01 basic biochemistry chemistry of life .pdf

Basic biochemistry

1. BASIC BIOCHEMISTRY
(DPH1/2)
01 Basic Organic Chemistry
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Mutamba Oscar Necmiah

2. WHAT IS BIOCHEMISTRY?
•Biochemistry = Chemistry of life.
•The study of chemical processes within and relating to
living organisms
•Biochemists use physical and chemical principles to
explain biology at the molecular level.
•Basic principles of biochemistry are common to all living
organism
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3. HOW DOES BIOCHEMISTRY IMPACT
YOU?
•Medicine (Clinical, Pharmacy, Biomedical etc)
•Agriculture
•Industrial applications
•Environmental applications
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4. PRINCIPLE AREAS OF
BIOCHEMISTRY
1.Structure and function of biological macromolecules
2.Metabolism – anabolic and catabolic processes.
3.Molecular Genetics – How life is replicated. Regulation of protein
synthesis
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5. BASIC PRINCIPLES OF
BIOCHEMISTRY
1.Cells are highly organized basic structural units of all living
systems. Maintenance of the ordered state requires constant
energy supply
2.Precise regulation and integration of thousands of chemical
reactions is required for maintenance of life
3.Certain reaction pathways are found in all organisms
4.All organisms utilize the same types of molecules e.g. CHOs,
Proteins, Lipids and Nucleic Acids
5.Instructions for growth, development and reproduction are
encoded in @ organism’s Nucleic acids
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6. ELEMENTS OF LIFE
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Most abundant,
essential for all
organisms
Less abundant,
essential for all
organisms
Trace levels,
essential for
all organisms
Trace levels,
essential for some
organisms

7. ORGANIC COMPOUNDS &
FUNCTIONAL GROUPS
Elements
Simple organic compounds (monomers)
Macromolecules (polymers)
Supramolecular structures
Organelles
Cells
Tissues
Organisms
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➢They lead to Organization of Life

8. MANY IMPORTANT BIOMOLECULES ARE POLYMERS
Lipids ProteinsCarbohydrate
s
Nucleic acids
Monomers Fatty acids,
Glycerol, etc
Amino
acids
Monosaccharide
s
Nucleotides
Polymers/
macromolecule
s
Lipids Protein sub
units
PolysaccharidesNucleic Acids
Supramolecular
Structures
Membranes Protein
complexes
e.g Cell walls Chromosomes
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All living things contain: Carbohydrates, Lipids, Proteins and Nucleic acids

9. IMPORTANT BIOMOLECULES
These biomolecules are formed through chemical bonds
or linkages.
Biochemical reactions of the compounds involve
breaking and making of Chemical bonds.
•Chemical bonds: Attraction between two or more atoms
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10. TYPES OF CHEMICAL BONDS.
Two major types:-
(i)Ionic Bond/Electrostatic/Salt Bridge:
One or more electrons from one atom are donated to another atom,
resulting in positive and negative ions which attract each other
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❑The atoms have a large
electronegativity difference.
❑Ionic bonding commonly occurs
inmetal saltssuch assodium
chloride(table salt)

11. •Interactions between oppositely charged groups/ions in
different molecules with ionizable groups
•E.g –vely charged RCOO
-
, Cl
-
, PO
4
-
, & +vely charged H
3N
+
-
R, H
+
,Na
+
,K
+
,Mg
2+
, Fe
2+
& Fe
3+
•5 Kcal/mole strong
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12. •(ii)Covalent chemicalbonds:Involve sharing of electrons by two atoms
and the electrons bind the atoms in a fixed orientation.
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❑The electronegativity difference
between the bonded atoms is small
or nonexistent.
❑Covalent bonds most common in
organic compounds.
❑Electron sharing stabilizes the
molecules.

