Biochemistry

For a reason why polymer chemistry has been briefly touched in the last subchapter of organic chemistry, this new chapter is written. Biochemistry describes the chemistry of animated nature. One often meets with very large molecules. Some students are therefore averse to this science. Do not worry, these are usually polymeric compounds: polysaccharides, polypeptides or DNA. All these macromolecules consist of repeating organic compounds.

 

The following topics are briefly discussed here. In doing so, you will be able to take advantage of the facts already discussed in this course.

 

• Carbohydrates
• Amino acids
• Nucleic acids
• Natural substances

 

Carbohydrates = sugar, starch and cellulose

 

From these substances plants are built, for animals they are the main component of food.

sugar

Sugar consist of 3 groups:

• Monosaccharides, simple sugars, e.g. glucose.
• Oligosaccharides consisting of two to five monosaccharide units, best known for our household sugar, saccharose, a disachharide of two monosaccharide units
• Polysaccharide, consisting of many monosaccharide units, starch (flour, etc.), cellulose and glycogen.

But let’s answer the first question:

Where does sugar (here glucose) come from?

Photosynthesis

The chlorophyll molecule is a complex compound. (See Chapter 6, complex compounds). It is a planar complex with 4 ligands and magnesium, Mg, as the central atom. Chlorophyll absorbs light in the red region of the continuous spectrum, λ ≅ 700 nm, which is why almost the entire plant kingdom appears with a green color.

The mechanism of photosynthesis is complicated and incomplete. According to James E. Huheey, a water molecule is coordinated at the complex perpendicular to the complex plane. The oxygen atom of the H2O molecule is to coordinate to the magnesium atom as a fifth ligand. One hydrogen atom is to form a hydrogen-bond with the carbonyl oxygen of the ester group of an adjacent chlorophyll molecule. This is followed by further steps.

(design below, is not exact).

Monosaccharides, simple sugars, monomeric units such as glucose, fructose or galactose. There are 3-, 5- and 6-membered hydroxy aldehydes and ketones. Each carbon atom containing no carbonyl group is linked to an OH group. There are 22 different simple sugars known. 7 of these are ketones. All sugars are turning ClockWise, D. Instead of R/S-, D/L-nomenclatura is used. Stucturs of simple sugars are  designated by Fischer-Projections. (chapter 10, Isomerie)

Trivial names are used for simple sugars. Instead of  R/S-nomenclature, simple sugars are usually described with the prefixes D (for clockwise) and L – (for conterclockwise). Crucial is to watch the second last carbon atom which is farthest away from the carbonyl group.

If that OH group is on the right, D- nomenclature is used. L-nomenclature is used when the OH-group is on the left.

Here are some examples: See picture below

 

Picture below: Ribose, a Ketopentose, essential compound of RNA and DNA. (See more about further below next)

.

 

 

 

 

⇑⇓

Structure below: open-chain glucose with intramolecular ring closure to the 6-ring. The non-bonding electron pair of the last OH group nucleophilically attacks the carbonyl carbon. Electron displacement and deprotonation of the last OH group, and protonation of the carbonyl group.

 

 

Picture above: α-D-glucose

Aldohexoses usually form six-membered rings, while 5-rings are predominantly formed from ketohexoses.

 

Oligosaccharides

Among the oligosaccharides, the most important Disachharides are mentioned here. They are formed by the condensation of 2 simple sugars (2 monosaccharides).

• The sucrose, condensation from glucose and fructose, household sugar, 6-ring and 5-ring.
• The maltose, condensation from 2 glucose units, malt sugar, 2 six-rings. Sugar of the malt cocoa and malt beer (Since maltose is very expensive, only slightly sweet and hardly soluble in water due to the lower dipole, saccharose is often added to these drinks.)
• The lactose, condensation from glucose and galactose. Milk sugar, 2 six-rings (lactose intolerance should always be treated. Milk sugar or milk is also highly recommended for older generations)

When 2 simple sugars condense to a disaccharide one molecule of water, H2O, is produced.

α-D-glucose + β-D-fructose → sucrose + H2O

 

Picture above: Sucrose, sugar, α-D-Glycopyranosyl–β-D-fructofuranoside

With acid or the enzyme invertase sucrose can be decomposed into the corresponding monosaccharides.

The disaccharide, sucrose, is contained in sugar beet and sugar cane and is mainly obtained therefrom.

 

Another disaccharide is maltose, the malt sugar, is a dimer of glucose:

Glucose + glucose → maltose + H2O         

Picture above: maltose, α-D-Glucopyranosyl–β-D-glucopyranose

The maltose can in turn be hydrolyzed with acid or the enzyme maltase to two molecules of glucose.

