Biochem Lecture 11- Proteins I

What is more common in proteins: alpha helices or beta sheets?

Alpha helices (even thought their area on a Ramachandran plot is smaller).

What is the structure of a beta strand?

The side chains alternate up and down. and the hydrophillic backbone isexposed to the environment.

What direction are proteins built in?

N to C terminus.

How do antiparallel beta sheets stack?

Stabilization with hydrogen bonds between two strands at a 1 to 1 correspondence with residues.

How do parallel beta sheets stack?

Stabilization with crosslinked hydrogen bonds between two strands at a 2 to 1 correspondence with residues (H bonds are with different residues).

What is an example of beta sheets being an important structural element?

Porins.

What are bends and loops in the secondary structure?

Reverse turn- 180 turn stabilized by hydrogen bonds. Loops- help different secondary motifs come together.

What is a leucine zipper? What level of structure is it?

Two alpha helices with many leucines recognize and coil each other, forming a coiled-coil. They have protein-protein interaction and protein-DNA interaction domains. Super secondary structure.

What is an omega loop?

A very sharp loop.

What are the two types of tertiary structures?

Globular and fibular.

What is myoglobin?

It is a protein that strongly holds onto oxygen. In the tertiary structure it has a heme prosthetic group that grabs the iron.

How can you alter part of a protein?

Mutating an amino acid can change often the structure of the protein in the domain that it is in. Depending on the protein the change can be isolated to that domain or affect other domains.

What is an intrinsically disordered domain?

A domain that never finds a confirmation that doesn’t have enough stability to maintain an ordered structure. Exploration of different conformations is driven by thermodynamics/the motion of atoms.

What protein is involved in ALS pathology?

TDP-43 has an intrinsically disordered C-terminus that may have amyloid-like properties, meaning that one form of the shape can propagate to other proteins. In people with ALS it stays that shape.

What are metamorphic proteins? What is a example?

Two protein structures (different functions) built from the same amino acid sequence. Lymphotactin.

What structure is hemoglobin?

Heterotetramer, homodimers each with an alpha and beta unit.

What is the structure of the coat of human rhinovirus?

Made of 60 copies of four subunits, quaternary structure.

Are prosthetic groups tertiary structures, quaternary structures, or its own thing?

Its own thing.

What is the structure of alpha-keratin?

Alpha-helical coiled-coiled structure, every seventh residue is leucine which interacts with each other due to the hydrophobic effect which makes it strong. Homodimer.

What are ways to denature proteins?

Heat, pH change, detergents, chaotropic agents, reducing agents.

What are examples of detergents? What do they do?

SDS, Triton-X 100. They are amphipathic molecules that cause water and lipids to mix.

What are examples of chaotropic agents? What do they do?

Guanidium ions and urea. They disrupt hydrogen bonding.

What are examples of reducing agents? What do they do?

DTT, beta-mercaptoethanol. Can break disulfide bridges.

What are the steps of the Anfinsen experiment?

1) Urea denatures the active protein by breaking hydrogen bonds 2) mercaptoethanol breaks the disulfide bridges 3) remove urea (readopts hydrogen bonding) 4) remove mercaptoethanol (reductant) to reform disulfide bridges (in presence of oxygen) 5) functional protein

What is the wrong order for renaturation of a denatured protein? What happens?

1) Remove mercaptoethanol to reform sulfide bridges while urea is still present 2) remove urea to reform hydrogen bonds. Disulfide bonds form randomly, so it will be stapled in the wrong order.