This document discusses biochemical molecules. It begins by explaining that all living organisms require biomolecules like organic and inorganic compounds. The four most common elements in living organisms are carbon, hydrogen, oxygen, and nitrogen. Biomolecules can be grouped as carbohydrates, lipids, proteins, nucleic acids, water, and minerals. Carbohydrates include monosaccharides, disaccharides, and polysaccharides. Lipids function as storage, structure, signaling, and pigments. Proteins are made of amino acids linked by peptide bonds that can fold into complex structures.

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Unit 2
Biochemical molecules
By the end of this section you should be able to:
• Group biochemical molecules as inorganic and organic.
• Explain which chemical elements are found most often in
biochemical molecules.
• Describe the properties of water.
• Explain the importance of water to living organisms.

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Introduction
 All living organisms require several compounds to
continue to live.
 We call these compounds biomolecules. The smallest unit
that make up a cell are called elements.
 The earth crust contains approximately 100 chemical
elements and yet only 16 of these are essential for life
 Biological molecules are often referred to as the molecules
of life (bio-molecules)

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The four most common element in living organism are
hydrogen ,carbon ,oxygen and nitrogen.
These four most common elements with Sulphur and
phosphorus that are known by the acronym SPONCH make up
more than 99% of the mass and the number of atoms found in
living organism.
The four most common element in the earth crust however are
oxygen , silicon , aluminum and sodium.
The biological importance of hydrogen, oxygen, nitrogen and
carbon is largely due to their ability to form more stable
covalent bonds than any other elements

4. 4
 Biological molecules are often referred to as the molecules
of life (bio-molecules)
oSuch as: organic and inorganic molecules.
 Organic bio-molecules includes :
 Carbohydrates
 Lipids
 Proteins &
 Nucleic acids
 They are important either structurally or functionally for
cells and, in most cases, they are important in both ways.
 Inorganic molecules includes :
oWater &
oMinerals
2. Biological Molecules

5. sucrose
2.1.Carbohydrates
• Consist of carbon, hydrogen and oxygen
with a ratio of 1:2:1,
• General formula (CH2O)n, n  3.
 All carbohydrates are aldehydes
or ketone, & all contain several
hydroxyl groups.
• Function:
1. Mediating interactions among and with
in cells(Glycoprotein)
2. Quick energy or fuels (glucose)
3. Metabolic intermediate (Pyruvate)
4. Energy storage (Starches, glycogen)
5. Structure (cellulose)
• cell wall in plants
glucose
C6H12O6
starch 5

6. 6
• Carbohydrates found in the form of either a sugar
or many sugars linked together, called saccharides.
• The word “saccharide” is derived from the Greek
sakcharon, meaning “sugar”).
• Based on the number sugar units they contain,they
categorized into three
1. Monosaccharides, simple sugars most abundant
in nature
2. Disaccharides with two monosaccharide units
joined by Glycosidic bond.
3. Polysaccharides are polymers containing more
than 2 monosaccharide units, and some have
hundreds or thousands of units.

8. 2.1.1 Monosaccharide's are simple sugars
• common monosaccharides are (Glucose, Galactose, Fructose)
 The two common tests for the presence of reducing sugar are Benedict's test
& Fehling's test.
 The basic units of carbohydrates
• Typically contain from three to seven carbon atoms.
• Are aldehyde or ketone derivatives
 All monosaccharides are reducing sugar, i.e. they carry out a type of
chemical reaction known as reduction reaction.
• Cannot be hydrolyzed to form simpler saccharides.
• Monosaccharides are classified according to:
1. Chemical nature of
their carbonyl group
a. Aldose: Glucose,
Galactose,
b. Ketose : Fructose
8

9. 2. The number of
their C atoms
3. OH- attachments position on chiral carbon atom
a) D sugars, The bottom of OH
attached to the right.
a) L sugars, The bottom of OH points
to the left.
Hexose
Heptose
Octose
Triose
Tetrose
Pentos e
Formula
Name
C3 H6 O3
C4 H8 O4
C5 H1 0 O5
C6 H1 2 O6
C7 H1 4 O7
C8 H1 6 O8
9