Maltose is the dimer of 2 glucose units and is only one third as sweet as sucrose. Beverages such as malt beer, available especially in Germany, and malt cocoa beverages are therefore often sweetened with sucrose sugar. Maltose is formed by enzymatic degradation of starch.

 

Lactose is a dimer of galactose and glucose.

Galactose + glucose → lactose + H2O

Picture above: Lactose, (milk sugar), β-D-galactopyranosyl–α-D-glucopyranose

In order to simplify drawing above, 4 ring-insidedirected and 3 outside of ring standing H-atoms and non-binding electrons of the oxygen atoms have been omitted. In most textbooks this is standard. Professors and assistants also teach in an analogous way.

The disaccharide lactose is the milk component of most mammals (ca 5%)

 

polysaccharides

Starch, cellulose and glycogen, all these monomers are polymers of glucose.

 

In all three natural polysaccharides, which are most frequently found, the monomer is always the glucose.

The starch is our daily food like potatoes, cereals and rice or bread and pasta. In vegetables and fruits starch often consists of the edible part.

The main components of starch are unbranched amylose and branched pectin. The two types of starch are separated in the hot water.

The amylose is composed of maltose units and preferably adopts a helical helical structure. Its molar mass is about 150000-600000.

The soluble pectin is branched at each twentieth to twenty-fifth glucose unit with another glucose chain. Its molar mass is 200,000 to 1 million

Picture below: Starch, Amylose, its preferable structure is helical.

Cellulose is the inedible part of the plant and has a rigid structure. Biologically, cellulose is the scaffold of the plant cell wall. Its solid structure owes cellulose to the effect observed by X-ray structure analysis that every second glucose monomer is rotated by 180 ° from the previous one. Because of this fact, cellulose enables the formation of hydrogen bonds.

Picture below: Cellulose, with hydrogen bonds between two chains

Cellulose serves as an important raw material in paper making. Calcium sulphate, Ca (HSO3)2, produces porous paper in sulphonic acids by dissolving wood (lignin and resin). e.g. Filter paper. Additional additives such as kaolin are necessary for writing and printing paper. To produce high gloss paper you need barium sufate.

 

Glycogen also polymers of glucose.

Glycogen has a similar structure to amylose and amylopectin, for it contains branches after every tenth glycose unit. Its molar mass is much greater and amounts to 100 million. Glycogen is used as an energy store in animals and humans and is mainly enriched in the liver and the dormant skeletal muscle.

If there is too little sugar in the living organism or blood, a specific enzyme, the phosphorylase, builds a terminal glucose molecule from the glycogen chain. The derivative α-D-glucopyranosyl-1-phosphate is formed. The dismantling takes place step by step. Because of strong branching, glycogen contains many end groups where the enzyme can begin to remove. The enzyme, phosphorylase, can only be removed to a limited extent, up to 4 glucose units away from the branch point.

Picture below: glucose units designated by zigzag lines. Phosphorylase only removes glucose units till 4 glucose units (or 2 maltose units) remain before branching. n = 4

A further 3 units are removed in one block by the enzyme, transferase, and re-attached to a chain which is also only 4 units away from the branch. Another enzyme, α-2,6, glucosidase, removes the only remaining glucose unit before branching. Once again, a unbranched chain has been formed. Again phosphorylase can  remove glucose-units up to 4 units before branching.

The removed glucose unit reacts via the glycolysis by means of several enzymes to pyruvic acid.

And now three reactions are possible, depending on Oxygen:

•  Pyruvic acid oxidizes to CO2 and H2O with sufficient oxygen supply.
•  If the oxygen content is too low, incomplete reductions to lactic acid are produced. 2-hydroxypropanoic acid. (see Organic Chemistry)
•  In an anaerobic condition, yeast organisms process pyruvic acid to ethanol, CH3CH2OH.

 

Amino acids, peptides and proteins

 

The amino acids are the building blocks of the proteins (proteins). Amino acids are also referred to as zwitterions because they each have an acidic carboxylic acid group, -COOH, and a basic amino group, -NH2.

In total, there are over 500 naturally occurring amino acids, but the proteins of all organisms from bacteria to humans show only 20 different amino acids. 12 of these amino acids are produced by the human body itself: glycine, alanine, proline, serine, tyrosine, aspargine, glutamine, arginine, histidine, cysteine, aspartic acid and glutamic acid.

Picture below:

The remaining 8 must be taken from the outside: valine, leucine, isoleucine, phenylalanine, threonine, lysine, tryptophan and methionine.

Picture below:

We have just learned that the simple sugars can form polymers.

