Download Organic Chemistry and the Four Classes of Macromolecules PPT

Organic Chemistry
Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based
compounds due to its ability to form large, complex, and
diverse molecules
• Proteins, DNA, carbohydrates, and other molecules that
distinguish living matter are all composed of carbon
compounds
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Carbon: Organic Chemistry
• The study of carbon compounds is called Organic
chemistry (main elements = CHONPS)
• Organic compounds range from simple molecules to
colossal ones
• Most organic compounds contain hydrogen atoms in
addition to carbon atoms with O, N and P among others
thrown in from time to time.
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Carbon has 4 valence electrons,
thus makes 4 bonds
• With four valence electrons, carbon
can form four covalent bonds with a
variety of atoms
• This ability makes large, complex
molecules possible
• In molecules with multiple carbons,
each carbon bonded to four other
atoms has a tetrahedral shape
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Those four bonds can vary…
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Carbon Skeletons Vary
• Carbon chains form the skeletons of most organic molecules and
can vary in length and shape
Functional Groups
A few chemical groups are key to the function of
biomolecules
• Distinctive properties of organic molecules depend
on the carbon skeleton and on the molecular
components attached to it
• A number of characteristic groups can replace the
hydrogens attached to skeletons of organic molecules
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Functional Groups
• FGs are the pieces that
are most commonly
involved in chemical
reactions
• The number and
arrangement of
functional groups give
each molecule its
unique properties
• Let’s meet the FGs
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Hydroxyl
STRUCTURE
(may be written
HO—)
EXAMPLE
Ethanol
Alcohols
(Their specific
names usually
end in -ol.)
NAME OF
COMPOUND
• Is polar as a result
of the electrons
spending more
time near the
electronegative
oxygen atom.
FUNCTIONAL
PROPERTIES
• Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
Carbonyl
STRUCTURE
Ketones if the carbonyl
group is within a
carbon skeleton
NAME OF
COMPOUND
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
EXAMPLE
Acetone
Propanal
• A ketone and an
aldehyde may be
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
groups).
FUNCTIONAL
PROPERTIES
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
NAME OF
COMPOUND
EXAMPLE
• Acts as an acid; can
FUNCTIONAL
PROPERTIES
donate an H+ because the
covalent bond between
oxygen and hydrogen is so
polar:
Acetic acid
Nonionized
Ionized
• Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion.
Amino
STRUCTURE
Amines
NAME OF
COMPOUND
EXAMPLE
•
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Glycine
Nonionized
•
Ionized
Found in cells in the
ionized form with a
charge of 1.
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
•
Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
FUNCTIONAL
PROPERTIES
•
Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
(may be
written HS—)
EXAMPLE
Cysteine
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
•
FUNCTIONAL
Contributes negative
charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
•
Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
Glycerol phosphate
NAME OF
COMPOUND
Methyl
STRUCTURE
Methylated compounds
EXAMPLE
•
Addition of a methyl group FUNCTIONAL
PROPERTIES
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
•
Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
NAME OF
COMPOUND
Example of FG in actionATP: Chemical Energy for Cells
• Adenosine triphosphate (ATP), is made of adenosine
bonded to three phosphate groups. Adding or
removing phosphate groups stores and releases
energy.
• Draw
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Organic Macromolecules:
Carbohydrates, Lipids, Proteins, and Nucleic Acids
The FOUR Classes of Large Biomolecules
• All living things are made of four classes of
biomolecules:
•
•
•
•
Carbohydrates
Lipids
Protein
Nucleic Acids
• Macromolecules are large molecules composed
of thousands of covalently bonded atoms
• Their structure determines their function!!!
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The FOUR Classes of Large Biomolecules
• Macromolecules are polymers, built
from monomers
• A polymer is a long molecule made of many similar building
blocks called monomers
• Three of the four classes of life’s organic molecules are
polymers
– Carbohydrates
– Proteins
– Nucleic acids
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Building polymers
• A dehydration reaction links
monomers together by
removing a water molecule
(leave space for a drawing!)
• Hydrolysis is the reverse,
and disassembles polymers
by adding water
• Why is water important for
food digestion?
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(Draw this!) Dehydration Synthesis
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(Draw this!) Hydrolysis
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Biomolecule 1: Carbohydrates
• Include sugars and sugar polymers called
starches. They provide chemical energy and
building material.
