Biochemistr

:Definition

Biochemistry is defined as the science which deals with

the chemical molecules and chemical processes and
. chemical reactions occurring in living cells

:I ms of studying of biochemistry

To study the structure , composition and chemical

:reactions of substances in living system by

. Isolation of molecules found in these cells -1

. Determine their structures -2

. Analyze how they function -3

Sciences to which biochemistry has a contribution -

: include

Microbiology-1

Immunology-2

Pharmacology-3

Toxicology-4

Pathology-5

Physiology-6

Biochemistry studies contribute to

. Diagnosis of diseases-1

.Treatment of diseases-2

.Preventation of diseases-3

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:Examples

A)Nucleic acids Genatic disease

B)Proteins Sickle cell ( anemia )

C)Lipids Arteriosclerosis

D)Carbohydrates Diabetes mellitus ( D.M )

:Bio molecules present in living cells

They are two types of molecules

A)Monomers : are smaller micro molecules that are put

together to make macro molecules examples: amino acids
., nucleotides , fatty acids and monosaccharide

: B)Macromolecules (polymers)

They are created when monomers are combined together -

by process called dehydration synthesis , ( also
called condensation reactions )

A molecule of water is removed from two monomers as -

.they are connected together to form the polymer

:Macro molecules present in living cells

Proteins 3-Lipids -1

Carbohydrate 4-Nucleic acids -2

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:A)Proteins

monomers: amino acids-

proteins have many functions within the cell membrane -

.structure , enzymes, ion channels and transporters

.e.g. enzymes and hormones

:B)Carbohydrates

monomers : monosaccharide-

e.g. starch , glycogen, cellulose-

.source and storage of energy and structural support -

:C)Lipids

monomers : fatty acids-

.e.g. : phospholipids and steroids-

. used as energy source and storage-

: D)Nucleic acids

monomers : nucleotides-

e.g.: RNA and DNA-

Genatic material which carries instructions for growth and -

.reproduction

:Organization of life depends on

Elements-1

Simble molecules-2

Macro molecules-3

Super molecular structures-4

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Cells-5

Tissues-6

Organs-7

Body-8

:Elements of life

.Elements are pure substances-

They are arranged in rows and columns based on their -

.properties

.Only 25 elements are essential to life -

:Atoms

Atoms are smallest particle of an element that has the -

.element's properties

(-) = electrons

(+) p= proton

n= neutron (o)

.Electrons used to form bonds with other elements -

:Example

:NaCl

Na23 (2,8,1) loses Na+ (2 ,8 ) 11

of 1

Cl35 (2,8,7) gains Cl- (2,8,8 ) 17

an electron

. Atoms bond with other atoms to become more stable -

make up 96% of living ( C , H , O , and N)-

.matter

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The remaining 4% consist of ca, p , k , Na , Cl , Mg -
.and S

Trace elements are those required by an organism in -

.minute quantities

Element Percentage of Human Body

Weight
O 65,0
C 18,6
H 9,5
N
Ca 1,5
P 1,0
K 0,4
S 0,3
Na 0,2
Cl 0,2
Mg 0,1
: Traceelements (less than 0.01% )

Boron ( B ) , Chromium (Cr ) ,Cobalt ( Co ), Cupper (Cu ) ,

Fluorine ( F ) ,Iodine( I ) ,Iron ( Fe ) , Manganese ( Mn ) ,
Molepednum ( Mo ) ,Selenium ( Se ) , Silecon (Si ) , Tin (Sn
.) , Vanadium ( V ), and Zinc ( Zn )

: Compounds-

They are combinations of elements-

Organic compounds : ( e.g.,: CH4 , CH3CH2OH)-

Inorganic compounds : (e.g. : NaCl )-

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: Electro negativity and polarity

: Electro negativity

It is ability of atom to attracted of electrons which bonded

. with other atom toward it

The more electronegative atom has slightly more negative

.charge ( more electron density )

Some of atoms that have high electro

: negativety

F>O>N = Cl > Br > S > C > H > metals

; Example

HF , CH3- C = N

N.B
The bond between two different atoms called polar -
bond , except the bond between ( C, H ) in
hydrocarbons such as : alkane called non polar
.bond
: Examples
O
HF , H C =N , CH3- C O H ,
CH3 CH3

