Transcript Carbon Based Macromolecules Organic Chemistry

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 air
How 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
H
C
C
H
H
H
H
H
H
H
C
C
C
H
H
H
Ethane
H
Propane
Carbon skeletons vary in length.
H
C
H
H
H
H
C
C
H
H
H
H
C
C
H
H
H
H
H
H
H
C
C
C
H
H
H
Butane
H
Isobutane
Skeletons may be unbranched or branched.
H
H
H
H
H
C
C
C
C
H
H
H
H
H
H
H
H
C
C
C
C
H
H
H
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
H
H
H
H
H
C
C
C
H
H
C
C
C
H
C
H
C
H
H
C
H
C
H
C
C
H
H
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Figure 3.1A
H
H
H
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
Structural
formula
Ball-and-stick
model
H
H
C
Space-filling
model
H
H
H
Methane
C
H
H
H
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 Groups
Hydroxyl group
Amino group
Carboxyl group
Phosphate group
- OH
- NH3+
- COOH
- 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
HYDROLYSIS
enzyme action at functional groups
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
OH
OH
Short polymer
Unlinked monomer
Dehydration
Dehydratio
reaction
n reaction
H2O
OH
O
H
H
H
Longer polymer
Figure 3.3A
H
H
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
Carbohydrates
SUGARS and STARCHES




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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
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Glycogen


Consists of glucose monomers
Is the major storage form of glucose in animals
Mitochondria
Giycogen
granules
0.5 m
Glycogen
Figure 5.6 (b) Glycogen: an animal polysaccharide
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
O
O
O
O
O
GLYCOGEN
O O
Cellulose fibrils in
a plant cell wall
O
O
O
O
O
O
O
O
O
O
CELLULOSE
OO
OO
O OH
OO
O OH
OO
O
OO
Figure 3.7
O
O O
O
Cellulose
molecules
O
O
O
Glycogen
granules in
muscle
tissue
Glucose
monomer
STARCH
Starch granules in
potato tuber cells
OO
OO
O O
O
O O
O
Cellulose
Is a major component of the tough walls that enclose plant
cells

Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
Figure 5.8
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH CH2OH
2
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
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
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Chitin, another important structural
polysaccharide
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
Is found in the exoskeleton of arthropods
Can be used as surgical thread
CH2O
H
O OH
H
H
OH H
OH
H
H
NH
C
O
CH3
(a) The structure of the (b) Chitin forms the exoskeleton
of arthropods. This cicada
chitin monomer.
is molting, shedding its old
exoskeleton and emerging
in adult form.
Figure 5.10 A–C
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
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
Lipids

Tend to be insoluble in water
Most include fatty acids
Fats and oils
Phospholipids
Waxes
Sterols - have no fatty acids
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.

Lipids
Structure:

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
H
C
H
OH
H
C
OH
H
C
OH
O C
HO
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
Fatty acid
(palmitic acid)
H
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
O
H
H
C
O
C
H
C
H
O
H
C
O
C
H
C
H
O
H
C
H
Figure 5.11
O
C
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
(b) Fat molecule (triacylglycerol)
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
H
C
H
H
C
H
H
H

Fats, also called triglycerides


Are lipids whose main function is energy storage
Consist of glycerol linked to three fatty acids
H
H
H
H C
C
OH OH
HO
Figure 3.8B
H
C H
OH
Glycerol
C O
H2O
CH2
CH2
CH2
CH2
CH2
Fatty acid
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
Figure 3.8C
H
H
H
C
C
C
O
O
O
C
O C
O C
H
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH3
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH3
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
Stearic acid
Figure 5.12 (a) Saturated fat and fatty acid

Unsaturated fatty acids

Have one or more double bonds
Oleic acid
Figure 5.12
(b) Unsaturated fat and fatty acid
cis double bond
causes bending
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
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
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
H3C
CH3
CH3
Figure 5.15
HO
CH3
CH3
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
PROTEINS
Proteins are macromolecules ( large molecules).
Proteins are put together with information stored in your
DNA
What are the building blocks of proteins?
Amino acids
A protein is a polymer constructed from amino acid
monomers
FUNCTIONS OF PROTEINS
1. Structural parts
Ex: 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 diseases
Ex: 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)

le 5.1
An overview of protein functions
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
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
Protein Structure
Proteins 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 protein
Amino 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 Acids
The central molecule is a carbon with an
amino group NH2 and a carboxyl group COOH attached to it.
Amino Acid Structure
carboxyl
group
amino
group
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.
Denaturation
What 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
Normal protein
Figure 5.22
Denatured protein
Renaturation
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
Leu Met
Asn Val
Pro
Val
Cys
Gly Glu
Primary structure
Thr
Gly
Ser Lys
Lys
Val
Arg
Ala
Pro
Leu Asp Ala Val Arg Gly
Ser
Amino acids
Figure 3.14A
Ala
Ile
Val
His
Phe
Val
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
Amino acids
Hydrogen
bond
O H
C
H
C
R
C
C
N H
N
O
C
H
O
C
C
N
O
H
O
C
N H
C
O
O
C
N
H O
C
N H
O C
N
O
C
CN
H
O
N
C
H
CC
N
O
H
H
C
C N
C
H
C N
H
O
CC
C
H
O
N
C
O
C
H
C
N
C
H
C
O
O
C R
H
H
CC N C
CN
C
C
C
Secondary structure
H
N
H
CC
H
N H
C
O
N H
O C
O
C C
N
N
O
O
H
N
C N C
C
O
CN
C
H
O
C
H
C
N
C
H
O
Alpha helix
Figure 3.14B
Pleated sheet
N
C
Tertiary Structure
heme group
Folding as a
result
of interactions
between R
groups
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
Polypeptide
chain
Quaternary structure
Transthyretin, with
four identical
polypeptide subunits
Figure 3.14D
Collagen
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
Groove
Figure 3.13A
Groove
Figure 3.13B
The four levels of protein structure
+H
3N
Amino end
Amino acid
subunits
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
bridges
broken
hair wrapped
around cuticles
different
bridges
form
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 DNA
The 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
Nucleotide Structure

Sugar



Ribose or deoxyribose
phosphate group
Base

Nitrogen-containing

Single or double ring structure

The monomers of nucleic acids are nucleotides

Composed of a sugar, phosphate, and nitrogenous
base
H
H
N
N
N
H
OH
O
P
N
O
CH2
Nitrogenous
base (A)
O
O
Phosphate
group
H
H
H
H
OH
Sugar
N
H
H
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
5’ end
5’C
O
3’C
O
O
5’C
O
3’C
OH
Figure 5.26
3’ end
(a) Polynucleotide,
or nucleic acid
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
A
C
C
T
G
G
A
T
C
G
A
T
T
A
Base
pair
G
T
A
A
T
A
C
T

The sugar and phosphate

Form the backbone for the nucleic acid or
polynucleotide
A
T
C
G
T
Sugar-phosphate
backbone
Nucleotide
Natural Toxins

Normal metabolic products of one species
that can harm or kill a different species

Natural pesticides

Compounds from tobacco

Compounds from chrysanthemum
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