Carbon Based Macromolecules

Organic Chemistry

The Molecules of Life

Macromolecules- macro=large

The molecules of life are “organic compounds”. All have C (carbon) as its backbone.

Carbon can share electrons with as many as 4 other atoms held together by covalent bonds. The four elements found in all living things are: C H O N

Terms to know: Organic compounds- carbon based molecules Hydrocarbons- compounds made up of only carbon and

hydrogen. ex: petroleum Carbon skeleton -a chain of carbon atoms Functional groups- groups of atoms that participate in

chemical reaction and are attached to the carbon skeleton. Ex: NH2 , -OH,

Hydrophilic- water loving Hydrophobic- fear or dislike of water Polymers- long chains made up of many subunits Monomers- one unit of a polymer

Producers Capture Carbon from the airHow carbon enters the world of living

things?

Using photosynthesis, plants and other producers turn carbon dioxide and

water into carbon-based compounds

These are called organic

Organic compounds have a carbon backbone

C-C-C-C-C-C-C-C-C-C-

Carbon chains vary in many ways

H H

HH

H H

Ethane Propane

HH

H H

H

H

H

H

H

H

Carbon skeletons vary in length.

H

H

H

H

H H

H H

H H

H H

H H

H H

H

H

H

H

H

H H H H

H

H

C

HH H

H H

H H

H

H

H

H H

H

H

HH

H

H

H H

H

H

Butane Isobutane

Skeletons may be unbranched or branched.

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

CC C

C

CC

H

CC

C

CC

C

Cyclohexane Benzene

Skeletons may be arranged in rings.

C C C C C

C C C C

C

C CC

CCC C CCCH H

Figure 3.1A

INTRODUCTION TO ORGANIC COMPOUNDS Life’s molecular diversity is based on the properties of carbon A carbon atom can form four covalent bonds

Allowing it to build large and diverse organic compounds

Structuralformula

Methane

H H

H

H H H

H

H

Ball-and-stickmodel

Space-fillingmodel

CC

The 4 single bonds of carbon point to the corners of a tetrahedron.

Figure 3.1A

Functional Groups

Atoms or clusters of atoms that are covalently bonded to carbon backbone

Give organic compounds their different properties

Examples of Functional GroupsHydroxyl group - OH

Amino group - NH3+

Carboxyl group - COOH

Phosphate group - PO3-

Types of Reactions

Hydrolysis reactions

Breaking down large polymers into smaller

monomers by adding water

Dehydration reactions

Joining monomers to form larger polymers by

removing water

Hydrolysis A type of cleavage reaction Breaks polymers into smaller units Enzymes split molecules into two or more

parts An -OH group and an H atom derived from

water are attached at exposed sites

enzyme action at functional groups

HYDROLYSIS

Fig. 3.4b, p. 37

Cells make most of their large molecules By joining smaller organic molecules into chains

called polymers Cells link monomers to form polymers

By a dehydration reaction

H

OH H

OH

H OH

Unlinked monomer

Dehydration reaction

Longer polymer

Short polymer

OH H

H OH

Unlinked monomer

Dehydration reaction

Short polymer

H2O

Figure 3.3A

Cells make a huge number of large molecules from a small set of small molecules

The four main classes of biological molecules Are carbohydrates, lipids, proteins, and nucleic acids

Many of the molecules are gigantic And are called macromolecules

CarbohydratesSUGARS and STARCHES

Function: Energy source Structure: all contain C H O The H to O ratio is 2:1. The same as water Hydrogen atoms are attached to carbons

to form a stable molecule. Sugar names end in “OSE”

Carbohydrates

Monosaccharides(simple sugars)

Oligosaccharides(short-chain carbohydrates)

Polysaccharides(complex carbohydrates)

Carbohydrates- sugars Monosaccharides: simple sugars. Have at least

two –OH (hydroxyl groups) attached to the carbon backbone.

