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Chapter 3
Biochemistry
1
Why study carbon?
• All living things are made of
cells
• Cells are…
– ~72% water
– ~3% salts
– ~25% carbon compounds
•
•
•
•
Carbohydrates
Proteins
Lipids
Nucleic acids
2
Carbon Chemistry
• Organic chemistry -study of
carbon compounds
• Carbon atoms can form
diverse molecules by bonding
to four other atoms
• Carbon has four valence
electrons and may form
single, double, triple, or
quadruple bonds
3
• The electron configuration of
carbon gives it covalent compatibility
with many different elements
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
H
O
N
C
4
Hydrocarbons
• Hydrocarbons are molecules
consisting of only carbon and
hydrogen
• Hydrocarbons are found in many of
a cell’s organic molecules
5
H H H
H H
(a) Length
C
H
H
H
C
C
C
C
H
H H H
Propane
H H
Ethane
H
(b) Branching
H
H H
H H
C
C
C
H H
H
H
C
H
H
C
H
H
C
C
C
H H H
H H
Butane
(c) Double bonds
H
isobutane
H
H
H H
C
C
C
C
H
H
H H
H
H C
(d) Rings
H
C
C
C
C
H
C
C
H
H
H
H
Cyclohexane
C
H H
C
H
1-Butene
H
H
H
H
H
C
H
H
2-Butene
H
H
C
C
C
C
H
C
Benzene
6
Functional Groups
• Functional groups
are the parts of
molecules involved in
chemical reactions
• They Are the
chemically reactive
Female lion
groups of atoms
within an organic
molecule
• Give organic
molecules distinctive
chemical properties Male lion
Estradiol
OH
CH3
HO
OH
CH3
CH3
O
Testosterone
7
• Six functional groups are important in the chemistry of life
– Hydroxyl – in alcohols, sugar
– Carbonyl – in sugars, amino acids, nucleotide bases
– Carboxyl – in amino acids, fatty acids; acts as an acid and
releases H+
– Amino – in amino acids; acts as a weak base
– Sulfhydryl – in amino acid cysteine; helps stabilize protein
structure
– Phosphate – in ATP, nucleotides, proteins, phospholipids;
acidic;
8
Some important functional groups of
organic compounds
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
O
OH
(may be written HO
STRUCTURE
CARBOXYL
C
C
OH
)
In a hydroxyl group (—
OH), a hydrogen atom is
bonded to an oxygen atom,
which in turn is bonded to
the carbon skeleton of the
organic molecule. (Do not
confuse this functional
group with the hydroxide
ion, OH–.)
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.

When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to a
hydroxyl group, the entire
assembly of atoms is called a
carboxyl group (—COOH).
9
• Some important functional
groups of organic compounds
AMINO
SULFHYDRYL
H
N
H
The amino group (—NH2)
consists of a nitrogen
atom bonded to two
hydrogen atoms and to
the carbon skeleton.
PHOSPHATE
O
SH
(may be written HS
)
O
P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen is
bonded to the carbon skeleton;
two oxygens carry negative
charges; abbreviated P . The
phosphate group (—OPO32–) is an
ionized form of a phosphoric acid
group (—OPO3H2; note the two
hydrogens).
10
Macromolecules
– Are large molecules composed of smaller
molecules
– Are complex in their structures
11
Macromolecules
•Most macromolecules are polymers,
built from monomers
• Four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
– Lipids
12
• A polymer
– Is a long molecule consisting of
many similar building blocks called
monomers
– Specific monomers make up each
macromolecule
– E.g. amino acids are the monomers
for proteins
13
How are organic compounds built?
• Enzymes (proteins) are needed to make
metabolic reactions proceed much
faster than they would on their own.
14
The Synthesis and Breakdown of
Polymers
• Monomers form larger molecules by
condensation reactions called dehydration
synthesis
HO
1
2
3
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
1
2
H
HO
3
H 2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
15
The Synthesis and Breakdown of
Polymers
• Polymers can disassemble by a cleavage
reaction -Hydrolysis (addition of water
molecules)
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
H
H 2O
HO
H
(b) Hydrolysis of a polymer
16
Carbohydrates
• Serve as fuel and building
material
• Include both sugars and
their polymers (starch,
cellulose, etc.)
