BIO151 - CH 3
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Chapter 3
The Chemistry of Organic Molecules
1
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2
3.1 Organic Molecules
• Organic molecules § carbon § hydrogen atoms.
• 4 Classes (biomolecules) exist in living organisms:
§ Carbohydrates § Lipids § Proteins § Nucleic Acids
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3
Inorganic versus Organic Molecules
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Carbon Chemistry § Carbon is a versatile atom. • It has four electrons in an outer shell that holds eight
electrons. • Carbon can share its electrons with other atoms to form
up to FOUR covalent bonds.
C
?
?
? ?
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Figure 3.1a
Carbon skeletons vary in length
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Figure 3.1b
Double bond
Carbon skeletons may have double bonds, which can vary in location
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Figure 3.1c
Carbon skeletons may be:
unbranched branched
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Figure 3.1d
Carbon skeletons may be arranged in rings
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§ The simplest organic compounds are hydrocarbons, which contain only carbon and hydrogen atoms.
§ The simplest hydrocarbon is methane, a single carbon atom bonded to four hydrogen atoms.
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10
The Carbon Skeleton and Functional Groups
• The carbon chain of an organic molecule is called its skeleton or backbone.
• Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structures and functions.
§ Determine the chemical reactivity and polarity of organic molecules
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Table 3.2
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Isomers
• Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms.
Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
glyceraldehyde dihydroxyacetone
OH OH
H H
H C C C H
O
OH OH
H O
H C C C H
H
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Biomolecules
• Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. § Usually consist of many repeating units
• Each repeating unit is called a monomer. • A molecule composed of monomers is called a polymer (many parts). – Example: amino acids (monomer) are joined together to form a protein (polymer)
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Fig. 3.3
Biomolecules
Polymer Category Subunit(s)
Polysaccharide Carbohydrates* Monosaccharide
Lipids
Proteins*
Nucleic acids*
Glycerol and fatty acids Fat
Polypeptide Amino acids
Nucleotide DNA,RNA
*Polymers © The McGraw Hill Companies, Inc./John Thoeming, photographer
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15
Synthesis and Degradation
• A dehydration reaction is a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is LOST during the reaction. § Used to connect monomers together to make polymers § Example: formation of starch (polymer) from glucose subunits (monomer)
• A hydrolysis reaction is a chemical reaction in which a water molecule is ADDED to break a covalent bond. § Used to breakdown polymers into monomers § Example: digestion of starch into glucose monomers
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monomer OH
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Synthesis and Degradation of Biomolecules
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monomer OH +
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+ monomer H monomer OH
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Synthesis and Degradation of Biomolecules
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monomer monomer
H2O
OH H +
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monomer monomer
monomer monomer
Dehydration reaction
H2O
OH H
a. Synthesis of a biomolecule
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+
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monomer monomer
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H2O
monomer monomer
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monomer monomer
Dehydration reaction
H2O
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monomer monomer
Hydrolysis reaction
OH H
b. Degradation of a biomolecule
H2O
monomer monomer
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monomer monomer
monomer monomer
dehydration reaction
monomer monomer
H 2 O
OH H
OH H
b. Degradation of a biomolecule
a. Synthesis of a biomolecule
H 2 O
monomer monomer
hydration reaction
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Synthesis and Degradation
• Enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions.
§ An enzyme is a molecule that speeds up a chemical reaction. • Enzymes are not consumed in the reaction. • Enzymes are not changed by the reaction.
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CARBOHYDRATES & LIPIDS Properties of:
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3.2 Carbohydrates
• Functions: § Energy source § Provide building material (structural role)
• Contain carbon, hydrogen and oxygen in a 1:2:1 ratio
• Varieties: monosaccharides, disaccharides, and polysaccharides
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• A monosaccharide is a single sugar molecule. • Also called simple sugars • Have a backbone of 3 to 7 carbon atoms • Examples:
§ Glucose (blood), fructose (fruit) and galactose • Hexoses -‐ six carbon atoms
§ Ribose and deoxyribose (in nucleotides) • Pentoses – five carbon atoms
Monosaccharides
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Fig. 3.6
H
C
HO a.
H OH
OH
6
5
4
3
1
c. d.
O O
H O H
H H
OH OH
OH H
HO b.
C6H12O6
CH2OH CH2OH C
C
H O
C 2 C
OH H
H
© Steve Bloom/Taxi/Getty
Glucose
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31
Disaccharides
• A disaccharide contains two monosaccharides joined together by dehydration synthesis.
• Examples: § Lactose (milk sugar) is composed of galactose and glucose.
§ Sucrose (table sugar) is composed of glucose and fructose.
