biochemistry course notes--lecture 3

8/7/2019 biochemistry course notes--lecture 3

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Lecture 3: Organic Chemistry as it Relates to Biochemistry

Fortunately, only a small fraction of the organic chemistry that you learned inprevious classes is required to get going in biochemistry:

A. Alkanes: Saturated Hydrocarbons

Nomenclature

Table 1: Molecular and Condensed Structural Formulas for the first ten normalalkanes:

When attached to other parts of organic molecules, alkane moieties are called„Alkyl groups‟

These alkyl groups can be straight-chain or branchedThe names and structures of those most commonly encountered inbiochemistry are listed in the table below

Note that the number of hydrogen atoms attached to the linking carbondetermines whether the alkyl group is referred to as „primary‟ (twohydrogens), „secondary‟ (one hydrogen) or „tertiary‟ (no hydrogens)

o e.g. butyl and isobutyl are primary; sec -butyl is secondary, and tert- butyl istertiary



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Table 2: The Most Important Alkyl Groups For Biochemistry

Physical properties

Alkanes and alkyl groups are nonpolar and therefore hydrophobic; they areinsoluble in water and are responsible for hydrophobic interactions

The density of hydrocarbons is considerably less than 1.0 (a typical value is0.7), which is why oil floats on water.

Chemical reactions

In the lab, alkanes are relatively unreactive in the sense that the structurescannot be modified in a controlled wayo They can however be burned with oxygen at high temperature to form

carbon dioxide and water, a reaction called combustion

E.g. : CH4 + 2O2 CO2 + 2H2O

o This reaction, which is vital to technology and to life, releases a lot ofenergy

o Alkanes are said to be saturated because they have the maximum numberof C-H bonds per carbon atom

o These energy-rich bonds enable alkanes to react with more oxygen (gramfor gram) than any other class of organic molecule

Alkanes are the most “energy-dense” organic fuels – more energy is releasedper gram than with other organic compounds

Cells also combust the hydrocarbon portions of food molecules, but in ahighly controlled way and at body temperature



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B. Alkenes – Unsaturated hydrocarbons

Structural characteristics

Alkenes are hydrocarbons with a double bond.

o Example: ethylene, CH2=CH2 The double bond is planar and rigido When other substituents are attached to it, the relative position of the

substituent is designated as cis (same side) or trans (opposite side):

o Note that the position of the substituents has a major effect on thecrowding of electron orbitals in the structure (affects stability)

Nomenclature

The standard nomenclature is to add an -ene ending to the root nameof the parent compound, as in ethylene(CH2=CH2)o This system is generally not used for biochemistry – instead, we

speak in terms of an unsaturated group in a molecule when there isa double bond.

o Fatty acids that contain a single double bond are called“monounsaturated”; those with more than one are“polyunsaturated”

Physical properties

Alkenes are nonpolar and hydrophobico Fatty acids with double bonds are essentially as hydrophobic as

saturated fatty acids.



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Reactions of biochemical importance

a. Hydrogenation (reduction) to alkanes:

>C=C< +2[H] >CH-CH<

o The brackets signify the addition of two hydrogen atoms withoutspecifying the nature of the reductant (i.e., the hydrogen source)

o In the lab, hydrogen gas can be used; cells use other reductants

b. Hydration to alcohols:

C. Aromatic Hydrocarbons


These are cyclic compounds with two or more double bonds that havemuch greater chemical stability than the C=C bonds of aliphaticalkenes

Benzene is the prototype, shown below. It is a resonance hybrid of twostructures, with six electrons shared by all six-carbon atoms:

An aromatic compound must meet two criteria:

1. The compound must have uninterrupted, cyclic cloud of electrons above

and below the plane of the molecule



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2. Its uninterrupted cloud must contain (4n + 2) electrons, where n is anywhole number

Nomenclature

The benzene ring as a substituent is called thephenyl groupo For example, benzene attached to

ethanol becomes „phenylethanol‟

The relationships of substituents on the ring itself are either ortho , meta , orpara , as shown below:

