Chapter 4 Carbon & the Molecular Diversity of Life

Chapter 4Carbon & the Molecular Diversity of Life

The Backbone of Biological Molecules• What compound makes up the majority of

matter in cells?

• Carbon is unparalleled in its ability to form large, complex, and diverse molecules• Proteins, DNA, carbohydrates

• Why is carbon so versatile?

Where do we ultimately get carbon to make the molecules necessary for life?

What about life elsewhere?

Do you think it is carbon-based life?

• Organic compounds range from simple molecules to colossal ones

• Most organic compounds contain hydrogen atoms in addition to carbon atoms• Hydrocarbons

Quick Review: What are the elements that are most common in biological compounds?◦O, H, S, P, and of course C

Organic chemistry is the study of carbon compounds

Vitalism - the idea that organic compounds arise only in organisms

Swedish scientist, Berzelius - The idea that there was a “life force” outside of physical & chemical laws

Organic chemistry - study of carbon based compounds

Organic Chemistry - OriginsFriedrich Wöhler accidentally created urea

in his labHermann Kolbe created acetic acid from

inorganic substanceStanley Miller demonstrated possible

origin of life through synthesis of organic compounds

Vitalism Mechanism◦the view that all natural phenomena, are subject to physical & chemical laws

Paradigm shift…

The Structure of Carbon Atoms

What is the electron configuration of carbon?

Why is the electron configuration important?

What kind of bond is carbon going to form?

The Formation of Bonds with Carbon

Four valence electrons = four covalent bonds (tetravalence)

Structure of Organic MoleculesWhat shape is a carbon molecule with four

single bonds?

Why is the bond angle the same for each bond?

LE 4-3

MolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene)

Structure of Organic Molecules

Carbon most commonly forms bonds with:OxygenNitrogenHydrogen

Brainstorm: Why do you think that these elements are the most likely to form organic compounds?

LE 4-4

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Hydrocarbons

Carbon is able to form long chains that vary in length and shape

LE 4-5

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene 2-Butene

Cyclohexane Benzene

Hydrocarbons

Only contain carbon and hydrogenMany organic molecules, such as fats,

have hydrocarbon components

Brainstorm: Why do you think that hydrocarbons might be important for biological processes?

LE 4-6

A fat molecule Mammalian adipose cells

100 µm

Fat droplets (stained red)

Isomers

Compounds with multiple possible structures and functions◦Structural isomers- arrangement of bonds and

atoms◦Geometric isomers- same covalent placement,

different spatial arrangements (e.g. cis/trans)◦Enantiomers- mirror images

LE 4-7

Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.

Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

L isomer D isomer

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

Enantiomers

Thalidomide ◦Treatment for morning sickness◦Causes limb deformities in newborns

Ethambutol◦Treatment for tuberculosis◦Causes blindness

Naproxen◦Treatment for arthritis◦Causes liver poisoning

Why is thalidomide especially dangerous?

LE 4-8

L-Dopa(effective againstParkinson’s disease)

D-Dopa(biologicallyInactive)

Functional GroupsMolecular structures that are responsible for

the chemical characteristics of a compoundMost reactions (in organic chemistry)

depend on the functional groups

Methylamine

LE 4-9

Estradiol

Testosterone

Male lion

Female lion

Know these functional groups!

◦Hydroxyl group OH◦Carbonyl group CO◦Carboxyl group COOH◦Amino group NH2

◦Sulfhydryl group SH◦Phosphate group PO4

LE 4-10aa

STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS

Alcohols (their specific names

usually end in -ol)

Ethanol, the alcohol present in

alcoholic beverages

FUNCTIONAL PROPERTIES

Is polar as a result of the

electronegative oxygen atom

drawing electrons toward itself.

Attracts water molecules, helping

dissolve organic compounds such

as sugars (see Figure 5.3).

LE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group is

within a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde may

be structural isomers with

different properties, as is the case

for acetone and propanal.

Aldehydes if the carbonyl group is

at the end of the carbon skeleton

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES

LE 4-10ac

STRUCTURE

NAME OF COMPOUNDS

Carboxylic acids, or organic acids

EXAMPLE

Has acidic properties because it isa source of hydrogen ions.

Acetic acid, which gives vinegarits sour taste

FUNCTIONAL PROPERTIES

The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,which is called a carboxylate group.

LE 4-10ba

STRUCTURE

NAME OF COMPOUNDS

Amine

EXAMPLE

Because it also has a carboxyl

group, glycine is both an amine and

a carboxylic acid; compounds with

both groups are called amino acids.

FUNCTIONAL PROPERTIES

Acts as a base; can pick up a

proton from the surrounding

solution:

(nonionized)

Ionized, with a charge of 1+,under cellular conditions

Glycine

(ionized)

LE 4-10bb

STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

Thiols

EXAMPLE

Ethanethiol

FUNCTIONAL PROPERTIES

Two sulfhydryl groups can

interact to help stabilize protein

structure (see Figure 5.20).

LE 4-10bc

STRUCTURE

NAME OF COMPOUNDS

Organic phosphates

EXAMPLE

Glycerol phosphate

FUNCTIONAL PROPERTIES

Makes the molecule of which it

is a part an anion (negatively

charged ion).

Can transfer energy between

organic molecules.

ATP: An Important Source of Energy for Cellular Processes

Adenosine triphosphate (ATP)- primary energy-transferring molecule in the cell

The Chemical Elements of Life: A Review

Why is the versatility of carbon so important for biological processes?

Exam practiceWhat is the reason why hydrocarbons are not

soluble in water? A) The majority of their bonds are polar

covalent carbon to hydrogen linkages. B) The majority of their bonds are nonpolar

covalent carbon-to-hydrogen linkages. C) They are hydrophilic. D) They exhibit considerable molecular

complexity and diversity. E) They are lighter than water.

Exam practice

Hydrocarbons mainly consist of H-C nonpolar covalent bonds and thus not soluble in water

The answer is B

Exam

Exam practice The two molecules shown in Figure 4.1 are

best described as A) optical isomers (enantiomers). B) radioactive isotopes. C) structural isomers. D) nonradioactive isotopes. E) geometric isomers.

Exam practice

The answer is C structural isomersThis is because structural isomers differ in

covalent patternsGeometric isomers differ in arrangement

about a double bondEnantiomers differ in spatial arrangement

around an asymmetric carbon (mirror images)

Functional Group Activity