Transcript Biochemistry - Austin Community College

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 water
molecule, forming a new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water
molecule, 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
• 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:
Triose sugars
(C3H6O3)
Pentose sugars
(C5H10O5)
Hexose sugars
(C5H12O6)
Glyceraldehyde
Ribose
Galactose
Glucose
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 and
ring forms
Abbreviated ring
structure
Monosaccharides: Hexoses
Monosaccharides: Pentsoses
Pentoses
(5-carbon sugars)
5 CH2OH
O
OH
1
4
H
H H
H
3
2
OH
OH
Ribose
5 CH2OH
O
OH
4
1
H
H
H
H
2
3
H
OH
Deoxyribose
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
Dehydration
reaction in the
synthesis of maltose
1–4
glycosidic
linkage
Glucose
Glucose
Dehydration
reaction in the
synthesis of sucrose
Maltose
1–2
glycosidic
linkage
Glucose
Fructose
Sucrose
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
Chloroplast
• Starch, a storage
polysaccharide of plants,
consists entirely of
glucose monomers
• Plants store surplus
starch as granules within
chloroplasts and other
plastids
Starch
1 µm
Amylose
Amylopectin
Starch: a plant polysaccharide
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 ()
a Glucose
b Glucose
a and b glucose ring structures
Starch: 1–4 linkage of a glucose monomers.
– Polymers with alpha
glucose are helical
– Polymers with beta glucose
are straight
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
Cellulose microfibrils
in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose
molecules
 Glucose
monomer
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 because they 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
Fatty acid
(palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
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
Glycerides
• Glycerol + 1 fatty acid = monoglyceride
• Glycerol + 2 fatty acids = diglyceride
• Glycerol + 3 fatty acids = triglyceride (also
called triacylglycerol or “fat”.)
Ester linkage
Fat molecule (triacylglycerol)
Saturated Fats
• Fats made from saturated fatty acids are called saturated
fats
• Most animal fats are saturated
• Saturated fats are solid at room temperature
• A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
Stearic acid
Saturated fat and fatty acid.
Unsaturated Fats
• Fats made from unsaturated fatty acids are called
unsaturated fats
• Plant fats and fish fats are usually unsaturated
• Plant fats and fish fats are liquid at room temperature and
are called oils
Oleic acid
Unsaturated fat and fatty acid.
cis double bond
causes bending
Fat Sources
• Most animal fats contain saturated fatty
acids and tend to be solid at room
temperature
• Most plant fats contain unsaturated fatty
acids. They tend to be liquid at room
temperature, and are called oils.
Phospholipids
• In phospholipids, two of the –OH groups on glycerol are joined to fatty
acids. The third –OH joins to a phosphate group which joins, in turn,
to another polar group of atoms.
• The phosphate and polar groups are hydrophilic (polar head) while the
hydrocarbon chains of the 2 fatty acids are hydrophobic (nonpolar
tails).
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Structural formula
Space-filling model
Phospholipid symbol
Phospholipids
Phospholipids
• When phospholipids are added to water, they orient so that the
nonpolar tails are shielded from contact with the polar H2O may form
micelles
• Phosopholipids also may self-assemble into a bilayer, with the
hydrophobic tails pointing toward the interior
• The structure of phospholipids results in a bilayer arrangement found
in cell membranes
Water
Lipid head
(hydrophilic)
Lipid tail
(hydrophobic)
Micelle
Water
Phospholipid bilayer
Water
Steroids
• Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component
in animal cell membranes
• Testosterone and estrogen function as sex
hormones
Proteins
• Proteins have many structures, resulting in a wide
range of functions
• They account for more than 50% of the dry mass
of most cells
• Protein functions
–
–
–
–
–
Structural support / storage / movement - fibers
Catalysis - Enzymes
Defense against foreign substances– Immunoglobulins
Transport – globins, membrane transporters
Messengers for cellular communications - hormones
Proteins
• A protein is composed of one or more polypeptides that
performs a function
• A polypeptide is a polymer of amino acids joined by
peptide bonds to form a long chain
• Polypeptides range in length from a few monomers to
more than a thousand
• Each polypeptide has a unique linear sequence of amino
acids
• A protein consists of one or more polypeptides which are
coiled and folded into a specific 3-D shape.