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 The bond between two atoms (non metals ) have -
equally electronegativity called non polar covalent
. bond

: Examples

H-H , O =O , N=N ( symmetrical molecules )

N. B

Any compound contains of fanctional group called polar -

.compound
e.g : CH3 OH , CH3 NH2 , H2O , NH3

..CH3 COOH , CH3CH2 F

Except any compound contains ( C , H ) only such as

. alkane , alkenes , alkynes called non polar compounds

CO2 non polar compound it has equall attraction of bond -

electrons

O=C=O

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 : Chemical Bonds

Bonding is the joining of two atoms in stable -

.arrangement

Bonding is favorable process because it lowers energy -

.required and increases stability of atoms

: Types of bonds-
. Ionic bonds-1

.Covalent bonds-2

: A)Ionic Bonds ( non covalent bond)

Ionic bonds result from the transfer of electrons from one -
.element to another

Atoms lose or gain electrons to form charged -

.particles ( ions )

Ionic bonds form when one atom ( positively charge ) -

gives one or more electrons to another atom( negatively
.charged ) to complete their outer energy levels

There is strongly attractive between opposite charges -

.( electrostatic attractive)

In ionic bind two atoms bonded together have -

.large electronegativity difference

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 . Ionic bond occurs between metal and nonmetal -

Ionic bond present in salts such as ; NaCL , CaCO3 ,

Na2CO3

:Example

NaCl

Na loss of an 1 Na+
-
e + Cl Gain of an 1e Cl

Na+ + Cl- combination NaCl compound

:B)Covalent bonds
Covalent bond result from the sharing of electrons -
.between two atoms

Atoms can share one or more than one between them -

.forming single , double and triple bond

: Example

O=O N=N
single bond double bond
triple bond H-H

: Types of covalent bonds

: Pola covalent bond -1

Occurs between unequal attraction of bond
.electrons , due to difference in electronegativity
: e.g
H Cl , H - C =N , NH3 , H 2O

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 ; Non covalent bond -2
Equal attraction of bond electrons ( they have
same electronegativity)
e.g ; H H , FF, O =O , N=N

:Chemical interaction

They are interactions exist between molecules (inter -

molecular forces)

:Types of interactions

.Vandderwaals forces-1

.Dipole-Dipole interaction-2

.Hydrogen bonding-3

:Van der waals forces -1

Van der waals forces are very week interactions caused -

by the momentary changes in electron density in the
molecules

or

caused by slight charge displacements and form

.induced dipole

Van der waals forces are the only attraction present-

between

non polar compounds i.g. (hydrocarbons)

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 Example : CH4 , CH3 - CH3 , CH=CH2

Bonding points increase with increasing of number of -

.carbon atoms

Example: CH3CH2CH3 > CH4

Dipole -Dipole -2 ;
forces
:
Dipole Dipole interactions occurs between the -
.permanent dipoles of two polar molecules

Dipole - Dipole interaction are much stronger thane week -

.vanderwaals forces

:Examples

acetone C3H6 ( CH3 - C - CH3 )-1

C3H6O > CH3CH2CH3 -2

.Higher b.p

:Hydrogen bonding -3

Hydrogen bonding occurs when a hydrogen atom bond -1

.to ( O , N or F ) atom in another molecules

e.g

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 O

H H. O H

Hydrogen bond

Any compound has ( O H or N H or NH2 ) can-

. formation hydrogen bonding with other molecules

e.g : CH3 - O-H , CH3 - COOH , CH3- NH2

According to the increasing of polarity , boiing -3

points and type of force

Hydrogen bond > dipole-dipole > van der waals

: Example

CH3CH2OH > CH3 O CH3 > CH3CH2CH3

Hydrogen bonds are still much weaker than any-4

.covalent bond

; Other forces between molecules

Electrostatic bonds
Result from the electrostatic attraction between-
two ionized groups of opposite charge such as
carboxyl ( - COO- ) and

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 amino ( - NH3 +
)

:Hydrophobic interaction -
Cause non polar groups such as hydrocarbons -
chains to associate with each other in an aqueous
. environment

Chemical equations
Reactants products

Chemical equation are simple way of showing chemical -

.reaction

A catalyst is a substance that speeds up the rate of -

.reactions

:Balancing equations

The number of atoms on the left side of the equation has -

to be equal to the number of atoms on the right side of
.the equation

:Example

4Na + O2 2Na2O

:Types of chemical reactions

:Synthesis or addition reactions -1

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Two or more simple substances combine to form a single -
.new substance

