Biochemistry PDF

‫‪Biochemistry‬‬
‫‪1‬‬ ‫‪-٣‬إيمان مرزا‬ ‫‪-٢‬ھديل الفرشي‬ ‫إعداد‪-١ :‬ريم السبيعي‬

‫‪ -٢‬ھتان بدر‬ ‫تنسيق‪ -١ :‬نورة نحاس‬
Lecture no (1)
Organic chemistry
An organic compound is one that has carbon as the

principal element
• Carbon is unique
• It has 6 electrons in its outer shell arranges 1s22s2sp2
• It has room for 4 bonds to 4 other atoms.
Organic compounds have specific geometry around the

carbon to carbon bond
Hydrocarbons:
• A hydrocarbon is a compound consisting of only hydrogen and
carbon.
• The carbon to carbon bond can be single, double, or triple bonds.
• The bonds are always nonpolar.
Carbon-to-carbon chains can be:
1-straight
2-branched
3-closed ring
2 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

‫ ھتان بدر‬-٢ ‫ نورة نحاس‬-١ :‫تنسيق‬
Types of Carbon Atoms :
• Primary carbon (1o)
a carbon bonded to one other carbon
• Secondary carbon (2o)
a carbon bonded to two other carbons
• Ter"ary carbon (3o)
a carbon bonded to three other carbons
Saturated compound:
Alkanes
The hydrocarbon that contain only single bond
End in –ane
• Methane CH4
• Ethane C2H6
• Propane C3H8

General formula of CnH2n+2
Simplest: Ehane, C2H6
Properties of Alkanes:
Unsaturated Hydrocarbons:
Alkene
• Alkene: hydrocarbon that contains one or more carbon-to-carbon

double bonds end in –ene
• Can have more hydrogen atoms added
• Very important in biological systems
• General formula :CnH2n

• Simplest: ethylene, C2H4
-Ethylene is the gas that ripens fruit, and a ripe

fruit emits the gas, which will act on unripe fruit.
Thus, a ripe tomato placed in a sealed bag with green tomatoes will
help ripen them.
Alkynes
• Alkyne: hydrocarbon that contains one or more carbon-to-carbon

triple bonds end in –yne
• General formula of CnH2n–2
• Simplest: acetylene, C2H2
Cyclic Hydrocarbons:
• Carbon atom chains in form of rings
• Can be represented by structural formulas or symbolic

representations

Cycloalkanes and Aromatic Hydrocarbons:
Cycloalkanes are alkanes (only carbon to carbon single bonds) which

form a ring structure
An aromatic compound is one that is based on the benzene ring (C6H6).
Structure: Alternating single & Double Bonding
A benzene ring that is attached to another compound is given the

name phenyl.

Functional Groups :
Group of atoms that gives a family of organic compounds its
characteristic chemical and physical properties.
Alkyl group: derived from alkane by removing a H
R stands for alkyl group in general
Halogens:
Halogens (F2, Cl2, Br2, I2,) can all add to a hydrocarbon to form am
alkyl halide.
When naming the halogen the –ine ending is replaced by –o
• Fluorine becomes fluoro
• Chlorine becomes chloro
• Bromine becomes bromo
• Iodine becomes iodo
Alcohol Family:
• Contain hydroxyl(OH) group
• Replace -e with -ol
• The simplest is: methanol ,CH3OH
• Produced industrially
– Mainly a chemical intermediate

C2H5OH, ethanol
• Made industrially and by fermentation
– Industrially produced alcohol has noxious substances added
• Small, simple alcohols tend to be toxic
Ethers:
• Two alkyl groups attached to same O
– Example :CH3CH2-O-CH2CH3
• Used mainly as solvent
• Little chemical reactivity
– Insoluble in water
– Highly flammable
Aldehydes and Ketones :

Both contain carbonyl group (C=O)
Aldehyde: R-CHO
Ketone: R-CO-R’
Common Aldehydes
Change -e ending to -al
Produced by oxidation of alcohols
Formaldehyde – used as a preservative
Larger ones used as fragrances