Ex: C6H12O6 glucose (blood sugar) one sugar unit,

the simplest carbohydrate. Fructose (fruit sugar) Soluble in water and sweet

tasting. Disaccharide. Short chain resulting from

covalent bonding of two monosaccharides. Sucrose (table sugar) is glucose + fructose Lactose (milk sugar) is glucose + galactose

Carbohydrates- starches Polysaccharides: many sugar units linked

together. Could be a chain of glucose.Examples: Starches( storage for plants) such as

potatoes, pasta, bread., glycogen (storage form of glucose) cellulose ( in plants cell walls) and chitin ( exoskeleton of insects) The stored form of glucose is called

Glycogen. It goes in your liver and muscle cells until you need it for energy.

Cellulose & Starch

Differ in bonding patterns between monomers

Cellulose - tough, indigestible, structural material in plants

Starch - easily digested, storage form in plants

Glycogen Consists of glucose monomers Is the major storage form of glucose in animals

Mitochondria Giycogen granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

Structural Polysaccharides Cellulose

Is a polymer of glucose

Starch and glycogen are polysaccharides That store sugar for later use

Cellulose is a polysaccharide found in plant cell walls

Starch granules in potato tuber cells

Glycogen granules in muscle tissue

Cellulose fibrils in a plant cell wall

Glucose monomer

Cellulose molecules

STARCH

GLYCOGEN

CELLULOSE

O O

OOOOOO

O O O

O

OO

OO

OO

OOOO

OO

OOO

OO

OOOO O

OOOOOO

OOOOOO

O

OH

OH

Figure 3.7

Cellulose

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHO

CH2OHO

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

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 unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

Is a major component of the tough walls that enclose plant cells

Cellulose is difficult to digest

Cows have microbes in their stomachs to facilitate this process

Figure 5.9

Glycogen

Sugar storage form in animals

Large stores in muscle and liver cells

When blood sugar decreases, liver cells convert glycogen back to glucose so the cells can use it

Chitin

Polysaccharide

Nitrogen-containing groups attached to glucose monomers

Structural material for hard parts of invertebrates,

Ex: exoskeleton of insects, cell walls of many fungi, lobster, shrimp shells

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.

O

CH2OH

OHH

H OH

H

NH

C

CH3

O

H

H

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

Lipids

Are the body richest source of energy. Each molecule of fat yields more than twice the energy than a carbohydrate (since they have more covalent bonds and energy is released when bonds are broken)

Lipids are a diverse group of hydrophobic molecules

Lipids Are the one class of large biological molecules that

do not consist of polymers Share the common trait of being hydrophobic

Most include fatty acidsFats and oils

Phospholipids

Waxes

Sterols - have no fatty acids

Lipids Tend to be insoluble in water

Lipids (fats, oils) Function: Long term storage of energy,

building of structures such as cell membranes and insulation.

Substances that are greasy or oily such as fats, oils, waxes, phospholipids, steroids .

Lipids are non polar, insoluble in water

(hydrophobic) but can dissolve in one another.

LipidsStructure: The building blocks of lipids are: FATTY ACIDS + GLYCEROL

Body fats are called triglycerides Made up of long carbon chains.

Fats

Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

(b) Fat molecule (triacylglycerol)

H HH H

HHH

HH

HH

HH

HH

HOH O HC

C

C

H

H OH

OH

H

HH

HH

HH

HH

HH

HH

HH

H

HCCC

CC

CC

CC

CC

CC

CC C

Glycerol

Fatty acid(palmitic acid)

H

H

H

H

HH

HH

HH

HH

HH

HH

HH

HH

HHHH

HHHHHHHHHHHH

H

HH

HH

HH

HH

HH

HH

HH

HH

HHHHHHHHHHH

HH

H

H H H H H H H HH

HH

H H H HH

HH

HHHHHH

HHHHH

HH

HO

O

O

O

OC

C

C C C CC

C C CC

C C CC

CC

C C

C

CCCCCCC

CCC

CCCCCC

C C C C C C CC

CC C C

CC

C

O

O

(a) Dehydration reaction in the synthesis of a fat

Ester linkage

Figure 5.11

Fats, also called triglycerides Are lipids whose main function is energy storage Consist of glycerol linked to three fatty acids

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

H2O

H H

HH

OHOH OH

H

HO

C O

C C C

Fatty acid

Glycerol

H HH

H H

CH2

O O O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH

CH2

CH2

CH2

CH2

CH2

CH2

CH3

C C C OOO

C C C

H

Figure 3.8B Figure 3.8C

Fatty Acids

Carboxyl group (-COOH) at one end

Carbon backbone (up to 36 C atoms)

Saturated - Single bonds between carbons

Unsaturated - One or more double bonds

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

Unsaturated fatty acids Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

LIPIDS Can be Saturated and unsaturated

depending on the length of the chain and the type of bonds between carbons.

