Media of Life

Ionization of Water
Acids, bases, and pH
Buffers
Physiological buffers

Monitoring Acidity
The Henderson-Hasselbalch
(HH) equation is derived from
the equilibrium expression
for a weak acid.

[A ]

pH = pKa + log
[HA]

Monitoring Acidity
The HH equation enables us to
calculate the pH during a titration and
to make predictions regarding buffer
solutions.
What is a titration?
It is a process in which carefully
measured volumes of a base are
added to a solution of an acid in order
to determine the acid concentration.

Monitoring Acidity
When chemically equal (equivalent)
amounts of acid and base are present
during a titration, the equivalence
point is reached.
The equivalence point is detected by
using an indicator chemical that
changes color or by following the pH
of the reaction versus added base,
i.e. a titration curve.

Titration Curve (HOAc with NaOH)

pH

moles OH per mole acid

Titration Curve (HOAc with NaOH)

At the equivalence point, only the

salt (NaOAc) is present in
solution.
At the inflection point, equal
moles of salt and acid are present
in solution.
[HOAc] = [NaOAc]
pH = pKa

Titration Curve (HOAc with NaOH)

The pKa for acetic acid is 4.76.

1. Calculate the relative percents of

acetic acid and acetate ion when
the acid is titrated with 0.7
equivalents of NaOH.
2. Use the Henderson-Hasselbalch
equation to calculate the pH at this
point.

Titration Curve (HOAc with NaOH)

0.7 equivalents of NaOH neutralizes 0.7 eq
of acid producing 0.7 eq of salt and leaving
0.3 eq of unneutralized acid.
pKa of HOAc is 4.76

pH = 4.76 + log [0.7]

[0.3]
30% acid and 70% salt.

pH=5.13

Buffer Solutions
Buffer: a solution that resists
change in pH when small amounts
of strong acid or base are added.
A buffer consists of:
a weak acid and its conjugate base or
a weak base and its conjugate acid

Buffer Solutions
Maximum buffer effect occurs at
the pKa for an acid.
Effective buffer range is +/- 1 of
the pK value for the acid or base.
eg. H2PO4-/HPO42-, Ka=7.20
buffer range 6.20 - 8.20 pH

Buffer Solutions
High concentrations of acid
and conjugate base give a
high buffering capacity.
Buffer systems are chosen
to match the pH of the
physiological situation,
usually around pH 7.

Buffer Solutions-4
Within cells the primary buffer is
the phosphate buffer:
H2PO4-/HPO42 The primary blood buffer is the
bicarbonate system: HCO3-/H2CO3.
Proteins also provide buffer
capacity. Side chains can accept
or donate protons.

Buffer Solutions
A zwitterions is a compound
with both positive and
negative charges.
Zwitterionic buffers have
become common because
they are less likely to cause
complications with
biochemical reactions.

Buffer Solutions
N-tris(hydroxymethyl)methyl2-aminoethane sulfonate
(TES) is a zwitterions buffer
example.
(HOCH2)3CN+H2CH2CH2SO3-

Buffer Solutions
Buffers work by chemically tying up
acid and base. Eg.:

HCO3- + H3O+

H2CO3 + H2O

H2CO3 + OH-

HCO3- + H2O

Buffer Solutions
Calculate the ratio of lactic acid to lactate
in a buffer at pH 5.00. The pKa for lactic
acid is 3.86

5.00 = 3.86 + log [lactate]

[lactic acid]
5.00-3.86 = log [lactate]
[lactic acid]
antilog 1.14 = [lactate]
= 13.8
[lactic acid]

Biomolecules
Biological Molecules
Monomers / Polymers
Sugar / Polysaccharide
Nucleotide / Nucleic Acids
Amino Acid / Polypeptides

Amino acids:
Amino acids are organic acids containing an
amine group. The most common amino acids are
the L- -amino acids.
It is important to understand the following about
amino acid structure:
Only 20 L- - amino acids are used to make
proteins.
Rare exceptions are bacterial membrane proteins,
which contain a few D-Amino Acids, modified
amino acids - primarily lysine and proline, and
occasional incorporation of the rare amino acid,
selenocysteine).

 The alpha position in all a. a. except

Glycine is a stereocenter (Chiral
molecules).
So all can exist as pairs of enantiomers.
All naturally occurring a. a. belong to the
same optical family (L-family)
CO2-

C
R

D-Family a.a.

O2C

NH3+

NH3+

R
L-family a.a.

 Side groups (labelled "R") are what

distinguish the amino acids from each
other.
Amino acids can exist as zwitterions substances containing equal numbers of
positive and negative charge - due to their
carboxyl and amine groups, which can be
negatively and positively charged,
respectively.
Several common amino acids found in
cells, such as ornithine and citrulline,
are not used to make proteins.