13. A covalent bond is formed
when electrons are shared
between atoms.
An ionic bond is formed
when electrons are
transferred from one atom
to the other.
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14. Characteristics Covalent Bonds Ionic Bonds
What is it?
•Sharing of pairs of electrons
between atoms and other covalent
bonds.
Electrostatic attraction between
oppositely charged ions in a chemical
compound.
Formation •Formed between two non-metals
that have similar
electronegativities.
•Neither atom is "strong" enough to
attract electrons from the other.
•Formed between a metal and a
non-metal.
•Non-metals(-ve ion) are "stronger"
than the metal(+ve ion) & can get
electrons very easily from the metal.
Polarity •Low •High
Shape •Definite shape •No definite shape
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15. INTERACTION IN POLAR AND NON
POLAR MOLECULES
Present in all biological structures and processes
Two main types:
(i) Covalent interactions:
-Very strong (> 100Kcal/mole) irreversible interactions at normal conditions
that lead to covalent bond formation
-Responsible for stability of biomolecules (Proteins, CH
2Os, Fats & Nucleic
Acids)
(ii) Non Covalent Interactions
❑Weak reversible interactions that include:-
(a)Electrostatic/ionic/salt bridge
(b)Hydrogen bond
(c)Van Der Waals interactions
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16. HYDROGEN BOND
H is shared between two other atoms of
higher electronegativity than H.
Can be formed between charged as
well as uncharged molecules.
May be Intramolecular
or intermolecular.
≈ 2–5 Kcal/mole.
Highly directional.
Strongest when the donor, H and
acceptor are collinear –as shown in the
fig.
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17. Hydrogen bonding is a force of attraction between a
hydrogen atom in one molecule and a small atom of high
electronegativity in another molecule.
It is usually an intermolecular force, not an intramolecular
force.
Hydrogen bonding has a very important effect on the
properties ofwaterand ice
Hydrogen bonding is also very important in proteins and
nucleic acids and therefore in life processes
The "unzipping" of DNA involves breaking of hydrogen bonds
that hold the two strands of the double helix together.
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18. VAN DER WAALS INTERACTIONS
•Weak Non specific attractive forces resulting from
temporary changes in electronic distribution around
neighboring atoms.
•Important in hydrophobic interactions of biomolecules ➔
association of non polar molecules in an aqueous (polar)
environment.
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19. HYDROPHILIC INTERACTIONS
Molecules that form hydrogen bonds with water are hydrophilic “water
loving” and those that can't bond with water are hydrophobic “water
hating”.
Hydrophilic molecules just dissolve in water, as they form H-bonds with
water molecules.
Examples
❑Proteins,
❑Carbohydrates,
❑Nucleic acids (DNA and RNA),
❑Salts (form ionic bonds),
❑Small molecules of metabolism (e.g. glucose, amino acids, ATP)
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20. HYDROPHOBIC MOLECULES
Don’t Make Hydrogen Bonds with Water
Float and don’t dissolve in water
Examples
▪fats,
▪steroids,
▪lipids,
▪aromatic compounds (such as some drugs)
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21. NON-COVALENT INTERACTIONS
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22. HOMOLOGOUS SERIES AND
FUNCTIONAL GROUPS
A functional group is an atom or group of atoms or types of
bonds which govern the chemical and physical behaviour of
molecules of the homologous series.
In Biochemistry we encounter compounds with one functional group and those
with more than one, or more than one type of functional groups
Homologous series is a series/group of structurally similar
compounds but each member differs from the proceeding
member by a constant difference e.g.-CH
2-
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23. TYPES OF HOMOLOGOUS SERIES
Homologous series General structure Functional group
Alkanes C
nH
2n + 2 -
Alkenes C
nH
2n -C=C-
Alkynes C
nH
2n-2 triple bond
Alcohols C
nH
2n+1OH Hydroxyl group
Aldehydes C
nH
2n+1CO Carbonyl group (Aldehyde)
Ketones C
nH
2nCO Carbonyl group (keto-)
Carboxylic acids C
nH
2n+1COOH Carboxyl group
Amines C
nH
2n+1NH
2 Amino group
