Introduction to biochemistry

Biochemistry

Biochemistry is the study of life cyclic processes in

terms of chemicals.

 It obtains information from the basic microorganisms

viz., bacteria, viruses, algae and fungi.

 It draws information on energetics from basic

thermodynamics.

 It couples them to show a path how life cycle

proceeds with the mutual cooperation of various
activities of the living beings.
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Biomolecules
 Biomolecules are the building blocks of the cell.

 They help in storing and releasing energy for biotransformations.

 They include
 Carbohydrates
 Lipids
 Proteins
 Nucleic acids

 Living organism contains a large number of biomolecules.

 Contain C, H, O, N

 eg. The bacteria which are the smallest cells contains 3000 kinds of
proteins,1000 kinds of nucleic acids.

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Elements present in biomolecules
Lipids - Primarily C, H and some O

Carbohydrates – C, H, O in a 1:2:1 ratio

Proteins – C, H, O, N

Nucleic Acids – C, H, O, N, P

Component % of t he total
cellular mass
Water 70-90
Proteins 10-15
Carbohydrates 3
Lipids 2
Nucleic acids 5-7
Ions 1
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Macromolecules
 A macromolecule is a molecule composed of a very large number
of atoms.

 But generally the use of term is restricted to molecules of more

than 100 atoms, and in particular to polymers.

 Many examples come from biology and in particular

biochemistry.

 These include proteins, starches, and nucleic acids (such as DNA),

which are sometimes called "biomacromolecules"

 Polymers: long molecules built by linking together small, similar

subunits (monomers)

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6 Biological molecules
Polymerisation process
 Monomers are made into polymers via dehydration reactions
 Polymers are broken down into monomers via hydrolysis
reactions

a. Dehydration synthesis
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Carbohydrates
 Carbohydrate are poly-hydroxyaldehydes or polyhydroxyketones
and their derivatives.

 Composing elements C, H, O.

 Hydrogen and Oxygen are in a ratio of 2:1.

 They have a general formula Cx(H2O)y

 Classified as
 Monosaccharides
 Oligosaccharides(di-and tri-saccharides).
 Poly-sacchrides

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 Groups of Carbohydrates

Carbohydrates

sugars

Monosaccharides Disaccharides Polysaccharides

(monomers) ( Dimers) (polymers)

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 Carbohydrates (or sugars)
Monosaccharides (C6H12O6
• Simple sugars (monosaccharides)
• Only one 3-C, 5-C, 6-C chain or ring involved

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 Monosaccarides are soluble in water and insoluble in non-polar
solvents.

 Various other monosaccharides based on the number of carbon atoms

are shown in the following table.

No. of C atoms Generic name of Examles

monosaccharide
3 Trioses Glyceraldehyde,
dihydroxyacetone
4 Tetroses Erythrose
5 Pentoses Rabinose, xylose,
ribose, rhmnose
6 Hexoses Glucose, galactose,
fructose, manose

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Epimers are defined as the sugars which have the same chemical
formula and structure except around one specific carbon atom.

Example: D-glucose and L-glucose are epimers with respect to

carbon atom2

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Disaccharides
Disacchrides are anhydrides of two monosaccharides.
Ex:
 Lactose: glucose + galactose
 Maltose: glucose + glucose
 Sucrose: glucose + fructose

sucrose 14
Condensation to form Disaccharides

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Polysaccharides
 Polysaccharides are also known as glycans.

 They are anhydrides of one or more monosaccharides in

which a large number of units are combined.

 Homopolysaccharides posses one repeating unit.

 Heteropolysacchrides contain more than one monosaccharide unit.