§ Maltose is composed of two glucose molecules.
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O O
OH glucose C6H12O6
HO
H H +
CH2OH CH2OH
glucose C6H12O6
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Synthesis and Degradation of Maltose
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glucose C6H12O6
CH2OH O O
OH HO
H H
+ dehydration reaction
glucose C6H12O6
CH2OH
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O O O O
OH water
HO
H H O + +
dehydration reaction H2O
maltose C12H22O11 glucose C6H12O6
CH2OH CH2OH CH2OH CH2OH
glucose C6H12O6
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O O O O
OH water
monosaccharide disaccharide water
HO
H H O
monosaccharide
+
+ +
+ de h yd r ation reaction
H2O
maltose C12H22O11 glucose C6H12O6
CH2OH CH2OH CH2OH CH2OH
glucose C6H12O6
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O O
O
maltose C12H22O11
CH2OH CH2OH
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O O
water
O + H2O
maltose C12H22O11
CH2OH CH2OH
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maltose C12H22O11
CH2OH O O
water
O + hydrolysis reaction
H 2 O
CH2OH
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O O O O
OH
water HO
H H O + +
hydrolysis reaction H2O
maltose C12H22O11 glucose C6H12O6
CH2OH CH2OH CH2OH CH2OH
glucose C6H12O6
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O O O O
OH water
monosaccharide disaccharide water
HO
H H O
glucose C6H12O6
monosaccharide
+
+ +
+ hydrolysis reaction H2O
maltose C12H22O11
CH2OH
glucose C6H12O6
CH2OH CH2OH CH2OH Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
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glucose C6H12O6 water
monosaccharide disaccharide water monosaccharide + +
dehydration reaction hydrolysis reaction
maltose C12H22O11 glucose C6H12O6
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Polysaccharides
• A polysaccharide is a polymer of monosaccharides. • Examples:
§ Starch provides energy storage in plants. § Glycogen provides energy storage in animals. § Cellulose is found in the cell walls of plants. § Chitin is found in the cell walls of fungi and
exoskeleton of some animals. § Peptidoglycan is found in the cell walls of bacteria.
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a. Starch
b . Glycogen
Amylose: nonbranched starch granule
glycogen granule
Amylopectin: branched
150 nm
250 m
Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
a: © Jeremy Burgess/SPL/Photo Researchers, Inc.; b: © Don W. Fawcett/Photo Researchers, Inc.
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3.3 Lipids
• Lipids are varied in structure. • Large nonpolar molecules that are insoluble in water • Functions:
§ Long-term energy storage § Structural components § Cell communication and regulation § Protection
• Varieties: fats, oils, phospholipids, steroids, waxes
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Triglycerides: Long-‐Term Energy Storage
§ Also called fats and oils § Functions: long-‐term energy storage and insulation
§ Consist of ONE glycerol molecule linked to THREE fatty acids by dehydration synthesis
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C H H
C H
C H H
OH
OH
OH
glycerol a. Formation of a fat
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+
C H H
C H
C H H
C O
C O
H
H
H H H H H
H C C C C C
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
OH
OH
OH C O H
H H H H
H C
C C C C
H H H
in
HO
HO
HO
3 fatty acids glycerol a. Formation of a fat
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3 H2O
3 H2O
+
C H H
C H
C H H
C O C O
H
H
H H H H H
H C C C C C
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
OH
OH
OH C O H
H H H H
H C
C C C C
H H H
in
HO
HO
HO
3 water molecules
3 fatty acids glycerol a. Formation of a fat
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
in
3 H2O
3 H2O
+
C H H
C H C H H
C O C O C O
H
H
H H
C C C C C
H H H H H
H
H H H H H
H H H H H H H
C C
H H
H
H H
H H H H H
C C C C C
C C C C C
H H H
H
H
H H H H H
H C C C C C
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 H H H H
H C
C C C C
H H H
in
OH
OH
OH HO
HO
HO
H
H
H
H
C
C
C O
H
O C O O C
H
O C
fat molecule 3 water molecules
3 fatty acids glycerol a. Formation of a fat
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• Fatty acids are either unsaturated or saturated. § Unsaturated -‐ one or more double bonds between carbons • Tend to be liquid at room temperature
– Example: plant oils
§ Saturated -‐ no double bonds between carbons • Tend to be solid at room temperature
– Examples: butter, lard
Triglycerides: Long-Term Energy Storage
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Fig. 3.10
in
3 H2O
3 H2O
+
C H H
C H
C H H
C O C O
C H H H H C H
C H C H H C O
C H H C H
H C H H C H
C H C H H C
H C H C H
H C H C H
C H H C H
H H
C H H H C H
H H H C H C H
C H H C O
C H H C H
H C H H C H
H H H C H C H
C H H C H
H C H H C H
H
C O
H
H
H H
C C C C C
H H H H H
H
H H
H H H
H H H H H H H
C C
H H
H
H H
H H H H H
C C C C C
C C C C C
H H H
H
H
H H H H H
H C C C C C
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 H
H H H
H C
C C C C
H H H
in
OH
OH
OH HO
HO
HO
HO
HO
unsaturated fat
unsaturated fatty acid with double bonds (yellow)
corn corn oil
butter
H
H
H
H
C
C
C O
H
O C
O
O C
H
O C
fat molecule 3 water molecules
3 fatty acids glycerol a. Formation of a fat
Types of fatty acids b. Types of fats c.
