Biochenistry Book

‫بسم هللا الرحمن الرحيم‬
‫‪BIOCHEMISTRY‬‬
‫‪1‬‬
Course outline
 Chapter one: carbohydrates
 Chapter two: lipids structure and
function
 Chapter three: proteins
 Chapter four: enzymes catalytic
reaction
 Chapter five cellular respiration
 Chapter six: vitamins
2
Course objectives
Upon completion of this course students will demonstrate
the basic knowledge of the following
1.Structures, names, and biological importance of a
variety of carbohydrates
2. Structures, names, and biological importance of a
variety of lipids
3.Structures and functions of amino acids and proteins
4.Functions of enzymes
5.structures and functions of DNA and RNA
6.Metabolism and energy production
3
Outline of instructions
 Carbohydrates
 Types of Carbohydrates
 Classification, structures and sources of some
important monosaccharaides
 Disaccharides
 Polysaccharides
4
Lipids
 Fatty acids
 Waxes, fats and oils.
 Chemical properties of triglycerides
 Solubility and polarity
 Phospholipids, steroids and other lipids
 Cell membrane
5
Amino acids (proteins)
 Amino acids and protein structures

 Functions of proteins
 Levels of protein structure
 Enzymes
6
Nucleic acid and protein syntesis
 Nucleosides and nucleotides
 The DNA double helix
 DNA replication
 Transcription and translation
 Genetic mutations
 Recombinant DNA
7
Bioenergetics (metabolism and
energy production)
 Glycolysis
 Citric acid cycle
 Oxidative phosphorylation and ATP
 Metabolic pathway of carbohydrates
 Metabolic pathway of lipids and amino acids
8
Chapter one
Carbohydrates
9
Carbohydrates are
 A major source of energy
from our diet.
 Composed of the elements
C, H, and O.
 Also called saccharides,
which means “sugars.”
10
Carbohydrates
 Are produced by photosynthesis
in plants.
 Such as glucose are synthesized
in plants from CO2, H2O, and
energy from the sun.
 Are oxidized in living cells
(respiration) to produce CO2,
H2O, and energy.
11
Types of Carbohydrates
The types of carbohydrates are
 Monosaccharides, the simplest carbohydrates.
 Disaccharides, which consist of two monosaccharides.
 Polysaccharides, which contain many
monosaccharides.
12
Monosaccharides
Monosaccharides consist of
 3 to 6 carbon atoms, typically.
 A carbonyl group (aldehyde or ketone).
 Several hydroxyl groups.
13
Aldoses
Aldoses are monosaccharides O
 With an aldehyde group. ║
 With many hydroxyl (─OH) C─H aldose
groups. │
triose (3 C atoms) H─ C─OH
tetrose (4 C atoms) │
pentose (5 C atoms) H─ C─OH
hexose (6 C atoms) │
CH2OH
Erythose, an aldotetrose
14
Ketoses
Ketoses are monosaccharides CH2OH
 With a ketone group. │
C=O ketose
 With many hydroxyl (─OH)
│
groups. H─ C─OH
triose (3 C atoms) │
H─ C─OH
tetrose (4 C atoms)
│
pentose (5 C atoms) H─C─OH
hexose (6 C atoms) │
CH2OH
Fructose, a ketohexose
15
Learning Check
Identify each as aldo- or keto- and as tetrose, pentose,
or hexose:
O
CH2OH
C H
C O
H C OH
HO C H
H C OH
H C OH
H C OH
CH2OH
H C OH
CH2OH
A B
16
Solution
A. aldohexose
B. ketopentose
17
Structures of Monosaccharides
18
Fischer Projections
A Fischer projection
 Is used to represent carbohydrates.
 Places the most oxidized group at the top.
 Shows chiral carbons as the intersection of vertical
and horizontal lines.
19
D and L Notations
In a Fischer projection, the −OH group on the
 Chiral carbon farthest from the carbonyl group
determines an L or D isomer.
 Left is assigned the letter L for the L-isomer.
 Right is assigned the letter D for the D-isomer.
20
Examples of D and L Isomers of
Monosaccharides
O
O
C H
C H O
HO H
H OH C H
H OH
HO H H OH
H OH
H OH H OH
H OH HO H
H OH
CH2OH CH2OH
CH2OH
D-glucose D-ribose L-galactose
21
Learning Check
Identify each as the D or L isomer.
A. B. C.
O CH2OH
C H O O
HO H C H HO H
HO H H OH H OH
HO H HO H H OH
CH2OH CH2OH CH2OH

__-ribose __- threose __- fructose
22
Solution
Identify each as the D or L isomer.
A. B. C.
O CH2OH
C H O O
HO H C H HO H
HO H H OH H OH
HO H HO H H OH
CH2OH CH2OH CH2OH

L-ribose L-threose D-fructose
23
D-Glucose
D-glucose is
 Found in fruits, corn
syrup, and honey.
 An aldohexose with
the formula C6H12O6.
 Known as blood sugar
in the body.
 The monosaccharide
in polymers of starch,
cellulose, and
glycogen.
24
Blood Glucose Level
In the body,
 Glucose has a
normal blood
level of 70-90
mg/dL.
 A glucose
tolerance test
measures blood
glucose for
several hours
after ingesting
glucose.
25
D-Fructose
D-fructose
 Is a ketohexose CH2OH
C6H12O6. C O
 Is the sweetest HO C H
carbohydrate.
H C OH
 Is found in fruit
juices and honey. H C OH
 Converts to CH2OH
glucose in the
body. D-Fructose
26
D-Galactose
D-galactose is O
 An aldohexose C6H12O6. C H
 Not found free in nature. H C OH
 Obtained from lactose, a HO C H
disaccharide.
HO C H
 A similar structure to
glucose except for the H C OH
–OH on C4. CH2OH
D-Galactose
27
Learning Check
Draw the structure and Fischer projection of D-fructose.
28
Solution
CH2OH CH2OH
│
C O C=O
HO C H HO H
H C OH
H OH
H C OH
CH2OH H OH
CH2OH
D-Fructose
Fischer projection 29
Cyclic Structures of
Monosaccharides
CH2OH
O
OH
OH OH
OH
Copyright © 2007 by Pearson Education, Inc

Publishing as Benjamin Cummings
30
Cyclic structures
 Are the prevalent form of monosaccharides with 5 or
6 carbon atoms.
O O
 Form when the hydroxyl group on C-5 reacts with the

aldehyde group or ketone group.
31
Cyclic Haworth Structures
Stable cyclic hemiacetals form
 When the C=O group and the
—OH are part of the same
molecule. CH2OH
 For hexoses, the hydroxyl group O
on C-5 reacts with the aldehyde
group or ketone group.
 The cyclic structure of a D-isomer
has the last CH2OH group located
above the ring.
32
Drawing the Cyclic Structure for
Glucose
STEP 1 Number the carbon chain and turn clockwise to
form a linear open chain.
H O
C
1
H C OH H OH H
2 H O
HO C H
3 HOCH2 C C C C C
H 4 C OH 6 5 4 3 2 1 H
H 5 C OH OH OH H OH
6 CH2OH
33
STEP 2 Bend the chain to
make a hexagon
 Bond the C5 –O– to C1. CH2OH
6
 Place the C6 group above O
5
the ring.
 Write the –OH groups on 4 1
C2 and C4 below the ring.

OH
OH 3 2 OH
 Write the –OH group on C3
above the ring. OH
 Write a new –OH on C1.
34
STEP 3 The new –OH on C1 is drawn
 Down for the  anomer.
 Up for the  anomer.
CH2OH CH2OH 
O O
OH
OH OH
OH OH OH
OH  OH
-D-glucose -D-glucose
35
Summary of the Formation of Cyclic
Glucose
Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings
36
-D-Glucose and β-D-Glucose in
Solution
When placed in solution,
 Cyclic structures open and close.
 -D-glucose converts to β-D-glucose and back.
 There is only a small amount of open chain.
CH2OH CH2OH CH2OH
H
O O O
O OH
OH C
OH OH H OH
OH OH OH
OH
OH OH
-D-glucose D-glucose (open) β-D-glucose
(36%) (trace) (64%) 37
Cyclic Structure of Fructose
Fructose
 Is a ketohexose.
 Forms a cyclic structure.
 Reacts the —OH on C-5 with the C=O on C-2.
CH2OH
CH2OH CH2OH CH2OH OH
C O O O
HO C H OH OH
H C OH OH CH2OH
H C OH OH OH
CH2OH
D-fructose α-D-fructose -D-fructose
38
Learning Check
Write the cyclic form of -D-galactose
O
C H
H C OH
HO C H
HO C H
H C OH
CH2OH
39
Solution
CH2OH
O
OH
OH
OH
OH
-D-galactose
40
Carbohydrates
Chemical Properties of
Monosaccharides
41
Reducing Sugars
Reducing sugars
 Are monosaccharides with a carbonyl group that
oxidizes to give a carboxylic acid.
 Undergo reaction with Benedict’s reagent (Cu2+) to
give the corresponding carboxylic acid.
 Include the monosaccharides glucose, galactose,
and fructose.
42
Oxidation of D-Glucose
O O
Glucose is oxidized
H to a carboxylic acid
C Benedicts C OH
reagent
H C OH H C OH
HO C H [O] HO C H
+ Cu 2+ + Cu2O(s)
H C OH H C OH
H C OH H C OH
Cu+ (reduced
CH2OH CH2OH form)
D-glucose D-gluconic acid
Glucose is a reducing
sugar 43
Reduction of Monosaccharides
D-Glucitol
The reduction of
monosaccharides
 Involves the carbonyl
group.
 Produces sugar
alcohols called alditols.
 Such as D-glucose
gives D-glucitol also
called sorbitol.
44
Learning Check
Write the products of the oxidation and reduction of
D-mannose.
O
C H
HO H
HO H
H OH
H OH
CH2OH
D-mannose
45
Solution
Write the products of the oxidation and reduction of
D-mannose.
O O
CH2OH C H C OH
HO H HO H HO H
Reduction Oxidation
HO H HO H HO H
H OH H OH H OH
H OH H OH H OH
CH2OH CH2OH CH2OH
D-mannitol D-mannose D-mannonic acid
46
Disaccharides
47
Important Disaccharides
A disaccharide
 Consists of two monosaccharides.
Monosaccharides Disaccharide
Glucose + glucose maltose + H2O
Glucose + galactose lactose + H2O
Glucose + fructose sucrose + H2O
48
Maltose
Maltose is
 A disaccharide also known as malt sugar.
 Composed of two D-glucose molecules.
 Obtained from the hydrolysis of starch.
 Linked by an -1,4-glycosidic bond formed from the
 −OH on C1 of the first glucose and −OH on C4 of
the second glucose.
 Used in cereals, candies, and brewing.
 Found in both the - and β - forms.
49
Formation of Maltose
50
Lactose
Lactose
 Is a disaccharide of β-
D-galactose and α- or
β-D-glucose.
 Contains a β -1,4-
glycosidic bond.
 Is found in milk and
milk products.
α-form
51
Sucrose
Sucrose or table sugar
 Is obtained from sugar cane and sugar beets.
 Consists of α-D-glucose and β-D-fructose..
 Has an α,β-1,2-glycosidic bond.
α-D-glucose
β-D-fructose 52
Learning Check
Write the structures and names of the two
monosaccharides that form when sucrose is
hydrolyzed.
53
Solution
α-D-glucose
β-D-fructose
54
Sweeteners
Sugars and artificial TABLE 15.2
sweeteners
 Differ in
sweetness.
 Are compared to
sucrose (table
sugar), which is
assigned a value
of 100.
60 000
55
Learning Check
Identify the monosaccharides in each of the following:

A. lactose
(1) α-D-glucose (2) β-D-fructose (3) β-D-galactose
B. maltose
C. sucrose
56
Solution
Identify the monosaccharides in each of the following:
A. lactose
(1) α-D-glucose (3) β-D-galactose
B. maltose
(1) α-D-glucose
C. sucrose
(1) α-D-glucose (2) β-D-fructose
57
Polysaccharides
58
Polysaccharides
Polysaccharides CH2OH
 Are polymers of D-glucose. O
 Include strach amylose and
amylopectin, starches made of OH
α-D-glucose. OH OH
 Include glycogen (animal starch
in muscle), which is made of α- OH
D-glucose.
 Include cellulose (plants and α-D-glucose
wood), which is made of
β-D-glucose.
59
Structures of Amylose and
Amylopectin
60
Amylose
Amylose is
 A polymer of α-D-
glucose molecules.
 Linked by -1,4
glycosidic bonds.
 A continuous
(unbranched)
chain.
61
Amylopectin
Amylopectin
 Is a polymer of α-D-
glucose molecules.
 Is a branched-chain
polysaccharide.
 Has α-1,4-glycosidic
bonds between the
glucose units.
 Has α-1,6-glycosidic
bonds to branches.

