Biochemistry I - Third Year

Lecture 1: Biochemistry I
Introduction to the macromolecules biochemistry
3rd stage
Anbar University-College of Pharmacy-Clinical Laboratory Sciences Department

2020-2021
Dr. Yousif H. Khalaf

[email protected]
▪ References:
✓ Harper’s Illustrated Biochemistry
✓ Lippincott Biochemistry
✓ Lehninger Principles of Biochemistry
✓ Stryer Biochemistry
Objectives of this semester
▪ To integrate key concepts describing the traditional core topics of biochemistry:
structure and metabolism
At the end of the semester the students should be able to understand
▪ The chemical structure, and function of all biomolecules present in the living
organisms
What is Biochemistry?
➢ Biochemistry is the science concerned with studying the various molecules that occur in living cells and
organisms and with their chemical reactions. Because life depends on biochemical reactions, biochemistry
has become the basic language of all biologic sciences.
➢ Biochemistry and medicine are intimately related. Health depends on a harmonious balance of biochemical
reactions occurring in the body, and disease reflects abnormalities in biomolecules, biochemical reactions, or
biochemical processes.
➢ Biochemical processes is the study of chemical processes within and relating to living organisms. By
controlling information flow through biochemical signalling and the flow of chemical energy through
metabolism.
➢ Biochemical approaches are often fundamental in illuminating the causes of diseases and in
designing appropriate therapies. The judicious use of various biochemical laboratory tests is an
integral component of diagnosis and monitoring of treatment.
➢ Biochemistry spills over into pharmacology, physiology, microbiology, toxicology, and clinical
chemistry. In these areas, a biochemist may investigate the mechanism of a drug action; engage in
viral research; conduct research pertaining to organ function; or use chemical concepts, procedures,
and techniques to study the diagnosis and therapy of disease and the assessment of health.
➢ The study of biochemistry shows how the collections of inanimate molecules that constitute living
organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws
that govern the nonliving universe
Introduction to the macromolecules biochemistry
➢ The cell is the fundamental unit of life

➢ Cells are composed of small molecules (water), macromolecules and organelles macromolecules fold
into complex 3D structure
➢ Macromolecules can be classified into 4 different categories: carbohydrates, proteins, lipids and
nucleic acids
➢ Each type possesses distinct chemical properties that suit it for the functions it serves in the cell
Carbohydrates
▪ Carbohydrates, contain a carbon backbone but they also contain many polar OH groups and are therefore
soluble in water - large carbohydrate molecules called polysaccharides consist of many small ringlike sugar
molecules , these sugar monomers are attached to one other by glycosidic bonds in a linear or branched array
to form the sugar polymer
▪ Carbohydrates release chemical energy and may also provide carbon skeletons for the synthesis of other
molecules.
▪ Important structural functions are also served by polysaccharides
▪ linear polysaccharides form a major component of plant cell walls and bacteria cell walls
Proteins
▪ Proteins the most complex macromolecules found in the cell.
▪ They are composed of linear polymers called polypeptides, which contain amino acids connected by
peptide bonds
▪ Each amino acid contains a central carbon atom attached to 4 groups:
carboxyl group, amino group, H atom and R group
▪ Some structural proteins interact with lipids in membrane structure. Others aggregate to form part of
cytoskeleton that helps to give the cell its shape.
▪ Others are the chief components of muscle or connective tissue
Enzymes
▪ Enzymes are major class of proteins which function as catalysts that accelerate chemical
reactions by lowering the activation energy
▪ Enzymes are proteins consisting of one or more polypeptide chains.
Lipids
▪ Lipids are primarily hydrocarbon structure. They tend to be insoluble in water and are
therefore particularly well suited to serve as a major component of the various membrane
in structure found in cells.
▪ lipids also serve as storing chemical energy to drive the metabolism of the cells.
▪ Lipids include fats, oils, phospholipids, steroids, and cholesterol.
▪ Formed by dehydration synthesis of one glycerol for every 3 fatty acids.
Nucleic acids
▪ Nucleic acids are the largest macromolecules in the cell.
▪ They are very long, linear polymers, called polynucleotides, composed of nucleotides
▪ A nucleotide contains
- 5 carbon sugar molecules
- One or more phosphate groups
- Nitrogenous base
▪ Five different type of nitrogenous bases are found in the two main type of nucleic acids,
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
▪ DNA contains the genetic information that is inherited when cells divide and organisms reproduce
▪ This genetic information is used in the cells to make ribonucleic acids and proteins
Some common functional groups in biomolecules
▪ 30 chemical elements are essential to organisms. The
four most elements in living organisms are hydrogen,
oxygen, nitrogen, and carbon, which together make
up more than 99% of the mass of most cells.
Carbohydrates
3rd Class

2020-2021

[email protected]
Learning outcomes
o To know the formation of carbohydrates

o To understand the nature of glycosidic bonds
o To understand the structural organisation of carbohydrates
o To appreciate the various functions of carbohydrates
Carbohydrates
▪ Carbohydrates, one of the four major classes of biomolecules along with

proteins, lipids, and nucleic acids.
▪ Carbohydrates are built from monosaccharides (carbon atoms bound to
hydroxyl groups, Empirical formula Cn(H2O)n
▪ Monosaccharides are linked together by glycosidic bonds to form di, oligo- and
a huge variety of polysaccharides
▪ Carbohydrates are aldehyde (CHO) or ketone (C=O) compounds with multiple
hydroxyl groups (Carbon-oxygen double bonds make the sugars reactive)
Importance of carbohydrates
• Carbohydrates serve as energy store and metabolic intermediates.
• Ribose and deoxyribose sugars form part of the structural framework of RNA and DNA.
• Carbohydrates are important for tissue formation
• Carbohydrates form the basis of human blood groups
• Polysaccharides are structural elements in the cell walls of bacteria and plants and in the
connective tissues of animals..
• Carbohydrates are linked to many proteins and lipids, where they play key roles in
mediating interactions among cells and interactions between cells and other elements in
the cellular environment.
Several classifications of carbohydrates
Classification of Carbohydrates
Carbohydrates can be classified into:
1- Monosaccharides - simple sugars with multiple OH groups. Based on number of
carbons.
2- Disaccharides: two monosaccharides covalently linked by glycosidic bond.
3- Oligosaccharides: several monosaccharides (3-9) joined by glycosidic bonds.
4- Polysaccharides: polymers consisting of chains of monosaccharide or disaccharide

units.
Monosaccharides
- The simplest of the carbohydrates
- Aldehydes or ketones
- Colorless, crystalline solids that are freely soluble in water but insoluble in
nonpolar solvents.
- They are important fuel molecules as well as building blocks for nucleic acids.
- The smallest monosaccharides are :
The sugars named in boxes are the most common in nature
(Pentose)
(Triose) (Tetrose)
(Hexose)
The sugars named in boxes are the most common in nature
▪ The names of all sugars end in – ose

▪ Hexoses are the nutritionally
important sugars.
D and L isomerism
▪ Isomers are molecules with the same kinds and numbers of atoms joined up in different ways.
▪ A carbon atom that contains 4 different chemical groups forms an asymmetric (chiral) center.
▪ The prefixes D and L designate the absolute configuration of the asymmetric carbon farthest
from the aldehyde or keto group.
▪ When the OH group on this carbon is on the right , the sugar is the D-isomer; when it is on the left, it
is the L-isomer.
▪ Glyceraldehyde has a single asymmetric carbon and, thus, there are 2 stereoisomers of this sugar.
▪ D-Glyceraldehyde and L-glyceraldehyde are mirror images of each other (enantiomers).
Ball-and-stick model
Stereoisomers and Epimers
▪ Stereoisomers have the same chemical formula but differ in the position of the OH group on 1 or
more of their asymmetric carbons.
▪ Epimers are stereoisomers that differ in the position of the OH group at only 1 of their
asymmetric carbons.
▪ D-glucose and D-galactose are epimers of each other, differing only at C4, and can be
interconverted in human cells by enzymes called epimerase.
▪ D-mannose and D-glucose are also epimers of each other, differing only at C2.
Fischer/Haworth projection
Glucose
1 (dextrose; grape sugar)
HC O
HC 2 OH open-chain form • Glucose in solution exists mostly in the ring form at
3 equilibrium, with less than 0.1% of the molecules in the
HO CH (Fischer projection)
open-chain form.
HC4 OH
HC5 OH • Fischer projections are useful for depicting carbohydrate
structures because they provide clear and simple views
6 CH2OH of the stereochemistry at each carbon center.
6
CH2OH
5
H O H
4 OH
H H 1 ring-form
2
OH 3 OH (Haworth projection)
H OH
glucose
Cyclization of Monosaccharide
• The predominant forms of ribose, glucose, fructose, and many other sugars in solution are not
open chains. Rather, the open-chain forms of these sugars cyclize into rings.
• For an aldohexose such as glucose, Formation of a hemiacetal by reaction of the C-1 aldehyde
group with the C-5 hydroxyl group to form an intramolecular hemiacetal. The resulting cyclic
hemiacetal, a six-membered ring, is called pyranose. because of its similarity to pyran.
1/3
Mutarotation
2/3
(Ring-form is energetically more stable)

▪ Similarly, the C-2 keto group in the open-chain form of a ketohexose, such as fructose, can form an
intramolecular hemiketal by reacting with either the C-6 hydroxyl group to form a six-membered
cyclic hemiketal or the C-5 hydroxyl group to form a five-membered cyclic hemiketal. The five-
membered ring is called a furanose because of its similarity to furan.
Pentoses and Hexoses Cyclize to Form Pyranose and furanose Rings
HC O aldehyde group HC O CH2OH

HC OH HC OH C O ketone group
HO CH HO CH HO CH
HC OH HO CH HC OH
HC OH HC OH HC OH
hemiketal
hemiacetal
CH2OH CH2OH CH2OH
6 CH2OH
CH2OH 6
1
5
O HO O HOCH2 O CH2OH
OH 5 HO
4 OH 1 2
2 4
OH OH OH
OH 3 3
OH OH OH
−D- glucose galactose fructose
pyranose pyranose furanose
Pentose sugars
Pentoses such as D-ribose and 2-Deoxy-D-ribose form furanose rings, as we have seen in the structure
of these units in RNA and DNA.
HC O HC O
HC OH HCH
HC OH HC OH
HC OH HC OH
CH2OH CH2OH
HOCH2 O OH HOCH2 O OH
OH OH OH
ribose deoxyribose
Components of RNA and DNA

Monosaccharides joined to alcohols and amines Through Glycosidic Bonds
▪ Facilitate their metabolism
▪ Linked to alcohols, amines and phosphates
▪ The OH group on the anomeric carbon of a cyclic sugar can react with an –OH or an –NH
group of another compound to form:
o O-glycosidic bond between a monosaccharide and an alcohol or two monosaccharides or between a
monosaccharide and a protein
o N-glycosidic bond between a monosaccharide and a nitrogenous base or the amino acid lysine of a
protein
Adenosine triphosphate
Phosphorylated sugars
• Addition of a phosphoryl group to the monosaccharide
• Makes sugars anionic
• Trap sugar within the cell
• Creates a reactive intermediate of sugar metabolism
Adenosine monophosphate
Sugar alcohols
o Formed by the reduction of the aldehyde group of glucose to a

H2OH hydroxyl group.
o Used in foods suitable for diabetics as it tastes sweet.
Also in cough syrup and sugar-free mints.
o Energy yield roughly half that of glucose.
Sorbitol
Nutritional classification of carbohydrates
sugars polysaccharides
starch
monosaccharides Glycogen
disaccharides Cellulose
oligosaccharides Dextrans
Disaccharide = condensation between two monosaccharides (O-glycosidic bond)
Oligosaccharides = 3 to 9 monosaccharides
Some hexose derivatives important in biology
Simple sugars
Glucose, mannose, galactose, fructose, sucrose, lactose and maltose.
The most common disaccharides are:
Sucrose (cane or beet sugar - made from one glucose and one fructose)
Maltose (made from two glucoses)
Lactose (milk sugar - made from one glucose and one galactose)
The formula of these disaccharides is C12H22O11

Sucrose
Sucrose (common table sugar) is obtained commercially from cane or beet. The anomeric carbon atoms
of a glucose unit and a fructose unit are joined in this disaccharide; the configuration of this glycosidic
linkage is α for glucose and β for fructose. Sucrose can be cleaved into its component monosaccharides
by the enzyme sucrase. Glucose Fructose
Lactose: (Sugar of milk)
Lactose is the most important carbohydrate in the milk of mammals, Cow’s milk contains 4.5% lactose,
while human milk contains up to 7.5%, consists of galactose joined to glucose by a β-1,4-glycosidic
linkage. Lactose is hydrolyzed to these monosaccharides by lactase in human beings and by β-
galactosidase in bacteria.
Galactose Glucose
Non-reducing end
Reducing end
Lactose
❖ An acetal is a molecule with two single bonded oxygens attached to the same carbon
atom.
❖ This prevents opening of the chain to the aldehyde form and renders the modified residue non-
reducing.
Milk intolerance
▪ Many adults are unable to metabolise the milk sugar lactose → gastrointestinal disturbances
▪ Decrease in lactase activity to 5 – 10% of the level at birth
▪ Lactose is used as energy source for microorganisms in the colon
Fermentation to lactate with production of methane (CH3OH) and hydrogen gas (H2).
Flatulence, diarrhea as lactate is osmotically active and draws water into the intestine
lactase
Lactose Glucose Galactose

Maltose – originally isolated from malt
Two D-glucose residues are joined by a glycosidic linkage between the α-anomeric form of C-1 on one
sugar and the hydroxyl oxygen atom on C-4 of the adjacent sugar. Maltose comes from the hydrolysis
of starch and is in turn hydrolyzed to glucose by maltase
Sucrase, lactase, and maltase are located on the outer surfaces of epithelial cells lining the small intestine.
Polysaccharides (also called glycans)
▪ Most carbohydrates found in nature occur as polysaccharides, polymers of medium to high molecular
weight.
▪ Homopolysaccharides are polymers of a single monosaccharide, whereas heteropolysaccharides
contain more than one type of monosaccharide ,Three important Polysaccharides are starch,
glycogen and cellulose
Starch – large molecule with variable number of glucose units; storage

carbohydrate of plant cells
Amylose – is a linear polymer of glucose linked with mainly (α-1,4) bonds
Amylopectin – chain of glucose molecules (α -1,4), every 30th glucose

branch to other glucose residues (α-1,6)
Glycogen - storage carbohydrate in animal cells (muscle and liver(

- similar to amylopectine, but branch every 10th glucose
Non-starch polysaccharides– not digested by human enzymes

- e.g. Cellulose (glucose linked β-1,4), chitin, pectin
The end of the polysaccharide with an anomeric C1 not involved in a glycosidic bond is called the
reducing end.
CH2OH CH2OH
1→6 links: branch points in
O O amylopectin and glycogen
OH OH
O O
O
OH OH
CH2OH CH2 CH2OH CH2OH
O O O O
OH OH OH OH
O O O O O
OH OH OH OH
Hydrolysis of starch by amylase in saliva and pancreatic juice results in formation of

