the chemical building blocks of life chapter 3. 38 biochemistry the study of the chemistry of life 4...
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The Chemical BuildingBlocks of Life
Chapter 3
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Biochemistry
• The study of the Chemistry of Life
• 4 Classes of Biological Molecules1.Carbohydrates2.Nucleic Acids3.Proteins4.Lipids
• The Classes are determined by the proportions of C, H, O in the molecule
• We will distinguish the structures and functions of each in living cells
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Biomolecules
• Organic Molecules – Composed of Carbon and Hydrogen– Elements Nitrogen, Oxygen, Phosphate, Sulfur
also included– These six elements compose 98.5% of body
weight (Saladin, 5th ed.)
• Some Inorganic molecules are incorporated as well – The Heme group in Hemoglobin contains Fe, for
example– Trace elements
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Biological Molecules
Biological molecules are composed of:
1. A Central Carbon or Carbon Chain
2. Functional Groups
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Organic Chemistry
• The carbon chain backbone of a molecule or Carbon Skeleton
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3
• Recall: Carbon makes 4 covalent bonds
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Functional Groups
• Functional Groups are specific combinations of bonded atoms attached to a Carbon Skeleton
• The Functional Groups determine the chemistry of the molecule
• Functional groups behave in chemically predictable ways
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Biological Molecules
• Biological molecules are typically Marcomolecules
- Very large molecules with high molecular weights
- DNA over a meter long
• Macromolecules are Polymers assembled from smaller Monomers
- Monomers - small, identical or similar subunits
- Polymers - covalently bonded monomers
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Monomers and Polymers
• Proteins• Amino Acid monomers polymerize to form proteins
• Nucleotides• Nucleotide monomers polymerize to form DNA and
RNA Macromolecules
• Carbohydrates• Simple sugar monomers polymerize to form
complex sugars
• Monosaccharides polymerize to form disaccharides, polysaccharides
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Polymerization• The joining monomers to form a polymer
• Dehydration Synthesis - the chemical reaction for how living cells form polymers
• A bond is formed between monomers and water is produced as a product of the reaction
• As the name implies, water is lost during the reaction
• Also known as Condensation
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Dehydration Synthesis
• A hydroxyl (-OH) group is removed from one monomer, and a hydrogen (H+) from another
• A new bond is formed between the monomers
• Water is released as a by-product
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Dehydration Synthesis• Monomers covalently bond together to form
a polymer with the removal of a water molecule– A hydroxyl group is removed from one monomer and a
hydrogen from the next
Monomer 1 Monomer 2
OH HO
OH– +
O
Dimer
(a) Dehydration synthesis
H+ H2O
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.15a
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Hydrolysis
• The reaction for the separation of joined monomers
• “Splitting with water”
• Opposite of dehydration synthesis– a water molecule ionizes into –OH and H+– the covalent bond linking one monomer to the other is
broken– the –OH is added to one monomer– the H+ is added to the other
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Hydrolysis• Splitting a polymer (lysis) by the addition of a water
molecule (hydro)– a covalent bond is broken
• All digestion reactions consists of hydrolysis reactions
OH HO
Monomer 1 Monomer 2
O
Dimer
(b) Hydrolysis
OH–+H+H2O
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.15b
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Biological Molecules
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1. Carbohydrates
The Saccharides (Sugars)
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1. CarbohydratesCarbohydrates
• Sugars, Starches, Fibers
• Names of carbohydrates often built from:– word root ‘sacchar-’ – the suffix ’-ose’– both mean ‘sugar’ or ‘sweet’
• monosaccharide or glucose
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1. Carbohydrates
• Carbohydrates are composed of carbon backbones with Hydroxyl Groups and a Carboxyl Group– R-OH– R-COOH
• The carbon backbone may be a in straight line or a closed ring of carbon atoms
• Polar and therefore Hydrophilic Molecules
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1. Carbohydrates
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1. Carbohydrates
• The Proportions of C, H, and O for Carbohydrates follow the General Formula:
