Download Ch.-3-Lecture

Eldra Solomon
Linda Berg
Diana W. Martin
www.cengage.com/biology/solomon
Chapter 3
The Chemistry of Life:
Organic Compounds
Albia Dugger • Miami Dade College
Organic Compounds
• In organic compounds, covalently bonded carbon atoms form
the backbone of the molecule
• The carbon atom forms bonds with more different elements
than any other type of atom
• More than 5 million organic compounds have been identified,
including large macromolecules (e.g. proteins) constructed
from modular subunits (e.g. amino acids)
3.1 CARBON ATOMS AND
ORGANIC MOLECULES
LEARNING OBJECTIVES:
• Describe the properties of carbon that make it the central
component of organic compounds
• Define the term isomer and distinguish among the three
principal isomer types
• Identify the major functional groups present in organic
compounds and describe their properties
• Explain the relationship between polymers and
macromolecules
Properties of Carbon
• A carbon atom can complete its valence shell by forming a
total of four covalent bonds
• Carbon-to-carbon bonds are strong and not easily broken
• Single bonds
• Double bonds
• Triple bonds
• Hydrocarbons (consisting only of carbon and hydrogen) can
exist as unbranched or branched chains, or as rings
Molecular Shapes
• The shape of a molecule is important in determining its
biological properties and function
• Carbon atoms link to one another and to other atoms to
produce a wide variety of 3-D molecular shapes, because
carbon’s four covalent bonds do not form in a single plane
• Freedom of rotation around each carbon-to-carbon single
bond permits organic molecules to assume a variety of
shapes, depending on degree of rotation
Organic Molecules
Fig. 3-1, p. 47
Carbon Bonding
Isomers
• The same components can link in more than one pattern,
generating a wide variety of molecular shapes
• isomers
• Compounds with the same molecular formulas but
different structures and properties
• Usually, one isomer is biologically active, another is not
• Three types: structural isomers, geometric isomers, and
enantiomers
Three Types of Isomers
• structural isomers
• Compounds that differ in covalent arrangements of atoms
• Large compounds have more possible structural isomers
• geometric isomers
• Compounds identical in arrangement of covalent bonds
but different in spatial arrangement of atoms
• enantiomers
• Isomers that are mirror images of each other
Structural Isomers
Geometric Isomers
Enantiomers
Functional Groups
• Hydrocarbons lack distinct charged regions, are insoluble in
water, and cluster together (hydrophobic interactions)
• Replacing one hydrogen with one or more functional groups
(groups that determine types of chemical reactions and
associations in which the compound participates) changes the
characteristics of an organic molecule
Functional Groups (cont.)
• Most functional groups readily form associations (such as
ionic and hydrogen bonds) with other molecules
• Polar and ionic functional groups are hydrophilic because
they associate strongly with polar water molecules
Important Functional Groups
• methyl group
• Nonpolar hydrocarbon group (R—CH3)
• The hydroxyl group (R—OH) is polar because of a strongly
electronegative oxygen atom
• The carbonyl group consists of a carbon atom that has a
double covalent bond with an oxygen atom
• aldehyde has a carbonyl group at the end of the carbon
skeleton (R—CHO)
• ketone has an internal carbonyl group (R—CO—R)
Important Functional Groups (cont.)
• The carboxyl group (R—COOH) consists of a carbon joined
by a double covalent bond to an oxygen, and by a single
covalent bond to another oxygen bonded to a hydrogen
• Carboxyl groups are essential constituents of amino acids
• An amino group (R—NH2) includes a nitrogen atom
covalently bonded to two hydrogen atoms
• Amino groups are components of amino acids and nucleic
acids
Important Functional Groups (cont.)