Physical properties

Similar to alkenes


Many important biomolecules are aromatico The reactions they undergo in the cell do not have clear

counterparts in organic chemistryo The cell has come up with novel ways to handle these unreactive

molecules, some of which we will discover in this course

D. Alcohols


These have the hydroxyl (-OH) functional groupThe best known example is ethyl alcohol, or ethanol (CH3CH2-OH)Aside from ethanol and methanol, pure alcohols of low molecular weight

are rare in human biochemistry



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o However, the hydroxyl group is found everywhere, such as incarbohydrates and in compounds with other functional groups.

Nomenclature

The -ol suffix is attached to the name of the appropriate alkyl groupBenzene with a single -OH attached to the ring is phenol

Physical Properties

The hydroxyl group is hydrophilic and much more soluble in water than ina hydrocarbon solvent (by a factor of about 5000)

o The first few members of the homologous series, up to butanol, aretherefore more soluble in water than in hydrocarbon solvents

The longer alcohols, such as octanol, are only sparingly soluble in water

Aliphatic alcohols are extremely weak acids, not significantly dissociated

at physiological pHo In strong alkali they can be made to dissociate to alkoxide anions:

ROH RO- + H+

Aromatic alcohols such as phenol are significantly acidic because thephenolate anion can be stabilized by resonance:


a. Oxidation to aldehydes andketones, usually viadehydrogenation.

b. Formation of esters andphosphoesters (e.g. withcarboxylic acids):



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c. Formation of hemiacetals and acetals

d. Dehydration to alkenes.

E Amines


These molecules contain the amino group (Nitrogen attached to four R/Hgroups)

The first member of the series is ammonia.o Ammonia

o Primary amines have one hydrogen replaced by R(two H‟s remain)

o Secondary amines have two hydrogens replacedby R (one H remains)

o Tertiary amines have all three hydrogens replacedby R (no H remains)

The R groups in secondary and tertiary amines may be the same or different.Note that the use of primary, secondary, and tertiary for amines is not quitethe same as for alcoholso For alcohols we look at how many R groups are on a carbo n; for amines

we look at how many are on the nitroge n

Nomenclature

Combine the alkyl prefix with the suffix “amine.”o For example, CH3NH2 is methylamine



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Physical properties

The amino group is hydrophilic, with a polarity similar to the hydroxyl groupo It is about 2000 times more soluble in water than in a hydrocarbon solvento Therefore, the first few members of the amine homologous series are

water-solubleImportantly, amines are bases that exist at physiological pH mainly in theprotonated form:

o The protonated forms are called ammonium ionso The ammonium ions are essentially insoluble in organic solvents


a. Formation of

amides

b. Formation of Schiff bases by condensation with aldehydes or ketones

c. Formation of Schiff bases by dehydrogenation.

F. Thiols/mercaptans


These compounds contain sulfur as RSH or RSR´

Nomenclature

The –SH group is called the thio- or the mercapto- group.Examples:



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Physical characteristics

The -SH group is not clearly polar or nonpolar, but somewhere in between.


a. Formation ofthioesters

b. Oxidation to disulfides viadehydrogenation

G. Aldehydes and ketones

Structural characteristics.

Both aldehydes and ketones have a carbonyl group, >C=O, composed of acarbonyl oxygen atomo Aldehydes have one –H attached to the

carbonyl carbon, whereas ketones havetwo alkyl groups.

Nomenclature

In IUPAC nomenclature, adehydes are named after the parent compound byattaching an -al suffix, whereas ketones are named by attaching a -one suffix.

The common names of aldehydes are derived from the names of thecorresponding carboxylic acids by replacing -ic acid by -aldehyde.

All members of the ketone family are named from the two groups attached tothe carbonyl, followed by ketone.

o Example: methyl ethyl ketone.

