Essential Cell Biology: Protein Structure and Function (Chapter 4)

A comprehensive set of Q&A flashcards covering protein structure, folding, domains, motifs, enzymes, regulation, post-translational modifications, protein purification, and common laboratory techniques based on the chapter notes.

What is the primary structure of a protein?

The linear sequence of amino acids in a polypeptide.

What are the two main types of protein secondary structure?

Alpha helices and beta sheets, stabilized by backbone hydrogen bonds.

How is an alpha helix stabilized?

Hydrogen bonds between the backbone C=O and N–H groups, typically every four residues.

What distinguishes a beta sheet from an alpha helix?

Beta sheets are formed by hydrogen bonds between neighboring strands and can be parallel or antiparallel.

What is the tertiary structure of a protein?

The final three-dimensional conformation of a single polypeptide chain.

What is the quaternary structure of a protein?

The arrangement of two or more polypeptide chains into a functional protein complex.

What is a protein domain?

A region of a polypeptide that can fold independently into a stable, compact structure and often has a function.

What is a protein motif?

A short, recurring sequence or structure that contributes to binding or stability but is not by itself a full functional protein.

What are intrinsically disordered regions?

Unstructured regions within proteins that lack a fixed three-dimensional structure but can be functionally important.

What is a chaperone in protein folding?

A protein that assists other proteins to fold correctly; many are heat shock proteins (HSPs).

What are disulfide bonds and where do they form?

Covalent S–S bonds between cysteine residues that form mainly in the endoplasmic reticulum to stabilize extracellular proteins.

What is denaturation and renaturation?

Denaturation is unfolding due to heat, pH, or chemicals; renaturation is refolding when denaturing conditions are removed.

Why is protein aggregation important?

Misfolded proteins can aggregate, contributing to neurodegenerative diseases (e.g., Alzheimer's, Huntington) and prion diseases.

What drives protein folding into a compact form in water?

Hydrophobic effect: nonpolar side chains cluster in a hydrophobic core away from water.

What are hydrogen bonds in proteins?

Noncovalent interactions stabilizing structure: backbone–backbone, backbone–side chain, and side chain–side chain bonds.

What is a peptide bond?

A covalent bond formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next, releasing water.

Polar covalent vs nonpolar covalent bonds in biomolecules?

Polar covalent bonds share electrons unequally due to electronegativity differences; nonpolar covalent bonds share electrons more equally.

What does the term ‘20 essential amino acids’ mean?

The standard set of amino acids; some must be obtained from the diet because the body does not synthesize them in sufficient amounts.

Which amino acids are acidic (negatively charged) at physiological pH?

Aspartic acid (Asp, D) and Glutamic acid (Glu, E).

Which amino acids are basic (positively charged) at physiological pH?

Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

Which amino acids are uncharged polar?

Serine (Ser), Threonine (Thr), Asparagine (Asn), Glutamine (Gln), Cysteine (Cys), Tyrosine (Tyr).

Which amino acids are nonpolar/hydrophobic?

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp).

What are the main forces driving protein folding besides hydrogen bonds?

Ionic interactions (salt bridges) and hydrophobic interactions forming a hydrophobic core.

What is protein aggregation and what diseases are associated with it?

Misfolded proteins aggregate into insoluble species; linked to neurodegenerative diseases and prion diseases.

What is a chaperone and what do they do?

A protein that assists the folding of other proteins, often part of the heat shock protein (HSP) family.

What is a binding site on a protein?

A region on the protein surface that interacts with another molecule via noncovalent bonds.

What is the structure of hemoglobin?

A tetramer with two alpha and two beta subunits; each subunit contains a heme group with iron for O2 binding.

What are fibrous proteins and give examples?

Elongated proteins such as collagen (triple helix) and elastin (cross-linked fibers) that provide structural support.

What is the role of enzymes and their active sites?

Enzymes catalyze chemical reactions; each enzyme has a specific substrate that binds to its active site to form an enzyme–substrate complex.

What are the main classes of enzymes and their general functions?

Hydrolases (hydrolyze bonds), Nucleases (cleave nucleic acids), Proteases (cleave proteins), Ligases (join molecules), Isomerases (rearrange bonds), Polymerases (synthesize polymers), Kinases (add phosphates), Phosphatases (remove phosphates), Oxidoreductases (redox), ATPases (hydrolyze ATP).

What is allosteric regulation?

Regulation where a protein has two or more binding sites that influence each other’s activity.

What is feedback inhibition?

Negative regulation where a downstream product inhibits an enzyme earlier in the pathway.

What is positive feedback in enzyme regulation?

A regulatory molecule stimulates an enzyme's activity, enhancing a process.