• The phosphate group (R—PO4H2) can release one or two
hydrogen ions, producing ionized forms with 1 or 2 units of
negative charge
• Constituents of nucleic acids and certain lipids
• The sulfhydryl group (R—SH), an atom of sulfur covalently
bonded to hydrogen, is found in thiols
• Important in proteins
Important Functional Groups
Table 3-1a, p. 50
Important Functional Groups
Table 3-1b, p. 50
Polymers
• Many biological molecules (such as proteins and nucleic
acids) consist of thousands of atoms (macromolecules)
• Most macromolecules are polymers, produced by linking
small organic compounds (monomers)
• Example: 20 monomers (amino acids) in proteins
Polyethylene: A Simple Polymer
Making and Breaking Polymers
• Polymers can be degraded to component monomers by
hydrolysis reactions
• Hydrogen from a water molecule attaches to one
monomer, and hydroxyl from water attaches to the
adjacent monomer
• Monomers become covalently linked by condensation
reactions (aka Dehydration synthesis)
• The equivalent of a molecule of water is removed during
reactions that combine monomers
Condensation and Hydrolysis Reactions
ANIMATION: Condensation and hydrolysis
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KEY CONCEPTS 3.1
• Carbon atoms join with one another or other atoms to form
large molecules with a wide variety of shapes
•
Hydrocarbons
• are nonpolar, hydrophobic molecules
• their properties can be altered by adding functional
groups:
• hydroxyl and carbonyl groups (polar), carboxyl and
phosphate groups (acidic), and amino groups (basic)
ANIMATION: Functional groups
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3.2 CARBOHYDRATES
LEARNING OBJECTIVE:
• Distinguish among monosaccharides, disaccharides, and
polysaccharides
• Compare storage polysaccharides with structural
polysaccharides
Carbohydrates
• Carbohydrates contain carbon, hydrogen, and oxygen atoms
in a ratio of approximately 1C:2H:1O (CH2O)n
• Sugars and starches (energy sources)
• Cellulose (structural component of plants)
• Carbohydrates contain one sugar unit (monosaccharides),
two sugar units (disaccharides), or many sugar units
(polysaccharides)
Monosaccharides are Simple Sugars
• monosaccharides
• Contain three to seven carbon atoms
• A hydroxyl group is bonded to each carbon except one
• One carbon is double-bonded to an oxygen atom
(carbonyl group), forming aldehydes and ketones
Monosaccharides
Glyceraldehyde (C3H6O3)
(an aldehyde)
Dihydroxyacetone (C3H6O3)
(a ketone)
(a) Triose sugars (3-carbon sugars)
Fig. 3-6a, p. 52
Ribose (C5H10O5)
(the sugar component of RNA)
Deoxyribose (C5H10O4)
(the sugar component of DNA)
(b) Pentose sugars (5-carbon sugars)
Fig. 3-6b, p. 52
Glucose (C6H12O6)
(an aldehyde)
Fructose (C6H12O6)
(a ketone)
Galactose (C6H12O6)
(an aldehyde)
(c) Hexose sugars (6-carbon sugars)
Fig. 3-6c, p. 52
Glucose
• Glucose (C6H12O6), the most abundant monosaccharide, is
used as an energy source in most organisms
• During cellular respiration, cells oxidize glucose molecules,
converting stored energy to a form used for cell work
• Homeostatic mechanisms maintain blood glucose levels
Glucose, Fructose, and Galactose
• Glucose and fructose are structural isomers: glucose is an
aldehyde and fructose is a ketone
• Glucose and galactose differ in the arrangement of the atoms
attached to asymmetrical carbon atom 4
• Molecules of glucose and other pentoses and hexoses in
solution are rings rather than extended straight carbon chains
Isomers of Glucose
• Two isomeric forms, differing in orientation of the hydroxyl
(OH) group attached to carbon 1, are important when glucose
rings join to form polymers
• In beta glucose (β-glucose) the hydroxyl group is on the same
side of the plane of the ring as the CH2OH side group
• In alpha glucose (α-glucose), it is on the side opposite the
CH2OH side group
Isomers of Glucose
Disaccharides
• A disaccharide (two sugars) contains two monosaccharide
rings joined by a glycosidic linkage, consisting of a central
oxygen covalently bonded to two carbons, one in each ring
• Common disaccharides:
• Maltose (malt sugar): 2 covalently linked α-glucose units
• Sucrose (table sugar): 1 glucose + 1 fructose
• Lactose (milk sugar): 1 glucose + 1 galactose
Hydrolysis of Disaccharides
Polysaccharides
• A polysaccharide is a macromolecule (a single long chain or
a branched chain) consisting of repeating units of simple
sugars, usually glucose
• Common polysaccharides:
• Starches: Energy storage in plants
• Glycogen: Energy storage in animals
• Cellulose: Structural polysaccharide in plants
Starches
• starch
• Form of carbohydrate used for energy storage in plants
• Polymer consisting of α-glucose subunits
• Starch occurs in two forms
• Amylose (unbranched chain)
• Amylopectin (branched chain)
• Plant cells store starch as granules in amyloplasts
Starch: A Storage Polysaccharide
Amyloplasts
(a) Starch (stained purple) is
stored in specialized organelles,
called amyloplasts, in these cells
of a buttercup root.