Dextrans
Glycogen
▪ Having a similar structure to amylopectin of starch, but more branches. and is commonly referred to as
animal starch.
▪ Glycogen does not possess a reducing end.
▪ The „reducing end“ glucose residue is not free but is covalently bound to a protein termed glycogenin
▪ Main storage of glucose in liver and skeletal muscle.
▪ The glycogen granules contain both glycogen and the enzymes of glycogen synthesis (Glycogenesis)
and degradation (Glycogenolysis).
Cellulose
• Cellulose is a polysaccharide of glucose found in plants, consists of linear chains of glucose units. It
is an unbranched polymer of glucose residues joined by β-1,4 linkages.
• The β configuration allows cellulose to form very long, straight chains. Fibrils are formed by parallel
chains that interact with one another through hydrogen bonds.
• The α-1,4 linkages in glycogen and starch produce a very different molecular architecture from that
of cellulose. A hollow helix is formed instead of a straightchain.
• These differing consequences of the α and β linkages are biologically important. The straight chain
formed by β linkages is optimal for the construction of fibers having a high tensile strength.
• Mammals lack cellulase and therefore cannot digest wood and vegetable fibers.
CH2OH 6CH OH
2 CH2OH CH2OH CH2OH
O 5 O O O H O OH
H H H H
H H H H H
OH H 1 O 4 OH H
1 O OH H O OH H O OH H
OH H H
H 2 H H
3
H OH H OH H OH H OH H OH
cellulose
Dextrans
• Dextrans are bacterial and yeast polysaccharides made up of (α1→6)-linked poly-D-glucose; all
have (α1→3) branches, and some also have (α1→2) or (α1→4) branches.
• Dental plaque, formed by bacteria growing on the surface of teeth, is rich in dextrans. Synthetic
dextrans are used in several commercial products (for example, Sephadex) that serve in the
fractionation of proteins by size-exclusion chromatography.
Chitin
▪ (a) A homopolymer of N-acetyl-D-glucosamine units in β-1,4 linkage, strengthens the
exoskeletons of arthropods
▪ (b) A spotted beetle (Pellidnota punetatia), showing its surface armor (exoskeleton) of
chitin.
Biochemistry of Nucleic acids
3rd stage

2020-2021

Nucleic acids
▪ Two types of Nucleic acids: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
▪ Storage and expression of genetic information.

▪ DNA: DNA is organic chemical of complex molecular structure that is found in all prokaryotic and
eukaryotic cells and in many viruses. It is also found in mitochondria and the chloroplasts of the
plants.
▪ The genetic information found in DNA is copied and transmitted from one generation to the next
through DNA replication.
▪ Nucleotides are the monomeric units of the DNA and RNA
o Heterocyclic nitrogenous base
o Sugar
o Mono, di, or triphosphate.

Bases present in DNA and RNA
▪ DNA and RNA contain the same purine bases: Adenine (A), Guanine (G), and pyrimidine base -
Cytosine (C)
▪ But they differ in their second pyrimidine base: DNA contains thymine (T), while RNA contains uracil
(U).
• The atoms in the rings of the bases are numbered 1 to 6 in pyrimidines and 1 to 9 in purines.
Bases present in DNA and RNA
Sugars present in DNA and RNA
o Pentoses (5-C sugars)

o Numbering of sugars is primed
Nucleosides
▪ linking one of the sugars with a purine or pyrimidine base through an N-glycosidic bond
▪ Purines are bonded to C1 of the sugar at their N9 atom.
▪ Pyrimidines are bonded to C1 of the sugar at their N1 atom.
▪ If the sugar is D-ribose, a ribonucleoside is produced , if the sugar is 2-deoxyribose a
Deoxyribonucleoside is produced.
▪ DNA: Deoxyadenosine, Deoxyguanosine, Deoxycytidine, and Deoxthymidine
▪ RNA: Adenosine, Guanosine, Cytidine, and Uridine

Ribonucleosides
N-glycosidic
bond
Phosphate Group
o Mono, di- or triphosphates
o Phosphates can be bonded to either C3 or C5 atoms of the sugar
Nucleotides
➢ A nucleotide is a nucleoside with an inorganic phosphate attached to a 5-hydroxyl
group of the sugar in ester linkage.
➢ The nitrogenous base is linked by an N-glycosidic bond to the anomeric carbon of
the sugar, either ribose or deoxyribose
➢ The names and abbreviations of nucleotides specify the base, the sugar, and the
number of phosphates attached.
Structure of nucleotides
Nucleotides
• In deoxynucleotides, the prefix “d” precedes the abbreviation. For example, ADP is Adenosine
diphosphate (the base Adenine attached to a ribose that has two phosphate groups) and dATP is
deoxyadenosine triphosphate (the base adenine attached to a deoxyribose with three phosphate
groups).
DNA is a polymer of deoxyribonucleotide RNA is a polymer of ribonucleotide

- Deoxyadenosine triphosphate (dATP) Adenosine triphosphate (ATP)
- Deoxyguanosine triphosphate (dGTP) Guanosine triphosphate (GTP)
- Deoxycytidine triphosphate (dCTP) Cytidine triphosphate (CTP)
- Deoxythymidine triphosphate (dTTP) Uridine triphosphate (UTP)
Nucleotides
Significances of nucleotides
o Building blocks of DNA and RNA.

o Essential carriers of chemical energy, especially ATP
o Components of the cofactors NAD, FAD, and coenzyme A
o Formation of activated intermediates such as UDP-glucose and CDP-
diacylglycerol.
o cAMP and cGMP, are also cellular second messengers.
▪ Cyclic AMP (cAMP), formed from ATP in a reaction catalyzed ▪ Nucleic acids: Phosphates can be
by adenylyl cyclase, is a common second messenger produced bonded to C3 and C5 atoms of the
in response to hormones and other chemical signals, used for sugar by phosphodiester bond
intracellular signal transduction, such as transferring into cells
the effects of hormones like glucagon and adrenaline, which
cannot pass through the plasma membrane
Anti-metabolites of nucleotides
▪ Anti-metabolites of purine/pyrimidine nucleotides are structural analogs of
purines and pyrimidines.
➢ They can interfere or inhibit synthesis pathway of purine or pyrimidine

nucleotides and further block synthesis of DNA, RNA, and proteins.
➢Widely used to control cancer.

Purine analogs
➢ 6-Mercaptopurine (6-MP) is analog of hypoxanthine.
OH SH
N N
N N
N N N N
H H
hypoxanthine 6-MP
6-MP nucleotide is analog of IMP
▪ Inosine monophosphate (IMP) or Inosinic acid is important
in metabolism. It is the ribonucleotide of hypoxanthine and
the first nucleotide formed during the synthesis of purine
nucleotides.
▪ It can also be formed by the deamination of adenosine
monophosphate by AMP deaminase
Pyrimidine analogs
➢ 5-fluorouracil (5-FU) is analog of thymine.
➢ Destroy structure of RNA
O O
F CH3
HN HN
O N O N
H H
5-FU thymine
There are two pathways leading to nucleotides
▪ De novo pathway: The synthesis of nucleotides begins with their

metabolic precursors: amino acids, ribose-5-phosphate, CO2, and one-
carbon units.
▪ Salvage pathway: The synthesis of nucleotide by recycle the free

bases or nucleosides released from nucleic acid breakdown.
o Some tissues and organs such as brain and bone marrow are only able
of synthesizing nucleotides by salvage pathway.
Degradation of nucleic acid
Nucleoprotein
In stomach Gastric acid and pepsin
Nucleic acid Protein
In small intestine Endonucleases: RNase and DNase

Nucleotide
Nucleotidase
Phosphate Nucleoside
Nucleosidase
Base Ribose
NH2 O Degradation of
Adenosine
C C N
N Deaminase
N C HN C Purine Nucleotides
CH CH
HC C HC C O
N N N
N
C N
Ribose-P Ribose-P
HN C
IMP CH
AMP
HC C
N N
Xanthine Oxidase H
Hypoxanthine
O O
C N C N
HN C HN C
C O CH
C C C C
O N N O N N
H H H H
GMP
Uric Acid Xanthine
(2,6,8-trioxypurine) The end product of purine metabolism

Gout
▪ Gout is a disorder of purine metabolism, occurs when uric acid crystallizes in the form of
monosodium urate
▪ A disease of the joints, usually in males, caused by an elevated concentration of uric acid
in the blood and tissues.
▪ The joints become inflamed and painful due to the abnormal deposition of crystals of
monosodium urate.
▪ The kidneys are also affected, because excess uric acid is deposited in the kidney tubules.
Allopurinol: inhibitor used to treat Gout
O O
C C H
N C
HN C HN C
CH N
HC C HC C
N N N
N H H
Hypoxanthine Allopurinol
Xanthine oxidase
Xanthine oxidase
Bases in DNA make hydrogen bonds
PURINE PYRIMIDINE PURINE PYRIMIDINE

DNA Structure
▪ DNA is a poly deoxyribonucleotide that contain many monodeoxyribonucleotide covalently
linked by phosphodiester bonds.
▪ Phosphodiester bonds join the 3´-OH group of one nucleotide to the 5´-OH group of the
next nucleotide.
Watson – Crick model of DNA structure
▪ 1953, Watson and Crick proposed a 3D for the DNA:
o Two helical polynucleotide chains, coiled about a common axis.

o The chains )strands( are anti-parallel, the 5-end of one strand is paired with the 3- end of the other
strand.
o The hydrophilic deoxyribose-phosphate of each chain is on the outside of the molecule, while the
hydrophobic bases are stacked on the inside.
o A purine on one strand forms H bonds with a pyrimidine on the other strand
o The bases of one strand of DNA are paired with the bases of the second strand, an Adenine is
always paired with a Thymine, while a Cytosine is always paired with a Guanine. Therefore one
polynucleotide chain of the DNA double helix is always the complement of the other. Given the
sequence of bases on one chain, the sequence of bases on the complementary chain can be
determined.
Watson – Crick model of DNA structure
Chargaff's rules
▪ In any samples of duoble–strand DNA:
o The amount of Adenine equals the amount of Thymine
o The amount of Guanine equals the amount of Cytosine
o The total amount of purines (A + G) equals the total amount of pyrimidines (T + C).
▪ The base pairs are held together by hydrogen bonds: two between A and T and three
between G and C.
o Base-pairing proved to be essential for determining the mechanism of DNA
replication (in which the copies of DNA are produced that are distributed to
daughter cells) and the mechanisms of transcription and translation (in which
mRNA is produced from genes and used to direct the process of protein
synthesis).
o As Watson and Crick suggested, base-pairing allows one strand of DNA to serve
as a template for the synthesis of the other strand.
o Base pairing also allows a strand of DNA to serve as a template for the synthesis
of a complementary strand of RNA.
Replication of DNA as suggested by Watson and Crick
▪ The preexisting or “parent” strands
become separated, and each is the
template for biosynthesis of a
complementary “daughter” strand
DNA can occur in different three-Dimensional (3D) Forms
DNA is a flexible molecule. Considerable rotation is possible around a number

of bonds in the sugar–phosphate (phospho-deoxyribose) backbone. Many
significant forms are described by Watson-Crick of DNA structure that are found in
cellular DNA. These structural variations generally do not affect the key properties
of DNA defined by Watson and Crick: strand complementary, anti-parallel strands,
and the requirement for A=T and G = C base pairs.
The B form (DNA double helix)
▪ Two helical polynucleotide chains, coiled about a common axis.
▪ Helix direction = Right-handed

▪ Strands are anti-parallel
▪ Diameter is 20 Å between base pairs
▪ Sugar-phosphates on the outside; purine and pyrimidine bases of both

strands on the inside of double helix .
▪ The offset pairing of the two strands creates a major groove and minor
groove on the surface of the double-helical
▪ H bonds between nitrogen bases and the van der Waals forces between
the stacked bases stabilize the structure of the double helix.
▪ Approx. 10 bases per helix turn and 34 Å between base pairs.

▪ Rise/turn of helix = 3.4 Å
DNA can exist in several structural forms. Two variations of the Watson-Crick form (B-DNA), are
A- and Z-DNA. These structural changes deepen the major groove while making the minor
groove shallower.
o The A form (devoid of water).

▪ Right-handed double helix, but the helix is wider (Diameter is 26 Å between base pairs)
▪ 11 base pairs per helical turn.
o The Z form
▪ Diameter is 18 Å between base pairs
▪ left-handed helix.
▪ 12 base pairs per helical turn
DNA Supercoiling
Supercoiling means the coiling of a coil. A telephone cord, for example, is typically a coiled wire. The
path taken by the wire between the base of the phone and the receiver often includes one or more
supercoils. DNA is coiled in the form of a double helix, with both strands of the DNA coiling around an
axis. The further coiling of that axis upon itself produces DNA supercoiling. When there is no net
bending of the DNA axis upon itself, the DNA is in a relaxed state.
Alternative structures triplex
▪ Several unusual DNA structures involve three or even four DNA strands can form a number of additional
hydrogen bonds
▪ Triple helical DNA containing 2 pyrimidine strands (T) and 1 purine strand (A)
▪ For example, Cytidine can pair with Guanosine (G=C), and Thymidine can pair with Adenosine (A=T).
▪ The N-7, O-6, and N-6 of purines, the atoms that participate in the hydrogen bonding of triplex DNA, are
often referred to as Hoogsteen positions, so called Hoogsteen pairing (Karst Hoogsteen 1963). Hoogsteen
pairing allows the formation of triplex DNAs.
Alternative structures tetraplex (Quadruplex)
▪ Base-pairing pattern in the guanosine tetraplex structure.
▪ 4 DNA strands can also pair to form a tetraplex (quadruplex), but this occurs readily only for
DNA sequences with a very high proportion of guanosine residues.
▪ The guanosine tetraplex, is stable over a wide range of conditions.
Several types of RNA and RNA polymerases
Messenger RNA (mRNA)
template for protein synthesis
RNA polymerase II (Pol II)
Transfer RNA (tRNA)

carries activated amino acids to ribosomes
RNA polymerase III (Pol III)
Ribosomal RNA (rRNA)

major component of ribosomes
RNA polymerase I (Pol I)
All require template DNA, ribonucleotides (ATP, GTP, UTP, CTP) and
a divalent metal ion (Mg2+)
RNA DNA
Biochemistry of Lipids
3rd stage

2020-2021

Lipids
▪ Organic compounds found every type of plant and animal cells. They contain
Carbon, Hydrogen, and Oxygen.
▪ Unlike the polysaccharides, proteins, and nucleic acids, lipids are not polymers.
They are mostly small molecules.
General properties of lipids:
o Insoluble in water.
o Soluble in nonpolar solvents such as chloroform and methanol.
o Water-hating nature is due to the predominance of hydrocarbon chains
o (-CH2- )n in their structure.
Function of lipids
▪ Energy storage molecules.Lipids are a source of high energy value:
➢ Fat: 1 gram = 9 calories
➢ Protein: 1 gram = 4 calories
➢ Carbohydrate: 1 gram = 4 calories

▪ Major structural elements of cell membrane and regulate the membrane permeability
▪ Serve as a source of fat soluble vitamins (A, D, K and E)
▪ Important as cellular metabolic regulators (steroid hormones and prostaglandins).

