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Biochemistry
Biochemistry has become the foundation for understanding all biological processes.

It has provided explanations for the causes of many diseases in humans, animals and plants.

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 Chapter 1
Chemical and biological
foundations of biochemistry

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 CHEMISTRY OF LIFE
basic chemical concepts

 Elements: simplest form of a substance

- cannot be broken down any further.
 Atom: the actual basic unit - composed
of protons, neutrons, and electrons.

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 THE ATOM
 The ATOM is the basic unit of matter.
 The atom is made up of 3 particles:
Particle Charge
PROTON +
NEUTRON No charge
ELECTRON -

 Isotopes are atoms that have same number

of protons and but different number of
neutrons.
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 Atoms are composed of two regions:
1- Nucleus: The center of the atom that
contains the mass of the atom (Proton &
Neutron).

2- Electron cloud: Region that surrounds the

nucleus.

 Electrons are not present within the atom,

instead they revolved around the nucleus of
the atom & form the electron cloud.

ATOMIC NUMBER = 3 (No. of PROTONS)

ATOMIC MASS = 6 (PROTONS + NEUTRONS)

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 COMPOUNDS
 A substance formed by the chemical combination
of 2 or more elements in definite proportions
 Ex: water, salt, carbon dioxide

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 TWO TYPES OF COMPOUNDS
1. Organic Compound: usually referred to as chemicals
of life - Contain C, H, and O in some ratio.
 Carbohydrates, Proteins, Lipids, Nucleic Acids

2. Inorganic Compound: usually "support" life - no

specific ratio of C, H, and O.
 Water (H2O), Carbon Dioxide (CO2)

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 CHEMICAL BONDS
 Chemical bonds hold the atoms in a molecule together.
 Types of chemical bonds:
1- Ionic bond.

2- Covalent bond.

3- Metallic bond.

4- Hydrogen bond.

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 IONIC BONDS
 Occur when 1 or more electrons are TRANSFERRED from one
atom to another.

 When an atom loses an electron(s) it becomes a positive charge.

 When an atom gains an electron(s) it becomes a negative charge
 These newly charged atoms are now called IONS.
 Example: NaCl (SALT)

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 COVALENT BONDS
 Occur when electrons are SHARED by atoms.
 These new structures that result from covalent bonds are called
MOLECULES.

 In general, the more chemical bonds a molecule has the more

energy it contains.

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 MIXTURES
 Mixture: is a material composed of TWO OR MORE ELEMENTS
OR COMPOUNDS THAT ARE PHYSICALLY MIXED.

 Types of Mixtures:
a- Homogeneous mixtures:
Examples: Sugar or salt in water
b- Heterogeneous mixtures:
Examples: A mixture of oil and water

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 SOLUTION
Two parts:

‫مذاب‬  SOLUTE – The substance that is being dissolved.

‫مذيب‬  SOLVENT - the substance in which the solute dissolves.

 Materials that do not dissolve are known as SUSPENSIONS. ‫معلق‬

 Blood is the most common example of a suspension.

 Cells & other particles remain in suspension.

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 FORMULA
 The chemical symbols and numbers that
compose a compound.
 Structural Formula – Line drawings of
the compound that shows the elements
in proportion and how they are bonded
 Molecular Formula – the ACTUAL
formula for a compound. C2H6O

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 CHEMICAL REACTIONS
 A process that changes one set of chemicals into another set of
chemicals.

 REACTANTS – elements or compounds that enter into a chemical

reaction.

 PRODUCTS – elements or compounds that are produced in a

chemical reaction.

 Chemical reactions always involve the breaking of bonds in

reactants and the formation of new bonds in products.

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 ‫اختيارات‬
‫حمض‬ ‫او توصيل‬

Acid & Base

 What are Acids and Bases?
Definition:

 “An Acid is a substance that can release a proton or hydrogen ion (H+)
when dissolved in water”

HCl H+ + Cl-

 “ A Base is a substance that can release a hydroxyl ion (OH-) when

dissolved in water”

NaOH Na+ +OH-

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 (‫تفاعالت التشرد )التفكك‬
‫يجي تعريف او معادلة‬
Neutralization Reactions

 An acid reacts with a base to produce a salt and water.

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 pH SCALE
The pH scale is a way of expressing the
strength of acids and bases. It’s measures
degree of substance alkalinity or acidity.

pH Range from 0 to 14

pH Under 7 = acid
pH 7 = neutral
pH Over 7 = base

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‫ممكن كتابة‬ Why is pH important in biology?
 pH affects solubility of many substances.
 pH affects structure and function of most proteins - including enzymes.
 Many cells and organisms (esp. plants and aquatic animals) can only
survive in a specific pH environment.
 Important point - ‫مهمة‬
 pH is dependent upon temperature

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 ‫تعريفه يجي في‬
‫االختبار‬

‫محلول واقي‬

Buffers
 Definition: A solution that resists change in pH. ‫توصيل التعريف‬
 Typically a mixture of the acid and base form of a chemical.
 Can be adjusted to a particular pH value

 Why use them?

 It is used to prevent any change in the pH. ‫ليش نستخدم كتابي‬
 The goal of the body is to maintain HOMEOSTASIS (neutrality) – to do this when
pH is concerned, we add weak acids & bases to prevent sharp changes in pH.
 Enzyme reactions and cell functions have optimum pH for performance.
 Important anytime, the structure and/or activity of a biological material must be
maintained.

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 ‫مبادئ‬
Principles of Biochemistry
 Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to maintain
the ordered state.

 Living processes contain thousands of chemical pathways.

Precise regulation and integration of these pathways are required
to maintain life

 Certain important pathways e.g. Glycolysis is found in almost all

organisms.

 All organisms use the following types of molecules: carbohydrates,

proteins, lipids & nucleic acids.

 Instructions of growth, reproduction and developments for each

organism are encoded in their DNA.

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 ‫تعاريف عن الخلية توصيل او اختيارات‬

Cells
 Basic building blocks of life.
 Smallest living unit of an organism.
 Grow, reproduce, use energy, adapt, respond to their
environment.
 Many cannot be seen with the naked eye.
 A cell may be an entire organism or it may be one of billions of
cells that make up the organism.
 Types of Cells: ‫كتابة‬

(a) Prokaryotic cell.

(b) Eukaryotic cell.

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For example of Prokaryotic cell ? Bacteria

Definition: Prokaryotic cells do not have a true nucleus and membrane-

bound organelles.

 The simplest form and the first type of cells are prokaryotic cells.