CnH2nOn – n = number of carbon atoms
– for glucose, n = 6, so formula is C6H12O6
– 2:1 ratio of hydrogen to oxygen
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1. Carbohydrates
• Names of carbohydrates:– Carbohydrates are classified for the number of
carbon atoms in the carbon backbone• Pentose, Hexose
– Many carbohydrates have common names• Glucose, Fructose, Sucrose, Lactose
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Carbohydrate Structure
• Numbering the C’s• Carbohydrates are classified by the number of
Carbon atoms they contain
• For Example: Ribose is a pentose sugar because it contains 5 carbon atoms Glucose is a hexose sugar
because it contains 6 carbon atoms
• Many Carbohydrates have informal names that do not provide information about the molecule
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Carbohydrate Structure
• Numbering the Carbons• Numbering System allows the molecules to be
described efficiently
• The Carbons of Carbohydrates are numbered
• For Example:• Describing locations of covalent bonds• Ribose vs 2’ Deoxy-ribose
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Carbohydrates
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Carbohydrates
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Carbohydrate StructureNumbering the Carbons Ribose vs. 2 Deoxyribose
• Ribose • 2’ Deoxyribose
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1. Carbohydrates
1.Monosaccharides
2.Disaccharides
3.Polysaccharides
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Carbohydrate Classification
1. Monosaccharides• Simple Sugars• Are not hydrolyzed into smaller carbohydrates
2. Disaccharides • On hydrolysis, are cleaved into two
monosaccharides
3. Polysaccharides • Are Hydrolyzed to more than 10 monosaccharides
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1. Monosaccharidesa. Structure
• There are over 200 different monosaccharides
• Monosaccharides differ in the number of carbon atoms they contain in the C-C backbone (Ex. hexose vs. pentose)
• Monosaccharides also differ in their STEREOCHEMISTRY – the 3 dimensional shape of the molecule
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Monosaccharides differ in their Stereochemistry - 3D shape
HexoseC6H12O6
PentoseC5H10O5
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Monosaccharides are Isomers
Glucose
HH
CH2OH
H
H
H
OH
OH
OH
O
HO
Galactose
H
H
H
H
H
OH
OH
OH
OHO
Fructose
HOCH2
OH
HO
OH
H
H
O
H
CH2OH
CH2OH
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.16
• Isomers – molecules with the same chemical
formula, but different structures
• 3 important monosaccharides– glucose, galactose and fructose
• Same molecular formula - C6H12O6
– isomers
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Carbohydrates
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Carbohydrates
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Chiral Molecules• Isomers that are mirror images of each other
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1. Monosaccharidesb. Functions
• Energy Source- Are efficiently oxidized for energy- The C-H bonds are high in energy- The C-H bonds are oxidized
• Most Important example: - Glucose in Cellular Respiration
C6H12O6 + 6 O2 6 H2O + 6 CO2 + EnergyGlucose Oxygen Water Carbon Dioxide
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2. Disaccharidesa. Structure
• Sugar molecule composed of 2 monosaccharides
• 3 important disaccharides– sucrose - table sugar
• glucose + fructose
– lactose - sugar in milk• glucose + galactose
– maltose - grain products• glucose + glucose
Sucrose
Lactose
Maltose
HO
H
H
H
H
H
H
H
H
H
H H
H
H HH
H
HH H
H
HH
H
H
H
H
H
H
HOOH
OH OH
OO
O
CH2OH
O
OH
HOOH OH
OH
OHOO
HO
OH
OH
OH
OH
OH
O
OO
CH2OH
CH2OH
CH2OH
CH2OH
CH2OHCH2OH
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.17
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2. DisaccharidesPolymerization
• Monosaccharides are joined together into chains through a Dehydration Reaction
• A dimer of two monosaccharides is formed
• Water is lost in the polymerization reaction
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Dehydration Synthesis
Glucose + Fructose = Maltose + H2O
Glucose + Glucose = Maltose + H2O
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Dehydration Reaction•Carbon 1 on the left glucose exchanges its bond with the hydroxyl group for a bond with the oxygen of the hydroxyl group on carbon 4 of the glucose on the right (OH is released)
•The oxygen of hydroxyl group of carbon 4 exchanges its bond with H for a bond with carbon 1 (H is released)
• OH + H yields H2O
1 4
23
4
5
6
111 4
H2O
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2. DisaccharidesHydrolysis Reaction
• Chains of Carbohydrates are cleaved into smaller chains and monosaccharides through Hydrolysis Reactions