Physical Characteristics

The >C=O group is polar, and is more soluble in water than in organicsolvents

The first four members of the homologous series are water-soluble



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a. Reduction to alcohols

This is the reverse of the dehydrogenation reaction described above inthe alcohol section

b. Formation of hemiacetals and hemiketals

This was described above in the section on alcohols

c. Formation of Schiff bases with amines

This was described in the section on amines

d. Aldol condensation/cleavage

This is one of several reactions involved in the making and breaking ofcarbon-carbon bonds, and will be discussed below

H. Carboxylic Acids


This class of compounds has the carboxyl group, which is often simply writtenas “COOH”

Nomenclature

Small carboxylic acids are named according to their common or IUPACnames, always ending with “ic acid” (e.g. formic acid)

Once the alkyl chain gets beyond the length of about 8, the carboxylic acidsare referred to as fatty acids

The carbon atoms in the chain are numbered from the carboxyl end (There isalso a Greek lettering system to indicate the relation of carbon atoms to theCOOH end)

Carboxylic acids are weak acids, dissociating in water to form a carboxylateanion



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o The salt of the acid is named by replacing the “–ic acid” with “–ate” o The dissociation of the .OH group in .COOH is more favorable than the

dissociation of .OH in an alcohol because the carboxylate anion isstabilized by resonance:

The carboxylate anion is extremelyhydrophilic, and essentially insoluble in organicsolvents

The anionic forms of fatty acids are strongly amphipathic – the carboxylate„heads‟ are hydrophilic whereas the hydrocarbon „tails‟ are very hydrophobic o This property is very important for the role if fatty acids and related

molecules in membrane formation

Reactions of biochemical significance

The most important is the formation of carboxylic acid derivatives, whichinclude esters, amides, thiolesters, and anhydrides:



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The above reactions exemplify a common feature of many biologicalreactions – dehydrations (aka condensations)o Dehydration reactions involve the combination of two functional groups

with the concomitant elimination of a water molecule

De- (loss of)

-hydration (water) o Dehydrations are often depicted as follows, with a „lasso‟ around the two

hydrogen atoms and one oxygen atom that will form H2O



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o Note that one hydrogen and one oxygen are derived from one of thereactants and the other hydrogen is derived from the other reactant

o Condensation reactions are very important for the synthesis of largebiological molecules:

The reverse reaction, hydrolysis, is equally important in biological chemistryo Hydrolysis reactions generally break down larger biological molecules into

their components parts, through the formal addition of a water molecule Hydro- (water) -lysis (breakage)

o Hydrolysis reactions are very important for the breakdown of largebiological molecules:

I.Phosphoric acid and its derivatives

This exceedingly important class of compounds is widely used in the

chemistry of the cello Important for energy supply (ATP), macromolecules (DNA, RNA),

biological signals (phosphorylation of proteins) and other processes

Much of the chemistry of phosphate is qualitatively similar to that of carboxylicacids



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J.Compounds with more than one functional group

1. Dicarboxylic acids

2. Keto acids.

keto acids

In these the keto group is adjacent to the carboxylic group

The most common in biochemistry is pyruvic acid and its salt,

pyruvate:



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The systematic name is .-keto followed by the name of the parent acid

This system is used for all keto acids other than pyruvate:

keto acids

In these the keto group is two carbons removed the carboxylic group:

keto acids readily undergo decarboxylation:

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Hydroxyacids.

-hydroxy acids

A hydroxy group is adjacent to the carboxylThe most common one in biochemistry is lactic acid and its salt, lactate

Other . -hydroxy acids are either named after the parent acid or givencommon names of their own

-hydroxy acids

A hydroxy group is two carbons removed from the carboxyl



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Polyfunctional groups with more than one hydroxyl are generallyclassified as carbohydrateso We will examine these separately later in the course

K. Heterocyclic compounds.

A heterocyclic compound is one that contains a ring with more than one kindof atom

These compounds are generally more important for their contribution to non-covalent interactions that any specific chemistry in which the are involved

Some of those encountered in biochemistry are shown below:

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biochemistry course notes--lecture 3

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