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24. IMPORTANT COMPOUNDS,
FUNCTIONAL GROUPS
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25. IMPORTANT COMPOUNDS,
FUNCTIONAL GROUPS
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27. •Aphosphoester bondis abondbetween the phosphorous atom of a
phosphate group and an oxygen atom.
•Phosphodiesterbonds, consist of twophosphoester bondsbetween a
phosphate group and two oxygen atoms.
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28. IMPORTANT COMPOUNDS & THEIR
FUNCTIONAL GROUPS
Compounds with – OH group - ALCOHOLS
Alcohols may be aliphatic or aromatic-with a ring).
CLASSIFICATION
(a) Classification According to the number of hydroxyl (-OH) groups:-
(i) Monohydric alcohols – having only one –OH group
e.g. CH
3 - OH – Methanol
CH
3CH
2 - OH – Ethanol
CH
3CH
2CH
2 - OH – Propanol
(ii) Dihydric alcohols – have 2 – OH groups
e.g. CH
2(OH)CH
2(OH) – Ethylene glycol
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29. •(iii) Polyhydric alcohols – Have more than two – OH groups
e.g. Glycerol: CH
2(OH)CH(OH)CH
2(OH)
propane -1,2,3-triol (GLYCEROL) a very important molecule
in biochemistry of Carbohydrates and lipids.
b) Classification According to kind of carbon atom
bearing the – OH group
(i) Primary (1
o
) alcohols – the carbon with the – OH
has at least two hydrogen atoms attached to it.
e.g. Methanol, ethanol, propan – 1 – ol
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30. •(ii) Secondary (2
o
) alcohols – the C atom with the
– OH has only one hydrogen atom attached to it
•e.g Propan – 2 – ol ; carbon number 2 has only one
hydrogen
iii)Tertiary (3
o
) alcohols – the carbon atom with the – OH
group has no hydrogen attached to it (i.e attached to 3 C
atoms);
carbon number 2 has no hydrogen atom.
e.g. 2 – methyl propan – 2 – ol;
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31. PHYSICAL PROPERTIES
Alcohols with 1 -12 carbon are liquids at room temperature, with 13C – 20C
– greasy, while those with >20C are solids
Have relatively higher boiling points than corresponding alkanes due to
ability to form intermolecular hydrogen bonds (H-Bonding) because of polar
–OH groups.
Volatilization of alcohols has to overcome H – Bonding.
They are polar and highly soluble in water since they can form hydrogen
bonds with molecules of water. But miscibility decreases with increase in R.
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32. CARBONYL COMPOUNDS
Have carbonyl (>C=O ) group.
Found in aldehydes and ketones
Examples of aldehydes;
H
2CO – Formaldehyde
CH
3HCO – Ethanal (Acetaldehyde)
C
6H
5HCO – Benzaldehyde
Examples of ketones;
CH
3COCH
3 - Dimethyl Ketone (Acetone)
C
6H
5CO C
6H
5 – Diphenyl Ketone
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33. PHYSICAL PROPERTIES OF
CARBONYL CPDS
Simple aliphatic aldehydes have unpleasant smell, ketones
have a pleasant smell.
They have lower boiling points (BPs) than alcohols since the
intermolecular hydrogen bonds formed are weaker than
those formed in alcohols. However their B.Ps are higher
than those of corresponding alkanes or non-polar cpds.
Both aldehydes and ketones are soluble in water due to
the fact that they can form H – bonds with water
molecules.
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34. AMINES
•Alkyl derivatives of ammonia (NH
3)
•R – NH
2, R – NHR, R – NR
2 – purely aliphatic amines
•Ar – NH
2 , Ar – NH Ar , Ar – N Ar
2 - purely aromatic amines or R – N Ar
2
(amines with both aliphatic and aromatic organic substituents).
•Classified into 1
0
, 2
0
and 3
0
amines depending on the number of hydrogens
replaced.
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35. •Examples:-
•CH
3 – NH
2 - Methylamine , a 1
0
aliphatic amine
•CH
3–NH-CH
3 - dimethylamine, a secondary
aliphatic amine
•CH
3CH
2-N(CH
2CH
3)
2 – triethylamine, a tertiary
aliphatic amine
•C
6 H
5 –NH- C
6 H
5 – a secondary aromatic amine.
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36. PHYSICAL PROPERTIES OF AMINES
•1
o
& 2
o
amines are polar and their molecules form
intermolecular hydrogen bonds with @ other.
•Thus boiling points are higher than corresponding alkanes.
•3
o
amines do not form these bonds.
•All amines can form hydrogen bonds with water molecules
hence are fairly soluble in water
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Hydrogen bond

