Chemistry, Water, and Buffers

M123
OUTLINES
Organic Chemistry Nomenclature -
Carbon
Geometry / Stereochemistry -
Electronegativity -
Hydrogen Bonding -
Covalent Bonding
Reduction / Oxidation (REDOX) -
Gibbs Free Energy -
ΔG = ΔH – TΔS
ΔG = ΔG°’ + RTln {[C]ceq[D]deq]} / {[A]aeq[B]beq}
Hydrophilic / Hydrophobic -
Amphiphilic -
Membrane lipids
Glycerophospholipids -
Sphingolipids
Lipid Bilayer
Water
Protein Folding -
 Partial Charges / Hydrogen Bonding -
Donor / Acceptor -
Base Pairing -
Ionization
pKa = -log Ka
pH = -log [H+]
pOH = -log[OH-]
Acids
Weak acid & Salt -
Buffering
Capacity
Titration
Henderson / Hasselbalch -
Charge estimates -
Strong vs Weak Acids -
Basic Chemistry
Geometry of Carbon
Tetrahedral
Handedness &
Stereochemistry
Basic Chemistry

Electronegativity: a measure of affinity or attractiteness of

nucleus has for electrons
Relative “pull” of nuclei for outer shell electrons
Hydrogen Bonds
Partial Negative & Partial Positive Charges
Arise From Different Electronegativities
Reduction / Oxidation

Reduction - Gain of electrons

Oxidation - Loss of electrons

H3CHC=O + NADH + H+<=> H3CH2COH + NAD+

Gibbs Free Energy

ΔG = ΔH - TΔS
aA + bB <=> cC + dD
Keq = {[C]ceq[D]deq]} / {[A]aeq[B]beq}

ΔG = ΔG°’ + RTln {[C] [D] ]} / {[A] [B] }

c
eq
d
eq
a
eq
b
eq

ΔG°’ = -RTlnKeq
Water & Buffers
Unequal sharing of electrons
Uneven Charge Distribution
Covalent bond
Dipolar
Hydrogen Bonds: always involve hydrogen
H-bonds are most: important: weak enough to be breakable and strong enough
to hold things together
Hydrophilic vs Hydrophobic
Amphiphilic: some where in between, have hydrophilic
characteristics and hydrophobic ones.
Soap and detergent
Other Amphiphilic Substances

Membrane Lipids
Glycerophospholip
ids
Sphingolipids
Other Amphiphilic Substances

Membrane Lipids
Glycerophospholip
ids
Sphingolipids
Lipid Bilayers
Protein Folding
Hydrophilic
Hydrophobic Outside
Inside

UNFOLDED FOLDED

Water’s Chemistry Affects Molecules

Hydrogen Bonding Between Water Molecules
Hydrogen Bonding Between Water and Other Molecules
Hydrogen Bonding Between Water and Other Molecules
Hydrogen Bonding in the Cell
Bond Strength
Ionization and Acid Strength: formation of ions by loss or gain of protons.
Gain of proton means gain of one positive charge, loss of proton means one
less of positive charge
Acid Measurement

pH = -Log[H ]
+

pOH = -Log[OH ] -

pH + pOH = 14
Weak Acid Dissociation :they are a very important components
in buffers , strong acids can’t act as buffers

why weak acids???because they dissociate partially when

dissolve in water , thus produce salts ( the other component of
buffers)
*Buffers contain weak acids and their salts
Weak Acid Dissociation

example : acetic acid(CH3COOH), COSIDERED AS : monoprotic (dissociate in water and produce one proton –
hydrogen ion- in order to produce salt
some weak acids are diprotic or triprotic or more ,what ever .(depend on how many protein produced when
they are dissociated in water .)
The monoprotic acids need 1 equivalent from strong base to release it , for example acetic acid
another example is carbonic acid (H2CO3) which considered as diprotic need 2 equivalent of stro, ng base to
release it , but when you talk about phosphoric acid “triprotic “ you need 3 equivalent
* monoprotic have 1 pka value , diprotic have 2 pka values , triprotic have 3 pka values, etc .