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 5 ‫تعداد في الهيكل‬
‫اختبار في التعاريف‬
Structure of Prokaryotic Cell :
A prokaryotic cell structure is as follows:
1.Capsule: It is an outer protective covering found in the
bacterial cells.
2.Cell Wall: It is the outermost layer of the cell which gives
shape to the cell.
3.Cell Membrane: This layer surrounds the cytoplasm and
regulates the entry and exit of substances in the cells.
4.Flagella: These are long structures in the form of a whip, that
help in the locomotion of a cell.
5.Nucleoid Region: It is the region in the cytoplasm where the
genetic material is present.

A prokaryotic cell lacks certain organelles like mitochondria and

Golgi bodies.

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 ‫تعداد املكونات‬
‫نفس قبل‬

4 ‫مكونات‬
Components of Prokaryotic Cells:
The prokaryotic cells have four main components:
1. Plasma Membrane: It is an outer protective covering which
separates the cell from the surrounding environment.
2. Cytoplasm: It is a jelly-like substance present inside the cell. All
the cell organelles are suspended in it.
3. DNA: It is the genetic material of the cell. All the prokaryotes
possess a circular DNA. It directs what proteins the cell creates.
It also regulates the actions of the cell.
4. Ribosomes: Protein synthesis occurs here.

Some prokaryotic cells possess cilia and flagella which helps in

locomotion.

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For example of Eukaryotic cell ? Animal and plants

Definition: Eukaryotic cells contain a membrane bound nucleus and

organelles.

 It 10 times larger than a prokaryotic cell and can be as much as 1000

times more in volume.

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 Eukaryotic cell
Two Main Types of Eukaryotic Cells

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 ‫هيكل اليو‬
Structure of Eukaryotic Cell:

Plasma Membrane
The outer lining, separate and protect cell from its surrounding
environment. A lipid/protein/carbohydrate complex, providing a barrier
and containing transport and signaling systems.

Nucleus
Double membrane surrounding the chromosomes and the nucleolus.
The nucleolus is a site for synthesis of RNA making up the
ribosome

Mitochondrion
Also known as “powerhouse of cells” because they produce energy.
Surrounded by a double membrane with a series of folds called cristae.
They help in the regulation of cell metabolism.

Chloroplasts
Similar to mitochondria but is found in plants where they convert light
energy (from the sun) into chemical energy (ATP) through the process
called photosynthesis.

How is the convert 29

Endoplasmic reticulum (ER)
Network of small, tubular structures forming channels within the cell.
It is present in two forms: rough endoplasmic reticulum (RER) contains
ribosomes and smooth endoplasmic reticulum (SER) that lacks ribosomes.

Ribosomes
Composed of proteins and ribonucleic acids (RNA) responsible
for protein synthesis.

Golgi apparatus
Responsible for transporting, modifying, and
packaging proteins and lipids into vesicles for delivery to targeted
destinations.

Lysosomes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps digest materials
ingested by the cell.

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Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.

Peroxisomes
Produce and degrade hydrogen peroxide, a toxic compound
that can be produced during metabolism.

Cell wall
Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm
Enclosed by the plasma membrane, liquid portion called cytosol
and it houses the membranous organelles.

Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its
shape and provides basis for movement.

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Similarities between prokaryotes and eukaryotes:
All cells, whether prokaryotic or eukaryotic, share these four features:
1. DNA
2. Plasma membrane
3. Cytoplasm
4. Ribosomes

Differences between prokaryotes and eukaryotes:

Prokaryote Eukaryote
Nucleus Absent Present
٢ ‫كتابة‬
Membrane-bound organelles Absent Present
Cell type Unicellular Mostly multicellular; some unicellular ٣ ‫او‬
Cell size Smaller (0.1-5 μm) Larger (10-100 μm)
Mitochondria Absent Present
DNA Form Circular Linear
Examples Bacteria Animals, plants
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36
 Bio-molecules
 Just like cells are building blocks of tissues likewise molecules are
building blocks of cells.

 Animal and plant cells contain approximately 10, 000 kinds of

molecules (bio-molecules)

 Water constitutes 50-95% of cells content by weight.

 Ions like Na+, K+ and Ca+2 may account for another 1%
 Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)
 Infinite variety of molecules contain C.

 Most bio-molecules considered to be derived from hydrocarbons.

 The chemical properties of organic bio-molecules are determined by
their functional groups. Most bio-molecules have more than one.

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 Many Important Biomolecules
are Polymers

‫مهم‬ • Biopolymers - macromolecules created by joining many

smaller organic molecules (monomers)

• Condensation reactions join monomers

(H2O is removed in the process)

• Residue - each monomer in a chain

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36
 Biomolecules – Structure
Anabolic

 Building block  Macromolecule

 Simple sugar  Polysaccharide
 Amino acid  Protein (peptide)
 Nucleotide  RNA or DNA
 Fatty acid  Lipid
Catabolic

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 ‫مهمني هذي والساليد الي بعده‬

Linking Monomers
Cells link monomers by a process
called dehydration synthesis
(removing a molecule of water)

Remove
H

H2O Forms

Remove OH

This process joins two sugar monomers

to make a double sugar
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 Breaking Down Polymers
 Cells break down
macromolecules by
a process called
hydrolysis (adding
a molecule of
water)

Water added to split a double sugar

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 Hydrocarbons ‫معانا‬
‫باالختبار‬
 A hydrocarbon is a compound consisting of only hydrogen (H)
and carbon (C).

 Hydrocarbons are the most simple organic compounds.

 For classification purposes, all other organic compounds are

considered derivatives of hydrocarbons.

 Hydrocarbons can be divided into aromatic and aliphatic

hydrocarbons.
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 The bonds are always nonpolar.
 The carbon-carbon bond can be single, double, or triple bonds.
 Alkanes are hydrocarbons with only single bonds.
 Alkenes are hydrocarbons with double bonds
 Alkynes are hydrocarbons with triple bonds

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 Chapter 2
Gene expression and the
synthesis of proteins

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 Gene Expression

 Gene: A gene is the sequence

of nucleotides in DNA encoding
for one polypeptide chain or
one mRNA molecule.
 Gene expression is assumed
to be controlled at various
points in the sequence leading
to protein synthesis.

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 Gene Expression
(From DNA to protein)
In all organisms, two steps are required to read the information
encoded in a gene's DNA and produce the protein it specifies.
First, the gene's DNA is transcribed to messenger RNA (mRNA).
Second, that mRNA is translated to protein.

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 Two steps are required
1. Transcription
The synthesis of mRNA uses the gene on the
DNA molecule as a template
This happens in the nucleus of eukaryotes
2. Translation
The synthesis of a polypeptide chain using the
genetic code on the mRNA molecule as its
guide.

