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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
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