BiochemistryBiochemistry is the study of the chemistry of

living organismsMuch of biochemistry deals with the large,

complex molecules necessary for life as we know it

However, most of these complex molecules are actually made of smaller, simpler units – they are biopolymers

There are four main classes of biopolymers – lipids, proteins, carbohydrates, and nucleic acids

1Tro: Chemistry: A Molecular Approach, 2/e

LipidsLipids are a family of compounds that are

generally insoluble in water (ie. Non-polar).Classes of Lipids:

Waxes = fatty acid and long chain alcohol (ester)Fats & Oils = glycerol + three fatty acidsPhospholipids = glycerol + 2 fatty acids +

phosphate + an amino alcoholSphingolipids = fatty acid + sphingosine +

phosphate + an amino alcoholGlycolipids = fatty acid + glycerol or sphingosine +

one monosaccharide.Steroids = a fused ring structure of three

cyclohexanes and one cyclopentane.

Fatty AcidsLong chain carboxylic acids.12 – 18 Carbon’s are the most common.Stearic acid is most often found in animal fat.

CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2COOH

And it can also be represented like this:

C

O

OH

Fatty AcidsCan be saturated – all C-C single bonds.Can be mono-unsaturated – one C-C double

bond.Ex) Oleic Acid found in olives and corn.CH3(CH2)7CH=CH(CH2)7COOH

Can be poly-unsaturated – more than one C-C double bond. Ex) Linoleic Acid found in soybeans and sunflowers.CH3(CH2)4CH=CHCH2CH=CH(CH2)4COOH

In the Unsaturated acids, the cis isomer is usually found.

Physical Properties of Fats and OilsThe repeating zigzag shape of saturated fatty acids

found in fats allows them to fit close together leading to strong attractions. As a result, a fat is solid at room temperature.

The unsaturated fatty acids found in oils do not stack together because of the double bonds. As a result, an oil is a liquid at room temperature.

Fats and OilsFats and oils are the most common lipids.Often called triglycerides because they are

a tri-ester of glycerol and three fatty acids.Tristearin consists of three stearic acid

molecules reacting with glycerol.

Reaction to Produce a Fat or Oil

+ 3 H2O

Steroids and CholesterolSteroids are any compounds

containing the steroid nucleus (Pictured at right).

Cholesterol is the most important and abundant steroid in the body.

You cannot exist without this substance!

The sex hormones and the adrenocortical hormones depend on cholesterol for their synthesis.

Cholesterol and Hormones

HO

CH3

CH3

H3C

CH3

CH3

HO

CH3OH

O

CH3OH

CH3

Cholesterol, Estrogen, and Testosterone

CarbohydratesSimple Sugars have the formula

Cn(H2O)n and were once thought to be “hydrates” of Carbon.

The Carbon cycle.

___________6CO2 + 6H2O + energy C6H12O6 + 6O2

_____________

Types of CarbohydratesMonosaccharides – do not hydrolyze

into smaller units.Disaccharides – consist of two mono

units joined together – these will hydrolyze.

Polysaccharides – consist of many mono units and are sometimes called “complex carbohydrates.”

MonosaccharidesHave between three and eight C atoms.Number of C’s determines whether it is a triose

(3), tetrose (4), pentose (5), hexose (6), etc.All have at least two –OH groups and the term

polyhydroxy- is sometimes used.Will also have either an aldehyde or ketone

group.Aldehyde = aldose and ketone = ketose.Molecules are written with the C backbone in a

vertical direction.

MonosaccharidesKetose or Aldose?How many chiral carbons?

C

C

H OH

CH2OH

O

CH2OH

Monosaccharides and ChiralityLarge monosaccharides have several

chiral C’s.If the lowest chiral C has the OH

group on the left, then it is called the L isomer. If it is on the right, then it is called the D isomer.

Hint: C’s with double to the O are not chiral and the -CH2OH groups are also not chiral.

GlucoseHow many chiral

carbons?Is this the D or L isomer?Note: D-glucose is

oxidized in the body to produce energy and L-glucose cannot be oxidized.

C

C

HHO

H OH

C

CH2OH

OHH

C

C

OHH

H O

Cyclic StructureIn solution, glucose and other mono-

saccharides become cyclic.

DisaccharidesComposed of two mono units.Some common ones are:

Sucrose = Glucose + FructoseLactose (Milk sugar) = glucose + galactoseMaltose = glucose + glucose

In the presence of water and an acid catalyst, these linked molecules will split apart back into their mono units.

