The Molecules of Life Biochem!

Chapter 9

Biochemistry

Carbohydrates, lipids, proteins, and the nucleic acids

All built from simple precursorsHow they are put together is the

key to their activity

Carbohydrates

Polymers built from repeating sugar molecules

Carbohydrates

Glucose – most common•Assembled one way = starch – our

main E source

•Assembled a different way = cellulose – main ingredient in wood and most plentiful organic substance on earth!

Lipids

Polymers built from long hydrocarbon chains of fatty acids

Proteins

Constructed from 20 different kinds of amino acids• Great structural

and functional variability

Types of Proteins

Collagen – major component of tendons, skin, and bones

Hemoglobin – transports O2 in the blood stream

Enzymes – catalyst that speeds up rxn’s in all living organisims

Biochem History Until early 19th century, it was thought that

living things had something called “vital forces” that was unique to only living things.

1828 – German Scientist Freidrich Wöhler synthesized Urea from ammonium cyanate (a mineral)• Urea is a waste product of animal metabolism

• NH4OCH H2NCONH2

Current Realizations

Any compound that exists in a living organism can be synthesized in a lab

Rxn’s of biomolecules depend on the functional groups

Functional Groups

Table of functional groupsAlso, carbon containing

derivatives of phosphoric acid [esters and anhydrides of phosphoric acid ADP, ATP

Amino Acids

20 A.A’s - usually found in proteinsGeneral structure in common with

variations in side chainsAmino acids contins amino groups

(RNH2, R2NH, R3N) and a carbonyl group (RCOOH)

Amino Acids

Both groups are bonded to the same carbon atom and labeled α carbon = the one next to the carbonyl group

Amino Acids

Carbon atoms in the R group are labeled using the Greek alphabet starting w/the C adjacent to the carbonyl group

α β γ δ ε

Alpha beta gama delta epsilon

Amino Acids

Identity of the amino acids depends on the nature of the R-group.

MonosaccharidesCarbohydrates have the general formula

Cn(H2O)n

• All carbohydrates are not just hydrates of water

Simple sugars (monosaccharides) are cmpds that contain a single carbonyl group & 2 or more hydroxyl groups• Either polyhydroxyaldehydes or

polyhydroxyketones

MonosaccharidesThe ones that contain aldehydes=aldasesThe ones that conatin ketones = ketoses6 Carbon sugars are most abundant in

nature but 2, 5 carbon sugars (ribose and deoxyribose) occur in the structures of RNA and DNA

The Structure of Nucleic Acid Monomers

The 2 kinds of nucleic acids are DNA and RNA

There are diffs and sims b/t the twoThey are macromolecules (very large

molecules) formed by polymerizing monomer units (nucleotides = monomer units of nucleic acids)

The Structure of Nucleic Acid Monomers

Nucleotides have a base, a sugar, and a phosphoric acid residue covalently bonded together Nucleic acids can be hydrolyzed to

their constituent nucleotides by acids, bases, or enzymes

The Structure of Nucleic Acid Monomers

The main distinction between the nucleotide monomers of DNA and RNA is the sugar portionDNA = deoxyribose

RNA = ribose

Nucleotide Base

The Structure of Nucleic Acid Monomers

Nucleic acid bases (aka nucleobases) = nitrogen-containing aromatic compounds that fall into 2 categories

1. Pyrimidines – cytosine (in RNA&DNA)/thymine (DNA in rarely in RNA)/uracil (only in RNA)

2. Purines adenine (RNA/DNA)/guanine (RNA/DNA)

Lipid Examples

Insoluble in H2O and soluble in organic solvents

Glycerol esters of fatty acids (long chain carbox.acids) & derivatives of these esters are imoportant examples of lipids

Another example = steroids

Biochem

Part II

Amino AcidsWe know that proteins are long chain of

amino acids linked together by peptide bonds between a + charged N (amino) group at one end and a – charged carbonyl group at the other end.• Along the chain is a series of side chains

that are different for each of the 20 amino acids

Amino AcidsDipeptide = 2 amino acidsTripeptide = 3The sequence of the amino acids is

most important• There are 8,000 ways to arrange them

• In a protein chain of 100 amino acids, there are more ways to arrange them than there are atoms in the universe

Of all the possible AA’s, only 20 are usually found in proteins!

General structure of an AA involves an amino group, a carboxyl group & both are bonded to the α C• The α C is also bonded to a H

and an R group (side chain)

• The R group determines the

identity of the AA

Amino AcidsOne of the most important

properties of a AA is its 3-d shape (stereochemistry)• Mirror images that are superimposable = achiral

• Mirror images that aren’t superimposable = chiral

• Many important molecules are chiral

• Frequently, chiral center is a C atoms bonded to 4 different groups

Amino AcidsGlycine is the only AA that doesn’t have

a chiral center (it’s R group is a single H, giving it 2H’s out of 4 groups)

All other AA have

2 stereoisomers

Amino AcidsDashed lines show behind the plane,

solid triangles show out of the plane

Amino AcidsIn biochemistry, we don’t use R&S

designations, instead D & L are usedL (laevus) and D (dexter) meaning left

and rightFor AA, D=amino group on right side,

L = amino group on the Left side

Amino Acids

AA in proteins are all L

Structures and Properties of the Individual AA’s

R group (thus the amino acids) are classified according to several criteria (two very important)

Polar or nonpolar nature of the side chain

Presence of an acidic or basic group in the side chain

Group 1 – AA Nonpolar side chainsAlanine, valine, leucine, isoleucine,

proline, phenylalanine, tryptophan, methionine

Group 2 - AA

With electrically neutral polar side chains (neutral pH)

Serine, threonine, tyrosine, cysteine

Group 3 – AA - carboxyl groups in their side chains

Glutamic acid and aspartic acidCarbonyl group can lose H+ (forming

carboxylate ion) so they are – charged at neutral pH

They frequently bond to –NH2 to form side chain amide groups yielding analogous AA glutamine & asparagine

Group 4 – AA

With basic side chains [+ charged at or near neutral pH

HistidineLysine Arginine

Others

Some other AA’s are known to occur in some, but not all proteins

Derived from common AA and are produced by the modification of the parent AA after the protein is synthesized by the organism

OthersHydroxyproline and hydroxylysine have

extra –OH groups on the side chainThyroxine (from tyrosine) has an extra

Iodine containing aromatic group on the side chain (found only in thyroglobuin, a protein in the thyroid)

The Peptide Bond AA are linked by covalent bonds joining

the α – carboxyl group with the α-amino group) splitting out an H2O

After the H2O elimination, the groups are linked amino acids residues

A bond formed this way is called a peptide bond (aka: amide bond)

Peptide Bond

The Peptide Bond In a protein many AA (usually more than

100) are linked by peptide bonds to form a polypeptide chain• A peptide is a compound formed by liking smaller

#’s of amino acids (two several dozen)

• The bond is a single bond with partial double bond character (resonance)