62
Glycogen
Glycogen
 Is the polysaccharide
that stores α-D-glucose
in muscle.
 Is similar to
amylopectin, but is
more highly branched.
63
Cellulose
Cellulose
 Is a polysaccharide
of glucose units in
unbranched chains.
 Has β-1,4-glycosidic
bonds.
 Cannot be digested
by humans because
humans cannot
break down β-1,4-
glycosidic bonds.
64
Learning Check
Identify the polysaccharides and types of glycosidic
bonds in each of the following:
A. B. C.
65
Solution
A. Cellulose -1,4-glycosidic bonds
B. Amylose -1,4-glycosidic bonds

Amylopectin -1,4-and -1,6-glycosidic bonds
C. Glycogen -1,4-and -1,6-glycosidic bonds

(more branched than amylopectin)
66
Chapter two
67
Lipid Structure and
Function
68
Common Physical Properties of Lipids
 Soluble in non-polar organic solvents

 Contain C, H, O
 Sometimes N & P
 Includes fats and oils – mostly triglycerides
 Fat: solid at room temperature
 Oil: liquid at room temperature
 More highly reduced than CHO
 2.25x more energy
69
Lipids
 Biomolecules soluble in organic solvents
 Roles
 Nutritional
 Structural
 regulatory
70
Types of Lipids
 Glycerol-based
 Sphingolipids
 Steroids
 Eicosanoids/leukotrienes
71
Storage Lipids
 Fatty acids
 Saturated and Unsaturated
 Relationship to melting point
 Triacylglycerides
 Glycerol + 3 fatty acids
 Waxes
72
Glycerol based fats
 Glycerol on the left
H2C OH  Esterifies to 3 fatty
acids
HC OH
HO CH2
73
Triacylglyerides
 Glycerol in blue
 Fatty acids in red
 Condensation
produces 3 water
molecules
 Very nonpolar…
excludes water
74
Lipids in Membranes:
 Phospholipids
 Cholesterol
 Glycolipds: Sugar group attached
 Proteins: either integral or peripheral
 Sphingolipids
75
Lipids or Glucose for Energy?
H2 H2 H2 H2 H2 H2 H2 H2
H3 C C C C C C C C C O
C C C C C C C C C
H2 H2 H2 H2 H2 H2 H2 H2 OH
HC O Energy-Containing Nutrients (C and H)

HO CH
HC OH
ATP Electron
H
+
Transport
Chain
HO CH
HO CH CO
2
CH 2 OH O2
H2O 76
Lipids or Glucose for Energy?
H2 H2 H2 H2 H2 H2 H2 H2
C C C C C C C C C
H2 H2 H2 H2 H2 H2 H2 H2 OH
More reduced state (more H bound to C)

HC O
 More potential for oxidation
HO CH
HC OH
HO CH
Less reduced state (more O bound to C)
HO CH  Less potential for oxidation
CH 2 OH 77
Energy from Lipids
 Compared to carbohydrates, fatty acids
contain more hydrogen molecules per unit of
carbon, thus, they are in a more reduced form
 Carbohydrates are partially oxidized so they
contain less potential energy (H+ and e-) per
unit of carbon
78
Functions and Properties
 Concentrated source of energy (9 kcal/gm)
 Energy reserve: any excess energy from
carbohydrates, proteins and lipids are stored
as triglycerides in adipose tissues
 Provide insulation to the body from cold
 Maintain body temperature
 Mechanical insulation
 Protects vital organs
79
 Electrical insulation
 Protects nerves, help conduct electro-chemical
impulses (myelin sheath)
 Supply essential fatty acids (EFA)
 Linoleic acid and linolenic acid
 Formation of cell membranes
 Phospholipids, a type of fat necessary for the
synthesis of every cell membrane (also
glycoproteins and glycolipids)
80
 Synthesis of prostaglandins from fatty acids
 Hormone-like compounds that modulates many body
processes
 Immune system, nervous systems, and GI secretions
 Regulatory functions: lower BP, blood clotting, uterine
contractions
 Help transport fat soluble vitamins
 Palatability and aroma
 Flavor and taste for some species!
 The satiety value – help control appetite
 Fullness; fats are digested slower
 Regulated through gastric inhibitory protein (GIP) and
cholecystokinin (CCK)
81
Physical Traits of Fatty Acids
 Form membranes, micelles, liposomes
 Orient at water : oil interface
 Contain hydrophobic and hydrophilic groups
 Lipid bilayer for membranes
 Micelles formed during digestion 82

 Fatty acids form “soaps” with cations
 Na & K soaps – water soluble
 Ca & Mg soaps – not water soluble
 Poorly digested
 Major issue in feeding fats to ruminants
83
 Unsaturated fatty acids oxidize spontaneously in
presence of oxygen
 Auto-oxidation, peroxidation, rancidity
 Free radicals formed
 Reduce nutritional value of fats
 Antioxidants prevent oxidation

 Vitamins C and E, selenium
84
Fatty Acid Structure
=O
-H
-H
H - C - ( C )n - C -
-H
-H
OH Carboxy
l group
Methy Carbon
l group(
group s) 85
Fatty Acids
 With a few exceptions, natural fatty acids:

 Contain an even number of carbon atoms
 Arranged in an unbranched line
 Have a carboxyl group (-COOH) at one end
 Have a methyl group (CH3) at the other end
86
87
Fatty Acid Chain Length
 Short chain: 2 to 6 C (volatile fatty acids)
 Medium chain: 8 – 12 C
 Long chain: 14 – 24 C
 As chain length increases, melting point

increases
 Fatty acids synthesized by plants and
animals have an even number of carbons
 Mostly long chain
 16C to 18C fatty acids are most prevalent
88
Fatty Acid Saturation
 Saturated - no double bonds
 Unsaturated – contain double bonds
 Monounsaturated – one double bond
 Polyunsaturated - >1 double bond
 The double bond is a point of unsaturation
 As number of double bonds increases, melting point
decreases
89
Saturated Fats
 All the chemical bonds between the carbon
are single bonds C-C-C-
 No double bonds
 No space for more H atoms; fully “saturated”
 Solid at room temperature
 Butter, shortening, lard, coconut oil, palm oil, and
fully hydrogenated vegetable oils
 Poultry skin, whole milk
90
Mono-Unsaturated Fatty Acids
 Only one double bond
 Therefore, two H atoms can be added
 Liquid at room temperature
 Olive oil, canola oil, peanut oil
 Other sources: avocado, almonds, cashews,
pecans and sesame seeds (tahini paste)
91
Poly-Unsaturated Fatty Acids
 Two or more double bonds
 Include omega-3 and omega-6 fatty acids
(essential fatty acids)
 Linolenic acid: omega 3 fatty acid
 Linoleic acid: omega 6 fatty acid
 Richest sources of poly-unsaturated fatty
acids include:
 Vegetable oils
 Corn, sunflower, safflower, cotton seed oils
92
Saturation
 Unsaturated fatty acids
 Converted to saturated fatty acids by rumen
microbes
 More susceptible to rancidity
 Oxidation of double bonds produces peroxides
and free radicals, which can cause damage to

other compounds
 Antioxidants
 Vitamins E, C
 Carotenoids
 Such as beta-carotene, lycopene
 Selenium
93
Hydrogenation of Fatty Acids
 To protect fats from becoming rancid, poly-
unsaturated fatty acids may be hydrogenated
 Increases saturation and stability - more resistant
to oxidation
 Unsaturated fats entering rumen are naturally
hydrogenated (“bio”-hydrogenated)
 Transforms the H-H configuration from cis to trans
configuration
 Trans configuration alters biological availability
 Trans configuration alters biological effects

 Suppresses de novo milkfat synthesis in mammary gland
94
Review of Fatty Acid Nomenclature
 Chain length
 Most fatty acids have an even number of carbons
 Fish oil is rich in odd-numbered FAs
 Double bonds
 Number
 Location from methyl or carboxyl end
 Degree of “saturation”
H H2 H H H2 H2 H2 H2
C C C C C C C C C
H2 H H H2 H H2 H2 H2 OH 95
Fatty-acid Nomenclature
 Named according to
chain length
 C18
H2 H2 H2 H2 H2 H2 H2 H2
C C C C C C C C C
H2 H2 H2 H2 H2 H2 H2 H2 OH
96
 Named according to the number of
double bonds
 C18:0
H2 H2 H2 H2 H2 H2 H2 H2
C C C C C C C C C
H2 H2 H2 H2 H2 H2 H2 H2 OH
Common
Common name:
name:
Stearic
Stearic acid
acid 97
double bonds
 C18:1
H2 H2 H2 H H2 H2 H2 H2
C C C C C C C C C
H2 H2 H2 H2 H H2 H2 H2 OH
Common
Common name:
name:
Oleic
Oleic acid
acid
98
double bonds
 C18:2
H2 H2 H H H2 H2 H2 H2
C C C C C C C C C
H2 H2 H H2 H H2 H2 H2 OH
Common
Common name:
name:
Linoleic
Linoleic acid
acid 99
double bonds
 C18:3
C C C C C C C C C
H2 H H H2 H H2 H2 H2 OH
Common
Common name:
name:
Linolenic
Linolenic acid
acid
100
 Named according to the
location of the first double bond from the non-
carboxyl end (count from the methyl end)
 Omega system (e.g., omega 3, 3)
 n–system (e.g., n–3)
C C C C C C C C C
H2 H H H2 H H2 H2 H2 OH101
H2 H2 H2 H H2 H2 H2 H2
C C C C C C C C C
H2 H2 H2 H2 H H2 H2 H2 OH
Omega 9 or n–9 fatty acid
H2 H2 H H H2 H2 H2 H2
C C C C C C C C C
H2 H2 H H2 H H2 H2 H2 OH
C C C C C C C C C
H2 H H H2 H H2 H2 H2 OH 102
Fatty Acid Synthesis Issues
Ω-3 Ω-6 Ω-9

C-C-C=C-C-C=C-C-C=C-C-C-C-C-C-C-C-COOH
 Animals can synthesize a fatty acid with a

double bond in the omega 9 position but not
at either 3 or 6 positions
 Omega-3 and omega-6 fatty acids must be
derived from diet
 Cold water fish accumulate high levels of
omega 3 fatty acids from their diet
103
Omega System and
Essential Fatty Acids
 Linoleic acid is an omega-6 fatty acid
 Linolenic and arachidonic acids are omega-3 fatty
acids
 Linoleic and linoleic acids are essential fatty acids
 Arachidonic acid can be synthesized from linoleic
acid, so not essential
 Exception is cats (of course)
104
 Named according to location of H’s

 Cis or trans fatty acids

Cis-9-octadecenoic acid Trans-9-octadecenoic acid

(Oleic acid) (Elaidic acid)
105
H2 H2 H2 H H2 H2 H2 O
H3 C C C C C C C C C C
C C C C H C C C C OH
H2 H2 H2 H2 H2 H2 H2 H2
H H2 H2 H2 O
C C C C C
H C C C C
C OH
H2 H2 H2 H2
H2 C
C H2
H2 C
C H2
H2 C
C H2
C C
H2
106
H 3
Isomers
 Geometrical isomers due  Chain branching

to double bond  Straight
 Cis  Synthesized by
 occurs naturally mammals and plants
 bend in acyl chain
 Branched
 Trans  Synthesized by
 Not as common
bacteria
 Found in hydrogenated
oils
 Results from bacterial
synthesis
 In fats in ruminants!!
 Straight acyl chains
107
Cis Fatty Acids
108
Melting Points
 Affected by chain length

 Longer chain = higher melting temp
Fatty acid: C12:0 C14:0 C16:0 C18:0 C20:0

Melting point: 44°C 58°C 63°C 72°C 77°C
Which fatty acids are liquid at room temperature?