Fig. 3-9a, p. 55
Glycogen
• glycogen
• Form in which glucose subunits are stored as an energy
source in animal tissues
• Similar in structure to plant starch but more extensively
branched and more water soluble
• In vertebrates, glycogen is stored mainly in liver and muscle
cells
Cellulose
• cellulose
• Insoluble polysaccharide composed of many joined
glucose molecules
• Structural component of plants (fibers)
• The most abundant carbohydrate
• Some microorganisms digest cellulose to glucose
• Humans lack enzymes to hydrolyze β 1—4 linkages
Cellulose: A Structural Polysaccharide
(a) Cellulose fibers from a cell wall. The
fibers shown in this electron micrograph
consist of bundles of cellulose molecules
that interact through hydrogen bonds.
Fig. 3-10a, p. 56
Carbohydrates With Special Roles
• amino sugars galactosamine and glucosamine
• Present in cartilage
• glycoproteins
• Functional proteins secreted by cells
• glycolipids
• Recognition compounds on surfaces of animal cells
KEY CONCEPTS 3.2
• Carbohydrates are composed of sugar subunits
(monosaccharides), which can be joined to form
disaccharides, storage polysaccharides, and structural
polysaccharides
3.3 LIPIDS
LEARNING OBJECTIVE:
• Distinguish among fats, phospholipids, and steroids, and
describe the composition, characteristics, and biological
functions of each
Lipids
• lipids
• Compounds soluble in nonpolar solvents, and relatively
insoluble in water (hydrophobic)
• Consist mainly of carbon and hydrogen, with few oxygencontaining functional groups
• Biologically important groups of lipids include fatty acids,
phospholipids, carotenoids, steroids, and waxes
• Some lipids are used for energy storage, structural
components of cell membranes, or important hormones
Triacylglycerol
Triacylglycerols (triglycerides or fats)
• Most abundant lipids in living organisms
• Form of reserve fuel storage
• Consists of glycerol joined to three fatty acids
1. glycerol
• A three-carbon alcohol with three hydroxyl (–OH) groups
2. fatty acid
• A long, unbranched hydrocarbon chain with a carboxyl
group (–COOH) at one end
Triacylglycerol: The Main Storage Lipid
ANIMATION: Triglyceride formation
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Saturated and Unsaturated Fatty Acids
• saturated fatty acids
• Contain the maximum number of hydrogen atoms
• Found in animal fat and solid vegetable shortening
• Solid at room temperature
• unsaturated fatty acids
• Include one or more pairs of carbon atoms joined by a
double bond (not fully saturated with hydrogen)
• Tend to be liquid at room temperature
Unsaturated Fatty Acids
• Each double bond produces a bend in the hydrocarbon chain
that prevents close alignment with an adjacent chains
• monounsaturated fatty acids
• Fatty acids with one double bond
• Example: Oleic acid
• polyunsaturated fatty acids
• Fatty acids with more than one double bond
• Example: linoleic acid
Shapes of Fatty Acids
• Saturated
• Monounsaturated
• Polyunsaturated
Trans Fats
• Food manufacturers hydrogenate or partially hydrogenate
cooking oils (convert unsaturated fatty acids to saturated fatty
acids) to make fat more solid at room temperature
• In naturally-occurring unsaturated fatty acids
• the hydrogens on each side of the double bond are on the
same side of the hydrocarbon chain (cis configuration)
• Artificial hydrogenation produces a trans configuration
• solid at room temperature and increases risk of
cardiovascular disease
Trans and Cis Isomers
Phospholipids
• Phospholipids are amphipathic lipids, with one hydrophilic
end and one hydrophobic end
• Hydrophilic head consists of a glycerol molecule,
phosphate group, and organic group (such as choline)
• Hydrophobic tail consist of two fatty acids
• Phospholipids are basic components of cell membranes
• Amphipathic properties of phospholipids cause them to
form lipid bilayers in aqueous (watery) solution
A Phospholipid
A Phospholipid Bilayer
Water
(b) Phospholipid bilayer. Phospholipids form lipid bilayers in
which the hydrophilic heads interact with water and the
hydrophobic tails are in the bilayer interior.