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* Gene expression to form
a specific polypeptide is
performed in 3 steps:

1- Transcription
( RNA production)
2- processing

3- Translation

DNA RNA Protein

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 1-Transcription
(RNA synthesis)
- RNA molecules are Nucleus
produced by copying
Gene
part of DNA into a
complementary
DNA
sequence of RNA.
- This process is started Transcription
and controlled by an messenger
RNA
enzyme called RNA
polymerase.
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 Types of RNA
Three types of RNA:
1- Messenger RNA (mRNA):
- Carries copy of a DNA sequence to the site of protein synthesis at the ribosome.
- Tells the ribosome what kind of protein to make
2- Transfer RNA (tRNA):
- Gets the right amino acid to make the right polypeptide protein according to mRNA
instructions.
3- Ribosomal RNA (rRNA):
- Part of the structure of a ribosome
- Helps in protein production

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 2. RNA Processing
- Introns are pulled out and exons come together.
- Introns are noncoding sections of an RNA transcript.
- Exons are coding sections of an RNA transcript.
- End product is a mature RNA molecule that leaves the nucleus to the cytoplasm
for protein synthesis.

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 3. Translation
(making proteins)

Three parts:
1- initiation: start codon (AUG)
2- elongation:
3- termination: stop codon (UAG)

Let’s make a PROTEIN!!!!.

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1- Initiation

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2- Elongation

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2- Elongation

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2- Elongation

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2- Elongation

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2- Elongation

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2- Elongation

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3- Termination

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 End product
The end products of protein synthesis is a
primary structure of a protein.

A sequence of amino acid bonded

together by peptide bonds.
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60
Chapter 3

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The Role of Energy and Metabolism

All organisms require energy to complete cellular

processes; metabolism is the set of the chemical reactions
that release energy for cellular processes.

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Types of Energy:

The various types of energy include

1-kinetic energy: is the energy associated with objects in

motion.

2-potential energy: is the type of energy associated with an

object’s potential to do work.

3-chemical energy: is the type of energy released from the

breakdown of chemical bonds and can be used for metabolic
processes

All organisms use different forms of energy to power the

biological processes that allow them to grow and survive.
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 Metabolism
Metabolism: All the chemical reactions that occur in the cells of
our bodies.

Catabolism (Catabolic reactions) catabolic

 Break down large molecules
 Produce energy
Anabolism (Anabolic reactions) anabolic

 Synthesize molecules (use small molecules to build large ones)

 Require energy

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Anabolic and catabolic pathways: Anabolic pathways are
those that require energy to synthesize larger molecules.
Catabolic pathways are those that generate energy by
breaking down larger molecules. Both types of pathways are
required for maintaining the cell’s energy balance.

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1-Anabolic Pathways:

Anabolic pathways require an input of energy to synthesize

complex molecules from simpler ones.

Examples:

a) The synthesis of sugar from CO2.

b) The synthesis of large proteins from amino acid.

c) The synthesis of new DNA from nucleic acid.

These processes are critical to the life of the cell, take place
constantly, and need energy provided by ATP and other high-
energy molecules like NADH and NADPH.

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2-Catabolic Pathways:

Catabolic pathways involve the degradation of complex

molecules into simpler ones, releasing the chemical energy.

Examples of energy-storing molecules:

a) Lipids

b) Carbohydrates

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 Digestion of Foods
Digestion is the first step of catabolism

 Carbohydrates glucose, fructose, galactose

 Proteins amino acids

 Lipids glycerol and

fatty acids
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The main 3 stages of catabolic reaction:

1-The first stage:

Large organic molecules, such as proteins, polysaccharides (carbohydrates)

and lipids are digested into their smaller components outside cells.

2-The second stage:

These smaller molecules are taken up by cells and converted to smaller

molecules, usually acetyl-CoA, which releases some energy.

3-The third stage:

The acetyl group on the acetyl-CoA is oxidized to H2O and CO2 in the citric
acid cycle and electron transport chain, releasing the energy that is stored in
NADH.

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70
1) Carbohydrate catabolism

Is the breakdown of carbohydrates into smaller units.

1. The major route of breakdown is glycolysis, where sugars such as

glucose and fructose are converted into pyruvate and ATP.

2. Pyruvate is an intermediate in several metabolic pathways, but the

majority is converted to acetyl-CoA and fed into the citric acid
cycle.

3. The most important product in the citric acid cycle is NADH and
NADH2
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Glycolysis: Oxidation of Glucose
Glycolysis generates
2 ATP molecules and 2 NADH + 2 H+
Two ATP used in adding phosphate groups to glucose
and fructose-6-phosphate (- 2 ATP)
Four ATP generated in direct transfer to ADP by two 3-
C molecules (+ 4 ATP)
Glucose + 2 ADP + 2 Pi + 2 NAD+
2pyruvate + 2 ATP + 2 NADH + 2 H+

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 Pathways for Pyruvate
Aerobic conditions:

O
||
CH3–C –COO- + NAD+ + CoA
pyruvate
O
||
CH3–C –CoA + CO2 + NADH + H+

acetyl CoA
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 Pathways for Pyruvate
Anaerobic conditions (No O2 available)

Reduce to lactate to replenish NAD+ for

glycolysis
O OH

|| |
CH3–C –COO- + NADH + H+ CH3–CH –COO- + NAD+
pyruvate lactate

enzyme: lactate dehydrogenase 74

 Learning Check
Match the following with the terms below:

(1) Catabolic reactions (2) Coenzymes

(3) Glycolysis (4) Lactate

A. Produced during anaerobic conditions

B. Reactions that convert glucose to pyruvate

C. Metabolic reactions that break down large molecules

to smaller molecules + energy

D. Substances that remove or add H atoms in

oxidation and reduction reactions
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 Solution
Match the following with the terms below:

(1) Catabolic reactions (2) Coenzymes

(3) Glycolysis (4) Lactate

A. 4 Produced during anaerobic conditions

B. 3 Reactions that convert glucose to pyruvate

C. 1 Metabolic reactions that break down large

molecules to smaller molecules + energy

D. 2 Substances that remove or add H atoms in

oxidation and reduction reactions

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2) Fat catabolism:

Fats are catabolized by hydrolysis to free fatty acids and glycerol.

1. The fatty acids are broken down by beta oxidation to release

acetyl-CoA, which then is fed into the citric acid cycle.

2. Fatty acids release more energy upon oxidation than

carbohydrates.

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 Chapter 4
Protein structure,
synthesis and degradation

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Proteins (polypeptide) are biomolecule composed of three or more

amino acids linked by synthesis reactions.