• As the name implies, the complex carbohydrates are “cleaved by water”
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2. DisaccharidesHydrolysis Reaction
Maltose + H2O = Glucose + Glucose
+ H2O
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3. Polysaccharides
a. Structure1. Multiple Monosaccharides linked together
b. Functions1. Structural Molecules
2. Signaling Molecules
3. Energy Storage
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3. Polysaccharides
• 3 Important Polysaccharides:1. Glucose2. Starch 3. Cellulose
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Glycogen
• Glycogen: energy storage polysaccharide in animals– long, branching chains of glucose monomers
– made by cells of liver, muscles, brain, uterus, and vagina
– liver produces glycogen when glucose blood level is high, then breaks it down when needed to maintain blood glucose levels
– muscles store glycogen for own energy needs
– uterus uses glycogen to nourish embryo
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GlycogenO
O
O
O
OO
O
O
OO
O
OO
O
O
O
O
O
O
OO
O
O
O
O O
O
OO
O OO
O
O
O
O
(a) (b)
CH2OHO
O O
O
O
O
O
CH2
O
O
O
OO
O
O
CH2OH
CH2OHCH2OH CH2OH
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.18
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Glycogen
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Glycogen Inclusions in a Liver Cell
Stryer's Biochemistry Fig. 23-2
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3. Polysaccharides• Starch: energy storage polysaccharide in
plants– only significant digestible polysaccharide in the human
diet
• Cellulose: structural molecule of plant cell walls- fiber in our diet
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3. Polysaccharides
b. Function
1. Structural MoleculesCellulose - plant cell walls
Chitin – Fungi cell walls
Peptidoglycan - Bacterial cell walls
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Carbohydrates
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Carbohydrates
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Carbohydrates
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Carbohydrate Functions
1.Structural:• Conjugated carbohydrates – covalently bound to lipid
or protein– glycolipids
• external surface of cell membrane
– glycoproteins• external surface of cell membrane
• mucus of respiratory and digestive tracts
– proteoglycans (mucopolysaccharides)
• gels that hold cells and tissues together
• forms gelatinous filler in umbilical cord and eye
• joint lubrication
• tough, rubbery texture of cartilage
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Glycoproteins on Cell Surface
Viral Bioinformatics Resource Center athena.bioc.uvic.ca/.../copy9_of_sample/surface
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3. Polysaccharides
Function
2. Signaling Molecules• GLYCOPROTEINS
– Carbohydrates bound to proteins – Example: Red Blood Cell Groups– Used by the Immune System to identify cells
• Antigenic – Are detected by the immune system and can cause an immune response
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3. Polysaccharidesb. Functions
3.Energy Storage– Excess glucose stored as Glycogen– Hydrolyzed to Glucose as needed
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2. Nucleic Acids
• DNA = Deoxyribonucleic Acid
• RNA = Ribonucleic Acid
• Function to store, transport, and control hereditary information
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2. Nucleic Acids• DNA (deoxyribonucleic acid)
– constitutes genes • instructions for synthesizing all of the body’s proteins
• transfers hereditary information from cell to cell and generation to generation
• RNA (ribonucleic acid) – 3 types– messenger RNA, ribosomal RNA, transfer RNA– 70 to 10,000 nucleotides long– carries out genetic instruction for synthesizing proteins– assembles amino acids in the right order to produce
proteins
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2. Nucleic Acids
• The Nucleic Acids are some of the largest organic compounds found in organisms
• Nucleic Acids are composed of Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorous atoms
• Nucleic Acids are components of DNA and RNA – the molecules responsible for the storage, transport and regulation of hereditary information
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2. Nucleic Acids
• Nucleotides are the uilding blocks of bucleic acids (DNA and RNA) and ATP
• 3 components of nucleotides1.Nitrogenous base2.Ribose Sugar (monosaccharide)
3.Phosphate groups
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2. Nucleic Acids
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The Nitrogenous Bases of Nucleotides
• There are 5 different Nitrogenous Bases to choose from when building Nucleic Acids:
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The Nitrogenous Bases of Nucleotides