▪ Protect the internal organs, serve as insulating materials and give shape and smooth
appearance to the body .
▪ Inner mitochondrial membranes, phospholipids participate in electron transport chain.
Arachidonic acid and some eicosanoid derivatives
▪ In response to hormonal signals, phospholipase A2 cleaves arachidonic acid–containing membrane phospholipids to

release arachidonic acid, the precursor to various Eicosanoids. These compounds include prostaglandins such as PGE1,
thromboxane A2, and leukotriene A4 . Nonsteroidal anti-inflammatory drugs (NSAIDs) such as aspirin and ibuprofen block the
formation of prostaglandins and thromboxanes from arachidonate by inhibiting the enzyme cyclooxygenase (prostaglandin H2
synthase)
Fatty acids
▪ Fatty acids are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons (C4 to C36).
The numbering of carbons in fatty acids begins with the C of the carboxylate group (COOH) .
▪ The most commonly fatty acids have even numbers of carbon atoms in an unbranched chain of 12 to
24 carbons; they are either saturated or unsaturated (one or more double bonds).
▪ The configuration of the double bonds in most unsaturated fatty acids is cis. Trans fatty acids correlate
with increased blood levels of LDL (bad cholesterol) and decreased HDL (good cholesterol)
▪ Short chain and unsaturation enhance the fluidity of fatty acids and their derivatives by lowering the
melting temperature.
▪ Fatty acids that contain multiple sites of unsaturation are termed polyunsaturated fatty acids (PUFAs).
The double bonds are separated by at least one methylene group.
Nomenclature of fatty acids
▪ The general rule is that total number of carbon atoms are written first, followed by the
number of double bonds, separated by a colon; for example, the 16-carbon saturated
palmitic acid is abbreviated 16:0, and the 18-carbon oleic acid, with one double bond, is
18:1
▪ The positions of double bonds, starting from the carboxyl end, are specified by superscript
numbers following the symbol Δ (delta); 18-carbon fatty acid with one double bond
between C-9 and C-10 and another between C-12 and C-13 is designated
Some Naturally Occurring Fatty Acids
Saturated and unsaturated lipids
▪ Saturated fatty acids have no double bond, general formula CH3-(CH2)n-COOH
▪ Unsaturated fatty acids have one or more double bonds
▪ In the fully saturated compounds, free rotation around each carbon–carbon bond gives
the hydrocarbon chain great flexibility; the most stable conformation is the fully
extended form, in which the steric hindrance of neighboring atoms is minimized.
▪ Double bond in oleic acid does not permit rotation and introduces a rigid bend in the
hydrocarbon tail
▪ In vertebrates, free fatty acids circulate in the blood bound noncovalently to a protein
carrier, serum albumin
Saturated and unsaturated fatty acid
a. Stearic acid b. Cis double bond (shaded) in oleic acid

c. Stabilized by many hydrophobic interactions

d. less stable aggregates
C16:0 C18:0 C18:1
Essential fatty acids (EFA)
▪ The fatty acids can not be synthesized by the body and, therefore, should be supplied in
the diet
▪ Only two fatty acids are known to be essential for humans: alpha-linolenic acid (Omega-3
fatty acid) and linoleic acid (Omega-6 fatty acid)
Functions of EFA
o Membrane structure and functions.
o Transport and oxidation of cholesterol. EFA tend to lower plasma cholesterol.
o Prevention of fatty liver.
o They are also needed for synthesis of eicosanoids (prostaglandins, prostacyclins).
Types of fat in our diet and body
▪ Triacylglycerols (triglycerides)
(3 fatty acids attached to glycerol)
▪ Phospholipids
(2 fatty acids and a head group attached to glycerol)
▪ Cholesterol
(4 ring hydrocarbon)
HO
Triacylglycerols
▪ Also referred to as triglycerides, fats, or neutral fats.
▪ Triacylglycerols are fatty acid esters of glycerol. They are composed of 3 fatty acids each in
ester linkage with a single glycerol.
▪ Triacylglycerols containing only saturated fatty acids
▪ Simple triacylglycerols contain only one type of fatty acid; mixed triacylglycerols, two or
three types.
▪ Triacylglycerols are primarily storage fats; they are present in many foods
▪ In some animals, triacylglycerols stored under the skin serve not only as energy stores but
as insulation against low temperatures.
Triacylglycerols (TGs)
▪ A compact, High-energy storage biomolecule
Ester bond
Glycerol Fatty acids
3
TGs are synthesised in a number of tissues: Liver, adipose tissue, intestinal tract
Fatty acid Glycerol-3

3 groups + Phosphate Triacylglycerol (TG)
2 types:
▪ TG synthesis from fatty acids made using glucose (glycolysis) or amino acid side chains (in Liver)
▪ TG synthesis during transport of dietary fat (in intestines and adipose tissue)
o TG cannot cross cell membranes: has to be broken down with the help of lipases to get in and
out of cells.
o TG are carried around the body by lipoproteins in the plasma:

➢ Very low density lipoprotein (VLDL): from liver to peripheral tissues.
➢ Chylomicrons: from intestine to peripheral tissues.
Triacylglycerols as stored fuels
▪ Two significant advantages to using triacylglycerols as stored fuels, rather than
polysaccharides such as glycogen and starch.
o Carbon atoms of fatty acids are more reduced than those of sugars, oxidation of
triacylglycerols yields more than twice as much energy, gram for gram, as the oxidation of
carbohydrates.
o Triacylglycerols are hydrophobic and therefore unhydrated, the organism that carries fat
as fuel does not have to carry the extra weight of water of hydration that is associated
with stored polysaccharides (2 g per gram of polysaccharide).
Structure of phospholipid
▪ Phospholipid as triglyceride except one molecule of
fatty acid is replaced by a phosphate group
▪ The phosphate group is polar and so is attracted to
water- therefore the phospholipid has two distinct
ends:
o A hydrophilic end (head) that dissolves in water
o A hydrophobic end (tail) that is (repels) repelled by
water
▪ This property causes phospholipids to spontaneously
form bilayer
Glycerophospholipids – general structure
▪ Most common phospholipid in animals tissues is phosphatidylcholine
Common headgroups
▪ Inositol
▪ Choline
▪ Serine
▪ Ethanolamine
O
H2C O P O Headgroup
O-
Phosphatidyl
Cellular Lipids – relative amounts and some major functions
NAME % GPL Comment

Phosphatidylinositol PI 10 Precursor of signal molecules
Phosphatidylethanolamine PE 30 Donor of functional group to membrane
proteins; required for certain ATPases
Phosphatidylcholine PC 50 Structural component of membrane;
precursor of some signal molecules
Phosphatidylserine PS 20 Important signal in apoptosis
GPL = glycerophospholipids
Sphingomyelin SM ‘parent’ sphingolipid; precursor of some signal
molecules; stabilises ‘lipid rafts’
Cholesterol 50-60% of all membrane lipids; important precursor of
other molecules
Cholesterol
▪ A 27 carbon lipid, it makes up 50-60% of all membrane lipid
▪ Cholesterol is exclusively found in animals tissues
▪ Amphipathic, with a polar head group (hydroxyl group) and a nonpolar hydrocarbon body (the steroid nucleus
and the hydrocarbon side chain at C-17)
▪ Major site of cholesterol synthesis is the liver with significant synthesis in intestines
▪ Precursor of steroid hormones, bile salts and Vitamin D
Classification of Lipids
▪ Simple lipids
▪ Compound (complex) lipids
▪ Derived lipids
▪ Simple lipids are esters of fatty acids with various alcohols.

R-COO-H + R- OH R-COO-R + H2O
Fatty Acid Alcohol Ester
a. Fats and Oils are esters of fatty acids with glycerol. Oil is a liquid unsaturated, tend to be
available in plants. while fat is a solid at room temperature .
CH2--–OH CH2—COO--R
3R – COOH + CH –---OH CH-----COO--R
CH2----OH CH2—COO—R
Fatty Acid Glycerol Fat
b. Waxes: esters of fatty acids (usually long chain ) with alcohol other than glycerol
▪ Biological waxes are using in the pharmaceutical and cosmetic. Lanolin, beeswax ,
carnauba wax are widely used in the manufacture of lotions and ointments
▪ Compound Lipids: esters of fatty acids with alcohols containing additional groups such
as phosphate, nitrogenous base, carbohydrate, protein etc.
They are divided into :
A- Phosphlipids
• There are two classes of phospholipids:

• 1- Glycerophospholipids: These phospholipids contain glycerol as the alcohol e.g.,
➢ Lecithin (glycerol + saturated fatty acid + phosphate+ choline).
➢ Cephalin: (glycerol + unsaturated fatty acid +phosphate+ ethanolamine)
2- Sphingophospholipids: Sphingosine is the alcohol in this group of phospho-lipids e.g.,

Sphingomyelin (Sphingosine + fatty acid +phosphate + choline ).
▪ Sphingomyelin is an insulating
material for nerve fibres
▪ It has a double behaviour
where it dissolves in fat and
polar solvents.
▪ It is found in the brain, kidney,
liver and blood
Compound Lipids:
b) Glycolipids: These lipids contain a fatty acid and carbohydrate. The alcohol is
Sphingosine (also called as glycosphingolipids) e.g., Cerebrosides (Sphingosine +
Cerebronic acid + Glucose or Galactose).
▪ Cerebroside is a key component of brain, spinal cord, and nervous cells
β-Glucocerebroside
C) Lipoproteins (Lipid transport to tissues)
▪ Lipids are hydrophobic and insoluble in aqueous environments. Therefore, special methods are
needed to transport them round the body.
▪ Lipoproteins: Macromolecular complexes of lipids and proteins. They are transport fat molecules,
such as triglycerides, phospholipids, and cholesterol within the water-based solution of the
bloodstream to all the cells and tissues of the body. Five types of lipoproteins
o Chylomicrons, transport dietary lipids (exogenous( from intestine to peripheral tissues.
o Very low density lipoproteins (VLDL), transport the lipids (endogenously synthesized) mainly TG from
liver to peripheral tissues.
o Low density lipoproteins (LDL) ("bad" cholesterol), transport cholesterol from liver to peripheral tissues.
o High density lipoproteins (HDL) ("good" cholesterol), carry cholesterol from peripheral tissues
to liver.
o Intermediate density lipoproteins (IDL).

3- Derived Lipids: are the derivatives obtained by the hydrolysis of simple and compound lipids. These
include fatty acids, alcohols, mono-and diacylglycerol, lipid soluble vitamins and steroids. The most
common derived lipids are steroids.
▪ Sterols are structural lipids present in the membranes of most eukaryotic cells. The characteristic
structure is the steroid nucleus, consisting of four fused rings, three with six carbons and one with five
▪ There are several steroids in the biological system. These include cholesterol, bile acids, vitamin D,
sex hormones, adrenocortical hormones
4- Neutral lipids : The lipids which are uncharged are referred to as neutral lipids e.g. triacylglycerols
Derivatives of cholesterol – steroid hormones
▪ Testosterone, the male sex hormone, is
produced in the testes.
▪ Estradiol, one of the female sex hormones,
is produced in the ovaries and placenta.
▪ Cortisol and aldosterone are hormones
synthesized in the cortex of the adrenal
gland; they regulate glucose metabolism
and salt excretion, respectively.
▪ Prednisolone and prednisone are synthetic
steroids used as anti inflammatory agents.
Bile acids
▪ Bile acids are polar derivatives of cholesterol that stored in the gallbladder after
secretion by the liver, and then release into small intestine to aid in the processes of
digestion and absorption of fats (emulsifying dietary fats to make them more readily
accessible to digestive lipases).
Derivatives of cholesterol – bile salts
Vitamin D (Solar vitamin)
Calcitriol
▪ Skin, UV irradiation breaks the bond between C9-C10 of 7 dehydrocholesterol

▪ liver, a hydroxyl group is added at C-25
▪ kidney, a second hydroxylation at C-1 produces the active hormone
Orientation amphipathic lipids
▪ Depending on the precise conditions and the nature of the lipids, three types
of lipid aggregates can form when amphipathic lipids are mixed with water
▪ Micelles
▪ Lipid bilayer
▪ liposome
Micelles
▪ When the amphipathic lipids are mixed in water (aqueous phase), the polar groups (heads) orient them selves
towards aqueous phase while the non-polar (tails) orient themselves towards the opposite directions. This
leads to the formation of micelles. Micelles formation facilitated by bile salts is very important for lipid
digestion and absorption.
▪ Micelles are water soluble molecules formed from aggregation of bile salts, fatty acids and mono-
glycerides in the intestine.
Lipid bilayer
▪ The hydrophobic portions in each monolayer, excluded from water, interact with each other.
▪ The hydrophilic head groups interact with water at each surface of the bilayer.
▪ Because the hydrophobic regions at its edges are transiently in contact with water, the
bilayer sheet is relatively unstable and spontaneously forms a third type of lipid aggregate:
o bilayer folds back on itself to form a hollow sphere, a vesicle or liposome
▪ Lipid bilayer are highly impermeable to ions and most polar molecules, but permeable to
nonpolar compounds; they are 5 to 8 nm (50 to 80 Å)
bilayer
▪ Fluid model for membrane structure. The fatty acyl chains in the interior of the membrane
form a fluid, hydrophobic region. The carbohydrate moieties attached to some proteins and
lipids of the plasma membrane are exposed on the extracellular surface of the membrane
lipid bilayer
▪ The central feature of biological membranes is a double layer of lipids, which are composed of
lipids and proteins
▪ Many membrane proteins contain covalently attached oligosaccharides. Plasma membrane
glycoproteins are always oriented with the carbohydrate-bearing domain on the extracellular
surface
▪ Some of the roles of oligosaccharides in the cell surface:
o Viruses that infect animal cells, such as the influenza virus, bind to cell surface glycoproteins
as the first step in infection.
o Bacterial toxins, such as the cholera and pertussis toxins, bind to a surface glycolipid before
entering
Liposomes
▪ By forming a sphere-shaped vesicles (liposomes), bilayers lose their hydrophobic edge
regions, achieving maximal stability in their aqueous environment. These bilayer liposomes
(phospholipid) enclose water, creating a separate aqueous compartment.
▪ The ability of liposomes to encapsulate hydrophilic or lipophilic drugs have allowed to

become useful drug delivery systems, e.g., Liposomes are used as carriers of drugs to
target certain tissue in cancer therapy.
Amino Acids
3rd Class