17
Sugars
• Monosaccharides
– Are the simplest sugars
– Can be used for fuel
– Can be converted into other
organic molecules
– Can be combined into polymers
18
• Examples of monosaccharides
Triose sugars Pentose sugars
(C3H6O3)
(C5H10O5)
Aldoses
H
C
O
H
O
H
C
C
H
O
C
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
HO
C
H
C
OH
H
H
C
OH
H
Glyceraldehyde
H
Ribose
H
H
H
C
OH
H
HO
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
H
Glucose
Galactose
H
C OH
C
O
H
C OH
C
O
O
C OH
H
C OH
HO
H
H
C OH
H
C OH
Dihydroxyacetone H C OH
H
C OH
H
C OH
H
H
O
H
H
C OH
C
Ketoses
Hexose sugars
(C6H12O6)
Ribulose
C H
H
Fructose
19
• Monosaccharides
– May be linear
– Can form rings
H
H
HO
H
H
H
O
1C
2
6CH
C
OH
C
H
C
OH
3
4
5
C
6
C
OH
OH
2OH
5C
H
4C
OH 3
H
OH
C
H
6CH
O
H
2C
OH
H
1C
H
O
H
4C
OH
2OH
5C
H
OH
3C
H
CH2OH
O
H
H
1C
2C
OH
OH
6
H
5
4
HO
H
OH
3
H
O
H
1
2
OH
OH
H
(a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.
20
• Disaccharides
– Consist of two
monosaccharides
– Are joined by a glycosidic
linkage
21
(a) Dehydration reaction
in the synthesis of
maltose. The bonding
of two glucose units
H
forms maltose. The
glycosidic link joins
the number 1 carbon
of one glucose to the HO
number 4 carbon of
the second glucose.
Joining the glucose
monomers in a
different way would
result in a different
disaccharide.
H
(b) Dehydration reaction
H
in the synthesis of
O
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
CH2OH
CH2OH
O
H
OH H
H
H
H
OH
HO
H
OH
H 2O
H
O
H
Glucose
CH2OH
H
O
H
HO
H 2O
O
H
H
OHOH
H
HO
H
O
H
H
OH
O
H
CH2OH
H
1–4
1 glycosidic
linkage
HO
OH
H
Fructose
H
O
H
H
O
H
H
OH
OH
Maltose
H
H
4
O
CH2OH
O
H
OH
Glucose
Glucose
CH2O
H
O
H
O
H
H
H
OH
CH2OH
CH2OH
H
HO
H
O
H
O
H
OH
H
1–2
H
glycosidic
1
linkage
O
CH2OH
O
2
H HO
H
CH2OH
OH H
Sucrose
22
Polysaccharides
• Polysaccharides (complex
carbohydrates)
– Are polymers of sugars
– Serve many roles in organisms
23
Storage Polysaccharides
Chloroplast
Starch
• Starch
– Is a polymer
consisting
entirely of
glucose
monomers
– Is the major
storage form of
glucose in plants
1 m
Amylose
Amylopectin
(a) Starch: a plant polysaccharide
24
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in
animals
Mitochondria Giycogen
granules
0.5 m
Glycogen
(b) Glycogen: an animal polysaccharide
25
Structural Polysaccharides
• Cellulose
– Is a polymer of glucose
– Its bonding arrangement stabilizes the
chains and make it resist being digested
26
– Has different glycosidic linkages than
starch
H
4
H
O
CH2O
H
O
HO
H H
H
O
H
H
H
O
H
 glucose
O
C
H
H
O
H
C
H
C
H
C
O
H
H
O
H
O
H
O
H
C
C
CH2O
H
O
H
O
H
H
H
4
H
O
O
H
H
O
H
1
H
 glucose
(a)  and  glucose ring structures
H
O
CH2O
H
O
O
H
1
O
4
CH2O
H
O
O
H
1
O
4
CH2O
H
O
O
H
1
O
4
CH2O
H
O
O
H
H
O
O
H
1
O
4
O
H
O
CH2O
H
O
O
H
O
O
H
O
O
O
H
H
H
(b) Starch: 1– 4 linkage of  glucose monomers
CH2O
H
O
O
H
1
O
H
O
O
H
O
O
CH2O
CH2O
O
O
H
H
H
H
(c) Cellulose: 1– 4 linkage of  glucose monomers
O
H
27
– Is a major component of the tough walls
that enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH
2
2OH
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
28
• Cellulose is difficult to digest
– Cows have microbes in their stomachs to
facilitate this process
29
• Chitin, another important structural
polysaccharide
– Is found in the exoskeleton of arthropods
– Can be used as surgical thread
– Has a nitrogen group
CH2O
H
O OH
H
H
OH H
OH
H
H
NH
C
O
CH3
(b) Chitin forms the exoskeleton
(a) The structure of the
of arthropods. This cicada
chitin monomer.
is molting, shedding its old
exoskeleton and emerging
in adult form.