• The simplest carbohydrates are monosaccharides, or
single sugars with formula ratios of 1C:2H:1O used for
quick energy (draw one)
• Carbohydrate macromolecules are polysaccharides,
or chains of sugars; often used to build cell parts or for
energy storage (draw one)
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Sugars: Monosaccharides
• Glucose (C6H12O6) is the most
common monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group
– The number of carbons in the
carbon skeleton
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Sugars: Disaccharides
• A disaccharide is formed when dehydration
reaction joins two monosaccharides
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Synthesizing Maltose & Sucrose
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Types of Polysaccharides
• Starch is a storage
polysaccharide of
plants that consists
entirely of glucose
monomers
• Plants store surplus
starch as granules
within chloroplasts
and other plastids
• The simplest form of
starch is amylose
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Types of Polysaccharides
• Glycogen is a
storage
polysaccharide in
animals (“animal
starch”)
• Humans and other
vertebrates store
glycogen mainly in
liver and muscle cells
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Types of Polysaccharides
• Cellulose is a polysaccharide used to build
plant cell walls
• Like starch, cellulose is a polymer of glucose,
but the glycosidic linkages differ
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Such Elegance!
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Polysaccharide
Random Acts of Biology
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
• Chitin is the structural polysaccharide in animal
exoskeletons (crunch!) and fungi cell walls
(surprise!)
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Biomolecule 2: Lipids
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or no
affinity for water (water fearing)
• Lipids are hydrophobic because they are nonpolar
• The most biologically important lipids are fats,
phospholipids, and steroids
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Fats: Start with a Simple Little
Glycerol Molecule
• Fats are constructed from two
types of smaller molecules:
glycerol and fatty acids
• Glycerol is a three-carbon alcohol
with a hydroxyl group attached to
each carbon
• A fatty acid consists of a carboxyl
group attached to a long carbon
skeleton
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Dehydration Rxn 1: Add a Fatty Acid
• Next, add a “fatty acid” through a dehydration
synthesis reaction
• What makes it an acid? The C double bond O,
single bond OH!
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Dehydration Rxn 2!!
• Next, add a SECOND “fatty acid” through a
dehydration synthesis reaction
Dehydration Reaction THREE!!!
• How many
water
molecules
will it take to
disassemble
this
molecule?
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Saturated or Unsaturated?
• Fats made from
saturated fatty acids
are called saturated
fats, and are solid at
room temperature
• Most animal fats are
saturated (lard)
• Saturated fatty acids have
the maximum number of
hydrogen atoms possible
and no double bonds, so
they are straight
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Saturated or Unsaturated?
• Fats made from
unsaturated fatty acids
are called unsaturated
fats or oils, and are
liquid at room
temperature
• Plant fats and fish fats
are usually unsaturated
• Unsaturated fatty acids
have one or more double
bonds, so they bend
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Fats: Major function is storage!
• The major function of
fats is long-term
energy storage!
• Humans and other
mammals store their
fat in adipose cells
• Adipose tissue also
cushions and
insulates the body
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Phospholipids
• Phospholipids are the
major component of all cell
membranes; b/c the
phosphate head is
hydrophilic and the lipid
tail is hydrophobic, they
self assemble into a bilayer in water (draw)
40
Hydrophobic tails
Hydrophilic head
A Single Phospholipid Molecule
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
(b) Space-filling model
(c) Phospholipid symbol
Steroids
• Steroids are lipids with a carbon skeleton
consisting of four fused rings
• The steroid Cholesterol is a component in animal
cell membranes
• Although cholesterol is essential in animals, high
levels in the blood may contribute to
cardiovascular disease
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Biomolecule 3: Proteins
• Proteins are very diverse.
• Cells are mostly made of Proteins, as they
account for more than 50% of the dry mass of
most cells
• Protein functions include structural support,
storage, transport, cellular communication,
movement, and defense (basically everything
that keeps you alive…)
• Let’s take a look at a few we’ll learn this year!
43
Enzymatic
Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Enzyme
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Storage
Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Ovalbumin
Amino acids
for embryo
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Hormonal
Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
High
blood sugar
Insulin
secreted
Normal
blood sugar
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Defensive
Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Antibodies
Virus
Bacterium
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Transport
Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Transport
protein
Cell membrane
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Receptor
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
Signaling
molecules
Receptor
protein
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Structural
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Collagen
Connective
tissue
60 m
Enzymes
• SPECIAL PROTEIN: Enzymes are protein
catalysts that speed up reactions; they are
reusable and specific to one function (based
on their shape)
51
Protein Monomer
• Amino acids are the
monomers of all
proteins.
• Amino acids differ in
their properties due to
differing side chains,
called R groups
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
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Polypeptides
• Polypeptide chains are made chained
arrangements of the 20 available amino acids
and then folded into proteins.
