Biochemistry: The Molecules of Life • Within cells, small organic molecules are joined together to form larger molecules • Macromolecules are large molecules composed of thousands of covalently connected atoms – Carbohydrates – Lipids – Proteins – Nucleic acids
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Biochemistry: The Molecules of Life Within cells, small organic molecules are joined together to form larger molecules Macromolecules are large molecules.
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Biochemistry: The Molecules of Life
• Within cells, small organic molecules are joined together to form larger molecules
• Macromolecules are large molecules composed of thousands of covalently connected atoms– Carbohydrates– Lipids– Proteins– Nucleic acids
Macromolecules - Polymers• A polymer is a long molecule consisting of many similar
building blocks called monomers• Most macromolecules are polymers, built from monomers• An immense variety of polymers can be built from a small set
of monomers• Three of the four classes of life’s organic molecules are
polymers:– Carbohydrates– Proteins– Nucleic acids
Polymers• Monomers form larger
molecules by condensation reactions called dehydration reactions
• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction
Short polymer Unlinked monomer
Dehydration removes a watermolecule, forming a new bond
Dehydration reaction in the synthesis of a polymer
Longer polymer
Hydrolysis adds a watermolecule, breaking a bond
Hydrolysis of a polymer
Carbohydrates• Carbohydrates serve as fuel and building material• They include sugars and the polymers of sugars• The simplest carbohydrates are monosaccharides,
or single (simple) sugars• Carbohydrate macromolecules are
polysaccharides, polymers composed of many sugar building blocks
Sugars
• Monosaccharides have molecular formulas that contain C, H, and O in an approximate ratio of 1:2:1
• Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules
• Glucose is the most common monosaccharide
• Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton
• 3 C = triose e.g. glyceraldehyde • 4 C = tetrose • 5 C = pentose e.g. ribose, deoxyribose • 6 C = hexose e.g. glucose, fructose, galactose • Monosaccharides in living organisms generally
have 3C, 5C, or 6C:
Monosaccharides
Triose sugars(C3H6O3)
GlyceraldehydeAld
ose
sK
eto
s es
Pentose sugars(C5H10O5)
Ribose
Hexose sugars(C5H12O6)
Glucose Galactose
Dihydroxyacetone
Ribulose
Fructose
Monosaccharides• Monosaccharides serve as a
major fuel for cells and as raw material for building molecules
• The monosaccharides glucose and fructose are isomers– They have the same chemical
formula– Their atoms are arranged
differently
• Though often drawn as a linear skeleton, in aqueous solutions they form rings Glucose Fructose
Monosaccharides
• In aqueous solutions, monosaccharides form rings
Linear andring forms
Abbreviated ringstructure
Monosaccharides: Hexoses
H H H H H
H
OH OH
OH O
OH H
OH O
CH2OH
Ribose
Pentoses (5-carbon sugars)
Deoxyribose
H H 4
5
1
3 2
4
5
1
3 2
CH2OH
Monosaccharides: Pentsoses
Disaccharides• A disaccharide is formed when a dehydration reaction joins two
monosaccharides• Disaccharides are joined by the process of dehydration synthesis• This covalent bond is called a glycosidic linkage
Glucose
Maltose
Fructose Sucrose
Glucose Glucose
Dehydrationreaction in thesynthesis of maltose
Dehydrationreaction in thesynthesis of sucrose
1–4glycosidic
linkage
1–2glycosidic
linkage
Disaccharides
• Lactose = Glucose + Galactose• Maltose = Glucose + Glucose• Sucrose = Glucose + Fructose• The most common disaccharide is
sucrose, common table sugar• Sucrose is extracted from sugar cane and
the roots of sugar beets
Polysaccharides• Complex carbohydrates are called polysaccharides
• They are polymers of monosaccharides - long chains of simple sugar units
• Polysaccharides have storage and structural roles
• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages
(a) Starch
(b) Glycogen
(c) Cellulose
Storage Polysaccharides - Starch
• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
• Plants store surplus starch as granules within chloroplasts and other plastids
Chloroplast Starch
1 µm
Amylose
Starch: a plant polysaccharide
Amylopectin
Storage Polysaccharides - Glycogen
• Glycogen is a storage polysaccharide in animals
• Humans and other vertebrates store glycogen mainly in liver and muscle cells
Mitochondria Glycogen granules
0.5 µm
Glycogen
Glycogen: an animal polysaccharide
Structural Polysaccharides• Cellulose is a major
component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
• The difference is based on two ring forms for glucose: alpha () and beta ()– Polymers with alpha
glucose are helical
– Polymers with beta glucose are straight
a Glucose
a and b glucose ring structures
b Glucose
Starch: 1–4 linkage of a glucose monomers.