Which fatty acids are solid at room temperature?
109
Chain Length
 In most fats with a mixture of fatty acids, the

chain length of the majority of fatty acids will
determine the “hardness” of the fat
 <10 carbons = liquid
 Between 10 and 20 carbons = ???
 <20 carbons = solid
Acetic Acid (2 C) Vinegar Liquid
Stearic Acid (18 C) Beef Tallow Solid
Arachidic Acid (20 C) Butter Solid
110
Melting Points
 Affected by number of double bonds

 More saturated = higher melting temp
Fatty acid: C18:0 C18:1 C18:2 C18:3

Melting point: 72°C 16°C –5°C –11°C
Which fatty acid is liquid at room temperature?

Which fatty acids are solid at room temperature?
111
Acids Carbons Double bonds Abbreviation Source
Acetic 2 0 2:0 bacterial metabolism
Propionic 3 0 3:0 bacterial metabolism
Butyric 4 0 4:0 butterfat
Caproic 6 0 6:0 butterfat
Caprylic 8 0 8:0 coconut oil
Capric 10 0 10:0 coconut oil
Lauric 12 0 12:0 coconut oil
Myristic 14 0 14:0 palm kernel oil
Palmitic 16 0 16:0 palm oil
Palmitoleic 16 1 16:1 animal fats
Stearic 18 0 18:0 animal fats
Oleic 18 1 18:1 olive oil
Linoleic 18 2 18:2 grape seed oil
Linolenic 18 3 18:3 flaxseed (linseed) oil
Arachidonic 20 4 20:4 peanut oil, fish oil
112
 Must be in diet
 Tissues can not synthesize
 Linoleic acid (18:2)
 Omega-6-FA
 Linolenic acid (18:3)

 Omega-3-FA
 Arachidonic (20:4)
 Not found in plants!
 Can be synthesized from C18:2 (linoleic acid) in
most mammals (except in cat)

 Essential nutrient in the diet of cats
113
Functions of Essential
Fatty Acids
 A component of the phospholipids in cell membranes
 Precursor for prostaglandins: arachidonic acid
 Important metabolic regulator
 Contraction of smooth muscle
 Aggregation of platelets
 Inflammation
114
 Since dietary poly-unsaturated fatty acids are
hydrogenated to saturated fatty acids in the rumen by
the microbes, how do ruminants meet their essential
fatty acid requirement?
 By-pass (rumen protected) lipids
 Microbial lipid synthesis
 Microbes don’t utilize lipids for energy, but they
do synthesize them for their cell membranes
115
 Deficiency of essential fatty acid intakes:
 Growth retardation
 Problems with reproduction
 Skin lesions
 Kidney and liver disorders
116
Simple Lipids
 Natural fats and oils
 Monoacyl glycerols (monoglycerides)
 Diacyl glycerols (diglycerides)
 Diglycerides found in plant leaves
 One fatty acid is replaced by a sugar (galactose)
 Triacyl glycerols (triglycerides)
 Triglycerides found in seeds and
animal adipose tissue

 Triacyl glycerols (triglycerides)
 Lipid storage form
 Where in the body? Adipocytes!!
 Most lipids consumed are triglycerides

117
Triglycerides
 Most common structure in dietary lipids

 Composed of one glycerol molecule and three fatty
acids connected by an ester bond (bond between an
alcohol and and organic acid)
 Fatty acids may be same or mixed
Fatty
Acid
Fatty
Glycero Acid
l
Fatty Acid
118
Triglyceride Structure
 Fatty acid composition of triglyceride varies
according to function
 Membrane lipids must be fluid at all temperatures
 Contain more unsaturated fatty acids
 Lipids in tissues subjected to cooling

(e.g., hibernators or tissues in extremities)
 Contain more unsaturated FAs
 Butterfat (milk fat) is fairly fluid

in spite of containing mostly saturated FAs
 Why? Chain length!!
119
Most Common Fatty Acids in Di-
and Triglycerides
Fatty acid Carbon:Double bonds Double bonds
Myristic 14:0
Palmitic 16:0
Palmitoleic 16:1 Cis-9
Stearic 18:0
Oleic 18:1 Cis-9
Linoleic 18:2 Cis-9,12
Linolenic 18:3 Cis-9,12,15
Arachidonic 20:4 Cis-5,8,11,14
Eicosapentaenoic 20:5 Cis-5,8,11,14,17
Docosahexaenoic 22:6 Cis-4,7,10,13,16,19
120
CH3(CH2)nCOOH
Factors Affecting Absorption of Lipids
 amount of fat consumed ( fat =  digestion = 

absorption)
 age of subject ( age =  digestion)
 emulsifying agents ( agent =  digestion)
 chain length of FA’s (> 18C =  digestibility)
 degree of saturation of FA ( sat =  digestibility)
 overheating and autooxidation (rancidification at double
bond)
 optimal dietary calcium = optimal FA absorption (high
Ca =  absorption)
121
Lipid Metabolism/Absorption
 short chain FA’s are absorbed and enter the portal

vein to the liver
 those FA’s with more than 10 carbons are
resynthesized by the liver to triglycerides
 they are then converted into chylomicrons and
pass to the lymphatic system
 some FA’s entering the liver are oxidized for
energy, others stored
 blood lipids: 45% P-lipids, 35% triglycerides, 15%
cholestrol esters, 5% free FA’s
122
Lipids
Phospholipids
Steroids and Cholesterol
Plasma (Cell)Membranes
123
Phosphoglycerides
 Most abundant lipids in cell membranes
 Control cell permeability
FATTY ACID
FATTY ACID
glycerol
Amino
alcohol
124
Lecithin
 Abundant in brain and nerve tissues
 Found in egg yolk, what germ, yeast
O
CH2 O C (CH2)14CH3
O
CH O C (CH2)14CH3
O
+
CH 2 O P O CH 2CH2N(CH3)3
O- choline, an amino alcohol
125
Sphingolipids
Esters of an 18-carbon alcohol sphingosine
FATTY ACID
sphingosine
Amino
alcohol
126
Sphingomyelin
Found in the myelin sheath

CH3(CH2)12CH=CH –CH–OH
O
sphingosine ‖ fatty acid
CH–NH –C –(CH2)14CH3
O
‖ + CH2 –O –P –O –CH2CH2 –
N–(CH3)3
‖
O– choline 127
Steroids
 Steroid nucleus
 3 cyclohexane rings
 1 cyclopentane ring
steroid nucleus 128

Cholesterol
 Most abundant steroid in the body

 Add methyl CH3- groups, alkyl chain, and
-OH to steroid nucleus
CH3 CH 3
CH3
CH3
CH 3
HO 129
Cholesterol in the Body
 Cellular membranes
 Myelin sheath, brain, and nerve tissue
 Bile salts
 Hormones
 Vitamin D
130
Bile Salts
 Synthesized in the liver from cholesterol
 Stored in the gallbladder
 Secreted into small intestine
 Mix with fats to break them part
 Emsulsify fat particles
131
Example of a Bile Salt
cholic acid, a bile acid

O
CH3
OH C N CH2 COO- Na+
CH3
H
CH3 gycine, an amino acid
HO OH
sodium glycocholate, a bile salt
132
Steroid Hormones
 Chemical messengers in cells

 Sex hormones
Androgens in males (testosterone)
Estrogens in females (estradiol)
 Adrenocorticosteroids from adrenal glands
mineralocorticoids (electrolyte balance)
glucocorticoids regulate glucose level
133
Sex Hormones
CH3 OH CH 3 OH
CH3 CH 3
O HO
t e s t o s t e ro n e e s t ra d io l
134
Plasma Membranes
 Surround cells
 Lipid bilayer of phospholipids
 Nonpolar hydrocarbon tails in center
 Polar (hydrophilic) sections on outside
 Some unsaturated fatty acids give flexibility
 Keep aqueous contents inside
 Allow certain biochemicals to pass through
135
Diagram of a Plasma Membrane
Polar sections
Nonpolar tails
136
Other Structures in Membranes
 Cholesterol molecules add strength
 Glycolipids on surface communicate with
other cells
 Proteins embedded in bilayer move
certain substances (water, K+, Cl-, HCO3-)
across the cell membrane
 Proteins on surface act as receptors for
hormones and other biochemicals
137
Learning Check PL1
Identify each lipid as: (1) phospholipid (2) steroid

(3) triglyceride (4) sphingolipid
A. Cholesterol
B. Glycerol, 2 fatty acids, phosphate, and choline
C. Glyceryl tristearate
D. Sphingosine, fatty acid, phosphate, and choline
E. Estradiol
F. Bile salts
G. Most of plasma membranes
138
Solution PL1
A. 2 steroid
B. phospholipid
C. 3 triglyceride
D. 4 sphingolipid
E. 2 steroid
F. 2 steroid
G. 1 phospholipid
139
Passive Transport
Selective permeability: integral membrane proteins
allow the cell to be selective about what passes
through the membrane.
Channel proteins have a polar interior allowing polar
molecules to pass through.
Carrier proteins bind to a specific molecule to facilitate
its passage.
140
Passive Transport
Channel proteins include:
-ion channels allow the passage of ions (charged
atoms or molecules) which are associated with water
-gated channels are opened or closed in response
to a stimulus
-the stimulus may be chemical or electrical
141
Passive Transport
Carrier proteins bind to the molecule that they transport
across the membrane.
Facilitated diffusion is movement of a molecule from

high to low concentration with the help of a carrier
protein.
-is specific
-is passive
-saturates when all carriers are occupied
142
Passive Transport
In an aqueous solution
-water is the solvent
-dissolved substances are the solutes
Osmosis is the movement of water from an area of

high to low concentration of water
-movement of water toward an area of high solute
concentration
143
144
Passive Transport
When 2 solutions have different osmotic concentrations
-the hypertonic solution has a higher solute
concentration
-the hypotonic solution has a lower solute
concentration
Osmosis moves water through aquaporins toward the
hypertonic solution.
145
146
Passive Transport
Organisms can maintain osmotic balance in different
ways.
1. Some cells use extrusion in which water is
ejected through contractile vacuoles.
2. Isosmotic regulation involves keeping cells
isotonic with their environment.
3. Plant cells use turgor pressure to push the cell
membrane against the cell wall and keep the cell
rigid.
147
Active Transport
Active transport
-requires energy – ATP is used directly or indirectly to
fuel active transport
-moves substances from low to high concentration
-requires the use of carrier proteins
148
Active Transport
Carrier proteins used in active transport include:
-uniporters – move one molecule at a time
-symporters – move two molecules in the same
direction
-antiporters – move two molecules in opposite
directions
149
Active Transport
Sodium-potassium (Na+-K+) pump
-an active transport mechanism
-uses an antiporter to move 3 Na+ out of the cell and
2 K+ into the cell
-ATP energy is used to change the conformation of
the carrier protein
-the affinity of the carrier protein for either Na+ or K+
changes so the ions can be carried across the
membrane
150
151
Active Transport
Coupled transport
-uses the energy released when a molecule
moves by diffusion to supply energy to active
transport of a different molecule
-a symporter is used
-glucose-Na+ symporter captures the energy
from Na+ diffusion to move glucose against a
concentration gradient
152
153
Bulk Transport
Bulk transport of substances is accomplished by
1. endocytosis – movement of substances into the
cell
2. exocytosis – movement of materials out of the
cell
154
Bulk Transport
Endocytosis occurs when the plasma membrane
envelops food particles and liquids.
1. phagocytosis – the cell takes in particulate matter
2. pinocytosis – the cell takes in only fluid
3. receptor-mediated endocytosis – specific
molecules are taken in after they bind to a receptor
155
156
157
158
Bulk Transport
Exocytosis occurs when material is discharged from
the cell.
-vesicles in the cytoplasm fuse with the cell
membrane and release their contents to the exterior
of the cell
-used in plants to export cell wall material
-used in animals to secrete hormones,
neurotransmitters, digestive enzymes
159
160
Chapter three
161
Proteins
162
Amino Acids
 Amino acids are building blocks for proteins
 They have a central α-carbon and α-amino and α-
carboxyl groups
 20 different amino acids
 Same core structure, but different side group (R)
 The α-C is chiral (except glycine); proteins contain only
L-isoforms.
 At physiological pH most AA occur as zwitterions.
163
Classification of Amino Acids
(based on polarity)
 Hydrophobic / non-polar R group(9): (Glycine, alanine,
valine, leucine, isoleucine, methionine, proline,
phenylalanine, tryptophan)
 Polar R group (net charge 0 at pH 7.4)(7): (Serine,
threonine, cysteine, tyrosine, asparagine, glutamine,
histidine)
 Polar R group (Charged ion at pH 7.4)(4): (aspartate,
glutamate, lysine, arginine)
164
Classification of Amino Acids
(Based on R-group)
 Aliphatic: gly (G), ala (A) , val (V), leu (L), ile (I)
 Aromatic: Trp (W), Phe (F), Tyr (Y), His (H),
 Sulphur : Met (M), Cys (C)
 Hydroxyl: Ser (S), Thr (T), Tyr (Y)
 Cyclic: pro (P)
 Carboxyl: asp (D), glu (E)
 Amine: lys (K), arg (R)
 Amide: asn (N), gln (Q)
165
Proteins
• Linear polymers of AA via amide linkages form