Another type of natural polymers are the polypeptides. The monomer is the 2-amino acids (also a-amino acid, see picture above). The peptide formation is actually a condensation as in the case of the oligosaccharide. The dipeptide (An analogue to the disaccharide) is formed by the reaction of an amino group, -NH2, with a carboxy group, -COOH. This creates a molecule of water. The linkage is an addition elimination mechanism as already known from organic chemistry.

The attack can also be done by alanine. This produces the dipeptide, glycilalanine, Gly–Ala. The carbonyl group now sits on the second carbon atom of the glycine.

 

A tripeptide is produced from 3 amino acids. Oligomers of amino acids are called peptides. The polypeptides can also be designated as polyamides, as in the organic chemical nomenclature. Long natural polymers of peptides are called proteins. These may contain more than 8000 amino acid units.

The proteins have the function of catalysts (enzymes) and also serve as transport and storage systems. Thus the oxygen transport through the protein, hemoglobin, and the replication of the chromosomes also takes place thanks to certain proteins.

A human average body (60kg) requires approx. 45 g of pure protein per day. This requirement corresponds to a portion of meager meat, poultry or fish (20g) 1 cup whole milk (9g) a piece of cheese (8g) an egg (6g) and a slice of bread (2g). Note: eggs, meat and fish should be eaten fresh. Eggs, no more than 8 days old no crack, no air chambers, and be transparent. Beef should be nice red and firm, pork white or pink. Important: Always keep fresh fish, otherwise it is poisonous!

For athletes, slimming and vegetarians. The amino acids methionine and lysine form in the liver of the human body the L-carnitine, a derivative, which plays an indispensable role in the fat burning in the muscles. Repetition, methionine, and lysine must be supplied from the outside; therefore, deficiency symptoms such as fatigue or sensitivity to cold are not uncommon in people who undergo radical slimming or in vegetarians.

The sequences, the arrangement of the 20 different amino acids, are precisely defined for all proteins.

Examples of oligopeptides and proteins:

Glutathione, Glu-Cys-Gly, tripeptide, component in living cells and in the eye lens.

Bovine insulin, 2 chains of 21 and 30 amino acids, a total of 51 amino acids and 3 disulfide bridges. Recall the rubber (subchapter polymerization, organic chemistry) due to the vulcanization of polyisoprene with sulfur. In insulin, which regulates the glucose content in the human body, there are 3 disulfide bridges. Two of them connect the two chains. The sulfur combines only with the amino acid cysteine, Cys.

Picture below:

The lack of insulin leads to diabetes. The replacement is made from the pancreas of slaughtering or genetically engineered and is thus commercially available. Further examples of proteins are enzymes, e.g. the digestive enzyme trypsin, toxins of fungi and snakes and some hormones:

vasopressin

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2

S —————————S

With disulfide bridge between the two cysteine, Cys.

Antidiuretic hormone, controls water excretion in the body.

Enzymes, digestive enzyme trypsin

The most common structures of long-chain proteins are helix and folded-leaf structure.

A superhelix can also be formed from the helix.

As it is often the case in biochemistry, the hydrogen bonds are responsible for helical, leaflet and superhelical structures.

More complex examples of long-chain proteins are myoglobin and hemoglobin, which surround a planar porphyrin complex with Fe as the central atom. The iron in the porphyrin complex is the cause of the red color of the blood. Function of hemoglobin is the oxygen withdrawal from the lungs and transport to the cells and organs.

 

nucleic acids

A nucleic acid consists of the following building blocks:

• One of the 5 bases: uracil (U), thymine (T), cytosine (C), adenine (A), guanine (G). These are heterocyclic amides and amines.
• One of the simple pentose sugars: β-D-ribose and 2-deoxy-β-D-ribose. (see the penultimate sub-chapter on carbohydrates, simple sugars). In the case of 2-deoxy-B-D-ribose, the OH group is absent from the second C atom to the right of the ether oxygen.
• Phosphoric acid. H3PO4, which connects the nucleic acids to each other via the sugar by condensation.

 

Image below: building blocks of the nucleic acid, (DNA and RNA), 2-deoxyribose and ribose according to Haworth representation:

 

Ribonucleic acid, RNA and deoxyribonucleic acid, DNA

The RNA is linked to phosphate (via phosphoric acid), ribose and one of the 4 bases, C, G, U or A. Uracil occurs only in the RNA!

The DNA contains instead of ribose, of 2-deoxyribose with the missing OH group at the second carbon atom to the right of the ether oxygen, hence the name deoxyribonucleic acid. The DNA contains one of the 4 bases, C, T, G or A. The DNA similar to RNA is linked to phosphate. Thymine occurs only in the DNA!

