Biochemistry.pptx

Biochemistry
Course Credit:3/5ECTS
2022
Itefa Degefa(Asst. Prof)
Dambi Dollo University
1

Biochemistry
Introduction
• Biochemistry is the science of the atoms and molecules in
living organisms.
• Is the branch of chemistry that deals with the chemical properties, composition,
and biologicallymediatedprocesses of complex substances in living systems.
• Its area encompasses the entire living world with the
unifying interest in the chemical structures and reactions
that occur in living systems
• Even the simplest of these cells is capable of carrying out a thousand or
more chemical reactions.
• These life processes fall under the heading of biochemistry
2

• Biochemical phenomena that occur in living organisms are extremely
complicated.
–In the human body, complex metabolic processes break down a
variety of food materials to simpler chemicals, yielding energy and
the raw materials to build body constituents, such as muscle,
blood, and brain tissue.
–It is found in all through science, medicine, and agriculture.
–Ultimately, most environmental pollutants and hazardous
substances are of concern because of their effects on living
organisms.
3

 knowledge of biochemistry can be applied to solve problems in:
–Medicine
–Dentistry
–Forensics
–Agriculture
–Industrial applications
–Environmental application, etc.
4

Biochemistry has also relation with disciplines like:
Genetics: study of Nucleic acids, their structures, and functions
constitute the core of Genetics.
Physiology: Biochemistry overlaps almost completely with
physiology (the study of biological processes and functions).
Immunology: a science that deals with defense mechanisms
against diseases, is considered a branch of Biochemistry.
5

Pathology: Biochemistry explains, at the molecular level,
the symptoms and pathogenesis of diseases.
Pharmacology and Toxicology: advances in these sciences
depend primarily on knowledge gained from Biochemistry
as drugs and poisons are metabolized inside the body in
enzyme-catalyzed biochemical reactions.
Biological Sciences (microbiology, Botany and Zoology)
use biochemical approaches in the study of different
aspects of these sciences.
6

Principal areas of biochemistry
– Structure and function of biological molecules
– Metabolism- anabolic and catabolic process
– Molecular genetics – how life is replicated, regulation of
protein synthesis
7

Study of Cell
According to Cell Theory
–Cells are the basic structural and functional units of life
–The activity of an organism depends on both the
individual and the collective activities of its cells
–The biochemical activities of a cell are dictated by their
organelles
–The continuity of life has a cellular basis
8

Characteristics of Cells
• Cells vary greatly in their size, shape, and function
–All cells are composed primarily of carbon, hydrogen,
nitrogen, and oxygen
–All cells have the same basic parts and some common
functions
–A generalized human cell contains the plasma membrane,
the cytoplasm, and the nucleus
9

Biochemistry of Cells
• Uses of Organic Molecules
Sugar: Cellulose, found in plant cell walls, is the most
abundant organic compound on Earth
Water: is about 60-90 percent and is used in most
reactions in the body. It is called the universal solvent
Carbon-based Molecules: Although a cell is mostly water,
the rest of the cell consists mostly of carbon-based
molecules
10

Organization of life
• Life is organizedas:
–Elements
–Simple organic compounds
(monomers)
–Macromolecules (polymers)
–Supramolecular structures
–Organelles
–Cells
–Tissues
–organisms 11

• Elements of life
–Most abundant, essential for all organisms: C, N, O, P, S, H
–Less abundant, essential for all organisms: Na, Mg, K, Ca, Cl
– trace level, essential for all organisms: Mn, Fe, Co, Cu, Zn
–Trace level, essential for some organisms: V, Cr, Mo, B, Al, Ga, Sn,
Si, As, Se, I
• Macromolecules in Organisms
–Many important bimolecular are polymers
–There are four categories of large molecules in cells:
Carbohydrates Proteins
Lipids Nucleic Acids
12

* Among the many events that occur in the life cell, multitude
of specific chemical transformations provide the cell with:
•usable energy
•the molecules needed to form its structure and
•coordinate its activities.
• Example
•Water
•inorganic ions
•small organic molecules (sugars, vitamins, fatty acids)
account for 75 – 80 percent of living matter by weight.
14

*Of these small molecules, water is by far the most
abundant.
*The remainder of living matter consists of
macromolecules, including proteins, polysaccharides, and
DNA.
*Cells acquire and use these two size classes of molecules in
fundamentally different ways.
*Ions, water, and many small organic molecules are
imported into the cell.
15

* Some small molecules function as precursors for synthesis of
macromolecules, and the cell is careful to provide the
appropriate mix of small molecules needed.
* Small molecules also store and distribute the energy for all
cellular processes
* they are broken down to extract this chemical energy, as
when sugar is degraded to carbon dioxide and water with the
release of the energy bound up in the molecule.
16

* Other small molecules (e.g., hormones and growth factors) act as
signals that direct the activities of cells and nerve cells
communicate with one another by releasing and sensing certain
small signaling molecules.
* The powerful effect on our body of a frightening event comes from
the instantaneous flooding of the body with a small-molecule
hormone that mobilizes the “fight or flight” response.
* Macromolecules are the most interesting and characteristic
molecules of living systems.
* in a true sense the evolution of life is the evolution of
macromolecular structures.
17

Catagories of Biomolecules:
• Biomolecules can be looked at in two major categories:
A. The small molecules:
–are going to be either metabolites or monomers from which the
macromolecules are built.
–Like oxygen (O2), H2O, CO2, NH3 or NH4+, NO3-, (PO43-) and
S042-)
B. The monomers and the associated macromolecules are divided into
four major:
– The sugars/polysaccharides/: Energy-yielding fuel stores and as
extracellular structural elements with specific binding sites for
particular proteins
18

–Nucleosides/ nucleotides: DNA Repository of hereditary
information (store and transmit genetic Information).
RNA Essentially required for protein biosynthesis and
some RNA molecules have structural and catalytic roles.
– The amino acids/proteins/: Catalytic activity (e.g. as
enzymes); structural elements, signal receptors, or
transporters that carry specific substances into or out of
cells
–The fatty acids/lipids/: structural components of
membranes, energy-rich fuel stores, and intracellular
signals
19

Chemical bonds in biochemical reactions
–Biomolecules /elements of the cell are interact each other with
certain types of interactions
–The major types of interactions are:
Covalent bonds:
–The strongest bonds that are present in biochemicals are, such as
the bonds that hold the atoms together within the individual
bases.
–A covalent bond is formed by the sharing of a pair of electrons
b/n adjacent atoms.
–More than one electron pair can be shared between two atoms to
form a multiple covalent bond. 20

Non-covalent bonds
Electrostatic interactions
–Are the interactions between oppositely charged groups
within or between biomolecules.
Hydrogen bonds
–These interactions are formed when a H- atom
covalently linked to O or N in one molecule (hydrogen
bond donor) interacts with a lone pair of electrons on O or
N of the neighboring molecule (hydrogen bond acceptor).
21

Vander Waals interactions
–is that the distribution of electronic charge around an
atom changes with time.
–At any instant, the charge distribution is not perfectly
symmetric.
–This transient asymmetry in the electronic charge around
an atom acts through electrostatic interactions to induce a
complementary asymmetry in the electron distribution
around its neighboring atoms.
• Hydrophobic associations
–refers to the tendency of non-polar compounds to self-
associate in an aqueous environment. 22

23
UNIT II
PROTEINS
• Proteins are large macro molecule most important
in living cells
• They can exist in various structures and types
based on their function
• They are synthesized from amino acids
• Before discussing more about protein let see what
amino acid is

24
Amino acids
• Are the building units of proteins
• Amino acids are molecules containing an amine group
and side chain that is specific to each amino acid.
• The key elements of amino acid are carbon, hydrogen,
oxygen and nitrogen.
• Amino acids are the basic structural building units of
protein and other biomolecules
• they are also utilized as an energy source

25
Amino acids have properties that are well-suited to carry
out a variety of biological functions
→Capacity to polymerize
→Useful acid-base properties
→Varied physical properties
→Varied chemical functionality

26
• The major parts of amino acids:
 carboxyl group
 amino group
 R group(side chain)
 Hydrogen
 alpha carbon
• Amino acids can differ in their side
chains (R).
• The alpha carbon is a chiral center.