A+B AB (anabolic reaction , need energy )

:Examples

C + O2 CO2

S + O2 SO2

:Decomposition or elimination reactions -2

.One substance breaks down into two or more products -

Synthesis and decomposition reactions are exactly -

OPPOSITE

A-B A + B (catabolic reaction gives energy )

:Examples

2H2O2 O2 + 2H2O

H2SO4 H2O + SO3

:Substitution or replacement reactions -3

Substitution is a reaction in which an atom or group of -

.atoms is replaced by another atoms or group of atoms

In the replacement reaction a compound reacts with -

.another compound to form two new compounds

AB + CD AD + BC

:Examples

AgNO3 + NaCl AgCl + NaNO3-1

HCl+ NaOH NaCl + H2O-2

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 : Organic chemistry
Organic chemistry is the study of compounds that -1
.contain carbon

e.g : CH3 CH3 , CH3OH , CH3 CH2CH2NH2

Carbon atom conform four covalent bonds with a-2

variety of atoms

C6 1S2 2S2 2P2

Hydrocarbons: are organic molecules consisting of only -3

.carbon and hydrogen they may aliphatic or aromatic

:Examples

CH3 CH2CH2CH3
aliphatic

:Functional groups-4

A functional groups an atom or group of atoms with -

.characteristic chemical and physical properties

.The functional group is the reactive part of the molecule -

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The properties of the major classes of organic compounds -
(carbohydrates , lipids , proteins and nucleic acid ) are
.determined mostly by their functional groups

Alkanes have ( C - C ) and ( C - H ) bonds so they have no -

. functional group , i.e. it have no reactive site

Alcohols have (OH) group as a functional group , so -

alcohol has polar group that makes it reactive and
.hydrophilic ( water soluble )

:The importance of functional groups

.Bonding and shape-1

.Type and strength of intermolecular forces -2

.Physical properties-3

.Nome clature-4

.Chemicla reactive-5

There are seven functional groups that are most

: important in the chemistry of life

Hydroxyl group (OH)-1

O
2-Carbonyi group ( C )

O
3-Carboxyl group ( C O H)

Amino group ( NH2 )-4

Sulfhydryl group ( SH )-5

Phosphate group ( PO4-2 )-6

Methyl group ( CH3 )-7

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 : hydroxly groups -1

Molecules have hydroxyl group are called alcohols ( C O -

H)

Their specific name names usually end in (-ol ) -

: Examples

CH3 OH (methanol )

CH3CH2CH (ethanol )

It is polar( water soluble)-

Hydroxyl group can form hydrogen bond with (H2O)-

.molecules and dissolve in water

groups found in carbohydrate and other many (OH)-

.cellular compounds

O
: 2-Carbonly (- C - )

O O
-Ketone ( R C R ) and aldehyde ( C H ) contain
.carbonyl groups

Ketones and aldehydes compounds differ in physical-

.and chemical properties

group is polar and contributes in making (CO)-

molecules water Soluble

.All sugar molecules have one carbonyl group

: Examples of aldehydes and ketones

O O
CH3 C CH3 CH3CH2 C H

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 acetone

propanal

: Carboxyl group ( - COOH ) -3

O
- ( C OH ) has both carbonyl and hydroxyl group attached
.to the same of carbon atom

Carboxyl group acts as an acid and can donate a proton -

.(H+)

.Carboxyl group dissociates partially into ( H +) and (Coo-)-

Found in cells in the ionized form and called a carboxylate -

.ion. (Coo- )

.Carboxyl groups including in amino acids and fatty acids -

O O
+
COH CO +H
-

Non ionized Ionized

: Amino group ( NH2) -4

The amino group consists of a nitrogen atom bonded to -

.two hydrogen atoms and to the carbon skeleton

Molecules containing amino groups are called amines ( R -

. NH2 )

Amino groups are basic and often become ionized by -

.addition of (H+) to form ( NH 3+ )

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 .Found in cell in the ionized form-

Found in amino acids , proteins and other N containing -

.compounds

:Examples

H
-Glycine H 2N C C OOH
H

H
-Alanine 2HN C COOH
CH3

H+
N H + H+ N H
H H

Non ionized ionized

:Sulfhydryl group ( S H ) -5

.Their specific names usually end in ( -thiol) -

:Examples

CH3 S H ( methane thiol )