Benzaldehyde – flavor in maraschino cherries
Common Ketones:
Change -e ending to -one
Acetone most common ketone
Used primarily as a solvent
Produced by oxidation of alcohols
Carboxylic Acid:
Contains C=O and –OH group on same carbon
Change -e to -oic acid
Acetic acid: acid in vinegar
The red ants, like other ants, make the simplest of the organic acids,
formic acid. The sting of bees, ants, and some plants contains formic
acid, along with some other irritating materials. Formic acid is HCOOH.
Esters:
Derived from carboxylic acids and alcohols
Tend to be fragrant
Methyl butyrate apple
Ethyl butyrate pineapple
Ethyl formate rum
Methyl salicylate wintergreen

Amines:
Contain N
May have 1, 2, or 3 alkyl or aroma<c groups
Most biological amines are amino acids
Building blocks of proteins
Amides:
N bonded directly to carbonyl group
Linkage that holds proteins together
Heterocyclic Compounds
Ring compounds that have something other than C in the ring
Occur in plants
Alkaloids: basic in solution
Examples: caffeine, morphine
Form basic structure of DNA

Lecture no (2)
Isomers
• Isomers: Compounds with same molecular formula but
different structures
• There is only one possible way that the carbons in methane (CH4),
ethane (C2H6), and propane (C3H8) can be arranged.
• However, carbons in butane (C4H10) can be arranged in two ways;

four carbons in a row (linear alkane) or a branching (branched
alkane). These two structures are two isomers for butane

Constitutional Isomers :
Are isomers that differ because their atoms are connected in a different
order.
e.g: C4H10 ( CH3CH2CH2CH3 )
Stereoisomers Isomers :
Are isomers that differ in arrangement of their atoms in space.
Enantiomers:
• Non-superimposable mirror image
Diastereomers:
Not mirror images
Number of possible isomers increases rapidly with the number of

carbons
C30H62 – >4 billion possible isomers
Different isomers are completely different compounds. They have

different structures, different physical properties such as melting point
and boiling point, and may have different physiological properties.
Lecture no (3)
Reaction of organic compound
Classification of organic reactions:

• substrate: the component whose carbon atom the reaction takes
place
• reagent: the component whose reacting centre is not a carbon

atom
Reagent:
1. elecrophiles: seek extra electrons that will give them a stable

valence shell of electrons
carboca<ons: HB, NO2B, NOB, SO3
2. nucleophiles: seek protons or some other positive center.
carbanions: halogenide ions,
H2O, ROH, RNH2, HC≡C
3. radical: having an unpaired electron, R·

Type of Organic reactions according to the structures of the
starting materials and products:
a) Substitution:
one group replaces another,
e.g. alkyl halides
subtypes: nucleophilic,electrophilic, radical
ABBC ACBB
b) Addition:
All parts of the adding reagent appear in the product, two molecules
become one
subtypes: nucleophilic, electrophilic, radical, concerted
ABB–C A –B –C
c) Elimination:
One molecule loses the elements of another small molecule
A –B –C ABBC
d) Rearrangement:
A molecule undergoes a reorganization of its constituent part
A –B –C A –C –B

e) Oxidative :
They can be sorted in one of the categories above, occur in alcohol
primary alcohols -------- aldehyde
primary alcohols -------- carboxylic acid (in special situation)
Secondary alcohols -------- ketone
Tertiary alcohols -------- don’t undergo oxidation
e.g:
RCH2- OH -------- RCO-OH ( carboxylic acid )
RCHOH- R --------- R-CO-R ( ketone)

Lecture no (4)
General chemistry
A Key part of any measurement is the unite.
SI: is interna<onal system of unite speciFes G base units:
1. Mass ( Kg)
2. Length (m)
3. Time (s)
4. Temperature (K)
5. Electric current (A)
6. Amount of substance (mole)
7. Luminous intensity (candela)
Derived Units:
units for quantities obtained by appropriate combinations of the base
units.
• Area of the rectangle =length x width
mx m
m2
• Speed = distance / time
m/s
Modified Units :
Modification of the basic units with decimal factors and prefixes
e.g.
1/10 = 10 -1
1/100 = 10 -2
1/1000 = 10 -3
Factor-label method:
Useful method in setting up unit conversion problems .
e.g.
Cm ------ dm
1. cm ------- m
2. m ------- dm
Temperature:
It is a quantity that determines the direction that heat will flow
spontaneously.
Three common scales used:
• Fahrenheit Scale
• Celcius
• Kelvin