Cellulose: 1–4 linkage of b glucose monomers.
Cellulose • Enzymes that digest starch by
hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose
• Cellulose in human food passes through the digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have symbiotic relationships with these microbes
Cellulosemolecules
Cellulose microfibrilsin a plant cell wall
Cell walls Microfibril
Plant cells
0.5 µm
Glucosemonomer
Lipids• Lipids are the one class of large biological molecules
that do not form polymers• Utilized for energy storage, membranes, insulation,
protection• Greasy or oily substances• The unifying feature of lipids is having little or no
affinity for water - insoluble in water • Lipids are hydrophobic becausethey consist mostly
of hydrocarbons, which form nonpolar covalent bonds
Fats• The most biologically important lipids are fats,
phospholipids, and steroids• Fats are constructed from two types of smaller molecules:
glycerol and fatty acids• Glycerol is a three-carbon alcohol with a hydroxyl group
attached to each carbon• A fatty acid consists of a carboxyl group attached to a long
carbon skeleton
Dehydration reaction in the synthesis of a fat
Glycerol
Fatty acid(palmitic acid)
Fatty Acids• A fatty acid has a long hydrocarbon chain with a
carboxyl group at one end.
• Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
• Unsaturated fatty acids have one or more double bonds, – Monounsaturated (one double bond)– Polyunsaturated (more than one double bond)
• H can be added to unsaturated fatty acids using a process called hydrogenation
• The major function of fats is energy storage
Stearate Oleate
Fats• Fats separate from water because water molecules form
hydrogen bonds with each other and exclude the fats
• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
• Two amino acids can join by condensation to form a dipeptide plus H2O.
• The bond between 2 amino acids is called a peptide bond.
Protein Conformation and Function• A functional protein consists
of one or more polypeptides twisted, folded, and coiled into a unique shape
• The sequence of amino acids determines a protein’s three-dimensional conformation
• A protein’s conformation determines its function
• Ribbon models and space-filling models can depict a protein’s conformation
A ribbon model
Groove
Groove
A space-filling model
Four Levels of Protein Structure• The primary structure of a protein is its unique sequence of amino
acids
• Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions among various side chains (R groups)
• Quaternary structure results when a protein consists of multiple polypeptide chains
Amino acidsubunits
pleated sheet
helix
Levels of Protein Structure
42
Interactions that Contribute to a Interactions that Contribute to a Protein’s ShapeProtein’s Shape
42 42 42
43
Enzymes as Catalysts• To increase reaction rates:
– Add Energy (Heat) - molecules move faster so they collide more frequently and with greater force.
– Add a catalyst – a catalyst reduces the energy needed to reach the activation state, without being changed itself. Proteins that function as catalysts are called enzymes.
Enzymes Are Biological Catalysts• Enzymes are proteins that carry out most catalysis in living
organisms.• Unlike heat, enzymes are highly specific. Each enzyme
typically speeds up only one or a few chemical reactions.• Unique three-dimensional shape enables an enzyme to
stabilize a temporary association between substrates.• Because the enzyme itself is not changed or consumed in
the reaction, only a small amount is needed, and can then be reused.
• Therefore, by controlling which enzymes are made, a cell can control which reactions take place in the cell.