peptides
(1-10), polypeptides (11-100) and proteins (>100)
Eg: Aspartame (2), glutathione (3), vasopressin
(9), insulin(51)
• Proteins have a amino-end and carboxyl-end
• In the lab, proteins can be hydrolyzed (to AA) by
strong acid treatment
• Physiologic hydrolysis by peptidases and
proteases 166
Protein function
• Catalysis (enzymes)
• Binding – transport (active/passive)
– Protein-DNA/RNA binding (e.g. histones,
transcription factors)
– Protein-protein interactions (e.g. antibody-
lysozyme)
– Protein-fatty acid binding (e.g.
apolipoproteins)
– Protein – small molecules (drug
interaction, structure decoding)
167
• Structural component
• Regulation
• Transcription regulation
• Signaling
• Immune system
• Motor proteins (actin/myosin)
168
Importance of Proteins
 Muscle structure depends on protein-protein interactions
 Transport across membranes involves protein-solute
interactions
 Nerve activity requires transmitter substance-protein
interactions
 Immune protection requires antibody-antigen interactions
169
Hierarchical nature of protein
structure
Primary structure (Amino acid sequence)
↓
Secondary structure （ α-helix, β-sheet ）
↓
Tertiary structure （ Three-dimensional structure
formed by assembly of secondary structures ）
↓
Quaternary structure （ Structure formed by more
than one polypeptide chains ）
170
171
Primary Structure
 Polypeptide chains 
Amino Acids
 Largest polypeptide
chain approx has
5000AA but most have
less than 2000AA
 Amino Acid Basic
Structure H2N-CH-
COOH
 Arrangement of the 20
amino acids in the
polypeptide is the amino
acid sequence which
composes the primary
structure of the protein
172
20 Amino Acids
Nonpolar,
hydrophobic
Polar, uncharged
Polar, charged
http://www.people.virginia.edu/~rjh9u/aminacid.html 173
Amino Acid Classification
Smal
l
A Venn diagram showing the relationship of the 20 naturally

occurring amino acids to a selection of physio-chemical properties
thought to be important in the determination of protein structure.
174
Bond Formation
 Linking two amino

acids together
 Definitions (N-
terminal, C-terminal,
polypeptide
backbone, amino
acid residue, side
chains)
http://web.mit.edu/esgbio/www/lm/proteins/peptidebond.html
175
Peptide Bond
http://cmgm.stanford.edu/biochem/biochem201/Slides/
176
Peptide Bond
 C-N bond length of the peptide is 10% shorter than that
found in usual C-N amine bonds
 Peptide bond planer
 ω, angle around peptide bond,
00 for cis, 1800 for trans
177
178
179
Secondary Structure
• Secondary structure is the initial folding
pattern (periodic repeats) of the linear
polypeptide
• 3 main types of secondary structure: α-
helix, β-sheet and bend/loop
• Secondary structures are stabilized by
hydrogen bonds
180
The α-helix
• The α-helix is right-handed or clock-wise (for L-isoforms

left-handed helix is not viable due to steric hindrance)
• The helix is stabilized by H-bonds between –N-H and –
C=O groups of every 4th amino acid
• α-helices can wind around each other to form ‘coiled coils’
that are extremely stable and found in fibrous structural
proteins such as keratin, myosin (muscle fibers) etc
181
182
Alpha Helix
183
http://cmgm.stanford.edu/biochem/biochem201/Slides/
Beta Sheet
184
Beta Sheet Features
 Sheets can be made up of any number of strands
 Orientation and hydrogen bonding pattern of strands
gives rise to flat or twisted sheets
 Parallel sheets buried inside, while Antiparallel sheets
occurs on the surface
185
Interactions
 Covalent bonds
Disulphide bond (2.2 0A) between two Cys residues
 Non-covalent bonds
 Long range electrostatic interaction
 Short range (4 0A) van der Waals interaction
 Hydrogen bond (3 0A)
186
Tertiary Protein Structure
 Defines the three dimensional conformation of an entire
peptide chain in space
 Determined by the primary structure
 Modular in nature
187
Aspects which determine tertiary

structure
Covalent disulfide bonds from between closely aligned
cysteine residues form the unique Amino Acid cystine.
 Nearly all of the polar, hydrophilic R groups are located
in the surface, where they may interact with water
 The nonpolar, hydropobic R groups are usually located
inside the molecule
188
Quaternary Structure
 Not all proteins have a
quaternary structure
 A composite of multiple
poly-peptide chains is
called an oligomer or
multimeric
 Hemoglobin is an
example of a tetramer
 Globular vs. Fibrous
189
Protein Folding
 Protein folding constitutes the process by which a poly-
peptide chain reduces its free energy by taking a
secondary, tertiary, and possibly a quaternary structure
190
Thermodynamics
 Proteins follow
spontaneous
reactions to reach
the conformation of
lowest free energy
 Reaction
spontaneity is
modeled by the
equation ΔG= ΔH-
TΔS
191
Factors Affecting Protein
Structure
 Disulfide bridges are formed when sulfhydryl
groups from different amino acids bind to form
a connection between the two amino acids. A
sulfhydryl group consists of a sulfur atom
combined with a hydrogen atom (–SH).
 Hydrogen bonding is the attraction of a
hydrogen atom to an electronegative atom
such as nitrogen (N), oxygen (O), or fluorine
(F). By itself, a hydrogen bond is quite weak;
but when many hydrogen bonds exist, such as
with the structure of DNA, collective hydrogen
bonding can be quite strong.
192
• Hydrophobic effect is the repulsion of
nonpolar molecules from water, which
is a polar substance. The nonpolar
chains of a polypeptide move into the
center of the structure away from the
water and towards other nonpolar
chains. Like is attracted to like, so
nonpolar substances attract each
other, whereas polar substances
attract each other. A nonpolar
substance and a polar substance will
repel each other. 193
• Polar interactions are the attraction of
negative side chains to positive side
chains. Ionic bonding is a polar
interaction. An ion is a positively- or
negatively-charged atom or molecule.
Ions are attracted to other ions of the
opposite charge so the binding of the
ions can result in a net charge of zero.
194
 Van der Waals forces are the weak
attractions and repulsions of
atoms. If an atom is within a certain
distance of another atom, they will
experience an attraction. If the
atoms are too close, there will be a
repulsion.
195
Chapter four
Enzymes
196
Enzyme Catalyzed Reaction
E
Enzyme
+ S
Substrate
E -S
Enzyme-Substrate
E P
+
Product
Complex
197
Enzymes – General properties
 All enzymes are proteins that function as biological
catalysts
 They are essential for reactions to occur in living (and dying) cells
 They can have a dramatic impact on the quality deterioration of
many foods
 They can be used to perform positive reactions in food and
beverage processing (also textile, leather and pharmaceutical
industry)
 Have specific ability to convert a particular substance into a
particular product
 Very rapid action
 Only need small amount
 Can easily control them by adjusting their environment, e.g. pH, T,
concentration…..
 They are all natural and non-toxic
198
Enzymes have one (or more) active sites in their structure that
have great specificity for certain substrates (bind only to
these) and catalyze their transformation into specific products
E E-S
E-S#
E+P
Change in
environment
199
Lactose Sucrose
200
 The reason enzymes are able to speed up chemical reactions so
much comes from their ability to bind to their substrates with very high
specificity and significantly lower the activation energy (Ea) of the
reaction converting a substrate to a product
 Speed up reactions by 103-1011 compared to other catalysts; 108-1020
compared to uncatalyzed reactions
A C
No enzyme A C
Free energy
E EA
Ea
Enzyme
E-S
E+S Ea
E+P
201
Progress of reaction
Classification of Enzymes
Class Reactions catalyzed

 Oxidoreductoases oxidation-reduction
 Transferases transfer group of atoms
 Hydrolases hydrolysis
 Lyases add/remove atoms
to/from a double bond
 Isomerases rearrange atoms
 Ligases combine molecules
using ATP 202
 There are six main types/groups of enzymes classified
based on their chemical reaction mechanism
1. Oxidoreductases
 Catalyze oxidations or reductions of substrates
 Some important food reaction examples:
 Lipid oxidation – lipoxygenase (adds an oxygen on fatty acids)
 Browning – polyphenol oxidase (oxidizes phenols in food)
2. Transferases
 Catalyze a shift of a chemical group from a donor to acceptor
substrate
 Not so important in foods
203
3. Hydrolases
 Catalyze the hydrolysis (with help of water) of substrates (i.e.
breaking of bonds)
 By far the most important enzymes with respect to food quality
and use in food processing

 Some important food reaction examples:
 Texture, protein modification – proteases (cleave the peptide

bond)
 Texture, carbohydrate modification – e.g. amylases (cleave
glycosidic bonds) and pectinases (act on several
groups/bonds)
 Hydrolytic rancidity, fat crystallization modification – lipases
(cleave ester bonds)
204
4. Lyases
 Catalyze the removal or addition of chemical groups
to substrates
5. Isomerases
 Catalyze intramolecular rearrangements
 An important food reaction example:

 Sweetness (Glu  Fru) – glucose isomerase (converts aldose to ketose)
6. Ligases
 Catalyze combinations of substrates
205
Factors affecting enzyme activity
1. Enzyme and substrate concentration
 When substrate concentration is kept constant the enzyme reaction
is proportional to the amount of enzyme (i.e. doubling enzyme will
double the speed of the reaction) up to a certain limit
Here you start to have more

enzyme than substrate and
rate starts to level off
There is no added benefit for a

food operation to have too
much enzyme ($$$).
That is why we have to study

the ideal concentration to206work
at
Chemical kinetics
120
100
C 80 S 1st Order Reaction

h v = k [S]
60
a
n 40
g
e 20 P
0
0 5 10 15 20 25 30 35 40
-20
Time
207
 Increasing the substrate concentration under fixed
enzyme concentration leads to a non-linear
increase in reaction velocity that can be explained
by the formation of the Enzyme-Substrate
complex:
k1 k2
E + S ↔ E-S ↔E + P
k-1
 This reaction curve is shared by most enzyme and