• DNA is composed of the Nitrogenous Bases: Thymine, Cytosine, Adenine, and Guanine
• RNA is composed of the Nitrogenous Bases: Uracil, Cytosine, Adenine, and Guanine
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Nitrogenous Bases of DNA
• Purines - double ring– Adenine (A)– Guanine (G)
• Pyrimidines - single ring– Cytosine (C)– Thymine (T)
• DNA bases - ATCG• RNA bases - AUCG
Figure 4.1b
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
C
NH2 N
NH
CCH
CH
N
N C
Adenine (A)
Purines
C
O N
NH
CCH
C N
HN C
NH2
Guanine (G)
HC
NH2
C
NH
C
HC N
O
Cytosine (C)
Uracil (U)
C
C
O
C
O
CH
HN CH
NH
NH
C
C
HC
CH3
NH
O
O
Thymine (T)
Pyrimidines
(b)
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The Nitrogenous Bases
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The Ribose Sugar of NucleotidesThe Nucleotides of DNA
• The name, Deoxyribonucleic Acid, tells us the structure of the ribose sugar in the Nucleotides of DNA
• It lacks a hydroxyl group at C2
The Nucleotides of RNA• The name, Ribonucleic acid, tells
us the structure of the ribose sugar in the RNA Nucleotides
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The Phosphate Group of Nucleotides
• Both The Phosphate Group and the Nitrogenous Base attach to the central Ribose Sugar
• The Phosphate Group Attaches at the 5’ Carbon of the Nucleotide• The Nitrogenous Base Attaches at the 1’ Carbon of the Nucleotide
• The Phosphate Group is important in forming the “Backbone” of the Nucleic Acid Molecule
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The Phosphate Group of Nucleotides
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Polymerization of Nucleotides to Make Nucleic Acids (DNA and RNA)
• Nucleotides are covalently bound together into long strands through a Dehydration Reaction
• The Phosphate of one Nucleotide is bound to the Ribose Sugar of an adjacent nucleotide
• These Phosphate-Ribose bonds form the backbones of the Nucleic Acid Molecules
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The Backbone is formed by multiple C3-C5 phospho-ribose linkages
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The Backbone is formed by multiple C3-C5 phospho-ribose linkages
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DNA Molecular Structure• DNA is a long threadlike
molecule with uniform diameter, but varied length– total length of 2 meters– average DNA molecule 2 inches
long
• 46 DNA molecules in the nucleus of most human cells (Chromosomes)
Figure 4.1a
HC
N C
N
NH2
NH
C
C
CH
N
H
CH2OHO
O
OH
P
H
HOH
HH
O
Adenine
Phosphate Deoxyribose(a)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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DNA Molecular Structure
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DNA Double Helix
• Two DNA strands are united by hydrogen bonds to form the double-helix
• DNA base pairing– A – T with 2 hydrogen bonds
– C – G with 3 hydrogen bonds
• Law of Complementary Base Pairing– one strand determines base sequence
of other
– One strand serves as the template for the complementary strand
Figure 4.2 partial
(b)
(c)
GC
Sugar–phosphatebackbone
Sugar–phosphatebackbone
G
A
C
T
AT
AT
GC
Hydrogenbond
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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Complementary Base Pairing
• To form the Double Stranded structure of DNA, two polynucleotide strands pair up through hydrogen bonds between specific Nitrogenous Bases:
• In DNA, Adenine pairs with Thymine via 2 Hydrogen bonds
• In DNA, Guanine pairs with Cytosine via 3 Hydrogen Bonds
• In RNA, Adenine pairs with Uracil via 2 Hydrogen Bonds
• A to T with two H-bonds, G to C with 3 H-bonds
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Complementary Base Pairing
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Fig. 3.16-1
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Nucleic Acids
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Nucleic Acids
RNA
• Contains ribose instead of deoxyribose
• Contains uracil instead of thymine
• Single polynucleotide strand
• Functions:
-Read the genetic information in DNA
-Direct the synthesis of proteins
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Fig. 3.16-2
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Nucleic Acids
Other nucleotides
• ATP: adenosine triphosphate
-primary energy currency of the cell
• NAD+ and FAD: electron carriers for many cellular reactions
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The Chemical BuildingBlocks of Life
Chapter 3 Sec. 2 Proteins and Lipids
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3. Proteins
• Protein - a polymer of amino acids
• Amino acids - the monomers of proteins
• 20 Amino acids are used to construct proteins
• Peptide Bonds form between adjacent amino acids
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Protein Functions1. Structure
