Lecture 2

Proteins, polypeptides, and amino acids

• Proteins - functions and synthesis

• Polypeptides

• Amino acids

• Ionisation and pI

• Primary Structure

• Peptide bonds
 Signalling between tissues and cells

Control proteins
What do proteins do? Receptors
Just about everything!!!!
Biosynthesis of proteins (translation)
Enzymes

Physiological functions
Breakdown of nutrients (fuels)

RNA transcription Structural proteins

Proteins are the working molecules of life.

Transport across membranes

Signalling molecules Biochemical functions

DNA replication Antibodies
Biosynthesis of cellular components

Carrier molecules
Cell structure (shape) and flexibility Movement
 Protein synthesis

Transcription
DNA
mRNA

Translation
mRNA

polypeptide

Campbell Fig 17.26

 Polypeptides are linear polymers of
amino acids.
1 333

There are 20 amino acids used to build proteins.

amino group

NH2

carboxyl group
H C COOH
R

-carbon
 The general structure of a polypeptide

Campbell Fig 5.18

 Proteins fold into complex shapes
1 333
Proteins are linear
polymers of amino
acids.
333

The biologically
functional forms of
proteins are folded
into specific
3-dimensional
structures.

1
 Staphlococcal
Myoglobin nuclease

Triose
phosphate Pyruvate
isomerase kinase
 Amino Acids are Stereoisomers
(optical mirror images)
All amino acids (except glycine) have four different
groups attached to the
-carbon.

Only L-amino acids are found in proteins.

H R R H

C
C

NH3+ COO- COO- NH3+

L isomer D isomer
 The properties of the 20 amino acids are a
function of their side-chains (R-groups).

Side chains vary in:

 Size.

 Shape.

 Charge.

 Hydrogen bonding capacity.

 Chemical reactivity.

Hydrophobic

Learn these

Phe Lys
Pro Ala
Gly Ser
Asp Cys

Hydrophilic

Campbell Fig 5.17

See also E&E p49-51
[36-7]
Amino Acids are Dipolar Ions at Physiological
pH

NH2 • uncharged
H C COOH
R

• in aqueous solution at pH 7
NH3+ “zwitterions”
H C COO-
R
The carboxyl group has lost a proton.

The amino group has gained a proton.
 Charge on Amino Acid Changes With pH
–NH3+ and –COO- groups change their ionisation state
with changes in pH.

H+ NH3+ H+ NH2
NH3+
H C COOH H C COO- H C COO-
R H+ R H+ R
Predominant Predominant Predominant
structure at pKa ~ 2.5 structure at pKa ~ 9.5 structure at
acid pH neutral pH alkaline pH

pKa = the pH at which a group is 50% dissociated

 If the pH is less than the pKa value
the proton is on.

If the pH is greater than the pKa value

the proton is off.
 Titration of Alanine
CH3 CH3 CH3
pKa 1 pKa 2
HC NH3+ HC NH3+ HC NH2
C OH C O- C O-
O +1
2.35 O 0 9.87 O -1

pH

Moles OH- Added

 Ionisation of Amino Acids

Some amino acids also have titrateable side chains.

Ex. The titration of glutamate (glutamic acid)

 Titration of Glutamate
(An acidic amino acid)
O O O O
-
C OH C OH C O C O-
(CH2)2 pKa 1 pKa2 (CH ) pKa 3
(CH2)2
(CH2)2 2 2
HC NH3+ HC NH3+ HC NH3+ HC NH2
C OH 2.1 C O- 4.07 C O- 9.47 C O-
+1 O 0O -1 O -2 O

pH

Moles OH- added

 pI

Isoelectric point: the pH at which a molecule

carries no NET charge

pI= 1 (pKi + pKj)

2