[PDF] Molecular diversity arises from variations in the carbon skeleton

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BIOLOGY 101

CHAPTER 4: Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

CONCEPTS:

4.1 Organic chemistry is the study of carbon compounds

4.2 Carbon atoms canform diverse molecules by bonding to four other atoms

Diversity in shape means diversity in function

4.3 A few chemical groups are key to molecular function

What characteristics of carbon make it such an excellent element to base life upon? Carbon can form long chains with other carbon atoms Carbon atoms form 4 covalent bondswith other atoms This allows for the formation of diverse branching(non-linear) structures

Varying the number of bonds also varies the anglesof bonds, and therefore, the shapes of molecules ʹ

this includes various types of isomers When combined with other atoms to form biological molecules, carbon tends to form polar covalent bonds, which creates polar molecules in an aqueous (polar) living world Carbon is one of the most abundantelements on Earth Carbon has both solidand gaseousforms (facilitates transfer and transformation)

ůĂŶƚƐĐĂŶƌĞĐLJĐůĞĐĂƌďŽŶďLJ͞fixing͟ŝƚĨƌŽŵŝƚƐŐĂƐĞŽƵƐĨŽƌŵ;CO2) into carbon containing molecules like

glucose. CO2is the source of carbon for all organic molecules

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.1 Organic chemistry is the study of carbon compounds:

Organic chemistry focuses on compounds containing carbon. Organic compounds can range from simplemolecules, such as CH4, to complexmolecules such as proteins, with thousands of atoms. Most organic compounds contain hydrogenatoms as well as carbon.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.1 Organic chemistry is the study of carbon compounds:

Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements. These otherelements commonly include hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and Sulfur (S)

CHNOPS

oRepresent the six atomsthat make up nearly all organic molecules ʹƚŚĞ͞ŵŽůĞĐƵůĞƐŽĨůŝĨĞ͟

C-C-C-C-C-C

H N O P S

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.1 Organic chemistry is the study of carbon compounds:

The overall percentages of the major elements of life (C, H, N, O, P, and S) are quite uniformfrom one

organism to another.

Because of ĐĂƌďŽŶ͛ƐǀĞƌƐĂƚŝůŝƚLJ, these few elements can be combined to build an inexhaustiblevarietyof

organic molecules.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.1 Organic chemistry is the study of carbon compounds:

Initially, organic molecules were defined as those that could only be synthesized by living organisms

Organic chemistry was later redefined as the study of carbon compounds, regardless of their origin. Organismsproduce the majority oforganic compounds. The laws of chemistry apply to both inorganic and organic compounds.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

A carbon atom has a total of 6 electrons: 2 in the first electron shell and 4 in the second shell. oCarbon will not form ionic bondsunder normal conditions. Gaining or losing 4 electrons takes a considerable amount of energy Carbon usually completes its valence shell by sharing electronswith other atoms in four covalent bonds, which may include single and double bonds. oCarbon-Carbon and Carbon-Hydrogen bonds are non-polar covalent bonds oCarbon bound to N,O,P, or S forms polar covalent bonds

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

This means that when carbon bonds to these atoms, it will generate polar molecules ʹthis is important in an aqueous environment!

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

The ability of carbon to form four covalent bonds makes large, complexmolecules possible. When a carbon atom forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedronwith bond angles of 109.5Σ. In molecules with multiple carbon atoms, every carbon atom bonded to four other atoms has a tetrahedral shape.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

The ability of carbon to form four covalent bonds makes large, complexmolecules possible. When a carbon atom forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedronwith bond angles of 109.5Σ. In molecules with multiple carbon atoms, every carbon atom bonded to four other atoms has a tetrahedral shape. When two carbon atoms are joined by a double bond, all bonds around those carbons are in the same planeas the carbons.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

The formation of single, double or triple bonds

changes bond angles, and therefore, shape

When the shape of a molecule changes, so

does its function.

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

The valencesof carbon and its partners can be viewed as the guidelines that determine the architecture of organic molecules In carbon dioxide (CO2), one carbon atom forms two double bonds with two oxygen atoms. In the structural formula, O=C=O, each line represents a pair of shared electrons. This arrangement completes the valence shells of all atoms in the molecule.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Although CO2is sometimes classified as either organic or inorganic, its importance to the living world is clear: CO2is the source of carbon for all organic molecules found in organisms CO2is usually fixedinto organic molecules by the process of photosynthesis.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

It is these organic molecules that make up all living things

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Carbon chains form the skeletons of most organic molecules. Carbon skeletons vary in lengthand may be straight, branched, or arranged in closed rings.