– keratin – tough structural protein• gives strength to hair, nails, and skin surface
– collagen – durable protein contained in deeper layers of skin, bones, cartilage, and teeth
2. Communication– some hormones and other cell-to-cell signals
– receptors to which signal molecules bind
1. ligand – any hormone or molecule that reversibly binds to a protein
• Membrane Transport– channels in cell membranes that governs what passes through
– carrier proteins – transports solute particles to other side of membrane
– turn nerve and muscle activity on and off
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Protein Functions 4. Catalysis
– enzymes
5. Recognition and Protection– immune recognition
– antibodies
– clotting proteins
• Movement– motor proteins - molecules with the ability to change shape
repeatedly
4. Cell adhesion– proteins bind cells together
– immune cells to bind to cancer cells
– keeps tissues from falling apart
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Amino Acid Structure
•A Central carbon with 4 attachments:
1.amino group (NH2)
2.carboxyl group (COOH)
3.radical group (R group)
4.hydrogen
• Properties of amino acid determined by -R group
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Amino Acid Structure
• By definition, all amino acids have the amine and carboxyl groups in common
• Amino differ in the side chains
• Different side chains give amino acids different chemical properties (for example, some amino acids are hydrophobic, some are hydrophilic)
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Page 46
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Representative Amino Acids
• Note: they differ only in the R group
Some nonpolar amino acids
Methionine
Tyrosine
H
N
C
C
H
S
O
(a)
OH
H CH2 CH2 CH3
Some polar amino acids
Cysteine
Arginine
H
N
C
C
H
O OH
H CH2 SH
CH2 OH
H
N
C
C
H
O OH
H (CH2)3 NH
NH2
NH2+
H
N
C
C
C
H
O OH
H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.23a
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Proteins
The structure of the R group dictates the chemical properties of the amino acid.
Amino acids can be classified as:1. nonpolar2. polar3. charged4. aromatic5. special functions (acidic, basic)
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Fig. 3.20
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Fig. 3.20-1
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Fig. 3.20-2
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Fig. 3.20-3
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Fig. 3.20-4
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Fig. 3.20-5
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Peptides• Peptide – any molecule composed of two or more
amino acids joined by peptide bonds
• Peptide Bond – joins the amino group of one amino acid to the carboxyl group of the next– formed by dehydration synthesis
• Peptides named for the number of amino acids– dipeptides have 2 – oligopeptides have fewer than 10 to 15 – polypeptides have more than 15– proteins have more than 50
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Amino AcidPolymerization
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The Formation of a Peptide Bond
Dehydration Reaction:The loss of water
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The Peptide Bond
• Amino acids are joined together into polypeptide chains through a DEHYDRATION REACTION
• Similarly, Polypeptide chains are cleaved apart through a HYDROLYSIS REACTION
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Hydrolysis Reaction
H2O
Hydrolysis Reaction:The Bond is Cleaved withwater
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Find the Peptide Bond
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Peptide BondTerminal Animo Group
Carboxyl Group
Amino GroupPeptide Bond
Side Chain
Side Chain
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Protein Structure and Shape
• Protein properties and functions depend on Protein Conformation
• Conformation – unique three dimensional shape of protein crucial to function
• Because of unique conformations, proteins are very specific to their functions
• Protein conformation depends on the environment
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Protein Structure and Shape
• Four Level of Protein Structure
1.Primary structure 2.Secondary structure3.Tertiary structure4.Quaternary structure
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Protein Structure and Shape
1. Primary structure – protein’s sequence amino acid– encoded in the genes
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Fig. 3.22-1
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Protein Structure and Shape
2. Secondary structure– coiled or folded shape held together by hydrogen
bonds– hydrogen bonds between slightly negative C=O
and slightly positive N-H groups
• Two secondary structure motifs: – Alpha Helix – springlike shape– Beta Helix – pleated, ribbonlike shape
