Transcript Lecture #3 - Suraj @ LUMS

Lecture 3
Chemicals of Life
Biochemistry
Content
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Elements
 Chemical Bonds
 Acids, Bases, Salts, pH and buffers
 Organic chemistry
 Water
Elements-1
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All matter is composed of varying amounts of
about 106 elements.
An element is a substance that cannot be split into
a simpler substance by chemical means e.g
carbon, nitrogen, and oxygen
Each element has its own unique properties.
The smallest particle of an element is an atom.
Elements combine to form compounds.
All matter is composed of atoms,a molecule is a
combination of atoms.
The Periodic Table
1 2 3 4 5 6 7 8
1 2 3 4 5 6 7 0
The Periodic Table is the collection of all known elements,
they are organized into groups based on shared properties
according to their atomic number.
Elements - 2
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Life requires 25 of the 106 elements
96% living things made of O (oxygen), H (hydrogen), C
(carbon) and N (nitrogen).
4% Ca (calcium), P (phosphate), K (potassium), and S
(sulphur).
Trace elements
Atom, elements, compound a substance of two or more
elements, atoms linked by chemical bonds e,g water H2O,
table salt NaCl, carbon dioxide CO2
Atomic Structure
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Made up of the following particles.
Particle
Location
Mass
Charge
Proton
Neutron
Electron
central
core
orbits
1 unit 1.7x10-24 g
1 unit
1/1870 unit
+1
0
-1
Atomic number represents the no. of protons in an
element
 Mass number the number of protons + neutrons
 Isotope atoms of elements with different no. of
neutrons.
Atomic Structure - Example
20p
20n
Calcium = Ca
Atomic no. = 20
Mass no. = 40
Electrons = 2, 8, 8, 2
6p
6n
Carbon = C
Atomic no. = 6
Mass no. = 12
Electrons = 2, 4
Chemical Bonds
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Electrons arranged in shells around nucleus:
–
–
–
–
–
1st shell 2 electrons,
2nd shell 8 electrons,
3rd shell 8 electronss,
4th shell 18 electrons,
5th shell 32 electrons.
Outer shell complete set of electrons – unreactive.
 Tendency is to try and obtain a full set of electrons
through reaction with other elements.
 Two types of interactions or bonds can be formed:
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– Ionic bonds
– Covalent bonds
Ionic Bonding - 1
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A transfer of electrons from one atom to
another.e.g
Sodium
Na
11 electrons (2,8,1)
11 protons
10 electrons
11 protons
Na+
Cation
+
+
Chlorine
Cl
17 electrons (2,8,7)
17 protons
18 electrons
17 protons
ClAnion
Ionic Bonding - 2
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Resulting compound is sodium chloride NaCl.
Compounds from the transfer of electrons are
called ionic compounds
Usually when metal reacts with a non-metal
The metal produces a cation and the non-metal an
anion.
The number of electrons transferred (loss/gain) is
the valency of the element.e.g Na and Cl have a
valency of 1 this is usually shown for ions Na+ Cl-
Covalent Bonding - 1
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Electrons are shared
 E.g 2 Chlorine atoms, each has 7 electrons
in outer shell.
 Each atom contributes an electron making a
Chlorine molecule (Cl2), covalency of 1.
Cl
Cl
Structural Formula
Cl Cl
Covalent Bonding - 2
Methane, CH4
Ethene, C2H4
H
H
C
H
C = 2, 4
H=1
H
H
H
C
H
H
H
H
C
H
C
H
Acids and Bases
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Hydrogen ions in a aqueous solution, H+
An acid is a substance that can act as a proton donor in an
aqueous solution.
When it completely dissociates into its constituent ions in
water you get a strong acid.
When a small proportion of the hydrogen ions dissociate a
weak acid is produced.
A base is a substance that reacts with an acid to form a salt
and water only, it is a hydrogen acceptor.
Most bases are insoluble in water, when they do dissolve
they produce a alkalis. E.g sodium hydroxide
pH
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The acidity and alkalinity of a solution is related
to the concentration of hydrogen ions in the
solution.
The pH is defined as the log to the base of 10 of
the reciprocal of the hydrogen ion concentration.
Pure water contains 1x10–7 moles of H+ /L
pH of water therefore log (1x107) = 7
A pH of 7 = neutral solution < = acid > = alkali
Range 0-14
Buffers
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Mixture of a weak acid and its soluble salt
Resists changes in pH.
If acidity increases the free anion from the salt
will mop up any free hydrogen ions.
If acidity decreases hydrogen ions released by the
anion.
Low pH
E.g HPO4 2- + H+
H2PO4High pH
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Proteins act as buffers and they are particularly
important in blood.
Organic Chemistry
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Organic chemistry based on the element
carbon.
 Organic compounds are usually defined as
containing carbon and at least one hydrogen
atom.
 Living organisms primarily composed of
organic molecules e.g carbohydrates.
Carbon
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Small atom with low mass.
Able to form strong covalent bonds.
Carbon atoms can join each other to form rings or
chains.
Very strong bonds hence very stable molecules.
Has the ability to form multiple covalent bonds with
other carbon atoms, oxygen and nitrogen.
Variation in organic molecules occurs through:
– Size (no. of carbon atoms)
– Chemistry (elements or functional groups attached to carbon atoms)
– Shape (angles of the bonds formed)
Functional Groups
Hydroxyl
Carbonyl
OH
C=O,
if oxygen on outside it is an aldehyde
if oxygen on the inside it is a ketone
Carboxyl COOH, the hydrogen tends to dissociate from
oxygen to produce organic ion and H+ ion
Amino
NH2
amines
Sulfhydrl SH
forms disulfide bridges in proteins chains
contribute toward function as enzyme
Phosphate (PO4)3 important in metabolism and information
storage
Methyl
CH3
Isomers
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The same atoms can often be arranged in various ways to form
compounds with different chemical properties.
Compounds that have the same molecular formulae but different
structures are known as ISOMERS.
There are 3 types:
1.
2.
Structural – differ in relationship between atoms in molecule
Geometric – atoms bonded to same partners but arranged differently
around double bond.
3.
Stereoisomers – mirror image
Stereoisomers- one active form one inactive, most sugars right
handed (D-sugars), left handed can be made commercially.
Human enzymes that break down sugars do not recognise Lsugars, but taste buts do. They are used as a sugar substitute,
where they produce sensation of sweetness not metabolised
hence do not contribute to weight gain.