 Amino acids are the monomeric units or

"building blocks" of proteins that are
joined together covalently in peptide
bonds

Amino acids are built into proteins by the

process of translation using the genetic
code.
O

O
NH2 - CH - C - OH
R

NH3 - CH - C - O
R

_
NH3 - CH - C - O

- NH - CH - C R

R
General structral
features of -amino
acids
+

Amino acids residue

(peptide unit)

NH3-CH-C(O) NH-CH-C(O)-O-

Peptide bond

Type

Side chain (R)

Name

Symbol

Non-polar
side chain

-H
- CH3

Glycine

Gly

Alanine

Ala

- CH (CH3)2

Valine

Val

- CH2CH(CH3)2

Leucine

Leu

-CH(CH3)CH2-CH3

Isoleucine

Ile

-CH2C6H5

Phenylalanine

Phe

Trptophan

Trp

Proline

Pro

(Proline is
the only 1 of
the standard
20 a.a. in
which the
amino group
is itself
joined to one
end of the
side chain)

CH2

N
H

OOC
H2N+

Type

Side chain (R)

- CH2OH
Side
chain has - CH(CH3)OH
a hydroxyl
group

Name

Symbol

Serine

Ser

Threonine

Thr

Tyrosine

Tyr

Aspartic
Side
- CH2CO2H
acid
chain has
a carboxyl
Glutamic
CH
CH
CO
H
2
2
2
group or
acid
amide
- CH2 CONH2
Asparagine
group
- CH2 CH2 CONH2 Glutamine

Asp
Glu
Asn
Gln

Type

Side chain (R)

Side
- (CH2)4NH2
chain has
(CH2)3NHC(NH)NH2
a basic
amino
N
group
CH
2

Side
chain
contains
sulphur

N
H

- CH2SH
- CH2 CH2 SCH3

Name

Symbol

Lysine

Lys

Arginine

Arg

Histidine

His

Cysteine

Cys

Methionine

Met

Sugars
Sugars and polymers of them are known as
carbohydrates because their general formulas can
all be written in a simple form as (CH2O)x, as if
they were a hydrated form of carbon. Another term
used to describe sugar-based molecules is rooted
in the word "saccharide" (from the Latin,
saccharum; meaning sugar).
Single units of sugar, such as glucose, are called
monosaccharides. Sugars can be readily linked
together to form disaccharides (contains two
sugars),olegosaccharides
(contains several
sugars) and polysaccharides (contains many
sugars).

CH

OH

CH2-OH

C-H

D-Erythrose

CH

C-H

D-Glyceraldehyde

OH

HO

OH

C H2-OH
O
OH

OH

OH

OH

HO

OH

H
H

C-H
OH
OH

HO
H

C-H
H
OH

OH

OH

OH

OH
C H2-OH

Altrose

HO

HO

C-H
H
H

HO
HO

OH

OH

HO

OH

OH

C H2-OH

Mannose

H
H

C H2-OH

C-H

OH

Xylose

C-H
OH
H
H
HO

Glucose

OH

C H2-OH

C H2-OH

C-H

OH

Arabinose

Allose

C H2-OH

Ribose

C H2-OH

O
C-H

HO

C H2-OH

O
C-H

OH

D-Threose

C H2-OH
O

C-H

Lyxose

O
C-H

C-H

C-H

OH
OH

HO
H

H
OH

H
HO

OH
H

HO
HO

H
H

HO

HO

HO

OH

OH

OH
C H2-OH

Gulose

OH
C H2-OH

Idose

C H2-OH

Galactose

C H2-OH

Talose

CH2OH

CH2OH

CH2OH
H

H
C
OH
HO

H
H

OH

-glucose

H
C
OH

C
OH

HO

H
C
OH

O
H

OH

Open form of
glucose

C
H

HO

OH
H

OH

C
H

-glucose

In aged glucose solutions, all three forms of glucose exist in equilibrium

Chair forms of glucose

H
C
HO

CH2OH
O
C
H
OH H
C
C
H

OH

-glucose

H
C
HO
H
C
OH

CH2OH
O
C
H
H
H
OH
O
C
C
C
H
OH H
Open form of
glucose

C
HO

CH2OH
O
C
H
OH H
C
C
H

OH

-glucose

OH
C
H

Twist this
end up

Chair form

Boat form
Then twist
this end down

Chair form

The
boat
form
is
another conformation
of the ring that permits
normal bond angles,
and
the
ring
has
enough flexibility to be
able to twist from the
chair to the boat form.

Ribose and 2-Deoxyribose

Ribose & 2-deoxyribose are aldopentoses
important to nucleic acid structures.
Both of them are building blocks of nucleic
acids, and each can exist in the three forms,
two cyclic hemiacetals and an open form.
HO CH2

H H
OH

OH

H
OH

- ribose

HO CH2

H H
OH

OH

-2-deoxyribose

Lipids
Lipids are a class of nonpolar molecules
that include the fats, fatty acids, lipid
soluble vitamins, cholesterol, waxes,
soaps, glycerophospholipids,
sphingolipids, and others.
Lipids are found in the membranes of
cells, the endoplasmic reticulum, and in
specialized fat storage cells called
adipocytes.