Fahrenheit Scale :
Freezing point is
• freezing point of H2O = 23 F temperature at which
both liquid and solid can
• Boiling point of H2O = 212F
coexist at the same
temperature
Celsius Scale:
• Freezing point = 0 C
• Boiling point = 100 C
100C = 180F
Kelvin (K) :
• SI temperature unit
• Water freezes at 2G3.15 K
Fehrenheit : F=9/5 (C+32)
Celcius : C= 5/9(F-32)
kelvin : K= C+273
Celcius : C=K- 27

Example :
• if it is 75 F what is it in K ?
Solution :
• First , convert to C
C=(G5-32) (5/9) = 23.9
• Then convert to K
K=CB2G3
K=23.9B2G3=29G
Density :
ratio of an object mass to its volume
Common units are : g/cm 3 or g/ml
Cm 3 = ml
e.g
Density of air = 0.0013 g/cm 3
Density of water = 1.0 g/cm 3

Specific gravity :
Ratio of the density of a substance (g/ml) to the density of water
(g/ml)
specific gravity dose not contain a unit
At 4 C , density of water is =1
At 4 C speciFc gravity = density of substance
Example:
At 4 C the Density of NaCl solu"on is 1.5 g /ml.whate is its specific

gravity?
Solution :
specific gravity = 1.5
Unite conversions:
• To convert a large unite to a smaller units : multiply
e.g :
5 Kg = 5 x 1000 = 5000 g
• To convert a smaller units to a larger units : divide
e.g :

5g = 5/1000 = 0.005 Kg
Example:
How many miligrams are in a Kilogram?
(Kg mg)
Solution:
1- Convert from Kg to g
1 Kg=103 g
2- Convert from g to mg
103 X 103 = 106

Precision and accuracy:
Accuracy precision
1)Correctness of single 1) Reproducibility

measurement (refer to how
the same measurement
an experimental
was repeated several times
measurement to true value
and the measurement close
to each other
2)Check by using a diﬀerent 2)Check by repeating

method measurement
3)Poor accuracy results 3)Poor precision results

from equipment error form poor techniques

Stoichiometry
Stoichiometry :
Quantitative measurement to carry out a chemical reaction
Mole concept :
1 atom C B 1 atom O ---------- 1 atom CO
1 mole C B 1 mole O ----------- 1 mole CO
The mole ratio is the same as the atom ratio
e.g.
What mole ra"o of C to Cl must be need to prepare C2Cl6 ?
Solution:
the ra<o is 2C to 6Cl = 1C to 3Cl
e.g.
How many moles of C are in 2 mole C2CL6 ?
Solution:
1 mol C2CL6 ---------- 2 mol C
2 mol C2CL6 ----------- xC
Mol of C= 2mol C2CL6 x 2 mol C/ 1 mol C2CL6 = 4 moles C

Atomic weight and atomic Number
Atomic number :
Is the number of proton found in the nucleus of an atom.
The atomic number is found in the periodic table above the

element
Atomic weight (atomic mass) :
is the mass of an atom, the total mass of protons, neutrons

and electrons in a single atom
The atomic weight is found in the periodic table below the element
Atomic weight = Weight of 1 mole
1 mole = 6.022 x 10 23 atoms
Atomic weight = Weigh of 6.022 x 10 23 atoms
Avogadro's number 6.022 x 10 23
e.g
What is the mass of one atom of Ca ?
Solution :
1 mole Ca = 6.022x 10 23 atoms
1 mole Ca = atomic mass

So atomic mass of Ca = 6.022 x 10 23 atoms
? g of Ca = 1 atom
? g of Ca (mass) = atomic mass of an element / 6.022x10 23
Molecular weight :
Sum of atomic weights for a molecule
Molecular weight = formula mass
e.g.
1 mole H2O = (1x2) B 16 = 18 g M.W
1 mole CO2 = 12 B (16x2) = 44g M.W.
Converting gram to mole and mole to gram:

Converting grams to moles :
Number of mole = weight/ molecular weight
e.g :
How many moles of C are in 50.5 g ?
Solution :
from periodic table : 1 mole of C------ 12 g
x mole of C ----- 50.5g
X mole of C = 50.5x1/12=4.62

Converting Moles To Grams:
Weight of substance = molecular weight x number of moles
e.g.
How many grams are there in 5 moles of oxygen ?
Solution :
1 mole ----------- 16 g
5 mole ----------- x g of oxygen
X g of oxygen = 5x16/1 = 80 g
Examples:
1- How many moles of Ca are needed to react with 3.5 mole Cl to

produce CaCL2 ?
Solution :
The correct ratio :
1mole of Ca B 2 mole Cl 1 mole CaCL2
We have :
? Mole Ca : 3.5 mole Cl
= 3.5 x 1 / 2 = 1.G5 mole Ca
2_How many grams of Ca should react with 50 g of Cl to produce

CaCl2?