Proteins are an important class of biological macromolecules which

are the polymers of amino acids.

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 Amino acids - Proteins:
 Amino acids:
• Building blocks of proteins.

• R Group (side chains) determines the

chemical properties of each amino acids.
• Also determines how the protein folds and
its biological function.

• Functions as transport proteins, structural

proteins, enzymes, antibodies, cell
receptors.

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Amino Acids are the Basic Structural Units of
Proteins

Stereo isomers of amino acids

(mirror images of each other).

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 Amino Acids are Linked by Peptide Bonds to
Form Peptide Chains
The peptide bond
The peptide bond is the bond between two amino acids.

Formation of a Peptide

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 Proteins are linear polymers of
amino acids
R1 R2

NH3＋ C COOー NH3＋ C COOー

＋ ＋
H H
A carboxylic acid
H2O H2O condenses with an amino
group with the release of a
R1 R2 R3 water
NH3＋ C CO NH C CO NH C CO

H Peptide H Peptide H
bond bond
The amino acid
sequence is called as
A
F
G S
T D
K A
primary structure
N G S

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84
85
 Structural of protein

1. Primary structure: the amino acid sequence

2. Secondary structure: (e.g. alpha helices, beta sheets).
3. Tertiary structure: (e.g.3-D shape).
4. Quaternary structure: Multiple polypeptides connect
(e.g. Hemoglobin).

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Types of protein structure
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 Primary structure

• The primary structure of protein refers to the sequence

of amino acids present in the polypeptide chain.

• Amino acids are covalently linked by peptide bonds.

• Each component amino acid in a polypeptide is called a

“residue” or “moiety”.

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 Secondary structure

 Secondary structure refers to highly regular local

sub-structures on the actual polypeptide
backbone chain.

 Two main types of secondary structure, the

alpha helix (α-helix) and beta sheets (β-sheets).

 These secondary structures are defined by

patterns of hydrogen bonds between the main-
chain peptide groups.

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 Beta sheets

β-sheets

- The beta sheet, (β-sheet) (also β-

pleated sheet) is a common motif of the
regular protein secondary structure.

- Beta sheets consist of beta strands (β-

strands) connected laterally by at least
two or three backbone hydrogen bonds,
forming a generally twisted, pleated
sheet.

- A β-strand is a stretch of polypeptide

chain typically 3 to 10 amino acids long .

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 Tertiary structure

 Tertiary structure is the three- dimensional

conformation of a polypeptide.

 The common features of protein tertiary

structure reveal much about the biological
functions of the proteins.

 The function of a protein depends on its

tertiary structure. If this is disrupted, it loses its
activity

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 Quaternary structure

 Quaternary structure is a larger assembly of

several protein molecules or polypeptide
chains usually called subunits .

 Sub units are held together by non covalent

interactions.

 Ex.: Hemoglobin

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 Proteins play key roles in a
living system
 Three examples of protein functions
 Catalysis: Alcohol
dehydrogenase
Almost all chemical reactions in a living oxidizes alcohols
cell are catalyzed by protein enzymes. to aldehydes or
ketones
 Transport:
Some proteins transports various
substances, such as oxygen, ions, and so
on. Haemoglobin
carries oxygen

 Information transfer:
For example, hormones.
Insulin controls
the amount of
sugar in the
blood

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Fibrous proteins have polypeptide chains
organized in long fibers or sheets

9/21/2023
 Water insoluble

Mrs. Hanadi Filmban

 Very tough physically, may be
stretchy

9
4
Globular proteins
have their chains folded into compact, rounded
shapes
 Easily water soluble

 Storage proteins function in

the storage of amino acids

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5
9/21/2023
Examples of globular proteins

9/21/2023
 Hormone proteins function as cellular messenger molecules
that help maintain homeostasis

Mrs. Hanadi Filmban

 Insulin: sends message “allow sugar into cells” (when blood
glucose levels are high, cells will transport glucose into the cells
for use or storage)

 Glucagon: sends message “we need more sugar in the blood”

(when blood glucose is too low, cells will release glucose)

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9/21/2023 Mrs. Hanadi Filmban
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Protein degradation:
1. Elimination of misfolded and damaged proteins:
- Environmental toxins, translation errors and genetic
mutations can damage proteins.
2. Regulation of cellular metabolism:
Increase or decrease the number of enzyme molecules and
regulatory substances
3. The generation of active proteins:
The proteolytic cleavage of the precursor generates an active
enzyme – proteases, lysosome
4. The recycling of amino acids

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2. Regulation of cellular metabolism:

Increase or decrease the number of enzyme molecules and

regulatory substances

3. The generation of active proteins:

The proteolytic cleavage of the precursor generates an active

enzyme – proteases, lysosome

4. The recycling of amino acids:

Generate free amino acids from short peptides that are

generated by the proteasome and other intracellular
proteases.

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 Chemical Modifications that Lead
to Protein Degradation
- The oxygen rich environment in which proteins exist tend to
produce a variety of chemical reactions in proteins.

- The oxidation of lipids, reducing sugars and amino acids

leads to the formation of carbonyls and carbonyl adducts.

- Racemization and isomerization of protein residues.

- The oxidatively modified proteins are not repaired and must
be removed -protein degradation.

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Denaturation

Denaturation results in disruption of the secondary,

tertiary, or quaternary structure of the protein

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Denaturation
 Disruption of secondary, tertiary and quaternary protein structure by:
1. heat/organics
2. acids/ bases
3. heavy metal ions

 Basically the protein is unfolded without changing

the primary structure resulting in the protein
changing its’ physical properties.

104
 Examples of denaturation
 Frying or boiling an egg

 Ironing or curling your hair

 Alcohol on cuts to denature proteins in bacteria

 Cooking food to denature proteins in bacteria

Protein function is lost during denaturation, which is often irreversible

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Even a slight change in the amino acid sequence
can cause the protein to malfunction

For example,
mis-formed hemoglobin causes sickle cell disease 104
 Chapter 5
Carbohydrates Metabolism

105
WHAT ARE CARBOHYDRATES?
 Carbohydrates (CHO) are single largest component of diet
besides water, providing 48% of caloric need (i.e, Energy).
In most CHO, the ratio of hydrogen to oxygen is 1:2:1.
They are a group of organic compounds whose carbons are
extensively hydrated (i.e, Charli carbon).

Remember:
They can also be defined as
aldehyde or ketone derivative of
polyhydric alcohols.

106
 Functions of Carbohydrates
1. Store energy in the form of starch (photosynthesis in plants)
or glycogen (in animals and humans).
2. Provide energy through metabolism pathways and cycles.
3. Supply carbon for synthesis of other compounds.
4. Form structural components in cells and tissues.
5. Intercellular communications.