2020-2021

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Structure of an amino acid
Example:
asymmetric carbon atom
(α- carbon), C is connected
to 4 different atoms.
▪ They have a carboxyl group and an amino group bonded to the same carbon atom.
▪ They differ from each other in their side chains, or R groups. which vary in structure, size,
and electric charge, and which influence the solubility of the amino acids in water
Structure of an amino acid
▪ For all the common amino acids except glycine, the α-carbon is bonded to 4 different
groups:
o Carboxyl group
o Amino group
o R group
o Hydrogen atom
▪ In glycine, the R group is another hydrogen
Gly G
▪ 20 different amino acids are commonly found in proteins
▪ The common amino acids of proteins have been assigned three-letter abbreviations
▪ Single-letter abbreviations are usually used to denote the amino acids in a polypeptide
sequence
▪ When a carbon atom has 4 different groups , they can be arranged in 2 stereoisomers
that represent mirror images of each other (enantiomers). This asymmetric carbon atom
is called a chiral center.
L-Alanine D-Alanine
▪ L-Amino acids are those with the amino group on the left,
and D-amino acids have the amino group on the right
▪ All amino acid residues in proteins are L- stereoisomers
Classification of Amino Acids
▪ Polar and Non-polar Amino Acids

▪ Chemical Classification of Amino Acids
▪ Nutritional classification of amino acids
▪ Metabolic classification of amino acids
Polar and Non-polar Amino Acids
▪ Amino acids can be grouped into two main classes based on polarity of the “R”
groups , or their tendency to interact with water at biological pH (near pH 7.0)
➢ polar amino acids: polar and hydrophilic (water-soluble)
➢ Nonpolar amino acids: nonpolar and hydrophobic (water-insoluble)
polar amino acids
▪ Uncharged R Groups: They contain functional groups that form hydrogen bonds with water
- Serine (hydroxyl group)
- Threonine (hydroxyl group)
- Cysteine (sulfhydryl group)
- Asparagine (amide group)
- Glutamine (amide group)
▪ Positively Charged (Basic) R Groups: The most hydrophilic R groups are those that are either
positively or negatively charged.
- Lysine (second primary amino group)
- Arginine (guanidino group)
- Histidine (imidazole group)
▪ Negatively Charged (Acidic) R Groups: Each of which has a second carboxyl group
- Aspartate
- Glutamate
Nonpolar amino acids
▪ Aliphatic amino acids are nonpolar and hydrophobic. They tend to cluster together within
proteins, stabilizing protein structure by means of hydrophobic interactions
▪ Methionine, amino acids containing sulfur, has a nonpolar thioether group in its side chain
▪ Proline has an aliphatic side chain with a distinctive cyclic structure
▪ Aromatic R Groups: phenylalanine, tyrosine, and tryptophan, with their aromatic side
chains, are relatively nonpolar (hydrophobic). All can participate in hydrophobic
interactions. However, the hydroxyl group of tyrosine can form hydrogen bonds (polar)
Polar and Non-polar Amino Acids
Chemical Classification of Amino Acids
▪ 20 amino acids found in proteins are also divided into 7 distinct groups:
1- Amino acids with Aliphatic side chains:
▪ Glycine (Gly)
▪ Alanine (Ala)
▪ Valine (Val)
▪ Leucine (Leu)
▪ Isoleucine (Ile)
2- Amino acids with side chains containing Hydroxylic (OH) groups:

▪ Serine (Ser)
▪ Threonine (Thr)
▪ Tyrosine (Tyr)
3- Amino acids with side chains containing Sulfur atoms:

▪ Cysteine (Cys)
▪ Methionine (Met)
4- Amino acids with side chains containing Acidic groups:
▪ Aspartic acid (Asp)
▪ Asparagine (Asn)
▪ Glutamic acid (Glu)
▪ Glutamine (Gln)
5- Amino acids with side chains containing Basic groups:

▪ Arginine (Arg)
▪ Lysine (Lys)
▪ Histidine (His)
6- Amino acids with side chains containing Aromatic rings:

▪ Phenylalanine (Phe)
▪ Tyrosine ( Tyr)
▪ Tryptophan (Trp)
7- Imino Acid:
▪ Proline (Pro)
Nutritional classification of amino acids
➢ Non-essential amino acids (NEAAs):
▪ can be synthesized inside the body
➢ Essential amino acids (EAAs):

▪ can not be synthesized by the body
▪ Their deficiencies in the diet result in diseases
o phenylalanine
o valine
o threonine
o tryptophan
o methionine
o leucine
o isoleucine
o lysine
o histidine
Metabolic classification of amino acids
▪ Amino acids are classified according to their metabolic fate into:
➢ Ketogenic amino acids:

o Leucine and lysine
➢ Both Ketogenic and glucogenic “mixed amino acids “

o Phenylalanine
o Tryptophan
o Tyrosine
o Isoleucine
➢ Glucogenic amino acids:

o All the remaining 14 amino acids are glucogenic .
Amino Acids, Peptides and Proteins
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2020-2021

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Amino Acids Can Act as Acids and Bases
▪ In solution, the free amino acids exist as the dipolar ion, or zwitterion, which can act as
either an acid (proton donor) or a base (proton acceptor). Ions in which the amino group is
positively charged and the carboxylate group is negatively charged.
▪ Substances having this dual nature are called Amphoteric
▪ Amino acids differ from each other in their side-chains (R) .Thus, the chemical properties of the
side chains determine how the protein folds, how it binds specific ligands, and how it interacts
with its environment (such as the aqueous medium of the cytoplasm).
▪ Tryptophan and tyrosine, and to a much lesser extent phenylalanine, absorb Ultraviolet light . This
accounts for the characteristic strong absorbance of light by most proteins at a wavelength of 280
nm, a property exploited by researchers in the characterization of proteins.
▪ Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine,
in which two cysteine molecules or residues are joined by a disulfide bond.
▪ Reversible formation of a disulfide bond by the oxidation of two molecules of cysteine.

Disulfide bonds between Cys residues stabilize the structures of many proteins
Titration Curves of Weak Acids
▪ Acid-base titration involves the gradual addition or removal of protons
▪ Titration is used to determine the amount of an acid in a given solution. A measured volume of the
acid is titrated with a solution of a strong base, (NaOH), of known concentration. The NaOH is added
in small increments until the acid is consumed (neutralized), as determined with an indicator dye or a
pH meter. The concentration of the acid in the original solution can be calculated from the volume
and concentration of NaOH added
▪ A plot of pH against the amount of NaOH added (a titration curve) reveals the pKa of the weak acid.
▪ At the midpoint of the titration, at which exactly 0.5 equivalent of NaOH has been added, one-half of
the original acid has undergone dissociation, so that the concentration of the proton donor, , now
equals that of the proton acceptor. At this midpoint, pH is exactly equal to the pKa
▪ The end point of the titration occurs at about pH 7.0: all the acid has lost its protons to OH
Titration Curves of Weak Acids
▪ Weak acids partially ionize to release a hydrogen ion, thus lowering the pH of the aqueous
solution. Weak bases accept a hydrogen ion, increasing the pH, and is expressed as a
dissociation constant, Ka
▪ The pKa expresses, on a logarithmic scale, the relative strength of a weak acid or base
▪ The stronger the acid, the lower its pKa; the stronger the base, the higher its pKa.
▪ The pKa can be determined experimentally; it is the pH at the midpoint of the titration
curve for the acid or base.
Amino Acids Have Characteristic Titration Curves
▪ At a physiologic pH of 7.4, the amino group on the amino acids carries a positive charge, and the
carboxylic acid group is negatively charged.
▪ the pKa, 50% of the molecules are dissociated into carboxylate anions and protons and at a
physiologic pH of 7.4, , more than 99% of the molecules are dissociated
▪ pKa values: pKa of the -COOH group in the range of 1.8 to 2.4, and pKa of the group in the
range of 8.8 to 11.0
▪ The characteristic pH at which the net electric charge is zero is called the isoelectric point or
isoelectric pH, designated pI
▪ Amino acids with an ionizable R group have more complex titration curves, with three possible
ionization steps (three stages); thus they have three pKa, values the pKa of the R group is
designated here as pKR
Titration curve of the diprotic form of glycine
▪ Glycine has two distinct stages.
▪ At low pH, the predominant ionic species of glycine is the fully protonated form,
▪ The first stage of the titration, as the pH is increased by the addition of OH, the -COOH group of
glycine loses its proton, the proton dissociates from the carboxylic acid group, and its charge
changes from zero to negative
▪ At the midpoint of the titration, a point of inflection is reached, where the pH is equal to the pKa
▪ The pH at the midpoint is 2.34, thus its –COOH group has a pKa (labeled pK1) of 2.34.
▪ As the titration proceeds, another important point is reached at pH 5.97. Here there is another
point of inflection, at which removal of the first proton is essentially complete (COOH) and removal
of the second ( ) has just begun. At this pH glycine is present largely as the dipolar
Titration curve of the diprotic form of glycine
▪ The second stage is removal of a proton from the group of glycine.

▪ The pH at the midpoint of this stage is 9.60, equal to the pKa (labeled pK2 ) for the
group.
▪ The titration is essentially complete at a pH of about 12, at which point the predominant
form of glycine is
▪ The characteristic pH at which the net electric charge is zero is called the isoelectric point
or isoelectric pH, designated pI.
▪ Glycine has no ionizable group in its side chain, the isoelectric point is simply the
arithmetic mean of the two pKa values:
pK1 carboxylic acid = 2.34
pK2 amino group = 9.60
pI = (pK1+ pK2)/2
pI = (2.34 + 9.60)/2
pI = 5.97
▪ Glutamine has a pI of 3.22, lower than that of glycine. This is due to the presence of
two carboxyl groups (Negatively charged)
pKR R group = 4.25
pI = (pK1+ pKR)/2
pI = (2.19 + 4.25)/2
pI = 3.22
▪ Histidine has a pI of 7.59 (the average of the pKa values of the amino and imidazole
groups) ,much higher than that of glycine. This is due to the presence of two amino
group (positively charged)
pKR R group = 6.0
pI = (pKR + pK2)/2
pI = (6.0 + 9.17)/2
pI = 7.59
pKa for the common amino acids found in protein
Peptides
▪ Peptides are chains of amino acids
▪ Two amino acid molecules can be covalently joined by peptide bond to yield a dipeptide.
▪ Three amino acids can be joined by two peptide bonds to form a tripeptide and so forth
▪ An amino acid unit in a peptide is often called a residue (the part left over after losing a hydrogen atom from its
amino group and the hydroxyl (OH) moiety from its carboxyl group)
(dehydration)
Dipeptide
Formation of a peptide bond by condensation

The pentapeptide Ser–Gly–Tyr–Ala–Leu
▪ In a peptide amino acid residue at the end with a free amino group is the amino
terminal or (N-terminal) , the residue at the other end , which has a free carboxyl
group is the carboxyl terminal (C-terminal) .
▪ Peptides are named beginning with the amino terminal and the sequence of amino
acids in a polypeptide is written starting with the amino terminal as number one.
▪ Polymerization of the 20 amino acids into polypeptide chain in cells is catalyzed by

enzymes and is associated with the ribosomes (protein translation).
Classification of peptides
▪ Oligopeptides: Short peptides containing 2 to 10 amino acid units
▪ Polypeptides: More than 10 amino acid units
Biological Activity of small Peptides

Glutathione: tripeptide (Glutamic acid-Cysteine-Glycine)
▪ Glutathione (GSH) is an antioxidant in plants, animals,

fungi, and some bacteria.
▪ Glutathione is capable of preventing damage to
important cellular components caused by Reactive
Oxygen Species (ROS) such as free radicals, peroxides,
lipid peroxides, and heavy metals
Biological Activity of small Peptides
Oxytocin and Vasopressin
▪ Oxytocin and Vasopressin are a nonapeptide hormones contain 9 amino acids which
released by the posterior pituitary.
▪ Oxytocin is released into the bloodstream as a hormone in labor. Thus, It plays a role
in birth (muscular contraction), bonding with the baby, and milk production.
▪ Vasopressin helps water reabsorption by renal tubules. It called “antidiuretic
hormone ADH”
Proteins
▪ Proteins are polymers of amino acids
▪ Proteins range in size from small peptides to very large polypeptides chains of 100 to
several thousand amino acid residues
▪ Proteins are the most abundant biological macromolecules occurring in all cells.
Classification of Proteins
Proteins can be classified according to
▪ Protein Function
▪ Shape
▪ Chemical Composition
Functions of Proteins
▪ Enzymes (Catalytic function)
- Hexokinase, mitogen-activated protein (MAP) kinases, and cysteine proteases
▪ Structural Proteins
- Collagen and tubulin
▪ Transport oxygen in blood and muscles
- Hemoglobin and myoglobin
▪ Receptors
- Toll-like receptors, insulin receptor
▪ Membrane Transport Proteins
- Na+/K+-ATPase, porins
▪ Hormones and Cytokines (Regulatory function)
-insulin and IL-1
▪ Carrier proteins
- Albumin and ferritin
▪ Antibodies (Protective function)
- IgG, IgM (immunoglobulin)
Shape of Protein
▪ Fibrous proteins
o Water insoluble
o Have a role as structural elements, e.g. Collagen, elastin, α-keratin and silk fibroin
▪ Globular proteins
o water soluble
o biologically active, e.g. Insulin, albumin, globulins and many enzymes
Chemical Composition of Proteins
Proteins are classified according to their chemical composition into
▪ Simple Proteins.
▪ Conjugated Proteins.
.
▪ Derived Proteins
▪ Simple Proteins
o Contain only amino acid residues and no other chemical constituents for example the
enzymes ribonuclease A and chymotrypsinogen
▪ Conjugated Proteins
o They are combinations of proteins with a nonprotein part
o The non–amino acid part of a conjugated protein is usually called its prosthetic group
o Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups (table below)
o Usually the prosthetic group plays an important role in the protein’s biological function
▪ Derived proteins:
o They are degradation products of native proteins as denatured proteins or hydrolytic
products as peptones and peptide.
Biochemistry of Proteins
3rd Class