37. CARBOXYLIC ( ORGANIC) ACIDS
Compounds that posses –COOH group
The group has both the CARBOnyl (>C=O) and a hydroXYL(– OH)
groups hence the name carboxyl gp.
Common in metabolism:
Examples;
1. Monocarboxylic acids – have one carboxyl gp
HCOOH – Methanoic (FORMIC) acid ; an irritating liquid produced by certain ants, wasps ,
bees & plants.
CH
3COOH – Ethanoic (ACETIC) acid; substance responsible for the sour taste of vinegar, a
product of metabolism in anaerobic conditions
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38. CH
3 CH
2COOH – Propanoic (PROPIONIC) acid; found in plant & animal
CH
3 CH
2 CH
2COOH – Butanoic (BUTYRIC) acid; found in rancid butter
CH
3 CH
2 CH
2 CH
2COOH – Pentanoic (VALERIC) acid
CH
3 (
CH
2 )
4 COOH – Hexanoic (CAPROIC) acid; found in goats milk
CH
3 (
CH
2 )
7 CH=CH (
CH
2 )
7 COOH – OLEIC acid
CH
3 (
CH
2 )
14 COOH - PALMITIC acid
CH
3 (
CH
2 )
16 COOH – STEARIC acid
Note: Last three above belong to a special group of carboxylic acids called
FATTY ACIDS
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39. . 2. DICARBOXYLIC ACIDS
– have 2 -COOH groups
•HOOCCOOH – Ethane dioic (OXALIC) acid
•HOOC CH
2COOH – propane dioic (MALONIC) acid
•HOOC (CH
2)
2 COOH – Butane dioic (SUCCINIC) acid; an important
intermediate in carbohydrate metabolism
•HOOC (CH
2)
3 COOH – Pentane dioic (GLUTARIC) acid
•HOOC (CH
2)
4 COOH – Hexane dioic(ADIPIC) acid; found in beet juice
3. Tri – and poly carboxylic acids; have more than two carboxyl groups.
They are rare.
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40. PHYSICAL PROPERTIES OF ORG.
ACIDS
•Highly polar & dimerize in liquid phase and in non aqueous solvents
forming intermolecular hydrogen bonds.
•Carboxylic acids have therefore higher boiling points than corresponding alcohols
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41. •The first 4 aliphatic carboxylic acids are soluble in water due to their
ability to form intermolecular hydrogen bonds with water.
•However solubility decreases with increase in chain length.
•Benzoic acid (C
6H
5COOH) is slightly soluble in cold water but readily
soluble in hot water.
•Compare bp of water and methanoic acid, Methanol and methanoic
acid, Ethanol and Ethanoic acid
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42. COMPOUNDS WITH COMBINATIONS OF
GROUPS
1)Combination of >C=O and - OH
A carbonyl group and more than one hydroxyl groups
Compounds are polyhydroxyaldehydes/ketones
Examples
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Aldehyde
Ketone
2,3 – dihydroxy propanal
1,3,4,5,6-pentahydroxy hexan -2-one
(GLYCERALDEHYDE) (FRUCTOSE)