Lipids
Hydrolysable
Lipids

Non-hydrolysable
Lipids

Sterols

Terpenes

Others

Waxes
Triacylglycerols

Animal
fats

Vegetable
oil

Esters of
glycerol

Esters of
sphingosine

Plasmalogens
Phosphatides

Cerebrosides

Sphingomyelins

 Lipids
are
broadly
subdivided
according
to
the
presence
of
hydrolysable
groups
(consist
of
compounds with one or more groups
that react with water) [ester groups]
Neutral fats include such familiar food
products as butter fat, tallow, olive oil,
palm oil, etc...
Non-hydrolysable group, which lack
group that react with water such as
steroids that include cholesterol and
many sex hormones.

Nucleotides
Ribonucleotides and deoxyribonucleotides
(collectively called nucleotides) are the building
blocks of the nucleic acids, RNA and DNA,
respectively. Nucleotides are composed of a
sugar, a phosphate, and a base.
The composition of DNA differs from that of RNA
in only two respects. First, DNA uses
nucleotides containing the sugar deoxyribose.
RNA's nucleotides contain the sugar ribose.
Second, DNA uses the bases adenine, guanine,
cytosine, and thyamine. RNA uses the bases
adenine, guanine, cytosine, and uracil.

base NH2

A nucloetide is
C
N
the repeating
C
phosphate N
unit of the DNA
CH
or RNA polymer. ester
C N
HC
The nitrogen
N
2base is attached
O3PO CH2
b to the ribose
O
(RNA) or
H
H
deoxyribose
H
(DNA) ring. The
H
sugar is
OH H
phosphorylated
deoxyribose sugar
at carbon 5

NH2

NH2
N

C N
N
O P O CH2
O
O
H
H
H
H
OH H
O

HC

CH

N
O

O P O CH2
O
H

2- deoxy

Deoxyadenosine
5-monophosphate

C
N

CH
CH

H
H

OH

Deoxycytidine
5-monophosphate

 Nucleotides differ from nucleosides in that

the latter do not contain phosphate, so we
sometimes refer to nucleotides as
nucleoside (mono, di, or tri)-phosphates. For
example, adenosine diphosphate is a
nucleotide
(also
called
ADP)
Deoxyribonucleotides (written with a 'd')
differ from ribonucleotides in containing
deoxyribose as the sugar moiety instead of
ribose.
In
some
naming
schemes,
deoxythymidine nucleotides are written
without the 'd', but the 'd' convention will be
used here.

Segment of DNA Chain

5-end
N

O
C

C N

C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O

guanine

CH

N
C

O
C

O
N
O P O CH2
O
O
H
H
H
H
H
O

3-5
link

CH3

C
CH

thymine

NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H

3-end

cytosine

Vitamins

Vitamins are organic molecules that

are essential to the biological
processes of higher organisms, but
cannot be synthesized by these
organisms. Examples include the fatsoluble vitamins A, D, E, and K and
the
water-soluble
B
complex
vitamins and ascorbic acid, also
known as vitamin C.

Hormones
A hormone is a substance that is synthesized and
secreted by specialized cells and carried via the
circulation to target cells, where it elicits specific
changes in the metabolic behavior of the cell by
interacting with a hormone-specific receptor.
Chemically, the hormones in vertebrate
metabolism include
(1) peptides or polypeptides, such as insulin or
glucagon
(2) steroid, including glucocorticoids and the sex
hormones
(3) amino acid derivatives, including the
catecholamines and thyroxine.

 Hormonal mechanisms include:

(1) enzyme activation or inhibition via second
messengers, as noted for epinephrine and
glucagons
(2) stimulation of the synthesis of particular proteins,
through activation of specific genes
(3) selective increases in the cellular uptake of certain
metabolites.
Among this last category are some receptors that
serve directly as ion channels, with hormone
binding causing a conformational change that opens
the channel, and other receptors that stimulate
uptake by still-unknown mechanisms, such as the
effects of insulin upon glucose uptake.

Biochemistry as a Biological Science

Distinguishing Characteristics of Living Matter
Constant renewal of a highly ordered structure
accompanied by an increase in complexity of
that structure.
Overcoming entropy requires energy.
Life is self-replicating.
Unit of Biological Organization: The Cell
Prokaryotes (Bacteria)
Eubacteria
Archaebacteria
Eukaryotes (Compartmentalization of
organelles) (animal and plant cells)
Windows on Cellular Functions: The Viruses

The Uses of Biochemistry

Agriculture
Medicine
Nutrition
Clinical Chemistry
Pharmacology
Toxicology