2020-2021

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Lecture outline
▪ Protein Denaturation
▪ Protein Purification
▪ Amino Acid Sequences
▪ Protein Structure
Protein Denaturation
▪ A loss of 3-dimensional structure sufficient to cause loss of function is called
denaturation.
▪ Most proteins can be denatured by:
Native state
o Heat, which affects the weak interactions in a protein (primarily hydrogen bonds) (active)
o Extremes of pH
o Organic solvents such as alcohol or acetone
o Solutes such as urea and guanidine hydrochloride
o Detergents
❖ Organic solvents, urea, and detergents act primarily by disrupting the Unfolded state
(inactive)
hydrophobic interactions that make up the stable core of globular proteins
❖ Extremes of pH alter the net charge on the protein, causing electrostatic
repulsion and the disruption of some hydrogen bonding.
❖ Loss of protein structure results in loss of function
Native state
▪ Denaturation of some proteins is reversible. This process is called renaturation. (active)
Protein purification
▪ A pure protein is essential before it’s properties and activities can be determined.
▪ How can one protein be purified from a complex mixture of proteins?
▪ Proteins can be purified according to solubility, size, charge, and binding properties
▪ Usually, protein mixtures are subjected to a series of separations, each based on a different
property to yield a pure protein.
▪ The source of a protein is generally tissue or microbial cells. The first step in any protein
purification procedure is to break open these cells, releasing their proteins into a solution
called a crude extract (Centrifugation)
▪ Commonly, the extract is subjected to treatments that separate the proteins into different
fractions based on a property such as size or charge, a process referred to as fractionation
Protein Purification
▪ Early fractionation steps in a purification utilize differences in protein solubility, which is a
complex function of pH, temperature, salt concentration ((NH4)2SO4), and other factors
▪ The solubility of proteins is generally lowered at high salt concentrations “salting out.” For
example, 0.8 M ammonium sulfate precipitates fibrinogen, a blood-clotting protein, whereas
a concentration of 2.4 M is needed to precipitate serum albumin.
▪ Proteins can be separated from small molecules by dialysis through a semipermeable
membrane (bag or tube), such as a cellulose membrane with pores. Molecules having
dimensions significantly greater than the pore diameter are retained inside the dialysis bag,
whereas smaller molecules and ions traverse the pores of such a membrane and emerge in
the dialysate outside the bag. This technique is useful for removing a salt or other small
molecule from the protein preparation
Fractionating Proteins by Column Chromatography
▪ The standard elements of a chromatographic column include a solid porous
material supported inside a column, generally made of plastic or glass.
▪ The solid material (matrix) makes up the stationary phase through which
flows a solution (the mobile phase)
▪ The solution that passes out of the column at the bottom (the effluent) is
constantly replaced by solution supplied from a reservoir at the top
▪ The protein solution to be separated is layered on top of the column and
allowed to percolate into the solid matrix
▪ Additional solution is added on top. The protein solution forms a band
within the mobile phase
▪ As proteins migrate through the column, they are retarded to different
degrees by their different interactions with the matrix material. The overall
protein band thus widens as it moves through the column
▪ Individual types of proteins (such as A, B, and C) gradually separate from
each other, forming bands within the broader protein band
▪ Separation improves (resolution increases) as the length of the column
increases. However, each individual protein band also broadens with time
due to diffusional spreading, a process that decreases resolution.
▪ In this example, protein A is well separated from B and C, but diffusional
spreading prevents complete separation of B and C under these conditions.
Column Chromatography
▪ Ion-exchange chromatography
▪ Size exclusion chromatography (also called gel filtration)
▪ Affinity chromatography
▪ High-performance liquid chromatography (HPLC)
o In most cases, several different methods must be used sequentially to purify a protein
completely, and many protocols may be tried before the most effective one is found
Ion-exchange chromatography
▪ Proteins can be separated on the basis of their net charge at a given pH
▪ The column matrix (stationary phase) is a synthetic polymer containing
bound charged groups; those with bound anionic groups are called
cation exchangers, and those with bound cationic groups are called
anion exchangers
▪ In the mobile phase (protein solution), proteins with a net positive
charge migrate through the matrix more slowly (due to its interaction
with the stationary phase) than those with a net negative charge
▪ The rate at which the protein solution can flow through the column
usually decreases with column length (More time)
▪ The resolution can decline as a result of diffusional spreading within
each protein band
Cation-exchange chromatography
Ion-exchange chromatography
▪ The affinity of each protein is affected by the pH (which determines the ionization state of the
molecule) and the concentration of competing free salt ions in the surrounding solution.
▪ Separation can be optimized by gradually changing the pH and/or salt concentration of the
mobile phase
▪ Proteins that have a low density of net positive charge will tend to emerge first, followed by
those having a higher charge density
▪ Positively charged proteins (cationic proteins) can be separated by chromatography on negatively
charged carboxy methyl-cellulose (CM-cellulose) Columns
▪ Negatively charged proteins (anionic proteins) can be separated by chromatography on positively
charged Diethylaminoethyl cellulose (DEAE-C) columns
Size exclusion chromatography (also called gel filtration)
▪ Separates proteins according to size

▪ The sample is applied to the top of a column matrix (solid
phase) consisting of porous beads made of an insoluble but
highly hydrated polymer such as dextran or agarose (which
are carbohydrates) or polyacrylamide
▪ Larger proteins migrate faster than smaller ones, because they
are too large to enter the pores in the beads and hence take a
more direct route through the column, around the beads
▪ Small proteins enter the cavities, and migrate through the
column more slowly as a result
Affinity chromatography
▪ It is based on the binding affinity of a protein.

▪ The beads in the column have a covalently attached chemical group.
▪ A protein with affinity for this particular chemical group will bind to
the beads in the column (bind to a ligand cross-linked to the beads),
and its migration will be retarded as a result
▪ After proteins that do not bind to the ligand are washed through
the column, the bound protein of particular interest is eluted
(washed out of the column) by a solution containing free ligand
high-performance liquid chromatography (HPLC)
▪ HPLC is a modern chromatographic methods
▪ The column materials themselves are much more finely divided and, as a consequence,
there are more interaction sites and thus greater resolving power.
▪ HPLC makes use of high-pressure pumps that speed the movement of the protein molecules
down the column
▪ It has Higher-quality chromatographic materials that can withstand the crushing force of the
pressurized flow. By reducing the transit time on the column
▪ HPLC can limit diffusional spreading of protein bands and thus greatly improve resolution.
Proteins can be separated by Electrophoresis
▪ It is based on the migration of charged proteins in an electric field.
▪ Electrophoresis of proteins is generally carried out in gels made up of the cross-linked
polymer polyacrylamide
▪ The polyacrylamide gel acts as a molecular sieve, slowing the migration of proteins
approximately in proportion to their charge-to-mass ratio
▪ Sodium dodecyl sulfate (SDS) is employed for estimation of purity and molecular weight
▪ SDS binds to most proteins in amounts roughly proportional to the molecular weight of
the protein, about one molecule of SDS for every two amino acid residues
▪ The bound SDS contributes a large net negative charge, rendering the intrinsic charge of
the protein insignificant. In addition, the native conformation of a protein is altered when
SDS is bound, and most proteins assume a similar shape
▪ Electrophoresis in the presence of SDS therefore separates proteins almost exclusively on
the basis of mass (molecular weight). Smaller polypeptides migrating more rapidly
Electrophoresis
▪ Electrophoresis separates proteins on the basis of molecular weight
▪ Different samples are loaded in the wells at the top of the polyacrylamide gel.
▪ The proteins move into the gel when an electric field is applied.
▪ The gel minimizes convection currents caused by small temperature
gradients, as well as protein movements other than those induced by the
electric field.
▪ Proteins can be visualized after electrophoresis by treating the gel with a
stain such as Coomassie blue, which binds to the proteins but not to the gel
itself
▪ Each band on the gel represents a different protein (or protein subunit);
smaller proteins move through the gel more rapidly than larger proteins and
therefore are found nearer the bottom of the gel.
Estimating the molecular weight of a protein
▪ The electrophoretic mobility of a protein on an SDS polyacrylamide
gel is related to its molecular weight
▪ Standard proteins of known molecular weight are subjected to
electrophoresis (lane 1). These marker proteins can be used to
estimate the molecular weight of an unknown protein (lane 2).
▪ Protein marker (also called a protein molecular weight marker, a
protein MW marker, or a protein ladder) is used to estimate the size
of proteins resolved by gel electrophoresis and to monitor transfer
efficiency from gel to blotting membrane.
Colour Protein Standard
▪ mPAGE™ Color Protein Standard is a mixture of ten recombinant

prestained proteins from 10 kDa to 203 kDa, covalently coupled
with different chromophores. It is designed for observing protein
separation during SDS-PAGE, verifying membrane transfer
efficiency, and approximating the molecular weight of proteins.
Determination of the amino acid composition of a polypeptide
▪ Sanger method: Sanger was the first
to determine the sequence of a
polypeptide.
▪ Identification of the amino-terminal Two approaches to
irreversible breakage
residue can be the first step in of disulfide bonds
sequencing a polypeptide.
o Insulin consists of the 21 amino acids
( A chain) and the 30 amino acids (B
chain) joined by disulfide bonds.
o Sanger reduced the disulfide bonds
by either oxidation or reduction
followed by acetylation
▪ Separated the A and B chains, and cleaved each chain into smaller peptides using trypsin,
chymotrypsin, and pepsin
▪ The resulting peptides were then isolated and treated with acid to hydrolyze peptide
bonds and generate peptides with as few as two or three amino acids
▪ Each peptide was reacted with 1-fluoro-2,4-dinitrobenzene (FDNB) (Sanger’s reagent),
which derivatizes the exposed α-amino group of amino terminal residues. The amino acid
content of each peptide was then determined.
Amino acid sequences can be determined by Edman Degradation
▪ The Edman degradation procedure labels and removes only the amino-terminal residue from a peptide, leaving all other
peptide bonds intact
▪ The peptide is reacted with phenylisothiocyanate (Edman's reagent) under mildly alkaline conditions, which converts the
amino terminal amino acid to a phenylthiocarbamoyl (PTC)
▪ The peptide bond next to the PTC adduct is then cleaved in a step carried out in anhydrous trifluoroacetic acid, with
removal of the amino-terminal amino acid as an anilinothiazolinone derivative
▪ The derivatized amino acid is extracted with organic solvents, converted to the more stable phenylthiohydantoin
derivative by treatment with aqueous acid, and then identified.
▪ After removal and identification of the amino terminal residue, the new amino-terminal residue so exposed can be
labeled, removed, and identified through the same series of reactions
▪ This procedure is repeated until the entire sequence is determined
▪ Edman degradation is carried out on a machine, called a sequenator,
▪ Edman degradation procedure reveals the entire sequence of a peptide (shorter peptides, 50-70 amino acids ), larger
polypeptides are often fragmented into smaller peptides for sequencing
Sanger’s method
Edman Degradation
Structural levels of proteins
▪ Proteins regardless of their function or biologic activity are built up from the same
basic set of the 20 standard amino acids
❖ What gives a protein enzymatic activity, another protein hormonal action , and
antibody activity ?
➢ Quite simply proteins differ from each other because each has a distinctive amino acid
sequence (primary structure) which direct folding of the protein once synthesized in
the cell.
Structural levels of proteins
o Four levels of protein structure are commonly defined
▪ Primary structure involves the linking of

L-amino acids by peptide bonds between
-COOH and –NH2 groups.
▪ Secondary structure: Proteins are highly

organized structures with some degree of
rigidity.
▪ Tertiary structure: Proteins are not loose,

floppy chains of amino acids.
▪ Quaternary structure: The higher levels

of structure are critical for determining a
protein’s function.
Primary Structure and Peptide Bonds
o The primary structure of a protein is the sequence of the amino acids present in polypeptide.
o It is written from the N-terminus to the C-terminus.
o The amino acids are joined by peptide bonds between –COOH and –NH2 groups
o The primary structure of a protein is the linear sequence of amino acids in the polypeptide chain.
O R
H
N H
OH N
R H O
Condensation
reaction H2O
O R
H
N
N
R H O
Secondary Structure
▪ Secondary structure refers to the special stable arrangements of amino acid by twisting
of the polypeptide chain.
▪ There are 3 main types of secondary structure:
o a-Helix
o b-Sheet
o Loops and Turns
▪ These structures are formed by bending or coiling of the amino acid chain,
which involves rotation around the N-Ca and the Ca-C bonds.
▪ The amount of rotation allowed depends on steric hindrance from the R (rest)
groups of the amino acids. Hence the primary structure also determines the
secondary structure
N-term The a-Helix
▪ The peptide bonds form the backbone (primary structure)
▪ right-handed helix
▪ 3.6 residues / turn
▪ 5.4 Å pitch (distance)
▪ R groups stick outside the spiral structure

▪ The helical structure is stabilized by intrachain hydrogen bonds
▪ H-bonding is between the C=O of one amino acid and the N-H of
another four residues forward in the chain
▪ Typically about 12-15 residues long, i.e. 3-4 turns and ~18 Å (1.8 nm).
C-term ▪ Segments, are found in many globular protein like myoglobin
b-Pleated Sheet Structure (b-sheet)
▪ The polypeptide chains in the β-pleated sheets is fully
extended into zigzag structure.
▪ The zigzag polypeptides are arranged side by side to form a
series of pleats.
▪ Typically: 6-10 residues per strand and 2-10 strands / sheet
▪ Can occur between separate peptide chains (e.g. silk fibroin)
or between segments of the same peptide chain where it
fold back upon itself “β-turn”.
• Parallel β-sheet: H-bonded chains
extend in the same direction ▪ Two types of β-pleated sheets exist : parallel and antiparallel
• Antiparallel β-sheet: opposite
direction ▪ The H-bonded structure is relatively strong and rigid so it is
an important part of many fibrous proteins.
▪ They are stabilized by H bond between N-H and carbonyl
antiparallel b-sheet parallel b-sheet groups of adjacent chains

Loops and Turns
▪ a-helices and b-sheets are stiff structures that don’t bend easily.
▪ More flexible parts to connect them are needed for a globular structure – loops
and turns.
▪ Non-repetitive structures, but still quite ordered.
▪ These often contain Gly and Pro, which are “helix-breakers” (permit an acute
angle at turn)
▪ Turns are short and ordered, containing 3-4 residues
▪ Loops/ Coils are longer (>6 residues) and more disordered
The b-Turn Loops & Coils
The C=O group of residue 1 of the tetrapeptide

forms a hydrogen bond with N-H of residue 4
and causes a hairpin turn
Tertiary Structure of Protein
▪ Defined as: 3-D folding of the secondary structural elements to give the
final, native conformation
▪ The tertiary structure is maintained by

o Ionic bonds
o Hydrogen bonds
o Hydrophobic interactions
o Van der Waals forces
o Disulfide bridges.
▪ Most proteins contain both a-helices and b-sheets (on average 30% of
each)
General Rules About 3 Structure
▪ Helices and sheets run across the protein.

