Download Introduction to Organic Chemistry

Organic Chemistry
How carbon based molecules
form the basis of life
Introduction
• Although cells are 70-95% water, the rest
consists mostly of carbon-based
compounds.
• Proteins, DNA, carbohydrates, and
lipids are the main carbon based
molecules found in living organisms.
– These other elements commonly include
hydrogen (H), oxygen (O), nitrogen (N), sulfur
(S), and phosphorus (P).
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Organic chemistry is the study of
carbon compounds
• The study of carbon compounds, organic
chemistry, focuses on any compound with
carbon (organic compounds).
– Organic compounds can range from the simple
(CO2 or CH4) to complex molecules, like
proteins.
• Carbon chains form the skeletons of most
organic molecules.
– The skeletons may vary in length and may be
straight, branched, or arranged in closed rings.
• Structure=function discussion
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 4.4
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Organic molecules
• Three of the four classes of macromolecules
form chainlike molecules called polymers.
– Polymers consist of many similar or identical
building blocks linked by covalent bonds.
• The repeated units are small molecules
called monomers.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The chemical mechanisms that cells use to
make and break polymers are similar for all
classes of macromolecules.
• Monomers are connected by covalent bonds
via a condensation reaction or dehydration
synthesis.
– This process requires
energy and is aided
by enzymes.
Fig. 5.2a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The covalent bonds connecting monomers in
a polymer are disassembled by hydrolysis.
– Hydrolysis reactions
dominate the
digestive process,
guided by specific
enzymes.
Fig. 5.2b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Functional Groups
Functional Groups cont.
Basic Review Questions
• Compare and contrast hydrolysis and
dehydration synthesis.
• Define the terms monomer and
polymer. Write an analogy to help you
remember the terms.
Introduction to Carbohydrates
• Carbohydrates are sugars that serve as
fuel and main carbon source.
• The simplest carbohydrates (monomers) are
monosaccharides or simple sugars.
• Disaccharides, double sugars, consist of
two monosaccharides joined by a
condensation reaction.
• Polysaccharides are polymers of
monosaccharides.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Monosaccharides generally have molecular
formulas that are some multiple of CH2O.
– For example, glucose has the formula C6H12O6.
– Most names for sugars end in -ose.
• Two monosaccharides can join to form a
dissaccharide via dehydration synthesis.
– Sucrose, table sugar, is formed by joining glucose and
fructose and is the major transport form of sugars in
plants.
– Lactose, sugar found in milk, is a disaccharide made
from galactose and glucose.
Fig. 5.5a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Starch is a storage polysaccharide
composed entirely of glucose monomers.
– Most monomers are joined by 1-4 linkages
between the glucose molecules.
Fig. 5.6a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Animals also store glucose in a polysaccharide
called glycogen.
• Humans and other vertebrates store glycogen in the
liver and muscles but only have about a one day
supply. Related to diabetes
Fig. 5.6b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Cellulose is a major component of the tough
wall of plant cells.
– Cellulose is also a polymer of glucose
monomers.
Fig. 5.7c
•In a human, the enzymes that digest starch cannot
hydrolyze the bonds in cellulose.
–Cellulose in our food passes through the digestive tract
and is eliminated in feces as “insoluble fiber”.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Carb Review Questions
• Explain the role of carbohydrates for
living things.
• If I gave you a list of chemical names,
how would you be able to identify the
carbohydrates?
• What types of bonds hold polymers of
carbohydrates together?
Introduction to Lipids
• Lipids (fats) are an exception among
macromolecules because they do not have
polymers.
• The unifying feature of lipids is that they all
have little or no affinity for water
(hydrophobic).
• A fat is constructed from two kinds of
smaller molecules, glycerol and fatty acids.
• The major function of fats is energy storage.
– A gram of fat stores more than twice as much
energy as a gram of a polysaccharide.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Building Blocks of Lipids
• Glycerol consists of a three carbon skeleton with
a hydroxyl group attached to each.
• A fatty acid consists of a carboxyl group attached
to a long carbon skeleton, often 16 to 18 carbons
long.
Fig. 5.10a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• In a fat, three fatty acids are joined to glycerol,
creating a triacylglycerol.
• Triglycerides are found in some of the foods we
eat, and are a rich energy source, although can
be linked to heart disease.
Fig. 5.10b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The three fatty acids in a fat can be the
same or different.
• Fatty acids may vary in length (number of
carbons) and in the number and locations of
double bonds.
– If there are no
carbon-carbon
double bonds,
then the molecule
is a saturated fatty
acid - a hydrogen
at every possible
position.
– Food: solid at room temp. Fig. 5.11a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
– If there are one or more carbon-carbon double
bonds, then the molecule is an unsaturated
fatty acid.
– Saturated fatty acids
are straight chains,
but unsaturated fatty
acids have a kink
wherever there is
a double bond.
– Food: tend to be
liquid at room temp
Fig. 5.11b
– The kinks provided by the double bonds prevent
the molecules from packing tightly together.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Phospholipids are major
components of cell membranes
• Phospholipids have two fatty acids attached
to glycerol and a phosphate group at the third
position.
– The phosphate at
the head makes it
hydrophilic
– Fatty acid tails
are hydrophobic
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 5.12
• At the surface of a cell phospholipids are
arranged as a bilayer.