gives us very useful information on the activity of
the enzyme and the affinity for its substrate
 Vmax gives us the maximum velocity that the enzyme
can produce (under the conditions tested) – the
higher the faster
 Km (determined as ½ Vmax) tells us the affinity of the
enzyme for its substrate
 Vmax/Km = catalytic efficiency (higher number means
more efficient)
208
At low [S]
[E] and [S] determine
rate A B
At high [S]
[E] determines rate
209
2. Temperature
 Enzyme reactions increase
with temperature up to a point
and then activity declines as
the enzyme becomes
denatured
 Different enzymes have
different temperature optima's
(the point when max activity is)
 Important to determine this to
be able to predict what type of
thermal treatment you need in
processing to inactivate
undesirable enzymes
210
3. pH
 All enzymes have a certain narrow range of pH where they
perform best
 Most active between 4.5-8
 Some active at very low (e.g. pepsin) or high pH
 Extremes of pH can affect the enzyme by denaturing it
(remember it is a protein) or affecting the charge of critical amino
acids in its active site (or charge on the substrate)
 For this reason pH control of foods with undesirable enzymes is
important
Trypsin
Pepsin
Activity
1 pH 12 211
4. Water activity
 Water can influence an enzyme in many ways
 It can be critical for the SP reaction (e.g. hydrolysis)
 It can be critical to solubilize the substrate and product
 It can be critical for the flexibility of the enzyme structure
 Water activity can be varied in foods to slow down enzymatic
activity
Enzyme 1
Enzyme 2
Activity
212
0 aw 1
5. Inhibitors
 We can use chemical compounds to inhibit or slow down the
activity of enzymes
1. Competitive inhibitors
 Compete with the substrate for the active site
 Enzyme can only bind to either S (substrate) or I (inhibitor) at one time
2. Non-competitive inhibitors
 Bind to enzyme at another site than active site
 Enzyme can bind to both S and I at the same time
3. Un-competitive inhibitors
 Can only bind to the E-S complex (the intermediate state)
 Enzyme binds first to S and then can bind to I
 These can be reversible or irreversible
 Some food use for these but many have flavor, odor, color and
toxicity problems, plus can be very expensive
213
214
215
Enzymes – Important food enzymes
HYDROLASES
 They all have in common that they break bonds with the help of water
1. Glycoside hydrolases
A) Enzymes that hydrolyze starch (glycosidic bonds)
 -amylase
 Hydrolyses -1-4 glycosidic bonds within starch
 Results in dextrins, maltose and maltotriose
 -amylase
 Hydrolyses -1-4 glycosidic bonds from the non-reducing end of starch
 Results in maltose
 Glucoamylase
 Hydrolyses -1-4 and -1-6 glycosidic bonds in starch
 Can hydrolyze all the way to glucose
 Pullulunase
 Hydrolyses -1-6 glycosidic bonds in starch
 These enzymes are naturally present in the food or are found in
microorganisms added to the food
216
 Food importance of the glycoside hydrolases
Corn syrup production

 Using a cocktail of enzymes
starch can be converted to
a glucose syrup (dextrose)
 Start with -amylase to
break amylose and
amylopectin to smaller units
 Then use glucoamylase to
break down to glucose
 If maltose is desired use -
amylase and pullulanase
217
Baking
 -amylases are important to “dextrinize” the disrupted starch
granules (rupture during milling) and the dextrins are then
hydrolyzed to maltose by -amylase  gives fermentable sugar
for yeast to produce CO2 (essential for rising of the bread)
 On baking there is further action of the amylases on the
gelatinized starch  plays an important role in the final texture
and quality of bread
 Amylases added to bakery products can minimize staling
 Need to add -amylases to some flours (what harvested in dry
climates)
Brewing
 High level of amylases in barley malt (no need to add more)
 During mashing (milled barley malt and water at 50C) amylases
hydrolyze starch to give maltose for yeast to utilize and produce
CO2 and ethanol 218
B) Invertase
 An enzyme that hydrolyzes the glycosidic bond
between glucose and fructose in sucrose
 Results in invert sugar (free glu and fru)
 Popular in the confectionary industry because invert
sugar is sweeter than sucrose and has less tendency

to crystallize
 Popular in soft candy fillings
C) Lactase
 An enzyme that hydrolyses the glycosidic bond
between galactose and glucose in lactose
 Increases sweetness and solubility of the sugar
 Done in the dairy industry to minimize crystallinization
in ice cream and to produce lactose free products 219

2. Pectinases
 Occur widely in fruits and vegetables and are responsible for
the degradation of pectic substances
 Pectin methyl esterase
 Hydrolyze the methyl ester linkages of pectin
 Causes loss of cloud in citrus juice (big problem)
C O O C H
O
3 C O O H
O
C O O C H
O
3 PME
O O O O
C O OCH 3 C O OH C O O CH 3
O O O
O O O O
O O O O
O O O
C O OH C O O C H3
O
Ca
C O O C H 3 C O O H C O O C H 3 O
O O O C O OH O C O O C H3
O O O
O O O
O O O
O O O O O C O OH O C O O C H3 O O
O
Ca
90C for 1 min

O O O O
O
C O O C H C O O H C O O C H C O OH C O O C H3
3 3
O O OO O O
O O O C O OH C O O C H3
O
O O O O
Ca
O O O O O
C O OH C O O C H3
O O O
O O O O
 Converts colloidal pectin to non-colloidal pectin

 We add this enzyme when clarity is desired (e.g. apple juice)
220
221
3. Proteases
 Enzymes that hydrolyze peptide bonds in proteins
A) Papain
 Found in papaya
 Broad pH (3-11) and temperature stability
 For this reason very popular for a variety of food
applications
1. Used as a meat tenderizer on inferior meat cuts (can also use
slice of pineapple on meat)
 The enzyme makes its way into the muscle and
hydrolyzes primarily connective tissue proteins (collagen
etc.) and softens muscle
 Have to use low amount to prevent liquefaction of muscle
 If you mix raw papaya into Jell-O it will not form a gel
 Other popular tenderizing enzymes are ficin (from figs),
bromelain (from pineapple) and microbial proteases
222
2. Papain can also be used to clear turbidity (chill haze) in
beer
 When bottled or canned beer is kept below 10C (50F) a haze
can form
 Interactions of proteins/polypeptides and tannins in beer
 This can be prevented using chill-proofing
 Protease (papain mostly used) added during post-fermentation
maturation to hydrolyze the proteins/polypeptides to prevent large
aggregates to form on cooling
223
B) Digestive proteases
 Trypsin & Chymotrypsin
 Found in animal pancreas
 Can cause quality problems in muscle foods if
contamination from intestines occurs (e.g. ground

products)  over-softening of the meat
 They are often used to make protein hydrolysates for
the food, beverage and the pharmaceutical industry

 Most active at pH 7-9
 Pepsin
 Very acidic activity optima (pH 1.8)
 Somewhat limits its use
 Used in cheese making, chillproofing and also in

making protein hydrolysates 224
 animal and fertilizer use primarily, some for food use

 Chymosin (rennin)
 Essential for the manufacture of good quality cheeses
 Found in the fourth stomach of suckling calf's
 Very expensive and “inhumane” to process now so it has been engineered
into a bacteria that mass produces it
 Has a very specific activity
 Hydrolyzes only one bond in к-casein, one of the many proteins that make up
the milk casein protein complex (к-, -, -casein)
 This breaks up the casein complex (micelle) and it aggregates leading to a clot,
the first step in cheese production
 Most other proteases can initiate a milk clot like chymosin but they would
continue the casein hydrolysis producing bitter peptides and eventually225
breaking the clot
C) Microbial proteases
 Several fungal and bacterial proteases are used in the food
industry
 Fungal proteases
 Some have almost equal ability to form cheese cloths like
chymosin
 A protease cocktail from Aspergillus oryzae is used to
partially break down bread proteins (glutens) to reducing

mixing time and making them more extensible
 Some are added to help with flavor and texture development
and speeding up fermentation in fermented dairy products

 Fungal proteases are also used to tenderize meat
 Bacterial proteases
 Subtilisin from Bacillus subtilisin is popular and is used in
combination with papain in beer chillproofing
226
4. Lipases
 Enzymes that all hydrolyze ester bonds between fatty acids and
a glycerol molecule
 Work at the water-oil interface
 Two classes
a) 1,3-lipases: preferentially hydrolyze ester bonds at SN1 and SN3
b) 2-lipases preferentially hydrolyze ester bonds at SN2
227
 Lipases have a dramatic impact on the quality of food
products
A) Lead to hydrolytic rancidity
 BAD when
 Free fatty acids released in muscle foods and react to proteins to denature them and give a tough texture
(happens on freezing muscle)
 they are not inactivated in milk; release short chain fatty acids that are very volatile and can also oxidize
 GOOD when
 Used in fermented products
 Extremely important in ripening of cheeses and dry-sausages
 Short chain fatty acids released from milk fat produces the characteristic odor and flavor of these products (C:8
especially)
228
229
B) They can be used to modify the properties of lipids
 Very popular application in the margarine industry to modify lipid
crystal structure to give different textures and melting points
 Also used to produce mono and diglycerides for use as emulsifiers
 A very unique reaction system must be used for these enzymes
since they are soluble in water but act on a lipid substrate
The enzyme is
located in the water
droplet of a water-in-
oil emulsion and acts
on the oil
surrounding the
230
water droplet
Corn
ISOMERASES Syrup
 They all catalyze the intramolecular

arrangement within a molecule
 Glucose isomerase
 The most important for the food industry
Glu isomerase
 Catalyzes isomeric rearrangement of pH 7
glucose to fructose (converts an aldose to a 50-60C
ketose)
 Gives a sweeter product than corn syrup
 Sweetness glu = 70; fru = 170; sucrose = 100
 Product called high fructose corn syrup
 Made from corn syrup (which is made by
amylase digestion of starch)
 Enzymes are immobilized in large columns
where the reaction takes place – can reuse 231
them
42% (HFCS) 52%
OXIDOREDUCTASES
 Enzymes that catalyze the oxidation
or reduction of substrates
A) Lipoxygenase
 Found in a wide variety of plants
(primarily legumes) and have also
been identified in animal tissue
(e.g. in the skin of fish)
 Specific for the oxidation of fatty
acids that have a cis, cis penta-
1,4-diene unit, so there are three
naturally occurring fatty acids that
can be substrates
 Linoleic acid (2 double bonds)
 Linolenic acid (3 double bonds)
 Arachidonic acid (4 double bonds)
232
 Importance of lipoxygenases in foods
 Desirable
 The enzyme plays a role in bleaching of wheat and soybean flours
 It contributes to the formation of S-S bonds in gluten in dough, thus
one does not have to add chemical oxidizers
 Undesirable
 Lipid oxidation and reactions of its products
 Breakdown products of hydroperoxides give off-flavors and odors
 Oxidation products (the free radicals or hydroperoxide) can bind and/or
oxidize proteins to lead to textural problems
 Lipid oxidation also leads to nutritional loss of essential polyunsaturated
fatty acids
 Vitamins may also be oxidized by the oxidation products
 Chlorophylls and carotenes can be bleached
 Its action can be effectively delayed by using antioxidants
233
Enzymes – Important food
enzymes
B) Polyphenol oxidase (PPO)
 Found in plants (fruits and
vegetables), animals (including
humans), insects and microbes
 Catalyzes the oxidation of phenolic
compounds (mono and/or
diphenols) in the presence of O2 to
give quinones which polymerize
into melanin pigments (desirable or
undesirable)
 Its activity can be inhibited by: Polymerizes  Melanins
 Removing O2 Undesirable browning of apples,
 pH < 4.5 (lemon juice) bananas, mushrooms, shrimp,
 Ascorbic acid (vit-C) (again, lemon lobster, human freckles?
juice) Up to 50% economic loss of tropical
 Bi-sulfites fruit due to PPO activity
 EDTA
Desirable browning of tea, coffee,
cocoa, raisins, prunes, tobacco,
234
human tan, freckles?
235
Learning Check
A. The active site is

(1) the enzyme
(2) a section of the enzyme
(3) the substrate
B. In the induced fit model, the shape of the

enzyme when substrate binds
(1) Stays the same
(2) adapts to the shape of the substrate
236
Solution
A. The active site is

(2) a section of the enzyme
B. In the induced fit model, the shape of the

enzyme when substrate binds
(2) adapts to the shape of the substrate
237
Learning Check
Surcease has an optimum temperature of

37°C and an optimum pH of 6.2. Determine
the effect of the following on its rate of
reaction
(1) no change (2) increase (3) decrease
A. Increasing the concentration of sucrose
B. Changing the pH to 4
C. Running the reaction at 70°C
238
Solution
Surcease has an optimum temperature of