Two sulfhydryl groups can interact to form a disulfide-

.group ( symbolized as S S )

.group is polar ( S H )-

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In some amino acids and proteins, sulfer is present in the -
form sulfhydryl groups or disulfide groups which
.help stabilize protein structure

:Examples

:Phosphate group ( PO4-2) -6

Compounds containing phosphate group are called -

.organic phosphatase

Phosphate group acts as an acid and can donate -

.two (H+)

Molecules containing phosphate groups have the -

.potential to react with water

Phosphate groups are found in phospholipids ,-

. A.T.P , A.D.P and nucleic acids

O O
R O P O H R O P O - + 2H+
-OH O

Non ionized

Ionized

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 :Methyl group ( CH3 ) -7

.Methyl group non polar ( hydrophobic )-

. Found in lipids , other membrane component -

: Examples

methylbenzene

:other functional groups you should know

O
RCOR RO
R

Ester
ether

:Examples

O
CH3 C O CH2CH3 CH 3 CH2 - O-
CH3

ethyl ethanoate ethyl methyl

ether

O O
CH3 C NH2 R C NH 2

ethanamide amide

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 Identification of functional groups in compounds

Alkanes: ( C-1
C)

Saturated hydrocarbons, they have only single -1

.bond

Alkanes contain straight or branched chains of carbon -2

.atoms and cyclic

:Examples

CH3
CH3CH2CH2CH3
CH3 C CH2 CH3

un branched
branched

.Alkanes have general molecular formula ( CnH2n+2 )-3

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 n= Number of carbon atom

:Some of alkanes-4

Methane CH4

Ethane C2H6

Propane C3H8

Butane C4H10

Pentane C5H12

Hexane C6H14

Heptane C7H16

Octane C8H18

Nonane C9H20

Decane C10H22

:Nomen cloture of alkanes

:Using the (IUPAC ) system

Choose the longest carbon chain in the molecule (parent -1

.chain)

:Example

CH3
CH3 CH2 C CH2 CH3
H

Identify the substituent groups attached to the parent -2

.chain

:Example

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 CH3 Cl CH2CH3
CH3 C -------- C ------- C ------ C CH3
H H H Br

Number the longest chain in the direction that -3

gives the lowest number to the substituent group
.at the first point of the branching

:Example

Cl
1- CH3 CH2 CH2 CH2 CH3
1 2 3 4 5

C hloro Pentane 2

Br CH3
2- CH3 C CH2 C CH2 CH3
H H
1 2 3 4 5 6

B romo 4 methyl hexane 2

When the same substituent appears more than once , -4

.. use the multiplying prefixes, di , tri , tetra , penta

:Example

Cl Cl
CH3 C C CH2 CH3

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 Cl H
1 2 3 4 5

tri chloro pentane 3 , 2 , 2

When two or more different substituents are present , -5

.they are listed in alphabetical order in the name

:Example

Br CH3
1- CH3 C CH2 C CH3
H H
1 2 3 4 5

B romo 4 methyl pentane 2

Br CH3 Cl
2- CH3 CH CH2 C CH CH3
H
1 2 3 4 5 6

Bromo 2 Chloro 3 methyl hexane 5

:Propenteis of alkanes

Alkanes contain only ( C C ) and ( C H ) so they have-1

.weak vander waals forces

Non polar alkanes are insoluble in H2O and soluble-2

.in organic solevents, ie. CCl4 , C6H6

Melting point and boiling point increase with the -3

.increase in number of carbons

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 :Example

CH3CH2CH2CH3 > CH3CH3

Higher b.p

M.P and b.p decrease with increase of the number of -4

.branches

:Example

CH3 CH 3
CH3 C CH2 CH3 > CH3 C CH3
Higher b.p H CH 3

5C , contain one branche 5C, contains two

branches

Alkanes have no reactive part ( have no function groups) -5

:and undergo few reactions

Combustion-1

Hologenation-2

Pyrolusis (cracking)-3

:A)Combustion

they burn in presence of oxygen to form carbon dioxide -

.(CO2) and water

CH4 + 2O2 CO2 + 2H2O + heat (energy)