▪ Turns and loops are usually at the edges.
▪ The core is densely packed and water is excluded
▪ The core has some flexibility but the edges are much looser.
▪ Cytosolic proteins are polar on the surface and hydrophobic inside.
▪ Membrane proteins are hydrophobic on the surfaces that are in contact with
the membrane.
3 Structure is determined by sequence
▪ Some simple principles contribute to determining the tertiary structure :

➢ Hydrophobic side chains do not like contact with water, and prefer to be
buried inside proteins.
➢ Polar side chains are hydrophilic and prefer to be on the surface in
contact with water.
▪ Unless it is a membrane protein, in which case the external environment
is hydrophobic, so the opposite is true.
o There are two general classes of proteins based on tertiary structure: fibrous
and globular.
▪ Fibrous proteins, which serve mainly structural roles, have simple repeating
elements of secondary structure.
▪ Globular proteins have more complicated tertiary structures, often containing
several types of secondary structure in the same polypeptide chain.
Within 3 Structure there are also Motifs and Domains
▪ Motifs are also called Super-secondary elements. They are

combinations of a few elements of secondary structure.
Examples: helix-loop-helix and zinc finger
▪ Domains are larger structures can fold stably and

independently, often with discrete functions or activities.
Examples: dehydrogenase domain
▪ Motifs and domains are important in providing help in folding

and providing stability to the protein. They have also been zinc finger
important in the evolution of proteins.
Some examples of globular 3 Structure
Triose Phosphate Isomerase Liver Alcohol Dehydrogenase
Sucrose Porin
Quaternary structure of protein
▪ Combination of two or more protein to form a large, biologically active protein
▪ Two kind of quaternary structure, both are multi-subunit proteins
o Homodimer: association between identical polypeptide chains
o Heterodimer: interactions between subunits of very different structures
4 structure (multiple subunits)
▪ Hemoglobin is a globular protein with 4 polypeptide chains bonded together.
▪ The 4 polypeptide chains consist of 2 alpha and 2 beta chains
▪ 4 haem groups each contain iron
heme
▪ Each haem group can carry one molecule of oxygen
Levels of structure in proteins
The primary structure consists of a sequence of amino acids linked together by peptide bonds and includes any
disulfide bonds. The resulting polypeptide can be coiled into units of secondary structure, such as an α-helix.
The helix is a part of the tertiary structure of the folded polypeptide, which is itself one of the subunits that
make up the quaternary structure of the multi-subunit protein
Enzymes
3rd Class

2020-2021

[email protected]
Learning outcomes
▪ To understand the function of the active site of enzymes

▪ To understand the role of cofactors in enzymes
▪ To know enzyme activity and specificity
▪ To understand the factors affecting enzyme activity
▪ To understand enzyme inhibition
Enzymes
▪ With the exception of a few catalytic RNAs, all known enzymes are proteins that act as catalysts to increase
the rate of biochemical reactions
▪ Enzyme-catalyzed reactions have three basic steps: Enzyme catalysts bind reactants (substrates), convert them
to products and release the products:
E+S E-S E-P E+P
▪ Enzymes, provide speed, specificity, and regulatory control to reactions in the body.
▪ Enzymes return to their original form at the end of reaction
▪ Have M.Weight ranging from about 12,000 to more than 1 million
▪ Substrate is the substance upon which the enzyme act. The substrates are bound to specific substrate binding
sites on the enzyme through interactions with the amino acid residues of the enzyme.
▪ Each enzyme selective for its substrates and ensures that only specific products are formed
▪ An enzyme-catalyzed reaction is take place within the confines of a pocket on the enzyme called the active site
Enzymes
▪ Enzymes provide a means for regulating the rate of metabolic pathways in the body
▪ In some diseases, especially genetic disorders, there may be deficiency or a total absence
of one or more enzymes
▪ Measurements of the activities of enzymes in blood plasma, erythrocytes, or tissue
samples are important in diagnosing certain illnesses
▪ Many drugs exert their biological effects through interactions with enzymes
▪ If an enzyme is broken down into its component amino acids, its catalytic activity is always
destroyed. Thus the primary, secondary, tertiary, and quaternary structures of protein
enzymes are essential to their catalytic activity.
▪ Many enzymes require an additional chemical component called a cofactor—either one or more inorganic
ions or a complex organic, or metalloorganic molecule called a coenzyme, some enzymes require both a
coenzyme and one or more metal ions for activity
Some Inorganic Elements That Serve as Cofactors for Enzymes
Some Coenzymes That Serve as Transient Carriers of Specific Atoms or Functional Groups
▪ Coenzyme
act as
transient
carriers of
specific
functional
groups
▪ A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein
is called a prosthetic group (a nonprotein group forming part of or combined with a protein.)
▪ Active enzyme together with its bound coenzyme and/or metal ions is called a holoenzyme.
The protein part of such an enzyme is called the apoenzyme or apoprotein
International Classification of Enzymes
▪ Enzymes usually have both a common name and a systematic classification that includes a formal name and an
Enzyme Commission (EC) number.
▪ The common names for most enzymes derive from their ability to catalyze a specific chemical reaction. In
general, an enzyme’s name consists of a term that identifies the type of reaction catalyzed followed by the
suffix-ase. e.g dehydrogenases remove hydrogen atoms, proteases hydrolyze proteins, and isomerases
catalyze rearrangements in configuration.
▪ Systematic name: each enzyme has a unique name and code number that reflect the type of reaction
catalyzed and the substrates involved. e.g “hexokinase” is designated “ATP:D-hexose-6-phosphotransferase
E.C. 2.7.1.1.” This identifies hexokinase as a member of class 2 (transferases), subclass 7 (transfer of a
phosphoryl group), sub-subclass 1 (alcohol is the phosphoryl acceptor). Finally, the term “hexose-6” indicates
that the alcohol phosphorylated is that of carbon six of a hexose.
International Classification of Enzymes
Biochemists have adopted a system for naming and classifying enzymes. This system divides enzymes
into six classes
1- Oxidoreductases: oxidation and reduction reactions
• dehydrogenases addition or removal of H
• peroxidases use as H2O2 as oxygen donor, forming H2O
2- Transferases: transfer a chemical group from one substrate to another

• kinases transfer phosphate from ATP onto substrate
3- Hydrolases: hydrolysis (water splits the bond) of C-O, C-N, O-P and C-S bonds (e.g. esterases, proteases,
phosphatases, deamidases)
4- Lyases: catalyze cleavage of C-C, C-O, C-N and other bonds by elimination, leaving double bonds, and also
add groups to double bonds (e.g. dehydratases, hydratases, decarboxylases)
5- Isomerases: intramolecular rearrangements (catalyze geometric or structural changes within a single molecule
6- Ligase (Synthetases) : formation of bonds between two substrates (frequently linked to utilization of ATP)
What is a catalyst ?
▪ The functional groups in the catalytic site of the enzyme activate the substrates and decrease the
energy needed to form the high-energy intermediate stage of the transition state complex
▪ The essence of catalysis is specific stabilisation of the transition state.
Transition state
➢ lowers the activation energy
➢ increased rate of reaction
➢ is not consumed in the reaction
➢ does not affect the reaction equilibrium
[A] + [B] [C] + [D]

reactants products
Enzymes as catalysts
▪ The enzymatic catalysis of reactions is essential to ▪ Folding of the protein brings side-chains of various
living systems amino acids that may be far apart in the primary
▪ Protein – large organic compound made of amino sequence into close juxtaposition, forming an
acids arranged in a linear chain and folded into a active site.
3-D structure
Tertiary structure
Stages in an enzyme-catalysed reaction
1 Substrates enter 2
active site.
Substrates are held
in active site by
weak interactions.
Substrates
Enzyme-substrate
Complex (E-S)
▪ How Enzymes Work Active • E-S & E-P: Transient complexes
site is
5 available
for new 3
substrates. Substrates are
converted to
Enzyme
products.
Enzyme-product
4 Products are Complex (E-P)
released.
Products
Overall it is a three-step reaction

E + S E-S E-P E+P
Properties of the active site
▪ Positioning of substrate molecules in the most favourable
relative orientation for the reaction to occur
▪ The active site is perfectly complementary to the transition state
▪ Amino acid side chains of the active site stabilise the electron
distribution of the transition state
▪ The substrate is strained on binding to the active site

➢ lowers the activation energy
➢ increases the reaction rate
▪ The transition state is rapidly converted to the product(s)
▪ The products bind less tightly to the enzyme and are released
The active site of an enzyme – substrate binding site
▪ Non-covalent interaction between the substrate and the amino side
–chain of the enzyme:
o Basic groups (Lys, His, Arg) → ionic bonds
o Acidic groups (Asp, Glu) → ionic bonds
o Hydrophobic interactions (Ala, Leu, Ile, Val, Met)
o Hydrophilic interactions with –OH or alcoholic groups (Ser,Thr, Tyr)
o Hydrophilic interactions with –SH or thiol groups (Cys)
o Hydrophilic interactions with amide groups (Asn, Gln)
o Aromatic interactions (Phe, Tyr, Trp)
The active site of an enzyme – catalytic site
Reactive groups at the enzyme surface catalyse the reaction by:
▪ Donating or withdrawing electrons

▪ Stabilizing or generating free radical intermediates
▪ Forming temporary covalent bonds (a transition state intermediate)
Enzyme-substrate interaction
lock-and-key
induced-fit Yeast hexokinase phosphorylation

of glucose
lock-and-key model
▪ The substrate binding site contains amino acid residues arranged in a complementary three-dimensional
surface that “recognizes” the substrate and binds it through multiple hydrophobic interactions, electrostatic
interactions, or hydrogen bonds. The amino acid residues that bind the substrate can come from very different
parts of the linear amino acid sequence of the enzyme. In the lock-and-key model, the complementarity
between the substrate and its binding site is compared to that of a key fitting into a rigid lock.
Induced fit model
▪ As the substrate binds, enzymes undergo a conformational change (“induced fit”) that repositions the side
chains of the amino acids in the active site and increases the number of binding interactions . The induced fit
model for substrate binding recognizes that the substrate binding site is a dynamic surface created by the
flexible overall three-dimensional structure of the enzyme.
▪ In addition to reactive groups from amino acids enzymes may contain non-
protein molecules also called cofactors and coenzyme:
➢ Metal group (e.g. hexokinase Mg2+)
➢ Coenzyme – tightly but not covalently bound organic molecule (NAD)
➢ Prosthetic group – covalently bound organic molecule (heme)
▪ Enzyme with prosthetic group = holoenzyme – catalytically active
▪ Enzyme protein without prosthetic group

= apoenzyme – catalytically inactive
Units of enzyme activity – catalytic activity
▪ How much substrate can be converted (product formed) in a given time

▪ Number of micromoles (µmol) of substrate converted to product per minute
under standard optimized conditions at 30°C
▪ 1 enzyme unit (EU) = 1 μmol min-1
Specificity
What does specificity mean ?
▪ The ability of an enzyme to select just one substrate and distinguish this substrate from a group of
very similar compounds is referred to as specificity, e.g. Glucokinase catalyzes the transfer of a
phosphate from ATP to carbon 6 of glucose
▪ Enzymes catalyse only one specific reaction. The enzyme converts this substrate to just one
product
▪ Shape, charge and conformation of the substrate are critically important for binding to an enzyme
▪ Specificity and speed of enzyme catalyzed reactions result from the unique sequence of specific
amino acids that form the three-dimensional (3D) structure of the enzyme.
Specific activity
▪ Activity of an enzyme per milligram (mg) of total protein (expressed in μmol min-1mg-1)
▪ Specific activity gives a measurement of the purity of the enzyme.
The reaction rate
▪ Generation of the reaction product with time
▪ Measured at a fixed enzyme concentration
▪ Defined temperature and pH
Why is it hyperbolic ?
o Accumulation of product
o Depletion of substrate
o Denaturation of enzyme
Factors affecting enzyme activity
▪ pH
▪ Temperature
▪ Concentration of enzyme
▪ Concentration of substrate
▪ Covalent modification of enzyme
▪ Inhibitors and activators
pH
▪ pH is a measure of the acidity or alkalinity of a solution
▪ Every enzyme has an optimum pH (or pH range) at which it has
maximal activity
o Acidic < 7.00 < Basic
o Neutral = pH 7.00
pH dependence of an enzyme-catalysed reaction
▪ Ionization state of amino acid side chains ▪ Binding of the substrate and catalysis
depends on the pH of the solution depend on pH
▪ e.g. pH optima for phosphatases in
the blood plasma
Acid phosphatase Alkaline Phosphatase
1
0.8
relative activity
0.6
0.4
0.2
0
1 2 3 4 5 6 7 8 9 10 11 12
pH
Temperature dependence of an enzyme-catalysed reaction
▪ Most human enzymes function optimally at a temperature of approximately 37℃
▪ Chemical reactions proceed faster at higher temperatures:
➢ molecules move faster, greater chance to collide
➢ electrons gain activation energy easier
▪ Denaturation of the enzyme → loss of hydrogen bonding → unfolding
→ precipitation → loss of activity
▪ The temperature optimum depends on the time of incubation
The effect of varying the amount of enzyme
relative activity
▪ Predictable linear increase in product
formation with increasing amount of
enzyme
enzyme concentration
Substrate concentration dependence of an enzyme-catalysed reaction
Vmax ▪ At a constant concentration of

enzyme, the reaction rate
Enzyme ± saturated increases with increasing
little change in rate with increasing substrate substrate concentration until a
maximal velocity is reached
▪ Km is an important
Concentration of substrate to achieve half the maximum
½ Vmax characteristic of enzyme-
with increasing substrate
rate of the reaction is Km, the Michaelis constant.

substrate interactions and is
Sharp increase in rate
independent of enzyme and

rate
substrate concentrations
[substrate]
Km
Kinetic Properties of Enzymes
▪ The equations of enzyme kinetics provide a quantitative way of describing the dependence of enzyme
rate on substrate concentration.
Michaelis-Menten equation
▪ The Michaelis-Menten model of enzyme kinetics applies to a simple reaction in which the enzyme and
substrate form an enzyme–substrate complex (ES) that can dissociate back to the free enzyme and
substrate.
▪ Relates the velocity (v) to the concentration of substrate [S] and the two parameters Km and Vmax
Michaelis-Menten equation (single-substrate reaction)
▪ Describes the dependence of rate of reaction on concentration of substrate at steady state (ES
formation balanced by its removal) and vast molar excess of substrate over enzyme [S]>>[E].
v
m
v rate of reaction
Vmax maximal rate of reaction
[S] concentration of substrate
Hyperbolic curve
Km Michaelis constant
Km, the Michaelis constant
▪ Low Km corresponds to high affinity for the substrate
▪ High Km corresponds to low affinity for the substrate
▪ Enzymes with a low Km compared with the concentration of substrate [S]
in the cell act at their maximum rate
→ modest changes in the concentration of substrate [S] have no effect on the rate of
reaction
▪ Enzymes with a high Km + small change in the concentration of substrate [S]
→large change in the rate of reaction
▪ Typical Km values: - Pyruvate carboxylase 60 µM for ATP
- Chymotrypsin 5 mM for peptide substrate
- Protein kinase 12 µM for ATP
The relevance of Km: two enzymes “competing” for substrate [S]
Enzyme A P
S
Enzyme B X
Enzyme A
low Km
rate
At low substrate concentration, enzyme A

with the lower Km will be favoured
Enzyme B
high Km
[substrate], mmol /L
Experimental determination of Km and Vmax
The Lineweaver-Burk double reciprocal plot
▪ Is transformations of the Michaelis-Menten Equation
▪ The Km and Vmax for an enzyme can be visually

determined from a plot of 1/v0 versus 1/S, called a
Lineweaver-Burk or a double reciprocal plot
▪ More accurate determination of Vmax
▪ Distinguishing between certain types of enzymatic
reaction mechanisms and in analyzing enzyme
inhibition
▪ (v0 = Initial velocity)
Most Biochemical Reactions Include Multiple Substrates
▪ Most reactions in biological systems usually include two substrates and two
products
▪ Multiple substrate reactions can be divided into two classes: sequential
displacement and double displacement
Enzymes with two substrates (sequential displacement)
A+B C+D
▪ All substrates must bind to the enzyme before any product is released. Consequently, a ternary
complex of the enzyme and both substrates forms
▪ Sequential reaction – each substrate binds in turn
(ternary complex = complex containing three different molecules A-E-B)
varying concentration of substrate B