Always when talk about buffers we must talk about PH, as buffers resist change in PH
PH : the measurement of protein concentration in the solution and is scale from 1 to 14 . And thematically
ph is measured by count the H+ in the solution and the same for poh we measure it by counting oh- in the
solution
ph= -log h3o
poh= -log oh
ph + poh = 14
why 14 because the concentration of oh- and h3o+ in the‫لاـماء لاـنقي‬
equal 10^-7 mol/L
IN OTHER SHAPE : 14 = -log( –oh ) –log(h3o+)
* to calculate the PH we must know the concentration of H3O+ OR OH—
so the really question now is to know how to calculate the concentration of H3O+ or OH- ??
BY using PH meter ,
Henderson Hasselbalch Equation
]3 )
O
2C
****weak acid , dossiate incompletely****
[ H
always remember that strong acids don’t make buffer because the dossiate ])
- ]/ c
completely in water thus don’t produce salt and as we know the3components A
O
of the buffers are salt and the weak acid which saltCcome- ]from [H
H /
- if we have nuitral water (ph=7), and then wegadd [
( base c
A or basic
o ( [
salt , the ph could jump from 7 to 10 due to+the l icreasingo g of l ,
oh-
l a
concentration ,,,,,, if we add strong baseKfor
p
a buffer
K a
+ solution
G tee ne r
for
a +
= ph after p adding
example has ph 4 , what is the range of
H
base ??? It will not jump , or there pwill not H
=
be high
I n
difference p K
,p
between the old and the new because the system of buffer = ] /
resist the change in ph , because in buffer solution there are
pH lt
some acid molecules didn’t associate thus they react with oh
S a
from added base and prevent the accumulation of oh- ( [
, so the change of ph will be very little . g
What will happen if we add strong acid ???the excess h+ will react with the salt ion and this will prevent the
accumulation of h ions , thus the ph won’t decrease much .
‫اول لاـمحـافظـة على وـضعـ اـالاتزـان الروـجوعـ‬
‫اـاـمظـ يحــ‬
‫لن‬ ,‫حـاـة اتزـان‬
‫يـ ل‬ ‫عدـة او حـمض على ناـمظـ فـ‬ ‫ لماـ نـضيف اـقـ‬: ‫الـزم نـعـرف مبادـ الـتشليهـ‬
‫على امـ كانعليهـ‬
e
‫يتكونمن حـمض ضـعيفو مـلحهـ‬ ‫يش لاـمنظم بــ‬ ‫همناـ لاـدقة و الرقـصـة و لـ‬ ‫بــ هل لاـهبد كلـهـ الـزم نـكون فــ‬ ‫ عدـ‬alu
a v
pK
no
v e d 7 6)
h a
A ci 4 .
ally ak ic d Ka =
n ti e A ( p
e W k
pKa and Acid Strength e ss ger ea cid
l, n r W cA
C o
H S tr a ke ceti
li ke a - W
e
s A
d s, p K
a - ) v
A ci ow p K .75
g L h = 3
n g
rt o Hi K a
S (p
c id
A
ic
o rm
F
 Buffers Rapid pH Change