107
CLASSIFICATION:
CHO are classified according to number of sugar units:
1. Monosaccharaides:
simple sugars; they can not be hydrolysed into simpler form
and are further classified according to no. of carbon
atoms per molecule.
a. Trioses: have 3 carbon atoms. Glyceraldehyde and
dihydroxyacetone.
b. Pentoses: have 5 carbon atoms. Ribose and ribulose.
c. Hexoses: Have 6 carbon atoms. Glucose and fructose

108
 Examples of the
most important &
common
Monosaccharaides

109
 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. In blood,

conc. Is 70-120 mg/dl

 Major building block of di- and poly saccharide

and is transported by blood to all cells where its

oxidized for energy. The monosaccharide in

polymers of starch, cellulose, and glycogen.

110
 D-Fructose
D-Fructose is CH2OH
 Is a ketohexose C6H12O6. C O
 Is the sweetest carbohydrate. HO C H
 Is found in fruit juices and honey. H C OH
 It is also a component of sucrose. H C OH
 Converts to glucose in the body. CH2OH

D-Fructose

111
 Galactose

Not found in nature as monosaccharide, but as a

part of a disaccharide, lactose.

Milk is the prime source of galactose.

Mammary glands convert glucose to galactose

then synthesize lactose.

112
 2- DISACCHARIDES:

They are composed of 2 monosaccharide units, with same or different.

Synthesis
C6H12O6 + C6H12O6 C12H22C11 + H2O
Hydrolysis/ digestion

They account for 35% of dietary carbohydrates.

Nutritionally important disaccharides are lactose, sucrose and Maltose.

The 2 sugars are joined by an O-glycosidic bond.

113
 Important Disaccharides
A disaccharide consists of two monosaccharides .

Monosaccharaides Disaccharide
glucose + glucose maltose + H2O
glucose + galactose lactose + H2O
glucose + fructose sucrose + H2O

114
 Maltose
Maltose is
 A disaccharide also known as malt sugar.

 Composed of two D-glucose molecules.

 Obtained from the hydrolysis of starch.

 Used in cereals, candies, and brewing.

 Found in both the - and β - forms.

115
Formation of Maltose

Free α-OH

116
LACTOSE: (milk sugar)
Major dietary CHO for infants.
Composed of galactose and glucose molecules
10% of total CHOs consumed. Lactose is the only natural source of galactose.
Lactose is hydrolysed to its monosaccharides by lactase in humans and by β-
galactosidase in bacteria.
Synthesized also during lactation.

Galactose is joined to glucose by

a β-1,4-glycosidic linkage.

117
 Sucrose:
It’s the main transport form of CHOs in plants.

Obtained from cane and beet commercially.

Made of 2 monosaccharides glucose and fructose which are

linked by a glycosidic linkage; α for glucose and β for fructose.

It can be cleaved to its 2 components by enzyme sucrase.

Provides 20-30% of the total calories (i.e one of the energy

source).
Sucrase/invertase
Sucrose ----------------------> Glucose + Fructose

118
3-Polysaccharides

119
 Polysaccharides
Polysaccharides include two main groups:

1. Homopolysacchrides
 Contain only one type of monosaccharaides units.

2. Hetero-polysacchraides
 Contain tow or more different monosaccharide
units.

120
A. Homopolysacchrides
 Are polymers of D-glucose.
 Include amylose and amylopectin,
CH2OH
starches made of α-D-glucose. O

 Include glycogen (animal starch in

OH
muscle), which is made of α-D- OH OH

glucose. OH

 Include cellulose (plants and α-D-Glucose

wood), which is made of β-D-
glucose.
121
 The three most important homo-

polysacchrides are all polymers of D-glucose.

 They differ only in the type of glycosidic

bond and the amount of the branches.

122
Examples of the
most important &
common
Polysaccharides

123
 Starch
 Starch is the storage form of glucose in plants and is
composed of two different kinds of polysacchrides :

 Amylose
 Amylopectin

124
 Glycogen
Glycogen
 Is the polysaccharide that
stores α-D-glucose in
muscle.
 Is similar to amylopectin,
but is more highly branched.
Each branch contains 8-12
glucose units.

125
 Cellulose
Cellulose
 Is a polysaccharide of
glucose units in un-branched
chains.
 Has β-1,4-glycosidic bonds.
 Cannot be digested by
humans because humans
cannot break down β-1,4-
glycosidic bonds.

126
Digestion of Carbohydrate:
A. More than 60% of our foods are carbohydrates. Starch,
glycogen, sucrose, lactose and cellulose are the chief
carbohydrates in our food. Before intestinal absorption, they
are hydrolysed to hexose sugars (glucose, galactose and
fructose).

B. A family of a glycosidases that degrade carbohydrate into

their monohexose components catalyzes hydrolysis of
glycocidic bonds. These enzymes are usually specific to the
type of bond to be broken.

127
Digestion of carbohydrate by salivary α -amylase in
the mouth
A. This enzyme is produced by salivary glands. Its optimum
pH is 6.7.
B. It is activated by chloride ions (cl-).
C. It acts on cooked starch and glycogen breaking α 1-4
bonds, converting them into maltose [a disaccharide
containing two glucose molecules attached by α 1-4 linkage].
This bond is not attacked by -amylase.

128
D: Because both starch and glycogen also contain 1-6 bonds,
the resulting digest contains isomaltose [a disaccharide in
which two glucose molecules are attached by 1-6 linkage].

E: Because food remains for a short time in the mouth,

digestion of starch and glycogen may be incomplete and
gives a partial digestion products called: starch dextrins
(amylodextrin, erythrodextrin and achrodextrin).

F: Therefore, digestion of starch and glycogen in the mouth

gives maltose, isomaltose and starch dextrins.

129
 III. ln the stomach:
carbohydrate digestion stops temporarily
due to the high acidity which inactivates
the salivary - amylase.

130
IV. Digestion of carbohydrate by the
pancreatic - amylase small intestine
in the small intestine.
A. α-amylase enzyme is produced by
pancreas and acts in small intestine.
Its optimum pH is 7.1.
B. It is also activated by chloride ions.
C. It acts on cooked and uncooked
starch, hydrolysing them into maltose
and isomaltose.

131
Final carbohydrate digestion by intestinal
enzymes:
A. The final digestive processes occur at
the small intestine and include the action of
several disaccharides. These enzymes are
secreted through and remain associated
with the brush border of the intestinal
mucosal cells.

