Download 3.1 Organic Molecules

1/24/2011
Essentials of
Biology
Sylvia S. Mader
3.1 Organic Molecules
•
Organic Chemistry
•
•
Chemistry of living world
Organic molecules contain carbon and
hydrogen.
•
Inorganic molecules do not (H2O)
Chapter 3
Lecture Outline
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Figure 3.1 Organic molecules as structural material
Figure 3.2 Hydrocarbons are highly versatile
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
H
H
C
C
H
H
C
C
H
H
H
H
H
H
H
C
C
C
C
H
H
H
H
C
H
H
H
H
Carbon chains can vary in length, and/or have double bonds,
and/or be branched.
H
b.
H
H
H
C
C
H
H
C
H
c.
38,000 a.
a: © Lary Lefever/Grant Heilman Photography; b: © Photodisc/Getty RF; c: © H. Pol/CNRI SPL/Photo Researchers, Inc.
• Carbon atom
 Total of six electrons – 4 in outer shell
 Almost always shares electrons with
CHNOPS to complete outer shell
 Can bond with as many as 4 other elements
 Most often shares electrons with other carbon
atoms
 Hydrocarbons – chains of carbon atoms
bonded only to hydrogen atoms
 Isomers – same number and kinds of atoms
in a variety of arrangements
C
C
H
C
C
H
H
C
H
H
H
H
C
C
C
H
H
Carbon chains can form rings of different sizes and
have double bonds.
• Organic molecules differ in
1. Size and shape of carbon skeleton or backbone
2. Functional group – specific combination of bonded
atoms that always has the same chemical properties
and always reacts the same way
 Reactivity of organic molecule largely dependent on
attached functional groups
 Often use R to stand for the rest of the molecule
• May have different properties
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Functional Groups
Groups
Structure
R
Hydroxyl
O
Found In
H
Figure 3.3
Functional groups
Alcohols, sugars
O
R
C
Carboxyl
4 categories
Amino acids,
fatty acids
O




H
H
R
Amino
Amino acids,
proteins
N
H
Sulfhydryl
R
S
Amino acids
cysteine, proteins
H
3.2 The Biological Molecules of Cells
Carbohydrates
Lipids
Proteins
nucleic acids
H
O
Phosphate
R
O
P
O
ATP
nucleic acids
H
O
R= remainder of molecule
Figure 3.4 Carbohydrates
Figure 3.5 Lipid foods
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Bread
Cheese
Ice cream
Oil
Corn
Potato
Lard
Rice
Butter
Pasta
Figures 3.6 Protein foods
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Meat
Monomers build polymers!
 Monomers – subunits
 Polymer – monomers joined
 Dehydration reaction
• Joins monomers to form polymers
• Equivalent of removing water molecule
Eggs
Milk
Tofu
Beans
Nuts
© The McGraw-Hill Companies, Inc./John Thoeming, photographer
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Figure 3.7 Synthesis of a polymer
Hydrolysis Reaction
 Breaks polymers apart into monomers (digestion)
monomer
monomer
OH
HO
monomer
OH
 Water is used to break the bond.
HO
dehydration reaction
polymer
+
O
a.)
2 H 2O
O
Dehydration synthesis reaction
Figure 3.7b Digestion of a polymer
 Almost universally used as immediate energy
source in living things
polymer
O
• Carbohydrates
 Play structural roles in cells
O
 Polymers of monomers called saccharide or
sugars
2 H 2O
hydrolysis reaction
 Monosaccharide, disaccharide, polysaccharide
monomer
monomer
OH
b.)
H O
monomer
OH
HO
Hydrolysis reaction
Figure 3.8
• Monosaccharides
 Single sugar molecule
 Simple sugars
Glucose
C6H12O6
6CH2OH
 3-7 carbon backbone
H
4C
 Glucose C6H12O6
HO
• 2 isomers – fructose and galactose
• Cells use glucose as energy source of choice
H
OH
3C
H
CH2OH
O
H
2C
OH
a.
O
H
H
H
H
C1
HO
OH
H
H
OH
OH
OH
C6H12O6
b.
O
O
• Ribose and deoxyribose found in RNA and DNA
 Ribose: C5H10O5
5C
Deoxyribose: C5H10O4
c.
d.