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
30
Lipids
• Lipids are a diverse group of
hydrophobic molecules
• Lipids
– Are the one class of large biological
molecules that do not consist of
polymers
– Share the common trait of being
hydrophobic
31
Fats
– Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty
acids
– Vary in the length and number and locations of
double bonds they contain
32
• Saturated fatty acids
– Have the maximum number of
hydrogen atoms possible
– Have no double bonds
Stearic acid
(a) Saturated fat and fatty acid
33
• Unsaturated fatty acids
– Have one or more double bonds
Oleic acid
(b) Unsaturated fat and fatty acid
cis double bond
causes bending
34
• Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of a
third fatty acid
35
• Phospholipid structure
– Consists of a hydrophilic “head” and
hydrophobic “tails”
CH2
CH2
O
O
P
O–
+
N(CH3)3
Choline
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
(b) Space-filling model
(c) Phospholipid
symbol
36
• The structure of phospholipids
– Results in a bilayer arrangement found in
cell membranes
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
37
Sterols
• Sterols (steroids)
– Are lipids characterized by a carbon
skeleton consisting of four fused rings
38
• One steroid, cholesterol
– Is found in cell membranes
– Is a precursor for some hormones
H 3C
CH3
CH3
CH3
CH3
HO
39
Proteins
• Proteins have many structures,
resulting in a wide range of
functions
• Proteins do most of the work in
cells and act as enzymes
• Proteins are made of monomers
called amino acids
40
• An overview of protein functions
41
• Enzymes
– Are a type of protein that acts as a
catalyst, speeding up chemical reactions
1
Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H 2O
Fructose
H O
4 Products are released.
3 Substrate is converted
to products.
42
Enzymes vs catalyst
43
Polypeptides
• Polypeptides
– Are polymers (chains) of amino acids
• A protein
– Consists of one or more polypeptides
44
• Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to
differing side chains, called R groups
45
Twenty Amino Acids
• 20 different amino acids make up
proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N
C
H
+
O–
C
CH2
O
H3N
C
H
Valine (Val)
Alanine (Ala)
CH
CH3
CH3
O
CH3
CH3
C
+
O–
CH2
O
C
H
Leucine (Leu)
H3C
H3N
+
O–
CH
C
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
CH2
O
H3N+
C
O–
Methionine (Met)
C
H
CH2
O
C
O–
Phenylalanine (Phe)
H3N+
C
H
O
C
H2C
CH2
H2
N
C
O
C
H
O–
Tryptophan (Trp)
Proline (Pro)
46
O–
OH
OH
Polar
H3N
+
CH2
C
O
C
H
CH
H3N
O–
Serine (Ser)
C
+
O
C
H3N
O–
H
+
CH2
C
H
O
C
CH2
H3N
O–
C
+
O
C
H
Electrically
charged
H3N
+
C
+
O–
O–
O
NH3+
NH2
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
H
O–
H3N
+
CH2
C
O
C
H
O–
H3N
+
CH2
C
H
Aspartic acid
(Asp)
O–
+
CH2
C
O
C
H
O–
Glutamine
(Gln)
Asparagine
(Asn)
C
C
C
H3N
Basic
O
C
CH2
O
H
Acidic
–O
CH2
H3N
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
Glutamic acid
(Glu)
O–
Lysine (Lys)
NH2+
H3N
+
CH2
O
C
NH+
H3N
+
CH2
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
47
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
48
Protein Conformation and
Function
• A protein’s specific conformation
(shape) determines how it functions
49
Four Levels of Protein Structure
• Primary structure
– Is the unique
sequence of amino
acids in a polypeptide
+H
3N
Amino
end
Amino
acid
subunits
Gly ProThrGly
Thr
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser
Pro
Ala
Glu Lle
Asp
Thr
Lys
Ser
Lys TrpTyr
Leu Ala
Gly
lle
Ser
Pro Phe
His Glu
AlaThrPhe Val
Asn
His
Ala
Glu
Val
Thr
Asp
Tyr
Arg
Ser
Arg
Gly Pro
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Tyr
Ser
Thr
Thr
Ala
Val
Val
Glu
Thr ProLys