132
B. The disaccharides include:
1. Lactase (β-galactosidase) which hydrolyses lactose into two molecules
of glucose and galactose:
Lactase
Lactose Glucose + Galactose

2. Maltase ( α-glucosidase), which hydrolyses maltose into two molecules

of glucose:
Maltase
Maltose Glucose + Glucose

3. Sucrase (α-fructofuranosidase), which hydrolyses sucrose into two

molecules of glucose and fructose:
Sucrase
Sucrose Glucose + Fructose

4. α - dextrinase (oligo-1,6 glucosidase) which hydrolyze (1 ,6) linkage of

isomaltose.
Dextrinase
Isomaltose Glucose + Glucose

133
 VI. Digestion of cellulose:
A. Cellulose contains β(1-4) bonds between
glucose molecules.
B. In humans, there is no β (1-4)
glucosidase that can digest such bonds. So
cellulose passes as such in stool.
C. Cellulose helps water retention during the
passage of food along the intestine  producing
larger and softer stools  preventing
constipation.

134
Dietary Fibers:

 The portion of dietary CHO unabsorbed following digestion by human or

bacterial enzyme activity are cellulose, hemicellulose, legnin, pectin and
gum are usually referred to as fibers.
 The body can not break them down and so they are not digested by the body
and have no nutritional importance.

Physiological Importance:
 The water holding capacity of dietary fibers is very high, so they increase the
bulk of stools and facilitate the passage through the colon and help prevent
constipation and incidence of colon cancer.
 They stimulate peristaltic movements of GIT by adding bulk to the intestinal
contents.
 They reduce blood cholesterol level(pectins tend to bind to cholesterol and
reduce its absorption and reabsorption from the intestinal tract.
 Too much fiber depresses the iron utilization and increases abdominal
fullness.

135
136
Lipid definition:
 Lipids are non polar organic compounds that contain hydrocarbons, which are
the foundation for the structure and function of living cells.
 Examples of Lipids: triglycerides, cholesterol, phospholipids, fatty acids and
lipid-soluble vitamins.
 It’s soluble in Non-polar environments thus not being water soluble because
water is polar.

General formula
of lipid

137
 Functions of lipids
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones

138
 Fatty Acids
 Represented by the chemical formula

R-COOH

139
 Fatty Acids Cont’:
 The physical and physiologic characteristics  depends on
the Length and the degree of un-saturation.

 Melting point increases  with chain length.

 Melting point decrease in un-saturations.

140
 Saturated and Unsaturated
Fatty Acids
 Fats that have no double bonds in the
hydrocarbon chain are “saturated”
with hydrogens and are very linear,
e.g. animal fats.
 Fats that have a double bond are
called unsaturated and have “kinks”
in the hydrocarbon chain, e.g. plant
oils.
 Unsaturated fats can be either
monounsaturated as shown or
polyunsaturated (more than one
double bond).
 Unsaturated fats are generally
healthier than saturated fats.
141
 Triglycerols
 Triglycerides

 Main storage forms of

fatty acid

 Esters of trihydric alcohol

 FAT STORAGE:
 ENERGY PRODUCTION
 HEAT PRODUCTION
 INSULATION

142
Lipid Molecule

143
 Phospholipids
 Are the main lipid constituents of the membrane

144
 Steroids
 Typically have a core structure
of four fused carbon rings Cholesterol

 Cholesterol is an example and

the “base steroid” from which
your body produces other
steroids.

 Many hormones and vitamins

are steroids.

145
 Cholesterol:

 Since cholesterol is
hydrophobic (water fearing)
and blood is hydrophilic (water
loving), the two do not mix.

 Cholesterol is carried through

the bloodstream in protein
packages called lipoproteins,
made up of lipid on the inside
and protein on the outside.

 Two kinds of lipoproteins carry

cholesterol throughout your
body.
- High density lipoproteins (HDL) - Low density lipoproteins (LDL)
146
 LDL and HDL cont’:
 LDL cholesterol is sometimes called bad cholesterol.
 High LDL cholesterol leads to a buildup of cholesterol in arteries. The
higher the LDL level in your blood, the greater chance you have of getting
heart disease.

 HDL cholesterol is sometimes called good cholesterol.

 HDL carries cholesterol from other parts of your body back to your liver.
The liver removes the cholesterol from your body. The higher your HDL
cholesterol level, the lower your chance of getting heart disease.

147
 Lipoprotein Profile
 Cholesterol levels are measured in milligrams (mg) of cholesterol per
deciliter (dL) of blood.
 Desirable or optimal levels for adults with or without existing heart
disease are:
 Total cholesterol: Less than 200 mg/dL.
 Low Density Lipoprotein (LDL) cholesterol: Less than 100 mg/dL.
 High Density Lipoprotein (HDL): 40 mg/dL or higher.
 Triglycerides: Less than 150 mg/dL.

 The National Cholesterol Education Program recommends that healthy

adults over 20 years of age have their cholesterol levels checked once
every 5 years.

148
 Hyperlipidemia can lead to disease
 When there is too much cholesterol /LDL in your body
(because of diet and the rate at which the cholesterol is
processed) it is deposited in arteries, including those of the
heart, which can lead to narrowing of the arteries and heart
disease.

 Studies of people with heart disease have shown that

lowering cholesterol/LDL reduces the risk for dying from
heart disease, having a heart attack, or needing heart bypass
surgery or angioplasty.
149
 Chapter 7
Nitrogen Metabolism

150
Source of nitrogen:

1. Atmospheric Nitrogen

 78% of atmosphere
 Plants cannot utilize this form
 Some Bacteria, Blue Green Algae, leguminous plants
2. Nitrates, Nitrites and Ammonia

3. Amino acids in the soil

 Many soil organisms use this form

4. Organic Nitrogenous compounds in insects:

151
Nitrogen Metabolism Overview

 It is the polymeric nitrogen containing compounds proteins

and nucleic acids that define the major attributes of organism
such as function and structure.

 The metabolism of nitrogen encompasses a number of

topics, including nitrogen fixation, the anabolism and
catabolism of amino acids, purines, etc.

 Atmospheric nitrogen is the ultimate source of this element in

biomolecules.

152
The topic of nitrogen metabolism includes:

1- Nitrogen Fixation

2- Biosynthesis and Breakdown of amino acids, purines and

pyrimidines.

153
1- Nitrogen Fixation

154
Classes of nitrogen fixation

155
Non biological N2 fixation

 Do not take place in the micro-organisms.

 Non biological N2 fixation is usually found in rainy seasons

during lightening, thunder, storms and atmospheric pollution.

