Organic Chemistry and Biochemistry

ANDREASREJBRAND NV3ANV2006-04-08Biochemistry

Organic chemistry and biochemistry

Organic chemistry and biochemistry

Table of Contents

Organic chemistry and biochemistry

Table of Contents

Preface

Part I: Organic chemistry

Alkanes

Isomers

Chain isomerism and nomenclature

Alkenes

Alkynes

Haloalkanes

Cycloalkanes

Aromatic hydrocarbons

Alcohols

Position isomerism

Molecules containing more than one hydroxyl group

Aldehydes

Carboxylic acids

Ketone

Thiols

Ethers

Amines

Amides

More aromatic compounds

Esters

Functional group isomerism

Stereoisomerism

Polymers

Part 2: Biochemistry

Carbohydrates

Amino acids

Proteins

Fibrous proteins

Globular proteins

Lipids

Nucleic acids

Vitamins

Vitamin A

B vitamins

Vitamin C

D vitamins

Other vitamins

Dietary minerals

Part 3: Physiological processes

Digestion

Absorption phase

Post absorption phase

Digestion of alcohols

Catabolism of digested molecules

Transportation molecules

Glycolysis

Pyruvate ions are converted to acetyl-CoA

Beta oxidation

Citric acid cycle

Final words

References

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Organic chemistry and biochemistry

Preface

The human being is a complex organism, completely made up of chemical compounds, of which most are organic. Organic compounds are in general made up of the atoms carbon, hydrogen, oxygen and nitrogen, even though other elements may occur as well, in smaller amounts. This document is meant to perspicuously describe organic chemistry and the compounds located and processes taking place in the human body. First, we shall study the structures and properties of the chemical compounds; then, we will study how these are digested and utilized in the body. We shall also study some of the chemical compounds used in products in the modern society asplastics, and other industrial applications of organic compounds.

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Organic chemistry and biochemistry

Part I: Organic chemistry

We shall begin to study the simplest organic compounds, the hydrocarbons, which only consist of carbon and hydrogen atoms.

Having four valence electrons, the carbon atom is able to covalently share four pairs of electrons with up to four other atoms. This is the fundamental principal concerning how hydrocarbons are formed. Besides the “normal” chemical formulas, discussing organic compounds, we also use structural formulas, specifying how the atoms are bond to each other. A complete two-dimensional structural formula consists of all atoms drawn on a plane with straight lines between then; each line symbolizes a shared pair of electrons. However, because organic compounds often are very large (containing many atoms), structural formulas are often abbreviated. Often hydrocarbons can be written as chains of carbon and hydrogen atoms, such as with heptane:

This formula may be abbreviated. First, we can write each “segment” as a local “normal” formula:

Furthermore, we can let all “standard segments” (CH2) be pre-understood:

At each joint, thus, there is a CH2 group.

Extremely many organic compounds are known, and many of them occur naturally on earth and have industrial applications (especially in the chemical, pharmaceuticaland food industries). As a consequence, in this document, we will only mention the occurrences and applications of the very most common organic compounds.

Alkanes

Alkanes are hydrocarbons where every carbon atom bonds four other atoms. Below, the simplest alkanes are described. The “C” column specifies the number of carbon atoms the compound contains, and the “phase” columnspecifies the phase (s: solid; l: liquid; g: gas) of the compound at STP (Standard Conditions for Temperature and Pressure; 273.15 K and 100 kPa).

C / Name / Trivial name / Formula / Structural formula / Phase
1 / methane / CH4 / / g
2 / ethane / C2H6 / / g
3 / propane / C3H8 / / g
4 / butane / C4H10 / / g
5 / pentane / C5H12 / / l
6 / hexane / C6H14 / / l
7 / heptane / C7H16 / / l
8 / octane / C8H18 / / l
9 / nonane / C9H20 / / l
10 / decane / C10H22 / / l

Table1Alkanes

All alkanes to the alkane with13carbon atoms, tridecane (C13H28)are liquids at STP. The 14 carbon atom alkane,tetradecane(C14H30),has a melting point of5.5°C; all larger alkanes are solids at STP.