Sucrose

PolysaccharidesThis is essentially a polymer of glucose units

(usually).Plant Starch exists in two forms: Amylose

and Amylopectin.Amylose is a long,continuous chain of glucose

molecules. Typically has 250 – 4000 units.Amylopectin is a branched chain of glucose

molecules. Branches are about every 25 units.

PolysaccharidesAnimal Starch is also called ___________. This

is essentially a branched chain as well.Branches are about every 10 – 15 units.

____________, found in cell walls of plants and animals, is also a long chain of glucose units much like amylose.

PolysaccharidesThe linkage between each unit in

cellulose is different ( linkage) and is resistant to hydrolysis.

Human’s do not possess the enzymes to break this material down for energy as some animals do.

We often refer to this material in our diet as “fiber.”

Amino Acids and Proteins

The Amino AcidsAre the building blocks of

all proteins.Twenty different versions

of these.All contain the carb. acid

and amine functional groups.

Center C is called the alpha Carbon and it is chiral (except in Glycine)

Abbreviated by three letter designations.

CN

R

C

H

H

HOH

O

Amino AcidsThe R groups can be non-polar, polar, acidic, or basic.

Alanine

Non-polar R group

Serine

Acidic R Group

The Peptide BondAmino acids link together by the

reaction of a carboxylic acid on one with the amine of another.

The linkage between the two is called a peptide bond.

Peptide Formation Reaction to form peptide bond between any

two amino acids is a condensation type:

Primary StructureChains of 3 – 50 amino acids are called

polypeptides.When more than 50 amino acids are joined,

we usually call it a protein. The specific sequence of amino acids in a

protein is called the primary structure. Our DNA codes for only a limited number of

specific sequences for making proteins.Approximately 100,000 different proteins

found in humans.

Secondary StructureThis refers to how the amino acids along the

polypeptide are arranged in space.The three most common types are:

Alpha Helix - which is a corkscrew shape of the chain that results from Hydrogen bonding between every fourth amino acid. All of the R groups then are pointed outward.

Beta-Pleated Sheet – rows of amino acids are held flat with HB keeping them rigid.

Triple Helix – is three peptide chains woven together like a braid. HB is also a powerful force that holds this together.

Alpha Helix & Beta-Pleated Sheet

Tertiary StructureThis is the overall 3D shape of the protein.The types and interactions of the R groups

are important in this area.Globular proteins, like hemoglobin and insulin,

have a very compact and round shape. The non-polar R groups point inward and the polar R groups point outward and this makes these proteins soluble in water.

Fibrous proteins, like keratin (hair, skin), consist of long, thin, fibrous shapes. Cross-linking is an important aspect and determines whether you have curly or straight hair.

Overview of Protein Structures

Albumin

Lysozyme

Nucleic AcidsBasic structure is a polymer of four different

bases.Each nucleotide consists of three parts: a

sugar, a base, and a phosphate group.

Nucleotide StructureEach nucleotide has three

parts – a cyclic pentose, a phosphate group, and an organic aromatic base

The pentoses are the central backbone of the nucleotide

The pentose is attached to the organic base at C1 and to the phosphate group at C5

The phosphate groups then link to each other to form a polymer

DNA and RNADeoxyribonucleic Acid is found primarily in the nucleus

of the cell.Ribonucleic Acid is found throughout the cell.The sugar molecule Ribose differs by a single oxygen

atom.

BasesIn DNA, the four cyclic bases are Adenine, Guanine,

Cytosine, and Thymine. In RNA, Thymine is replaced by Uracil.

Base Pairing in DNA

Base Pairing in DNAThe bases in nucleic acids are

complementary – they precisely pair with another base.

Adenine pairs with Thymine via two hydrogen bonds

Guanine pairs with Cytosine via three hydrogen bonds

Linking Nucleotides

Linking Nucleotides

Genetic StructureEach sequence of three nucleotides is called

a codonA codon codes for one amino acidAGT = SerineACC = ThreonineThis is universal for all living things!

DNA Double Helix

DNA Double HelixBase pairing generates the helical

structureIn DNA, the complementary bases

hold strands together by H-bondingallow replication of strand

DNA Replication

Protein SynthesisTranscription → translationIn nucleus, DNA strand at gene separates and a

complementary copy of the gene is made in RNAmessenger RNA = mRNA

The mRNA travels into the cytoplasm where it links with a ribosome

At the ribosome, each codon on the RNA codes for a single amino acid, and these are joined together to form the polypeptide chain

47Tro: Chemistry: A Molecular Approach, 2/e

48Tro: Chemistry: A Molecular Approach, 2/e