Asn
c
o
o–
Carboxyl end
50
• Secondary structure
– Is the folding or coiling of the polypeptide
into a repeating configuration
– Includes the  helix and the  pleated
sheet
 pleated sheet
Amino acid
subunits
O H H
C C N
C N
H
R
R
C C N
O H H
C
C
R
N H
C
H
R
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C H
C
H
R
R
C
R
R
O H H
C C N
C C N
OH H
R
R
R
O
O H H
C C N
O
H
O H H
C C N
C C N
OH H
R
O
C
H
H
N HC N H C N H C N
C
H
H
C
O
C
O
R
R
C
R
O
C
H
H
NH C N
C
H
O C
R
R
C C
O
R
H
C
N HC N
H
O C
H
 helix
51
• Tertiary structure
– Is the overall three-dimensional shape of
a polypeptide
– Results from interactions between amino
acids and R groups
Hyrdogen
bond
CH22
CH
O
H
O
H 3C
CH
CH3
H 3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+-O C CH2
Ionic bond
52
• Quaternary structure
– Is the overall protein structure that
results from the aggregation of two or
more polypeptide subunits
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
53
Review of Protein Structure
+H
3N
Amino end
Amino acid
subunits
helix
54
What Determines Protein
Conformation?
• Protein conformation Depends
on the physical and chemical
conditions of the protein’s
environment
• Temperature, pH, etc. affect
protein structure
55
•Denaturation is when a protein
unravels and loses its native
conformation
(shape)
Denaturation
Normal protein
Denatured protein
Renaturation
56
The Protein-Folding Problem
• Most proteins
– Probably go through several
intermediate states on their way to a
stable conformation
– Denaturated proteins no longer work
in their unfolded condition
– Proteins may be denaturated by
extreme changes in pH or
temperature
57
Sickle-Cell Disease: A Simple Change
in Primary Structure
• Sickle-cell disease
– Results from a single amino acid
substitution in the protein
hemoglobin
58
Normal hemoglobin
Primary
structure
Val
His Leu Thr Pro Glul Glu
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Val
His Leu Thr Pro


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Val Glu
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
QuaternaryHemoglobin A
structure
Function
Sickle-cell hemoglobin
. . . Primary
Quaternary
structure
Function
10 m
...
Exposed
hydrophobic
region
 subunit




10 m
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity
to carry oxygen
is greatly
reduced.
Red blood
cell shape
Fibers of
abnormal
hemoglobin
deform cell into
sickle shape.
59
Nucleotides
• Consist of sugar, phosphate
group, and nitrogen-containing
bases
• ATP – adenosine triphosphate
contains 3 phosphate groups;
important source of energy
• Coenzymes – enzyme helpers
that accept hydrogen atoms
and electrons
60
Nucleic Acids
• Nucleic acids store and transmit
hereditary information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleotide sequences
on DNA
61
The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
62
Deoxyribonucleic Acid
• DNA
– Stores information for the synthesis
of specific proteins
– Found in the nucleus of cells
63
DNA Functions
– Directs RNA synthesis (transcription)
– Directs protein synthesis through RNA
DNA
(translation)
1 Synthesis of
mRNA in the nucleus
NUCLEUS
2 Movement of
mRNA into cytoplasm
via nuclear pore
mRNA
CYTOPLASM
mRNA
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
64
The Structure of Nucleic
Acids
5’ end
• Nucleic acids
– Exist as polymers called
polynucleotides
5’C
O
3’C
O
O
5’C
O
3’C
(a) Polynucleotide,
or nucleic acid
OH
3’ end
65
• Each polynucleotide
– Consists of monomers called nucleotides
– Sugar + phosphate + nitrogen base
Nucleoside
Nitrogenous
base
O

O
P
5’C
O
CH2
O
O
Phosphate
group
3’C
Pentose
sugar
(b) Nucleotide
66
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