BIOC 460 EXAM 2

Flashcard #1
Term: What are the key aspects covered in protein studies?
Definition: Understanding three-dimensional protein structure, how proteins function, the mechanisms of ligand binding and release, and the various interactions they partake in.

Flashcard #2
Term: Why is amino acid sequence important?
Definition: The amino acid sequence (primary structure) dictates the protein's three-dimensional structure and, consequently, its function.

Flashcard #3
Term: What is the purpose of primary amino acid sequence comparisons?
Definition: To identify similarities and differences between proteins, infer evolutionary relationships, and predict functional commonalities or divergences.

Flashcard #4
Term: What is a consensus sequence?
Definition: A sequence pattern that represents the most common amino acids found at each position in a group of related protein sequences, often indicating a functionally important region.

Flashcard #5
Term: What is a signature sequence?
Definition: A short, conserved amino acid sequence motif characteristic of a protein family or domain, often indicative of a specific function or evolutionary origin.

Flashcard #6
Term: Define homologs, paralogs, and orthologs.
Definition: Homologs: Proteins related by evolutionary descent from a common ancestor. Paralogs: Homologs within the same species that arose by gene duplication. Orthologs: Homologs in different species that arose from a speciation event.

Flashcard #7
Term: What are conserved substitutions of amino acids and their significance?
Definition: Replacements of an amino acid by another with similar biochemical properties (e.g., nonpolar for nonpolar), which often do not significantly alter the protein's structure or function, indicating evolutionary preservation of function.

Flashcard #8
Term: How does amino acid sequence conservation relate to evolutionary relationships between organisms?
Definition: Greater similarity in amino acid sequences between proteins from different organisms suggests a closer evolutionary relationship, as critical protein functions and structures are often conserved across species.

Flashcard #9
Term: What are the four levels of protein structure?
Definition: Primary: Amino acid sequence. Secondary: Local folded structures (alpha-helices, beta-sheets). Tertiary: Overall three-dimensional shape of a single polypeptide chain. Quaternary: Arrangement of multiple polypeptide chains (subunits) in a protein complex.

Flashcard #10
Term: How do bioenergetics influence protein structure state?
Definition: Protein folding is primarily driven by thermodynamic principles, where proteins seek the lowest energy conformation. Noncovalent interactions contribute to the overall stability, and the cell expends energy (ATP) through chaperones to assist in proper folding to achieve this stable state.

Flashcard #11
Term: What forces stabilize protein structure?
Definition: Mainly noncovalent interactions: 1. Hydrophobic effect: Exclusion of nonpolar groups from water. 2. Hydrogen bonds: Between polar side chains and peptide backbone atoms. 3. Ionic interactions (salt bridges): Between charged amino acid side chains. 4. Van der Waals interactions: Weak attractive forces between all atoms. 5. Disulfide bonds: Covalent links between cysteine residues (in tertiary/quaternary).

Flashcard #12
Term: Where do different forces predominate in protein stabilization?
Definition: Hydrophobic interactions prevail in the protein's interior, sheltered from water. Hydrogen bonds and ionic interactions are common on the surface and within the protein. Disulfide bonds are crucial for extracellular and some intracellular proteins.

Flashcard #13
Term: How does resonance affect the peptide bond?
Definition: The peptide bond has partial double-bond character due to resonance between the carbonyl oxygen and the amide nitrogen, making it rigid and planar, restricting rotation around the C-N bond.

Flashcard #14
Term: Which bonds in a polypeptide show rotation, and which do not?
Definition: No rotation: The peptide bond (C-N bond within the main chain) due to partial double-bond character. Rotation: Bonds adjacent to the alpha-carbon: the N-extCextalphaextCextalpha bond (phi, extphiextphi) and the extCextalphaextCextalpha-C bond (psi, extpsiextpsi).

Flashcard #15
Term: What are dihedral angles in proteins?
Definition: Torsion angles around a chemical bond, representing the rotation between two planes. In proteins, phi (extphiextphi) and psi (extpsiextpsi) are the most important, defining the conformation of the polypeptide backbone.

Flashcard #16
Term: Which dihedral angles are associated with which bonds in a polypeptide chain?
Definition: Phi (extphiextphi) angle: Rotation around the N-extCextalphaextCextalpha bond. Psi (extpsiextpsi) angle: Rotation around the extCextalphaextCextalpha-C bond.

Flashcard #17
Term: What is a Ramachandran plot and what information does it provide?
Definition: A plot of phi (extphiextphi) versus psi (extpsiextpsi) dihedral angles for amino acid residues in a protein, showing sterically allowed and disallowed conformations. It helps visualize common secondary structures (alpha-helices and beta-sheets) and assess the quality of protein structures.