43. Generally they are called CARBOHYDRATES
They exhibit properties of aldehydes and ketones
They exhibit a phenomenon called optical isomerism
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44. 2) COMBINATION OF >C=O &
These are called ketoacids
Exhibit properties of carbonyl compounds and organic acids
E.g:
(PYRUVIC ACID)
PYRUVATE
Pyruvate is an end product when glucose is broken down to provide
energy during aerobic glycolysis.
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3 – oxo butanoic acid
(ACETOACETIC ACID) important
intermediate in fat breakdown
α-KETOGLUTARIC ACID
Intermediate in the TCA

46. 3.COMBINATION OF - OH &
(HYDROXYACIDS)
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2 – hydroxyethanoic acid
(GLYCOLIC ACID)
Occurs in beet root and unripe
grapes
2 – hydroxypropanoic acid (LACTIC ACID
or LACTATE)
Widely distributed, occurs in milk due to
fermentation of lactose.
It is also formed from glucose breakdown
in the body during strenuous exercises
under limited supply of oxygen.

47. •Malic acid
•A naturally occurring acid found in
many fruits, including apples, grapes,
and pears.
•A saturated dicarboxylic acid that is
involved in many biochemical
processes in the body, including the
production of energy and the
metabolism of carbohydrates.
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3(or β) – hydroxybutyric/butanoic acid
•NOTE: β – hydroxybutyric acid, acetoacetic acid and acetone are
important by-products of fatty acid breakdown after prolonged starvation.
•They are collectively referred to as Ketone Bodies.
•The brain uses these compounds as an alternative source of energy.
•Simple detection of elevated levels of ketone bodies is by the characteristic
sweet smell of acetone, emitted in a person’s breath or sweat.

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Has 6 C, 3 -COOH groups and 1-OH group
3 – hydroxy-pentane – 1,3,5 trioic acid (CITRIC ACID)
A naturalpreservative which occurs naturally incitrus fruits & also used to
add an acidic or sour taste to foods & drinks
An important intermediate in the citric acid or TCA or Kreb’s cycle.

50. 4. CPDS WITH – COOH & – NH
2
ATTACHED TO THE SAME CARBON
ATOM
Examples;
Amino acids or amino derivatives
of carboxylic acids.
To be considered in detail separately.
They also exhibit a phenomenon called optical isomerism
To be considered in detail in structural biochemistry.
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51. NUCLEIC ACIDS:-
•Molecules that contain many nucleotide molecules
•Each nucleotide molecule has a
a. nitrogenous base (purine or pyrimidine)
b.phosphate group and
c.5 carbon monosaccharide (ribose or deoxyribose) .
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52. AMIDES
•Derived from carboxylic acids by replacement of the - OH group of the
acid with an amino group
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53. ISOMERISM
Different compounds have the same molecular formula but
different structural formulae.
different physical properties (melting point, boiling point etc.).
OR may also have very different chemical properties
depending on the type of isomerism present.
Two main types: Structural (constitutional) Isomerism &
stereoisomerism
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55. STEREOISOMERISM
Compounds have same formula, same chemical bonds, but different spatial
arrangements.
I.I. Geometric (cis – trans) Isomerism – occurs in cpds in which free
rotation is impossible due to presence of double bonds or cyclic structures.
•Eg (a) FUMARIC & MALEIC ACIDS
• MP =286
0
C 130.5
0
C
• BP = 380
0
C 355
0
C
•
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(b)

