Proteins

What is a condensation reaction?

Release of water during bond formation

What is a peptide bond?

- Joins two amino acids

- rigid and planar

What configuration do peptide bonds assume?

trans configuration

Why is the trans form favored in peptide bonds?

Less steric collisions occurs in the trans form than the cis form

Where does free rotation occur?

Around the alpha carbon and the carbonyl carbon (psi) and nitrogen atom (phi).

What allows proteins to fold in different ways?

Rotation around bonds.

What are the levels of structure in a protein?

Primary, Secondary, Tertiary, and Quaternary

The structure of a protein is determined by the...

Amino acid sequence

What is the primary structure of a protein?

The linear sequence of amino acids of a polypeptide chain

What determines the charge of a protein at a given pH?

The pKa of the dissociation of protons by the carboxyl, amino, and the side chain groups.

What is the isoelectric point?

The pH at which the net charge of the molecule is zero.

If the pH is lower than the pKa, then the protein is ________ protonated.

more

If the pH is higher than the pKa, then the protein is _____ protonated.

less

What is the pKa value of the amino group at the N termini?

~9

What is the pKa value of the carboxyl group at the C termini?

~2

What is the secondary structure of proteins?

Form recurring localized structures within regions of the polypeptide chain

What are two common regular secondary structures?

Alpha helix and Beta sheet

What are three irregular secondary structures?

Loops, turns, and coils

Alpha helices are ______ handed structures

right

How is the peptide backbone of alpha helices formed?

H-bonds between each carbonyl oxygen atom and amide hydrogen atom 4 residues apart (occurs within the same strand)

Where are alpha helices found?

Globular, membrane spanning, and DNA binding proteins

Which amino acid is absent from the helical region?

Proline

Why is proline absent from the helical region?

Proline doesn't have an amide nitrogen for H-bonding and the appropriate bond angles to fit within the helix.

Beta sheets are composed of __________.

Strands/chains

How are the strands/chains held together in Beta sheets?

Hydrogen bonding

When does optimal hydrogen bonding in Beta sheets occur?

When strands are pleated (bent)

What directions can Beta sheet strands run?

Opposite (anti parallel) or same (parallel) direction.

What is the anti-parallel arrangement?

- Composed of the same strand that folds back on it's self

- Atoms involved in H-bonding are directly opposite to each other

What is the parallel arrangement?

- Atoms involved in H-bonding are skewed.

- One amino acid is H-bonded to two amino acids in the opposite strand.

What is a Beta turn?

-Irregular secondary structure

- Consist of 4 successive residues that connect B-strands in anti-parallel arrangement

What is the second and third residue in B-turns

Second residue is proline

Third residue is glycine.

How many residues are loops?

6 - 16 residues long

Where are loops and turns found?

On the surfaces of proteins which are involved in interaction with other molecules

What are Motifs?

- Secondary structures that form a pattern

What are two examples of a structural motif?

- Helix turn helix motif found in DNA binding proteins.

- Ba Ba B structural motif found within a domain of the enzyme lactose dehydrogenase.

What is the tertiary structure of a protein?

- Folding of the secondary structures

- Specifies the location of each atom in a protein

- Structural elements fold into 3D

Are the tertiary structures rigid or dynamic and flexible?

Dynamic and flexible

What types of bonding hold tertiary structures together?

Ionic interactions, H-bonds, disulfide bonds, and hydrophobic interactions.

Ionic interactions

Occurs between amino acids whose side chains are charged

Disulfide bridges

- Formed between two cysteine residues within and between polypeptide chains.

- Oxidation of the sulfhydryl groups of the free cysteine residues results in the formation of covalent disulfide bridges.

What is the Insulin structure?

Chain A and B are connected by two disulfide bridge (intermolecular), and a single disulfide bridge exists in chain A (intramolecular).

H-bonding

- Occurs between amino acids with polar and charged side groups.

- H-bonding also occurs between unpaired polar NH and CO groups of the main chain to exist in hydrophobic environments (a-helices, B-sheets).

Hydrophobic interactions

- Strong tendency for hydrophobic amino acid residues to cluster together resulting in the expulsion of water.

- An increase in entropy gives rise to an energetically stable overall structure

Van der Waals interaction

The compact structure of a protein is further stabilized by these forces between the tightly packed hydrocarbon side chains.

In cystolic globular proteins, the polar amino acids are found make up the ________ of the protein, while the non-polar or hydrophobic make up the ______ of the protein. (Myoglobin)

Surface

Core

In transmembrane proteins. the non-polar amino acids make up the ________ of the protein, while the polar residues make up the _______ of the protein. (Bacterial porins; B-barrels)

Surface

Core

What is an example of a transmembrane protein?

B2-Adrenergic receptor

What is the B2-Adrenergic receptor?

- Seven transmembrane helices form a cylindrical structure.

- Loops connecting helices form the hormone-binding site of the external side of the PM, and a binding site for a G-protein on the intracellular side.

What are protein domains?

Continuous stretches of amino acids of a polypeptide that fold independently into distinct 3D structures from the rest of the proteins

What is an example of a protein domain?

Cell surface protein CD4 consists of 4 identical domains

What is the Quaternary structure of proteins?

- Combination of 2 or more polypeptide chains (subunits)

- Many proteins function as dimers, tetramers, and oligomers

- The subunits are arranged in a geometrical and spatial manner

- A subunit is known as a protomer

What is it called when the quaternary structure contains identical subunits?

Homo

What is it called when the quaternary structure contains different subunits?

Hetero

E. coli Formate transporter has 5 similar subunits and would be classified as...

homopentameric protein

A G protein with 3 different subunits would be classified as...

Heterotrimeric protein

Hemoglobin consists of 4 polypeptide chains: a1, a2, B1, B2, and would be classified as...

Heterotetrameric

What is a native protein?

- The final 3D structure of a protein.

- Most proteins will fold by themselves into the native structure.

What happens if proteins misfold?

They would aggregate, be degraded by proteolytic enzymes, or be refolded by chaperones (heat shock proteins).

What happens when a polypeptide chain begins folding?

- It will continue refolding and find several metastable intermediates (high energy) until it finds the confirmation with lowest native energy.

- These are kinetic barriers. Slows the process down.

What factors cause protein denaturation?

pH, temperature, and the nature of the solvent

How does temperature denature proteins?

When the temperature is increased, the rotational and vibrational energies in bonds increases.

How does pH denature proteins?

Changes in pH will disrupt ionic and H bonds

How do solvents denature proteins?

Can disrupt hydrophobic interactions

What is protein denaturation?

Disruption of 3D structure resulting in loss of function

What are prions?

- Proteins that act as templates for other prion proteins to misfold and resist degradation

- Cause neurodegenerative diseases.

How are prion diseases acquired?

By infections (mad cow disease) or through sporadic or heritable mutations (Creutzfeldt Jakob Disease (CJD)

What are the two confirmations of prions?

PRPc and PRPsc

Which prion confirmation does not contain the disease?

PRPc

Which prion confirmation does contain the disease?

PRPsc

PrPc is predominantly consist of _________, while PrPsc is enriched with _________

a-helices

b-sheets

How are prions resistant to degradation?

PRPsc aggregation into a multimeric complex which is resistant to proteolytic degradation

Does PRPc normally convert to PRPsc?

No, PRPc does not convert to PRPsc because of high activation energy.

Certain structural domains are binding sites for specific molecules, called a _________, or for other proteins

ligand

The 3D native structure of a protein has the _______ energy

lowest