1 / rate
A+E A-E
increasing [B]
A-E + B A-E-B C-E-D C-E + D
C-E E+C
converging lines
1 / [substrate A]
Enzymes with two substrates (double displacement)
▪ In double-displacement, or Ping-Pong, reactions, one or more products are released
before all substrates bind the enzyme
▪ The defining feature of double-displacement reactions is the existence of a
substituted enzyme intermediate, where the altered enzyme forms a second complex
with another substrate molecule, and the second product leaves
▪ Substrate 1 may transfer a functional group to the enzyme (to form the covalently
modified E), which is subsequently transferred to substrate 2. This is called a Ping-
Pong or double-displacement mechanism.
▪ Reactions that shuttle amino groups between amino acids and α -ketoacids are
classic examples of double-displacement mechanisms.
Enzymes with two substrates (double displacement)
▪ The Michaelis Menten equation is also applicable to bisubstrate reactions, which occur by
ternary-complex or Ping-Pong (double-displacement) pathways
▪ Ping-pong reaction – one substrate reacts, and modifies enzyme, then second substrate reacts
varying concentration of substrate B

with modified enzyme
increasing [B]
1 / rate
A+B C+D
A+E A-E C-E* C + E*
B + E* B-E* D-E D+E
parallel lines
1 / [substrate A]
Allosteric enzymes
▪ Allosteric enzymes- enzymes with cooperative substrate binding
▪ contain binding sites “other” (“allo”) than substrate binding sites.
▪ often in multi-subunit complex, more than one active site in the complex.
▪ binding of substrate to the active site of the first subunit leads to change in
conformation facilitating binding of substrate to the other active sites
Enzyme inhibitors
▪ Decrease the enzyme’s ability to bind substrate or/and lower the enzyme’s catalytic activity
▪ Many drugs and toxic agents act by inhibiting enzymes
Type of enzyme inhibitors
▪ Reversible inhibitors
▪ Irreversible inhibitors (inactivators)
Enzyme inhibitors
Reversible inhibitors Irreversible inhibitors
▪ Non-covalent binding to enzyme ▪ Tightly Bind to enzyme covalently
▪ Many are relatively unspecific ▪ Many are substrate analogues
▪ Mechanism: blocking substrate ▪ Undergo part of reaction

binding or hindering catalytic steps ▪ Transition state covalent intermediate
does not break down
Irreversible inhibitors
▪ Dissociates very slowly from its target enzyme because it has become tightly bound to the
enzyme
▪ Some irreversible inhibitors are important drugs. Penicillin acts by covalently modifying
the enzyme transpeptidase, thereby preventing the synthesis of bacterial cell walls and
thus killing the bacteria. Aspirin acts by covalently modifying the enzyme cyclooxygenase,
reducing the synthesis of inflammatory signals.
Competitive inhibitor
▪ Competes with the substrate for binding at the active site
▪ Inhibition is a function of the relative affinities of the substrate and the
inhibitor for binding the enzyme
▪ Inhibition is a function of the relative concentrations of substrate and
inhibitor
E +S+I E-S E-P E+P

E+S+I E-I
▪ Vmax is unchanged, Km is increased
▪ If enough substrate is added, it overcomes the inhibitor

Competitive inhibitor
▪ Methotrexate is a structural analog of tetrahydrofolate, a coenzyme for the enzyme
dihydrofolate reductase, which plays a role in the biosynthesis of purines and
pyrimidines. It binds to dihydrofolate reductase 1000-fold more tightly than the
natural substrate and inhibits nucleotide base synthesis. It is used to treat cancer.
Non-competitive inhibitor
▪ Binds to the enzyme at a position separate from the active site
▪ No competition for binding with the substrate
▪ The apparent affinity for the substrate is unchanged, but the rate of reaction is slowed
slow
E+S+I E-S + I E-S-I E-P-I E+P+I
▪ Km is unchanged, Vmax is decreased
▪ Adding more substrate has no effect on the rate of reaction

Mixed inhibitors
▪ Mixed inhibitors do not bind in the active site
▪ Inhibitor can bind prior to substrate or to the enzyme-substrate complex
▪ Mixed inhibitors distort the substrate binding site which affects:
- apparent substrate affinity
- catalytic turn-over (slowing catalysis)
▪ Mixed inhibitors can either:
- increase or decrease Km
- decrease vmax
Allosteric inhibitors
▪ Increase the Km and hence lower
the apparent affinity of the enzyme
for its substrate
▪ A decrease in the substrate affinity

leads to a decrease of enzyme
activity (at subsaturating levels of
substrate present in the cell)
Hormones 3rd Class

2020-2021

[email protected]
Hormones
▪ Hormones are chemical messengers formed in specific tissues. They are transferring
information and instructions from one set of cells to another, and serve to coordinate
metabolic activities, regulate growth, maintain homeostasis of essential nutrients, sexual
function, and prepare the organisms for reproduction
▪ Hormone is released in small amount from glands, and is transported in the bloodstream
to target organs or other cells to modify their structures and functions.
▪ Hyposecretion or hypersecretion of any hormone can be harmful to the body. Controlling
the production of hormones can treat many hormonal disorders in the body
▪ Most glands of the body delivery their secretions by means of ducts. These are called
exocrine glands.
▪ There are few other glands that produce chemical substance that they directly secrete
into the blood stream for transmission to various target tissues, which have cells
possessing the appropriate receptor. These are ductless or endocrine glands. The
secretions of endocrine glands are called as hormones.
Hormones and target cells
▪ Most hormones circulate in blood, coming into contact with essentially all cells. However, a
given hormone usually affects only a limited number of cells, which are called target cells. A
target cell responds to a hormone when it express a specific receptor for that hormone.
▪ The hormone binds to the receptor protein, resulting in the activation of a signal transduction
mechanism that ultimately leads to cell type-specific responses
▪ A target cell is defined by its ability to selectively bind a given hormone to its receptor.
Several biochemical features of this interaction:
o binding should be specific
o binding should be saturable
o binding should occur within the concentration range of the expected biologic response
The target cell concept and hormone receptors
Several factors determine the response of a target cell to a hormone.
▪ Factors that affect the concentration of the hormone at the target cell
▪ Factors that affect the actual response of the target cell to the hormone
▪ Factors that affect the concentration of the hormone at the target cell
o The rate of synthesis and secretion of the hormones.
o The proximity of the target cell to the hormone source (dilution effect).
o The dissociation constants of the hormone with specific plasma transport proteins .
o The conversion of inactive or sub-optimally active forms of the hormone into the
fully active form.
o The rate of clearance from plasma by other tissues or by digestion, metabolism, or
excretion.
▪ Factors that affect the actual response of the target cell to the hormone
o The number, relative activity, and state of occupancy of the specific receptors on the plasma
membrane or in the cytoplasm or nucleus.
o The metabolism (activation or inactivation) of the hormone in the target cell
o The presence of other factors within the cell that are necessary for the hormone response.
o Up- or down-regulation of the receptor consequent to the interaction with the ligand.
▪ Although their varying actions and differing specificities depending on the target organ, the
hormones have several characteristics in common with enzymes:
o Act as body catalysts.
o Not consumed in the reaction
o Required only in small quantities
▪ Hormones differ from enzymes in the following ways:
o Hormones are produced in an organ other than that which they ultimately perform their
action
o Hormones are secreted in blood prior to use. Because of the small amounts of the hormones
required , blood levels of the hormones are extremely low
o Structurally, Hormones are not always proteins.
What is the endocrine system?
▪ The endocrine system is made up of glands and the hormones that they secrete.
▪ Although the endocrine glands are the primary hormone producers, they can also produce and
release by:
o brain
o Heart
o Lungs
o Liver
o Skin
o Thymus
o gastrointestinal mucosa
o placenta
▪ The endocrine system regulates all biological processes in the body from conception through
adulthood and into old age, including the development of the brain and nervous system, the growth
and function of the reproductive system, as well as the metabolism and blood sugar
What is the endocrine system?
▪ The primary endocrine glands are:

o The pituitary (the master gland)
o Pineal, thyroid, parathyroid
o Islets of Langerhans
o Adrenals
o Ovaries in the female
o Testes in the male
General mechanisms of hormone action
▪ Hormone action begins with the binding of the hormone to a receptor on (or in) a target cell,
binding of hormone molecule induces a conformational change in its receptor. Hence, the
hormone-receptor interaction can be transduced from one molecule to another, cell may then
➢ Synthesis new molecules
➢ Change permeability of membrane
➢ Alter reaction
▪ Each target cell responds to hormone differently
▪ Liver cells: insulin stimulates glycogen synthesis
▪ Adipose cells: insulin stimulates triglyceride synthesis
Regulation of hormones action
▪ Regulated by signals from nervous system, chemical changes in the blood or by other
hormones
▪ Negative feedback control (most common)
o Increase/decrease in blood level is reversed (maintains hormone levels within narrow ranges)
▪ Positive feedback control
o The change production by hormone causes more hormone to be released
▪ Disorders involve either hyposecretion or hypersecretion of hormone
Diseases associated with the Endocrine system
▪ Overproduction of a hormone
▪ Underproduction of a hormone
▪ Non-functional receptor that cause target cells to become insensitive to hormones
▪ Knowledge of hormone biosynthesis, secretion, and interaction with target cells is

essential to an understanding of biochemical basis of these disorders
Thyroid hormones
▪ T3 and T4: thyroid hormones responsible for our metabolic rate, protein synthesis,
breakdown of fats, use of glucose for ATP production
▪ Calcitonin (CT) a hormone secreted by the thyroid that has the effect of lowering blood
calcium, responsible for building of bone
▪ Most hormones fall into three classes:
o Polypeptide (synthesised from large precursors)
o Steroids hormones are derivatives of cholesterol
o Amino acids derivatives (thyroids and epinephrine are amino acids derivatives)
Pathway of thyroxine (T4) and
triiodothyronine (T3) synthesis. Thyroid
cells actively transport iodine (I-), which
is incorporated into a few tyrosine

residues of thyroglobulin by the enzyme
iodoperoxidase. After condensation of
iodinated tyrosine residues, the
thyroglobulin is proteolytically degraded
liberating T4 and T3
Goiter
▪ Iodine deficiency causes thyroid to enlarge as it tries to produce thyroxine
▪ Mechanism:
▪ Hyperthyroidism means too much thyroid hormone
▪ Hypothyroidism means too little thyroid hormone and is a common problem
▪ Thyroid cancer is a fairly common malignancy, however, the vast majority have excellent
long term survival
▪ Thyroiditis is an inflammatory process ongoing within the thyroid gland
▪ Solitary thyroid nodules: defined as swelling benign within an normal gland
Diseases associated with the adrenal cortex
Two diseases associated with the adrenal cortex
▪ Cushing’s disease
▪ Addison's disease
o Cushing’s disease: adenoma in the pituitary gland produces large amount of

Adrenocorticotropic hormone (ACTH) causing the adrenal gland to produce
elevated level of cortisol
▪ Symptoms:
o Weigh gain
o Hair loss
o Hyperpigmentation
o Hypercalcemia
Addison's disease
▪ Addison's disease (Chronic adrenal insufficiency, hypocortisolism, and hypoadrenalism)
▪ is a rare, chronic endocrine disorder in which the adrenal gland do not produce sufficient
steroid hormones (glucocorticoids and often mineralocorticoids)
▪ It characterized by a number of relatively nonspecific symptoms such as abdominal pain
and weakness
Symptoms:
o Nausea
o Fever
o Vomiting
o Fatigue
▪ Three actions were defined to describe how the signal is distributed for a particular hormonal
pathway
▪ Endocrine action: the hormone is distributed in blood and binds to distant target cells.
▪ Paracrine action: the hormone acts locally by diffusing from its source to target cells in the
neighborhood.
▪ Autocrine action: the hormone acts on the same cell that produced it.
Two important terms are used to refer to molecules that bind to the hormone-binding sites of
receptors:
Agonists are molecules that bind the receptor and induce all the post-receptor events that
lead to a biologic effect.
Antagonists are molecules that bind the receptor and block binding of the agonist, but fail to
trigger intracellular signaling events. Hormone antagonists are widely used as drugs.
▪ The hormones are categorized based on the location of their specific cellular receptors and
the type of signals generated.
▪ Group I hormones interact with an intracellular receptor and group II hormones with
receptor recognition sites located on the extracellular surface of the plasma membrane of
target cells.
▪ The hormones generate signals at or within target cells, and these signals regulate a variety
of biologic processes which provide for a coordinated response to the stimulus.
Hormone Action and Signal Transduction
▪ A hormone-receptor interaction results in generation of an intracellular signal that can

either regulate the activity of genes, thereby altering the amount of certain proteins in
the target cell or affect the activity of specific proteins, including enzymes and transporter
proteins.
▪ The signal can influence the location of proteins in the cell and can affect general
processes such as protein synthesis, cell growth, and replication, often through effects on
gene expression
▪ Many pharmacotherapeutic agents are aimed to target signal transduction pathways
Vitamins 3rd Class

2020-2021

[email protected]
Objectives
▪ Vitamins
o Introduction
o General characteristics
o General functions
o Classification
o Structure
o Individual characteristics
o Individual function
o Deficiency
Definition of Vitamins
▪ Vitamins are organic compounds in food that are required in small amounts for
growth and maintaining good health. They are released , absorbed and transported
with the fat of the diet.
▪ The word vitamin comes from the Latin word vita, means life
▪ Organic nutrients with on-caloric
▪ Help body processes; digestion, absorption, metabolism, growth etc.
▪ Some appear in food as precursors or provitamins
Classification of vitamins
On the basis of their solubility, there are 2 classes of vitamins

▪ Fat soluble vitamins
▪ Water soluble vitamins
Fat soluble vitamins
o are A, D, E and K
o Found in the fats and oils of food
o Absorbed into the lymph and carried in blood with protein transporters =
chylomicrons.
o Vitamins that dissolve in fat, because fat is easily story on our body, these vitamins
can be stored within our fat
o They can accumulate and be saved for later use
o Stored in liver and body fat and can become toxic if large amounts are consumed.
Water soluble vitamins
▪ Include B complex (B1, B2, B3, B5, B6, B7, B9 and B12) and vitamin C
▪ Found in vegetables, fruit and grains, meat
▪ Absorbed directly into the blood stream
o Vitamins that dissolve in water, because our body is a watery environment,
these vitamins can move through our body pretty easily, and they can also be
flushed out the kidneys
o Not stored in the body and toxicity is rare, smoking cause decreased
absorption.
Classification of vitamins
Fat versus Water Soluble Vitamins
Water Soluble Fat Soluble
Absorption Directly to blood Lymph via CM
Transport free Require carrier