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Fig. 3.21a
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Fig. 3.22-2
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Fig. 3.22-3
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Protein Structure and Shape
3. Tertiary structure
– further bending and folding of proteins into globular and fibrous shapes
– further folding due to Hydrogen bonding or other R group interactions within the chain, hydrophobic/hydrophilic interactions
• globular proteins –compact tertiary structure well suited for proteins embedded in cell membrane and proteins that must move about freely in body fluid
• fibrous proteins – slender filaments better suited for roles as in muscle contraction and strengthening the skin
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Fig. 3.21a
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Fig. 3.21b
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Fig. 3.21c
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Fig. 3.21d
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Fig. 3.21e
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Fig. 3.22-4
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Protein Structure and Shape
3. Tertiary structure
• Tertiary Structure of polypeptides forms Domains
• Domains are 3D functional regions of a polypeptide strung together on the polypeptide chain
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Fig. 3.23
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Protein Structure and Shape
• Quaternary structure– associations of two or more separate polypeptide chains– the chains are not covalently bonded
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Fig. 3.22
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• Proteins that contain a non-amino acid moiety called a prosthetic group
• Hemoglobin contains four complex iron containing rings called a heme moieties
Conjugated Proteins
Quaternary structure
Association of two ormore polypeptide chainswith each other
Beta chain
Betachain
Hemegroups
Alphachain
Alphachain
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.24 (4)
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Structure of Proteins
C
C=O
C=O
C=O
HN
HN
HN
NH O=C
C
C
C
CC
C
CC
C
C
O=C
O=C
C
NH O=C
NH
NH
C=O HN
C=O HN
CH
N CC
O
O O
O
CC
OC
NH
CC
NH
NH
C
Amino acids
Peptidebonds
Primary structure
Sequence of aminoacids joined bypeptide bonds
Secondary structure
Alpha helix or betasheet formed byhydrogen bonding
Betasheet
Chain 1Chain 2
Alphahelix
Quaternary structure
Association of twoor more polypeptidechains with eachother
Beta chain
Betachain
Heme groups
Alphachain
Alphachain
Tertiary structure
Folding and coilingdue to interactionsamong R groups andbetween R groupsand surrounding water
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.24
C=O H N
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Proteins
• Protein folding is aided by Chaperone Proteins• Endoplasmic Reticulum, Golgi Appartus
Fig. 3.24
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Protein Denaturation
• A change in the shape of a protein, usually causing loss of function
• Caused by changes in the protein’s environment
- pH- temperature- concentration
• Protein ‘unfolding’- looses layers of structure as conditions deviate- Quaternary Tertiary Secondary Primary
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Protein Denaturation
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Protein ‘Renaturation’
• Protein conformation can be restored if conditions are returned to normal
Secondary Tertiary Quaternary
• Conformation cannot be restored if primary structure is lost
• Because protein function depends on conformation, proteins work best in their specific environments
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Fig. 3.26
Protein ‘Renaturation’
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Enzymes• Enzymes - special class of proteins that functions as
biological catalysts – facilitate chemical reactions
• The Rules to be an Enzyme
1. It is a protein molecule that speeds up a chemical reaction2. Enzymes are not changed during the reaction3. Enzymes can be re-used many times
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Enzymes• Enzymes - proteins that function as biological
catalysts – facilitate chemical reactions – regulate chemical reactions– permit reactions to occur rapidly at normal body
temperature
• The Rules to be an Enzyme
1. It is a protein molecule that speeds up a chemical reaction• Enzymes are not changed during the reaction• Enzymes can be re-used many times
• Naming Convention– named for enzyme substrate with -ase as the suffix
• amylase enzyme digests amylose (a starch)
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Enzyme Structure
• Substrate - substance an enzyme acts upon