It is of two types:

A. Physical

B. Chemical

156
A. Physical

157
B. Chemical (Haber’s Process)

By using a temperature of about 500 C and a pressure of about

1000 atm, there is about 50% conversion of N2 to NH3.

158
1- Biological N2 fixation

 Conversion of elemental nitrogen or gaseous nitrogen into

nitrogenous compounds or salts by certain microorganisms
like bacteria ,blue green algae, fungi etc. is called biological
nitrogen fixation.

OR: Fixation of atmospheric Nitrogen into nitrogenous salts

with the help of micro-organisms

159
Nitrification: a process by which ammonia is converted by bacteria
into nitrates (NO3-)

Denitrification: a process which return nitrogen (NO3 - and NO2 -) to

the atmosphere

- Biological N2 fixation is carried by two types of micro- organisms.

Eg Symbiotic and non-symbiotic.

160
Biological N2 Fixation Carried out by two types of micro-
organisms:

1- symbiotic

2- non-symbiotic (free living micro- organisms)

161
Symbiotic N2 Fixation

The Fixation of free nitrogen of the soil by microorganisms

living symbiotically inside the plant.

Three categories :

 Nodule formation in leguminous plants

 Nodule formation in non-leguminous plants

 Non nodulation

Nodules may buried in soil even after harvesting – continue

nitrogen fixation 162
Non-symbiotic N2 fixation

The Fixation of free nitrogen of the soil by all those micro-

organisms living freely or outside the cell is called as non-
symbiotic biological N2 fixation.

 Aerobic

 Anaerobic

 Blue green algae

163
Steps in Nitrogen Fixation:

1. Atmospheric nitrogen is reduced by the addition of hydrogen atoms.

2. As a result the bonds between the two nitrogen atoms ( )

are broken down resulting in the formation of ammonia.

164
3. Nitrogen fixation thus requires the following three components:

1) A strong reducing agent

2) ATP to transfer hydrogen atoms to di-nitrogen.

3) enzyme systems

4. Ammonia thus formed as a result of nitrogen fixation is used for

the synthesis of amino acids (the building blocks for the synthesis
of proteins).

165
2- Amino acid
anabolism and
catabolism
166
Anabolism: also known as biosynthesis, build things and
consumes energy.

Catabolism: destructive metabolism, breakdown of amino acid

to form energy.

167
Amino Acid Biosynthesis (Anabolism)

 Biosynthesis of Glutamate from α-ketoglutarate (Reductive

amination)

 The production of glutamine from glutamate (Amidation)

168
The common features in amino acid biosynthesis:

1. Transamination

2. One-carbon transfer

Transamination: the transfer of amino groups from one

molecule to another; an important process in the anabolism and
catabolism of amino acid.

169
Example of transamination reactions:

170
Amino Acid Catabolism

What is the role of the urea cycle in amino acid Break

down?

It is the central pathway in nitrogen metabolism. The urea cycle

is a liver resident process removing nitrogen in form of
ammonia to be excreted from the body.

171
Urea Cycle: The urea cycle consists of five reactions:

1. Carbamoyl Phosphate + Ornithine = Citrulline

2. Citrulline + Aspartate = Arginosuccinate

3. Cleavage of Arginosuccinate = Arginine & Fumarate

4. Cleavage of Arginine Releases Urea & re-forms Ornithine

5. Control of the Urea cycle Involves Carbamoyl Phosphate

Synthetase

172
173
Purine Catabolism

The end product of

purine catabolism in
man is uric acid. It is
formed primarily in the
liver and excreted by the
kidney in the urine

174
Gout

 Is a disease in humans that is caused by the over production

of uric acid.

 Deposits of uric acid (which is barely soluble in water)

accumulate in the joints of hands and feet. Allopurinol is a
compound used to treat gout; it

 inhibits the degradation of hypoxanthine to xanthine

 inhibits the degradation of xanthine to uric acid

 preventing the buildup of uric acid deposits.

175
Chapter 8
Enzymes

176
 Enzyme

•Enzymes are biological catalysts.

•Many proteins act as biological catalysts or enzymes.
•Thousands of different enzymes exist in the body.
•A Catalyst is defined as "a substance that increases
the rate of a chemical reaction without being itself
changed in the process.”

177
 Enzymes

 Enzymes are proteins that control the rate of

chemical reactions by weakening bonds, thus
lowering the amount of activation energy
needed for the reaction .
 They catalyze nearly all the chemical reactions
taking place in the cells of the body.

 Not change or consumed during reaction.

 Reusable.

178
 Importance of Enzyme
1. Enzymes play an important role in Metabolism,
Diagnosis, and Therapeutics.

2. All biochemical reactions are enzyme catalyzed in the

living organism.

3. Level of enzyme in blood are of diagnostic importance

e.g. it is a good indicator in disease such as myocardial
infarction.

4. Enzyme can be used therapeutically such as digestive

enzymes.

179
 Structure of enzymes
Enzymes

Complex (protein part and nonprotein Simple (only protein)

part – cofactor)

Apoenzyme
Cofactor
(protein part)

Prosthetic groups Coenzyme

-usually small inorganic -large organic
molecule or atom; molecule
-usually tightly bound -loosely bound to
to apoenzyme apoenzyme
180
 4. Classification of enzymes

(1). By their composition

1). Monomeric enzyme
2). Oligomeric enzyme
3). Multienzyme complex: such as
Fatty acid synthase

181
 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

182
 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

183
 How enzymes work
1) Enzymes lower a
reaction’s activation
energy
 All chemical reactions have
an energy barrier, called the
activation energy, separating
the reactants and the
products.
 activation energy: amount of
energy needed to disrupt
stable molecule so that
reaction can take place.

184
Enzymes
Lower a
Reaction’s
Activation
Energy
185
186
 The active site of the enzyme
 Enzymes bind substrates to their active site and
stabilize the transition state of the reaction.

Active site: The area on the enzyme where the

substrate attach to.

Enzymes are usually very large proteins and the

active site is just a small region of the enzyme
molecule.

187
Active sites:
Enzyme molecules contain a special pocket or cleft called the
active sites.

188
Substrate: Is the reactant in biochemical
reaction.

When the substrate binds to an enzyme it

forms an enzyme-substrate complex.

