Fundamentals of Protein Structure

Proteins play key roles in a living system

Three examples of protein functions
Catalysis:
Almost all chemical reactions in a living cell are catalyzed by protein enzymes.
Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones

Transport:

Some proteins transports various substances, such as oxygen, ions, and so on.

Haemoglobin carries oxygen

Information transfer:

For example, hormones.

Insulin controls the amount of sugar in the blood

Amino acid: Basic unit of protein

R
Amino group

NH3

Different side chains, - R, determin the COO properties of 20 Carboxylic acid group amino acids.

An amino acid

20 Amino acids
Glycine (G)
Alanine (A) Valine (V) Isoleucine (I) Leucine (L) Proline (P) Methionine (M) Phenylalanine (F)

Tryptophan (W)

Asparagine (N)

Glutamine (Q)

Serine (S)

Threonine (T)

Tyrosine (Y)

Cysteine (C)

Asparatic acid (D) Glutamic acid (E)

Lysine (K)

Arginine (R)

Histidine (H)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

Proteins are linear polymers of amino acids

R1 R2 NH3 C COO NH3 C COO H H A carboxylic acid
H 2O H2 O

R1
H
A

R2
Peptide bond
S

R3
Peptide bond

condenses with an amino group with the release of a water

NH3 C CO NH C CO NH C CO H
T D

H
A

The amino acid sequence is called as primary structure

Amino acid sequence is encoded by DNA base sequence in a gene

DNA molecule G C G C T T A A G C G C DNA base C G sequence C G A A T T C G C G

Amino acid sequence is encoded by DNA base sequence in a gene

T
T
TTT TTC TTA TTG CTT CTC CTA CTG ATT ATC ATA ATG GTT GTC GTA GTG Phe Leu

C
TCT TCC TCA TCG CCT CCC CCA CCG ACT ACC ACA ACG GCT GCC GCA GCG

Second letter A
Ser TAT TAC TAA TAG CAT CAC CAA CAG AAT AAC AAA AAG GAT GAC GAA GAG Tyr Stop His Gln Asn Lys Asp Glu

G
TGT TGC TGA TGG CGT CGC CGA CGG AGT AGC AGA AGG GGT GGC GGA GGG Cys Stop Trp Arg T C A G T C A G T C A G T C A G

Third letter

Leu

Pro

First letter

Ile Met Val

Ser Arg

Thr

Ala

Gly

Gene is proteins blueprint, genome is lifes blueprint

DNA Gene

Protein

Each Protein has a unique structure

Amino acid sequence

NLKTEWPELVGKSVEE AKKVILQDKPEAQIIVL PVGTIVTMEYRIDRVR LFVDKLDNIAEVPRVG

Folding!

Basic structural units of proteins: Secondary structure

-helix -sheet

Secondary structures, -helix and -sheet, have regular hydrogen-bonding patterns.

Three-dimensional structure of proteins

Tertiary structure

Quaternary structure

Hierarchical nature of protein structure

Primary structure (Amino acid sequence) Secondary structure -helix, -sheet Tertiary structure Three-dimensional structure formed by assembly of secondary structures Quaternary structure Structure formed by more than one polypeptide chains

Close relationship between protein structure and its function

Example of enzyme reaction
substrates enzyme

Hormone receptor

Antibody

A B

enzyme

Matching the shape to A

enzyme

Digestion of A!

A
Binding to A