What is phosphorylation and why is it important?

Addition of a phosphate group from ATP to Ser/Thr/Tyr by a kinase; can change activity and promote complex formation.

What is ubiquitylation (ubiquitination)?

Attachment of ubiquitin to a protein, often signaling it for degradation by the proteasome.

What is the proteasome?

A large protease complex that degrades polyubiquitinated proteins.

What are motor proteins and how do they move?

Motor proteins convert ATP hydrolysis into directed movement along cytoskeletal filaments, via a cycle of conformational changes.

What are GTP-binding proteins and their role as molecular switches?

Proteins active when bound to GTP and inactive when GDP; reactivated by GDP–GTP exchange.

What is the role of antibodies in the lab?

Antibodies (heavy and light chains linked by disulfide bonds) are used to detect specific antigens in various assays.

How can proteins be visualized and detected experimentally?

Techniques include SDS-PAGE, Western blotting, immunostaining, and immunohistochemistry with labeled antibodies.

What is isoelectric focusing?

Separation of proteins by their isoelectric point (pI) in a pH gradient, where they carry no net charge.

What is two-dimensional gel electrophoresis?

Separation of complex protein mixtures first by isoelectric focusing (pI) and then by SDS-PAGE (size).

What is chromatography in protein purification and its main types?

Separation based on charge (ion-exchange), size (gel filtration), or specific interactions (affinity chromatography).

What is the purpose of affinity chromatography?

Matrix is linked to a molecule that binds specifically to the protein of interest, allowing highly purified isolation.

What is SDS-PAGE used for?

A denaturing gel electrophoresis technique that separates proteins by molecular weight.

What is a protein’s relationship to matrices and binding partners in purification?

Proteins can be purified by exploiting their charge, size, or specific binding to a matrix or ligand.

What is the primary structure of a protein?

The linear sequence of amino acids in a polypeptide.

What are the two main types of protein secondary structure?

Alpha helices and beta sheets, stabilized by backbone hydrogen bonds.

How is an alpha helix stabilized?

Hydrogen bonds between the backbone C=O and N–H groups, typically every four residues.

What distinguishes a beta sheet from an alpha helix?

Beta sheets are formed by hydrogen bonds between neighboring strands and can be parallel or antiparallel.

What is the tertiary structure of a protein?

The final three-dimensional conformation of a single polypeptide chain.

What is the quaternary structure of a protein?

The arrangement of two or more polypeptide chains into a functional protein complex.

What is a protein domain?

A region of a polypeptide that can fold independently into a stable, compact structure and often has a function.

What is a protein motif?

A short, recurring sequence or structure that contributes to binding or stability but is not by itself a full functional protein.

What are intrinsically disordered regions?

Unstructured regions within proteins that lack a fixed three-dimensional structure but can be functionally important.

What is a chaperone in protein folding?

A protein that assists other proteins to fold correctly; many are heat shock proteins (HSPs).

What are disulfide bonds and where do they form?

Covalent S–S bonds between cysteine residues that form mainly in the endoplasmic reticulum to stabilize extracellular proteins.

What is denaturation and renaturation?

Denaturation is unfolding due to heat, pH, or chemicals; renaturation is refolding when denaturing conditions are removed.

Why is protein aggregation important?

Misfolded proteins can aggregate, contributing to neurodegenerative diseases (e.g., Alzheimer's, Huntington) and prion diseases.

What drives protein folding into a compact form in water?

Hydrophobic effect: nonpolar side chains cluster in a hydrophobic core away from water.

What are hydrogen bonds in proteins?

Noncovalent interactions stabilizing structure: backbone–backbone, backbone–side chain, and side chain–side chain bonds.

What is a peptide bond?

A covalent bond formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next, releasing water.

Polar covalent vs nonpolar covalent bonds in biomolecules?

Polar covalent bonds share electrons unequally due to electronegativity differences; nonpolar covalent bonds share electrons more equally.

What does the term ‘20 essential amino acids’ mean?

The standard set of amino acids; some must be obtained from the diet because the body does not synthesize them in sufficient amounts.

Which amino acids are acidic (negatively charged) at physiological pH?

Aspartic acid (Asp, D) and Glutamic acid (Glu, E).

Which amino acids are basic (positively charged) at physiological pH?

Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

Which amino acids are uncharged polar?

Serine (Ser), Threonine (Thr), Asparagine (Asn), Glutamine (Gln), Cysteine (Cys), Tyrosine (Tyr).

Which amino acids are nonpolar/hydrophobic?

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp).

What are the main forces driving protein folding besides hydrogen bonds?