– Again, the hydrophilic heads are on the outside
in contact with the aqueous solution and the
hydrophobic tails from the core.
– The phospholipid bilayer forms a barrier between
the cell and the external environment.
• They are the major component of
membranes.
Fig. 5.12b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Steroids include cholesterol
and certain hormones
• Steroids are lipids with a carbon skeleton
consisting of four fused carbon rings.
– Different steroids are created by varying
functional groups attached to the rings.
– Cholesterol, an important steroid, is a component
in animal cell membranes.
Fig. 5.14
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Lipid Review Questions
• Please list at least three jobs that lipids play
in living organisms.
• Differentiate between saturated and
unsaturated fats. Be able to give an example
of each.
• Compare and contrast the amount of energy
stored in a lipid versus a carbohydrate.
Explain why this might be the case.
Introduction to Proteins
• Proteins are instrumental in about
everything that an organism does.
– These functions include structural support,
storage, transport of other substances,
intercellular signaling, movement, and defense
against foreign substances.
– Proteins are the enzymes in a cell, speeding up
chemical reactions.
• Proteins are the most structurally complex
molecules known.
– Each type of protein has a complex threedimensional shape or conformation.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Amino acid=monomer of a protein
• Amino acids consist of four components
attached
to a central carbon.
• These components include a
hydrogen atom, a carboxyl
group, an amino group, and
a variable R group
(or side chain).
– Differences in R groups
produce the 20 different
amino acids.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• One group of amino acids has hydrophobic
R groups.
Fig. 5.15a
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Another group of amino acids has polar R
groups, making them hydrophilic.
Fig. 5.15b
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The last group of amino acids includes
those with functional groups that are
charged (ionized) at cellular pH.
– Some R groups are bases, others are acids.
Fig. 5.15c
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Amino acids are joined together when a
dehydration reaction removes a hydroxyl
group from the carboxyl end of one amino
acid and a hydrogen from the amino group
of another.
– The resulting covalent bond is called a peptide
bond.
Fig. 5.16
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• All protein polymers are constructed from
the same set of 20 monomers, called amino
acids.
• Polymers of proteins are called
polypeptides.
• A protein consists of one or more
polypeptides folded and coiled into a
specific conformation.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
A protein’s function depends
on its specific conformation
• A functional proteins consists of one or more
polypeptides that have been precisely twisted,
folded, and coiled into a unique shape.
• It is the order of amino acids that determines what
the three-dimensional conformation will be.
Fig. 5.17
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Levels of Organization
• Three levels of structure: primary,
secondary, and tertiary structure, are
used to organize the folding within a single
polypeptide.
• Quarternary structure arises when two or
more polypeptides join to form a protein.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The primary
structure of a protein
is its unique sequence
of amino acids.
– The precise primary
structure of a protein is
determined by
inherited genetic
information.
– Central dogma:
DNA --> RNA --> Protein
Fig. 5.18
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
•Even a slight change in primary structure can affect a
protein’s conformation and ability to function.
•In individuals with sickle cell disease, abnormal
hemoglobins, oxygen-carrying proteins, develop because
of a single amino acid substitution.
Fig. 5.19
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The secondary structure of a protein
results from hydrogen bonds at regular
intervals along the polypeptide backbone.
– Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
Fig. 5.20
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Tertiary structure is determined by a
variety of interactions among R groups and
between R groups and the polypeptide
backbone.
Fig. 5.22
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Quarternary structure results from the
aggregation of two or more polypeptide
subunits.
– Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides.
Fig. 5.23
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 5.24
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 5.25
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Protein Review Questions
• What are the monomers of a protein called?
How many different monomers are there?
• What types of bonds hold the primary
structure of a protein together?
• What types of bonds hold the secondary,
tertiary and quaternary structures of a protein
together?
• Please explain at least two roles of proteins in
living things.
Introduction to Nucleic Acids
• The amino acid sequence of a polypeptide
is programmed by a gene.
• A gene consists of regions of DNA, a
polymer of nucleic acids.
• DNA (and their genes) is passed by the
mechanisms of inheritance. Organisms
inherit DNA from their parents.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Nucleic acids store and
transmit hereditary information
• There are two types of nucleic acids:
ribonucleic acid (RNA) and
deoxyribonucleic acid (DNA).
• DNA provides direction for its own replication.
• DNA also directs RNA synthesis and, through
RNA, controls protein synthesis.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The flow of genetic information is from DNA ->
RNA -> protein (central dogma).
– Protein synthesis occurs
in cellular structures
called ribosomes.
– In eukaryotes, DNA is
located in the nucleus,
but most ribosomes are
in the cytoplasm with
mRNA as an
intermediary.
Fig. 5.28
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
A nucleic acid strand is a polymer of
nucleotides
•
•
Nucleic acids are polymers of monomers
called nucleotides.
Each nucleotide consists of three parts:
1. a nitrogen base
2. a pentose sugar (ribose in RNA, deoxyribose in
DNA)
3. a phosphate group.
– Polynucleotides are synthesized by
connecting the sugars of one nucleotide to
the phosphate of the next with a
phosphodiester bond.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 5.29
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
RNA structure: DNA Structure:
Single Strand Double Helix
Nucleic Acid Review Questions
• What are the monomers of nucleic acids
called? What are the three things the
monomers are composed of?
• Please explain the central dogma of
inheritance.
• Compare and contrast the structures of
DNA and RNA.