Unsaturated: Double bonds join the carbon atoms. Oily

liquids at room temperatures. Olive, corn, peanut, canola oils

Saturated :single bonds join the carbons. Solid at room temperature. Butter, lard, bacon, chicken fat and all animal fats, triglycerides.

Fats

Fatty acid(s)

attached to

glycerol

Triglycerides are

most common

Phospholipids

Main components of cell

membranes

The structure of phospholipids

Results in a bilayer arrangement found in cell membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

Sterols or steroids Lipids whose carbon chains form 4 rings

Ex; cholesterol

Cholesterol is important in making cell membranes and used to make male and female sex hormones.

Too much cholesterol in your blood can cause atherosclerosis ( lipid deposits, plaques, build up inside the walls of blood vessels)

One steroid, cholesterol

Is found in cell membranes Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

Anabolic steroids Synthetic ( made in the lab) male sex

hormone Causes build up of muscle mass Serious side effects such as:Depression, mood swings, liver damage, cancer,

high blood pressure, stunted growth. In males, reduced testosterone production and sex

drive shrunken testicles, infertility in females, masculine characteristics Illegal to use but some athletes use it

Waxes Long-chain fatty acids linked to long

chain alcohols or carbon rings

Firm consistency, repel water

Important in water-proofing

PROTEINSProteins are macromolecules ( large molecules). Proteins are put together with information stored in your DNA

What are the building blocks of proteins?Amino acidsA protein is a polymer constructed from amino acid monomers

FUNCTIONS OF PROTEINS1. Structural partsEx: providing structural support in the form of collagen (cartilage),

muscle (actin and myosin), hair and nails (keratin), blood,connective tissue

2. Transport Ex: Hemoglobin transports oxygen to all cell of the body

3. Chemical messengers and signals ex: hormones such as growth hormone and neurotransmitters

4. Receptors and channels in cell membranes regulate traffic in and out of cells and allows cells to communicate with

each other

5. Defense against diseasesEx: antibodies and toxins

6. Enzymes facilitate and speed up chemical reactions in cells

FUNCTIONS: Structural parts of cells, forms muscles, blood, skin, hair (keratin),

microfilaments, connective tissue (collagen).

Biocatalysts, enzymes are proteins that facilitate chemical reactions in cells.

Transport proteins. Hemoglobin in blood transports oxygen

Chemical messengers (hormones). Regulate how and when certain processes occur in an organism.

Chemical signals allow cells to communicate with each other (neurotransmitters between nerve cells).

Receptors and channels in cell membranes. Pumps in membranes regulate traffic in and out of cells

Defense against diseases (antibodies)

An overview of protein functions

Table 5.1

HOW ENZYMES FUNCTION?

Enzymes speed up the cell’s chemical reactions by lowering energy barriers

In other words enzymes work by lowering the activation energy, which means lowering the amount of energy needed to get a reaction going.

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.

22

4 Products are released.

Figure 5.16

Protein StructureProteins are composed of amino acids joined together by peptide bonds.

There are 20 different amino acids and the sequence and number of amino acids determines the kind of proteinAmino acids are composed of CHON. some add S (sulphur)

A chain of amino acids is called a polypeptide chain. It is joined by peptide bonds which are formed by dehydration reactions.

PROTEINS Proteins are macromolecules (large) composed

of amino acids joined together by peptide bonds (covalent bonds).

The smaller units, amino acids, form long chains of hundreds of amino acids. (there are 20 amino acids )The proteins of each organism are unique.

Humans proteins are different from dogs and different from fish. The more closely related two organisms are the more their proteins resemble each other.

Amino AcidsThe central molecule is a carbon with an

amino group NH2 and a carboxyl group -COOH attached to it.

Amino Acid Structure

aminogroup

carboxylgroup

R group

The central molecule is Carbon and they have an amino group NH2, or NH3 hydrogens and an acid group –COOH plus a variable functional group ®

How can you make thousands of proteins from 20 amino acids? Different arrangements or sequence

STRUCTURE AND SHAPE The SHAPE of a protein determines its

function.