189
Enzymatic reaction steps

1. Substrate approaches active site

2. Enzyme-substrate complex forms
3. Substrate transformed into products
4. Products released
5. Enzyme recycled
190
Mechanism of Action of Enzymes

1- Lock-and-Key Model

2- Induced Fit Model

191
 Lock-and-Key Model
 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
 This is an older model, however, and does not work for all
enzymes

192
 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

193
 Enzyme-substrate complex
Step 1:
Enzyme and substrate combine to form complex

194
 Enzyme-Product complex
Step 2:
An enzyme-product complex is formed.

195
 Product
Step 3:
The enzyme and product separate

196
 Factors affecting enzyme
activity
1. Concentration of substrate
2. Concentration of enzyme
3. Temperature
4. pH
5. Cofactors and Coenzymes
6. Inhibitors

197
 Inhibition of enzyme activities

• Inhibitor: any molecule which acts

directly on an enzyme to lower its
catalytic rate is called an inhibitor.
• Some enzyme inhibitors are normal
body metabolites.
• Other may be foreign substances,
such as drugs or toxins.

198
Enzymes involved in breakdown reactions

Catalase
Hydrogen peroxide Water + Oxygen

Amylase
Starch Maltose

Lipase Fatty acids + Glycerol

Fat
Pepsin
Protein Amino acids

199
Enzymes involved in Synthesis reactions
Leaves make glucose.

Glucose is used by
leaves as energy
source or transported
to root for storage.

Roots convert glucose

into G-1-P.
Phosphorylase
converts G-1-P into
starch. 200
 Enzymes involved in Synthesis reactions
What is phosphorylase?
Phosphorylase is an enzyme that synthesises starch.
What is substrate of phosphorylase?
Glucose-1-phosphate
What is the product?
Starch
phosphorylase

glucose-1-phosphate starch
201
 Enzyme Summary

Enzyme Substrate Product(s) Degradation

or synthesis?
Amylase Starch Maltose Degradation
Catalase Hydrogen Oxygen and Degradation
peroxide water
Pepsin Protein Amino acids Degradation
Phosphorylase Glucose-1- Starch Synthesis
phosphate
Lipase Fat fatty acids Degradation

202
 Enzymes in clinical diagnosis
 An enzyme test is a blood test or urine test that measures levels
of certain enzymes to assess how well the body’s systems are
functioning and whether there has been any tissue damage.

203
 Chapter 9
Control of chemical process signal-molecules
specialty functions

204
 Cell Communication

 Cells communicate with one another through

 Direct channels of communication
 Specific contact between cells
 Intercellular chemical messengers

205
 Cell Communication
 To survive, cells must
 Communicate with their neighbors
 Monitor environmental conditions
 Respond appropriately

206
 The Cellular Internet
 Cell-to-cell communication is essential for
multicellular organisms
 Biologists have discovered some universal
mechanisms of cellular regulation

• A signal transduction pathway is a series of

steps by which a signal on a cell’s surface is
converted into a specific cellular response

• Signal transduction pathways convert signals on

a cell’s surface into cellular responses
207
 Types of Chemical
Signaling
• Chemical signaling between
cells is one of the most
important ways that activities of
tissues and organs are
coordinated.
• The nervous system is the other
major coordinating system in
animals, but even here chemical
signaling is used between
adjacent neurons.

208
Modes of cell-cell signaling
1. Direct cell-cell or cell-matrix
2. Indirect: Secreted molecules.
A. Endocrine signaling. The signaling molecules are hormones
secreted by endocrine cells and carried through the circulation
system to act on target cells at distant body sites.
B. Paracrine signaling. The signaling molecules released by one
cell act on neighboring target cells (neurotransmitters).

C. Autocrine signaling. Cells respond to signaling molecules that

they themselves produce (response of the immune system to
foreign antigens, and cancer cells).

209
 Local and Long-Distance Signaling
 Cells in a multicellular organisms communicate by
chemical messengers

 Animal and plant cells have cell junctions that directly

connect the cytoplasm of adjacent cells

 In local signaling, animal cells may communicate by direct

contact

 In many other cases, animal cells communicate using local

regulators, messenger molecules that travel only short
distances

 In long-distance signaling, plants and animals use

chemicals called hormones

210
211
 Some signaling molecules

1. Steroid hormones
This class of molecules diffuse across the plasma membrane and bind to
receptors in the cytoplasm or nucleus. They are all synthesized from cholesterol.

2. Nitric oxide (NO) and Carbon Monoxide (CO)

NO, a simple gas, is able to diffuse across the membrane, and alters the
activity of intracellular target enzymes. It’s extremely unstable, so its effects are
local. Ex. It signals the dilation of blood vessels.

3. Neurotransmitters
They signal from neuron to neuron or from neuron to other target cell (ex. muscle cell ).

212
 The Three Stages of Cell Signaling

 The cells receiving signals through three processes:

1. Reception
2. Transduction
3. Response

213
1- Reception: A signal molecule binds to a receptor
protein, causing it to change its shape.

The binding between a signal molecule (ligand) and

receptor is highly specific

A conformational change in a receptor is often the

initial transduction of the signal

Most signal receptors are plasma membrane proteins

214
A. Intracellular Receptors
 Some receptor proteins are intracellular, found in the
cytosol or nucleus of target cells.
 Small or hydrophobic chemical messengers can
readily cross the membrane and activate receptors.
 Examples of hydrophobic messengers are the steroid
and thyroid hormones of animals.
 An activated hormone-receptor complex can act as a
transcription factor, turning on specific genes.
215
B. Receptors in the Plasma Membrane
Most water-soluble signal molecules bind to specific
sites on receptor proteins in the plasma membrane
There are three main types of membrane receptors:
1. G-protein-linked receptors
2. Receptor tyrosine kinases
3. Ion channel receptors

216
1- G-protein-linked receptor is a plasma membrane receptor that works with the
help of a G protein.
2- Receptor tyrosine kinases are membrane receptors that attach phosphates to
tyrosine.
 A Kinase, alternatively known as a phosphotransferase, is a type of enzyme that transfers phosphate
groups from high-energy donor molecules, such as ATP, to specific substrate. The process is referred to
as phosphorylation.

3- An ion channel receptor acts as a gate when the receptor changes shape.
 When a signal molecule binds as a ligand to the receptor, the gate allows specific ions, such as Na+ or
Ca2+, through a channel in the receptor.

 Calcium ions (Ca2+) act as a second messenger in many pathways, because cells can regulate its
concentration.
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2- Transduction: Many of molecular interactions relay
signals from receptors to target molecules in the cell.

Transduction usually involves multiple steps.

The molecules that relay a signal from receptor to

response are mostly proteins.

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3- Responses

The response may occur in the cytoplasm or in

the nucleus.

Many signaling pathways regulate the synthesis

of enzymes or other proteins.

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Termination of the Signal

 Inactivation mechanisms are an essential

aspect of cell signaling.

 When signal molecules leave the receptor,

the receptor reverts to its inactive state.

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