saturated fat saturated fatty acid with no double bonds
mil
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• Most animal fats • have a high proportion of saturated fatty acids, • can easily stack, tending to be solid at room
temperature, and • contribute to atherosclerosis, in which lipid-containing
plaques build up along the inside walls of blood vessels.
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§ Most plant and fish oils tend to be • high in unsaturated fatty acids • liquid at room temperature • Good source of dietary fats
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Phospholipids: Membrane Components • Structure is similar to triglycerides
§ Consist of ONE glycerol molecule linked to TWO fatty acids and a modified phosphate group • The fatty acids are nonpolar and hydrophobic. • The modified phosphate group is polar and hydrophilic.
• Function: form plasma membranes • In water, phospholipids aggregate to form a lipid bilayer. § Polar phosphate heads are oriented towards the water. § Nonpolar fatty acid tails are oriented away from water.
• Nonpolar fatty acid tails form a hydrophobic core.
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Fig. 3.11
.
O
R O P O 3 O
Polar Head
glycerol
fatty acids
phosphate
Phospholipid structure a.
Nonpolar Tails
b. Plasma membrane of a cell
CH2 CH2 CH2
O O C CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3
CH2
O
C CH2 CH2 CH2 CH2 CH2 CH2
insi
de c
ell
outs
ide
cel
l
CH
1 2
Phospholipids Form Membranes
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• Composed of four fused carbon rings § Various functional groups attached to the carbon skeleton
• Functions: component of animal cell membrane, regulation • Cholesterol makes the bilayer stronger, more flexible but less fluid, and less permeable to water-‐soluble substances such as ions and monosaccharides.
• Examples: cholesterol, testosterone, estrogen
• Cholesterol is the precursor molecule for several other steroids.
Steroids: Four Fused Carbon Rings
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b . T e s t o s t e r o n e
HO a. Cholesterol
c. Estrogen
OH CH3
O
CH3
OH CH3
CH3
HC CH3
HC CH3
HO
(CH2)3
© Ernest A. Janes/Bruce Coleman/Photoshot
CH3
CH3
Steroid Diversity
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• Long-‐chain fatty acid bonded to a long-‐chain alcohol
• Solid at room temperature
• Waterproof
• Resistant to degradation • Function: protection • Examples: earwax, plant cuticle, beeswax
Waxes
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Waxes
a. b. Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
a: © Das Fotoarchiv/Peter Arnold, Inc.; b: © Martha Cooper/Peter Arnold, Inc.
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PROTEINS & NUCLEIC ACIDS Properties of:
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3.4 Proteins
• Proteins are polymers of amino acids linked together by peptide bonds. § A peptide bond is a covalent bond between amino acids.
• Two or more amino acids joined together are called peptides. § Long chains of amino acids joined together are called polypeptides.
• A protein is a polypeptide that has folded into a particular shape and has function.
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Functions of Proteins
• Metabolism
§ Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells.
• Support
§ Keratin and collagen
• Transport
§ Hemoglobin and membrane proteins
• Defense
§ Antibodies
• Regulation
§ Hormones are regulatory proteins that influence the metabolism of cells.
• Motion
§ Muscle proteins and microtubules
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C
H
R
acidic group
amino group
COOH H2N
R = rest of molecule
Amino Acids: Protein Monomers • There are 20 different common amino acids. • Amino acids differ by their R groups.
