Lesson 2.2. Protein Structure

Primary Protein Structure

4 TYPES OF PROTEIN STRUCTURES:

• structure sequence of a chain of amino acids

Secondary Protein Structure

4 TYPES OF PROTEIN STRUCTURES:

• local folding of the polypeptide chain into helices or sheets

Tertiary Protein Structure

4 TYPES OF PROTEIN STRUCTURES:

• 3-D folding pattern of a protein due to side chain interactions

Quaternary Protein Structure

4 TYPES OF PROTEIN STRUCTURES:

• protein consisting of more than one amino acid chain

Primary Structure of Proteins (1° Structure)

order in which AA residue are specifically linked to each other in a protein chain

shape and function

The 1° structure defines the protein’s a.__________________. It is dictated by the b.______________________ in the gene.

a = ?

DNA base sequence

The 1° structure defines the protein’s a.__________________. It is dictated by the b.______________________ in the gene.

b = ?

number of AA residue, kind, and order of attachment

Each protein has its own unique AA sequence: ___________________________, are all important

Frederick Sanger

British biochemist who won the 1958 Nobel Prize for Chemistry with his discovery of the structure of proteins using insulin

insulin

the first protein

protein backbone

In a peptide chain, the linkage of each amino acid makes the ______________ and the R groups are all left outside the backbone.

trans-position

The C=O and -NH groups are always in a.___________ of each other. The linkage is planar resulting to a b.____________________.

a = ?

zigzag arrangement

The C=O and -NH groups are always in a.___________ of each other. The linkage is planar resulting to a b.____________________.

b = ?

similar, not identical

The 1° structure of a specific protein will always be the same regardless the species it is extracted from. It is _____________________________ because there are some residues that differ.

Secondary Structure of Proteins (2° Structure)

After folding of the 1° structure, the peptide chain will be able to achieve its native conformation — this is important for its function.

3D arrangements / regular folding

The 2° structure is:

a. ordered ________________________ in localized regions of a peptide chain

b. the ___________________ of AA residues in a polypeptide chain

c. result of the folding of 1° structures which is formed and stabilized by ________ between amide proton (-NH) and carbon oxygen (C=O)

d. dictated by the ___________ based on the AA residue present in the chain

a = ?

spatial arrangement

The 2° structure is:

a. ordered ________________________ in localized regions of a peptide chain

b. the ___________________ of AA residues in a polypeptide chain

c. result of the folding of 1° structures which is formed and stabilized by ________ between amide proton (-NH) and carbon oxygen (C=O)

d. dictated by the ___________ based on the AA residue present in the chain

b = ?

H-bonding

The 2° structure is:

a. ordered ________________________ in localized regions of a peptide chain

b. the ___________________ of AA residues in a polypeptide chain

c. result of the folding of 1° structures which is formed and stabilized by ________ between amide proton (-NH) and carbon oxygen (C=O)

d. dictated by the ___________ based on the AA residue present in the chain

c = ?

1° structure based on the AA residue

The 2° structure is:

a. ordered ________________________ in localized regions of a peptide chain

b. the ___________________ of AA residues in a polypeptide chain

c. result of the folding of 1° structures which is formed and stabilized by ________ between amide proton (-NH) and carbon oxygen (C=O)

d. dictated by the _____________________________ present in the chain

d = ?

2° Structure: Alpha Helix

adopts to a shape that resembles a coiled spring or helix which coils every 3.6 AA residue held together by H-bonds

similar conformations

2° Structure: Alpha Helix

a. All must have ______________________ in order for the helix to coil.

b. All the R-groups will __________________ because of inadequate space inside the helix.

c. Even _____________________ do not fit in the space inside the helix due to the tightness of the coil.

a = ?

extend outward

2° Structure: Alpha Helix

a. All must have ______________________ in order for the helix to coil.

b. All the R-groups will __________________ because of inadequate space inside the helix.

c. Even _____________________ do not fit in the space inside the helix due to the tightness of the coil.

b = ?

solvent molecules

2° Structure: Alpha Helix

a. All must have ______________________ in order for the helix to coil.

b. All the R-groups will __________________ because of inadequate space inside the helix.

c. Even _____________________ do not fit in the space inside the helix due to the tightness of the coil.

c = ?