57. (II) OPTICAL ISOMERISM
•Cpds have same formula, same chemical bonds, different spatial
arrangement but are not superimposable.
•Are mirror images of one another
•exist as two isomers known asenantiomers.
•Optical isomers are named like this because of their effect on plane
polarized light.
A solution of one enantiomer rotates the plane of polarization in a clockwise direction.
This enantiomer is dextrorotatory (d) & is the(+)form.
A soln of the other enantiomer rotates the plane of polarisation in an anti-clockwise
direction. This enantiomer is levorotatory (l)& is the (-)form.
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58. REACTIONS COMMON IN
BIOCHEMISTRY
•Biochemical reactions of compounds involve breaking and making of
chemical bonds.
•Involves cleavage of bonds → reactive intermediates → new bond
formation.
•Reactive intermediates may be:-
Electrophiles(e – acceptors/proton donors-acids)
Nucleophiles (e – donors/proton acceptors-bases)
❖free radicals (act as electrophiles).
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59. Free radicals and C cations are e-deficient species and in
rxns they seek extra electrons (Electrophiles).
C anions are e-rich species and in rxns they seek a proton or
some other +ve charge to neutralize their charges
(Nucleophiles).
Examples
Free radicals: -C
.
, H
.
,R
.
Electrophiles: H
+
, Br
+
, Cl
+


Nucleophiles:
-
OH, I
-
, NH
3, H
2O, ROH, RO, Cl
-
, etc.
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60. HETEROLYTIC/ HOMOLYTIC
CLEAVAGE
•Reactions may be Heterolytic or homolytic.
•Homolytic cleavages involve formation of free radicals which then combine
to form final product.
•Heterolytic reactions- Involves cleavage of bonds →
reactive intermediates → new bond formation.
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61. The most frequently encountered reactions E.g.
➢Oxidation
➢Reduction
➢Substitution rxns
➢Addition
➢Elimination
➢Rearrangement
➢Polymerisation
➢Esterification, etc
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62. 1. OXIDATION
-Addition of oxygen
-Removal of hydrogen
-Removal of electrons
•E.g.
•1
0
Alcohols→ Aldehydes→ Organic acids
•2
0
alcohols → Ketones →??
•3
0
alcohols → ??
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63. 2. REDUCTION REACTIONS
opposite of oxidation.
-Addition of hydrogen e.g. to aldehydes, C=C,
-Addition of electrons
-Removal of oxygen
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Forward reaction
Lactate is oxidized (H
removed).
NAD
+
is oxidizing agent.
Reverse reaction
Pyruvate is reduced (H added).
NADH

is reducing agent.

64. REDOX REACTIONS
▪Involve the transfer of electrons from one member
to another.
▪Involve both Oxidation and reduction rxns
▪Oxidation: a loss of electrons
▪Reduction: a gain of electrons
▪Oxidizing agent: the electron acceptor
▪Reducing agent: the electron donor
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65. •In Biochemistry redox reactions are usually
recognized by the following changes:
• Oxidation occurs when a molecule loses two
hydrogens and/or gains an oxygen.
• Reduction occurs when a molecule gains two
hydrogens and/or loses an oxygen.
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66. 3. CONDENSATION
•Small molecules (monomers) are joined to build
macromolecules by the removal of water.
•H from one atom and OH from the other combine to form
water.
•E.G. Sucrose (a sugar) can be produced by a condensation
reaction of glucose and fructose (glycosidic bond).
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67. 4. HYDROLYSIS
•Macromolecules are broken down into smaller
molecules.
•Reverse of condensation (above).
•Water cleaves (splits) a covalent bond and inserts
itself.
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68. 5.ESTERIFICATION
•– rxn between an alcohol & acid to form an ESTER Bond found in esters
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69. SUBSTITUTION RXNS
•– one atom or gp of atoms substituted by another
•e.g. –OH in alcohols with a halogen
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CH
3
CH
2
CH
2
CH
2
–OH + HBr CH
3
CH
2
CH
2
CH
2
–Br+ H
2
O

70. 7. ADDITION:
▪two molecules combine to give one. One molecule usually has
multiple bonds.
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O
OC
O
C
C
H
H
OC
O
OC
O
C
CH
2
HOH
+H
2
O
Addition occurs at Multiple bonds like C=C, >C=O, >C=C<

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73. 10. POLYMERIZATION
Monomers form
polymers through
condensation –
this is
polymerization
Polymers are
broken down
through hydrolysis.
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