Eg: Starch, Cellulose, Glycogen, Chitin

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Importance:
 Energy storage: sucrose is a store of energy in sugarcane and sugar
beets
 Energy transport: carbohydrate is transported in plants as sucrose.
 Functions of carbohydrates include:
 serving as precursors for building many polymers
 storing short-term energy
 providing structural building materials
 serving as molecular "tags" to allow recognition of specific cells and
molecules

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Protein
 Proteins are polypeptides. They are linear chains of amino
acids linked by peptide bonds.
 Each protein is a polymer of amino acids.
 As there are 20 types of amino acids (e.g., alanine, cysteine,
proline, tryptophan, lysine, etc.,

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Protein
 Protein is a heteropolymer.

 A homopolymer has only one type of monomer repeating ‘n’

number of times.

 C,H,O,N and some have S. (a few might also have P due to addition of P in
modification process but P is not a component of amino acids)

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Peptide bonds occur between amino acids
The COOH group of 1 amino acid binds to the NH2 group of
another amino acid to form a peptide bond. 21 21
20 different amino acids

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Fig. 3.21

Protein structure

The chain (polymer) of amino acids forms a variety of loops, coils, and folded sheets
from an assortment of bonds and attractions between amino acids within the chain(s)
 Shape of proteins are important because
 This determines how they interact with other molecules
 This determines their particular function 25
 There are four levels of protein structure
• Primary = sequence of AA’s
• Secondary = forms pleated
sheet, helix, or coil
• Tertiary = entire length of AA’s
folded into a shape
• Quaternary = several AA
sequences linked together

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Importance of proteins

 They are considered to be the beginners and builders of

biochemical reactions.

 They occupy a central position in the construction and functioning

of living matter.

 All enzymes are proteins and they catalyse biochemical reactions.

 They help in the transport of oxygen into blood, transmission of

nerve impulses, etc.

 Protein constitute a major part of the animal tissues.

 Some proteins transport nutrients across cell membrane, fight

against infectious organisms
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 Lipids
 Lipids are a class of compounds which are fatty/oil in nature and
present in all cells and tissues.

 Lipids include various biomolecules whose common property is

their insolubility in water.

 Composing elements C, H, O
 Include:
 fats
 oils
 Waxes
 Phospholipids
 steroids: sex hormones and cholesterol
 some vitamins
 glycolipids (lipids with carbohydrates attached)

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 Lipid structure
 Most lipids are composed of a glycerol molecule with attached
fatty acids

GLYCEROL FATTY ACIDS

Fatty acid
Glycerol

Fatty acid
Triglyceride
Fatty acid

Phospholipid GLYCEROL
HYDROPHOBIC END

Fatty acid
Glycerol

Fatty acid

PO4
FATTY ACIDS
HYDROPHYLIC END 30
Saturated fatty acids

Their fatty acids

 have no double bonds between carbon atoms(have maximum number of
hydrogen atoms)
 Straight structure
 Unhealthy fats usually from animal sources
 Solid at room temperature(20°C)
 Eg- lauric acid, myristic acid, palmitic acid, stearic acid, etc.

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Unsaturated fats

Their Fatty acids have:

 Have some carbon atoms that are double bonded(not fully
hydrogenated)
 Kinked in shape
 Healthy
 From plant sources
 Liquid at room temperature (20°C)
 Eg- palmitoleic acid, oleic acid, elaidic acid , linoleic acid, linolenic
acid, etc.

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 Saturated vs unsaturated fats and diet
• The saturated acids end in –anoic, e.g., octadecanoic acid for 18-carbon
saturated fatty acid and unsaturated acids end in –enoic acid, e.g.,
octadecenoic acid.

• Saturated fats raise LDL-cholesterol levels in the blood (animal fats, dairy,
coconut oil, cocoa butter)

• Polyunsaturated fats leave LDL-cholesterol unchanged; but lower HDL-

cholesterol (safflower and corn oil)

• Monounsaturated fats leave LDL and HDL levels unchanged (olive oil,
canola, peanut oil, avocados)

• One variety of polyunsaturated fat (Omega-3 fatty acids) guards against

blood clot formation and reduce fat levels in the blood (certain fish,
walnuts, almonds, and tofu)

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Forming a triglyceride
 Unlike other classes of biomolecules, lipids do not form large
polymers
 Two or three fatty acids are usually polymerized with glycerol, but
other lipids, such as steroids, do not form polymers.