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Figure 3.9 Breakdown of maltose, a disaccharide
• Disaccharides
 2 monosaccharides bonded together
 Maltose – yeast breaks down maltose in beer
for energy and produces ethyl alcohol.
O
O
Role of Maltase?
maltose
O
Hydrolysis
H2O
yeast
• Fermentation
O
 Sucrose – table sugar
 Lactose – milk sugar
O
glucose
Fermentation
• Polysaccharides
Figure 3.10 Starch and glycogen structure and function
 Polymers of monosaccharides
starch granule in potato cell
 Some function as energy storage molecules.
nonbranched
• Plants store glucose as starch.
• Animals store glucose as glycogen.
 Some function as structural components.
• Cellulose – plant cell walls
branched
 Most abundant of all organic molecules
 Digested only by some microbes
• Chitin – crab, lobster, insect exoskeletons
Figure 3.10 continued
57
a. Starch structure
Figure 3.10 continued
cellulose fibers in plant cell wall
glycogen granules in liver cell
H bond
20
c. Cellulose structure
highly branched
59,400
b. Glycogen structure
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• Lipids
 All are insoluble in water.
Figure 3.11 Preening in birds
 Due to long nonpolar hydrocarbon chains
 few hydrophilic functional groups
 Very diverse structures and functions
 Fats and oils used for long term energy
storage and insulation
 Oil may help waterproof skin, hair, and
feathers.
• Fats and oils
 Triglyceride composed of 1 glycerol and 3 fatty
acids
Figure 3.12 Synthesis and breakdown of fat
H
H
C
H
H
H
H
H
H
H
OH
HO
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
H
H
H
H
H
H
H
R
O
H
C
OH
+
C
HO
H
H
H
H
H
H
H
C
C
C
C
C
C
C
H
H
H
H
H
H
H
R
H
dehydration
reaction
C
O
C
C
H
H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
C
O
OH
HO
R
H
C
H
O
C
H
H
C
C
C
C
C
C
H
H
H
H
H
H
H
O
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
O
H
hydrolysis
reaction
O
H
O
C
O
C
H
C
C
R
R
+
3 H2O
R
H
Glycerol
Fatty acids are either…
3 Fatty acids
Fat
(triglyceride)
3 waters
Figure 3.13 Fatty acids
 Saturated – no double bonds between
carbon atoms
• Butter is solid at room temperature.
 Unsaturated – one or more double bonds
between carbon atoms
canola oil
• Oils liquid at room temperature
• Trans fatty acids have been artificially
hydrogenated to make them more solid.
bend caused by
double bond
carboxyl group
C18H34O2
a. Oleic acid, a monounsaturated fatty acid (one double bond) found in canola oil .
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Figure 3.13 continued
Figure 3.13 continued
butter
donut
carboxyl group
C18H36O2
b. Stearic acid, a saturated fatty acid (no double bonds) found in butter.
carboxyl group
C18H34O2
c. Elaidic acid, a trans fatty acid (one double bond) found in many snack foods.
R
• Phospholipids
polar head
O
phosphate
group
O–
P
Figure 3.14
Phospholipids from
membranes
O
H
 Form bulk of plasma membrane
 One end of molecule water-soluble
HCH
HC
C
• Polar phosphate head
 Other end of molecule not water-soluble
• Nonpolar fatty acid tails
nonpolar tails
O
O
C
O
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HC
HCH
HCH
glycerol
CH
O
fatty acids
HC
inside of cell
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
H
HCH
HCH
outside of cell
H
a. Phospholipid structure
• Steroids
 Lipids made of four
fused rings
 No fatty acids but
are insoluble in
water
 Derived from
cholesterol
 Differ only in
functional groups
b. Plasma membrane of a cell
• Steroids
 Lipids made of four
fused rings
 No fatty acids but
are insoluble in
water
 Derived from
cholesterol
 Differ only in
functional groups
Figure 3.15 Steroid diversity
H3C
CH3
CH3
CH3
CH3
HO
a. Cholesterol
OH
CH3
CH3
O
b. Testosterone
OH
CH3
HO
c. Estrogen
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Anabolic Steroids
Figure 3.16 Types of
proteins
• Proteins
 Many functions: support,
metabolism (enzymes),
transport, defense,
regulation, and motion
 Synthetic anabolic
steroids are
controversial.
