basics of biochemistry

1. Introduction to biochemistry
AMNU 214

2. Course grade distribution
Final Exam 40%
Mid Term Exam 20%
Quizzes 20%
Assignments 20%
Total 100%

8. Proteins
Proteins are polymers of amino acids
Each has a unique 3D shape
Amino acid sequences vary
Proteins are major component of cell parts
The provide:
support and structural components
Several types of proteins are identified:
receptor, contractile, defense, enzymes,
structural

9. Building Blocks: Amino Acids
There are 20
different types
of amino acids
All have this
general formula
The R group is a
variable group

11. Polar vs. Non-polar Amino Acids
 Some amino acids are polar while some are non-polar

12. Amino acids may be either polar or non-polar depending on the composition of their
side chain
Polar amino acids have hydrophilic R groups, while non-polar amino acids have
hydrophobic R groups

13. The localization of polar and non-polar amino acids will be determined by the
type of protein and its function:
Water soluble proteins:
•Non-polar amino acids tend to be found in
the center of the molecule (stabilize the
structure)
•Polar amino acids tend to be located on the
protein surface (capable of interacting with
water molecules)

15. Membrane-bound proteins:
•Non-polar amino acids tend to be
located on the regions of the surface in
contact with the membrane
•Polar amino acids will generally line
interior pores (to create hydrophilic
channels)

16. Significance of polar & non-polar amino acids
polar amino acids non-polar amino acids
 Hydrophilic
 can make hydrogen bonds
 found in hydrophilic
channels & parts of proteins
projecting from membranes
 found on surface of water-
soluble proteins
 hydrophobic
 forms van der Waals
(hydrophobic interactions)
with other hydrophobic amino
acids
 found in proteins in interior of
membranes
 found in interior of water-
soluble proteins

17. Peptide Bonds
 Proteins are formed
by condensation
 A peptide bond is
formed

18. Four levels of protein structure

19. Primary Structure
 Primary structure is a
chain of amino acids
 number & unique
sequence of amino acids
determine the properties
of primary structure
 each position is occupied
by one of 20 different
amino acids
 sequence of amino acids
is determined by DNA
sequence in genes
 linked by peptide bonds

20. Secondary structure
 formed by interaction
between amino and carboxyl
i.e. -NH and -C=O groups
 weak hydrogen bonds are
formed between – H & = O
 there are two types: a-helix
and b-sheet
 α- helix formed / polypeptide
coils up e.g. sheep wool
 β- pleated sheet formed e.g.
silk in spider web
 regular repeated folding of
amino acid chain
 secondary structure is
stabilized by hydrogen bonds

21. Tertiary structure
 These are globular proteins
with irregular conformation
 tertiary structure is the
folding up of the polypeptide
chain, secondary structure or
alpha helix
 it gives three dimensional
globular shape i.e. shape of
active site
 the structure is stabilized by
disulphide bridges, hydrogen,
ionic& hydrophobic bonds
 tertiary structure used as
enzymes to catalyze
biochemical reactions

22. Quaternary structure
 made of several
polypeptide subunits
joined together
 they maybe conjugated
proteins i.e. proteins
which combine with a
prosthetic group (non-
protein molecules)
 prosthetic groups
includes: metals e.g. iron
in haemoglobin, nucleic
acids as in ribosomes ,
carbohydrates as in
glycoprotein or lipids as
in glycolipids

23. Denaturation of Proteins
 change in protein’s
usual regular
structure due to:
 High temp
 Change in pH
 Addition of organic
solvent (alcohol,
acetone)
 These factors break
the bonds that
stabilize the
structure

24. Protein Functions
Function Examples
 Structure
 Transport
 Enzymes
 Movement
 Hormones
 Antibodies
 storage
 – collagen/keratin/fibrin
 – myoglobin/hemoglobin, bind &
transport oxygen
 – lysozyme, speeding up metabolic
reactions
 – actin (and myosin tropomyosin (and
troponin)
 – insulin, regulate blood glucose
 – immunoglobulin
 – albumin in egg, casein in milk