Flashcard #18
Term: What are the common secondary structures found in proteins?
Definition: Alpha-helices, beta-sheets (composed of beta-strands), and beta-turns (or reverse turns).

Flashcard #19
Term: How do phi (extphiextphi) and psi (extpsiextpsi) angles determine secondary structure?
Definition: Specific combinations of phi (extphiextphi) and psi (extpsiextpsi) angles allow for the formation of stable, repeating hydrogen bonding patterns that define secondary structures like alpha-helices and beta-sheets, by minimizing steric clashes.

Flashcard #20
Term: Describe the alpha-helix: structure, handedness, stabilization, diameter, and length per turn.
Definition: Structure: A coiled polypeptide chain. Handedness: Typically right-handed. Stabilization: Hydrogen bonds between the carbonyl oxygen of residue nn and the amide hydrogen of residue n+4n+4. Diameter: Approximately 5.4extA˚5.4extA˚ (Cextalphaextalpha to Cextalphaextalpha distance). Length per turn: Approximately 5.4extA˚5.4extA˚ (pitch), with 3.63.6 residues per turn.

Flashcard #21
Term: How does amino acid sequence affect alpha-helix stability?
Definition: Bulky or charged residues close together (e.g., proline introduces a kink), or long runs of similarly charged residues, can destabilize an alpha-helix. Amino acids with small, uncharged side chains are often preferred.

Flashcard #22
Term: Explain the alpha-helix dipole and the importance of amino acids at its ends.
Definition: The alignment of peptide bond dipoles along the helix axis creates an overall net positive dipole at the N-terminus and a net negative dipole at the C-terminus. Charged amino acids (e.g., negatively charged at the N-terminus, positively charged at the C-terminus) can stabilize this dipole.

Flashcard #23
Term: Describe beta-strands and beta-sheets.
Definition: Beta-strands: Extended polypeptide segments where the backbone is nearly fully extended. Beta-sheets: Formed by multiple beta-strands aligned side-by-side, stabilized by hydrogen bonds between adjacent strands. Can be parallel or antiparallel.

Flashcard #24
Term: What are beta-turns, their types, and common amino acids involved?
Definition: Beta-turns (reverse turns): Short, tight turns that connect strands of antiparallel beta-sheets, reversing the direction of the polypeptide chain, involving 4 residues. Types: Type I and Type II, differing in dihedral angles. Common amino acids: Proline (at position 2, often to introduce a kink) and glycine (at position 3, due to its flexibility) are frequently found in beta-turns.

Flashcard #25
Term: What is circular dichroism (CD) and what does it reveal about protein secondary structure?
Definition: CD spectroscopy measures the differential absorption of left and right circularly polarized light by chiral molecules. It generates characteristic spectra for different secondary structures (e.g., alpha-helix, beta-sheet), allowing for the estimation of their proportion in a protein or changes upon folding/unfolding.

Flashcard #26
Term: What is tertiary structure and how is it stabilized?
Definition: Tertiary structure: The complete three-dimensional conformation of a single polypeptide chain, including all secondary structural elements and side chains. Stabilization: Primarily by noncovalent interactions (hydrophobic effect, H-bonds, ionic bonds, van der Waals forces) and sometimes covalent disulfide bonds.

Flashcard #27
Term: What are the major structural classes of proteins?
Definition: Globular proteins (compact, spherical, water-soluble, diverse functions) and fibrous proteins (elongated, insoluble, structural roles).

Flashcard #28
Term: What is a coiled-coil structure?
Definition: A stable, rod-like protein structure formed by two or more alpha-helices wrapped around each other, often stabilized by hydrophobic interactions at the interface of the helices (e.g., leucine zipper).

Flashcard #29
Term: Describe two examples of fibrous proteins: alpha-keratin and collagen.
Definition: Alpha-keratin: A right-handed alpha-helix that forms a left-handed coiled-coil dimer, rich in cysteine (disulfide bonds), found in hair, nails. Collagen: A triple helix (left-handed helices coiled in a right-handed superhelix), rich in Gly, Pro, and 4-hydroxyproline, found in connective tissues.

Flashcard #30
Term: How are the protomers (subunits) of alpha-keratin and collagen held together?
Definition: Alpha-keratin: Coiled-coil dimers are stabilized primarily by hydrophobic interactions, and larger filaments are linked by disulfide bonds. Collagen: Three polypeptide chains (alpha-chains) are held together by hydrogen bonds, particularly involving 4-hydroxyproline.