The simplest hydrocarbon, methaneis an odourless gas. In industrial production of the gas, however, odoriferous gasses are often added (often sulphurous compounds), so that gas leakages easily can be detected. Methaneis abundant in the earth’s mantleand on the ocean bed,and is a main component in natural gas, which is used as a fuel, for instance for heating and generation of electricity.

Through the reaction

methaneis fully combusted.

The process of digestion of some animals also produces methane. Moreover, methaneis abundant on other celestial bodies in our solar system, for instance on Jupiter’s moon Titan, the only moon in the solar system known to have a thick atmosphere, of which approximately 1.6% is methane. Methanehas also been detected in interstellar gas clouds.Also many larger alkanes are naturally occurring, both on earth and at other locations in space.

Petrol, which is used as a fuel in smaller engines (e.g. motorcycles, cars and smaller aircraft), is largely a solution of alkanes;often, the carbon atom numbers are between six and ten.

Isomers

Two compounds sharing the same chemical formula but having two distinct structural formulas are isomers to each other. There are different types of isomerism, described by the list below.

• Structural isomerism
• Chain isomerism
• Position isomerism
• Functional group isomerism
• Stereoisomerism
• Cis-trans isomerism
• Enantiomersisomerism

Structural isomerism occurs between two compounds when the atoms in the first compound are not bonded to the corresponding atoms in the second compound. Concerning stereoisomerism, on the other hand, all atoms in the first compound are in fact bonded to corresponding atoms in the second compound, but in different directions in three-dimensional space.

Chain isomerism and nomenclature

Chain isomerism occurs when the carbon chains differ between two molecules. For instance, the following molecules are chain isomers to each other.

The two molecules share the common formula C5H12, but the atoms are bonded to each other forming two distinct structures. We recognize the first molecule as pentane. Thus, the second molecule is an isomer of pentane, or iso-pentane. We can also find an isomer of hexane:

The first molecule is hexane, whereas the other may be called iso-hexane. However, there are more than one candidates of the “iso-hexane” name. Below, all possible chain isomers of hexane are drawn.

To unambiguously name an isomer, one has decided to use the following rules:

1. Find the longest continuous carbon chain in the molecule; this is called the root chain. The straight alkane with the same number of carbon atoms as the root chain will make up the “last name” of the molecule. To be able to follow the following steps, we must also number the carbon atoms in the root chain, so that the carbon atom bonding a branch and being as close to one of the two ends of the root chain as possible, will be assigned a number as low as possible.
2. The groups branched from the root chain will be named individually and receive the new “–yl” suffix, declaring that they are just groups branched from the root chain. Concerning alkanes, these groups will get the “–yl” suffix instead of “–ane”.

one / (mono)
two / di
three / tri
four / tetra

1. The names of all groups will be written before the “last name” of the molecule. Before each group name, the number of the carbon atom to which the group is bonded, is declared. Between numbers and names and between different group declarations, hyphensare used as separators.

1. If a certain group occurs more than once, a “counter” is written before the group name (without any separator), according to the table to the right. The carbon atom numbers of the groups are separated by commas.
2. The group names before the “last name” of the molecule are sorted alphabetically. Counters (di, tri, and tetra) are excluded.

For instance, the two isomers of hexane will be named as follows.

Below is a somewhat more complicated example.

Alkenes

Sometimes a carbon atom bonds only three other atoms; in such cases, exactly one of these bonds must be a double bond, i.e. two pairs of electrons are shared between these atoms. A compound with one or more double bonds is said to be unsaturated, and is able to add two new atoms at the position of the double bond, which then will be converted to a single bond. In structural formulas, double bonds are drawn as two parallel lines. The “last name” of a molecule containing double bonds willend with “–ene” instead of “–ane”.Concerning the carbon numbering, it is important to make sure, that the carbon atoms participating in the double bond will be located in the root chain and receive as low numbers as possible. This is more important than the root chain’s being as long as possible. The number of a double bond equals the number of the carbon atom participating in the bond and being as close as possible to one of the terminating points of the chain. The number of the double bond is written just before the “last name” of the molecule.

Study the two following structures as examples.

A more “technical” name of the second molecule above would be 6[1propene1yl]-dodecane.

