1. LESSON PLAN 1 2 Introduction to biochemistry I and II 2,3 2+1
Week
Total Hours
Contents 1 2
Introduction to biochemistry I and II
2,3
2+1
Carbohydrates 3
Lipid 4 5 6 7
8, 9
9,10
1+1
Enzymes: Biological catalyst 10
Test 2 – amino acid and protein 11 12
13,14 14
Test 3 – enzymes and nucleic acid
15, 16
Final examination (26/10/09 – 15/11/09)
LESSON PLAN
Semester break
1+1
Lipid 1
Test 1 – carbohydrate and lipid
Proteins: Amino acids
Proteins
Enzymes: Biological catalyst
Hari Raya break (19 – 27 Sept)
Nucleic Acid
Overview of metabolism

2. Protein: MONOMER – AMINO ACID

3. Proteins are polymers of amino acids.
What is protein?
Proteins are polymers of amino acids.
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure

4. What is amino acid?
Amino acid: a compound that contains both an amino group and a carboxyl group attach to -carbon
-carbon also bound to side chain group, R
R gives identity to amino acid

5. Terminology
 - carbon = the carbon that attach next to the carboxyl group
 - amino group = amino group that attach to -carbon
Other type of amino group – eg. in Lysine, has
-amino group
Lysine

6. Amino acid All 20 are -amino acids
2. For 19 of the 20, the -amino group is primary; for proline, it is secondary amino acid
-Amino acid has an amino group attached to the carbon (-carbon) adjacent to the carboxyl group

7. Amino acids as dipolar ions
Generic amino acid at physiological pH amino acids exist as dipolar ionic species (have positive and negative charge on the same molecule) - zwitterion form
Physiological pH
Amino acid is an amphoteric molecule – act either as an acid or a base
Amino acids as dipolar ions
 - carboxyl group  carboxylate ion
 - amino group  protonated amino acid

8. Enantiomer
The amino acids can exist in two enantiomeric forms (nonsuperimposable mirror image) forms – exceptional for glycine
Two steroisomers of amino acids are designated L- or D-.
L – amino acid: abundant in nature, found in proteins, amino group on the left
Mirror plane
a carbon

9. Amino acid
Only the L - form of amino acids is commonly found in proteins.
Depending on the nature of the R group, amino acids are classified into four groups.
1. nonpolar
2. polar – neutral/uncharged side chain
3. acidic
4. basic
Vs monosaccharide : D - form
Polar, charged

10. Classification of amino acid
Nonpolar (9 amino acids)
Polar neutral/uncharged (6 amino acids)
charged basic (3 amino acids)
acidic (2 amino acids)

11. Classification of amino acids
Simplest amino acid due to the R group = H
No stereoisomer because the is achiral
Nonpolar

12. Amino acids with nonpolar side chains - hydrophobic
Aliphatic cyclic structure – N is bonded to C2 atoms
Amino group of become secondary amine – often called an imino acid
Amino acids with nonpolar side chains - hydrophobic

13. Polar uncharged Amide bond – highly polar Phenol
Thiol / sulfhydryl group – polar
– under oxidizing condition, with other thiol groups to form disulfide bridges (-S-S-) – important in 3o structure

14. Polar charged
Basic
Aspartate
Acidic
Glutamate

15. Essential Amino acid
An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet.
vs non-essential amino acid

16. Ionization of Amino Acids
• Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge
In acidic solution – as base (protonation)
In basic solution – as acid (deprotonation)

17. Ionization of amino acids
At physiological pH, the carboxyl group of the amino acid is negatively charged and the amino group is positively charged.
Amino acids without charged side chains (Group 1 and 2) are zwitterions and have no net charge. (H3+N-HCR-COO- ).
A titration curve shows how the amine and carboxyl groups react with hydrogen ion.

18. Titration of amino acid
At low pH a nonacidic/nonbasic amino acid is protonated and has the structure H3N+HCRCOOH (amino acid in cationic form)
Increase of pH, dissociation of proton (H+) from –COOH group form H3N+HCRCOO- (amino acid in zwitterionic form)
At pK1, amount of cationic form = amount of zwitterionic form
Beyond pK1, additional base ions will results in all amino acids in cationic forms deprotonated to zwitterionic forms – all amino acids have no net charge
pI = isoelectric point = pH at which the amino acid has no net charge/all amino acids are in zwitterionic form
Increase of pH beyond pI, will cause the dissociation of H+ / deprotonation
from H3N+ resulting in formation of H2NHCRCOO- (anionic form)
Increase of pH, more dissociation of proton (H+) from –H3N+group, more amino acids in anionic form
At pK2, amount of zwitterionic form = amount of anionic form

19. Titration of Alanine
• When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion
Anionic form
pI (isoelectric point) = pH at which the amino acid has no net charge/ all amino acids are in zwitterionic form
All amino acids are in the zwitterion form – at isoelectric point (pI)
Cationic form

20. Titration of amino acid
pK1 and pK2 are proton dissociation constant from carboxyl group and amino group
From titration of amino acid, the pI can be calculated
The charge behavior of acidic and basic amino acids is more complex. – Group Polar/charged amino acid

21. Terminology
• peptide: the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain • dipeptide: a molecule containing two amino acids joined by a peptide bond • tripeptide: a molecule containing three amino acids joined by peptide bonds • polypeptide: a macromolecule containing many amino acids joined by peptide bonds • protein: a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains
Primary structure = one polypeptide

22. Protein: 1o , 2o and 3o structure

23. Peptide * * * * *
Amino acid residue: a monomeric unit of amino acids

24. PROTEIN STRUCTURE :OVERVIEW

25. Primary structure
Primary (1o) Structure = sequence of a chain of amino acids. Determines the final structure, eventually the properties of proteins

26. Peptide bond The amino acids are linked through peptide bond
Peptide bond: the special name given to the amide bond between the -carboxyl group of one amino acid and the -amino group of another amino acid
peptide bond – covalent bond

27. Peptide bond: Feature 5 1 2 3 4
Free rotation
COO-
NH3+
Peptide bond – in trans configuration, acts as a rigid and planar unit. Has limited rotation around the peptide bond (C-N).

