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Organic Chemistry

The Structure and Function of

Macromolecules

•Organic compounds contain carbon and are associated with living things.

•Carbon is so vital to life, an entire branch of chemistry is devoted to its study: organic chemistry

Carbon!

Characteristics of Carbon!

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The Molecules of Life

• Overview:– Another level in the hierarchy of

biological organization is reached when small organic molecules are joined together

– Atom molecule macromolecule

Macromolecules

Large molecules are called macromolecules

The macromolecules are composed of submits called MONOMERS.

A POLYMER is composed of many monomers.

Building PolymersWhy it is called Dehydration

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Macromolecules

•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers

– Carbohydrates– Proteins– Nucleic acids– Lipids

CARBOHYDRATES

LIPIDS

PROTEINS

NUCLEIC ACIDS

4 Classes of Biological Macromolecules

CARBOHYDRATESCARBOHYDRATESMonomer is monosaccharide Monosaccharides are the simple

sugars• They contain C, H and O in a 1:2:1 ratio

and may be represented by the general formula CH2O

glucose fructose

Complex CarbohydratesComplex CarbohydratesTwo monosaccharides = a disaccharide More than two = polysaccharide

+ H2O

glucose fructose

sucrose

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Complex CarbohydratesComplex Carbohydrates

• Serve as fuel (energy) and building material (cellular structure)

• Include both sugars and their polymers (starch, cellulose, glycogen, chitin)

Complex CarbohydratesComplex Carbohydrates

Glycogen (animals) Starch (plants) are energy

storing Cellulose is in plant cells Chitin is the major component

in the exoskeleton of arthropods

Complex CarbohydratesComplex Carbohydrates

Monosaccharides– May be linear– Can form rings

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H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

HOH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

OH3

O H OO

6

1

Figure 5.4

Complex CarbohydratesComplex Carbohydrates

Examples of monosaccharides

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Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

oses

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Ket

oses

FructoseFigure 5.3

Complex CarbohydratesComplex CarbohydratesDisaccharides

– Consist of two monosaccharides– Are joined by a glycosidic linkage

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

O H

CH2OH

CH2OH HO

OHH

CH2OH

HOH H

H

HO

OHH

CH2OH

HOH H

O

O H

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Storage Polysaccharides• Starch

– Is a polymer consisting entirely of glucose monomers

– Is the major storage form of glucose in plants

• Glycogen– Consists of glucose

monomers– Is the major storage

form of glucose in animals

Chloroplast Starch

Amylose Amylopectin

1 m

Starch: a plant polysaccharide

Mitochondria Giycogen granules

0.5 m

Glycogen: an animal polysaccharide

Glycogen

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Structural Polysaccharides

• Cellulose– Is a polymer of glucose– Has different glycosidic

linkages than starch

(c) Cellulose: 1– 4 linkage of glucose monomers

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO4 OH

CH2OHO

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OHO

OH

OH

HO4

O1

OH

O

OH OHO

CH2OHO

OH

O OH

O

OH

OH

(a) and glucose ring structures

(b) Starch: 1– 4 linkage of glucose monomers

1

glucose glucose

CH2OH CH2OH

1 4 41 1

Figure 5.7 A–C

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Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OHO

OOHO

CH2OHO

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OHO

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unit

of the plant cell wall.

A cellulose moleculeis an unbranched

glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

– Cellulose is a major component of the tough walls that enclose plant cells

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• Cellulose is difficult to digest– Cows have microbes in their stomachs to

facilitate this process

Figure 5.9

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• Chitin, another important structural polysaccharide– Is found in the exoskeleton of arthropods– Can be used as surgical thread

(a) The structure of the chitin monomer.

OCH2OH

OHHH OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging

in adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Figure 5.10 A–C

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Lipids• Lipids are a diverse group of hydrophobic molecules

– Are the one class of large biological molecules that do not consist of polymers

– Share the common trait of being hydrophobic– fats and oils– waxes – sterols

Monomer is the fatty acidStructure is mostly C and H

Fig. 3.8a, p. 40stearic acid oleic acid linolenic acid

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Fats– Are constructed from two types of smaller molecules, a

single glycerol and usually three fatty acids– Vary in the length and number and locations of double

bonds they contain

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• Saturated fatty acids– Have the maximum number of hydrogen

atoms possible– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

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• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

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• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a

third fatty acid

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• Phospholipid structure– Consists of a hydrophilic “head” and

hydrophobic “tails”

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• The structure of phospholipids– Results in a bilayer arrangement found in cell

membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

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LipidsLipids• Function– Energy Storage– Fats store twice as many

calories as carbohydrates– Protection of vital organs

and insulation– Fat is stored in adipose

cells.