• A protein consists of one or more polypeptides
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Hydrophobic Amino Acids
Nonpolar side chains; hydrophobic
Side chain
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Hydrophilic Amino Acids
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Electrically charged Amino Acids
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Peptide Bonds
• Amino acids are linked by peptide bonds
(through dehydration synthesis)
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to more
than a thousand monomers (Yikes!)
• Each polypeptide has a unique linear sequence
of amino acids, with a carboxyl end (C-terminus)
and an amino end (N-terminus)
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Peptide Bonds
58
Peptide Bonds
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Protein Structure & Function
• At first, all we have is a string of AA’s bound with
peptide bonds.
• Once the string of AA’s interacts with itself and its
environment (often aqueous), then we have a
functional protein that consists of one or more
polypeptides precisely twisted, folded, and coiled into
a unique shape
• The sequence of amino acids determines a protein’s
three-dimensional structure
• A protein’s structure determines its function
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Protein Structure: 4 Levels
• Primary structure is the amino acid chain pipe
cleaner
• Secondary structure consists of alpha helices
(coils) or beta pleats (folds) coiled/folded pipe
cleaner
• Tertiary structure is determined by interactions
among side chains (IMFs and bonds) within the
helix/pleat pipe cleaner connected to itself with
paper clip
• Quaternary structure consists of multiple
polypeptide chains multiple pipe cleaners
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Primary Structure
• Primary structure,
the sequence of
amino acids in a
protein, is like the
order of letters in a
long word
• Primary structure is
determined by
inherited genetic
information
Secondary Structure
• The coils and folds of
secondary structure
result from hydrogen
bonds between repeating
constituents of the
polypeptide backbone
• Typical secondary
structures are a coil called
an  helix and a folded
structure called a 
pleated sheet
63
Tertiary Structure
• Tertiary structure is determined by interactions
between R groups, rather than interactions
between backbone constituents
• These interactions between R groups include
actual ionic bonds and strong covalent bonds
called disulfide bridges which may reinforce the
protein’s structure.
• IMFs such as London dispersion forces (LDFs
a.k.a. and van der Waals interactions), hydrogen
bonds (IMFs), and hydrophobic interactions
(IMFs) may affect the protein’s structure
64
Tertiary Structure
65
Quaternary Structure
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope
66
Four Levels of Protein Structure Revisited
67
Sickle-Cell Disease:
A change in Primary Structure
• A slight change in primary structure can affect a
protein’s structure and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in
the protein hemoglobin
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Sickle-Cell Disease:
A change in Primary Structure
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Changing Protein Structure
• Proteins are fragile. The environment can affect
protein structure and therefore function.
• Alterations in pH, salt, temperature, etc can
cause a protein to unravel; this is denaturing
and the protein doesn’t function anymore
• A denatured protein is biologically inactive
70
Biomolecule 4: Nucleic Acids
• Nucleic acids store, transmit, and help
express hereditary information
• The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a
gene
• Genes are made of DNA, a nucleic acid
made of monomers called nucleotides
71
Two Types of Nucleic Acids
• There are two types of nucleic
acids
– Deoxyribonucleic acid
(DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its
own replication
• DNA directs synthesis of
messenger RNA (mRNA) and,
through mRNA, controls protein
synthesis
• Protein synthesis occurs on
ribosomes
72
Figure 5.25-1
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
The Components of Nucleic Acids
• Nucleic Acids are made of monomers called
nucleotides, which consist of a nitrogenous
base, a pentose sugar, and a phosphate group
(draw)
76
Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
Nucleoside
Nitrogenous
base
5C
1C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
Phosphate
group
(b) Nucleotide
3C
Sugar
(pentose)
The Devil is in the Details
• Types of nitrogenous bases
– Pyrimidines (cytosine, thymine, and uracil)
have a single ring, that has six-members
– Purines (adenine and guanine) have two rings;
a six-membered ring fused to a five-membered
ring
• DNA vs. RNA nucleotides:
• In DNA, “T” is used and the sugar is deoxyribose; in
RNA, “U” is used and the sugar is ribose
78
The Devil is in the Details
• The backbone of both NAs are made
of phosphate-sugar covalent bonds.
VERY STRONG!
79
The Devil is in the Details
• When NAs link sides it is with hydrogen bonds
between complementary base pairs (A w/ T, C
w/ G). WEAK BOND!
• Complementary pairing can also occur between
two RNA molecules or DNA to RNA
• Note: In RNA, thymine is replaced by uracil (U)
so A and U pair
80
5
3
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
3
5
(a) DNA
Base pair joined
by hydrogen bonding
(b) Transfer RNA