Solution:
The ra<o should be 1 mole Ca : 2 moles Cl
Convert grams to moles :
1 mole Cl 35.5 g
? 50 g
50x1/35.5 = 1.4 mole Cl available
The ra<o should be 1 mole Ca : 2 moles Cl
? : 1.4 mole Cl
=1.4 x 1 / 2 = 0.G mole Ca
3- How many grams are in 0.7 moles of Ca ?
M.W. of Ca = 40 g
Solution :
weight of substance =moles x M.W
= 0.G moles x 40 g = 28 g of Ca
Summary:
Moles = weight (g) / M.W(g)
Weight = M.W x moles
Number of atoms in a molecule=

Weight of substance x Avogadro`s number / M.W
Example :
How many atoms of C are in 4 x 10 -8 g C3H8 ?
Solution :
Number of atoms = (4 x 10 -8 ) (6.022x 10 23) / 44 g
= 0.54 x 10 15
Mul<ply the answer by 3 because there are 3 carbon atoms
= 3 x 0.54 x 10 15 = 1.64 x 10 15

Lecture no (5)
Expression of solution concentration
Molarity (M):
M= number of moles of solute / volume of solution.
Unit : (mole)/(L) or (mmole)/(ml)
Examples:
1- Calculate the molarity of a 2L solu"on that contains 10 moles of

NaOH.
Solution:
M= 10/2 = 5M
2-What is the molarity of a solu"on that has 18.23 g HCl in 2 L?
Solution:
mol.wt of HCl =1B35.5 =36.5g/ mol
number of moles = weight of substance / molecular weight
No. of mol = 18.23 /36.5=0.50 mol
molarity HCl= 0.50 mol/2 L=0.25 M

Molality (m):
m = number of moles of solute / kg of solvent.
Unit: (Mole) /( Kg )
Examples:
1- What is the molality of solu"on that contains 330g of CaCl2 per kg

of solvent.
Solution:
Number of moles= wt / mol.wt
=330/110.98 = 3 mole
m= number of moles of solute / kg of solvent.
= 3/1 = 3 molal of solu<on of CaCl 2
2- How many grams of NaOH are needed to make 2 molal solu"on?
solution:
m = number of moles of solute / kg of solvent
number of moles = wt/ mol.wt
mol.wt of NaOH = 23 B 16 B1=40
so,
2 = (wt / 40 ) / 1 = 80 g.

Normality:
N= number of equivalents of solute / liter of solution.
Equivalents = the amount of replaceable H or OH or valence
Equivalents wt = mol.wt/ valance
No. of grams of solute
Equivalent wt of solute
N= 1 L of solu<on
In case of acid: e.g .H2SO4 ,eq.wt = 98/2=49
In case of bases: e.g. Ba(OH)2 ,eq.wt =171/2=85.5
In case of salts: e.g. NaCl ,eq.wt = 58.5/1=58.5
Examples:
(1) Calculate the normality of solu"on containing 98 g of H2SO4 in 0.5

L solution?
Solution:
normality= (98/ 49.4) / 0.5 = 4 eq / L

Interconversion between molarity &normality:
N=nxM
N= normality
n= valance
M= molarity
Example:
2.3 molar HCl solu"on,what is the normality?
Solution:
N= 1x 2.3 =2.3
Mole fractions:
The ratio of number of moles of one component to the total number of
moles of all component in solution.
Xa = n A / n A + n g +…..+n n
Xa= mole fraction
nA= number of mole of component A
nA+ng+……+nn= total number of moles
Example:
What is the mole frac"on of ethyl alcohol & H2O if 0.5 mol. Of ethyl
alcohol & 1,5 mol. Of H2O is mixed?