Heat and extremes in pH “denature” proteins.

Ex: boiling breaks the chemical bonds and the protein changes shape so it can’t work anymore.

Proteins are made up of 20 amino acids in different combinationslinked by peptide bonds.

DenaturationWhat is a denatured protein? Disruption of three-dimensional shape Breakage of weak bonds Destroying protein shape disrupts function, it doesn’t function

What causes denaturation? pH Temperature Excessive salinity

Denaturation

Is when a protein unravels and loses its native conformation

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

Why is it so dangerous to have a very high fever? Denaturation of your enzymes

Since enzymes make all the chemical reactions happen better and faster, the reactions won’t be happening and the body stops functioning.

Protein Conformation and Function A protein’s specific conformation

Determines how it functions

LEVELS OF STRUCTURE The sequence of amino acids in a chain is unique

for each protein and it is called its PRIMARY STRUCTURE.

SECONDARY STRUCTURE: When the primary structure twists, coils or folds.

TERCIARY STRUCTURE:The folded peptide chain folds back on itself forming a three dimensional shape, which in turn determines its function.

QUATERNARY STRUCTURE: The overall structure that results from the aggregation and coiling together of two or more peptide chains. Ex: hemoglobin

Primary Structure Sequence of amino acids

Unique for each protein

Two linked amino acids = dipeptide

Three or more = polypeptide

Backbone of polypeptide has N atoms:

-N-C-C-N-C-C-N-C-C-N-

Primary Structure of protein

The sequence of amino acids in a chain is its primary structure. It is unique for each protein

a.a a.a a.a a.a a.a a.a

Primary Structure A protein’s primary structure

Is the sequence of amino acids forming its polypeptide chains

Levels of Protein Structure

Primary structure GlyThr

Gly GluSer Lys

Cys

Pro

Leu Met

Val

Lys

Val

Leu Asp Ala Val Arg Gly SerPro

Ala

Ile

Asn Val

Ala

ValHis

Val

Amino acids

PheArg

Figure 3.14A

Secondary Structure

Hydrogen bonds form between different parts of polypeptide chain

These bonds give rise to coiled or extended pattern

Helix or pleated sheet

Secondary structure A protein’s secondary structure

Is the coiling or folding of the chain, stabilized by hydrogen bonding

Figure 3.14B

Secondary structure

C

N

O C

C

N H

OC

C

H

Hydrogenbond

O C

N H

C

CO

N H

OC

C

N H

C

N

O C

C

N H

OC

C

N H

CO

C

H

N H

CO

HC R

HN

Alpha helix

CN

H

C C

HH

O

N

RC C

O

N

H

O

CC N

H

C C

O

N

H

O

CC N

H

C

O

CN

H

O

CC N

H

C

O

O

C

C

N

H

C C

O

N

H

CC

O

N

H

C

C

O

N

H

CC

O

N

H

CC

O

N

H

C

C

O

N

H

C

C

O

H

N

C

Pleated sheet

Amino acids

Tertiary Structure

Folding as a

result

of interactions

between R

groups

heme group

coiled and twisted polypeptide chain of one globin molecule

Quaternary Structure

Some proteins

are made up of

more than one

polypeptide chain

Hemoglobin

Quaternary Structure A protein’s quaternary structure

Results from the association of two or more polypeptide chains

Quaternary structure

Transthyretin, withfour identical

polypeptide subunits

Figure 3.14D

Polypeptidechain

Collagen

GrooveGroove

Figure 3.13BFigure 3.13A

A protein’s specific shape determines its function A protein consists of one or more polypeptide chains

Folded into a unique shape that determines the protein’s function

The four levels of protein structure

+H3NAmino end

Amino acidsubunits

helix

Sickle-Cell Disease: A Simple Change in Primary Structure Sickle-cell disease

Results from a single amino acid substitution in the protein hemoglobin

A Permanent Wave

hair wrapped around cuticles

differentbridges form

bridgesbroken

TALKING ABOUT SCIENCE Linus Pauling contributed to our understanding of the chemistry of life

