 1. Chemical components
 2. Molecular structures
 3. Structure-function relationship
 4. Physical and chemical properties
 5. Exploration of proteins

Proteins are macromolecules composed of amino acids linked together through peptide bonds .

Element components of proteins

 major elements
C, H, O, N, S.
trace elements
P, Fe, Cu, Zn, I, …


The average nitrogen content in proteins is about 16%.
The protein quantity can be estimated.
protein in 100g sample = N per gram x 6.25 x 100

The basic building blocks of proteins
Amino Acids only 20 types of amino acids are used for protein synthesis in biological systems.
L-α-Amino acid

H
2
N
COOH
C
¦Á
H
R
²à Á´
¹² ͬ²¿ ·Ö


Amino acids are grouped as
(1) non-polar, hydrophobic;
(2) polar, neutral;
(3) acidic;
(4) basic.


Gly
optically inactive

Pro Having a ring structure and imino group

Cys active thiol groups to form disulfide bond

A peptide is a compound of amino acids linked together by peptide bonds .

A peptide bond is a covalent bond formed between the carboxyl group of one AA and the amino group of its next AA with the elimination of one H2O molecule.

Glutathione (GSH)
As a reductant to protect nucleic acids and proteins
Peptide hormones
Neuropeptides responsible for signal transduction

Section 2
Molecular Structures of Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Spatial structure

The primary structure of proteins is defined as a linear sequence of amino acids joined together by peptide bonds.
Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment, that is, the relative positions of backbone atoms of this peptide segment.
H-bonds are responsible for stabilizing the secondary structure.

Repeating units of Ca-C(=O)-N(-H)-
Ca constitute the backbone of peptide chain.
Six atoms, Ca-C(=O)-N(-H)-Ca , constitute a planer peptide unit.

Four common types of secondary structure




α-helix
β -pleated sheet
β -turn random coil

When several local peptides of defined secondary structures are close enough in space, they are able to form a particular structure---
Motif .
Zinc finger
HLH (helix-loop-helix)
HTH (helix-turn-helix)


The tertiary structure is defined as the three-dimensional arrangement of all atoms of a protein.

Five types of interactions stabilize the protein tertiary structure.




• hydrophobic interaction
• ionic interaction
• hydrogen bond
• van der Waals interaction

• disulfide bond

Large polypeptides may be organized into structurally close but functionally independent units--Domain

Chaperones are large, multisubunit proteins that promote protein foldings

The quaternary structure is defined as the s p a t i a l a r r a n g e m e n t o f multiple subunits of a protein.
These subunits are associated through H-bonds, ionic interactions , and hydrophobic interactions .

From primary to quaternary structure


Constituents simple protein conjugated protein = protein + prosthetic groups
Overall shape
Globular protein long/short < 10
Fibrous protein long/short > 10

Section 3 Structure-Function
Relationship of Proteins

Relationship between primary structure and function
Primary structure is the fundamental to the spatial structures and biological functions of proteins.

1.
2.
Proteins having similar amino acid sequences demonstrate the functional similarity .
The alternation of key AAs in a protein will cause the lose of its biological functions .

Relationship between spatial structure and function

A particular spatial structure of a protein is strongly correlated with its specific biological functions .

1.The denatured protein remains its primary structure , but no biological function.
2.
Allosteric change of hemoglobin by O
2

Section 4 Physical and Chemical
Properties of Proteins
1.
Amphoteric


The pH at which the protein has zero net-charge is referred to as isoelectric point (pI)

Hydration shell and electric repulsion make proteins stable in solution.

3 Protein denaturation renaturation, precipitation and coagulation

The process in which a protein loses its native conformation under the t r e a t m e n t o f d e n a t u r a n t s i s referred to as protein denaturation .
•
Applications sterilization, lyophilization



Trp, Tyr, and Phe have aromatic groups of resonance double bonds .
Proteins have a strong absorption at 280nm



Biuret reaction
Ninhydrin reaction


Isolation and purification
• Centrifugation
• Dialysis
• Precipitation
• Chromatography
• Electrophoresis

Protein Sequence Determination


Edman degradation
Deduction from DNA sequence





Circular dichroism spectroscopy
X-ray crystallography
Nuclear magnetic resonance spectroscopy
Computer simulation