37°C and an optimum pH of 6.2. Determine
the effect of the following on its rate of
reaction
(1) no change (2) increase (3) decrease
A. 2, 1 Increasing the concentration of
sucrose
B. 3 Changing the pH to 4
C. 3 Running the reaction at 70°C
239
Nucleic acids
240
DNA (Deoxyribonucleic Acid)
“The Blueprint of Life”
DNA Structure & Function
241
A. What is DNA?
1. Organic molecule
2. Nucleic acid
242
B.Where is it located?
1. Nucleus
2. Chromosomes
DNA
243
Nucleotides
Nucleic acids consist of nucleotides that

have a sugar, nitrogen base, and phosphate
Base
PO4
Sugar
nucleoside
244
Nitrogen-Containing Bases
O
NH2
H CH3
N N
N
N O N
N
H H
adenine (A) thymine (T)
O NH2 O
H N CH3 H CH3
N N N
NH2 N N O N O N
H H H
guanine (G) cytosine (C) uracil (U)
245
Sugars
HOCH2 O OH HOCH2 O OH
OH OH OH (no O)
ribose deoxyribose
246
D. What is DNA’s Function?
 Hereditary Instructions
 Chemical code for every trait
 “Blueprint” for making Proteins
247
Chromosome DNA Code:
Genes = Hair
 Segments of DNA
Color
 Code for a trait
Eye
Color
248
DNA Chromosome Code:
Acid Acid
Sugar-T-A-
Triplets=
Sugar
Acid Acid  Sets of 3
Sugar-G-C-
Sugar Nucleotides
Acid Acid
Sugar-C-G-
Sugar
 Code for
Trait
249
DNA Replication
 Chromosomes double
 Mitosis
 Late Interphase
 2n to 4n
250
E. Steps for DNA Replication:
1. DNA untwists
2. DNA unzips
3. Corresponding base pairs
Line up
In sets of 3
nucleotides (triplets)
Or “codons”
4. DNA reforms
5. 2 strands twist into helix
Identical
251
Strand
RNA Ribonucleic Acid
“DNA messenger & taxi”
II. RNA Structure & Function
252
A. What is RNA?
1. Organic
Molecule
2. Nucleic Acid
3. mRNA=
messenger
tRNA=
transfer
253
B. Where is RNA located?
1. mRNA in
nucleus &
mRNA
cytoplasm
2. tRNA only mRNA
in
cytoplasm tRNA
254
B. What is RNA’s structure?
1. Nucleotides=
 Acid a. Phosphoric Acid
 Sugar-Base b. Ribose sugar
 Acid c. Nitrogenous
 Sugar-Base Bases:
 Acid Adenine-Uracil
 Sugar-Base Guanine-Cytocine
 Acid 2. Single Strand
 Sugar-Base 3. No Twisted helix 255
Comparison of RNA & DNA:
 Acid Acid Acid

 Uracil
Sugar-Base Sugar-Base-Sugar
Thymine
 Acid Acid Acid
 Sugar-Base
Sugar-Base-Sugar
 Acid
 Sugar-Base Acid Acid
Deoxy-
Sugar-Base-Sugar
 Acid ribose
 Ribose
Sugar-Base Acid Acid
RNA DNA Ladder 256
D. What are RNA’s functions:
1. mRNA=
 Copies the DNA
code
 Deliveries
message to
Ribosome
 Protein Factories
257
RNA function cont.
2. tRNA:
 in cytoplasm
 Picks up an amino acid
 “Taxis” the aa to the Ribosome protein factories
258
III. Protein Synthesis
Assembling Proteins from the DNA

Instructions
259
A. Transcription:
1. mRNA is copied off of DNA
2. In nucleus
3. Steps:
I. DNA untwists
II. DNA unzips
III. RNA codons line up
260
Transcription: mRNA has:
 Ribose sugar
 Uracil instead
mRNA of thymine
A bases
U  Nuclear
T membrane
allows it to
A leave!
C
G
G
C
DNA Code
261
Transcription in
The nucleus
DNA mRNA copy
262
B. Translation
 Conversion of the
message (mRNA Code)
 Into a protein
 By the ribosome
factories
263
tRNA taxi
B.Translation A
1. mRNA arrives at the
Ribosome
2. tRNA picks up an amino
acid
3. tRNA delivers the aa to
U
the ribosome
4. aa are assembled into
polypeptide proteins C
G
U A G C
mRNA code 264
DNA Replication and Repair
 Enzyme regulated
 Hydrogen bonds
break
 Attachment of
nucleotides to new
strands
 DNA polymerases
DNA ligases
 New strand is half
old, half new 265
Detailed Look at Replication
 In this replication fork the

helicases have unwind the
DNA.
 Binding proteins are
breaking the base pairs.
 DNA polymerase is copying
each strand; one side
continuous and the other in
smaller fragments.
 DNA ligase binds smaller
fragments together to
produce identical copies.
266
Transcription and Translation:
DNA
Transcription
RNA
Translation
Protein
267
Transcription vs. Translation Review
Transcription Translation
 Process by which  Process by which
genetic information information
encoded in DNA is encoded in mRNA
copied onto is used to
messenger RNA assemble a protein
 Occurs in the at a ribosome
nucleus  Occurs on a
 DNA mRNA Ribosome
 mRNA protein
268
Chapter five
269
Cellular Respiration
270
Harvesting Chemical
Energy
C6H12O6 + 6O2 6H2O + 6CO2 + Energy
271
What is cell respiration???
 Respiration: the process of breaking down food
molecules into usable energy
 THE GOAL:
 Create ATP for cells to use
 Free up electrons—have high energy
272
 A catabolic, exergonic, oxygen (O2) requiring

process that uses energy extracted from
macromolecules (glucose) to produce energy
(ATP) and water (H2O).
C6H12O6 + 6O2  6CO2 + 6H2O + energy
glucose ATP
273
Question:
 In what kinds organisms does cellular
respiration take place?
274
Plants and Animals
 Plants - Autotrophs:
Autotrophs self-producers.
 Animals - Heterotrophs: consumers.
275
Mitochondria
 Organelle where cellular respiration takes place.
Inner Matrix
membrane space Cristae
Outer
membrane
Inner
membrane
276
Redox Reaction
 Transfer of one or more electrons from one
reactant to another.
 Two types:
1. Oxidation
2. Reduction
277
Oxidation Reaction
 The loss of electrons from a substance.
 Or the gain of oxygen.
oxygen
Oxidation
C6H12O6 + 6O2 6CO2 + 6H2O + energy
glucose ATP
278
Reduction Reaction
 The gain of electrons to a substance.
 Or the loss of oxygen.
oxygen
Reduction
C6H12O6 + 6O2  6CO2 + 6H2O + energy

glucose ATP
279
Breakdown of Cellular
Respiration
 Four main parts (reactions).
1. Glycolysis (splitting of sugar)

a. cytosol, just outside of mitochondria.
2. Grooming Phase
a. migration from cytosol to matrix.
280
Breakdown of Cellular
Respiration
3. Krebs Cycle (Citric Acid Cycle)
a. mitochondrial matrix
4. Electron Transport Chain (ETC) and

Oxidative Phosphorylation
a. Also called Chemiosmosis
b. inner mitochondrial membrane.
281
1. Glycolysis
 Occurs in the cytosol just outside of
mitochondria.
 Two phases (10 steps):
A. Energy investment phase
a. Preparatory phase (first 5 steps).
B. Energy yielding phase
a. Energy payoff phase (second 5 steps).
282
1. Glycolysis
A. Energy Investment Phase:
Glucose (6C) C-C-C-C-C-C
2ATP
2 ATP - used
0 ATP - produced
0 NADH - produced
2ADP + P
Glyceraldehyde phosphate (2 - 3C) C-C-C C-C-C

(G3P or GAP)
283
1. Glycolysis
B. Energy Yielding Phase
Glyceraldehyde phosphate (2 - 3C)

(G3P or GAP) GAP GAP
C-C-C C-C-C
4ADP + P 0 ATP - used

4 ATP - produced
2 NADH - produced
4ATP
C-C-C C-C-C
(PYR) (PYR)
Pyruvate (2 - 3C)
(PYR)
284
1. Glycolysis
 Total Net Yield
2 - 3C-Pyruvate (PYR)
2 - ATP (Substrate-level Phosphorylation)
2 - NADH
285
10 Steps of Glycolysis
 Step 1
The enzyme hexokinase phosphorylates (adds a

phosphate group to) glucose in the cell's cytoplasm.
In the process, a phosphate group from ATP is
transferred to glucose producing glucose 6-
phosphate.
Glucose (C6H12O6) + hexokinase + ATP → ADP +

Glucose 6-phosphate (C6H11O6P1)
286
Step 2
The enzyme phosphoglucoisomerase converts
glucose 6-phosphate into its isomer fructose 6-
phosphate. Isomers have the same molecular
formula, but the atoms of each molecule are
arranged differently.
Glucose 6-phosphate (C6H11O6P1) +

Phosphoglucoisomerase → Fructose 6-
phosphate (C6H11O6P1)
287
Step 3
 The enzyme phosphofructokinase uses
another ATP molecule to transfer a phosphate
group to fructose 6-phosphate to form
fructose 1, 6-diphosphate.
Fructose 6-phosphate (C6H11O6P1) +

phosphofructokinase + ATP → ADP + Fructose 1, 6-
diphosphate (C6H10O6P2)
288
Step 4
 The enzyme aldolase splits fructose 1, 6-diphosphate
into two sugars that are isomers of each other. These
two sugars are dihydroxyacetone phosphate and
glyceraldehyde phosphate.
Fructose 1, 6-diphosphate (C6H10O6P2) + aldolase → Dihydroxyacetone

phosphate (C3H5O3P1) + Glyceraldehyde phosphate (C3H5O3P1)
289
Step 5
 The enzyme triose phosphate isomerase rapidly inter-converts the
molecules dihydroxyacetone phosphate and glyceraldehyde phosphate.
Glyceraldehyde phosphate is removed as soon as it is formed to be
used in the next step of glycolysis.
Dihydroxyacetone phosphate (C3H5O3P1) → Glyceraldehyde phosphate

(C3H5O3P1)
Net result for steps 4 and 5: Fructose 1, 6-diphosphate (C6H10O6P2) ↔ 2

molecules of Glyceraldehyde phosphate (C3H5O3P1)
290
Step 6
The enzyme triose phosphate dehydrogenase serves two functions in this
step. First the enzyme transfers a hydrogen (H-) from glyceraldehyde
phosphate to the oxidizing agent nicotinamide adenine dinucleotide (NAD+)
to form NADH. Next triose phosphate dehydrogenase adds a phosphate
(P) from the cytosol to the oxidized glyceraldehyde phosphate to form 1, 3-
diphoshoglyceric acid. This occurs for both molecules of glyceraldehyde
phosphate produced in step 5.
A. Triose phosphate dehydrogenase + 2 H- + 2 NAD+ → 2 NADH + 2 H+

B. Triose phosphate dehydrogenase + 2 P + 2 glyceraldehyde phosphate
(C3H5O3P1) → 2 molecules of 1,3-diphoshoglyceric acid (C3H4O4P2)
291
Step 7
The enzyme phosphoglycerokinase transfers a P from 1,3-
diphoshoglyceric acid to a molecule of ADP to form ATP. This
happens for each molecule of 1,3-diphoshoglyceric acid. The
process yields two 3-phosphoglyceric acid molecules and two ATP
molecules.
2 molecules of 1,3-diphoshoglyceric acid (C3H4O4P2) +

phosphoglycerokinase + 2 ADP → 2 molecules of 3-
phosphoglyceric acid (C3H5O4P1) + 2 ATP
292
Step 8
The enzyme phosphoglyceromutase relocates the P from 3-

phosphoglyceric acid from the third carbon to the second carbon to
form 2-phosphoglyceric acid.
2 molecules of 3-Phosphoglyceric acid (C3H5O4P1) +

phosphoglyceromutase → 2 molecules of 2-Phosphoglyceric acid
(C3H5O4P1)
293
Step 9
 The enzyme enolase removes a molecule of water from 2-
phosphoglyceric acid to form phosphoenolpyruvic acid (PEP).
This happens for each molecule of 2-phosphoglyceric acid.
2 molecules of 2-Phosphoglyceric acid (C3H5O4P1) + enolase →

2 molecules of phosphoenolpyruvic acid (PEP) (C3H3O3P1)
294
Step 10
 The enzyme pyruvate kinase transfers a P from PEP to ADP to
form pyruvic acid and ATP. This happens for each molecule of
PEP. This reaction yields 2 molecules of pyruvic acid and 2 ATP
molecules.
2 molecules of PEP (C3H3O3P1) + pyruvate kinase + 2 ADP → 2

molecules of pyruvic acid (C3H4O3) + 2 ATP
295
Fermentation
 Occurs in cytosol when “NO Oxygen” is present

(called anaerobic).
 Remember: glycolysis is part of fermentation.
fermentation
 Two Types:
1. Alcohol Fermentation
2. Lactic Acid Fermentation
296
Alcohol Fermentation
 Plants and Fungi  beer and wine
2ADP 2ATP
C +2 P 2NADH 2 NAD+
C
C C
C
C Glycolysis C
C
C C
C
2 Ethanol
2 Pyruvic 2CO2
2 NAD+ 2NADH acid released
glucose
297
Alcohol Fermentation
 End Products: Alcohol fermentation
2 - ATP (substrate-level phosphorylation)

2 - CO2
2 - Ethanol’s
298
Lactic Acid Fermentation
 Animals (pain in muscle after a workout).
2ADP 2ATP
C
+2 P
C 2NADH
C 2 NAD+
C C
C
Glycolysis C C
C
C C
C
2 Pyruvic 2 Lactic
2 NAD+ 2NADH
acid
acid
Glucose
299
Lactic Acid Fermentation
 End Products: Lactic acid fermentation
2 - ATP (substrate-level phosphorylation)

2 - Lactic Acids
300
2. Grooming Phase
 Occurs when Oxygen is present (aerobic).