10. • Glucose (C6H12O6), the most abundant monosaccharide,
which used as an energy source in most organisms.
• Glucose and fructose are structural isomers
• Monosaccharaides exist in two forms:
i. Straight chain form
ii. Ring form
10

11. 2.1.2. Disaccharides(Sucrose,Lactose,Maltose)
• Formed by condensation rxn b/n 2 monosaccharides with
special type of covalent bonds known as Glycosidic bond
• Maltose & lactose are reducing sugars while sucrose is the
only common non-reducing sugar
• All are isomers with molecular formula C12H22O11
• On hydrolysis they yield 2 monosaccharide.
• Soluble in water
• There are 3 main disaccharides:
1. Sucrose= sugar in cane
2. Lactose=sugar in milk
3. Maltose=sugar in malt
11

12. • Summary on structure of Disaccaraides
Sucrose =fructose + glucose Lactose =Galactose + Glucose
Maltose= Glucose +Glucose

13. c) Polysaccharides
 polysaccharides are polymers of monosaccharides.
 They function chiefly as food & energy stores (e.g. starch in
plants & glycogen in animals) & as structural material (e.g.
cellulose).
 Chitin & Murein are compounds closely related to
polysaccharides.
 Chitin is closely related to cellulose in structure & function as
being a structural polysaccharide.
 It occurs in cell wall of fungi & exoskeleton of arthropods.
 Murein acts as the strengthening material of bacterial cell wall.
 Pectin are polysaccharides of galactose & galacturonic acid
residues, & is an important component of the first layer of a cell
wall.
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14. POLYSACCHARIDES
14
STORAGE FUNCTION
1. Starch
– energy storage in
plants
» potatoes
2. Glycogen
– energy storage in
animals
– in liver
STRUTURAL
3. Cellulose
– structure in plants
» cell walls
4. Chitin
– structure in
arthropods &
fungi
» exoskeleton
1.Storage function
 in animals in the form of
Glycogen and starch in
animals
2. Structural function
Cellulose and chitin

15. 2.2. Lipids
• Lipids are a heterogeneous group of compounds.
• They consist mainly of carbon and hydrogen, with few
oxygen-containing functional groups.
• Lipids are mainly insoluble in water and soluble in organic
solvents (such as ether and chloroform).
Functions
1. As Storage function (fatty acids, oils, triacylglycerols, waxes)
2. As Structural function (Phospholipids, glycolipids, sterols)
3. As Signaling and Cofactor function ( Steroid hormones)
4. As Pigment function (Carotenoids)
15

16. 2.2. 1. Triacylglycerol ( fat), the main
storage lipid
• The triacylglycerols most abundant lipids in living organisms
commonly known as fats.
• Because it contains three fatty acids, a fat molecule is called
a triglyceride.
• A triacylglycerol consists:
1. Glycerol, a three-carbon alcohol that contains three
hydroxyl (￢OH) groups, and
2. 3 Fatty acid chain, a long, unbranched hydrocarbon
chain with a carboxyl group (￢COOH) at one end.
16

17. • The glycerol’s hydroxyl groups reacts with the
carboxyl group of a fatty acid
• By the formation of a covalent linkage known as an
ester bond
• There are 2 types of Fatty Acids
A. Saturated fatty acids
 Contain the maximum possible number of hydrogen
atoms
 Form single C-C bond
 Tend to be solid at room temperature.
17

18. 18

19. B. Unsaturated fatty acids
 One or more adjacent pairs of carbon atoms joined by a
double bond
 Therefore, they are not fully saturated with hydrogen.
I. Mono unsaturated fatty acids,
 Fatty acids with one double bond
II. Poly unsaturated fatty acids
 FA with more than one double bond
 Liquid at room temperature.
• B/C each double bond produces a bend in the
hydrocarbon chain that prevents it from aligning closely
19

