Biochemistry

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Biochemistry or biological chemistry is the study of

organs as well as organism structure and function.[4] Biochemistry is closely related to molecular biology, the study of the molecular mechanisms of biological phenomena.[5]

Much of biochemistry deals with the structures, bonding, functions, and interactions of biological

nutritional deficiencies.[9] In agriculture, biochemists investigate soil and fertilizers with the goal of improving crop cultivation, crop storage, and pest control. In recent decades, biochemical principles and methods have been combined with problem-solving approaches from engineering to manipulate living systems in order to produce useful tools for research, industrial processes, and diagnosis and control of disease—the discipline of biotechnology.[10]

History

Carl Cori jointly won the Nobel Prize in 1947 for their discovery of the Cori cycle
at RPMI.

At its most comprehensive definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life. In this sense, the history of biochemistry may therefore go back as far as the

enzymes and the dynamic nature of biochemistry, represent two examples of early biochemists.[18]

The term "biochemistry" was first used when Vinzenz Kletzinsky (1826–1882) had his "Compendium der Biochemie" printed in Vienna in 1858; it derived from a combination of

Zeitschrift für Physiologische Chemie (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study.[19][20] The German chemist Carl Neuberg however is often cited to have coined the word in 1903,[21][22][23] while some credited it to Franz Hofmeister.[24]

DNA structure (1D65​)[25]

It was once generally believed that life and its materials had some essential property or substance (often referred to as the "

Krebs cycle
(citric acid cycle), and led to an understanding of biochemistry on a molecular level.

Another significant historic event in biochemistry is the discovery of the

Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi) in the silencing of gene expression.[33]

Starting materials: the chemical elements of life

The main elements that compose the human body shown from most abundant (by mass) to least abundant

Around two dozen

animals. For example, ocean algae use bromine, but land plants and animals do not seem to need any. All animals require sodium, but is not an essential element for plants. Plants need boron and silicon
, but animals may not (or may need ultra-small amounts).

Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium and phosphorus—make up almost 99% of the mass of living cells, including those in the human body (see composition of the human body for a complete list). In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more.[35]

Biomolecules

The 4 main classes of molecules in biochemistry (often called biomolecules) are carbohydrates, lipids, proteins, and nucleic acids.[36] Many biological molecules are polymers: in this terminology, monomers are relatively small macromolecules that are linked together to create large macromolecules known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis. Different macromolecules can assemble in larger complexes, often needed for biological activity.

Carbohydrates

Carbohydrates
Glucose, a monosaccharide
A molecule of sucrose (glucose + fructose), a disaccharide
Amylose, a polysaccharide made up of several thousand glucose
units

Two of the main functions of carbohydrates are energy storage and providing structure. One of the common sugars known as glucose is a carbohydrate, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.[citation needed]

The simplest type of carbohydrate is a

hemiketal group, depending on whether the linear form was an aldose or a ketose.[38]

In these cyclic forms, the ring usually has 5 or 6 atoms. These forms are called

]

Two monosaccharides can be joined by a

ester bond into a disaccharide through a dehydration reaction during which a molecule of water is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed hydrolysis. The best-known disaccharide is sucrose or ordinary sugar, which consists of a glucose molecule and a fructose molecule joined. Another important disaccharide is lactose found in milk, consisting of a glucose molecule and a galactose molecule. Lactose may be hydrolysed by lactase, and deficiency in this enzyme results in lactose intolerance
.

When a few (around three to six) monosaccharides are joined, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses.[39] Many monosaccharides joined form a polysaccharide. They can be joined in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers. Cellulose is an important structural component of plant's cell walls and glycogen is used as a form of energy storage in animals.

Saccharose
does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

Lipids

palmitoyl chains attached to a glycerol backbone. At the bottom is the common phospholipid, phosphatidylcholine.[41]

aromatic (with a cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid.[42]

Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).[citation needed]

Most lipids have some

amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol
, the polar group is a mere –OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Lipids are an integral part of our daily diet. Most

pharmaceutical products, either as co-solubilisers (e.g. in parenteral infusions) or else as drug carrier components (e.g. in a liposome or transfersome
).

Proteins

carboxyl
group on the right

polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues.[43]

Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined as a dipeptide
A schematic of hemoglobin. The red and blue ribbons represent the protein globin; the green structures are the heme groups.