28. Secondary structure
The planar peptide group and free rotating bonds between C-N and C-C are important
Two types: -helix and -pleated sheet
2o structure: involves the hydrogen-bonded arrangement of the backbone of the protein
N O

29. Secondary structure: -helix
Structural features:
One polypeptide chain
Hydrogen bonds between the -CO and the –NH in the same polypeptide chain (intrachain)
The hydrogen bonds are parallel to the helix axis
Winding can be right- or left- handed (L- amino acid favor right-handed) 
H bond 
N O

30. Secondary structure: -pleated sheet
Structural features:
More than one polypeptide chain
Two types: antiparallel and parallel pleated sheet
Hydrogen bonds between the -CO and the –NH in the same polypeptide chain or with other polypeptide chain (interchain)
The hydrogen bonds are perpendicular to the direction of chain    

31. Secondary structure: -pleated sheet
antiparallel pleated sheet = peptide chains are in the opposite directions
parallel pleated sheet = chains are in the same direction, the N- and C- terminal ends are aligned

32. Tertiary structure Tertiary structure
Results from folding and packing of secondary structure
Bring together amino acid residues far apart, permitting interactions among their side chains
Tertiary structure
Is the three-dimensional arrangement of all atoms in protein molecule

33. Tertiary structure
Is the three-dimensional arrangement of all atoms in protein molecule
Involves non-covalent interaction and covalent bonds
Hydrogen bonds between the side chain
Hydrophobic interaction
Electrostatic interactions/attractions
Disulfide bonds – between the R group
Complexation with metal ions

34. Forces in 3˚ Structure Noncovalent interactions, including
hydrogen bonding between polar side chains, e.g., Ser and Thr
hydrophobic interaction between nonpolar side chains, e.g., Val and Ile
electrostatic attraction between side chains of opposite charge, e.g., Lys and Glu
electrostatic repulsion between side chains of like charge, e.g., Lys and Arg, Glu and Asp
Covalent interactions: Disulfide (-S-S-) bonds between side chains of cysteines

35. Native conformation: three-dimensional shape of a protein with biological activity
Tertiary or quaternary structures

36. Quaternary structure 2 3 4 1 Final level of protein structure
Association of more than one polypeptide chain to form a complex
Subunit = individual parts of a large protein molecule = polypeptide chain
Quaternary structure is the result of noncovalent interactions between two or more protein chains.
Noncovalent interactions
electrostatics,
hydrogen bonds,
hydrophobic 2 3 4 1

37. Quaternary Structure
Oligomers are multisubunit proteins with all or some identical subunits.
The subunits are called protomers.
two subunits are called dimers
four subunits are called tetramers

38. Structure of Hemoglobin
Quaternary structure
If a change in structure on one chain causes changes in structure at another site, the protein is said to be allosteric.
Many enzymes exhibit allosteric control features.
Hemoglobin is a classic example of an allosteric protein. – oxygen = positive cooperativity
Has four subunits = tetramers
Overall structure 22
Heme - Fe
Structure of Hemoglobin

39. Classification of protein
Proteins are classified in two ways:
Shape
Composition

40. Fibrous Proteins
Fibrous proteins: contain polypeptide chains organized approximately parallel along a single axis. They
consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature

41. Globular Proteins
Globular proteins: proteins which are folded to a more or less spherical shape
they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of -helix and -sheet

42. Comparison of Shapes of Fibrous and Globular Proteins

43. Proteins by Composition
Simple protein (apoprotein)
Contain only amino acids
ex. serum albumin and keratin
Conjugated protein
simple protein (apoprotein)
prostetic group (nonprotein)
ex. Glycoproteins, lipoproteins, metaloproteins - hemoglobin
Holo-
protein

44. Denaturation
Definition – complete loss of organized structure in a protein, destroys the physiological function of the protein.
Definition – The unfolding of protein
Eg. During cooking of egg
Albumin (white egg) – denatured by heat and changes from a clear, colorless solution to a white coagulum
Often irreversible – denatured protein cannot returned to its native biological form – lost of biological function – why microbes die when boiling

45. Due to loss of 2o 4o of protein structure, but not 1o , the amide bond (peptide bond) is intact

46. Denaturation Several ways to denature proteins
• Heat –  in temp,  vibrations within the molecule, the energy of these vibrations can disrupt the 3o
• pH –  or  pH, affect the charges of protein, the electrostatic interactions that normally stabilize the native conformation is reduced.
• Detergents (eg. SDS) - disrupt hydrophobic interactions, if the detergent is charged, this can also disrupt electrostatic interactions
• Reducing agents(eg. Urea) – will form stronger H bonds, stronger than within the protein. Also disrupt the hydrophobic interaction
• Heavy metal ions
Mechanical stress

47. Denaturation
Reversible denaturation – organic solvents (ethyl alcohol or acetone), urea, detergents and acid or base
Denaturants disrupt only noncovalent interactions not the covalent linkages of the primary structure
If removed, possible protein to unwound to native structure
eg. pH – addition of picric acid, protein (casein) precipitate
addition of NaOH, the solution clear

48. Denaturation -mercaptoethanol example of reversible denaturation.
-mercaptoethanol reduced the disulfide
bridges of protein  the unfolding of
3o structure,
the removal of -mercaptoethanol
will cause the oxidation of SH group
to form disulfide bridges again
and the 3o structure is recovered.

49. Protein
Functions