Solution:
X(H2O)= 1.5/(0.5B1.5)= 0.G5
X(C2H5OH)=0.5/(0.5B1.5)= 0.25
Dilution of solution:
The process of reducing the concentration of a solute in solution usually
by mixing with solvent.
Example:
What is the concentra"on of solu"on produced by dilu"ng 100ml of

1.5 M NaOH to 2L?
Solution:
M1XV1=M2XV2 (1= ini<al, 2= Fnal)
M1=1.5M , M2=??
V1=100 ml , V2=2000ml
1.5 x 100 = M2 x 2000
M2= 0.0G5M

Lecture no (6)
Acid and base
Arrhenius Acids and Bases:

Acid: substance that produce Hydronuim ions in aqueous solution .
e.g. HCl, CH3COOH, HNO3

Hydronium Ion:
Hydronium Ion is a
+
HC1 + H2O = H3O + CL solvated proton.
In water solvent it is a
hydrated proton.
HB(aq) = H3OB =
Hydronium ion
Base: substance that produces Hydroxide ion in a aqueous solution
e.g. NaOH, Ca (OH)2
NaOH+ H2O = Na+ + OH-
Examples of strong acids:
H2SO4 Sulfuric Acid
HNO3 Nitric Acid

Examples Weak Acids:
Organic carboxylic acids R-COOH
Weak acids ionize less than 10%
Dissociation:
a) Strong acids and bases:
HCl B H2O ----- H3OB(aq) B CL (aq)
HCLO4 B H2O ---- H3OB B CLO4-(aq)
NaOH B H2O ---- NaB B OH-(aq)
b) Weak acids and bases :
do not dissociate completely
CH3COOH B H2O ---- H3OB B CHCOO-
NH3 B H2O ---- NH4B B OH-
Lowery-Bronested Theory :
-Acid: Substance that donates protons (HB)
e.g : HBr, HCI , H2SO4
-Base: Substance that accepts protons

e.g: NH3 , NaOH
Conjugate Acid- Base Pairing :

-Conjugate Acid: An acid produced by base accepting a proton
-Conjugate Base: A base produced by an acid donating a proton
HA B H2O = H 3 OB B A-
Acid base conj.Acid conj.base
H3O is conj.acid of base H2O
A- is conj.base of acid HA
* The stronger the Acid the weaker the conjugate Base
* The stronger the Base the weaker the conjugate Acid
Monoportic acid: An acid which gives one hydrogen ion per molecule
of acid
e.g. HCl, CH3COOH
Diprotic acid : An acid that gives two hydrogen ions per molecule of
acid
e.g. H2SO4 HB B HSO4-

HSO4 HB B SO4--
Triprotic acid : An acid that gives three hydrogen ions per molecule of
acid
e.g. H3PO4 HB B H2PO4-
H2PO4- HB B HPO4--
HPO4-- HB B PO4---
Polyprotic acid :An acid that gives more than one hydrogen ion per
molecule, includes diprotic and triprotic.
Lewis Definition of Acid and Base:

-Acid: Electron acceptor
e.g. Transition metal cations, Boron compounds, Aluminum compounds
-Base: Electron donor
e.g. Organic Amines, Alcohol
Autoionization (self ionization) of water:

Autoionization : when water molecules react with one another to form
ions
2H2O = H3OB (aq) B OH- (aq)

Kw:
Kw = [H3O+] [OH-]
Kw= 1 X 10-14 at 25oC
Kw : called ion product of water ( The product of the concentration of

H3OB and OH ions)
pH Scale :
pH = G
Neutral solution ( Hydronium ion and Hydroxide ion concentrations are

equal )
pH < G
Acidic solution ( Hydronium ion concentration is greater than

Hydroxide ion concentrations )
pH>G
Basic solution ( Hydronium ion concentrations is less than Hydroxide

ion concentration )
Relationship Between pH and Hydronium ion Concentration :

pH = -log[H3O+]
[ H3O] = Antilog ( -pH )

Determining Hydronium and Hydroxide Concentrations using Kw
Expression :
[H3O+] = Kw / [OH- ]
[OH- ] = Kw / [H3O+]
Kw = 1 X 10-14
Other "p" Scale :
pOH = - log [OH-]
[OH-] = Antilog (-pOH)
pKw = - log Kw = - log (1 X 10-14) = 14
pKa = -log Ka
pKb = -log Kb
Relationship between pH and pOH:

pKw = pH + pOH

Two methods of determining pH experimentally:
1- pH Meter
2- Acid – Base chemical indicators
pH Calculations:
1- [ H+] = 6.7 X10 -3 M
pH = - log [HB]
pH = - log [HB] = 2.2
2- [H+] , if the pH is 4.5
[HB] = Antilog (-pH0) = Antilog (- 4.5) = 3.2 X 105 M
pOH Calculation:
pH B pOH = 14
pOH = 14 – pH , pH = 14 – pOH
Example :
Determining the following :
1-[NaOH] = 1.7 X10-14 M ( determine pH)
pOH = - log [OH]
pOH = -log [NaOH] = 3.8 , pH = 10.2