 2 Pyruvate (3C) molecules are transported through
the mitochondria membrane to the matrix and is
converted to 2 Acetyl CoA (2C) molecules.
Cytosol 2 CO2
C
C
C Matrix
2 Pyruvate C-C
2 NAD+ 2NADH 2 Acetyl CoA
301
2. Grooming Phase
 End Products: grooming phase
2 - NADH
2 - CO2
2- Acetyl CoA (2C)
302
 Location: mitochondrial matrix.
 Acetyl CoA (2C) bonds to Oxalacetic acid

(4C - OAA) to make Citrate (6C).
 It takes 2 turns of the krebs cycle to oxidize
1 glucose molecule.
Mitochondrial
Matrix
303
1 Acetyl CoA (2C)
OAA (4C) Citrate (6C)
2 CO2
Krebs
Cycle
FADH2 (one turn) 3 NAD+
FAD
3 NADH
ATP 304
ADP + P
2 Acetyl CoA (2C)
Citrate (6C)
OAA (4C)
4 CO2
Krebs
Cycle
2 FADH2 (two turns) 6 NAD+
2 FAD
6 NADH
2 ATP 305
2 ADP + P
 Total net yield (2 turns of krebs cycle)
1. 2 - ATP (substrate-level phosphorylation)

2. 6 - NADH
3. 2 - FADH2
4. 4 - CO2
306
Steps of the Krebs cycle
307
308
1. In the first step, coenzyme A transfers a two-carbon
acetyl group to the oxaloacetate, a four-carbon
compound. This forms the six-carbon molecule
citrate.
2. In step two, the citrate rearranges to form six-carbon
isocitrate.
309
3. In the third step, the isocitrate is oxidized and
a carbon dioxide molecule is removed. The result is a
five-carbon molecule alpha-ketoglutarate and the
reduction of NAD+ to NADH and H+.
4. In the fourth step, the alpha-ketoglutarate is
oxidized, carbon dioxide is again removed, and
coenzyme A is added. This forms the four-carbon
compound succinyl-CoA. Like the prior step, during
oxidation, NAD+ is reduced to NADH and H+.
310
5. In step five, coenzyme A is removed from
succinyl-CoA, resulting in the production of
succinate,
6. Then, succinate is oxidized to form fumarate
7. In step seven, water is added to the
fumarate, resulting in malate. Finally, malate is
oxidized, resulting in oxaloacetate.
311
8. During this final oxidation, NAD+ is reduced to NADH
and H+. For each Krebs Cycle, two molecules of carbon
dioxide are formed and oxaloacetate is regenerated.
This process allows for the next stage of glucose
oxidation.
312
Oxidative Phosphorylation (Chemiosmosis)
 Location: inner mitochondrial membrane.
 Uses ETC (cytochrome proteins) and ATP

Synthase (enzyme) to make ATP.
 ETC pumps H+ (protons) across innermembrane
(lowers pH in innermembrane space).
Inner
Mitochondrial
Membrane
313
 The H+ then move via diffusion (Proton Motive

Force) through ATP Synthase to make ATP.
 All NADH and FADH2 converted to ATP during
this stage of cellular respiration.
respiration
 Each NADH converts to 3 ATP.
 Each FADH2 converts to 2 ATP (enters the ETC

at a lower level than NADH).
314
Inner Matrix
membrane space Cristae
Outer
membrane
Inner
membrane
315
4. ETC and Oxidative Phosphorylation
(Chemiosmosis for NADH)
Intermembrane Space higher H+

concentration
1H+ 2H+ 3H+ H+ ATP
Synthase
Inner
E T C Mitochondrial
Membrane
O2
2H+ + 1/2
H2O
ADP + P
ATP
NADH NAD+
H+
+ H+
(Proton Pumping)
lower H+
concentration
Matrix 316
4. ETC and Oxidative Phosphorylation
(Chemiosmosis for FADH2)
Intermembrane Space higher H+

concentration
1H+ 2H+ H+ ATP
Synthase
Inner
E T C Mitochondrial
Membrane
ADP + P
FADH2 FAD+
2H+ +
H2O H+ ATP
+ H+ 1/2O2
(Proton Pumping)
lower H+
concentration
Matrix 317
TOTAL ATP YIELD
1. 04 ATP - substrate-level phosphorylation
2. 34 ATP - ETC & oxidative phosphorylation
38 ATP - TOTAL YIELD
ATP
318
Eukaryotes
(Have Membranes)
 Total ATP Yield
02 ATP - glycolysis (substrate-level phosphorylation)
04 ATP - converted from 2 NADH - glycolysis
06 ATP - converted from 2 NADH - grooming phase
02 ATP - Krebs cycle (substrate-level phosphorylation)
18 ATP - converted from 6 NADH - Krebs cycle
04 ATP - converted from 2 FADH2 - Krebs cycle
36 ATP - TOTAL
319
18
320
Maximum ATP Yield for Cellular
Respiration (Eukaryotes)
Glucose
Cytosol
Mitochondria
Glycolysis 2 Acetyl CoA Krebs
Cycle
2 Pyruvate
2NADH 2 ATP
6NADH 2FADH2 (substrate-level
phosphorylation)
2NADH
ETC and Oxidative
Phosphorylation
2 ATP
(substrate-level
phosphorylation) 2ATP 4ATP 6ATP 18ATP 4ATP 2ATP
321
36 ATP (maximum per glucose)

Prokaryotes
(Lack Membranes)
 Total ATP Yield
02 ATP - glycolysis (substrate-level phosphorylation)
06 ATP - converted from 2 NADH - glycolysis
06 ATP - converted from 2 NADH - grooming phase
02 ATP - Krebs cycle (substrate-level phosphorylation)
18 ATP - converted from 6 NADH - Krebs cycle
04 ATP - converted from 2 FADH2 - Krebs cycle
38 ATP - TOTAL
322
Question:
 In addition to glucose, what other various
food molecules are use in Cellular
Respiration?
323
Catabolism of Various
Food Molecules
 Other organic molecules used for fuel.
1. Carbohydrates: polysaccharides
2. Fats: glycerol’s and fatty acids
3. Proteins: amino acids
324
Lipids metabolism
 Glycerol and fatty acids
 both oxidized as fuel
 Fatty acids
 converted to acetyl CoA by β-oxidation
325
Catabolic Pathways
326
327
OXIDATION OF FATTY ACIDS:
KETOGENESIS
 The initial event in the utilization of fat as an energy
source is the hydrolysis of triacylglycerol by lipases
328
 Epinephrine, norepinephrine, glucagon, and
adrenocorticotropic hormone stimulate the adenylate
cyclase of adipose cells, and thus cause lipolysis.
329
Fatty acids are synthesized and degraded
by different mechanisms:
 Fatty acids are both oxidized to acetyl-CoA and

synthesized from acetyl-CoA. Although the staring
material of one process is identical to the product of the
other, fatty acid oxidation is not the simple reverse of fatty
acid biosynthesis. It is an entirely different process taking
place in separate compartment of the cell. This allows
each process to be individually controlled.
330
Fatty acids are synthesized and degraded by
different mechanisms:
Synthesis Oxidation
Cytosol Mitochondrial matrix
Intermediates are covalently Bonded to CoA
linked to ACP Degradative enzymes are
Fatty acid synthase contain not associated
multi enzyme activities Utilizes NAD+ and FAD as
Utilizes NADP+ as coenzymes
coenzyme Generates ATP
Requires both ATP and Aerobic process
bicarbonate ion
331
Step 1: Activation of fatty acids to acyl-CoA: Acyl-CoA
synthetics are found in the endoplasmic reticulum,
peroxisomes, and inside and on the outer membrane of
mitochondria. Several acyl-CoA synthetics have been
described, each for fatty acids of different chain length.
R-COO- + CoA + ATP + H20 Acyl CoA + AMP + 2Pi + 2H+
332
Step 2: Long-chain fatty acids penetrate inner
mitochondrial membrane as carnitine derivatives. Carnitine
(ß-hydroxy-g-trimethylammonium butyrate) is widely
distributed and abundant in muscle. Carnitine
palmitoyltransferase-I, present in the outer mitochondrial
membrane, catalyzes the following reaction:
333
334
Step 3: ß-oxidation of fatty acids involves successive cleavage with
release of acetyl-CoA. Fatty acid oxidase are found in the mitochondrial
matrix or inner membrane adjacent to the respiratory chain in the inner
membrane.
335
Oxidation of unsaturated fatty acids occurs by
a modified -oxidation pathway:
336

Oxidation of fatty acids produces a large quantity of ATP:
Palmitoyl CoA + 7 FAD + 7 NAD+ + 7 CoA + 7H2O

8 acetyl CoA + 7 FADH2 + 7 NADH + 7 H+
Oxidation of NADH - 3ATP

'' FADH2 - 2 ATP
'' Acetyl-CoA - 12 ATP

7 FADH2 yields 14
7 NADH yields 21
8 acetyl-CoA yields 96

Total 131 ATP

2 high energy phosphate bonds are consumed in the activation of palmitate

Net yield is 129 ATP or 129 X 51.6 = 6656 kJ
337
TRIACYLGLYCEROLS ARE HIGHLY
CONCENTRATED ENERGY STORES
The initial event in the utilization of fat as an energy source

is the hydrolysis of triacylglycerol by lipases.
338
-Reduced and anhydrous; Complete oxidation of fatty acids yields 9 kCal/g, where as, proteins and
carbohydrates yield 4 kCal/g.