Fig. 3-13b, p. 58
Carotenoids
• carotenoids
• Orange and yellow plant pigments
• Insoluble in water, with an oily consistency
• Function in photosynthesis
• Consist of 5-carbon hydrocarbon monomers (isoprene
units)
• Most animals convert carotenoids to vitamin A, which can be
converted to the visual pigment retinal
Isoprene-Derived Compounds
Steroids
• steroid
• Consists of carbon atoms arranged in four attached rings
• Side chains distinguish one steroid from another
• Synthesized from isoprene units
• Steroids of biological importance include cholesterol, bile
salts, reproductive hormones, cortisol and other hormones
secreted by the adrenal cortex
• Plant cell membranes contain molecules similar to cholesterol
Steroids
Chemical Mediators
• Some chemical mediators (used for communication or
internal regulation) are produced by modification of fatty acids
removed from membrane phospholipids
• Lipid chemical mediators include prostaglandins and certain
hormones
KEY CONCEPTS 3.3
• Lipids store energy (triacylglycerols) and are the main
structural components of cell membranes (phospholipids)
3.4 PROTEINS
LEARNING OBJECTIVES:
• Give an overall description of the structure and functions
of proteins
• Describe the features that are shared by all amino acids
and explain how amino acids are grouped into classes
based on the characteristics of their side chains
• Distinguish among the four levels of organization of
protein molecules
Proteins
• proteins
• Macromolecules composed of amino acids
• Characteristic forms, distributions, and amounts of protein
determine what a cell looks like and how it functions
• Most enzymes are proteins
• enzymes
• Molecules that accelerate chemical reactions that take
place in an organism
Protein Functions
Table 3-2, p. 60
Amino Acids
• amino acids
• Subunits of proteins
• Have an amino group (NH2) and a carboxyl group (COOH)
bonded to the alpha carbon
• Amino acids in solution at neutral pH are mainly dipolar ions
• Each COOH donates a proton and becomes COO• Each NH2 accepts a proton and becomes NH3+
Amino Acid at pH 7
Fig. 3-16, p. 61
Amino Acids in Proteins
• Twenty amino acids are found in most proteins, identified by a
variable side chain (R group) bonded to the α carbon
• Amino acids are grouped by properties of their side chains
• Nonpolar side chains are hydrophobic
• Polar side chains are hydrophilic
• A side chain with a carboxyl group is acidic
• A side chain that accepts a hydrogen ion is basic
• Some proteins have additional amino acids
20 Common Amino Acids
20 Common Amino Acids
20 Common Amino Acids
20 Common Amino Acids
20 Common Amino Acids
20 Common Amino Acids
Essential Amino Acids
• Animal cells can manufacture some, but not all, biologically
significant amino acids
• essential amino acids
• Amino acids an animal can’t synthesize in amounts
sufficient to meet its needs and must obtain from the diet
• Differs in different species
• Nine essential amino acids for adult humans:
• Isoleucine, leucine, lysine, methionine, phenylalanine,
threonine, tryptophan, valine, histidine
Peptide Bonds
• Amino acids combine chemically by a condensation reaction
between the carboxyl carbon of one amino acid and the
amino nitrogen of another amino acid
• Two amino acids combine to form a dipeptide
• A longer chain of amino acids is a polypeptide
• peptide bond
• Covalent carbon-to-nitrogen bond linking two amino acids
Peptide Bonds
ANIMATION: Peptide bond formation
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Polypeptides and Proteins