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21. • Food manufacturers commonly hydrogenate or partially
hydrogenate cooking oils to make margarine and other
foodstuffs, converting unsaturated fatty acids to
saturated fatty acids and making the fat more solid at
room temperature.
• This process makes the fat less healthful because
saturated fatty acids in the diet are known to increase the
risk of cardiovascular disease
21

22. 2.3.Protein
is a compound made of small carbon compounds called amino
acids
Amino acids are small compounds that are made of carbon,
nitrogen, oxygen, hydrogen, and sometimes sulfur
All amino acids share the same general structure.
They have central carbon atom with four covalent
bonds.

24. 2.3. 1.Proteins are built from a collection of 20 amino acids
• Amino acids (monomers) are the building blocks of proteins (polymer).
• An amino acid consists of:
1. A central carbon atom, called the α-carbon,
2. An amino group (-NH+3)
3. A carboxylic acid group (-COO),
4. A hydrogen atom (H), and
5. A distinctive R group (the side chain).
• Only L amino acids are found in proteins which found in our body.

25. Essential and Non-Essential Amino Acids
 An essential amino acid is one, which must be included in the diet because
either it cannot be made in the body at all, or it is made too slowly to meet
needs.
 Non-essential amino acid that can be synthesized in the cell or in the body.
• Essential amino acids are 10 amino acids not synthesized by
the body and must be consumed from proteins in the diet.
Arginine(Arg)* Methionone(Met) Leucine(Leu)
Histidine(His)* Phenylalanine(Phe) Lysine(Lys)
Isoleucine(Ile) Threonine(Thr) Tryptophan(Trp)
Valine(Val)

26. 2.3.2 Levels of structure in proteins
• The linear sequence of amino acid residues in a polypeptide
chain determines the three dimensional configuration of a
protein.
• The structure of a protein determines its function.
• Generally there are four generally recognized levels of protein
structure:
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

27. 1. Primary Structure: Amino acids are linked by peptide bonds to form
polypeptide chains
• Consists of a liner sequence of amino acids linked together by peptide bonds and
includes any disulfide bonds.
• These liner sequence of amino acids in a peptide is characteristic of that protein.
• It determine other structure.

28. 2. Secondary Structure: Polypeptide Chains Can Fold into
Regular Structures (Alpha Helix and Beta Sheet)
• Two major secondary structure are α- helix and ß-strand.
1. α- helix
 Polypeptide chain twists into tightly packed rod.
• Within the helix, the COO- group of each amino acid is hydrogen
bonded to the NH group of the amino acid four residues along the
polypeptide chain.
• Generally, the alpha helix is a coiled structure stabilized by intra-
chain (the same chain) hydrogen bonds.

29. Figure: Alpha helix structure of proteins

30. 2. ß-strand
 The polypeptide chain is nearly fully extended.
• Two or more strands connected by NH-to-CO hydrogen bonds
come together to form sheets.
• A β sheet is formed by linking two or more β strands by
hydrogen bonds.
• β sheets can be purely antiparallel, purely parallel, or mixed
• Generally, Beta sheets are stabilized by hydrogen bonding
between polypeptide strands

31. Figure: Beta sheet structure of proteins

32. Tertiary Structure of proteins
3. Tertiary Structure:: Water-soluble proteins fold in to
compact structures with non-polar cores.tt
32
• It defines the overall folding of a polypeptide chain and
stabilized by (Globular vs Fibrous proteins):
1. Ionic bond (between NH3+ and COO-),
2. Weak van der Waals forces,
3. Hydrogen bonding,
4. Hydrophobic interactions and
5. Disulphide (-SS-) bridges b/n -SH groups of cysteine
• In the polypeptide chain hydrophobic side chains are buried
and its polar, charged chains are on the surface.
• Generally, water-soluble proteins fold into compact structures
with nonpolar cores.

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Figure: Tertiary structure of proteins.