If two or more double bonds exist within the same molecule (on the same root chain), the correct counter is written before the “–ene” suffix of the “last name”. The numbers of the double bonds are separated by commas. Study the examples below.

An unsaturated compound can be saturated by adding extra atoms and losing the double bond in the process. The following reaction is a typical addition reaction.

Ethene (ethylene) is a transmitter substance (a hormone) in plants and is also a very technically important alkene. Ethene is first and foremost used for production of polyethene (polyethylene) plastics – one of the most commonly used plastics in the modern society. Polyethene is a polymer of ethene, i.e. a macromolecule compiled of numerous small ethene molecules.

Double bonds are –unlike single bonds – not dynamic: the two sides of the bond cannot rotate in relation to each other. Below, four molecules are drawn. The molecules on the first row are derivatives of alkanes, where the molecules on the second row are derivatives of alkenes. Whereas the two alkane derivatives are identical to each other, the two alkene derivatives represent two distinct molecules, being stereoisomers to each other.

Alkynes

Triple bonds, where three pairs of electrons are shared, are dealt with analogous to double bonds. Here the “–yne” suffix is used instead of “–ene” that is used for alkenes.

In the following example, in the name of the molecule, we specify the position numbers of the double and triple bonds just before the “–ene” and “–yne” suffixes.

Haloalkanes

Hydrogen atoms in hydrocarbons may be substituted for other atoms, particularly halogens. These molecules are called haloalkanes, and are named by adding the names of the halogen atoms and their positions before the “last name” of the molecule. Study the following example.

Cycloalkanes

A cycloalkane is a cyclic alkane, i.e. an alkane without any terminating ends.

Cyklohexaneand cyklopentaneare quite stable cycloalkanes, compared to cyklobutaneand the instable cyklopropane molecule.

Aromatic hydrocarbons

Hydrocarbons derived from benzene are called aromatic hydrocarbons. Benzene is a cyclic hydrocarbon where – as one said some years ago – every other carbon-carbon-bond is a double bond. This definition, however, is inappropriate, because benzene does not behave as an unsaturated compound.

With modern terminology, one realizes that the two following (resonance) structures are possible:

Instead of writing these two possible forms of benzene, one usually says that the six[1] additional bonding electrons are delocalized and belong equally to every carbon atom. To draw this, the delocalized electrons are drawn as a circle:

One can consider the two “conventional” double bond models above as two “extremes” of electron positions in the molecule, whereas the model of the benzene molecule should be described using the modern form, a “mean” of the two extremes, or aresonance hybrid. The resonance hybrid is more stable than any of its extremes. Benzene is a colourless and fragrant liquid at room temperature (melting point at 5.5 °C)and has been shown to be a carcinogen.

Two common derivatives of benzene are methylbenzene (toluene) and dimethylbenzene (xylene). These compounds can be derived from benzene if one or two hydrogen-to-methyl-substitutions are performed, respectively.

Of course, there are three structural isomers of xylene:

Toluene and xylene are colourless liquids. They are, for instance, used in petroleum, as solvents and in synthesis of other chemicals.

Alcohols

We shall now study more complex organic compounds than simple hydrocarbons (and haloalkanes, which we also have studied). If a hydrogen atom in a hydrocarbon is replaced with another group (not a hydrocarbon group), the molecule may obtain completely new properties. Such a group is called a functional group. First, we will study alcohols, organic compounds with the –OH functional group, the hydroxyl group. We shall begin to study alcohols that are direct derivatives of the alkanes, with only one of the two outermost hydrogen atoms substituted with a hydroxyl group. The names of these compounds are derived from the name of the corresponding alkane, adding the “–ol” suffix.