Carbon skeletons may include double bonds.

Atoms of other elements can be bonded to the atoms of the carbon skeleton. Hydrocarbonsare organic molecules that consist of only carbon and hydrogen atoms.

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Hydrocarbonsare the major component of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that lived millions of years ago. Fatsare biological molecules that have long hydrocarbon tailsattached to a nonhydrocarbon component.

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton oPetroleumand fatare non-polarcompounds that cannot dissolve in water because of their many nonpolar covalent carbon-hydrogen bonds. Hydrocarbons can undergo reactions that release a relatively large amount of energy.

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Isomersare compounds that have the same molecular formulabut different structuresand, therefore, different chemical properties Structural isomershave the same molecular formula but differ in the covalent arrangement of atoms. Structural isomers may also differ in the location of the double bonds.

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Cis-transisomershave the same covalent partnerships but differ in the spatial arrangement of atoms around a carbon-carbon double bond. Consider a simple molecule with two double-bonded carbons, each of which has an H and an X attached to it. The arrangement with both Xson the same sideof the double bond is called a cis isomer; the arrangement with the Xson opposite sidesis called a transisomer.

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton

The double bond does notallow the atoms

to rotate freely around the bond axis.

Double bonds not only change bond angles, but

also create molecules that can be isomers, having different functions

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Enantiomersare isomers that are mirror imagesof each other. Enantiomers are possible when four different atoms or groups of atoms are bonded to an asymmetric carbon. The four groups can be arranged in space in two different waysthat are mirrorimagesof each other. They are like left-handedand right-handedversions of the molecule. Usually one is biologically active, while the other is inactive

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Even subtle structural differences in two enantiomers may have important functional significance because of emergent properties from specific arrangements of atoms. An example of this is a comparison of R and S forms of the enantiomers for Ibuprofenand Albuterol

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton oS-Ibuprofen is 100x more potent than the

R form

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Even subtle structural differences in two enantiomers may have important functional significance because of emergent properties from specific arrangements of atoms. An example of this is a comparison of R and S forms of the enantiomers for Ibuprofenand Albuterol

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton oS-Ibuprofen is 100x more potent than the

R form

oS-Albuterol counteracts its active R form

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms:

Summary of different forms of isomers

Carbon and the Molecular Diversity of Life:

Molecular diversity arises from variations in the carbon skeleton

4.3 A few chemical groupsare key to molecular function:

The distinctive properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the chemical groups attached to that skeleton.

If we start with hydrocarbonsas the simplest organic molecules, characteristic chemical groups can replace

one or more of the hydrogen atoms bonded to the carbon skeleton of a hydrocarbon.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

oThe addition of chemical groups brings different functionsand shapesto molecules

4.3 A few chemical groupsare key to molecular function:

These chemical groups may be involved in chemical reactions or may contribute to the shape and function of the organic molecule in a characteristic way, giving it unique properties. As an example, the basic structureof testosterone(a male sex hormone) and estradiol(a female sex hormone) is the same.

Both are steroidswith four fused carbon rings, but the hormones differ in the chemical groups attached to

the rings.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groupsare key to molecular function:

These chemical groups may be involved in chemical reactions or may contribute to the shape and function of the organic molecule in a characteristic way, giving it unique properties. As an example, the basic structure of testosterone(a male sex hormone) and estradiol(a female sex hormone) is the same.

Both are steroidswith four fused carbon rings, but the hormones differ in the chemical groups attached to

the rings.