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 Phospholipids and cell membranes
• P-lipids make up the majority of cell membranes including:
– The plasma membrane
– Nuclear envelope
– Endoplasmic reticulum (ER)
– Golgi apparatus
– Membrane-bound vesicles

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 Importance; Biological Role

 Used to store energy (approx 36 kj/gram)

Mitochondrion
(false color TEM)

Fat cell

Lipids are often stored in special

adipose tissue, within large fat cells
Lipids are concentrated sources of energy and can be
broken down (through fatty acid oxidation in the
mitochondria) to provide fuel for aerobic respiration

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Importance; Biological Role

 Water proofing of some surfaces

 Transmission of chemical messages

via hormones

Waxes and oils, when

secreted on to
surfaces provide
waterproofing in
plants and animals.

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 Importance; Biological Role

 An important structural component of membranes

Phospholipids are the primary structural component

of all cellular membranes, such as the plasma
membrane (false color TEM above).

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Importance; Biological Role

 acts as a shock absorber and good insulator

The white fat tissue (arrows) is

visible in this ox kidney

Fat absorbs shocks.

Organs that are prone to
bumps and shocks (e.g.
kidneys) are cushioned with
a relatively thick layer of fat.
Stored lipids provide insulation
in extreme environments.
Increased body fat levels in
winter reduce heat losses to the
environment.
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Importance of lipids

Lipids perform many important functions in biological systems, including:

 contributing to the structure of membranes that enclose cells and cell compartments
 protecting against dessication (drying out)
 storing concentrated energy
 insulating against cold
 absorbing shocks
 regulating cell activities by hormone actions

Steroids function both as hormones (such as the sex hormones estrogen and testosterone)
and as structural material (such as cholesterol, an integral part of animal cell membranes).

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Nucleic Acids
 Nucleic acids are the polymers of nucleotides, which can store
genetic information in each cell.

 Composing elements: C, H , O, P, N.

 Nucleic acids are built from subunits called nucleotides. Each

nucleotide has three components:
 a ring-shaped molecule belonging to the class of purine or pyrimidine
bases
 a 5-carbon, or pentose, sugar
 one or more phosphate groups

eg :Deoxyribonucleic Acid (DNA)

Ribonucleic Acid (RNA)

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Nucleic Acids

 These molecules are responsible for all of our genetic

information.

 There are 5 different types of nucleotides in the cell;

 Adenine
 Thymine
 Guanine
 Cytosine
 Uracil.

 The bonds that form between nucleotides are called

phosphodiester bonds.

 Nucleotides as ATP is the energy currency of the cell.

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There are two types of nucleic acids:

Deoxyribonucleic acid (DNA), which serves as a cellular database

by storing an immense amount of information about all the
polypeptides a cell can potentially make.

Ribonucleic acid (RNA), which occurs in several different forms

(messenger RNA, ribosomal RNA, transfer RNA) and is needed to
convert DNA information into polypeptide sequences; in some
viruses, RNA serves as the primary database with no DNA
involvement; certain RNAs have catalytic ability similar to that of
protein enzymes called ribozymes.

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DNA and RNA

• DNA = deoxyribonucleic acid

• DNA is a double polymer (chain)
• Each chain is made of nucleotides
• The 2 chains bond together to form
a helix

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Fig. 3.14

One polymer of nucleotides on one “backbone” of nucleic acid

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Fig. 3.15

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Functions of nucleic acids

 The main function is to store and transfer genetic information.

 To use the genetic information to direct the synthesis of new

protein.

 DNA controls the synthesis of RNA in the cell.

 RNA also directs the production of new protein by transmitting

genetic information to the protein building structures.

 The function of the double helix of the DNA is that no disorders

occur in the genetic information if it is lost or damaged.
 Thank you

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