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H Sample Amino Acids with Nonpolar (Hydrophobic) R Groups
C C H O
O C H
C O O
C H
C O O
C C H O
O S
C C O O
C C H O
O C
O C C H O
O C C H O
O C
O
C C H O
O C
O O
C C H O
O
C
C C H O
O
C H
C O O
C H
C O O
C H
C O O
C C H O
O C C
O O
CH2
H3N+
H3C CH3
H3N+
(CH2)2
CH3
H3N+
CH2
H3N+
H3N+
CH2
SH OH
CH
H3N+ H3N+ H3N+
CH2 (CH2)2
H3N+
CH2
N+H3
OH
H3N+
CH3
NH2
H3N+
H3N+
CH2
CH2
COO-
H3N+ CH2
CH2
CH2
H3N+
(CH2)3
NH
N+H2
NH2
H3N+
CH2
NH
N+H histidine (His) arginine (Arg) aspartic acid (Asp) lysine (Lys) glutamicacid (Glu)
asparagine (Asn) threonine (Thr)
Sample Amino Acids with Polar (Hydrophilic) R Groups
proline (Pro) leucine (Leu) phenylalanine (Phe) methionine (Met) valine (Val)
CH CH3
CH2 CH
CH2 H2N+
H2C
glutamine (Gln)
cysteine (Cys) serine (Ser)
tyrosine (Tyr) OH
CH
Sample Amino Acids with Ionized R Groups
CH3
NH2
H
CH2
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amino acid
amino group
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Synthesis and Degradation of a Peptide
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+
amino acid amino acid
acidic group amino group Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
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dehydration reaction
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amino acid amino acid
acidic group amino group
water
peptide bond
dipeptide
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dehydration reaction
amino acid amino acid
acidic group amino group
Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
water
peptide bond
dipeptide
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dehydration reaction hydrolysis reaction
water
peptide bond
dipeptide amino acid amino acid
acidic group amino group Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.
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71
Levels of Protein Structure
• Proteins cannot function properly unless they fold into their proper shape. § When a protein loses it proper shape, it said to be denatured. • Exposure of proteins to certain chemicals, a change in pH, or high temperature can disrupt protein structure.
• Proteins can have up to four levels of structure:
§ Primary § Secondary § Tertiary § Quaternary
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• Several Roles for proteins:
• Enzymes**
• Structural
• Storage
• Contractile
• Transport
• Defensive
• Signal
• Receptor
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Four Levels of Protein Structure
§ Primary • The sequence of amino acids
§ Secondary • Characterized by the presence of alpha helices and beta (pleated) sheets held in place with hydrogen bonds
§ Tertiary • Final overall three-‐dimensional shape of a polypeptide
• Stabilized by the presence of hydrophobic interactions, hydrogen bonding, ionic bonding, and covalent bonding
§ Quaternary • Consists of more than one polypeptide
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COO–
hydrogen bond
Primary Structure
This level of structure is determined by the sequence of amino acids coded by a gene that joins to form a polypeptide.
Secondary Structure
Hydrogen bonding between amino acids causes the polypeptide to form an alpha helix or a pleated sheet.
Β (beta) sheet = pleated sheet α alpha) helix
C N R
C R
C N
C R
C
N C
R N
C R
N R
N C
N R
CH
CH
CH
CH
CH
CH
CH
CH
Tertiary Structure
disulfide bond
Quaternary Structure
This level of structure occurs when two or more folded polypeptides interact to perform a biological function.
hydrogen bond
Interactions of amino acid side chains with water, covalent bonding between R groups, and other chemical interactions determine the folded three-dimensional shape of a protein.
peptide bond amino acid
H3N+
C C
C C
C C
C
C C C
C C
C C
C
C C
C C
C C
C
R
R
R R
R
R R
R R
O
O
O O
O O
O
O O
O
O
O N
N N N
N N
N
N N N N C
H H H
H H H
H H
H H
C O O
O O
O O
O H H
H H
H
H
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§ Proteins consisting of one polypeptide have three levels of structure.
§ Proteins consisting of more than one polypeptide chain have a fourth level, quaternary structure.
• Primary • Single chain
• Secondary • Pleated sheet • Alpha Helix
• Tertiary • Quaternary
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77
Examples of Fibrous Proteins
a. b. c.
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§ A protein’s three-‐dimensional shape • typically recognizes and binds to another molecule and • enables the protein to carry out its specific function in a
cell.
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Protein-‐Folding Diseases
• Chaperone proteins help proteins fold into their normal shape.
§ Defects in chaperone proteins may play a role in several human diseases such as Alzheimer disease and cystic fibrosis.
• Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs.
§ Mad cow disease is one example of a TSE disease.
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3.5 Nucleic Acids
• Nucleic acids are polymers of nucleotides.
• Two varieties of nucleic acids: § DNA (deoxyribonucleic acid)
• Genetic material that stores information for its own replication and for the sequence of amino acids in proteins.
