Protein Structure and Function Lecture Flashcards

Flashcards testing concepts of protein structure, chemical bonding, functional classes, denaturation, protein turnover via the ubiquitin-proteasome system, and enzyme mechanisms based on lecture transcript notes.

What are the four levels of protein structure and their basic descriptions?

Primary structure is the amino acid sequence; secondary structure is the formation of $\alpha$-helices and $\beta$-sheets; tertiary structure is the overall 3-dimensional shape and domain assembly; quaternary structure consists of more than one polypeptide chain.

How many total amino acids are found in proteins, and how are they classified based on synthesis by the human body?

There are $20$ amino acids found in proteins, categorized into $8$ essential amino acids (which the body does not synthesize) and $12$ non-essential amino acids.

What general chemical components are common to all $20$ amino acids attached to the central alpha carbon?

All $20$ amino acids contain a carboxyl group ($-COOH$), an amino group ($-NH_2$), a hydrogen atom ($-H$), and a unique side chain ($R$-group) attached to the central alpha carbon.

Which three amino acids contain an $-OH$ group that can be phosphorylated by protein kinases?

Serine ($\text{Ser}$), Threonine ($\text{Thr}$), and Tyrosine ($\text{Tyr}$).

Which amino acid contains a sulfhydryl ($-SH$) group and can form disulfide bonds?

Cysteine ($\text{Cys}$).

How is a peptide bond formed and what structural level does it stabilize?

A peptide bond is a covalent bond formed via dehydration synthesis between the carboxyl group of one amino acid and the amino group of a neighboring amino acid; it stabilizes primary structure.

What type of chemical bonding stabilizes secondary protein structures such as $\alpha$-helices and $\beta$-sheets?

Hydrogen bonding between the $C=O$ and $N-H$ groups of the polypeptide backbone (not involving side chains).

What is a protein domain?

A distinct functional or structural area within a single polypeptide chain that folds independently of the rest of the polypeptide.

What types of noncovalent interactions help stabilize tertiary protein structure?

Hydrophobic interactions, hydrogen bonds, ionic bonds, and Van der Waals attractions.

What is the only covalent bond that stabilizes tertiary protein structure?

The disulfide bridge (or disulfide bond), formed between two Cysteine ($\text{Cys}$) side chains.

What is the difference between a homodimer and a heterodimer in quaternary protein structure?

A homodimer contains two identical polypeptide chains (same amino acid sequence), whereas a heterodimer contains two different polypeptide chains (different amino acid sequences).

How many Cysteine residues must a single polypeptide chain contain to form an intra-chain disulfide bond that stabilizes tertiary structure?

At least $2$ Cysteine residues.

Which levels of protein structure are affected when noncovalent bonds are disrupted by a chemical agent?

Secondary, tertiary, and quaternary structures are affected, while primary structure remains intact because covalent peptide bonds are not broken.

What is a ligand and how is it held in a protein's binding site?

A ligand is any molecule that binds to a protein; it fits precisely into a binding site and is held in place by multiple weak noncovalent bonds.

What is protein denaturation and what factors can cause it?

Denaturation is the change of a protein's 3-dimensional shape due to environmental changes (such as temperature, pH, or electrolyte concentration), which disrupts noncovalent bonds without breaking primary peptide bonds.

What is the function of the ubiquitin-proteasome system in cellular protein turnover?

Ubiquitin ligases tag specific damaged, misfolded, or short-lived proteins with a ubiquitin chain, marking them for recognition and degradation by the proteasome into amino acids or small peptides.

What are the structural components of the proteasome and their respective functions?

The proteasome consists of two $19S$ caps that recognize the ubiquitin tag, unfold the protein, and feed it into a central $20S$ cylinder containing proteases that degrade the protein.

How do enzymes increase the rate of biochemical reactions?

Enzymes act as catalysts that speed up reaction rates by lowering the activation energy ($E_A$) required to convert substrates into transition states and products.

What are the specific functions of Kinases and Phosphatases?

Kinases add phosphate groups to molecules, while Phosphatases remove phosphate groups from molecules.

What is the key functional distinction between a coenzyme and a cofactor?

A coenzyme is a small organic molecule that functions as a transient carrier of a functional group (such as $NAD^+$ carrying $H^+$), whereas a cofactor is an inorganic ion or molecule required for enzyme activity (such as $Fe^{2+}$, $Cu^{2+}$, or $Se$).