Resist Changes in pH
Limited pH Change
Weak Acid Systems

Buffering Capacity

Rapid pH Change
‫دنا نــحكيعن اـل‪Titration‬‬
‫ي لاــشكل لاــسـابـق بــــ‬
‫فـــ‬
‫و بنا ناخذ مثال الكاربونيك اسيد و بدنا نعتبره مونوبروتوك عشان نسهل دراسته‬
‫و للعلم الكاربونيك اسيد بفر منيح بيشتغل باالمعاء الدقيقة‬
‫هسا الحمض الضعيف بعمله ‪ titration‬عن طريق اضافة قاعدة قوية‬
‫مبدا ال ‪ titration‬بيعتمد ع انه هل الحمض الضعيف يتاين بشكل كامل‬
‫بالمخطط السابق درجة الحموضة بعد اضافة ايونات الهيدروكسيل درجة الحموضةزادت بشكل حاد‬
‫بعد هيك استقرت و كان التغير كثير طفيف و معدل تغير درجة الحموضة منخفض و بعد هيك رجعت‬
‫تزيد و بعدين صار تزيد بشكل حاد مرة ثانية‬
‫مربـعـ اـل ‪Buffering‬‬
‫لـــ‬ ‫شكل لاــسـابـق اـنـتبهـ‬
‫بــــ‬
‫لاــ‬
‫و هو المنطقة اللي بشتغل فيها الحمض كبفر و بكونمعدل التاين للحمض يساوي معدل عدم التاين‬
‫يعني بكلمات اخرى بكون نص الحمض متاين و معطينا ايونات هيدروجين و الملح و النص االخر غير‬
‫متاين اطالقا‬
‫و اـشيمهمـ اـنـهـ اـل‪PH=pka‬‬
‫‪Ph = pka , ph = 5.37-7.37 , pka = -1--+1‬‬
‫بالشكل السابق في نقطتين مهمين ‪ ,‬نقطة كان في عندنا بس حمض من دون ملح و كان الغير شديد‬
‫و نقطة كان في عندنا ملح فقط و من دون حمض و بينهم كانت منطقة ال ‪ buffering‬قبلها‬
Acids With Multiple pKa Values
‫شوية حكي عن المخط السابق‬
The amino acid has chiral carbon atom (center carbon ) attached to 4 groups
1-carboxyl G ,,,,,,,, 2-amino G ,,,,,,,,,3- H atom ,,,,,,,,4-the variable G (R G)
Here we have three dissociable groups ( carboxyl group(alpha group because it
attached to alpha carbon “ chiral carbon “ , the carboxyl group of the variable
group (beta group because it attached to beta carbon (carbon of R group ) and
finally the amino group which called alpha amino group because it attached to
alpha carbon )
*in other word we have : a-carboxyl , b-carboxyl and a-amino .
Highest pka : a-amino> b-carboxyl> a-carboxyl
‫ركز مع المخطط السابق عشان نفهم التاين االول و الثاني و الثالث و عشان نفهم انه في عندنا ثالث‬
‫مناطق للبفر و انه ما في بعد التاين الثالث كمان تاين و الزم نفهم تغير الشحنة مع كل تاين و نكون‬
‫قادرين نحدد الشحنة و صيغة المركب بعد كل تاين‬ .
There is another term to know : Pi
Pi: isoelectric point: ph at which the molecule carries no charge .
We must be able to identify the value of Pi .
Pi= (pka1 +pka2)/2
‫من المخطط السابق بنشوف نقطة يكون فيها معظم الحمض يكون فيها متاين لشكل يكون فيه ال‬
pka ‫ باخد المتوسط الحسابي بقيم ال‬pi ‫يحمل شحنة ( متعادل ) و بنحسب عندها ال‬
 ‫لما يكون حمض ‪ mulitprotic‬بيكون عندنا اكثر من قيمة لل ‪ pka‬كل تاين له قيمة معينة‬
‫‪Monoprotic – 1 pka value‬‬
‫‪Diprotic -2 pka vale one for each ionization .‬‬
‫‪Triprotic – 3 pka values one for each ionization .‬‬
‫لـــ اـقل‪ ph ,,,,‬و اـعلي ‪pka‬‬
‫لاــتايـن االـخـير هـ‬ ‫لـــ اـعلي ‪ ph‬و اـقل ‪Pka‬‬
‫لاــتايـن اـالول هـ‬
‫‪ .‬لهدا التاين االول هو االسرع ‪ ,‬االقوي و االسهل‬
‫كنهل لاــحمض مـلاــتيبروـتـيك‪ ,‬كــل* ‪Pka value‬‬
‫يشتغل كـبـفـر و لـــ‬
‫بــــ‬ ‫يعندنا حمض ضـعيفو‬
‫هسـا ادا كـان فـــ‬
‫في حوليها منطقة بفر‬
‫مثال ‪ H2co3‬بالمرة االولي لما يتاين و يعطينا ‪ Hco3-‬بيشتغل مع الحمض كبفر و بالمرة الثانية لما يتاين الي‬
‫خـتالف قـيمة اـل‪Pka‬‬
‫اــفـر نــظرـا الـــ‬
‫منطقـة لب‬
‫بــــ‬ ‫اــفـريـنهو‬
‫ين لب‬
‫كن االـخـتالف بــــ‬
‫يشتغلمعـ لاــحمض كـبـفـر و لـــ‬
‫بــــ‬ ‫‪Co3 -2‬‬
‫‪This is important in our bodies ‬‬
‫انه عندنا منطقتين للكاباسيتي للبفر و كدا‬
Estimating Weak Acid Charge

1. If pH > pKa by one or more pH units - Proton OFF

2. If pH < pKa by one or more pH units - Proton ON

-COOH vs -COO-
-NH3+ vs -NH2
*handerson-haselbalch equation very important to understand

*pka and ka are constant

Ph= pka +log(salt/acid)

The equation depend only on the concentration of salt and acid .

Very important to know how the buffer resist the change in ph