The DNA is almost the operating system of the living being: cell, plant, animal, human being. The DNA is located in the center of each cell and is called the nucleus. Therein the genetic information is stored.

Chemically, the DNA is nothing else but a polymer of the four different nucleic acids, which differ only from the four different bases,

Adenine, cytosine, guanine and thymine. The DNA consists of 2 chains arranged in parallel and forming a double helix.

The chain is linked to adjacent deoxyribose sugar via the phosphate and thus forms the polymer. The two chains in parallel are paired with 2 specific bases

• thymine – Adenine (AT or TA)
• guanine – cytosine (GC or CG)

via hydrogen bonds. (N—H) or (O—H

Picture below: Detail from the DNA with the sequence: GC-AT-CG

Picture below: Double helix of DNA. The red edge of the outside indicates the phosphoric acid, the blue lines the sugar, deoxyribose.

The rectangle shows the section of the sequence G-C, A-T, C-G of the picture above:

The mean diameter of a helix is ​​about 2000 pm, (10exp-12m), the distance between the bases is about 340 pm. The turns repeat about every 3400 pm.

During cell division, the two DNA spirals separate the corresponding bases temporarily and release their H-bonds. The two separated chains now build each a new corresponding chain. The separated chains serve as a kind of template.

They use corresponding nucleotides (as triphosphate) from the environment, in the restoration of the H-bonds diphosphate is split off.

There are 2 new helices with exact the same sequence. Picture below:

From the DNS together with most natural compounds also the proteins are produced. Parallel to the DNA, the RNA (ribonucleic acid) builds up with the same complementary base sequence as in the duplication. Example: An area of ​​the DNA contains the sequence: G, A, C, as in the rectangle in the picture above. Such is the complementary sequence of the RNA: C, U, G. In RNA, there are the same 4 bases as in DNA, with one exception. Instead of the base thymine, the RNA uses the base uracil (see further above).

While the RNA contains about 500 base units, depending on the size of the protein, there are about 100 million with the DNA.

The RNA is also called matrix-RNA, mRNA.

An amino acid arises due to a particular sequence of 3 bases of RNA. They form the corresponding code for the corresponding amino acid. This code is called codon. Example CUG. From this codon, (cytosine, uracil, guanine) arises the corresponding amino acid, leucine. The same amino acid can be generated from one of several different codons. Thus leucine can be formed from one of the following different condones: UUA, UUG, CUU, CUC, CUS, CUG (CUG see example above).

List of amino acids and the corresponding codons: Picture below

The process of protein synthesis via ribosomes. These consist of proteins, transfer RNA and anticodon. The exact procedure is explained in detail in the study of biochemistry.

 

The codon AUG initiates the beginning of a protein or polypeptide chain. The codon AUG (chain start) is called chain initiation.

One of the codons UGA, UAA and UAG is at the end of a protein or polypeptide chain.

The process of protein synthesis via ribosomes. These consist of proteins, transfer RNA and anticodon. The exact procedure is explained in detail in the study of biochemistry.

 

Example: sickle cell anemia as gene defect (Source: K. Peter C. Vollhardt, Organic Chemistry, VCH GmbH 1988)

The mRNA gene encoding a protein chain of hemoglobin starts with the following sequence: AUG GUG CAC CUG ACU CCU GAG GAG AAG ……

The first codon is AUG, The Chain Start. This is followed by GUG = valine, Val, CAC = histidine, His see last picture above.

 The codon GAG corresponds to the amino acid, glutamic acid, Glu.

 Glu is a compound with a fairly high dipole, which is also responsible for a functioning blood clotting.

 Now the A of GAG is replaced by U (by mutation). Instead of GAG, the codon GUG stands for Valin, Val. With Val, we now have a relatively non-polar amino acid in contrast to Glu.

 The resulting altered structure (tertiary structure) of hemoglobin results in clots in the blood due to relatively bad water solubility. The blood vessels can become blocked.

 

Literature

• K. Peter C. Vollhart, Organic Chemistry, VCH Publishing Company, D-6940 Weinheim (BRD) 1988, 1990
• Peter Sykes, Reaction mechanisms of organic chemistry, VCH Publishing Company, D-6940 Weinheim (BRD) 1988
• Charles E. Mortimer, The basic knowledge of chemistry, Georg Thieme Publishing Company, Stuttgart . New York 1987, 5th Edition
• James E. Huheey, Inorganic chemistry, Harper & Row, Publishers, Inc. New York, N.Y. 10022 USA, 3rd Edition 1988

 

 

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