• Two enatiomers possible for most amino acids
 L-form
 D- form
• The L-form is found almost exclusively in naturally occurring
proteins
27
• In amino acids that have a carbon chain attached to the α–carbon
the carbons are labeled in order as α, β, γ, δ, and so on.
• For example

• Amino acids have high melting point solids because amino acids are
ionic compounds under normal conditions
C
O
OH
R
NH3
C
O
O
R
NH3
C
O
O
R
NH2
LOW pH
Zwitterion
NEUTRAL
Carboxylate Form
HIGH pH
ammonium Form
29
• Isoelectric Point is the pH at which an amino acids or peptide carries no net charge. i.e.
[RCOO-] = [RNH3
+]
• So, for basic R-groups, we require higher pHs, and for acidic R-groups we require lower pHs
e.g. Isoelectric point for Gly pH = 6.0
Asp pH = 3.0
Lys pH = 9.8
Arg pH = 10.8

• Numbering of carbon in amino acids is as the following
A
30

Classification of Amino Acids:
• Common amino acids can be placed in five basic
groups depending on their R substituents:
• Nonpolar, aliphatic
• Aromatic
• Polar, uncharged
• Positively charged
• Negatively charged
31

Based on essentiality
Essential Amino Acids:
– A human gets most the amino acid requirement from dietary protein.
Those which cannot be synthesised are called essential amino acids .
– Essential amino acids: Val, Leu, Ile, Met**, Phe**, Trp,Thr, Lys, His**,
Arg**
Non-Essential amino acids :
– Gly, Ala, Tyr, Cys, Ser, Asp. Glu, Gln,Asn, Pro.
– They are synthesized in the body from Metabolic Precursor as while by
modifications other amino acids by the following methods.
» Ammonia fixation: e.g Plants and many bacteria.
» Transamination:
» Modification of essential amino acids: e.g : Tyr and cys
from phe and Met respectively.
» Modification of non-essential amino acids: e.g Gly from
ser and Pro from glu.
35

36
Anabolic/catabolic responses
and tissue pH regulation
→Glutamic acid
→Glutamine
The urea cycle and Nitrogen
Management
→Arginine
→Citrulline
→Ornithine
→Aspartic acid
→Asparagine
Essential amino acids for proteins
and energy
→Isoleucine
→Leucine
→Valine
→Threonine
→Histidine
→Lysine
→Alpha-Aminoadipic acid
Classification according to functions
Sulfur containing amino acids for
methylation and glutathione
→Methionine
→Cystine
→Homocysteine
→Cyststhionine
→taurine

37
Neurotransmitters and precursor
phenylalanine
→Tyrosine
→Tryptophan
→Alpha-Amino-N-Butyric Acid
→Gamma-Aminobutyric Acid
Methylhistidines
→1-methylhisidine
→3-methylhistidine
Precursors to home, Nucleotides
and Cell Membranes
→Glycine
→Serine
→Sarcosine
→Alanine
→Ethanolamine
→Phospethanolamine
→Phosphoserine
Bone collagen specific amino acids
→Proline
→Hydroxyproline
→hydroxylysine

• Proteins are formed when amino acids join
together by forming peptide bonds
38
Biochemistry 2017

C
O
OH
N
H
H
N
H
H
• Proteins are chains of amino acids.
• They are polypeptide molecules that contain many peptide subunits.
39

Structure of peptides
 The peptide bond is an amide bond.
 Amides are very stable and neutral.
Biochemistry 2017 40

Peptide Bond Formation
41
• Amino acids are covalently linked by amide bonds (Peptide Bonds)
 The resulting molecules are called Peptides & Proteins
N
C R
R'
O
N
C R
R'
O

ΩHormones and pheromones
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly
mating)
Ω Neuropeptides
– substance P (pain mediator)
42
ΩAntibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)
Ω Protection, e.g., toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
Peptides: A Variety of Functions

Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly:
cofactors
 functional non-amino acid component
 metal ions or organic molecules
coenzymes
 organic cofactors
 NAD+ in lactate dehydrogenase
prosthetic groups
 covalently attached cofactors
 heme in myoglobin
other modifications 43

Protein Structure
Proteins are large, complex molecules that serve diverse
functional and structural roles within cells.
Proteins are polymers of amino acids linked by covalent
peptide bonds – leads to different conformations
Protein’s native conformation – has biological activity
Protein structure is often discussed in terms of a
hierarchy
44

• Primary Structure of Proteins:
– The sequence of amino acids in a protein held by peptide
bonds into polypeptide is called the primary structure of the
protein.
• Secondary Structure of Proteins
– A regular arrangements of aas that are located near to each
other in the linear sequence.
– created by spatial arrangements and interactions of aa
residues that are near one another in the linear sequence.
45

• Example of secondary structure is
– α-Helix: Rotation of ‘peptide
planes’ between α–C gives
rise to angles (φ and ψ) which
determine the folding pattern
of peptide .
46
β-pleated sheets& β bends
• Polypeptides (2-5 chains) run in-
line with each other and H
bonding stabilizes the structure.
When the polypeptide chains run
in parellel direction to each other,
called ‘parallel β-pleated sheets’
and when they run in opposite
direction to each other, called
‘anti-parallel β-pleated sheets’.

Tertiary structure
• 3D-space, how secondary structural features- helices, sheets, bends,
turns, and loops- assemble to form domains and how these domains
relate spatially to one another in to functional 3D structure of a
protein formed by complicated folding and super-folding of the
peptide chain into globular or fibrous form of different size.
• Stabilized by interactions through R-groups of composite amino
acids utilizing van derWaals, ionic, hydrophobic, H-bonds and
disulfide bonds.
47

Quaternary structure
– Specifies the nature of association of more than one polypeptides in
a defined geometric positional configuration to make a functional
protein
– Many proteins contain 2, 3, 4 or more subunits: dimeric,
trimeric, tetrameric or oligomeric proteins
– Polymeric proteins could be hetero-oligomers (i.e., several
polypeptides each with different sequence) or homooligomers
(i.e., several polypeptides of the same type).
– Oligomeric proteins are very common among enzymes e.g.
carbonic anhydrase is composed of 27 polypeptides.
49

• E.gs of quaternary structure is Hemoglobin, the O2 carrying protein
of the blood, contains two α and two β subunits arranged with a
quaternary structure in the form, α1β1 α2β2 (tetrameric). Hb is a
hetero-oligomeric protein.
50

51
Functional Groups
There are certain groups of atoms that are frequently attached to the
organic molecules and these are called functional groups.
These are things like
# hydroxyl groups which form alcohols,
#carbonyl groups which form aldehydes or ketones,
#carboxyl groups which form carboxylic acids, and
#amino groups which form amines.

52
Major Protein Functions
* Growth and repair
* Energy
* Buffer -- helps keep body pH constant
Dipeptide
• Formed from two amino acid subunits
• Formed by the process of Dehydration Synthesis
• amino acid + amino acid --- dipeptide + water

53
Hydrolysis of a dipeptide
1. Breaking down of a dipeptide into amino acids dipeptide +H2O --->
aminoacid + amino acid

Classification of Proteins
• Simple: hydrolyze to amino acids only.
• Conjugated: bonded to a non-protein group, such as sugar, nucleic
acid, or lipid.
• Fibrous: long, stringy filaments, insoluble in water, function as
structure.
• Globular: folded into spherical shape, function as:
Enzymes
Hormones
Transport
54

Protein denaturation
• Protein denaturation involves a change in the protein structure (generally an
unfolding) with the loss of activity.
• Water is critical, not only for the correct folding of proteins but also for the
maintenance of this structure.
• Heat denaturation and loss of biological activity has been linked to the breakup of
the 2-D-spanning water network around the protein (due to increasing hydrogen
bond breakage with temperature), which otherwise acts restrictively on protein
vibrational dynamics
• The free energy change on folding or unfolding is due to the combined effects of
both protein folding/unfolding and hydration changes.
55

# Disruption of the normal structure of a protein, such that it
loses biological activity.
# Usually caused by heat or changes in pH.
# Usually irreversible. A cooked egg cannot be “uncooked.”
 Denaturation by pH High or low extremes of pH
 Detergents – disrupt electrostatic (hydrophobic) interactions
 Urea or guanidine disrupt hydrogen bonding
 β-mercaptoethanol – reduces disulfide bridges/bonds
56

Role of Nucleic acids in Biosynthesis of proteins
• Proteins are synthesized in our cell by passing through the central
dogma from nucleic acid.
• In the synthesizing of protein, nucleic acid has great role because anti
codon sequence of amino acids are encoded by codon sequences on
nucleic acids.
– You know as Proteins are critically important as active
participants in cell structure and function.
– The primary role of DNA is to store the information needed for
the synthesis of all the proteins that an organism makes.
57

– genes that encode an amino acid sequence are known as structural
genes.
– The RNA transcribed from structural genes is called messenger
RNA (mRNA).
– Thus, mRNA is used to specify the sequence of amino acids within
a polypeptide
– The main function of the genetic material is to encode the
production of cellular proteins in the correct cell, at the proper
time, and in suitable amounts.
– This is an extremely complicated task because living cells make
thousands of different proteins. 58

– During Translation, the Genetic Code Within mRNA Is
Used to Make a Polypeptide with a Specific Amino Acid
Sequence
– The ability of mRNA to be translated into a specific
sequence of amino acids relies on the genetic code.
– The sequence of bases within an mRNA molecule
provides coded information that is read in groups of three
nucleotides known as codons
59

– The sequence of three bases in most codons specifies a specific
amino acid.
– These codons are termed sense codons.
– For example, the codon AGC specifies the amino acid serine,
whereas the codon GGG encodes the amino acid glycine.
– The codon AUG, which specifies methionine, is used as a start
codon; it is usually the first codon that begins a polypeptide
sequence.
– The AUG codon can also be used to specify additional methionines
within the coding sequence.
60

Assignment
1. What is the difference between codon and
anticodon?
2. List and discuss factors that affect enzymes
activity
3. What is sense codon and non sense codon?
4. Do you think all proteins are synthesized
from Nucleic acid? Why?
5. Write a short note on plasma proteins and
their functions.
61