2-[H+] = 5.2 X 10-14 (determine pOH)
pH = [HB] = 11.2
pOH = 14 – 11.2 = 2.8
3-if the pH is 4.5 (determine [OH-])
pOH = 14 – 4.5 = 9.5
[OH-] = Antilog [-pOH ] = Antilog [- 9.5 ] = 3.2 X 10-10M

Lecture no (7)
Cont.Acid and base
Acid Dissociation Constant (Ka):

The strength of a weak acid can be express a an equilibrium
HA(aq) B H2O ------------ H3OB(aq) B A-(aq)
The strength of a weak acid is related to its equilibrium constant Ka
Ka = [A-] [H3O]
[HA]
Base Dissociation Constant (Kb):

The strength of a weak base can be express b an equilibrium
B(aq) B H2O(aq) ------------- BHB(aq) B OH-(aq)
The strength of a weak base is related to its equilibrium constant, Kb
Kb = [OH-] [BHB]
[B]
Percent ionization:
Percent ionization = [H+] × 100%
Stronger base, Kb increase pKb decrease
Stronger acid, Ka increase pka decrease

Example :
What are the concentra"on of all species present in a 0.50 M solu"on

of ace"c acid (ka for ace"c acid = 1.8 × 105)
Solution :
CH3COOH -------- H+ + CH3COO-
Initial 0.5 M 0 0
Change -X BX BX
Final (0.5-X) X X
Ka = [HB] [HCOO-]
[CH3COOH
1.8 × 10 -5 = [X] [X]
[0.5 – x]
X = 3.0 × 10 -3
Concentra"on of CH3COOH
= 0.50 – 3 × 10 -3 = 0.50 M

Concentration [H+] = [CH3COO-]
= 3.0 × 10 -3 M
Indicator (In) :
Are weak organic acid or bases
HIn --------- HB B In –
InOH --------- OH- B In –
Indicator Color change pH range in which

color change occur
Phenolphthalein Colorless to pink (8.2-10)
Thymolblue Red to yellow (1.2-28)
Neutralization Reaction:
Example:
How many ml of 0.025 M H2SO4 are required foe neutralize 525 ml of

0.06 M KOH . what is the pH of neutralized solu"on .
Solution :
N of KOH = nM =1×0.066 = 0.06 N

N of H2SO4 = nM = 2× 0.025 = 0.05 N
Na × Va = Nb × Vb
0.05 × Va = 0.06 × 525
Va = 630 ml
pH of neutralized solu"on = 7
Titration curve of strong acid with strong base :

Titra<on of a strong acid with a strong base, 25 ml ,O.1M HCL vs. O.1
M NaOH
1) before star"ng the "tra"on :
[HB] = O.1
pH = -log 0.1 , pH= I
2) aSer adding 5 ml of 0.1 M NaOH to 5 ml of 0.1 M HCL
Mol of HCl= M × L = 0.1 × 0.025 = 0.0025
Mol of NaOH = M × L = 0.1 × 0.005 = 0.0005
Mol of HCl remaining (unreacted) = 0.0025 – 0.0005 = 0.002
M of HCl [HB] = 0.002/0.03 = 0.066G
pH = -log 0.066G
pH = 1.18

3) at equivalent point (add 25 ml 0.1 M NaOH to 25 ml 0.1 M HCL):
The solu<on is neutral pH = G
Because strong acid and strong base release some no. of HB & OH-ions
Respective they combine to form water so the resultant is neutral pH

=G
4) After adding 26 ml of 0.1 M NaOH to 25 ml 0.1 M HCL:
Mol of HCl = M × L = 0.1 × 0.025
= 0.0025
Mol of NaOH = M × L = 0.1 × 0.026
= 0.0026
Mol of NaOH leU aUer neutral = 0.0026 – 0.0025
= 0.0001
M of NaOH [OH-] = 0.0001/0.051
= 0.00196 = 1.96 × 10 -3
pOH = -log (OH)
pOH = - log 1.96 × 10 -3
pOH = 2.G2
pH B pOH = 14
pH= 11.3