34. 4. Quaternary Structure: Polypeptide chains can assemble
into multi subunit structures.
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• Proteins consisting of more than one polypeptide chain and
each individual polypeptide chain is called a subunit.
• Quaternary structure can be as simple as two identical
subunits or as complex as dozens of different subunits.
• In most cases, the subunits are held together by non-
covalent bonds.
• Generally, polypeptide chains can assemble into multi-
subunit structures.

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Figure: Quaternary structure (hemoglobin) of proteins

36. 36

37. Table: Summary of Protein Structural
37

38.  Nucleic acids are made of polymers of nucleotides.
 Individual nucleotides comprise three parts:
o Phosphoric acid:
o Pentose sugar: (deoxyribose in DNA nucleotides and ribose in
RNA nucleotides).
o Organic bases: – Adenine, Cytosine, Guanine and either
Thymine (DNA) or Uracil (RNA).
 Nucleic acid can be categorized as DNA or RNA
 The three components of a nucleotide are combined by
condensation reactions to give a nucleotide and linked with a
phosphodiester bonds.
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2.4.Nucleic Acid

39. • Genetic information is encoded by molecules called nucleic
acids.
• There are two related types of nucleic acid, deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA).
• The master copy of each cell’s genome is stored on long
molecules of DNA, which may each contain many thousands
of genes.
• In contrast, RNA molecules are much shorter, are used to
transmit the genetic information to the cell machinery, and
carry only one or a few genes.

40. • DNA and RNA are linear polymers made of subunits known as
nucleotides.
• Each nucleotide has three components:
• a phosphate group,
• a five-carbon sugar, and
• a nitrogen-containing base.
• The phosphate groups and the sugars form the backbone of
each strand of DNA or RNA.
• In DNA, the sugar is always deoxyribose.
• Whereas, in RNA, the sugar is ribose. Both sugars are
pentoses, or five-carbon sugars.
• There are four d/f nitrogenous bases in each type of nucleic
acid and their order determines the genetic information.
2.4.1. Chemical Structure of Nucleic Acids

41.  The phosphate group is joined to the sugar on either side by
ester linkages, and the overall structure is therefore a
phosphodiester linkage.
 The phosphate group linking the sugars has a negative charge.

42. • There are five different types of nitrogenous bases associated
with nucleotides.
• DNA contains the bases adenine, guanine, cytosine and
thymine.
• These are often abbreviated to A, G, C and T, respectively.
• RNA contains A, G and C, but T is replaced by uracil (U).
• T in DNA and U in RNA are equivalent.
• The bases found in nucleic acids are of two types,
pyrimidines and purines.
• The smaller pyrimidine bases contain a single ring where as
the purines have a fused double ring.
• thymine,uracil and cytosine (CUT) are pyrimidines;
and
• Adenine and guanine are purines

44. 1. The sugar in RNA is ribose but DNA contain the
sugar deoxyribose
2. DNA contain thymine where as RNA contains the
ribonucleotide of uracil.
3. RNA typically exists as a single strand, whereas
DNA exists as a double-stranded helical molecule.
4. DNA is more stable than RNA.
2.3.2. The difference between RNA and DNA

47. Inorganic biomolecules ( water and minerals)
Water
 Of the smaller molecules, water is the most abundant, typically making
up between 60-95% of the fresh mass of living organism.
 Without water, life could not exist on this planet.
 It is important for two reasons.
 First it is a vital chemical constituent of living cells, & Secondly it
provides an environment for those organisms that live in water.
 The interesting chemical & physical properties of water are due to its
small size, its polarity & to hydrogen bonding between its molecules
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48. Properties of water
 Liquid at room temperature
 Very high latent heat
 Very high latent heat of vaporization (evaporation of water
needs great deal of heat)
 Very high latent heat of fusion (much heat must be removed
before freezing occurs)
 Very high surface tension
 Very low viscosity
 High surface cohesion (water molecules adhere to surfaces)
 High surface tension (water column does not break or pull apart
under tension
 Universal solvent
 High transmission of visible light (water is colorless)
 Water as reagent
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