• They are variants of
testosterone.
 Some athletes use
anabolic steroids to
build up their
muscles quickly.
Structural proteins
• pose serious health
risks
Transport proteins
• Proteins composed of amino
acid monomers
Contractile proteins
Figure 3.17 Amino acids
H
H2N
H
COOH
C
H2N
CH
 Central carbon bonded to
hydrogen atom, amino group,
carboxyl group, and a side
chain, or R group
H3C
C
COOH
CH2
CH3
NH
valine (Val)
(nonpolar)
amino
group
 20 different amino acids
carboxyl
group
H
H
N
C
H
H2N
OH
 Differ according to R group
tryptophan (Trp)
(nonpolar)
H
O
C
COOH
C
H
CH2
R
group
H2N
CH2
COOH
CH2
COO–
SH
glutamate (Glu)
(ionized)
cysteine (Cys)
(nonpolar)
Amino acid
a.
C
b.
Figure 3.18
Synthesis and degradation of peptide
• Peptides
 Peptide bond – formed by dehydration
reaction between 2 amino acid monomers
 Peptide – 2 or more amino acids covalently
linked
 Polypeptide – chain of many amino acids
joined by peptide bonds
 Amino acid sequence determines final
three-dimensional shape of protein.
 Protein shape determines its_____?______
peptide
bond
H
H
N
H
C
R
O
H
OH
H
C
R
N
Amino acid
C
O
dehydration
reaction
C
H
H
OH
hydrolysis
reaction
Amino acid
H
H
O
N
C
C
R
R
N
C
H
H
O
H2O
C
OH
Dipeptide
Water
• Peptides
 Peptide bond – formed by dehydration reaction between 2 amino
acid monomers
 Peptide – 2 or more amino acids covalently linked
 Polypeptide– chain of many amino acids joined by peptide bonds
 Protein – chain of more than 100 amino acids
• Structure determines function
 Amino acid sequence determines the three-dimensional shape
of protein.
 Protein shape determines its_____?______
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Protein Shape
Shape of proteins
 Function determined by three-dimensional shape
• Proteins have four levels of structure.
• Denature – loss of structure and function
 A change in pH or temperature may denature a protein
Protein Structure Introduction
• Four Levels of Protein Structure
Primary Protein Structure
 Primary structure – amino acid sequence
Secondary Protein Structure
• Under genetic control – Changes in DNA may affect primary
structure
Tertiary Protein Structure
 Secondary structure – portions of chain form helices or
pleated sheets.
Quaternary Protein Structure
 Tertiary structure – overall three-dimensional shape of
interacting secondary structures
 Quaternary structure – more than one polypeptide chain
interacting
Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings
Levels of protein organization
Figure 3.19
Primary structure: sequence of amino acids
• A change in the
primary structure of
a protein affects its
ability to function.
H
N
H
• Changing one
amino acid in
hemoglobin causes
sickle-cell disease.
Figure 3.19
(cont.)
Secondary structure: alpha helix and pleated sheet
H
C
N
C
C
H
C
N
HO
N
O
O
C C
N
C
H
N
H
C
H
C
N
C
C
C
O
O
N C
O
H
C
C C N C
O
C
N
C
C
O
N C
H
H
Quaternary structure: more than one polypeptide
H
N
H
C
O
alpha helix
Figure 3.19 continued
C C
H
C
pleated sheet
O
N
C
O
hydrogen
bond (red)
• Only one small change (mutation) in the hemoglobin gene
leads to the production of sickle-cell hemoglobin protein
H
C
N
C
C
O
HO
C
O
N C
H
N
C
C
O
H
C N
HO
C
C C N
O
HO
N
C
C
globular shape
H
C N
O
Tertiary structure: overall 3-D shape
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Four levels of Protein
Structure
What Determines the Primary Structure of Protein?
1. Primary Structure
• The order of ________________ in a gene
determines the primary structure of a protein
2. Secondary
Structure
– Gene: segment of DNA that “codes” for the
production of a _______________
– DNA is a nucleic acid
• Let’s learn about nucleic acids
3. Tertiary
Structure
4. Quaternary
Structure
Figure 3.24
• The genetic instructions in DNA
Nucleic Acids
– Must be translated from “nucleic acid language” to
“protein language.”