• Active Site - area of an enzyme where the chemical activity takes place– The active site is specifically shaped to bind to a
certain substrate– The active site is usually a cleft or indented area of
a protein– The active site is lined with various R groups that
provide the chemical activity
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How Enzymes Work:
• Enzymes Lower the Activation Energy - energy needed to get reaction started– enzymes facilitate molecular interaction
• Enzymes lower the Activation Energy by:1.Bringing the chemically active portions (functional
groups, for example) of Substrates together2.Destabilizing Substrates, making them more prone to
break or form bonds3.Decreasing Entropy – Enzymes hold substrates in
place, increasing the chance that chemical reactions will occur
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Enzymes and Activation Energy
Time
Free e
nerg
y c
onte
nt
Time
Energy levelof products
Energy levelof reactants
Activationenergy
Netenergyreleasedbyreaction
Activationenergy
Netenergyreleasedbyreaction
(a) Reaction occurring without a catalyst (b) Reaction occurring with a catalyst
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.26a, b
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Enzyme Structure and Action
• Enzyme/Substrate Complex:
E + S ES EP E + P
1. The Enzyme and the Substrate come together (E+S)
2. The Enzyme/Substrate Complex is formed (ES)
3. The Enzyme’s Substrate is changed to the Enzyme’s
Product in the active site of the enzyme (EP)
4. The Enzyme and Product Separate (E+P)
5. The Enzyme is free to bind to another Substrate
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Enzyme Structure and Action
• Substrate approaches active site on enzyme molecule
• Substrate binds to active site forming enzyme-substrate complex– highly specific fit –’lock and key’
• enzyme-substrate specificity
• Enzyme breaks covalent bonds between monomers in substrate
• adding H+ and OH- from water – Hydrolysis
• Reaction products released – glucose and fructose
• Enzyme remains unchanged and is ready to repeat the process
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Enzymatic Reaction Steps
Sucrase (enzyme)
1 Enzyme and substrate
Sucrose (substrate)
Enzyme–substrate complex
2
Enzyme and reaction products
3
Glucose Fructose
O
O
Active site
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.27
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• Reusability of enzymes– enzymes are not consumed by the reactions
• Astonishing speed– one enzyme molecule can consume millions of substrate
molecules per minute
• Factors that change enzyme shape– pH and temperature– alters or destroys the ability of the enzyme to bind to
substrate – enzymes vary in optimum pH
• salivary amylase works best at pH 7.0• pepsin works best at pH 2.0
– temperature optimum for human enzymes – body temperature (37 degrees C)
Enzymatic Action
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The Allosteric Site
• The allosteric site is another binding area of the enzyme
• The allosteric site binds a substance other than the substrate
• Binding at the allosteric site can induce a change in the shape of the protein and affect the active site
• *Noncompetitive inhibitors bind to allosteric sites
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Conformational Change
• The change in the shape of the protein induced by binding at an allosteric site is known as a CONFORMATIONAL CHANGE
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Protein Specificity
• The Quaternary Shape of a Protein gives the Active Site Specificity
• Specific Receptors• Specific Antigens• Specific Antibodies• Specific Substrates
• Specificity is important for enzyme action and function
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Protein Specificity
• Lock and Key Hypothesis:• The Substrates of Protein Active Sites fit like a key
fits into a lock
• Induced Fit Hypothesis:• The Active Site of a Protein changes shape as a it
binds to its substrate to create a very specific fit
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Conformational Change Example:Hemoglobin
• Hemoglobin is the protein in Red Blood Cells that carries Oxygen
• One molecule of Hemoglobin has four active sites – each active site can bind to one molecule of oxygen
• Hemoglobin undergoes conformational changes at each of its oxygen binding sites as molecules of oxygen bind
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Hemoglobin
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Conformational Change Example:Hemoglobin
• As each oxygen binding site binds a molecule of oxygen, a conformational change is induced to the rest of the oxygen binding sites
• With the binding of every O2, the other O2 binding sites have a weaker attraction for O2
• How is this important physiologically?