– Finally, three codons —UAA, UAG, and UGA—are used to end
the process of translation and are known as stop codons.
– They are also called termination or nonsense codons.
– An mRNA molecule also has regions that precede the start codon
and follow the stop codon.
– Because these regions do not encode a polypeptide, they are called
the 5ʹ-untranslated region and 3ʹ-untranslated region,
respectively.
– The codons in mRNA are recognized by the anti codons in transfer
RNA (tRNA)molecules

– Anti codons are three-nucleotide sequences that are complementary to codons in
mRNA.
– The tRNA molecules carry the amino acids that correspond to the codons in the
mRNA.
– In this way, the order of codons in mRNA dictates the order of amino acids
within a polypeptide.
– Because polypeptides are usually composed of 20 different kinds of amino acids,
a minimum of 20 codons is needed to specify each type.
– With four types of bases in mRNA (A, U, G, and C), a genetic code containing
a three-base codon system can specify 43, or 64, different codons.
– Because the number of possible codons exceeds 20—which is the number of
different types of amino acids—the genetic code is termed degenerate.
63

Metabolism and Catabolism of proteins
Metabolic pathways fall into three categories:
1. Anabolic pathways: are those involved in the synthesis of
compounds. They are endergonic
2. Catabolic pathways: breakdown of larger molecules:- involving
oxidative reactions; they are exergonic.
3. Amphibolic pathways: acting as links between the anabolic and
catabolic pathways, eg, the citric acid cycle.
66

Dietary Protein Is Enzymatically Degraded to amino acids.
– Entry of dietary protein into the stomach stimulates secrete the
hormone gastrin, which in turn stimulates the secretion of HCl by
the parietal cells and pepsinogen by the chief cells of the gastric
glands.
– As the acidic stomach contents pass into the small intestine, the
low pH triggers secretion of the hormone secretin into the blood.
– Secretin stimulates the pancreas to secrete HCO3-into the small
intestine to neutralize the gastric HCl.
– The digestion of proteins now continues in the small intestine.
69

• Arrival of amino acids in the upper part of the intestine causes release
into the blood of the hormone cholecystokinin, which stimulates
secretion of several pancreatic enzymes .
• Trypsinogen, chymotrypsinogen, and procarboxypeptidases A and B,
the zymogens of trypsin, chymotrypsin, and carboxypeptidases A and
B, are synthesized and secreted by the exocrine cells of the pancreas.
• Degradation of the short peptides in the small intestine is then
completed by other intestinal Peptidases.
• Tendopeptidases
• aminopeptidases
• Carboxypeptidases
• the final end product → free amino acids.
70

Amino acid Catabolism
1. Transamination and deamination:
– Transamination: means the reversible transfer of an amino
group from alpha amino acid to an alpha keto acid forming a new
amino acid and a new alpha keto acid.
– Is the process by which amino groups are removed from amino acids and
transferred to acceptor keto acids to generate the amino acid version of the
keto acid and the keto acid version of the original amino acid
– The reactions are catalyzed by group of enzymes known as transaminases or
aminotraferases with pyridoxal phosphate (PLP) as a coenzyme.
71

Functions Of Transamination
– Transfer of –NH2 from most amino acids to alpha KGA to form
glutamate.
– This is very important since Glutamate is the only deaminable amino
that can release free NH3 suitable for urea synthesis.
– Synthesis of non-essential amino acids, through reactions of alpha-keto
acids with Glutamate.
– Transamidation to form amide of aminoacids, sugaramines and
nitrogenous bases and conversion of C-skeleton of amino acids into
ketone bodies or Glucose for energy production during
starvation.
– Diagnostic importance (ALT and AST) such as liver function test.
– Connection between CHO and protein metabolism through
glycolysis and Krebs' cycle, e.g., pyruvate, Oxaloacetic acids and -KGA.

74
Deamination
• Irreversible removal of –NH2 from amino acids as free NH3.
• Most amino acids are ‘deaminable’, undergo deamination in
liver/kidneys.
• Oxidative and non-oxidative deamination of amino acid has an
important contribution to the over all N metabolism.
Several routes for deamination:
1. Oxidative deamination: (combined with removal of H).

1. Non-oxidative deamination:
– Dehydratase (combined with removal of water).
– Desulfhydrase (combined with removal of hydrogen sulfide,
H2S).
– Specific deamination (is not associated with other reactions).
75

• Urea cycle:
– Urea is the main disposal form of amino groups
derived from protein.
– Liver is the only tissue that synthesizes urea from
NH3 and CO2.
– And diffuses freely into the blood and is cleared
through the kidneys for excretion in urine.
– The cycle operates partly in mitochondria and
partly in the cytoplasm of liver cells.
77

ENZYMES
• Enzymes are proteins that increase the rate of reaction by lowering the
energy of activation
– They catalyze nearly all the chemical reactions taking place in the cells
of the body.
– Not altered or consumed during reaction and reusable
 most enzyme names end in -ase
 enzymes lower the energy needed to start a chemical reaction
energy)
 begin to be destroyed above 45øC. (above this temperature all proteins
begin to be destroyed)
• catalyst: inorganic or organic substance which speeds up the rate of a
chemical reaction without entering the reaction itself
• enzymes: organic catalysts made of protein 80

Importance
• Enzymes play an important role in:
*Metabolism,
*Diagnosis
*Therapeutics.
• All biochemical reactions are enzyme catalyzed in
living organism.
• Level of enzyme in blood are of diagnostic
importance e.g. it is a good indicator in disease such
as myocardial infarction.
• Enzyme can be used therapeutically such as digestive
enzymes. 81

82
Naming Enzymes
 The name of an enzyme in many cases end in –ase
– For example, sucrase catalyzes the hydrolysis of sucrose
 The name describes the function of the enzyme
– For example, oxidases catalyze oxidation reactions
 Sometimes common names are used, particularly for the
digestion enzymes such as pepsin and trypsin
 Some names describe both the substrate and the function
– For example, alcohol dehydrogenase oxides ethanol

83
• Enzyme Classification
Enzymes are classified into six functional classes (ec number
classification) by the international union of biochemists (IUB)
on the basis of the types of reactions that they catalyze
EC 1. Oxidoreductases
EC 2. Transferases
EC 3. Hydrolases
EC 4. Lyases
EC 5. Isomerases
EC 6. Ligases

84
Principle of the international classification
• Each enzyme has classification number consisting of four
digits:
– Example, EC: (2.7.1.1) Hexokinase
EC: (2.7.1.1) these components indicate the following groups of
enzymes:
EC refers to Enzyme Commission
2. Is Class (Transferase)
7. Is Subclass (Transfer Of Phosphate)
1. Is Sub-sub Class (Alcohol Is Phosphate Acceptor)
1. Specific Name: Atp,d-hexose-6-phosphotransferase
(Hexokinase)

85
Enzyme kinetics
• Kinetics is the study of reaction rates (velocities).
# Study of enzyme kinetics is useful for measuring
→concentration of an enzyme in a mixture (by its catalytic
activity),
→its purity (specific activity),
→its catalytic efficiency and/or specificity for different
substrates
→comparison of different forms of the same enzyme in
different tissues or organisms,
→effects of inhibitors (which can give information about
catalytic mechanism, structure of active site, potential
therapeutic agents...

86
• Dependence of velocity on [substrate] is described for
many enzymes by the Michaelis-Menten equation:
• This equation illustrates in mathematical terms the
relationship b/n initial reaction velocity V0 and
substrate concentration [S],

• The mathematical equation explaining the qualitative
r/n ship b/n the [S] & V of enzyme-catalyzed reactions
assuming that;
I. E-S complex formation is the necessary step,
II. The rate of enzyme catalyzed reactions is
determined by the rate of conversion of E-S
complex to the P and E,
III. A single S yields a single P,
IV. A limited [enzyme] but an excess substrate
87

• Michaelis-Menten equation in three different conditions:
1. At a very low substrate conc. ([S]<< Km value).
2. At high substrate conc. ([S]>> Km value)
3. At substrate conc. [S] = Km value
88

Mechanism of action Estimation
• It is thought that, in order for an enzyme to affect the rate of
reaction, the following events must take place;
1. The enzyme must form a temporary association with the
or substances whose reaction rate it affects. These substances are
known as substrates.
2. The association between enzyme and substrate is thought to form
close physical association between the molecules and is called the
enzyme-substrate complex.
3. While the enzyme-substrate complex is formed, enzyme action
takes place.
4. Upon completion of the reaction, the enzyme and product(s)
separate. The enzyme molecule is now available to form additional
complexes.
90

Important terms to understand biochemical nature and activity of
enzymes
• Active site:
 The area on the enzyme where the substrate or substrates
attach to is called the active site.
 Enzymes are usually very large proteins and the active site is
just a small region of the enzyme molecule.
 Enzyme molecules contain a special pocket or cleft called
active sites.
• Substrate :
 Is the reactant in biochemical reaction
 When a substrate bind to an enzyme it forms an enzyme
substrate complex
 In enzymatic reactions, the substance at the beginning
of the process, on which an enzyme begins it’s action is
called substrate.
91

Models of the enzyme catalyzed reaction
"Lock and Key Theory“
each enzyme is specific for one and only one substrate (one
lock - one key)
this theory has many weaknesses, but it explains some basic
things about enzyme function
In the lock-and-key model of enzyme action:
- the active site has a rigid shape
- only substrates with the matching shape can fit
- the substrate is a key that fits the lock of the active site
92

93
#Induced Fit Model:
• In the induced-fit model of enzyme action:
- the active site is flexible, not rigid
- the shapes of the enzyme, active site, and substrate adjust to
maximize the fit, which improves catalysis
- there is a greater range of substrate specificity
• This model is more consistent with a wider range of enzymes

94
# Apoenzyme And Holoenzyme
• The enzyme without its non protein moiety is termed as
apoenzyme and it is inactive.
• Holoenzyme is an active enzyme with its non protein
component.

Important terms
Cofactor:
– A cofactor is a non-protein chemical compound that is
bound (either tightly or loosely) to an enzyme and is
required for catalysis.
Types of Cofactors
• Coenzyme:
– The non-protein component, loosely bound to
by non-covalent bond.
• Examples: vitamins or compound derived from
• Prosthetic group:
– The non-protein component, tightly bound to the
apoenzyme by covalent bonds is called a Prosthetic group.
96

Enzyme Specificity
Enzymes have varying degrees of specificity for substrates
 Enzymes may recognize and catalyze:
- a single substrate
- a group of similar substrates
- a particular types of bond
See the following
97

99
What Affects Enzyme Activity?
 Three factors:
1. Environmental Conditions
2. Cofactors and Coenzymes
3. Enzyme Inhibitors
Environmental Conditions
1. Extreme Temperature are the most dangerous
– high temperature may denature the enzyme.
1. pH (most like 6 - 8 pH near neutral)
2. substrate concentration .
99

• Optimum temperature: The temp at which enzymatic reaction occur
fastest.
100

101
• pH also affects the rate of enzyme-substrate complexes
• Most enzymes have an optimum pH of around 7 (neutral)
• However, some prefer acidic or basic conditions

Substrate Concentration and Reaction Rate
• The rate of reaction increases as substrate concentration increases
(at constant enzyme concentration)
• Maximum activity occurs when the enzyme is saturated (when all
enzymes are binding substrate)
102
Biochemistry 2017

103
Cofactors and Coenzymes
• Inorganic substances (zinc, iron) and vitamins
(respectively) are sometimes need for proper enzymatic
activity.
• For example: Iron must be present in the quaternary
structure - hemoglobin in order for it to pick up oxygen.

104
3. Enzyme Inhibitors
• Competive - mimic substrate, may block active site, but
may dislodge it.

Enzyme Inhibitors
• Noncompetitive
105

QUIZ(5)
1. Define enzymes
2. What are catalysts?
3. What is the difference between active site
and substrate site?
4. Why enzymes can not function above their
optimum temperature?
5. Define cofactors

CARBOHYDRATES
• are one of the three major classes of biological molecules.
• are the most abundant biological molecules.
• their name derived from the general formula Cn(H2O).
• A carbohydrate is a compound containing the elements
– carbon,
– hydrogen
– Oxygen
• The ratio of hydrogen to oxygen is the same as in water
(two hydrogen's to one oxygen.)
107

The basic building blocks of carbohydrate molecules
are the monosaccharides –glucose, fructose and
galactose.
Living things use carbohydrates as a key source of
ENERGY!
Plants use carbohydrates for structure (cellulose)
Carbohydrates are hydrates of carbon
108

Functions of Carbohydrate
• Breakdown of carbohydrates provides energy.
• Glycolipids and glycoproteins are glycoconjugates involved in
recognition between cell types or recognition of cellular structures by
other molecules
• Variety of important functions in living systems:
– nutritional (energy storage, fuels, metabolic intermediates)
– structural (components of nucleotides, plant and bacterial cell
walls, arthropod exoskeletons, animal connective tissue)
– informational (cell surface of eukaryotes -- molecular
recognition, cell-cell communication)
– osmotic pressure regulation (bacteria) 109

110
Based on the complexity carbohydratees may be
A. Monosaccharides (simple sugars)
– all have the formula C6 H12 O6
– all have a single ring structure (glucose is an example)
– simple sugars with multiple OH groups.
– Based on number of carbons (3, 4, 5, 6), a monosaccharide:
 triose,
 tetrose,
 pentose or
 Hexose
 Monosaccharides cannot be broken down into simpler sugars
under mild conditions.

111
Three carbons
Five carbons
Four carbons

113
Cyclic structure of monosaccharide
• Those greater than 4C are tend to cyclic structure
• The stable ring structures may be pyran(a six member ring) or
furan(a five member ring)

Isomerism in Carbohydrates
• Stereoisomerism: The total number of possible
stereoisomers of a compound is given by the Vont Hoff’s
rule, i.e., " 2n", where; n is the number of asymmetric carbon
atoms. Stereoisomer's can be of four types:
– Anomers (ɑ- and β-): These are isomers that differ in
distribution of H and OH groups around the asymmetric
anomeric carbon atom after cyclization of the molecule,
e.g., ɑ- and β-glucopyranose.
– Enantiomers (D- and L-isomers): These isomers differ
in distribution of H and OH groups around the sub-
terminal asymmetric carbon atoms.
115

• D-form has the OH group to the right, whereas, this group
is on the left in the L-form.
• Therefore, the two D- and L-forms appear as mirror images
of each other. Metabolically, these two forms are massively
different.
• D & L designations are based on the configuration about the
single asymmetric Carbon in glyceraldehyde.
116

117
CHO
C
CH2OH
HO H
CHO
C
CH2OH
H OH
CHO
C
CH2OH
HO H
CHO
C
CH2OH
H OH
L-glyceraldehyde
D-glyceraldehyde
L-glyceraldehyde
D-glyceraldehyde

118
Isomers
 Isomers are molecules that have the same molecular
formula, but have a different arrangement of the atoms in
space (different structures).
– For example, a molecule with the formula AB2C2, has two
ways it can be drawn:
Isomer 2
Isomer 1

119
Examples of isomers:
1. Glucose
2. Fructose
3. Galactose
4. Mannose are same chemical formula C6H12O6

EPIMERS
 EPIMERS are sugars that differ in configuration at ONLY 1
POSITION
• Examples of epimers :
– D-glucose & D-galactose (epimeric at C4)
– D-glucose & D-mannose (epimeric at C2)
– D-idose & L-glucose (epimeric at C5)

B. Disaccharides (double sugars)
 Two monosaccharides can form a covalent bond between them to form
a disaccharide sugar.
 There are three kinds of disaccharides.
Sucrose is a compound containing a glucose joined to a fructose.
Sucrose is commonly called table sugar.
Maltose is a disaccharide containing two glucose molecules held
together by a covalent bond.
Lactose is a sugar found in milk formed by the combination of
glucose and galactose.
 All have the formula C12 H22 O11; sucrose (table sugar) is an example
121

C. Oligosaccharide
– Oligo--Greek, few
– Definition: 2-20 monosaccharide units
– More than 20 monosaccharide units is a
polysaccharide
– Higher order oligosaccharides are named:
–tri-,
–tetra-,
–penta-, etc.
– Structures may be predominately linear or
branched
122

Structural features
Linear
– Features a head-to-tail linkage
– 1 reducing end
– 1 non-reducing end
Branched
– 1 reducing end
– Several to many non-reducing endsSuc
– sucrose is NOT a reducing sugar.
• Oligosaccharides that are covalently attached to proteins or
to membrane lipids may be linear or branched chains
123

H O
OH
O
H
HN
H
OH
CH2OH
H
C CH3
O
-D-N-acetylglucosamine
CH2 CH
C
NH
O
H
serine
residue
• O-linked oligosaccharide chains of glycoproteins vary in complexity.
• They link to a protein via a glycosidic bond between a sugar residue
& a serine or threonine OH.
• O-linked oligosaccharides have roles in recognition, interaction, and
enzyme regulation.
124

D. Polysaccharides
 When many monosaccharide molecules are joined
together with covalent bonds, we have a polysaccharide.
 Glycogen is a polysaccharide containing many hundreds of
monosaccharide subunits.
 Glycogen is a food stored in the body for energy.
 An important structural polysaccharide is cellulose.
 Cellulose is in wood and the cell walls of plants.
 shirt you're wearing, cotton, that's cellulose.
 Polysaccharides are also found in the shells of
crustaceans such as crabs and lobsters as a material
called chitin. 125

Cont,…
Generally, there Forms of three or more simple sugar units
Glycogen - animal starch stored in liver & muscles
Cellulose - indigestible in humans - forms cell walls
Starches - used as energy storage
126

Functions:
– storage
– structure
– recognition
– Lower the osmotic pressure.
– Starch and glycogen are energy storage molecules.
– Chitin and cellulose are structural molecules.
– Cell surface polysaccharides are recognition molecules.
– Carbohydrates also can combine with lipids to form
glycolipids OR With proteins to form glycoprotein
Nomenclature
1. Homo polysaccharide
2. Hetero polysaccharide
127

How are complex carbohydrates formed and broken down?
Dehydration Synthesis
– Combining simple molecules to form a more complex one with
the removal of water
– Polysaccharides are formed from repeated dehydration syntheses
of water
For example:
monosaccharide + monosaccharide ----> disaccharide + water
– (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O)
128
Hydrolysis
Addition of WATER to a compound to split it into smaller subunits
also called chemical digestion
eg. disaccharide + H2O ---> monosaccharide + monosaccharide
(C12H22O11 + H2O ---> C6H12O6 + C6H12 O6 )

Metabolism of carbohydrates
• Carbohydrates are stored as a form of glycogen in animals and
microorganisms and, starch in plants
• In vertebrates, glycogen is found primarily in the liver and skeletal
muscle
• Glycogen is stored in large cytosolic granules.
• The glycogen in muscle is there to provide a quick source of energy
for either aerobic or anaerobic metabolism
• the catabolic pathways includes
– from glycogen to glucose 6-phosphate==glycogenolysis
– from glucose 6-phosphate to pyruvate==glycolysis
– then turn to the anabolic pathways from pyruvate to
glucose==gluconeogenesis
– from glucose to glycogen==glycogenesis
129

• When glycogen in the skeletal muscle and liver starts to break down
the glucose units of the outer branches of glycogen enter the
glycolytic pathway through the action of three enzymes:
• glycogen phosphorylase
• glycogen debranching enzyme
• phosphoglucomutase.
• Glycogen phosphorylase catalyzes the reaction in which glycosidic
linkage between two glucose residues at a non reducing end of
glycogen undergoes attack by inorganic phosphate (Pi), removing
the terminal glucose residue as alpha-D glucose 1-phosphate
130

• Glucose 1-phosphate, is converted to glucose 6-phosphate by
phosphoglucomutase which catalyzes the reversible reaction
• in skeletal muscle, The glucose 6-phosphate formed from glycogen
can enter glycolysis and serve as an energy source to support muscle
contraction
• In liver cell, glucose 6-phosphate converted to glucose in the
indoplasmic reticulum lumen and released into the blood when the
blood glucose level drops by enzyme, glucose 6-phosphatase,
131

Glycolysis and Gluconeogenesis
• Glycolysis is the process when glucose molecule degraded from glycogen
is converted to pyruvate molecule
• gluconeogenesis occurs primarily in the liver, where its role is to provide
glucose for export to other tissues when glycogen stores are exhausted.
• They are opposing pathways
• Glucose occupies a central position in the metabolism of plants, animals,
many microorganisms.
• It is relatively rich in potential energy, and thus a good fuel;
the complete oxidation of glucose to carbon dioxide and
water proceeds with a standard free-energy change of 2,840 kJ/mol
134

• When energy demands increase, glucose can be released from
these intracellular storage polymers and used to produce ATP either
aerobically or anaerobically
• In animals and vascular plants, glucose has three major fates:
– it may be stored (as a polysaccharide or as sucrose)
– oxidized to a three-carbon compound (pyruvate) via glycolysis to
provide ATP and metabolic intermediates
– oxidized via the pentose phosphate (phosphogluconate) pathway to
yield ribose 5-phosphate for nucleic acid synthesis and NADPH
for reductive biosynthetic processes
135

• a molecule of glucose is degraded in a series of enzyme-catalyzed
reactions to yield two molecules of the three-carbon compound
pyruvate.
• During the sequential reactions of glycolysis, some of the free energy
released from glucose is conserved in the form of ATP and NADH.
• Fermentation is also the general term for the anaerobic degradation
of glucose or other organic nutrients to obtain energy, conserved as
ATP.
• Because living organisms first arose in an atmosphere without
oxygen, anaerobic breakdown of glucose is probably the most ancient
biological mechanism for obtaining energy from organic fuel
molecules. 137

Two Phases of Glycolysis
• The breakdown of the six-carbon glucose into two molecules of the
three-carbon pyruvate occurs in ten steps
– the first five of which constitute the preparatory phase
• 1st glucose is phosphorylated at the hydroxyl group on C-6 and
form D-glucose 6-phosphate
• 2nd D-glucose 6-phosphate is converted to D-fructose 6-
phosphate
• 3rd D-fructose 6-phosphate is again phosphorylated on C-1 and
produce D-fructose 1,6-bisphosphate
• 4th Fructose 1,6-bisphosphate is split to yield two three-carbon
molecules, dihydroxyacetone phosphate and glyceraldehyde 3-
phosphate
• 5th dihydroxyacetone phosphate is isomerized to a second
molecule of glyceraldehyde 3-phosphate 138

• Two molecules of ATP are invested before the cleavage of
glucose into two three-carbon pieces; later there will be a good
return on this investment.
• The six to ten step is called Pay off phase
– 6th Each molecule of glyceraldehyde 3-phosphate is oxidized and
phosphorylated by inorganic phosphate to form 1,3-
bisphosphoglycerate
– 7th Energy is then released as the two molecules of 1,3
bisphosphoglycerate are converted to two molecules of
pyruvate(through step 7-10)
139

– Much of this energy is conserved by the coupled phosphorylation of four
molecules of ADP to ATP
– Energy is also conserved in the payoff phase in the formation of two
molecules of NADH per molecule of glucose
• Totally, 10ATP is produced. But by payoff of 2ATP consumed in preparatory
phase the net is 8ATP molecule.
• In the sequential reactions of glycolysis, three types of chemical
transformations are particularly noteworthy:
1. degradation of the carbon skeleton of glucose to yield pyruvate,
2. phosphorylation of ADP to ATP by high-energy phosphate
compounds formed during glycolysis, an
3. transfer of a hydride ion to NAD forming NADH
140

Fates of Pyruvate
1st route
– Pyruvate is oxidized, with loss of its carboxyl group as CO2, to
yield the acetyl group of acetyl-coenzyme A;
– The acetyl group is then oxidized completely to CO2 by the citric
acid cycle.
– The electrons from these oxidations are passed to O2 through a
chain of carriers in the mitochondrion, to form H2O.
– The energy from the electron-transfer reactions drives the synthesis
of ATP in the mitochondrion
143

2nd route
• pyruvate is reduced to lactate via lactic acid fermentation.
• When vigorously contracting skeletal muscle must function
under low oxygen conditions (hypoxia), NADH cannot be
reoxidized to NAD, but NAD is required as an electron acceptor
for the further oxidation of pyruvate.
• Under these conditions pyruvate is reduced to lactate,
accepting electrons from NADH and thereby regenerating the
NAD necessary for glycolysis to continue.
144

3rd route
• pyruvate catabolism leads to ethanol.
• In some plant tissues and in certain invertebrates, protists, and
microorganisms such as brewer’s yeast, pyruvate is converted under
hypoxic or anaerobic conditions into ethanol and CO2, a process
called ethanol (alcohol) fermentation
145

Production of Acetyl-CoA
• In aerobic organisms, glucose and other sugars, fatty acids, and most amino
acids are ultimately oxidized to CO2 and H2O via the citric acid cycle and
the respiratory chain.
• Before entering the citric acid cycle, the carbon skeletons of sugars and fatty
acids are degraded to the acetyl group of acetyl-CoA,
• Pyruvate, the product of glycolysis, is converted to acetyl-CoA, the starting
material for the citric acid cycle, by the pyruvate dehydrogenase complex.
• This is done when pyruvate from glycolysis, is oxidized to acetyl-CoA and
CO2 by the pyruvate dehydrogenase (PDH) complex
• The overall reaction catalyzed by the pyruvate dehydrogenase complex is an
oxidative decarboxylation, an irreversible oxidation process in which the
carboxyl group is removed from pyruvate as a molecule of CO2 147

• The combined dehydrogenation and decarboxylation of pyruvate to the acetyl group
of acetyl-CoA requires the sequential action of
• three different enzymes and
• Pyruvate dehydrogenase (E1)
• dihydrolipoyl transacetylase(E2)
• dihydrolipoyl dehydrogenase (E3)
• five different coenzymes
• thiamine pyrophosphate (TPP),
• flavin adenine dinucleotide (FAD),
• coenzyme A (CoA, sometimes denoted CoA-SH)
• nicotinamide adenine dinucleotide (NAD)
• lipoate.
148

• Four different vitamins required in human nutrition are vital components of
this system:
• thiamine (in TPP)
• riboflavin (in FAD)
• niacin (in NAD)
• pantothenate (in CoA).
• FAD and NAD are electron carriers and TPP as the coenzyme of pyruvate
decarboxylase
149

150
• Since two molecule of pyruvate is formed from one glucose molecule,
when each of these pyruvates is converted to two molecules of acetyl
coA, two molecules of NADH are formed i.e., 6ATP

Citric Acid Cycle(Krebs’ cycle)
• It is called Krebs‟ cycle in honour of the discoverer Sir Hans Adolf
Krebs also called Tricarboxylic acid cycle (TCA) ,citric acid cycle
and Yet another name is given as “common pathway”
• It is the cyclic pathway by which active acetate (acetyl-CoA) is
completely oxidized into CO2, with electron-containing hydrogen
transfer to FADH2 and NADH.H+.
• eight successive reaction steps of the citric acid cycle taking place as
citrate formed from acetyl-CoA and oxaloacetate is oxidized to yield
CO2 and the energy of this oxidation is conserved in the reduced
coenzymes NADH and FADH2.
151

• Importance of Kreb's Cycle:......
• Energy Production ATP, FADH2, NADH,
• Production of CO2,
• Raw material for biosynthesis
• Regulation of metabolic pathways.
• Acetyl-CoA + 3NAD+ + FAD+ + GDP + Pi + 2H2O  CoASH
+3NADH.H+ + FADH2 + GTP/ATP + 2CO2
Bioenergetics of Krebs' cycle:
• 30 ATP are produced from oxidation of two pyruvates to CO2 and H2O.
• Since 6NADH=18ATP
• 2FADN2= 4ATP
• 2GTP =2ATP
• 2NADH=6ATP(preparatory phase of TCA)
The Net produced =30ATP
152

• Other Monosaccharides Enter the Glycolytic Pathway at Several
Points
– In most organisms, hexoses other than glucose can undergo
glycolysis after conversion to a phosphorylated derivative.
– D-Fructose, present in free form in many fruits and formed by
hydrolysis of sucrose in the small intestine of vertebrates, is
phosphorylated by hexokinase:
154
• This is a major pathway of fructose entry into glycolysis in the
muscles and kidney.
• In the liver, however, fructose enters by a different pathway.
• The liver enzyme fructokinase catalyzes the phosphorylation of
fructose at C-1 rather than C-6:

• The fructose 1-phosphate is then cleaved to glyceraldehyde and
dihydroxyacetone phosphate by fructose 1-phosphate aldolase:
155
• Dihydroxyacetone phosphate is converted to glyceraldehyde 3
phosphate by the glycolytic enzyme triose phosphate isomerase.
• Glyceraldehyde is phosphorylated by ATP and triose kinase to
glyceraldehyde 3-phosphate:

156
• Thus both products of fructose 1-phosphate hydrolysis enter the
glycolytic pathway as glyceraldehyde 3- phosphate.
• Similarly, D-Galactose, a product of hydrolysis of the disaccharide
lactose (milk sugar), passes in the blood from the intestine to the
liver, where it is first phosphorylated at C-1, at the expense of ATP,
by the enzyme galactokinase:
• The galactose 1-phosphate is then converted to its epimer at C-4, glucose 1-
phosphate, by a set of reactions in which uridine diphosphate (UDP) functions as
a coenzyme-like carrier of hexose groups

• The epimerization involves first the oxidation of the C-4 --OH group
to a ketone, then reduction of the ketone to an --OH, with inversion of
the configuration at C-4.
• NAD is the cofactor for both the oxidation and the reduction.
• Defects in any of the three enzymes in this pathway cause
galactosemia in humans.
• In galactokinase deficiency galactosemia, high galactose
concentrations are found in blood and urine.
• Infants develop cataracts, caused by deposition of the galactose
metabolite galactitol in the lens.
157

Gluconeogenesis
• In mammals, some tissues depend almost completely on glucose for
their metabolic energy.
• For the human brain and nervous system, as well as the
erythrocytes, testes, renal medulla, and embryonic tissues, glucose
from the blood is the sole or major fuel source.
• The brain alone requires about 120 g of glucose each day—more
than half of all the glucose stored as glycogen in muscle and liver.
• However, the supply of glucose from these stores is not always
sufficient; between meals and during longer fasts, or after vigorous
exercise, glycogen is depleted.
• For these times, organisms need a method for synthesizing glucose
from noncarbohydrate precursors.
• This is accomplished by a pathway called gluconeogenesis
(“formation of new sugar”), which converts pyruvate and related
three- and four-carbon compounds to glucose
159

• Gluconeogenesis occurs in all animals, plants, fungi, and
microorganisms.
• The reactions are essentially the same in all tissues and all species.
• The important precursors of glucose in animals are three-carbon
compounds such as
Lactate
pyruvate
Glycerol
certain amino acids
 In mammals, gluconeogenesis takes place mainly in the liver, and to a
lesser extent in renal cortex.
 Seven of the steps in gluconeogenesis are catalyzed by the same
enzymes used in glycolysis; these are the reversible reactions.
160

• Three irreversible steps in the glycolytic pathway are bypassed by
reactions catalyzed by gluconeogenic enzymes:
1. conversion of pyruvate to PEP via oxaloacetate, catalyzed by
pyruvate carboxylase and PEP carboxykinase;
2. dephosphorylation of fructose 1,6-bisphosphate by FBPase-1
3. dephosphorylation of glucose 6-phosphate by glucose 6-
phosphatase.
• Formation of one molecule of glucose from pyruvate requires 4 ATP,
2 GTP, and 2 NADH; it is expensive
161

162
Glycolysis
Gluconeogenesis

Pentose Phosphate Pathway of Glucose Oxidation
• In addition to converting glucose to pyruvate , lactate, etanol and etc
it can be converted to pentose which lead to specialized products
needed by the cell
• In some tissues the oxidation of glucose 6-phosphate to pentose
phosphates by the pentose phosphate pathway (also called the
phosphogluconate pathway or the hexose monophosphate pathway
• In this oxidative pathway, NADP+ is the electron acceptor, yielding
NADPH.
• Rapidly dividing cells, such as those of bone marrow, skin, and
intestinal mucosa, use the pentoses to make RNA, DNA, and such
coenzymes as ATP, NADH, FADH2, and coenzyme A.
163

LIPIDS
Are Fats, oils, waxes, steroids
Chiefly function in:
– energy storage,
– protection, and
– insulation
Contain:
– carbon,
– hydrogen, and
– oxygen but the H:O is not in a 2:1 ratio
Tend to be large molecules
They are made of fatty acids and glycerol
165

167
An example of a neutral lipid
 Neutral lipids are formed from the union of one glycerol molecule and
3 fatty acids
– 3 fatty acids + glycerol ----> neutral fat (lipid)
 Fats -- found chiefly in animals
 Oils and waxes -- found chiefly in plants
 Oils are liquid at room temperature, waxes are solids
 Lipids along with proteins are key components of cell membranes
 Steroids are special lipids used to build many reproductive hormones
and cholesterol

• Triglycerides – Fats & Oils
– Predominate form of fat in foods and major storage form of fat in
the body
• Fatty Acids & Triglycerides
– glycerol + 3 fatty acids  triglyceride + H2O
168
• Organic acid (chain of carbons with hydrogen attached) that has an
acid group at one end & a methyl group at the other end

 Length of carbon chain
Stearic acid – 18-carbon, saturated
Simplified structure
169
Fatty Acids carbon chains, vary in:
1. Length – affects absorption
2. Saturation –chemical structure; affects cooking & storage properties and health

 Saturation
 Saturated fatty acid – carbon chains filled with hydrogen atoms (no
C=C double bonds)
 Saturated fat – triglyceride containing 3 saturated fatty acids, such as
animal fats (butter, lard) & tropical oils (palm, coconut)
 Appear solid at room temperature
170

171
• Unsaturated fatty acid – carbon chains lack some hydrogen (>1 C=C
double bond)
• Appear liquid at room temperature
• Monounsaturated fat – triglyceride containing fatty acids with 1
double bond; i.e. canola & olive oil
• Polyunsaturated fat- triglycerides containing a high % of fatty acids
with >2 double bonds; i.e. corn, safflower, soybean, sunflower oils
and fish;

 Location of double bonds
– Omega number – refers to the position of the double bond nearest the methyl (CH3)
end of the carbon chain
* Omega-3 fatty acid
* Omega-6 fatty acid
172

Hydrogenated – addition of hydrogen to unsaturated fat
1. Makes it more “solid” or firm
2. Effects on stability and protects against oxidation; more “shelf-
stable”
3. Widely used by food industry in margarine, shortening, peanut
butter, baked goods & snack food
 Cist vs. trans-fatty acids
• In nature, most double bonds are cis meaning that the hydrogens next
to the double bonds are on the same side of the carbon chain
• When a fat is partially hydrogenated, some of the double bonds
change from cis to trans
173

Phospholipids
 similar to triglycerides in structure except only 2 fatty acids +
choline
 Phospholipids in foods: Lecithin, egg yolks, soybeans, wheat germ,
peanuts
Functions
• part of cell membranes and acts as an emulsifier (helps keep fats in
solution)
– Not a dietary essential; made by the liver
175

Functions of Fats
 In the body, fats provide:
1) Energy – 9 kcals/gm
a. Supplies 60% of body’s energy needs at rest
b. Stored as adipose tissue
2) Insulation & protection
3) Cell membrane constituents
 In foods, fats:
1. Provide energy (9 kcal/gm)
2. Contribute flavor, aroma, and tenderness
3. Carry fat-soluble vitamins (A,D,E & K)
4. Provide a source of essential fatty acids
176
Biochemistry, 2017

177
Essential fatty acids
Health Effects of Fats
Excess fat intake contributes to many diseases including:
Obesity
Diabetes
Cancer
Heart disease
How?
1. High fat diets = high kcal diets
2. High saturated fat intake raises blood cholesterol
3. High fat intakes may promote cancer

178
Classification of Lipids
Based on the structure and function
– Lipids that do not contain fatty acids: cholesterol,
terpenes, …
– Lipids that contain fatty acids (complex lipids)
– Storage lipids and membrane lipids
Storage Lipids
• The fats and oils used almost universally as stored forms of
energy in living organisms are derivatives of fatty acids.
• Fatty acids are hydrocarbon derivatives
• Fatty acids are carboxylic acids with hydrocarbon chains
ranging from 4 to 36 carbons long (C4 to C36).
• A simplified nomenclature for unbranched fatty acids
specifies the chain length and number of double bonds,
separated by a colon.

179
Two conventions for naming fatty acids.

The most commonly occurring fatty acids have even numbers of
carbon atoms in an unbranched chain of 12 to 24 carbons.
The family of polyunsaturated fatty acids (PUFAs) with a double
bond between the third and fourth carbon from the methyl end of
the chain are of special importance in human nutrition.
PUFAs with a double bond between C-3 and C-4 are called
omega-3 (ω-3) fatty acids, and those with a double bond between
C-6 and C-7 are omega-6 (ω-6) fatty acids.
180

 Triacylglycerols
– are fatty acid esters of glycerol
– The simplest lipids constructed from fatty acids are the
triacylglycerols, also referred to as triglycerides, fats, or neutral
fats.
– Triacylglycerols are composed of three fatty acids each in ester
linkage with a single glycerol.
– Triacylglycerols Provide Stored Energy and Insulation
– In vertebrates, specialized cells called adipocytes or fat cells,
store large amounts of triacylglycerols as fat droplets that nearly
fill the cell
182

 Triacylglycerols are also stored as oils in the seeds of many types of
plants, providing energy and biosynthetic precursors during seed
germination.
 Adipocytes and germinating seeds contain lipases, enzymes that
catalyze the hydrolysis of stored triacylglycerols, releasing fatty acids
for export to sites where they are required as fuel.
Waxes
 Waxes are esters of long-chain saturated and unsaturated fatty acids
with long-chain alcohols
 Insoluble and have high melting points
 Variety of functions:
 Storage of metabolic fuel in plankton
 Protection and flexibility for hair and skin in vertebrates
 Protection from evaporation in tropical plants
 Used by people in lotions, ointments, and polishes
183

Structural Lipids in Membranes
 In glycerophospholipids and some sphingolipids, a polar
head group is joined to the hydrophobic by a
phosphodiester linkage are the phospholipids.
Other sphingolipids lack phosphate but have a simple sugar
or complex oligosaccharide at their polar ends; these are
the glycolipids.
Glycerophospholipids are derivatives of phosphatidic acid
Glycerophospholipids, also called phosphoglycerides, are
membrane lipids in which two fatty acids are attached in
ester linkage to the first and second carbons of glycerol.
184

the backbone of phospholipids
Glycerophospholipids
185

 The properties of head groups determine the surface properties of
membranes
 Different organisms have different membrane lipid head group
compositions
 Different tissues have different membrane lipid head group
compositions
 Examples of Glycerophospholipids: Phosphatidylcholine
 Phosphatidylcholine is the major component of most eukaryotic cell
membranes
186

 Many prokaryotes, including E. coli cannot synthesize this lipid; their
membranes do not contain phosphatidylcholine
 Some Glycerophospholipids have Ether-Linked Fatty Acids
 Some animal tissues and some unicellular organisms are rich in ether
lipids, in which one of the two acyl chains is attached to glycerol in
ether, rather than ester, linkage.
 Example Ether lipids: Plasmalogen
187

Vinyl ether analog of phosphatidylethanolamine
Common in vertebrate heart tissue
Also found in some protozoa and anaerobic bacteria
Function is not well understood
Resistant to cleavage by common lipases
Increase membrane rigidity
Sources of signaling lipids
May be antioxidants
188

Sterols
 Important part of:
1. Sex hormones – testosterone
2. Vitamin D
3. Bile (aids fat digestion)
4. Adrenal hormones – cortisol
5. Cholesterol – in foods and made by the liver; dietary sources
include egg yolks, liver, meats, dairy products
Sterols Have Four Fused Carbon Rings
 Sterols are structural lipids present in the membranes of most
eukaryotic cells.
 Cholesterol
the major sterol in animal tissues
is amphipathic with a polar head group (the hydroxyl group
at C-3) nonpolar hydrocarbon body, about as long as a 16-
carbon fatty acid in its extended form.
189

 Bile acids are polar derivatives of cholesterol that act as detergents
in the intestine, emulsifying dietary fats to make them more readily
accessible to digestive lipases.
191

 Most bacteria lack sterols
 Mammals obtain cholesterol from food and synthesize it de novo in
the liver
Physiological role of sterols
 Cholesterol and related sterols are present in the membranes of most
eukaryotic cells.
 Modulate fluidity and permeability
 Thicken the plasma membrane
However,
 Cholesterol, bound to proteins, is transported to tissues via blood vessels
 Cholesterol in low-density lipoproteins tends to deposit and clog arteries
 Many hormones are derivatives of sterols
192

Steroid Hormones
Steroids are oxidized derivatives of sterols
Steroids have the sterol nucleus, but lack the alkyl chain found in
cholesterol. This makes them more polar than cholesterol.
Steroid hormones are synthesized in gonads and adrenal glands
from cholesterol
They are carried through the body in the blood stream, usually
attached to carrier proteins
Many of the steroid hormones are male and female sex hormones
193

Lipids as Signals, Cofactors, and Pigments
Eicosanoids
 Carry Messages to Nearby Cells
 are paracrine hormones, present in small amounts but play vital
roles as signaling molecules between nearby cells
 are derived from arachidonic acid (20:4(Δ5,8,11,14), the 20-
carbon polyunsaturated fatty acid from which they take their
general name.
195

196
There are three classes of eicosanoids:
1. Prostaglandins (PG)
• contain a five-carbon ring originating from the chain of
arachidonic acid.
2. Thromboxanes
• have a six-membered ring containing an ether.
• They are produced by platelets (also called thrombocytes) and
act in the formation of blood clots and the reduction of blood
flow to the site of a clot.
3. Leukotrienes contain three conjugated double bonds.

Functions:
‾ Inflammation and fever (prostaglandins)
‾ Formation of blood clots (thromboxanes)
‾ Smooth muscle contraction in lungs (leukotrienes)
‾ Smooth muscle contraction in uterus (prostaglandins)
‾ Generally, the followings are eight categories of lipids
197

198
Storage protein and membrane protein

199
Metabolism of dietary lipids:
• Lipids are a heterogeneous group of water- insoluble (hydrophobic)
Organic molecules.
• Hydrophobicity is due to the long – hydrocarbon chains.
• Body lipids are generally found either:
A. Compartmentalized: e.g., Membrane- associated lipids or as
droplets of fat TAGs in adipose tissue.
B. Transported in plasma in association with protein as lipoprotein
particles (chylomicrons)
• The classification of blood lipids is distinguished based upon the
density of the different lipoproteins.

Digestion, absorption and utilization of dietary lipids:
• Dietary lipids mainly contains
• 90% triacylglycerol (TAG)
• 10%:cholesterol
• cholesteryl esters phospholipids and
• non-esterified fatty acids (NEFAs).
• Processing of dietary lipids in the stomach
• In infants digestion begins in stomach catalyzed by the acid-stable lingual
lipase
• However, the rate of hydrolysis is slow because the lipid is not yet
emulsified.
• These TAG molecules can be degraded by a separate gastric acid lipase.
• This enzyme is active only at neutral pH and therefore, is active in
neonates whose stomach pH is nearer to neutrality.
• Overall in adults, dietary lipids are not digested to any extent in the
mouth or the stomach.
201

Emulsification of dietary lipids in the small intestine
• Emulsification increases the surface area of the hydrophobic lipid
droplets so that the digestive enzymes which work at the interface of
the lipid droplet and the surrounding aqueous duodenal contents can
act effectively.
• Emulsification is accomplished by two complementary mechanisms:
– The use of the amphipathic surface active properties of bile salts
synthesized in the liver and stored in the gall bladder and
mechanical mixing of peristalsis.
202

Fate of FFAs:
I. Directly enter adjacent muscle cells or adipocytes.
II. May be transported in blood in association with serum
albumin, until they are taken by cells.
III. Most cells can oxidize FFAs to obtain energy (ATP).
IV. Adipocytes can also re-esterify free-fatty acids to
produce TAG molecules, which are stored until the FAs
are needed by the body.
203

Fate of glycerol
• Glycerol is used by the liver to produce glycerol-3-phosphate, which
can enter glycolysis or gluconeogenesis by oxidation to
dihydroxyacetone phosphate.
Oxidation of fatty acids
• Fatty acids may be oxidized to acetyl-CoA (β-oxidation) or esterified
with glycerol, forming TAG (fat) as the body’s main fuel reserve
204

• β-Oxidation of fatty acids
• The major pathway for catabolism of saturated fatty acids is a mitochondrial
pathway called β-oxidation, in which two-carbon fragments are successively
removed from the carboxyl end of the fatty acyl CoA, producing acetyl CoA, NADH,
and FADH2.
1.Transport of long-chain fatty acids (LCFA) into the mitochondria:
– After a LCFA enters a cell, it is converted in the cytosol to its fatty acyl CoA
derivative by long-chain fatty acyl CoA synthetase (thiokinase)
– Because β-oxidation occurs in the mitochondrial matrix, the fatty acid
must be transported across inner mitochondrial membrane which is
impermeable to CoA.
– Therefore, a specialized carrier transports the long-chain acyl group from the
cytosol into the mitochondrial
206

Oxidation of Fatty Acids by β-oxidation Produces a Large Quantity of
ATP
• For example palmitic acid is 16-carbon fatty acid ,which is common
edible fatty acid.
• When oxidized by oxidation it can be splitted to 8 molecules of acetyl
CoA (2-carbon molecule).
• And each molecule of acetyl-coA produce 12 mol of ATP. See the
following figure.
209

NUCLEIC ACIDS
• The nucleotides plus molecules derived from them ( he final class of
biomolecules to be considered, i.e., nucleic acids), represent a clear case in
which last is not least.
• “Nucleotides themselves participate in a plethora of crucial supporting roles
in cell metabolism, and the nucleic acids provide the script for everything
that occurs in a cell” (Lehninger, Nelson and Cox, 1993).
• Nucleotides are energy-rich compounds that drive metabolic processes
(esp., biosynthetic) in all cells.
• They also serve as chemical signals, key links in cellular systems that
respond to hormones and other extracellular stimuli, and are structural
components of a number of enzyme cofactors and metabolic intermediates.

• The nucleic acids (DNA and RNA) are the molecular repositories for
genetic information and are jointly referred to as the ‘molecules of
heredity’.
• The structure of every protein, and ultimately of every cell
constituent, is a product of information programmed into the
nucleotide sequence of a cell’s nucleic acids

Chemistry And Their Biological Significance
• Friedrich Miescher(1869), a 25-year old Swiss chemist, isolated
nuclei from pus cells (white blood corpuscles) and found that they
contained a hitherto unknown phosphate-rich substance, which he
named nuclein.
• In 1871 He continued his studies on salmon sperm, a prime source of
nuclein and isolated it as a nucleoprotein complex, when he
prophetically wrote: “It seems to me that a whole family of such phosphorus-
containing substances, differing somewhat from each other, will emerge, as a group
of nuclein substances, which perhaps will deserve equal consideration with the
proteins.”
213

• In 1874, that he isolated pure nucleic acid from the DNA-protamine
complex in salmon sperm nuclei.
• In 1899Altmann, found that the nuclein had acid properties and hence
introduced the term nucleic acid to replace nuclein.
• In 1880s, Fischer discovered purine and pyrimidine bases in nucleic
acids.
• In 1881, Zacharis identified nuclein with chromatin.
• In 1882, Sachs stated that nucleins of sperm and egg are different
• In 1884, Hertwig claimed that nuclein is responsible for the
transmission of hereditary characteristics.
214

• in 1894, Geheimrat Albrecht Kossel, of the University of Heidelberg,
Germany, recognized that histones and protamines are associated with
nucleic acids and also found that the histones were basic proteins.
• He was honoured with Nobel Prize for Physiology or Medicine in
1910 for demonstrating the presence of two purine and two
pyrimidine bases in nucleic acids.
• In 1894, cytosine was identified and in 1909, uracil was isolated.
• in 1910 Levene, a Russian-born biochemist, recognized the 5-carbon
ribose sugar and later also discovered deoxyribose in nucleic acids.
• In 1914, Robert Feulgen, another German chemist, demonstrated a
colour test known as Feulgen test for the deoxyribonucleic acid.
215

• In 1931 P.A. Levine stressed that there are 2 types of nucleic acids, viz.,
deoxyribonucleic acid and ribonucleic acid.
• In 1941, Caspersson and Brachet, independently, related that nucleic acids
were connected to protein synthesis.
• In 1944 Oswald T. Avery, Colin M. MacLeod and Maclyn McCarty, first of all
demonstrated that DNA is directly involved in inheritance.
• In 1952 Alfred D. Hershey and Martha J. Chase of Cold Spring Harbor Lab.,
New York,, demonstrated that only the DNA of T4 bacteriophage enters the host, the
bacterium Escherichia coli, whereas the protein
(i.e., capsid) remains behind.
• They, thus, confirmed that DNA is the genetic material of most living organisms.
• In 1957, Matthew S. Meselson and Franklin H. Stahl at California Institute of
Technology, presented evidence that nucleic acid forms the genetic material.
216

• In 1953, James D. Watson and Francis H.C. Crick constructed the
double helical model forthe DNA molecule which could successfully
explain DNA replication.
• In 1957, Arthur Kornberg proved the Watson-Crick model in the cell-
free system.
• In 1967, he also synthesized a molecule of DNA from the 6,000
nucleotides.
Structural components of RNA and DNA
• There are two kinds of nucleic acids, deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA).
217

219
Pentose Sugar
Phosphoric acid
Components of Nucleotides

Nitrogenous Bases
Pyrimidine Derivatives
220
Uracil (C4H4O2N2) Thymine (C5H6O2N2) Cytosine (C4H5ON3)
Purine Derivatives
Adenine (C5H5N5) Guanine (C5H5ON5)

Functions of Nucleotides
1. As carriers of chemical energy
221

2. As components of enzyme factors.
• Many enzyme cofactors and coenzymes (such as coenzyme A, NAD+
and FAD) contain adenosine as part of their structure
222

3. As chemical messengers.
• The cells respond to their environment by taking cues from
hormones or other chemical signals in the surrounding
medium.
• The interaction of these chemical signals (first messengers)
with receptors on the cell surface often leads to the
formation of second messengers inside the cell, which in
turn lead to adaptive changes inside the cell.
• Often, the second messenger is a nucleotide. For example
– adenosine 3′, 5′- cyclic monophosphate (cyclic AMP or cAMP)
– Guanosine 3′, 5′- cyclic monophosphate(cGMP)
223

Catabolism of nucleic acids
Nucleotide Degradation
• Most foodstuffs, being of cellular origin, contain nucleic acids.
• Dietary nucleic acids survive the acid medium of the stomach; they are
degraded to their component nucleotides, mainly in the duodenum, by
pancreatic nucleases and intestinal phosphodiesterases.
• These ionic compounds, which cannot pass through cell membranes, are
then hydrolyzed to nucleosides by a variety of group-specific nucleotidases
and nonspecific phosphatases.
• Nucleosides may be directly absorbed by the intestinal mucosa or first
undergo further degradation to free bases and ribose or ribose-1-
phosphate through the action of nucleosidases and nucleoside
phosphorylases:
224

225
• Radioactive labeling experiments have demonstrated that only a
small fraction of the bases of ingested nucleic acids are incorporated
into tissue nucleic acids.
• Evidently, the de novo pathways of nucleotide biosynthesis largely
satisfy an organism’s need for nucleotides.
• Consequently, ingested bases, for the most part, are degraded and
excreted.
• Cellular nucleic acids are also subject to degradation as part of the
continual turnover of nearly all cellular components.

Catabolism of Purines
• The major pathways of purine nucleotide and deoxynucleotide catabolism in
animals are diagrammed as follow
226

Fate of Uric Acid
• In humans and other primates, the final product of purine degradation
is uric acid, which is excreted in the urine.
• The same is true of birds, terrestrial reptiles, and many insects, but
these organisms, which do not excrete urea, also catabolize their
excess amino acid nitrogen to uric acid via purine biosynthesis.
• In all other organisms, uric acid is further processed before excretion
• Mammals other than primates oxidize it to their excretory product,
allantoin, in a reaction catalyzed by the Cu-containing enzyme urate
oxidase.
227

• A further degradation product, allantoic acid, is excreted by teleost
(bony) fish.
• Cartilaginous fish and amphibia further degrade allantoic acid to urea
prior to excretion.
• Finally, marine invertebrates decompose urea to their nitrogen
excretory product, NH4+
228

• The most prevalent cause of gout is impaired uric acid excretion(lead poisoning).
• Gout may also result from a number of metabolic insufficiencies, most of which are
not well characterized.
• Uric acid overproduction is also caused by glucose-6-phosphatase deficiency
• The increased availability of glucose-6-phosphate stimulates the pentose phosphate
pathway (Section 23-4), increasing the rate of ribose-5-phosphate production and
consequently that of PRPP, which in turn stimulates purine biosynthesis.
• Gout may be treated by administration of the xanthine oxidase inhibitor allopurinol,
a hypoxanthine analog with interchanged N7 and C8 positions.
229

Catabolism of Pyrimidines
• Animal cells degrade pyrimidine nucleotides to their component bases
• These reactions, like those of purine nucleotides, occur through
dephosphorylation, deamination, and glycosidic bond cleavages.
• The resulting uracil and thymine are then broken down in the liver
through reduction rather than by oxidation, as
occurs in purine catabolism.
• The end products of pyrimidine catabolism, β -alanine and β-
aminoisobutyrate, are amino acids and are metabolized as such.
• They are converted, through transamination and activation reactions,
to malonylCoA and methylmalonyl-CoA
231

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