2° Structure: Beta-pleated Sheet

A structure in which two fully extended protein chain segments in the same/different molecules are held together by H-bonds

alternating top and bottom

2° Structure: Beta-pleated Sheet

a. R-groups are found in _________________________ position.

b. Intermolecular and intramolecular interactions are held by ____________.

c. The ___________________ is a common example of a betapleated sheet.

a = ?

H-bonding

2° Structure: Beta-pleated Sheet

a. R-groups are found in _________________________ position.

b. Intermolecular and intramolecular interactions are held by ____________.

c. The ___________________ is a common example of a betapleated sheet.

b = ?

“U-turn” structure

2° Structure: Beta-pleated Sheet

a. R-groups are found in _________________________ position.

b. Intermolecular and intramolecular interactions are held by ____________.

c. The ___________________ is a common example of a betapleated sheet.

c = ?

Parallel Beta-Pleated Sheet

• both peptide chains are orientated in the same direction

• do not align H-bonds perfectly

Anti-Parallel Beta-Pleated Sheet

• where the peptide chains are orientated in a different direction

• Anti-parallel sheets has the O, N, and H atoms fully collinear with each other resulting to maximum H-bonding

2° Structure: Unstructured

A structure which is neither a helix or beta-pleated sheet that provides flexibility to protein structures to interact with different substances

large R-groups

2° Structure: Unstructured

a. The presence of _______________ disrupt the helix or beta-pleated sheet.

b. It is a __________ among protein structure since only portions of peptide exhibit 2° structure.

c. These structures are all ____________ within a given protein

a = ?

common

2° Structure: Unstructured

a. The presence of _______________ disrupt the helix or beta-pleated sheet.

b. It is a __________ among protein structure since only portions of peptide exhibit 2° structure.

c. These structures are all ____________ within a given protein

b = ?

identical

2° Structure: Unstructured

a. The presence of _______________ disrupt the helix or beta-pleated sheet.

b. It is a __________ among protein structure since only portions of peptide exhibit 2° structure.

c. These structures are all ____________ within a given protein

c = ?

Tertiary Structure of Proteins (3° Structure)

This is the overall 3D shape resulting from interaction between widely separated AA side chains

biologic function

3° structure defines the ___________________ of the protein

3° Structure: Disulfide bonds

This a covalent bonds between CYS residues and are the strongest of all. The linkage causes the chains to twist and bend.

3° Structure: Hydrogen bonding

• occur between amino acids with polar R-groups (-OH, -NH2, COOH, CONH2)

• relatively weak and it can be easily disrupted by changes in pH and temperature

3° Structure: Hydrophobic interactions

• It occurs due to the non-polar groups orienting inwards away from common polar solvents.

• These interactions are momentary, weak forces (London dispersion) that is common with alkyl-aryl side chains.

• However, it poses a cumulative strength due to their abundance in a peptide chain.

Quaternary Structure of Proteins (4° Structure)

This is the highest level of protein organization and only exist in multimeric proteins (with 2 or more polypeptide chains). Each subunit is generally dependent (not bound) to others.

even

Quaternary Structure of Proteins (4° Structure):

a. It usually contains _________ number of subunits

b. held together by _________________________________________ (similar to those in 3° structure)

c. These structures are ____________________ in changing cellular conditions but are easily restored as cellular conditions are return to normal.

a = ?

H-bonding, electrostatic, and hydrophobic interactions

Quaternary Structure of Proteins (4° Structure):

a. It usually contains _________ number of subunits

b. held together by _________________________________________ (similar to those in 3° structure)

c. These structures are ____________________ in changing cellular conditions but are easily restored as cellular conditions are return to normal.

b = ?

easily broken down

Quaternary Structure of Proteins (4° Structure):

a. It usually contains _________ number of subunits

b. held together by _________________________________________ (similar to those in 3° structure)

c. These structures are ____________________ in changing cellular conditions but are easily restored as cellular conditions are return to normal.

c = ?

G-Protein

A trimer with 3 nonidentical chains

Hemoglobin

A tetramer with 2 identical α and β-subunit

K-channel

A tetramer with 4 identical chains