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Cofactors and Coenzymes• Cofactors
– about 2/3rds of human enzymes require a nonprotein cofactor
– inorganic partners (iron, copper, zinc, magnesium and calcium ions)
– some bind to enzyme and induces a change in its shape, which activates the active site
– essential to function
• Coenzymes– organic cofactors derived from water-soluble vitamins
(niacin, riboflavin)– they accept electrons from an enzyme in one metabolic
pathway and transfer them to an enzyme in another
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Coenzyme NAD+
• NAD+ transports electrons from one metabolic pathway to another
Pi+ADP
Glycolysis Aerobic respiration
Glucose Pyruvic acid
Pyruvic acid CO2 + H2O
ATP
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.28
e–NAD+ e–
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Metabolic Pathways• Chain of reactions, with each step usually catalyzed
by a different enzyme
• α β γ A → B → C → D
• A is initial reactant, B+C are intermediates and D is the end product
• Regulation of metabolic pathways – activation or deactivation of the enzymes – cells can turn on or off pathways when end products are
needed and shut them down when the end products are not needed
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4. Lipids
• Lipid molecules are composed of Carbon, Hydrogen, and Oxygen atoms
• The proportion of oxygen is much lower in lipids than it is in carbohydrates
• A high proportion of nonpolar C – H bonds causes the molecule to be hydrophobic
• Lipids are insoluble in water
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Lipids
• Two main categories of lipids
1. Fats (Triglycerides)2. Phospholipids
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1. Triglycerides
• Molecule for energy storage– store twice as much energy as carbohydrates
• Animal fats are are solid at room temperature
- Adipose tissue, waxes
• Plant fats (oils) are liquid at room temperature
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1. Triglycerides
• Composed of 2 Parts:a.Glycerol Molecule
b.Three Fatty Acids (tri)
• 3 fatty acids covalently bonded to a glycerol molecule – each bond formed by dehydration synthesis– broken down by hydrolysis
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a. Glycerol
• Glycerol is a 3 carbon molecule with 3 hydroxyl groups
• One, two, or three fatty acids can bind at the locations of the Hydroxyl Groups to form a lipid
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b. Fatty Acids• Chain of 4 to 24 carbon atoms
– carboxyl (acid) group on one end, methyl group on the other and hydrogen bonded along the side
Figure 2.19
C
H H H H H H H H H H H H H H HO
HOH H H H H H H H H H H H H H H
C C C C C C C C C C C C C C C H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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Fatty Acids
• Classes of Fatty Acids a.Saturated - carbon atoms saturated with hydrogen b.Unsaturated - contains C=C bonds without hydrogenc.Polyunsaturated – contains many C=C bonds
Figure 2.19Palmitic acid (saturated)CH3(CH2)14COOH
C
H H H H H H H H H H H H H H H
O
HO
H H H H H H H H H H H H H H H
C C C C C C C C C C C C C C C H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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Fatty Acids
a. Saturated Fatty Acids- carbon backbone saturated with hydrogen - Contains C-C Single Bonds only
Figure 2.19Palmitic acid (saturated)CH3(CH2)14COOH
C
H H H H H H H H H H H H H H H
O
HO
H H H H H H H H H H H H H H H
C C C C C C C C C C C C C C C H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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Saturation
A Saturated Fatty Acid
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Fatty Acids
b.Unsaturated Fatty Acids- contains C=C bonds, therefore fewer hydrogens
c.Polyunsaturated - contains many C=C bonds
Figure 2.19
C
H H H H H H H H H H H H H
O
HO
H H H H H H H H H H H H H
C C C C C C C C C C C C C C C H
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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Saturation
• An Unsaturated Fatty Acid
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Examples of Fatty Acids
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Saturation
• The Saturation or Unsaturation of the Fatty Acids affects the properties of the lipid
• Unsaturations put “kinks” in the fatty acids
• Kinks in the fatty acids prevent them from stacking together, making them less stable solids
• Unsaturated Fats are usually liquids at room temperature – plant fats (oils)
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Saturation
• Saturated fats are not kinked• They stack together making the lipid more
stable solids
• Saturated Fats are usually solid at room temperature – animal fats and waxes
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Saturation
• Saturated Fatty Acids
• Unsaturated Fatty Acids
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Triglyceride Synthesis
A Dehydration Rxn.
A Triglyceride + 3H2OGlycerol + 3 Fatty Acids
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Saturated Fats
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Unsaturated Fats
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2. Phospholipids
• Similar to triglycerides except that one fatty acid is replaced by a phosphate group
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Phospholipids• Phospholipids are Amphiphilic molecules
– fatty acid “tails” are hydrophobic– phosphate “head” is hydrophilic
Polar Head Group
Nonpolar Hydrocarbon Tail
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Phospholipids
• Because of Hydrophobic/ Hydrophilic Interactions, phospholipids spontaneously form micelles or lipid bilayers in water
• These structures cluster the hydrophobic tail regions of the phospholipid toward the inside and leave the hydrophilic head regions exposed to the water environment.
• Lipid bilayers are the basis of biological membranes
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Micelle
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Phospholipid Bilayer