§ RNA (ribonucleic acid) • Perform a wide range of functions within cells which include protein synthesis and regulation of gene expression
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Structure of a Nucleotide
• Each nucleotide is composed of three parts:
§ A phosphate group § A pentose sugar § A nitrogen-‐containing (nitrogenous) base
• There are five types of nucleotides found in nucleic acids. § DNA contains adenine, guanine, cytosine, and thymine. § RNA contains adenine, guanine, cytosine, and uracil.
• Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand.
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S
C
O P nitrogen-
containing base
pentose sugar
5'
4' 1' 2' 3'
phosphate
Nucleotides
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S
C O
–O P O O
O– P nitrogen-
containing base
phosphate
pentose sugar Nucleotide structure a.
5'
4' 1' 2' 3'
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S
C
O –O P O
O
O–
H
O C C
C C H
H H
H
P nitrogen- containing base
phosphate
pentose sugar deoxyribose (in DNA)
Nucleotide structure a.
OH
OH CH2OH
5'
4' 1'
2' 3'
b. Deoxyribose versus ribose
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S
C O
–O P O O
O–
H
O C C
C C H
H H
H
O C C
C C H
H H
H
P nitrogen- containing base
phosphate
pentose sugar ribose (in RNA) deoxyribose (in DNA)
Nucleotide structure a.
OH OH OH
OH OH
CH2OH CH2OH
5'
4' 1'
2' 3'
b. Deoxyribose versus ribose
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H O
N
N H O N
C C C
C
C C
C C
H O N H N
N N
N
H N N
N C C C
C T U G A
Purines Pyrimidines
HN CH
CH CH
CH
CH HC CH
HN CH
guanine adenine uracil in RNA
Pyrimidines versus purines c.
cytosine thymine in DNA
NH2
HN CH3
NH2
H2N
O O O
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S
C O
–O P O O
O–
H
O C C
C C H
H H
H
O C C
C C H
H H
H O
N
N H O N
C C C
C
C C
C C
H O N H N
N N
N
H N N
N C C C
H
C T U G A
P nitrogen- containing base
phosphate
pentose sugar ribose (in RNA) deoxyribose (in DNA)
Nucleotide structure a.
Purines Pyrimidines
OH OH OH
OH OH
HN CH
CH CH
CH
CH HC CH
HN CH
guanine adenine uracil in RNA
Pyrimidines versus purines c.
cytosine thymine in DNA
CH2OH CH2OH
NH2
HN CH3
NH2
H2N
O O O
5'
4' 1'
2' 3'
b. Deoxyribose versus ribose
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88
Structure of DNA and RNA
§ The backbone of the nucleic acid strand is composed of alternating sugar-‐phosphate molecules.
§ RNA is predominately a single-‐stranded molecule. § DNA is a double-‐stranded molecule.
• DNA is composed of two strands held together by hydrogen bonds between the nitrogen-‐containing bases. The two strands twist around each other to form a double helix.
– Adenine hydrogen bonds with thymine
– Cytosine hydrogen bonds with guanine
• The bonding between the nucleotides in DNA is referred to as complementary base pairing.
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Chargaff’s Rule
89
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Fig. 3.19 O
H S
S
S
S
P
P
P
P
N N N N
N N
N N
N N
N N
CH3
NH2
NH2
Backbone
NH2
Cytosine
Phosphate
Ribose Adenine Uracil
Guanine C G P
S A U
U
G
A
C O
Nitrogen-containing bases
O O
RNA Structure
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A T
N N N H
O N H
H
N N N
H
H
O
N H O N N N
N C
N s u g a r
s u g a r O N H
N
A A
T G G
C
G C
C
c. Complementary base pairing
Sugar
Thymine Adenine
Phosphate Guanine Cytosine
cytosine (C) guanine (G)
sugar
sugar
thymine (T) adenine (A)
CH3
Double helix b. a. Space-filling model
C G P
S A T
― ― ―
―
H
T
© Photodisk Red/Getty RF
DNA Structure
Complementary Base Pairing in
DNA
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A Special Nucleotide: ATP
• ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates.
• ATP is a high-‐energy molecule due to the presence of the last two unstable phosphate bonds.
• Hydrolysis of the terminal phosphate bond yields:
§ The molecule ADP (adenosine diphosphate)
§ An inorganic phosphate § Energy to do cellular work
• ATP is called the energy currency of the cell.
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ATP
N N N
N + + P P P P P P N N N
N ENERGY
phosphate diphosphate
ADP
triphosphate
ATP b.
NH2 NH2
H2O
adenosine triphosphate c. a.
adenosine adenosine
c: © Jennifer Loomis / Animals Animals / Earth Scenes