:B)Hologenation

Alkanes react with the (Cl2 , Br2 ) at high temperature to-

.yield chlorinated and brominated alkanes

:Example

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 CH4 + Cl2
CH3Cl + HCl

:C)Pyrolysis (cracking)

Cracking is process that splits long chain alkanes at high -

.temperature into shorter chain alkanes and hydrogen

Alkanes 400 600 CO smaller alkane + alkanes + H2

Alkenes: ( C = C )-2
General molecular formula (CnH2n)-

Trans more stable cis-

C C
C C

Cis 2 butene Trans 2 butene

Alkynes: (C C )-3

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 General formula (CnH2n -2 )-

Example: CH3 C C CH3 , H C CH

: Nomen culature of alkenes and alkynes

Nomenclture of alkenes and alkynes ( using IUPAC

system )

Change the (ane) ending of the parent alkane to the-1

.suffix (ene) for alkenes and (yne) for alkynes

The longest chain containing (C C ) double bond or -2

triple bond are numbered in a direction that give the
.lowest possible number

:Examples

CH3 C H = CH C CH3 -1
1 2 3 4 5

methyl 2 pentene 4

1 2
CH2 CH3
2- CH3 C = CH CH2 CH2CH3
3 4 5 6 7

methyl 3 3
heptene

: :Properties of alkenes and alkynes

.Alkenes and alkynes non polar molecules-1

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 Alkenes and alkynes are very active they can react-2
with many compounds , because of the presence of double
.and triple bonds in their molecule

Addition reactions -

oxidation
reactions

:Addition reactions-1

A)Hydro halogenations addition ( H X ) i.e. (x = Cl ,

.Br , and I )

:Examples

H Br
1- CH3 CH = C H2 + HBr CH3 C C
H

B)Halogenation addition (X2)

(X2 = Cl2 , Br2 and I2)

:Examples

Br Br
1- CH3 C = C C H3 + Br2 CH3 C C
CH3

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 C) Hydration : is addition of water to an alkenes and
. alkynes to form an alcohol

:Examples

OH H
O 1- CH3 C CH CH 3
C CH CH3 C CH3

OH
2- CH3 CH CH2 + H2O CH3 C CH3
H

: Oxidation reduction reactions-2

Oxidation results an increase in the number of ( C H ) -

bonds or

.decrease in the number of ( C H ) bonds

Reduction results of an a decrease in the number of ( C -

.O ) bonds or an increase the number of ( C H ) bonds

{Reduction is the opposite of oxidation }

Oxidation

Decreasing number of C H bonds

RC = CR C = C RC

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 CH
H H

Increasing number of ( C H ) bonds reduction

Reduction

Oxidation

Increasing in ( C-O ) bonds ( Oxidation)

H H H
H HCH HCH
C O C O O C H
H H OH

Increasing in ( C H ) bonds ( Reduction)

: Aromatic hydrocarbons

Cyclic compound contains several decrease of un -1

saturated double bonds . Example : Benzene ( C 6H6 )

:Benzene structure-2

A)Most contain six membered ring and three double

.bonds

.Should be planar-

.All ( C C ) bond lengths should be equal -

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Compounds containing two or more benzene rings that -
share (C C ) bonds called polycyclic aromatic
.hydrocarbons

:Nomen clature of Benzene Derivatives

To name of benzene with one substituent, name the -

.substituents and add the word benzene

: Examples

Ortho, para, or meta are use to describe the-

.position of the two substituents

:Examples

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 : Properties of aromatic hydrocarbons
Non polar-1

Insoluble in H2O-2

.More stable than normal unsaturated compounds-3

CL2 No reaction + -4

:Biomedical important of hydrocarbons

:Hydrocarbons form lipids which are important for -

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 Formation of complexes such as phospholipids -1
(important for formation of cell membrane) and
prostaglandins (control blood pressure and cause
.inflammation)

.Absorption of fat Soluble vitamins -2

Production of energy in the body because of presence of -3

.(C C ) and (C H ) bonds

Cholesterol is a group of lipids having four rings joined -4

.together (constituent of membrane structure )

Hydrocarbons form parts of many medicines used

: for treatment of

.Diseases-1

.Used in the labs to diagnose many of diseases -2

Used as fuel to run the ambulances used to carry -3

.patients

Combustion of alkanes provides heat for hospitals and -4

.homes

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