• A protein consists of one or more polypeptide chains, with
hundreds of amino acids joined in a specific linear order
• The 20 types of amino acids in proteins are like letters of a
protein alphabet; each protein is a very long sentence made
up of amino acid letters
• An almost infinite variety of protein molecules is possible,
differing in number, types, and sequences of amino acids
Protein Shape
• Polypeptide chains are twisted or folded to form a protein with
a specific conformation (3-D shape)
• Some form long fibers
• Globular proteins are folded into spherical shapes
• A protein’s function is determined by its conformation
• An enzyme’s shape allows it to catalyze a specific
chemical reaction
• A protein hormone’s shape allows it to combine with
receptors on its target cell
Four Levels of Protein Organization
• There are four main levels of protein organization: primary,
secondary, tertiary, and quaternary
• primary structure
• The sequence of amino acids in a polypeptide chain
• Specified by instructions in a gene
• Higher orders of structure (secondary, tertiary, quaternary)
derive from interactions among the specific amino acids in the
sequence (primary structure)
Primary Structure of a Polypeptide
• Glucagon, a very small polypeptide made up of 29 amino
acids, represented in a linear, “beads-on-a-string” form
• One end has a free positive ion (NH3+) ; the other has a free
negative ion (COO-)
Fig. 3-19, p. 64
Levels of Protein Organization (cont.)
• secondary structure
• Two common types: α-helix and β-pleated sheet
• Both types may occur in the same polypeptide chain
1. α–helix (helical coil)
• Hydrogen bonds form between oxygen and hydrogen
• Basic structural unit of fibrous, elastic proteins
2. β-pleated sheet
• H-bonds form between regions of polypeptides chains
• Proteins are strong and flexible, but not elastic
Secondary Structure of a Protein
ANIMATION: Secondary and tertiary
structure
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Levels of Protein Organization (cont.)
• tertiary structure
• Overall 3-D shape of an individual polypeptide chain
• Determined by four main factors involving interactions
among R groups of the same polypeptide chain
• Four factors in tertiary structure:
• 3 weak interactions (hydrogen bonds, ionic bonds, and
hydrophobic interactions)
• Strong covalent bonds (disulfide bridges between
sulfhydryl groups of two cysteines)
Tertiary Structure of a Protein
Levels of Protein Organization (cont.)
• quaternary structure
• 3-D structure resulting from two or more polypeptide
chains interacting in specific ways to form a biologically
active molecule
• Examples:
• Hemoglobin, a globular protein consisting of 4 polypeptide
chains (2 alpha chains and 2 beta chains)
• Collagen, a fibrous protein with 3 polypeptide chains
Quaternary Structure of a Protein
Amino Acid Sequence
Determines Conformation
• In vitro, a polypeptide spontaneously folds into its normal,
functional conformation
• In vivo (within the living), proteins (molecular chaperones)
mediate the folding of other protein molecules
• Molecular chaperones
• are thought to make the folding process more efficient,
and to prevent partially folded proteins from becoming
inappropriately aggregated
Protein Conformation
Determines Function
• Overall structure of a protein determines biological activity
• Biological activity can be disrupted by a change in amino acid
sequence that results in change in protein conformation
• Example: sickle cell anemia
Protein Conformation
Determines Function (cont.)