• The shape of a protein determines its function.
Amino Acids
• Amino acids are monomers of polypetides
• They composed of a carboxyl group, amino group, and an
“R”Group
• Amino acids differ in their properties due to differing side
chains, called R groups
• Cells use 20 amino acids to make thousands of proteins
 carbon
Amino
group
Carboxyl
group
Amino Acids
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
O–
H
Glycine (Gly)
C
H
H3N+
C
CH
CH3
CH3
O
C
H3N+
C
C
O–
Alanine (Ala)
CH2
CH2
O
O–
CH3
CH3
O
H3C
H3N+
C
H
Valine (Val)
Leucine (Leu)
C
O
C
O–
O–
H
CH
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H3N+
C
O–
H
Methionine (Met)
Figure 5.17
CH2
O
C
CH2
O
H3 N+
C
C
O–
H
Phenylalanine (Phe)
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
H
Tryptophan (Trp)
Proline (Pro)
Amino Acids
OH
NH2 O
C
NH2 O
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
C
SH
CH3
OH
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
O–
H3N+
CH2
O
H3N+
C
C
Electrically
charged
CH2
H3N+
C
O
O–
H
H3N+
NH3+
O
C
O
C
O–
H
C
CH2
CH2
CH2
CH2
CH2
C
O
CH2
C
O–
H3N+
C
H
NH2+
C
H3N+
H3N+
C
Lysine (Lys)
C
H
CH2
O–
NH
CH2
CH2
O
H
Glutamic acid
(Glu)
NH+
NH2
CH2
H
Aspartic acid
(Asp)
O–
H
C
CH2
C
H3N+
C
Basic
O–
O
CH2
O
Asparagine Glutamine
(Gln)
(Asn)
Tyrosine
(Tyr)
Acidic
–O
C
O–
H
Cysteine
(Cys)
Threonine (Thr)
C
CH2
O
C
O–
O
C
O–
Arginine (Arg)
Histidine (His)
Amino Acids and Peptide Bonds
• 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 threedimensional conformation
• A protein’s conformation
determines its function
• Ribbon models and spacefilling models can depict a
protein’s conformation
Groove
A ribbon model
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
 pleated sheet
Amino acid
subunits
 helix
Levels of Protein Structure
Interactions that Contribute to a Protein’s Shape
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.
Energy released Energy supplied
Activation Energy and Catalysis
Activation
energy
Activation
energy
Reactant
Reactant
Product
Uncatalyzed
Product
Catalyzed
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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- substrate
complex
The Catalytic Cycle Of An Enzyme
1 The substrate, sucrose, consists
of glucose and fructose bonded together.
Glucose
Fructose
2 The substrate binds to the enzyme,
forming an enzyme-substrate
complex.
Bond
H2O
Active site
Enzyme
3 The binding of the substrate
and enzyme places stress on
the glucose-fructose bond,
and the bond breaks.
4 Products are
released, and the
enzyme is free to
bind other
substrates.
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
Normal protein
Denatured protein
Renaturation
Effects of Temperature and pH
• Each enzyme has an optimal temperature in
which it can function
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
Rate of reaction
(heat-tolerant)
bacteria
0
20
40
Temperature (Cº)
(a) Optimal temperature for two enzymes
80
100
Effects of Temperature and pH
– Each enzyme has an optimal pH in which it
can function
Optimal pH for pepsin
(stomach enzyme)
Rate of reaction
Optimal pH
for trypsin
(intestinal
enzyme)
3
4
0
2
1
(b) Optimal pH for two enzymes
Figure 8.18
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
DNA
Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
Synthesis
of protein
Polypeptide
Amino
acids
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
Nucleoside
Nitrogenous
base
Phosphate
group
Nucleotide
3 end
Pentose
sugar
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 sixmembered 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
Cytosine
C
Thymine (in DNA) Uracil (in RNA)
U
T
Purines
Adenine
A
Guanine
G
Pentose sugars
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
5 end
3 end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
5 end
New
strands
5 end
3 end
5 end
3 end
ATP
• Adenosine triphosphate (ATP), is the primary energytransferring 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