Proteins can have structural and/or functional roles. For instance, movements of the proteins

disulfide linkages between their amino acids. Antibodies are specific through variation based on differences in the N-terminal domain.[44]

The

substrates; they then catalyze the reaction between them. By lowering the activation energy
, the enzyme speeds up that reaction by a rate of 1011 or more; a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

The structure of proteins is traditionally described in a hierarchy of four levels. The

quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.[45]

Examples of protein structures from the Protein Data Bank
Members of a protein family, as represented by the structures of the isomerase domains

Ingested proteins are usually broken up into single amino acids or dipeptides in the

glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine
, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.

If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to form a protein.

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free

Unicellular organisms release the ammonia into the environment. Likewise, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle
.

In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like sequence alignments and structural alignments are powerful tools that help scientists identify homologies between related molecules. The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

Nucleic acids

deoxyribonucleic acid
(DNA); the picture shows the monomers being put together.

genetic information in all living cells and viruses.[2] The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group.[46]

Structural elements of common nucleic acid constituents. Because they contain at least one phosphate group, the compounds marked nucleoside monophosphate, nucleoside diphosphate and nucleoside triphosphate are all nucleotides (not phosphate-lacking nucleosides).

The most common nucleic acids are

hydrogen bonds
with certain other nitrogenous bases in a complementary strand of nucleic acid (similar to a zipper). Adenine binds with thymine and uracil, thymine binds only with adenine, and cytosine and guanine can bind only with one another. Adenine and Thymine & Adenine and Uracil contains two hydrogen Bonds, while Hydrogen Bonds formed between cytosine and guanine are three in number.

Aside from the genetic material of the cell, nucleic acids often play a role as

second messengers, as well as forming the base molecule for adenosine triphosphate
(ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

Metabolism

Carbohydrates as energy source

Glucose is an energy source in most life forms. For instance, polysaccharides are broken down into their monomers by enzymes (glycogen phosphorylase removes glucose residues from glycogen, a polysaccharide). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. [47]

Glycolysis (anaerobic)

A summary pathway diagram of glycolysis, showing the multi-step conversion of glucose to pyruvate. Each step in the pathway is catalysed by a unique enzyme.
G6P
F6P
1,3BPG
3PG
2PG
PEP
Pyruvate
HK
PGI
PFK
TPI
GAPDH
PGK
PGM
ENO
PK
The image above contains clickable links
The
pyruvate via a series of intermediate metabolites.    Each chemical modification is performed by a different enzyme.    Steps 1 and 3 consume ATP
and    steps 7 and 10 produce ATP. Since steps 6–10 occur twice per glucose molecule, this leads to a net production of ATP.

Glucose is mainly metabolized by a very important ten-step

pyruvate. This also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents of converting NAD+ (nicotinamide adenine dinucleotide: oxidized form) to NADH (nicotinamide adenine dinucleotide: reduced form). This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g. in humans) or to ethanol plus carbon dioxide (e.g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.[48]

Aerobic

In

electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle).[49]
It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

Gluconeogenesis

In

anaerobic metabolism
, converting glucose to lactate. The combination of glucose from noncarbohydrates origin, such as fat and proteins. This only happens when
Krebs Cycle. Large scale protein and fat catabolism usually occur when those suffer from starvation or certain endocrine disorders.[50] The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.[51]

Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics, and molecular biology

Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas developed in the fields of genetics, molecular biology, and biophysics. There is not a defined line between these disciplines. Biochemistry studies the chemistry required for biological activity of molecules, molecular biology studies their biological activity, genetics studies their heredity, which happens to be carried by their genome. This is shown in the following schematic that depicts one possible view of the relationships between the fields:

  • Biochemistry is the study of the chemical substances and vital processes occurring in live organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are applications of biochemistry. Biochemistry studies life at the atomic and molecular level.
  • Genetics is the study of the effect of genetic differences in organisms. This can often be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms that lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knockout" studies.
  • Molecular biology is the study of molecular underpinnings of the biological phenomena, focusing on molecular synthesis, modification, mechanisms and interactions. The central dogma of molecular biology, where genetic material is transcribed into RNA and then translated into protein, despite being oversimplified, still provides a good starting point for understanding the field. This concept has been revised in light of emerging novel roles for RNA.
  • drug molecules
    ).

See also

Lists

See also

Notes

a.

date is glucose, compared with 24% fructose and 8% sucrose. However, peaches contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%).[52]

References

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Cited literature

Further reading

External links