Storage Circulate freely In cells with fat
Excretion In urine Stored with fat
Toxicity Less likely More Likely
Requirements Every 2-3 days Every week
CM= Chylomicrons
General characteristics of vitamins
▪ Some of vitamin cannot to be synthesized by the body
▪ Significant amounts of fat soluble vitamins can be stored in human adipose tissues
and the liver
▪ Water soluble vitamins cannot be stored in human tissues, their excess is excreted
with urine
o Synthetic vitamins are identical to natural vitamins
o Following growth and development, vitamins remain essential nutrients for the
healthy maintenance of the cells, issues and organs
General Functions of vitamins
Vitamins are helpful for the health and life of the body in the following respects
▪ Help health protection by build up the resistance of the body against diseases
▪ Prevent and cure various diseases caused by deficiency of vitamins
▪ Help the digestion and utilization of mineral salts and carbohydrates in the body
▪ Help maintenance of health and normal growth
▪ Stimulate and give strength to digestive and nervous system
Vitamin A
▪ Vitamin A is a group of unsaturated nutritional organic compounds that includes,
retinol, retinal, retinoic acid, and several provitamin A carotenoids (beta-carotene)
▪ Retinol is the active form of vitamin A, which is found only in animal sources
▪ Found in animal and plant sources
o Vitamin A Functions o Vitamin A deficiency
▪ Vision (11-cis-retinol bound to rhodopsin ▪ Night blindness
detects light in our eyes)
▪ Xerophthalmia (Development of a peculiar
▪ Gene transcription condition around the eyes)
▪ Bone growth ▪ Decreased resistance to infections
▪ Embryonic development and Reproduction ▪ Dry skin, hair or nails
▪ Cell division and differentiation
▪ Healthy Skin
▪ Regulate Immune System
▪ Antioxidant activity
Vitamin D
▪ Vitamin D refers to a group of fat soluble secosteroids (similar lipid-soluble molecules) that have a hormone-like
function
▪ The active molecule binds to intracellular receptor proteins
▪ The most prominent actions-of the active molecule are to regulate the plasma levels of calcium and phosphorus.
▪ Vitamin D – precursor is cholesterol, converted by UV from sunlight exposure, therefore is a “non-essential”
vitamin. It also called sunshine vitamin
▪ Vitamin D is available in two forms:
o Cholecalciferol (Vitamin D3) is made from 7- dehydrocholesterol in the skin of animals and humans
o Calciferol (Vitamin D2) is obtained artificially by irradiation of ergo-sterol and is called ergocalciferol
Vitamin D3 (cholecalciferol) Vitamin D2 (ergocalciferol)
Vitamin D3 can be obtained in diet, or derived from cholesterol in a reaction that requires
UV light.
UV light
Skin
liver
kidney
Vitamin D3 calcitriol (1,25-dihydroxycholecalciferol)

▪ Vitamin D binds to a “vitamin D binding protein” (VDP) for transport to target organs.
▪ Vitamin D is not active itself (it’s a prohormone); it is modified to yield biologically active
forms, such as calcitriol.
▪ Calcitriol is a transcription factor, influencing expression of proteins involved in calcium
absorption and transport.
▪ Calcitriol is normally made in the kidney
1,25-dihydroxycholecalciferol
Calcitriol
Role of vitamin D
▪ Maintaining adequate plasma levels of calcium (Calcium balance):
o Stimulates calcium removal from bone
o Increasing uptake of calcium by the intestine
o Minimizing loss of calcium by the kidney
▪ is essential for the proper utilization of calcium and phosphorus to produce normal,
healthy bones and teeth
▪ Promotes bone growth and maintenance
▪ Cell differentiation
▪ Stimulates maturation of cells – heart and brain
▪ Important for immune system function
▪ Blood pressure regulation
Vitamin D Deficiencies
▪ Rickets (children)
▪ Osteomalacia (adults)
Toxicity of Vitamin D
▪ Vitamin D can be stored in the body and is slowly metabolized.
▪ High doses can cause loss of appetite, nausea, thirst, stupor.
▪ Enhanced calcium absorption and bone resorption results in hypercalcemia which can
lead to deposition of calcium in many organs particularly the arteries and kidney.
Vitamin E
▪ Vitamin E refers to a group compounds that include both tocopherols and tocotrienols.
▪ The word tocopherol is derived from the word toco meaning child birth and pheros
meaning to bear
▪ Essential for normal reproduction in many animals, hence known as anti-sterility vitamin
▪ It also called anti-aging factor
α-tocopherol
Function of vitamin E
▪ Anti-oxidant (minimize the damage of free radicals)
▪ protects cell membrane
▪ Enhances immune system
▪ Protects lipids and prevents the oxidation of polyunsaturated fatty acids in various tissues
▪ Protects RBC from hemolysis by oxidizing agents
Vitamin K
▪ It naturally produced by intestinal bacteria
▪ It is essential for product of a type of protein called prothrombin and other factor involve
in blood clotting mechanism
▪ It includes two natural vitamins
o K1 phylloquinone
o K2 menaquinones
Function of vitamin K
▪ Vitamin K is fat soluble vitamin with a specific coenzyme function. It is required in the
hepatic synthesis of prothrombin and blood clotting factors.
▪ Vitamin K helps blood clotting, essential to stop bleeding from wounds.
▪ Necessary for the maintenance of normal blood coagulation.
▪ It prevents hemorrhage only in cases when there is defective production of prothrombin.
▪ Oxidative phosphorylation
o It acts as a cofactor in oxidative phosphorylation associated with lipid
Vitamin K deficiency
▪ Deficiencies are rare but
▪ Seen in infants, Newborns are given a dose of vitamin K at birth.
▪ After prolonged antibiotic therapy, and in patients with decreased bile production.
▪ People with vitamin K deficiency may experience easy bruising nosebleeds
❖ Toxicities >1000 mg/day:

➢ Rupture of RBCs
➢ Jaundice
Water soluble vitamins
▪ Essential coenzymes required in energy releasing mechanisms
▪ Act as coenzymes for metabolism of carbohydrates, proteins, and fats
✓ B1-thiamine
✓ B2-riboflavin
✓ B3-Niacin
✓ B5-pantothenic acid
✓ B6- pyridoxine
✓ B7-Biotin
✓ B9-folic acid
✓ B12-cobalamin
✓ Ascorbic acid
Thiamine (vitamin B1)
▪ It is colourless basic organic compound composed of a sulphated pyramiding ring
▪ It is synthesized only in bacteria, fungi and plants
▪ Thiamine pyrophosphate (TPP) is the biologically active form of the vitamin. It serves as a
coenzyme in the oxidative decarboxylation of α-keto acids.
o Important in:
▪ Producing energy from carbohydrates
▪ Nerve function
Thiamine
o Deficiency of vitamin 1 causes beriberi (Muscle atrophy, neurological problems)

▪ Wernicke-korsakoff syndrome (Characterized by apathy, loos of memory)
Riboflavin (vitamin B2)
▪ It is yellowish green fluorescent compound
▪ It is widely involved in oxidation reduction reaction
▪ Riboflavin is a precursor for FAD and FMN.
▪ The word Riboflavin derived from 2 sources
o Ribose-mean many ribose sugar found in several vitamins
o Flavin-yellow
▪ Light can destroy riboflavin, so purchase milk in opaque containers.
❖ NAD= Nicotinamide adenine dinucleotide

❖ FMN= Flavin mononucleotide
Riboflavin (vitamin B2)
Important in:
▪ Energy production
▪ Carbohydrate, fat, and protein metabolism
▪ Formation of antibodies and red blood cells (RBCs)
▪ Cell respiration
▪ Maintenance of good vision, skin, nails, and hair
Deficiency of vitamin B2 can causes:

▪ Itching and burning eyes (eye abnormalities)
▪ Cracks and sores in mouth and lips ( fissuring at the corners of the mouth )
▪ Glossitis (the tongue appearing smooth and purplish).
Niacin (vitamin B3)
▪ Vitamin B3 niacin or nicotinic acid
▪ It is a pyridine derivative and is precursor of the NAD (Nicotinamide adenine dinucleotide)
▪ Essential for metabolism of carbohydrate, fat and protein

▪ Pellagra
o Dermatitis
Pantothenic acid (vitamin B5)
▪ This word derived from Greek word pantos meaning everywhere
▪ Part of coenzyme A
▪ Essential for metabolism of carbohydrate, fat and protein
Pantothenic acid
Pyridoxine (vitamin B6)
▪ Vitamin B6 refers to a group of chemical very similar compounds, pyridoxine,
pyridoxal and pyridoxamine, all derives of pyridine, which can be interconverted
in biological systems
▪ Its active form of B complex, pyridoxal 5-phosphate (PLP) serves as a cofactor in
many enzyme reactions in amino acid, glucose, and lipid metabolism
▪ PLP is a covalently linked cofactor to transaminases, and some decarboxylases,
and glycogen phosphorylase; these are called “PLP-dependent enzymes
pyridoxal 5-phosphate pyridoxine pyridoxamine

Pyridoxine (vitamin B6)
Important in:
▪ Production of red blood cells (RBCs)
▪ Enhances immune system
▪ Nervous system functions
▪ Reducing muscle spasms
▪ Keep blood sugar (glucose) in normal ranges
▪ Maintaining proper balance of sodium and phosphorous in the body
▪ Coenzyme for a large number of enzymes particularly those that catalyze reactions
involving amino acids (transamination, deamination, decarboxylation).
Deficiency symptoms of B6
▪ Associated with neurological symptoms such as depression, irritability, nervousness

and mental confusion due to decrease synthesis of serotonin, Gamma Aminobutyric
Acid (GABA), adrenaline norepinephrine.
▪ Anemia
Biotin (vitamin B7)
▪ Coenzyme for carboxylase enzymes
▪ Involved in the synthesis of fatty acid, isoleucine and valine,
and gluconeogenesis
Folic acid (vitamin B9)
Important in:
▪ Formation of red blood cells (RBCs)
▪ Nerve function
▪ DNA reproduction
Folic acid
▪ Necessary for growth and division of all body cells
▪ Prevention of anemia
▪ Essential for the health of skin and hair
▪ Fat and proteins metabolism to energy production
▪ Pregnancy- Folic acid is an important nutrient for pregnant women and her developing
fetus, also it improves the lactation
o Very important in early pregnancy (important for rapidly dividing cells )
Deficiency of vitamin B9
Deficiency of folic acid can causes:

▪ Anemia
▪ Nerve damage
▪ Hypersensitive skin
Cobalamin (vitamin B12)
▪ Also known as anti-pernicious anemia vitamin.
▪ synthesized only by microorganisms
▪ Production of red blood cells
▪ Nervous: It improves concentration, memory and balance
▪ Promotes growth and increase appetite
▪ Important for metabolism of carbohydrate, protein, fat
and folic acid
Cobalamin
Deficiency of vitamin B12

▪ Pernicious anemia due to defect to absorb the vitamin from the intestine, not by an
absence of the vitamin in the diet.
▪ Low levels of hemoglobin
▪ Irreversible nerve cell death
Ascorbic acid (vit C)
▪ Ascorbic acid (Toxic to viruses, bacteria, and some malignant tumor cells)
▪ In almost all organisms, ascorbic acid is synthesized from glucose
.
Functions of vitamin C in the body
▪ Protects the body from free radicals (antioxidant)
▪ Maintenance of bones and proper adrenal thyroid gland
▪ Helps form connective tissue (Collagen), and as a cofactor for several enzymes.
▪ Helps healing of wounds
▪ Helps in absorbing iron
▪ keep the gums healthy
▪ Stimulates immune functions
▪ prevention of heart disease and cancer
Deficiency of vitamin C can causes
▪ Weight loss
▪ Scurvy (swollen and painful joints and bleeding gums, poor wound healing, and bleeding
from the skin may occur, and finally death from infection or bleeding)
▪ Reduced resistance to colds and infections
▪ poor wound healing and fractured bones
▪ Spongy gums loose of teeth
▪ Harmful effects in larger doses: (over 1000mg/ dose)

▪ Diarrhea
❖ Chewable tablets (may cause damage to teeth)

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Lecture 1: Biochemistry I

Introduction to the macromolecules biochemistry

Anbar University-College of Pharmacy-Clinical Laboratory Sciences Department

Dr. Yousif H. Khalaf

➢ The cell is the fundamental unit of life

Anbar University-College of Pharmacy-Clinical Laboratory Sciences Department

Dr. Yousif H. Khalaf

o To know the formation of carbohydrates

▪ Carbohydrates, one of the four major classes of biomolecules along with

• Carbohydrates are important for tissue formation

• Carbohydrates form the basis of human blood groups

2- Disaccharides: two monosaccharides covalently linked by glycosidic bond.

3- Oligosaccharides: several monosaccharides (3-9) joined by glycosidic bonds.

4- Polysaccharides: polymers consisting of chains of monosaccharide or disaccharide

▪ The names of all sugars end in – ose

(Ring-form is energetically more stable)

HC O aldehyde group HC O CH2OH

CH2OH CH2OH CH2OH

Components of RNA and DNA

o Formed by the reduction of the aldehyde group of glucose to a

o Energy yield roughly half that of glucose.

Disaccharide = condensation between two monosaccharides (O-glycosidic bond)

The most common disaccharides are:

Maltose (made from two glucoses)

The formula of these disaccharides is C12H22O11

▪ Decrease in lactase activity to 5 – 10% of the level at birth

▪ Lactose is used as energy source for microorganisms in the colon

Lactose Glucose Galactose

Starch – large molecule with variable number of glucose units; storage

Amylose – is a linear polymer of glucose linked with mainly (α-1,4) bonds

Amylopectin – chain of glucose molecules (α -1,4), every 30th glucose

Glycogen - storage carbohydrate in animal cells (muscle and liver(

Non-starch polysaccharides– not digested by human enzymes

Hydrolysis of starch by amylase in saliva and pancreatic juice results in formation of

Anbar University-College of Pharmacy-Clinical Laboratory Sciences Department

Dr. Yousif H. Khalaf

▪ Storage and expression of genetic information.

o Heterocyclic nitrogenous base

o Mono, di, or triphosphate.

o Pentoses (5-C sugars)

▪ Purines are bonded to C1 of the sugar at their N9 atom.

▪ Pyrimidines are bonded to C1 of the sugar at their N1 atom.

▪ If the sugar is D-ribose, a ribonucleoside is produced , if the sugar is 2-deoxyribose a

▪ DNA: Deoxyadenosine, Deoxyguanosine, Deoxycytidine, and Deoxthymidine

▪ RNA: Adenosine, Guanosine, Cytidine, and Uridine

DNA is a polymer of deoxyribonucleotide RNA is a polymer of ribonucleotide

o Building blocks of DNA and RNA.

➢ They can interfere or inhibit synthesis pathway of purine or pyrimidine

➢Widely used to control cancer.

▪ De novo pathway: The synthesis of nucleotides begins with their

▪ Salvage pathway: The synthesis of nucleotide by recycle the free

Nucleic acid Protein

In small intestine Endonucleases: RNase and DNase

(2,6,8-trioxypurine) The end product of purine metabolism

PURINE PYRIMIDINE PURINE PYRIMIDINE

o Two helical polynucleotide chains, coiled about a common axis.

DNA is a flexible molecule. Considerable rotation is possible around a number

▪ Helix direction = Right-handed

▪ Sugar-phosphates on the outside; purine and pyrimidine bases of both

▪ Approx. 10 bases per helix turn and 34 Å between base pairs.