• Nucleic acids are information storage molecules.
– They provide the directions for building proteins.
• There are two types of nucleic acids:
– DNA, deoxyribonucleic acid
– RNA, ribonucleic acid
Figure 3.20
DNA and RNA are polymers of Nucleotides
C
phosphate
P
5'
4'
nitrogencontaining
base
O
S
1'
•
•
•
•
Each DNA
nucleotide has
one of the
following bases:
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
2'
3'
sugar
Nucleotide: phosphate – sugar – Nitrogen base
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Nitrogen Bases in DNA: A, T, G, C
• Nucleotide monomers are linked into long chains.
– These chains are called polynucleotides, or DNA
strands.
– A sugar-phosphate backbone joins them together.
DNA and RNA Structure
DNA structure with base pairs: G with C and A with T
Figure 3.20
DNA Structure
• Sugar: ?????
H
N
H
O
N
N
H
N
N
O
H
– Complementary base pairing
H
A
T
• Double Helix: Two strands of DNA join together
N
N
C
G
• Bases: ?????
N
Guanine (G)
G
C
A
Cytosine (C)
• Adenine (A) with ______________
H
T
N
N
H
CH3
O
C
N
N
N
H
Hydrogen
bond (red)
Adenine (A)
• Cytosine (C) with ______________
N
N
O
• Genetic information stored in sequence of _??___
Thymine (T)
(DNA only)
DNA Structure
RNA Structure
• Sugar: Deoxyribose
• Ribonucleic Acid
• Bases: A, T, G, C
• Single strand of
RNA nucleotides
• Double Helix: Two strands of DNA join together
– Complementary base pairing
• Adenine (A) with thymine (T)
• Cytosine (C) with guanine (G)
• Genetic information stored in sequence of bases
• Sugar: ribose
• Bases: A, U, G, C
– Uracil (U)
instead of
thymine (T)
RNA Nucleotide
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Figure 3.20 continued
Relationship between proteins and nucleic acids
• Sequence of ______1________in DNA determines sequence of
_________2_______in a protein.
RNA structure with bases G, U, A, C
G
bases
O
P
NH
U
N
P
A
Sugar – Phosphate Backbone
O
Uracil (U)
(RNA only)
• Sequence of ______3_______determines proteins structure and
_____4_______.
• Small changes in the DNA may cause large changes in the
________5________ the DNA codes for.
• Sickle cell disease
P
C
–
Individual’s red blood cells are sickle-shaped.
–
One amino acid difference
–
Inherited disease
P
Relationship between proteins and nucleic acids
Figure 3.21 Sickle cell disease
• Sequence of bases (or nucleotides) in DNA determines sequence
of amino acids in a protein.
• Sequence of amino acids determines proteins structure and
function.
• Small changes in the DNA may cause large changes in the
protein the DNA codes for.
normal red
blood cells
H2N
Val
His
Leu
Thr
Pro
Glu
Glu
Leu
Thr
Pro
Val
Glu
Normal hemoglobin
H2N
Val
His
sickled red blood cell
• Sickle cell disease
–
Individual’s red blood cells are sickle-shaped.
–
One amino acid difference
–
Inherited disease
Sickle cell hemoglobin
© Eye of Science/Photo Researchers, Inc.
Evolution Connection:
DNA and Proteins as Evolutionary Tape Measures
• Evolutionary relationships between organisms can
be assessed.
DNA and
Proteins as
Evolutionary
Tape Measures
• Compare nucleotide sequences in DNA and amino
acid sequences in proteins
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5.2 ATP: Energy for Cells
Figure 5.4 The ATP cycle
• Adenosine triphosphate
 Energy currency for cells
 Cells use ATP to carry out nearly
all activities
 3 phosphate groups makes it
unstable
 Easily loses a phosphate group
to become ADP (adenosine
diphosphate)
 Continual cycle of breakdown
and regeneration
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
ATP
energy for cellular work
(e.g., protein synthesis,
muscle contraction)
energy released during
cellular respiration
Figure 5.3 ATP
ADP +
P
• ATP releases energy quickly
• Amount of energy released is usually just
enough for a biological purpose
• Breakdown can be easily coupled to an energyrequiring reaction
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