A 70 kg man: 100,000 kCal in triacylglycerols
25,000 kCal in proteins (muscles)
600 kCal in glycogen
400 kCal in glucose

-Triacylglycerols constitute about 11 kg of his total body weight. If this amount were stored in
glycogen, his total body weight would be 55 kg greater.
-In mammals, the major site of accummulation of triacylglycerols is the cytoplasm of adipose cells (fat
cells). Droplets of triacylglycerol coalesce to form a large globule, which may occupy most of the cell
volume.
-Adipose cells are specialized for the synthesis and storage of triacylglycerols and for their mobilization
into fuel molecules that are transported to other tissues by the blood.
339
PROTEINS CARBOHYDRATES FATS
Amino GlycolysisGlycerol Fatty

acids acids
Glucose
G3P
Pyruvate
CO2
Acetyl
coenzyme
A
Citric
acid
cycle
Electron
transport and
chemiosmosis
End 340
products: NH3 H2O CO2

Fig. 8-12, p. 186
PROTEINS CARBOHYDRATES FATS
Amino Glycolysis Glycerol Fatty

acids acids
Glucose
G3P
Pyruvate
CO2
Acetyl
coenzyme
A
Citric
acid
cycle
Electron
transport and
chemiosmosis
Stepped Art
End 341
products: NH3 H2O CO2
Fig. 8-12, p. 186
KEY CONCEPTS
 Nutrients other than glucose, including many
carbohydrates, lipids, and amino acids, can be
oxidized by aerobic respiration
342
343
Protein Turnover and Amino
Acid Catabolism
344
Overview: dietary origin of amino acids
INGESTED PROTEIN
PEPSIN
STOMACH
PEPTIDES
TRYPSIN
CHYMOTRYPSIN
SMALLER PEPTIDES CARBOXYPEPTIDASES
AMINOPEPTIDASE
SMALL INTESTINE
+ SHORT PEPTIDES
BLOODSTREAM
345
Nitrogen Balance
N balance - Amount of N consumed equals N released. True of
healthy, well-fed adult ( ~75% of AAs from body protein turnover
is re-used for synthesis of new protein; remaining ~25% is
converted to other N-containing compounds or oxidized)
Negative N balance- More N leaves than enters; Occurs in either
protein malnutrition or disease( protein-derived AAs are used for
energy)
Positive N balance- Incorporating more N than losing due to
growth/tissue replacement; Occurs in infants and children.
346
Oxidation of AAs as fuel occurs
to significant extent in three conditions
1) Normal turnover of proteins, if amino acid

levels are high
2) High protein diet (amino acids not stored)
3) Starvation or disease state
347
Amino acid catabolism
 What happens to the carbon skeleton?
 How does amino acid catabolism yield energy?
 20 catabolic pathways converge to form 7 products
1. Pyruvate
2. -ketoglutarate
3. Succinyl-CoA
4. Fumarate
5. Oxaloacetate
6. Acetyl-CoA
7. Acetoacetyl-CoA
 Glucogenic vs. ketogenic
348
349
Amino Acid Carbon Skeletons
Amino acids, when deaminated, yield -keto

acids that, directly or via additional reactions,
feed into major metabolic pathways (e.g., Krebs
Cycle).
Amino acids are grouped into 2 classes, based
on whether or not their carbon skeletons can be
converted to glucose:
 glucogenic
 ketogenic.
350
Carbon skeletons of glucogenic amino acids are
degraded to:
 pyruvate, or
 a 4-C or 5-C intermediate of Krebs Cycle. These
are precursors for gluconeogenesis.
Glucogenic amino acids are the major carbon
source for gluconeogenesis when glucose
levels are low.
They can also be catabolized for energy, or
converted to glycogen or fatty acids for energy
storage.
351
Carbon skeletons of ketogenic amino acids are
degraded to:
 acetyl-CoA, or
 acetoacetate.
Acetyl CoA, & its precursor acetoacetate, cannot
yield net production of oxaloacetate, the
gluconeogenesis precursor.
For every 2-C acetyl residue entering Krebs
Cycle, 2 C leave as CO2.
Carbon skeletons of ketogenic amino acids can
be catabolized for energy in Krebs Cycle, or
converted to ketone bodies or fatty acids.
They cannot be converted to glucose. 352
COO COO
CH2 CH2
CH3 CH2 CH3 CH2
HC N H 3+ + C O C O + HC N H 3+
COO COO COO COO
a la n in e  -k e to g lu ta ra te p y r u v a te g lu ta m a t e
A m in o t r a n s f e r a s e ( T r a n s a m in a s e )
The 3-C -keto acid pyruvate is produced from

alanine, cysteine, glycine, serine, & threonine.
Alanine deamination via Transaminase directly
yields pyruvate. 353
H 2O H 2O N H 4+ O
H   
HO CH2 C COO H 2C C COO H 3C C COO
N H 3+ N H 3+
s e rin e a m in o a c ry la te p y ru v a te
S e rin e D e h y d ra ta s e
Serine is deaminated to pyruvate via Serine

Dehydratase.
Glycine, which is also product of threonine catabolism,
is converted to serine by a reaction involving
tetrahydrofolate (to be discussed later). 354
COO COO
COO CH2 COO CH2
CH2 CH2 CH2 CH2
HC N H 3+ + C O C O + HC N H 3+
COO COO COO COO
a s p a r ta t e  -k e to g lu t a r a te o x a lo a c e ta te g l u t a m a te
A m in o tr a n s f e r a s e ( T r a n s a m in a s e )
The 4-C Krebs Cycle intermediate oxaloacetate is
produced from aspartate & asparagine.
Aspartate transamination yields oxaloacetate.
Aspartate is also converted to fumarate in Urea
Cycle. Fumarate is converted to oxaloacetate in 355
Krebs cycle.
H 2N O

C H 2O N H 4+ C O O
CH2 CH2
HC N H 3+ HC N H 3+
COO COO
a s p a r a g in e a s p a r ta te
A s p a ra g in a s e
Asparagine loses the amino group from its R-

group by hydrolysis catalyzed by Asparaginase.
This yields aspartate, which can be converted to
oxaloacetate, e.g., by transamination.
356
The 4-C Krebs Cycle intermediate succinyl-
CoA is produced from isoleucine, valine, &
methionine.
Propionyl-CoA, an intermediate on these
pathways, is also a product of -oxidation of
fatty acids with an odd number of C atoms.
357
Proteins are degraded into amino acids.
Protein turnover is tightly regulated.
First step in protein degradation is the removal of the
nitrogen
Ammonium ion is converted to urea in most mammals.
Carbon atoms are converted to other major metabolic
intermediates.
Inborn errors in metabolism
358
 Amino acids are also a source of nitrogen for other
biomolecules.
359
Excess amino acids cannot be stored.
Surplus amino acids are used for fuel.
 Carbon skeleton is converted to
Acetyl–CoA
Acetoacetyl–CoA
Pyruvate
Citric acid cycle intermediate
 The amino group nitrogen is converted to urea and
excreted.
Glucose, fatty acids and ketone bodies can be formed
from amino acids.
360
Protein Degradation
Dietary proteins are a vital source of amino acids.
Discarded cellular proteins are another source of

amino acids.
361
Dietary Protein Degradation
 Dietary proteins are hydrolyzed to amino acids and
absorbed into the bloodstream.
362
Cellular Protein Degradation
 Cellular proteins are degraded at different rates.
 Ornithine decarboxylase has a half-life of 11

minutes.
 Hemoglobin lasts as long as a red blood cell.
 Υ-Crystallin (eye lens protein) lasts as long as

the organism does.
363
Removal of Nitrogen
 The first step in amino acid degradation is the
removal of the nitrogen.
 The liver is the major site of protein degradation in

mammals.
 Deamination produces α-keto acids, which

are degraded to other metabolic
intermediates.
364
Conversion to Ammonium Ions
 α–Amino groups are converted to
ammonium ions by the oxidative
deamination of glutamate
365
Transamination
 Generally these enzyme funnel amino groups to α–
ketoglutarate.
 Aspartate transaminase
 Alanine transaminase
366
Deamination
 Glutamate dehydrogenase
367
Deamination
 In most terrestrial vertebrates the ammonium ion is
converted to urea.
368
Serine and Threonine
 The β–hydroxy amino acids,
serine and threonine, can
be directly deaminated
369
Transporting Nitrogen to Liver
Urea is produced in the Liver
The alanine cycle is used to transport nitrogen to the
liver
370
Ammonium Ion
 Ammonium ion is converted into urea in most terrestrial
vertebrates
371
The Urea Cycle
372
Formation of Carbamoyl Phosphate
 Carbamoyl synthetase
 Free NH4 reacts with HCO3 to form carbamoyl
phosophate.
 Reaction is driven by the hydrolysis of two
molecules of ATP
373
Formation of Citrulline
 Ornithine transcarbamoylase
 Citrulline is formed from transfer of the carbamoyl
group to the γ-amino group of ornithine.
374
Formation of Arginosuccinate
 Condensation of citrulline with aspartate to form
arginosuccinate
 Two equivalent of ATP are required.
375
Formation of Arginine and Fumarate
 Arginosuccinase
 Cleaves arginosuccinate to form arginine and
fumarate
376
4.1 Formation of Urea
 Arginase
 The arginine is hydrolyzed to produce the urea
and to reform the ornithine.
 The ornithine reenters the mitochondrial matrix.
377
Linked to Citric Acid Cycle
 The urea cycle is linked to the citric acid cycle: Kreb’s Bi-
cycle!!
378
Carbon Atoms
 The carbon atoms of degraded amino acids emerge as
major metabolic intermediates.
 Degradation of the 20 amino acids funnel into 7
metabolic intermediates
 Acetyl–CoA
 Acetoacetyl–CoA
 Pyruvate Ketogenic

α-Ketoglutarate

Succinyl–CoA
Glucogenic

Fumarate

Oxaoloacetate
379
Carbon Atoms
Ketogenic Glucogenic Both
leucine serine isoleucine
lysine threonine phenylalanine
aspartic acid tryptophan
glutamic acid tyrosine
asparagine
glutamine
glycine
alanine
valine
proline
histidine
arginine
methionine
cysteine
380
Carbon Atoms
381
Pyruvate Entry Point
382
Oxaloacetate Entry Point
 Aspartate
 Transamination to oxaloacetate
 Asparagine
 Hydrolysis to Aspartate + NH4+
 Transmination to oxaloacetate
383
α–Ketoglutarate Entry Point
 Five carbon amino acids
384
 Histidine
385
 Proline and Arginine
386
Succinyl–CoA Entry Point
 Methionine, Valine & Isoleucine
387
Succinyl–CoA Entry Point
 Methionine
 Forms S-Adenosylmethionine
388
Branched-chained Amino Acids
389
Aromatic Amino Acids
 Phenylalanine
390
 Tetrahydrobiopterin - electron carrier
391
Aromatic Amino
Acids
 Phenylalanine & Tyrosine
392
 Tryptophan
393

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‫بسم هللا الرحمن الرحيم‬

 Amino acids and protein structures

CH2OH CH2OH CH2OH

CH2OH CH2OH CH2OH

Draw the structure and Fischer projection of D-fructose.

Copyright © 2007 by Pearson Education, Inc

 Form when the hydroxyl group on C-5 reacts with the

C2 and C4 below the ring.

Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

D-glucose D-gluconic acid

D-mannitol D-mannose D-mannonic acid

Identify the monosaccharides in each of the following:

A. Cellulose -1,4-glycosidic bonds

B. Amylose -1,4-glycosidic bonds

C. Glycogen -1,4-and -1,6-glycosidic bonds

 Soluble in non-polar organic solvents

HC O Energy-Containing Nutrients (C and H)

More reduced state (more H bound to C)

 Regulatory functions: lower BP, blood clotting, uterine

 Micelles formed during digestion 82

 Major issue in feeding fats to ruminants

 Antioxidants prevent oxidation

 With a few exceptions, natural fatty acids:

 As chain length increases, melting point

and free radicals, which can cause damage to

 Trans configuration alters biological effects

Ω-3 Ω-6 Ω-9

 Animals can synthesize a fatty acid with a

 Named according to location of H’s

Cis-9-octadecenoic acid Trans-9-octadecenoic acid

 Geometrical isomers due  Chain branching

 Affected by chain length

Fatty acid: C12:0 C14:0 C16:0 C18:0 C20:0

Which fatty acids are liquid at room temperature?

 In most fats with a mixture of fatty acids, the

Stearic Acid (18 C) Beef Tallow Solid

Arachidic Acid (20 C) Butter Solid

 Affected by number of double bonds

Fatty acid: C18:0 C18:1 C18:2 C18:3

Which fatty acid is liquid at room temperature?

 Linolenic acid (18:3)

 Can be synthesized from C18:2 (linoleic acid) in

most mammals (except in cat)

do synthesize them for their cell membranes

animal adipose tissue

 Most lipids consumed are triglycerides

 Most common structure in dietary lipids

 Lipids in tissues subjected to cooling

 Butterfat (milk fat) is fairly fluid

 amount of fat consumed ( fat =  digestion = 

 short chain FA’s are absorbed and enter the portal

Found in the myelin sheath

steroid nucleus 128

 Most abundant steroid in the body

cholic acid, a bile acid

 Chemical messengers in cells

Identify each lipid as: (1) phospholipid (2) steroid

Facilitated diffusion is movement of a molecule from