C / Name / Trivial name / Formula / Structural formula / Phase
1 / methanol / wood alcohol / CH3OH / / l
2 / ethanol / grain alcohol / C2H5OH / / l
3 / propanol / C3H7OH / / l
4 / butanol / C4H9OH / / l
5 / pentanol / C5H11OH / / l
6 / hexanol / C6H13OH / / l
7 / heptanol / C7H15OH / / l
8 / octanol / C8H17OH / / l
9 / nonanol / C9H19OH / / l
10 / decanol / C10H21OH / / l

Table3Some simple alcohols

We see that the alcohols in general have higher boiling points than the corresponding alkanes, which, of course, is true because the hydroxyl groups allow the molecules to form hydrogen bonds. Having amelting point at 24-27 °C, dodecanol, C12H25OH is the first alcohol in this category beinga solid at room temperature. Methanol and ethanol are sometimes used as solvents and, increasingly often, as fuels (particularly ethanol). These compounds are also produced by anaerobic bacteria.Despite being a toxic, in some cultures ethanol is used as beverage.Furthermore, essentially all alcohols mentioned above have industrial applications.

Position isomerism

Two molecules being identical to each otherexcept for a functional group’s being bonded to distinct atoms are positional isomers to each other. Thus, to name a particular positional isomer of an alcohol, the position of the hydroxyl group must be specified. Study the following molecules as an example.

To be correct, we should accordingly name the alcohols in the table above 1-propanol, 1-butanol, 1-pentanol etc.

Molecules containing more than one hydroxyl group

An alcohol may contain more than one (1) hydroxyl group. The name of such an alcohol must specify the positions of all hydroxyl groups, and add the correct counter before the “–ol” suffix. We shall now study some common compounds containing multiple hydroxyl groups.

C / Name / Trivial name / Formula / Structural formula / Phase
2 / ethane-1,2-diol / ethylene glycol / C2H4(OH)2 / / l
3 / propane-1,2,3-triol / glycerol, glycerin, glycerine / C3H5(OH)3 / / l

Table4Some alcohols containing multiple hydroxyl groups

The most well-known application of ethanediol is probably as a component in automotive antifreeze. If the antifreeze solution in a car consists of 50% ethanediol and 50% water, the freezing point of the solution will drop to −35 °C, preventing the solution from freezing during winter. Propanetriol is a main component of all fats.

An alcohol is said to be primary (with respect to a specific hydroxyl group) if the carbon atom bonding the hydroxyl group at most forms a bond to one other carbon atom. If it, on the contrary, forms bonds to two other carbon atoms, the alcohol is said to be secondary; if it bonds three other carbon atom, the alcohol is said to be tertiary. All alcohols in Table 3 are primary. Ethanediol is primary with respect to its both hydroxyl groups as well as the outermost hydroxyl groups in propanetriol, whereas the hydroxyl group in the middle actually is secondary.

Rn symbolizes any hydrocarbon chain. Now, we shall study what happens when primary, secondary and tertiary alcohols are oxidized.

Aldehydes

Aldehydes are compounds containing the –CHO functional group, the aldehyde group.

Aldehydes are formed when primary alcohols are oxidized. The reaction is shown below.

If we oxidize the (primary) alcohols from Table 3, we will obtain the simplest aldehydes. These are named adding the “–al” suffix to the name of the corresponding alkane, in analogy to how alcohols are named (using the “–ol” suffix).

C / Name / Trivial name / Formula / Structural formula / Phase
1 / methanal / formaldehyde / HCHO / / g
2 / ethanal / acetaldehyde / CH3CHO / / l
3 / propanal / propionaldehyde / C2H5CHO / / l
4 / butanal / C3H7CHO / / l
5 / pentanal / C4H9CHO / / l
6 / hexanal / C5H11CHO / / l
7 / heptanal / C6H13CHO / / l
8 / octanal / C7H15CHO / / l
9 / nonanal / C8H17CHO / / l
10 / decanal / C9H19CHO /

Table5Some aldehydes

Methanal is produced naturally during forest fires and is also present in automobile exhaust gasses and tobacco smoke. Killing bacteria, methanal-water solution (formalin) is industrially used as a disinfectant and preservative to, for instance, animals in glass jars at museums. Methanal is also used to dry out skin, for instance to treat warts and in the plastics industry. Chiefly, however, methanal is used to synthesize other compounds.

Ethanal is produced by plants and is naturally occurring in bread and in ripe fruits. Industrially, ethanal is mostly used in the synthesis of other compounds. Both methanal and ethanal are suspected to be carcinogenic. Heptanal and octanal are used in paints, and several of the aldehydes above are used within the pharmaceutical industry.