• Denaturation of a protein:
• When a protein is heated, subjected to significant pH
change, or treated with certain chemicals, its structure
becomes disordered and peptide chains unfold
• Change in shape is typically accompanied by loss of
normal function (biological activity)
• Denaturation generally cannot be reversed
Misfolded Proteins in Human Diseases
• Studies of protein folding, and the relationship between
protein activity and conformation, are of medical importance
• Serious diseases in which misfolded proteins play an
important role include mad cow disease and related diseases
in humans (caused by misfolded proteins called prions),
Alzheimer’s disease, and Huntington’s disease
KEY CONCEPTS 3.4
• Proteins have multiple levels of structure and are composed
of amino acid subunits joined by peptide bonds
3.5 NUCLEIC ACIDS
LEARNING OBJECTIVES:
• Describe the components of a nucleotide
• Name some nucleic acids and nucleotides, and discuss
the importance of these compounds in living organisms
Nucleic Acids
• Nucleic acids transmit hereditary information and determine
what proteins a cell manufactures
• Deoxyribonucleic acid (DNA)
• Composes the hereditary material of the cell (genes)
• Contains instructions for making proteins and RNA
• Ribonucleic acid (RNA)
• Used in processes that link amino acids form polypeptides
• Ribozymes act as specific biological catalysts
Nucleotides
• Nucleic acids are polymers of nucleotides
• Nucleotides are made up of three parts:
1. A five-carbon sugar, either deoxyribose (in DNA) or
ribose (in RNA)
2. One or more phosphate groups (make the molecule
acidic)
3. A nitrogenous base (nitrogen-containing ring compound)
Nitrogenous Bases
• Nitrogenous base may be either a double-ring purine or a
single-ring pyrimidine
• DNA contains four nitrogenous bases:
• Two purines: adenine (A) and guanine (G)
• Two pyrimidines: cytosine (C) and thymine (T)
• RNA contains the purines adenine and guanine, and the
pyrimidines cytosine and uracil (U)
Purines and Pyrimidines
Nucleic Acid Structure
• Nucleic acids are chains of nucleotides joined by
phosphodiester linkages (a phosphate group and covalent
bonds that attach it to sugars of adjacent nucleotides)
• RNA is usually composed of one nucleotide chain
• DNA consists of two nucleotide chains held together by
hydrogen bonds in a double helix
RNA: A Nucleic Acid
• A nucleic acid molecule
is uniquely defined by
its specific sequence of
nucleotides, which acts
as a code
Nucleotide
Uracil
Adenine
Phosphodiester
linkage
Cytosine
Guanine
Fig. 3-24, p. 69
Nucleotides and Energy
• adenosine triphosphate (ATP)
• Composed of adenine, ribose, and three phosphates
• Primary energy molecule of all cells
• Is converted to cyclic adenosine monophosphate
(cyclic AMP, or cAMP) by the enzyme adenylyl cyclase
• guanosine triphosphate (GTP)
• Transfers energy by transferring a phosphate group
• Cyclic guanosine monophosphate (cGMP), has a role
in certain cell signaling processes
Cyclic Adenosine
Monophosphate (cAMP)
• The single phosphate
is part of a ring
connecting two regions
of the ribose
Fig. 3-25, p. 69
Dinucleotides
• nicotinamide adenine dinucleotide
• Primary role in oxidation and reduction reactions in cells
• Oxidized form (NAD+) is converted to a reduced form
(NADH) when it accepts electrons
• NADH transfers electrons, along with their energy, to other
molecules
KEY CONCEPTS 3.5
• Nucleic acids (DNA and RNA) are informational molecules
composed of long chains of nucleotide subunits
• ATP and some other nucleotides have a central role in energy
metabolism
ANIMATION: Nucleotide subunits of DNA
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3.6 IDENTIFYING
BIOLOGICAL MOLECULES
LEARNING OBJECTIVE:
• Compare the functions and chemical compositions of the
major groups of organic compounds: carbohydrates,
lipids, proteins, and nucleic acids
Classes of Biologically Important Organic
Compounds
Classes of Biologically Important Organic
Compounds
Table 3-3c, p. 70