Protein Structure and Function

These flashcards cover key concepts in protein structure and function as presented in the lecture notes.

What is the three-dimensional structure of a protein called?

Conformation

What are peptides?

Short chains of amino acids (2-30 residues) connected by peptide bonds.

What is the primary structure of a protein?

The linear sequence of amino acids.

What comprises secondary structure in proteins?

Local folding into structures such as alpha helices and beta strands.

What type of hydrogen bonding stabilizes alpha helices and beta sheets?

Hydrogen bonds between the backbone amide (N-H) and carbonyl (C=O) groups of amino acids.

What interactions are necessary for tertiary structure formation?

Hydrophobic interactions, hydrogen bonds, ionic interactions, van der Waals interactions, and sometimes disulfide bonds.

How does quaternary structure form?

One protein interacts with another protein using the same interactions as tertiary structure.

What are protein domains?

Modules of tertiary structure that can be functional or structural.

What is the role of molecular chaperones?

They assist in the proper folding of proteins and prevent misfolding.

What is the role of enzymes in biochemical reactions?

They catalyze reactions by lowering the activation energy.

What is the Michaelis constant (Km)?

It measures the affinity of an enzyme for its substrate.

What is the significance of phosphorylation in proteins?

It regulates protein activity and function.

What are common methods used in protein purification?

Centrifugation, electrophoresis, and chromatography.

What is the purpose of Western blotting?

To detect specific proteins using antibodies after electrophoresis.

What is mass spectrometry used for in protein research?

To analyze protein mass and sequence.

What does the term 'induced fit' refer to in enzyme function?

The conformational change of an enzyme to better fit the substrate during binding.

What are the types of post-translational modifications?

Phosphorylation, ubiquitination, glycosylation, and proteolytic cleavage.

What is the pulse-chase experiment used for?

To track the fate of proteins over time after synthesis.

How is the structure of proteins determined?

Using techniques like X-ray crystallography, NMR, and cryo-electron microscopy.

What are intrinsically disordered proteins?

Proteins that do not have a single stable conformation but can fold into various structures upon interaction.

What is the impact of misfolded proteins?

They can lead to diseases such as Alzheimer's and Parkinson's.

What defines the four broad structural categories of proteins?

Globular, fibrous, integral membrane proteins, and intrinsically disordered proteins.

What is the 'oil drop model' of protein folding?

A model describing protein folding where hydrophobic residues tend to bury themselves in the interior of the protein (like oil drops aggregating in water), minimizing their contact with the aqueous cellular environment, while hydrophilic residues remain on the surface.

Enzyme A has a '$K<em>m$' of '$2$ mM' for substrate X, while enzyme B has a '$K</em>m$' of '$10$ mM' for substrate Y. Which enzyme has a higher affinity for its substrate?

Enzyme A has a higher affinity for its substrate. A lower '$K_m$' value indicates a higher affinity of the enzyme for its substrate because less substrate concentration is needed to reach half of the maximum reaction velocity.

Proteolytic degradation is one way to regulate protein function. Which of the following is used to degrade poly-ubiquitinated proteins?

Proteasomes