Chapter 4

Chapter 4

How does carbon account for the large diversity of biological molecules?

• Organic chemistry – study of compounds containing carbon

• Accounts for small molecules (methane) to large molecules (proteins)

What are the hypotheses about the natural origin of life on Earth?

• Vitalism– Belief in a life force outside the jurisdiction of

physical and chemical laws– Provided for foundation of organic that eventually

began to undermine its very foundation– Who first provide great doubt about vitalism?• Wohler who made urea• Followed by Kolbe who made acetic acid

Stanley Miller

Who was Stanley Miller and what was his contribution?

– Experimented to see if complex organic molecules could arise spontaneously under conditions thought to have existed on the early Earth

– His experiment supported the idea that abiotic synthesis of organic compounds could have been an early stage in the origin of life

LE 26-2

Water vaporCH4

NH3 H 2

Electrode

Condenser

Coldwater

Cooled watercontainingorganicmolecules

Sample forchemical analysis

H2O

Energy Source

Who was Stanley Miller and what was his contribution?

– Helped shift from vitalism to mechanism

What is mechanism?• View that physical and chemical laws govern all natural phenomena,

including the processes of life

How does carbon form a wide selection of diverse molecules?

• Carbon has 6 electron– 2 first electron shell– 4 in second shell (4 valence electrons)• This shell can hold 8• Would have to donate or accept 4 to complete valence shell and

become ion– Generally complete valence shell by covalently bonding sot

that 8 electrons (4 from itself, 4 from another) are shared• Called tetravalence

– Leads to carbon’s versatility to make complex molecules

– Generally forms a tetrahedral shape

Most Frequent Partners

• Oxygen• Hydrogen• Nitrogen

• Can also form covalent bonds to other carbon atoms, linking the atoms into chains of a huge variety

What is the benefit of having a carbon skeleton?

• Vary in length• Can be straight, branched, or in rings, double

bonds, single bonds, etc

What is a hydrocarbon?

• Organic molecules consisting of only carbon and hydrogen

• Wherever electrons are available for covalent bonding, atoms of hydrogen are attached to the carbon skeleton

• Many of cell’s organic molecules have regions consisting of only carbon and hydrogen

• Many of the compounds are hydrophobic because of the non-polar carbon-to-hydrogen linkages

• Reactions generally release a relatively large amount of energy

What is an isomer?

• Compounds that have the same number of atoms and the same element composition, but are arranged differently

Kinds of Different isomers

• Structural• Geometric• enantiomers

Kinds of Different isomers

• Structural– Differ in the covalent arrangement of atoms– two substances having the same

molecular formula but different physical and chemical properties because the arrangement of their component atoms is different.

– Also known as Constitutional ISomers

Kinds of Different isomers• Geometric– Have same covalent partnerships but differ in

spatial arrangement– Due to inflexibility of double bonds– two or more coordination compounds which

contain the same number and types of atoms, and bonds (i.e., the connectivity between atoms is the same), but which have different spatial arrangements of the atoms.

– Not all coordination compounds have geometric isomers.

Kinds of Different isomers

• Geometric– Due to inflexibility of double bonds• Two types:

– cis isomer-» the two groups are on the same side of the double bond

– trans isomer-» the two groups are on opposite sides

• Note that these two structures contain the same number and kinds of atoms and bonds but are non-superimposable. The isomer in which like ligands are adjacent to one another is called the cis isomer. The isomer in which like ligands are opposite one another is called the trans isomer.

Kinds of Different isomers

• enantiomers– isomers that are mirror images of each other– Occurs when there are asymmetric carbons• Carbon is attached to 4 different atoms or groups of

atoms– Two forms:• Right-handed• Left-handed

– Generally one is biologically active, while the other is not

Kinds of Different isomers

What chemical groups are key to the functioning of biological molecules?

• chemical groups are key to the functioning of biological molecules?– Hydrocarbons-• Simplest organic molecules• Underlying framework for more complex organic

molecules

Hydrocarbon tails

Hydrocarbon Tails of a Phospholipid

Structural formula Space-filling model Phospholipid symbol

Hydrophilichead

Hydrophobictails

Fatty acids

Choline

Phosphate

Glycerol

Hydr

oph o

bic t

a ils

Hydr

o ph i

l ic h

ead

Cell Membranes

What chemical groups are key to the functioning of biological molecules?

– The groups attached to the hydrocarbons can participate in chemical reactions or can contribute to function indirectly by their effects on molecular shape

– These chemical groups can affect molecular function by becoming directly involved in chemical reaction

Functional Groups

• Participates in chemical reactions in a characteristic ways

• 7 chemical groups are important to biological processes

Functional groups serve important purposes in molecules

Estradiol

Testosterone

Male lion

Female lion

7 Chemical Groups Important to Biological Processes

• Hydrophilic and can act as functional groups– Hydroxyl– Carbonyl– Carboxyl– Amino– Sulfhydryl– Phosphate

LE 4-10aa

STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS

Alcohols (their specific namesusually end in -ol)

Ethanol, the alcohol present inalcoholic beverages

FUNCTIONAL PROPERTIES

Is polar as a result of theelectronegative oxygen atomdrawing electrons toward itself.

Attracts water molecules, helpingdissolve organic compounds suchas sugars (see Figure 5.3).

LE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group iswithin a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is the casefor acetone and propanal.

Aldehydes if the carbonyl group isat 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 carboxylgroup, glycine is both an amine anda carboxylic acid; compounds withboth groups are called amino acids.

FUNCTIONAL PROPERTIES

Acts as a base; can pick up aproton from the surroundingsolution:

(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 caninteract to help stabilize proteinstructure (see Figure 5.20).

LE 4-10bc

STRUCTURE

NAME OF COMPOUNDS

Organic phosphates

EXAMPLE

Glycerol phosphate

FUNCTIONAL PROPERTIES

Makes the molecule of which itis a part an anion (negativelycharged ion).

Can transfer energy between organic molecules.

• Not reactive and acts as a recognizable tag on biological molecules– methyl

7 Chemical Groups Important to Biological Processes