelled from a mass ofwater.[1] (Strictly speaking, there is no repulsive force involved; it is an absence of attraction.)

Hydrophobic molecules tend to be non-polar and, thus, prefer other neutral molecules and non-polar solvents. Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle.

Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, and chemical separation processes to remove non-polar substances from polar compounds.[2]

Hydrophobic is often used interchangeably with lipophilic, “fat-loving.” However, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions—such as the silicones and fluorocarbons.

The term hydrophobe comes from the Ancient Greek ὑδρόφοβος, “having a horror of water”, constructed from ὕδωρ, “water”, and φόβος, “fear”.[3]

A hydrophilic molecule or portion of a molecule is one whose interactions with water and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents.[2][3] They are typically charge-polarized and capable of hydrogen bonding. This makes these molecules soluble not only in water but also in other polar solvents.

Hydrophilic molecules (and portions of molecules) can be contrasted with hydrophobic molecules (and portions of molecules). In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiphilic molecules is the lipids that comprise the cell membrane. Another example is soap, which has a hydrophilic head and a hydrophobic tail, allowing it to dissolve in both water and oil.

Hydrophilic and hydrophobic molecules are also known as polar molecules and nonpolar molecules, respectively. Some hydrophilic substances do not dissolve. This type of mixture is called a colloid.

An approximate rule of thumb for hydrophilicity of organic compounds is that solubility of a molecule in water is more than 1 mass % if there is at least one neutral hydrophile group per 5 carbons, or at least one electrically charged hydrophile group per 7 carbons.[4]

Hydrophilic substances (ex: salts) can seem to attract water out of the air. Sugar is also hydrophilic, and like salt is sometimes used to draw water out of foods. Sugar sprinkled on cut fruit will “draw out the water” through hydrophilia, making the fruit mushy and wet, as in a common strawberry compote recipe.

Metabolism

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Metabolism (from Greek: μεταβολή metabolē, “change”) is the set of life-sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestionand the transport of substances into and between different cells, in which case the set of reactions within the cells is calledintermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter by way of cellular respiration, andanabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell’s environment or to signals from other cells.

The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food.

A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species.[2] For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants.[3] These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy.