Lipids;

The Hydrophobic Molecules

1.
1. Fats
Fatsstore
storelarge
largeamounts
amountsof
ofenergy
energy
2.
2. Phospholipids
Phospholipidsare
aremajor
majorcomponents
componentsof
ofcell
cellmembranes
membranes
3.
3. Steroids
Steroidsinclude
includecholesterol
cholesteroland
andcertain
certainhormones
hormones
1) Fats:
 Lipids are an exception among macromolecules because
they do not have polymers.
 The unifying feature ‫ لاــصفة ل ُاــم َميـٍزة‬of lipids is that they all
have little or no affinity for water ‫الـ ـَتــمتزج لبــاــماء‬.
 This is because their structures are dominated by non-polar
covalent bonds.
 Lipids are the components‫ ُمكونات‬of fats, and are highly
diverse in form and function.
 Although fats are not polymers, they are large
molecules assembled from ‫ تــتكونمن‬smaller molecules by
dehydration reactions.
 A fat is constructed from two kinds of smaller
molecules, glycerol and fatty acids ‫ أـحماضدُهنية‬.
Glycerol H
O H H
Fatty Acid
H H
H C C C H
OH C C C
H C OH H H
Ester link H H H
H C OH
H C OH Dehydration

H
A fat is composed of three fatty acids linked with one glycerol molecule.

Fats are classified into Saturated ‫ مـشبعـ‬and Un-saturated ‫ غريـ مشبعـ‬fats

Glycerol consists of a three C skeleton with an OH group attached to each C.

A fatty acid consists of a carboxyl group (COOH) attached to a long carbon

skeleton, often 16 to 18 carbons long.
 The many non-polar C-H bonds in the long hydrocarbon skeleton
make fats hydrophobic.
 In a fat, three fatty acids are joined to glycerol by an ester linkage, ‫راـبطة‬
‫ إـستيرية‬creating a triacylglycerol( = triglyceride) .
 Fatty acids may vary‫ تــختلف‬in length (number of carbons) and in the
number and locations of double bonds.
 If there are no carbon-carbon double bonds, then the molecule is a
saturated fatty acid ‫( مشبعـ‬has H at every possible position).

•If there are one or more carbon-carbon double bonds, then the
molecule is an unsaturated fatty acid ‫حـض دـهنى غريـ مـشبعـ‬
‫اـم‬ - formed by the
removal of H atoms from the carbon skeleton.
 A)- Saturated Fats ‫الـدهون لاــمشبعـة‬

The Fatty acid components are saturated (there is no double bonds

between the carbons. All C are linked with H.
Thus, it is saturated with H.

Most animal fats are saturated.

They are solid at room temperature.
Saturated fats-rich diet results in Atherosclerosis‫ لاـتصلب لاـشـريانى‬.

B)- Un-saturated Fats ‫الدـهون‬ ‫لاـغريـ مـشبعـة‬

These double bonds are formed by the removal of H atoms.
Most vegetable fats (oils) and fish fats are unsaturated.
They are liquid at room temperature.
They can be synthetically converted to saturated (solid) by adding H
(Hydrogenation ‫ﭽـة‬ ‫) َ ل ْه‬.
َ ‫اـدـ َر‬
 The major function of fats is energy storage.
 A gram of fat stores more than twice as much energy as
a gram of a polysaccharide.
 Humans and other mammals store fats as long-term
energy reserves‫ كمخزونطاقة طويل المدى‬in adipose cells ‫خاليا دهنية‬.
 2) Phospholipids;
Are major components of cell membranes

 Phospholipids have two fatty acids attached to glycerol and a

phosphate group at the third position.
 The phosphate group carries a negative charge.

• The interaction of
phospholipids with
water is complex.

• The fatty acid tails are

hydrophobic, but the
phosphate group and
its attachments form a
hydrophilic head.
  When phospholipids are added to
water, they self-assemble ‫تتشكل ذاتيا‬
into aggregates‫ تجمعات‬with the
hydrophobic tails pointing toward
the center and the hydrophilic
heads on the outside.
 This type of structure is called a
micelle ‫ الـزهرة‬.

• At the surface of a cell phospholipids

are arranged as a bilayer ‫ بطـقـة مـزدوـجة‬.
– Again, the hydrophilic heads are on
the outside in contact with the aqueous
solution‫ لاـمحلول لاـمائـى‬and the
hydrophobic tails in the core ‫ لاـمركز‬.
– The phospholipid bilayer ‫بطـقـة مـزدوـجة‬
forms a barrier ‫جز‬ ‫ اـحـ‬between the cell
and the external environment ‫لاـبيئة‬
‫جـ‬
‫لاـخـاريـة‬ .
• They are the major component of cell
membranes.
3) Steroids:
Include cholesterol and certain hormones
 Steroids are lipids with a carbon skeleton consisting of four fused
‫ ملتحمة‬carbon rings.
 Different steroids are created by varying functional groups attached to
the rings.

• Cholesterol, an important
steroid, is a component in
animal cell membranes.

• Cholesterol is also the precursor ‫ لاــمادـة لاــخام‬from which all other

steroids are synthesized.
• Many of these other steroids are hormones, including the sex

hormones.
• While cholesterol is clearly an essential molecule, high levels of
 ***
Fats
(Composed of Lipids)

Saturated
Saturated Unsaturated
Unsaturated Phospholipids
Phospholipids Steroids
Steroids
Animal Fats Vegetable Fats Bi-layer of cell Sex Hormones
membrane & Cholesterol

Hydrogenation
‫ﭽـــــــــة‬
َ ‫َهـ ْد َر‬
 CHAPTER
THE STRUCTURE AND 5
FUNCTION
THE STRUCTURE AND
OF MACROMOLECULES
FUNCTION OF
MACROMOLECULES
4- Nucleic Acids:
The Informational Polymers

1. Nucleic acids store and transmit

hereditary information ‫لاــمعلوـمات الـوراـثـية‬
2. A nucleic acid strand is a polymer
of nucleotides
3. Inheritance is based on
replication of the DNA
double helix
 DNA Structure ***

 DNA is located in the nucleus

 There are two types of nucleic acids

ribonucleic acid (RNA)
And
deoxyribonucleic acid (DNA).
Structures of nucleic acids (DNA & RNA) ***

3 5 o Phosphate Bases
group
o P o
o DNA Adenine
Base nucleotide
(A)
5 CH2 o Purine
4 H H 1
H
H
Guanine
3 2H (G)
o
Deoxyribose sugar
o P o
o
Base Cytosine
CH2 o (C) Pyrimidine
H H
H
H Thymine
3
5 3 H
(T)
Sugar-phosphate backbone
• The PO4 group of one
nucleotide is attached
to the sugar of the next
nucleotide in line‫ىـ صـف‬
‫فـ‬
‫مستقيم‬.

• The result is a
“backbone” of
alternating‫تــــدـل‬
‫با‬
phosphates and
sugars, from which the
bases starts.
 Nitrogenous bases ‫لاــنيتروجينية‬ ‫لاــقواـعد‬

3 5
Hydrogen bonds

Cytosine Guanine
Nitrogenous bases
(C) (G)

Thymine Adenine
(T) (A)
Uracil (U)
Pyrimidines Purine
5 3
Sugar-phosphate
backbones
 ***
DNA
• Adenine (A) would
form 2 hydrogen
bonds only with
thymine (T)

• Guanine (G) would

form 3 hydrogen
bonds only with
cytosine (C).
 ***

DNA & RNA

CH2 o CH2 o
H H
H H H
H H
H H
OH
Deoxyribose sugar (O Ribose sugar
on C2 is missed) (no missed O)

Deoxiribo-Nucleic-Acid Ribo-Nucleic-Acid

Double stranded nucleic acid Single stranded nucleic acid

Bases: A, G, C, T Bases: A, G, C, U
 The nucleic acid ***

 Nucleic acids are polymers of monomers called nucleotides.

 Each nucleotide consists of three parts: a nitrogen base, a pentose

sugar, and a phosphate group.

 The nitrogen bases (rings of carbon and nitrogen) come in two types:
Purines and Pyrimidines.

 The pentose sugar joined to the nitrogen base is ribose in

nucleotides of RNA and deoxyribose in DNA.

 The only difference between the sugars is the lack‫ نقص‬of an oxygen
atom on carbon 2 in deoxyribose.
 ***
 Polynucleotides are synthesized by connecting the
sugars of one nucleotide to the phosphate of the next
with a phosphodiester link.

 This creates a repeating backbone of sugar-phosphate

units with the nitrogen bases as appendages.
 The sequence of nitrogen bases along a DNA or mRNA
polymer is unique for each gene.
 Genes are normally hundreds to thousands of
nucleotides long.
 The linear order ‫ لاــترتيب لاــتتابعى‬of bases in a gene specifies ‫ُ يــحدد‬
the order of amino acids ‫( تــرتيب اـألحماض اـألمينية‬the monomers of a
protein).
 Inheritance is based on replication of the DNA double helix

 An RNA molecule is single polynucleotide chain (single strand).

 DNA molecules have two polynucleotide strands (double strand)
that spiral around ‫ تــدور حـلزونيا‬to form a double helix ‫ حـلزونمزدوج‬.
 The sugar-phosphate
backbones of the two
polynucleotides are on
the outside of the
helix.

 Pairs of nitrogenous
bases (one from each
strand) connect the
polynucleotide chains
with hydrogen bonds.

 Most DNA molecules

have thousands to
millions of base pairs
‫( زوج من لاــقواـعد‬bP).
 Because of their shapes, only some bases are compatible ‫ متواـفـقة‬with
each other.
 Adenine (A) always pairs with thymine (T) and guanine (G) with
cytosine (C).
 With these base-pairing rules, if we know the sequence of bases on
one strand, we know the sequence on the opposite ‫ لاــمقابل‬strand.
 The two strands are complementary ‫مكملين لـبعضهما‬.
 During preparations for cell division each of the strands serves as a
template ‫قــاــب نـسخ‬
‫ ل‬to order nucleotides into a new complementary
strand.
 This results in two identical copies ‫ نـسختينطبق اـألصل‬of the original
double-stranded DNA molecule.
 The copies are then distributed ‫ تــوزع‬to the daughter cells.

 This mechanism ensures that the genetic information is transmitted

to the new cells.
 ***

RepeatedSugar
Repeated Sugar--Phosphate
Phosphate DNA backbone
DNA backbone
Sugar–Phosphate-Base
Sugar–Phosphate-Base One nucleotide
One nucleotide
Polynucleotide
Polynucleotide DNA Molecule
DNA Molecule

DNA Double
DNA Double stranded
stranded

RNA single
RNA single stranded
stranded

DNA A G C T A T C

mRN T
U C G A T
U A G
A
 INTRODUCTION
CHAPTER 5
TO
THE STRUCTURE AND
FUNCTION OF
METABOLISM
MACROMOLECULES
Section B: Enzymes
1. Enzymes speed up metabolic reactions by lowering energy barriers
2. Enzymes are substrate specific
3. The active site in an enzyme’s catalytic center
4. A cell’s physical and chemical environment affects enzyme activity

Pages 96 - 103
 Hydrolysis of sucrose (table sugar)

Dehydration
Glucose + Fructose Sucrose

Hydration
Glucose + Fructose (H2O)
Sucrase
Hydrolysis of sucrose in the presence of Sucrase results in
its two monosaccharide components.

This process include:

1- breaking the bond between Glucose and Fructose;

2- Then, forming new bonds with H+ and OH- from water

This process consumes ‫ستهلك‬

‫ تــ‬energy (Activation Energy; EA)
Enzymes speed up metabolic reactions by lowering energy
barriers ‫حـواـجز لاــطاقة‬

A catalyst ‫ ال ُمحفز‬is a chemical agent that changes the rate of a reaction

without being consumed ‫ دون أـن ُ يــستهلك‬by the reaction.
An enzyme is a catalytic protein.
Chemical reactions between molecules involve both bond breaking
and bond forming.
To hydrolyze (hydration) sucrose, the bond between glucose and fructose
must be broken via hydrolysis in the presence of sucrase (the catalyst).

Sucrase
 Enzymes and Activation Energy

Activation Energy: is the amount of energy needed for the

reaction (between enzyme & substrate) to complete (to break the bonds)

Raising the temperature for these reactions to complete will

either denature the compounds or kill the cell.
Thus, organisms must therefore use a catalyst ‫ عاـمـلمحفـز‬.
Catalyst: is a chemical agent that accelerate the reaction
without being consumed by the reaction.

Enzyme is a catalytic protein‫ محزفـ‬/‫م اـسـعد‬ ‫ينـ‬

‫وترـبـ‬

Enzyme is a specific ‫ متخصص‬catalyst for specific reactants at

any time in the cell (e.g. Sucrase for only Sucrose).
Activation energy: is the amount of energy necessary to push the
reactants over an energy barrier.

At the transition state, the molecules

are at an unstable point.

The difference between free energy

of the products and the free energy of
the reactants is the delta G.

Enzyme speed reactions by

lowering EA. The transition
state can then be reached even at
moderate temperatures.
 Enzymes are substrate specific
 The substrate ‫ المادة المطلوبهضمها‬is a reactant which binds to an enzyme.
 When a substrate binds to an enzyme, the enzyme catalyzes‫ يسهل‬the
conversion‫ تحويل‬of the substrate to the product ‫ مكوناتها البنائية‬.
 Sucrase (catalyst) is an enzyme that binds to sucrose (substrate) and breaks
the disaccharide into fructose and glucose (products).

Enzyme (a catalyst)
Substrate Product (s)

Sucrase
Sucrose + H2O Glucose + Fructose

Specificity of enzyme ‫خصصية اـإلنزيـم‬ ‫ تــــ‬refers to its Active Site ‫لاــمركز‬

‫ لاــنشط‬which fit to‫ ـ ُيـــناسب‬the surface of substrate.
 The active site is an enzyme’s catalytic center

The active site of an enzymes is typically a pocket or groove‫شكل الجيب‬

on the surface of the enzyme into which the substrate fits.
The specificity of an enzyme is due to the fit between the active site
and that of the substrate.
As the substrate binds, the enzyme changes shape to fit the substrate,
bringing chemical groups in position to catalyze the reaction.

Fig. 6.14
Catalytic Cycle of Enzyme
 Active site of enzyme and Catalytic Cycle

Sucrose Sucrase

Glucose

Fructose
H2O
 Catalytic Cycle of Enzyme

1- The substrate binds to the active cite of enzyme.

2- This forms an Enzyme-Substrate complex (via weak

hydrogen bonds).

3- The active cite catalyses the conversion of the

substrate to final products (original components) by
breaking bonds.
4- The resulting products release from the enzyme.

5- The enzyme starts another reaction over and over again.

6- Thus, the enzyme can have a huge metabolic effects in
the catalytic cycle.
A single enzyme molecule can catalyze thousands or more reactions a
second.

Enzymes are unaffected by the reaction and are reusable ‫ يـُعاد استخدامها‬.

Most metabolic enzymes ‫ اإلنزيمات األيضية‬can catalyze a reaction in both the

forward and reverse direction.
The actual direction depends on the relative concentrations of products and
reactants.
Enzymes catalyze reactions in the direction of equilibrium‫ التعادل‬.

Enzymes lower activation energy and speed a reaction.

The rate that a specific number of enzymes converts substrates to

products depends in part on substrate concentrations.

At some substrate concentrations, the active sites on all enzymes are

engaged ‫ مشغولة‬, called enzyme saturation‫ التشبع اإلنزيمى‬.
 Cellular factors affecting enzyme activity

 Some conditions lead to the most active conformation and lead to

optimal rate of reaction. These factors are:-

1. Temperature: has a major

impact on reaction rate.
 As temperature increases,
reaction between substrate and
active sites occur faster.
 However, at some point
thermal increase begins to
denature the substrate.
 Each enzyme has an optimal
temperature‫ درـجة حرـارة ُمثلى‬.
 Cellular factors affecting enzyme activity

2. pH also influences the reaction rate, each enzyme has

an optimal pH falls between pH 6 - 8 for most
enzymes.
 However, digestive enzymes in the
stomach are designed to work best at
pH 2 while those in the intestine are
optimal at pH 8, both matching
their working environments.

Fig. 6.16b, page 100

3. Cofactors (coenzymes): ‫لاــعـواـمـل لاــمساـعدة‬
A non-protein helpers for catalytic activity of enzymes. They bind
permanently ‫ دـائـما‬to the enzyme and include two types:-
a) Inorganic cofactors, include zinc, iron, and copper.
b) Organic cofactors, include vitamins or molecules derived
from vitamins.
 Enzyme inhibitors:‫ـثـبّطات اـإلنزيـمات‬
ِ ‫ُم‬

They are molecules that prevent enzymes from catalyzing reactions.

 If thy covalently bind with enzyme, inhibition is irreversible‫غير منعكس‬.
 If binding is weak, inhibition may be reversible‫منعكس‬.
ُ
 If the inhibitor binds to the same site as the substrate, then it
called competitive inhibition‫ تثبيط تنافسى‬.

• If the inhibitor binds somewhere

other than the active site, then it
called noncompetitive inhibition.
 Types of Inhibitors:

A- Competitive: That resemble the substrate molecule and thus competes

the attach to the active site (blocking the active site).

B- Noncompetitive: They do not compete the substrate directly at the active

site. Rather, they bind with another part of the enzyme resulting in
changing enzyme shape. Finally, deactivate ‫ ـ ُيـــخمد‬the active site.

Activation and inhibition of enzymes are essential

for metabolic control
The insecticide DDT is inhibitor for key enzymes of nervous system.
Many antibiotics (e.g. Penicillin) inhibits enzymes that help bacteria to
make their cell walls.