The Handerson Hasselbalch Equation:
[A-]
pH = pKa B Log ----------------
[HA]
[A-] = conjugate base - the deprotonated specie
[HA] = conjugate acid - the protonated specie
Buffer solution :
Solution whose pH does not change very Much when H3OB or OH- ions
are added to it.
The buffer often made by combining approximately equal amount of

weak acid and conjugate base.
If OH- is added, it will be removed by reaction with weak acid
OH- + HA ------- A + H2O
If H3O+ is added, it will be removed by reac"on with a weak base.
H3O+ + A --------HA + H2O

A little more conjugate acid – the pH is slightly less than pKa
A little more conjugate base – the pH is slightly greater than pKa
Buffer capacity :
Is the ability to absorb acids or bases without being affected much.
Buffers and Blood :

Control of blood pH:
oxygen is transported primarily by hemoglobin in the red blood cells
CO2 is transported both in plasma and the blood cells
CO2(aq) B 2H2O --------- H2CO3 -------- H3OB(aq) B Hco-3(aq)
The amount of CO2 helps control blood pH
1)Too much CO2 :
respiratory arrest (hypoventilation)
pH goes down , acid level goes up ( acidosis )
solution : ventilate and give bicarbonate via IV

2)too little CO2 :
anxiety (hyperventilation)
pH goes up, acid level goes down ( alkalosis )
solution : rebreath CO2 in paper bag to raise level
normal blood pH is fom 7.35 – 7.45
going outside of this range can be very dangerous or deadly .
Acidosis and Alkalosis:
-Metabolic acidosis :
Can be caused by uncontrolled diabetes mellitus, diarrhea, aspirin,

overdose and heavy exercise.
-Metabolic alkalosis
Caused by prolonged vomiting, excessive use of bicarbonate for

treating an upset stomach.


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‫‪Biochemistry‬‬

‫‪1‬‬ ‫‪-٣‬إيمان مرزا‬ ‫‪-٢‬ھديل الفرشي‬ ‫إعداد‪-١ :‬ريم السبيعي‬

An organic compound is one that has carbon as the

• It has 6 electrons in its outer shell arranges 1s22s2sp2

• It has room for 4 bonds to 4 other atoms.

Organic compounds have specific geometry around the

• The carbon to carbon bond can be single, double, or triple bonds.

• The bonds are always nonpolar.

Carbon-to-carbon chains can be:

2 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

a carbon bonded to one other carbon

• Secondary carbon (2o)

a carbon bonded to two other carbons

• Ter"ary carbon (3o)

a carbon bonded to three other carbons

The hydrocarbon that contain only single bond

3 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

Simplest: Ehane, C2H6

• Alkene: hydrocarbon that contains one or more carbon-to-carbon

• Can have more hydrogen atoms added

• Very important in biological systems

• General formula :CnH2n

4 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

-Ethylene is the gas that ripens fruit, and a ripe

• Alkyne: hydrocarbon that contains one or more carbon-to-carbon

• General formula of CnH2n–2

• Simplest: acetylene, C2H2

• Can be represented by structural formulas or symbolic

5 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

Cycloalkanes are alkanes (only carbon to carbon single bonds) which

An aromatic compound is one that is based on the benzene ring (C6H6).

Structure: Alternating single & Double Bonding

A benzene ring that is attached to another compound is given the

6 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

Alkyl group: derived from alkane by removing a H

R stands for alkyl group in general

When naming the halogen the –ine ending is replaced by –o

• Fluorine becomes fluoro

• Chlorine becomes chloro

• Bromine becomes bromo

• Iodine becomes iodo

• Contain hydroxyl(OH) group

• Replace -e with -ol

• The simplest is: methanol ,CH3OH

– Mainly a chemical intermediate

• Made industrially and by fermentation

– Industrially produced alcohol has noxious substances added

• Small, simple alcohols tend to be toxic

• Used mainly as solvent

• Little chemical reactivity

Aldehydes and Ketones :

Change -e ending to -al

Produced by oxidation of alcohols

Formaldehyde – used as a preservative

Larger ones used as fragrances

8 ‫إيمان مرزا‬-٣ ‫ھديل الفرشي‬-٢ ‫ريم السبيعي‬-١ :‫إعداد‬

Change -e ending to -one

Acetone most common ketone

Used primarily as a solvent

Produced by oxidation of alcohols

Change -e to -oic acid

Acetic acid: acid in vinegar

Methyl butyrate apple