Substrate Specificity of Enzymes• Almost all enzymes are globular proteins with one or more active sites on their surface.• The substrate is the reactant an enzyme acts on• Reactants bind to the active site to form an enzyme-substrate complex.• The 3-D shape of the active site and the substrates must match, like a lock and key• Binding of the substrates causes the enzyme to adjust its shape slightly, leading to a
better induced fit.• When this happens, the substrates are brought close together and existing bonds are
stressed. This reduces the amount of energy needed to reach the transition state.
Substate
Active site
Enzyme
Enzyme- substratecomplex
1 The substrate, sucrose, consistsof glucose and fructose bonded together.
Bond
Enzyme
Active site
The substrate binds to the enzyme, forming an enzyme-substrate complex.
2
H2O
The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks.
3
Glucose Fructose
Products are released, and the enzyme is free to bind other substrates.
4
The Catalytic Cycle Of An Enzyme
Conformational Change and Enzyme Activity• In addition to primary structure, physical and chemical conditions can
affect conformation
• Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel
• This loss of a protein’s native conformation is called denaturation
• A denatured protein is biologically inactive
Denaturation
Renaturation
Denatured proteinNormal protein
Effects of Temperature and pH• Each enzyme has an optimal temperature in
which it can function
Optimal temperature for enzyme of thermophilic
Rat
e o
f re
actio
n
0 20 40 80 100Temperature (Cº)
(a) Optimal temperature for two enzymes
Optimal temperature fortypical human enzyme
(heat-tolerant) bacteria
Effects of Temperature and pH– Each enzyme has an optimal pH in which it can function
Figure 8.18
Rat
e o
f re
actio
n
(b) Optimal pH for two enzymes
Optimal pH for pepsin (stomach enzyme)
Optimal pHfor trypsin(intestinalenzyme)
10 2 3 4 5 6 7 8 9
Nucleic Acids
• Nucleic acids store and transmit hereditary information
• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid
The Roles of Nucleic Acids• There are two types of nucleic
acids:– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
• Protein synthesis occurs in ribosomes
NUCLEUS
DNA
CYTOPLASM
mRNA
mRNA
Ribosome
Aminoacids
Synthesis ofmRNA in the nucleus
Movement ofmRNA into cytoplasmvia nuclear pore
Synthesis of protein
Polypeptide
The Structure of Nucleic Acids• Nucleic acids are
polymers called polynucleotides
• Each polynucleotide is made of monomers called nucleotides
• Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group
• The portion of a nucleotide without the phosphate group is called a nucleoside
5 end
3 end
Nucleoside
Nitrogenousbase
Phosphategroup
Nucleotide
Pentosesugar
Nucleotide Monomers• Nucleotide monomers are made
up of nucleosides and phosphate groups
• Nucleoside = nitrogenous base + sugar
• There are two families of nitrogenous bases: – Pyrimidines have a single six-
membered ring– Purines have a six-membered ring
fused to a five-membered ring
• In DNA, the sugar is deoxyribose• In RNA, the sugar is ribose
Nitrogenous bases
Pyrimidines
Purines
Pentose sugars
CytosineC
Thymine (in DNA)T
Uracil (in RNA)U
AdenineA
GuanineG
Deoxyribose (in DNA)
Nucleoside components
Ribose (in RNA)
Nucleotide Polymers• Nucleotide polymers are linked
together, building a polynucleotide• Adjacent nucleotides are joined by
covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next
• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
• The sequence of bases along a DNA or mRNA polymer is unique for each gene
The DNA Double Helix• A DNA molecule has two
polynucleotides spiraling around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel
• One DNA molecule includes many genes
• The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C
Sugar-phosphatebackbone
3 end5 end
Base pair (joined byhydrogen bonding)
Old strands
Nucleotideabout to beadded to anew strand
5 end
New strands
3 end
5 end3 end
5 end
ATP• Adenosine triphosphate (ATP), is the primary energy-
transferring molecule in the cell • ATP is the “energy currency” of the cell• ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups• The energy stored in the bond that connects the third
phosphate to the rest of the molecule supplies the energy needed for most cell activities