Ionic interactions (salt bridges) and hydrophobic interactions forming a hydrophobic core.

What is protein aggregation and what diseases are associated with it?

Misfolded proteins aggregate into insoluble species; linked to neurodegenerative diseases and prion diseases.

What is a chaperone and what do they do?

A protein that assists the folding of other proteins, often part of the heat shock protein (HSP) family.

What is a binding site on a protein?

A region on the protein surface that interacts with another molecule via noncovalent bonds.

What is the structure of hemoglobin?

A tetramer with two alpha and two beta subunits; each subunit contains a heme group with iron for O2 binding.

What are fibrous proteins and give examples?

Elongated proteins such as collagen (triple helix) and elastin (cross-linked fibers) that provide structural support.

What is the role of enzymes and their active sites?

Enzymes catalyze chemical reactions; each enzyme has a specific substrate that binds to its active site to form an enzyme–substrate complex.

What are the main classes of enzymes and their general functions?

Hydrolases (hydrolyze bonds), Nucleases (cleave nucleic acids), Proteases (cleave proteins), Ligases (join molecules), Isomerases (rearrange bonds), Polymerases (synthesize polymers), Kinases (add phosphates), Phosphatases (remove phosphates), Oxidoreductases (redox), ATPases (hydrolyze ATP).

What is allosteric regulation?

Regulation where a protein has two or more binding sites that influence each other’s activity.

What is feedback inhibition?

Negative regulation where a downstream product inhibits an enzyme earlier in the pathway.

What is positive feedback in enzyme regulation?

A regulatory molecule stimulates an enzyme's activity, enhancing a process.

What is phosphorylation and why is it important?

Addition of a phosphate group from ATP to Ser/Thr/Tyr by a kinase; can change activity and promote complex formation.

What is ubiquitylation (ubiquitination)?

Attachment of ubiquitin to a protein, often signaling it for degradation by the proteasome.

What is the proteasome?

A large protease complex that degrades polyubiquitinated proteins.

What are motor proteins and how do they move?

Motor proteins convert ATP hydrolysis into directed movement along cytoskeletal filaments, via a cycle of conformational changes.

What are GTP-binding proteins and their role as molecular switches?

Proteins active when bound to GTP and inactive when GDP; reactivated by GDP–GTP exchange.

What is the role of antibodies in the lab?

Antibodies (heavy and light chains linked by disulfide bonds) are used to detect specific antigens in various assays.

How can proteins be visualized and detected experimentally?

Techniques include SDS-PAGE, Western blotting, immunostaining, and immunohistochemistry with labeled antibodies.

What is isoelectric focusing?

Separation of proteins by their isoelectric point (pI) in a pH gradient, where they carry no net charge.

What is two-dimensional gel electrophoresis?

Separation of complex protein mixtures first by isoelectric focusing (pI) and then by SDS-PAGE (size).

What is chromatography in protein purification and its main types?

Separation based on charge (ion-exchange), size (gel filtration), or specific interactions (affinity chromatography).

What is the purpose of affinity chromatography?

Matrix is linked to a molecule that binds specifically to the protein of interest, allowing highly purified isolation.

What is SDS-PAGE used for?

A denaturing gel electrophoresis technique that separates proteins by molecular weight.

What is a protein’s relationship to matrices and binding partners in purification?

Proteins can be purified by exploiting their charge, size, or specific binding to a matrix or ligand.

What are the diverse functional categories of proteins?

Proteins serve as enzymes, structural components, transport molecules, signaling molecules, motor proteins, storage proteins, and immune defense agents.

How does a protein's primary sequence dictate its higher-order structures?

The unique linear sequence of amino acids (primary structure) contains all the information needed for a protein to spontaneously fold into its specific secondary, tertiary, and in some cases, quaternary structures.

What is the role of chaperonins like GroEL/GroES in protein folding?

Chaperonins are specific types of chaperones that form barrel-shaped complexes, providing an isolated environment where proteins can fold correctly, often involving ATP hydrolysis.

What is glycosylation and why is it important for protein function?

Glycosylation is the enzymatic addition of carbohydrate chains to proteins, playing crucial roles in cell-cell recognition, cell signaling, protein stability, and proper protein targeting/localization.

What are van der Waals forces, and how do they contribute to protein stability?

Weak, transient attractive forces between electron clouds of closely approaching atoms; they are numerous in a tightly packed protein interior, contributing significantly to overall stability.

What are the primary experimental techniques used to determine the exact three-dimensional atomic structure of proteins?

X-ray crystallography (for crystallized proteins) and Nuclear Magnetic Resonance (NMR) spectroscopy (for proteins in solution) are key methods to determine detailed protein structures.