Chapter 1

Protein

Contents

1.
2.
3.
4.
5.

Chemical components
Molecular structures
Structure-function relationship
Physical and chemical properties
Exploration of proteins

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

Section 1
Chemical Components
of
Proteins

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 estimate

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--Amino acid

L--Amino acid
COOH
H2N

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

Having a ring structure and imino group

Cys

active thiol groups to form disulfide

bond

optically inactive

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 active
peptides

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

Primary 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.

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

-helix
-pleated sheet
-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 thespatial 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 <

Fibrous protein

long/short >

10

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

Example
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.

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 zero 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
The process in which a protein
coagulation
loses its native conformation
under the treatment of
denaturants is referred to as
protein denaturation.

Applications
sterilization, 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
Protein
Isolation and purification
Centrifugation
Dialysis
Precipitation
Chromatography
Electrophoresis

of

Protein Sequence
Determination

Edman degradation
Deduction from
DNA
sequence

Structure
Determination

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