As a result, testosterone and estradiol have different shapes, causing them to interact differently with

many targets throughout the body.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

In many cases, chemical groups known as functional groups affect molecular function through their direct involvement in chemical reactions. Seven chemical groups are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methylgroups. All (except the methyl group) contribute to the polar natureof biological molecules, with the hydroxyl group having the greatest effect Methyl groups are not reactivebut change the shape of molecules and can serve as important markers on organic molecules

4.3 A few chemical groups are key to molecular function:

In a hydroxylgroup -OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. Organic molecules become water solubleand hydrogen bond with water when they contain two or more hydroxy groups. Organic compounds with hydroxyl groups are alcohols and carbohydrates. Ethanol mixes with water onlybecause of the Hydroxyl group it possesses

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

A carbonylgroup (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the endof the skeleton, the compound is an aldehyde. If the carbonyl group is withinthe carbon skeleton, the compound is a ketone. Isomerswith aldehydes and those with ketones have different properties. The double bond in carbonyl groups makes isomerspossible

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

Compounds with carboxylgroups are carboxylic acids. A carboxyl group acts as an acidbecause the combined electronegativitiesof the two adjacent oxygen atoms increase the chance of dissociation of hydrogenas an ion (H+).

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

An aminogroup (ͶNH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton.

Organic compounds with amino groups are amines.

The amino group acts as a basebecause it can pick up a hydrogen ion (H+) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

A sulfhydrylgroup (ͶSH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. Organic molecules with sulfhydryl groups are thiols. Two sulfhydryl groups can react, forming a covalent bond. This 'cross-linking' helps stabilize protein structure

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

A sulfhydrylgroup (ͶSH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. Organic molecules with sulfhydryl groups are thiols. Two sulfhydryl groups can react, forming a covalent bond. This 'cross-linking' helps stabilize protein structure Cross-linking of cysteinesin hair proteins maintains the curliness or straightness of hair.

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

Perms use reducing agentsto break cysteine

bridges. This allows peptide chains to slip into a new shape.

Perms are then neutralized(usually hydrogen

peroxide) to reform cysteine disulfide bridges and lock in the new shape

4.3 A few chemical groups are key to molecular function:

A phosphategroup (ͶOPO32оͿĐŽŶƐŝƐƚƐŽĨĂƉŚŽƐƉŚŽƌƵƐĂƚŽŵďŽƵŶĚƚŽĨŽƵƌŽdžLJŐĞŶĂƚŽŵƐ;ƚŚƌĞĞ

with single bonds and one with a double bond). A phosphate group connects to the carbon backbone via one of its oxygen atoms. Phosphate groups are anionswith two negative charges because 2 protons dissociate from the oxygen atoms. One function of phosphate groups is to transfer energybetween organic molecules

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

A phosphategroup (ͶOPO32оͿĐŽŶƐŝƐƚƐŽĨĂƉŚŽƐƉŚŽƌƵƐĂƚŽŵďŽƵŶĚƚŽĨŽƵƌŽdžLJŐĞŶĂƚŽŵƐ;ƚŚƌĞĞ

with single bonds and one with a double bond). A phosphate group connects to the carbon backbone via one of its oxygen atoms. Phosphate groups are anionswith two negative charges because 2 protons dissociate from the oxygen atoms. One function of phosphate groups is to transfer energybetween organic molecules Phosphate groups confer polarityto otherwise nonpolar phospholipids

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

4.3 A few chemical groups are key to molecular function:

Adenosine triphosphate, or ATP, is the primary energy transfer molecule in living cells. oATP consists of an organic molecule called adenosineattached to a string of three phosphate groups. oWhen one inorganic phosphate ion is split off as a result of a reaction with water, ATPbecomes adenosine diphosphate, or ADP.

oŶĂƐĞŶƐĞ͕͞stores͟ƚŚĞƉŽƚĞŶƚŝĂůƚŽƌĞĂĐƚǁŝƚŚǁĂƚĞƌ͕ƌĞůĞĂƐŝŶŐĞŶĞƌŐLJƚŚĂƚĐĂŶďĞƵƐĞĚďLJ

the cell.

Carbon and the Molecular Diversity of Life:

ATP is an important source of energy for cellular processes

4.3 A few chemical groups are key to molecular function:

A methylgroup (ͶCH3) consists of a carbon atom bonded to 3 hydrogen atoms. Methyl groups are generally non-reactive, but can change the shapeof molecules or serve as

ŵŽůĞĐƵůĂƌ͚ƚĂŐƐ͛ĨŽƌŵŽůĞĐƵůĞƐ

The methylation of DNA nucleotides is a mechanism to deactivate genes

Carbon and the Molecular Diversity of Life:

Carbon: the Backbone of Life

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