SterolsSterols

Characterized by a carbon skeleton consisting of four fused rings

Steroids- differ from other lipids in structure but are classified as a lipid because they are insoluble in water

– Examples• Cholesterol• Progesterone• Vitamin D

ProteinsProteins• Many structures, resulting in a wide range of

functions

• Amino acids are the building blocks of proteins.

• Needed for

• Structural support and movement(bone, cartilage, muscle)

• Storage/transport molecules (hemoglobin)

• Hormones (insulin-sugar breakdown)

• Enzymes (control of cellular reactions)

• Amino acids joined together by special covalent bonds called peptide bonds

Amino AcidAmino Acid -COOH, which is a

carboxyl group (acidic).

-NH2, which is an amino group (basic).

-H hydrogen. -R which varies

depending on the amino acid

Amino AcidAmino Acid All 20 different amino acids 10 essential - you must get them from food10 non-essential – your body can make themThe amino acids are the alphabet in which the proteins are written.

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• Enzymes– Are a type of protein that acts as a catalyst,

speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

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4 Products are released.

Figure 5.16

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Twenty Amino Acids

• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

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O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NHCH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

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Protein Conformation and Function

• Instrumental in nearly everything organisms do; 50% dry weight of cells

• The most structurally sophisticated molecules known

• A protein’s specific conformation (shape) determines how it functions

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Four Levels of Protein Structure

• Primary structure– Is the unique sequence

of amino acids in a polypeptide

Figure 5.20–

Amino acid subunits

+H3NAmino

end

oCarboxyl end

oc

Gly ProThr GlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaVal ArgGly

SerPro

Ala

Gly

lle

SerProPheHis Glu His

Ala

GluValValPheThrAla

Asn

AspSer

Gly ProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

Glu Lle Asp

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O C helix

pleated sheet

Amino acidsubunits NC

H

C

O

C N

H

CO H

R

C NH

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NCO

R

C

H

NH

H

C

R

C

O

C

O

C

NH

H

R

C

C

ON

HH

C

R

C

O

NH

R

C

H C

ON

H H

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N HO C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

C

H C

O

N

H

C

• Secondary structure– Is the folding or coiling of the polypeptide into a

repeating configuration– Includes the helix and the pleated sheet

H H

Figure 5.20

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• Tertiary structure– Is the overall three-dimensional shape of a

polypeptide– Results from interactions between amino

acids and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

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• Quaternary structure– Is the overall protein structure that results from

the aggregation of two or more polypeptide subunits

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Review Structure of ProteinsReview Structure of Proteins

• Primary Structure - the sequence of amino acids, which form a chain

• Secondary structure

•Alpha helix

•Beta-sheets

•Random coil

• Tertiary structure – folding of the coil

• Quaternary structure – two or more chains joined together

Types of ProteinsTypes of Proteins

Normal Sickle cell

Sickle cell disease, abnormal hemoglobins, is due to a single amino acid substitution.

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What Determines Protein Conformation?

• Protein conformation depends on the physical and chemical conditions of the protein’s environment

• Temperature, pH, etc. affect protein structure

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•Denaturation is when a protein unravels and loses its native conformation(shape)

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

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Types of ProteinsTypes of Proteins

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Nucleic Acids

• Nucleic acids store and transmit hereditary information

• Genes– Are the units of inheritance– Program the amino acid sequence of

polypeptides– Are made of nucleotide sequences on

DNA

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Nucleic AcidsNucleic Acids Provide blueprint of life Nucleotides are the monomers that make

– DNA – RNA – ATP

Nitrogen Base Pentose (5 carbon sugar) Phosphate

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Nucleotide BasesNucleotide Bases

PyrimidinesC = CytosineT = ThymineU = Uracil

PurinesA = AdenineG = Guanine

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CH

CHO

CN

H

CH

HNC

O

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

N

HCNHH

CC

N

NH

CNH2

AdenineA

GuanineG

Purines

OHOCH2

H

H H

OH

H

OHOCH2

H

H H

OH

H

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’

OH H2’

1’

5”

4’

3’ 2’

1’

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Deoxyribonucleic acid (DNA)

– Double stranded– Form double helix– Stores hereditary

information– Provides instruction

for every protein in the body

Nucleic AcidsNucleic Acids

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Ribonucleic acid (RNA)– Single stranded– Builds proteins– Acts as enzymes– Three types

• mRNA• tRNA• rRNA

Nucleic AcidsNucleic Acids

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Adenosine triphosphate (ATP)

– Called Life’s Energy Currency

– Single nucleotide – Energy storing phosphate

groups– Energy transfer and

storage used by all cells– Energy is released by

breaking high energy phosphate bond

Nucleic AcidsNucleic Acids

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