Chapter 1

Protein

Contents

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

What are proteins?

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

Section 1 Chemical Components of

Proteins

major elements C, H, O, N, S. trace elements P, Fe, Cu, Zn, I, …

Element components of proteins

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

only 20 types of amino acids are used for protein synthesis in biological systems.

L-α-Amino acid

The basic building blocks of proteins

Amino Acids

L-α-Amino acid

COOH

C HH2N

R

¹² ͬ²¿ ·Ö¦Á

²à Á´

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

Special amino acids

Gly

Pro

Cys

optically inactive

Having a ring structure and imino group

active thiol groups to form disulfide bond

Peptide

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

peptide bond

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.

Biologically activepeptides

Glutathione (GSH) As a reductant to protect nucleic acid

s and proteinsPeptide hormones Neuropeptides responsible for signal

transduction

Section 2 Molecular Structures of Proteins

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

Spatial structure

Primary Structure The primary structure of proteins is def

ined as a linear sequence of amino acids joined together by peptide bonds.

Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

Secondary 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

                                                       

                                       

Motif

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)

Tertiary Structure

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

Domain

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

Chaperon

Chaperones are large, multisubunit proteins that promote protein foldings

Quaternary Structure

The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein.These subunits are associated

through H-bonds, ionic interactions, and hydrophobic interactions.

From primary to quaternary structure

Protein classification 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 structu

re and function Primary structure is the fundamental t

o the spatial structures and biological functions of proteins.

Example

1. Proteins having similar amino acid sequences demonstrate the functional similarity.

2. 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.

Example

1.The denatured protein remains its primary structure, but no biological function.

2. Allosteric change of hemoglobin by O2

Section 4 Physical and Chemical Properties of Proteins

1. Amphoteric

isoelectric point (pI) The pH at which the protein has zer

o net-charge is referred to as isoelectric point (pI)

2. Colloid property

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 treatment of denaturants is referred to as protein denaturation.

• Applicationssterilization, lyophilization

4 UV absorption

Trp, Tyr, and Phe have aromatic groups of resonance double bonds.

Proteins have a strong absorption at 280nm

5 Coloring reactions

Biuret reaction Ninhydrin reaction

Section 5 Exploration of Protein

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

Protein Sequence Determination

Edman degradation Deduction from DNA sequence

StructureDetermination

Circular dichroism spectroscopy X-ray crystallography Nuclear magnetic resonance spectr

oscopy Computer simulation