Linus Pauling made important contributions To our understanding of protein structure and

function

Figure 3.15

NUCLEIC ACIDS Nucleic acids are information-rich polymers of nucleotides

Nucleic acids such as DNA and RNA Serve as the blueprints for proteins and thus control

the life of a cell

Nucleic acids store and transmit hereditary information

Genes Are the units of inheritance Program the amino acid sequence of polypeptides Are made of nucleic acids

Stretches of a DNA molecule are called genes

What information is in the genes? Program the amino acid sequences of

proteins

The Roles of Nucleic Acids

There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

DNA

Stores information for the synthesis of specific proteins

Functions of nucleic acids Nucleic Acids store and transmit hereditary

information Organisms inherit DNA from their parents. Each DNA molecule consists of thousands of

genes. DNA provides direction for its own replication When a cell divides DNA is copied and passed to

the next generation of cells.

NUCLEIC ACIDS Nucleic acids are informational polymers a

polymer of nucleotides., their function is to store information.

There are two types of nucleic acids: DNA, dioxiribonucleic acid and RNA,

ribonucleic acid. DNA (and its genes) is passed by heredity The amino acid sequence of a polypeptide

(a proteins) is programmed by a gene. A gene consists of a region of DNA,

DNA directs RNA synthesis.

DNA controls protein synthesis through RNA .

DNA is NOT directly involved in the activities of a cell, the proteins do. Proteins are responsible for implementing the instructions contained in DNAThe flow of genetic information is:From DNA (genes) to RNA to Protein

Structure of Nucleic Acids Nucleic acids are polymers of nucleotides. ( nucleotide

is the monomer)

Each nucleotide consists of three parts and only differ in their bases

A nitrogen base, a 5 carbon (pentose) sugar and a phosphate group.

Nucleotide Functions

Energy carriers Coenzymes

Chemical messengers

Building blocks for nucleic

acids

Sugar Ribose or deoxyribose

phosphate group

Base Nitrogen-containing

Single or double ring structure

Nucleotide Structure

The monomers of nucleic acids are nucleotides Composed of a sugar, phosphate, and nitrogenous

base

Sugar

OH

O P O

O

CH2

H

O

H H

OH H

H

N

N

H

N

N H

HH

N

Phosphategroup

Nitrogenousbase (A)

Some nucleotides function as energy carriers. ATP is an energy carrier One nucleotide, ATP is very important to

metabolism because it can transfer a phosphate group to many other molecules, energizing them to enter a reaction.

Some nucleotides are coenzymes and electron carriers. These enzyme helpers can transfer hydrogen atoms and electrons from molecules to other reaction sites.

Ex: NAD and FAD

The Structure of Nucleic Acids Nucleic acids

Exist as polymers called polynucleotides

(a) Polynucleotide, or nucleic acid

3’C

5’ end

5’C

3’C

5’C

3’ endOH

Figure 5.26

O

O

O

O

The sequence of bases along a nucleotide polymer

Is unique for each gene

DNA and RNA are assembled from four kinds of nucleotides DNA is a double strand while RNA is a single

strand In RNA uracil takes the place of thyamine The nitrogen bases are of two types: purines

and pyrimidines Purines are a double ring structure (have two

rings) . One with 6 and one with 5 components Adenine and Guanine Pyrimidines have only one ring ( 6 members) Cytosine, Thyamine and Uracil

Because of their shape, only some bases are compatible with each other A with T adenine---thyamine G with C guanine---cytosine

DNA

Double-stranded Consists of four

types of nucleotides A bound to T C bound to G

DNA consists of two polynucleotides Twisted around each other in a double helix

C

TA

GC

C G

T A

C G

A T

A

G C

A T

A T

T A

Basepair

T

The sugar and phosphate Form the backbone for the nucleic acid or

polynucleotide

Sugar-phosphatebackbone

T

G

C

T

A Nucleotide

Normal metabolic products of one species

that can harm or kill a different species

Natural pesticides Compounds from tobacco

Compounds from chrysanthemum

Natural Toxins

Negative Effects of Pesticides May be toxic to predators that help fight pests May be active for weeks to years Can be accidentally inhaled, ingested, or

absorbed by humans Can cause rashes, headaches, allergic

reactions