Flashcard #31
Term: Explain the role of 4-hydroxyproline, vitamin C, and their connection to collagen structure and scurvy.
Definition: 4-hydroxyproline: A modified amino acid crucial for stabilizing the collagen triple helix via hydrogen bonds. Vitamin C (ascorbate): A required cofactor for prolyl hydroxylase, the enzyme that converts proline to 4-hydroxyproline. Scurvy: A disease caused by vitamin C deficiency, leading to unstable collagen (due to insufficient 4-hydroxyproline) and symptoms like bleeding gums and poor wound healing.

Flashcard #32
Term: What is the Protein Data Bank (PDB) and its significance?
Definition: A publicly available repository of experimentally determined three-dimensional structures of proteins, nucleic acids, and complex assemblies. It's crucial for structural biology research, drug discovery, and understanding biological function.

Flashcard #33
Term: Differentiate between protein motifs (folds) and domains.
Definition: Motif (fold): A recurring supersecondary structure, a specific combination of secondary structures (e.g., beta-alpha-beta loop) with a characteristic geometry, often associated with a particular function. Domain: A stable, independently folding unit within a polypeptide chain, often associated with a specific function or binding capability. Proteins can have multiple domains.

Flashcard #34
Term: What are intrinsically disordered proteins/regions (IDPs/IDRs), their properties, and benefits?
Definition: IDPs/IDRs: Regions of proteins that lack a fixed, stable three-dimensional structure under physiological conditions. Properties: Highly flexible, dynamic, often rich in polar and charged amino acids. Benefits: Can interact with multiple partners, facilitating molecular recognition, signaling, and regulation, often undergoing a disorder-to-order transition upon binding.

Flashcard #35
Term: What is the SCOP2 database, its usefulness, and what it tells us about protein motifs, structure, and relationships?
Definition: SCOP (Structural Classification of Proteins) and its successor SCOP2, is a hierarchical database that classifies protein domains based on their structural and evolutionary relationships. It helps understand how motifs assemble into domains, how domains combine, and infers evolutionary connections between functionally distinct proteins.

Flashcard #36
Term: What are the advantages and limitations of X-ray crystallography for protein structure determination?
Definition: Advantages: Provides high-resolution atomic structures, applicable to very large proteins and complexes. Limitations: Requires protein crystallization (difficult for many proteins), provides a static snapshot, may not resolve flexible regions.

Flashcard #37
Term: What are the advantages and limitations of NMR spectroscopy for protein structure determination?
Definition: Advantages: Determines structures in solution (mimicking physiological conditions), can capture dynamic information, and resolve flexible regions. Limitations: Limited to relatively small proteins (typically less than  50extkDa 50extkDa), requires high protein concentration and isotopic labeling.

Flashcard #38
Term: What is proteostasis?
Definition: The cellular process of maintaining the proper balance of protein synthesis, folding, trafficking, function, and degradation to ensure cellular health and function.

Flashcard #39
Term: What are potential outcomes of a partially-folded protein?
Definition: Partially-folded proteins can expose hydrophobic regions, leading to aggregation, misfolding, loss of function, and potentially toxic protein deposits, contributing to various diseases.

Flashcard #40
Term: What are chaperones and what are their roles in protein folding?
Definition: Chaperones are proteins that assist in the proper folding of other proteins, prevent aggregation, and facilitate refolding of denatured proteins, often by binding to exposed hydrophobic regions.

Flashcard #41
Term: Describe the function of Hsp70 chaperones.
Definition: Hsp70 chaperones bind to unfolded or partially folded proteins, especially to hydrophobic sequences, in an ATP-dependent manner. They prevent aggregation and help stabilize newly synthesized or stress-denatured proteins, preparing them for further folding or transport.

Flashcard #42
Term: Explain the function and mechanism of GroEL/GroES chaperonins.
Definition: GroEL/GroES are chaperonin complexes that form a 'folding cage.' GroEL provides an isolated environment for misfolded proteins to refold, and GroES acts as a lid. ATP hydrolysis drives conformational changes, releasing the protein, often in a more folded state.

Flashcard #43
Term: What is protein denaturation, how is it measured, and what are its features, including TmTm? Definition: Denaturation: The loss of protein's native three-dimensional structure (secondary, tertiary, quaternary) due to disruption of noncovalent forces, leading to loss of function. Measurement: Can be measured by changes in activity, UV absorbance, circular dichroism, or fluorescence. Features: Often cooperative and reversible (for some proteins). TmTm (melting temperature): The temperature at which 50% of the protein is denatured.

Flashcard #44
Term: Describe the ribonuclease refolding experiment (Anfinsen's experiment) and its importance.
Definition: Anfinsen denatured bovine pancreatic ribonuclease A with urea (disrupts noncovalent bonds) and mercaptoethanol (reduces disulfide bonds), causing it to lose activity. Upon removal of denaturants, the protein spontaneously refolded to its native, active state. This experiment demonstrated that the primary amino acid sequence contains all the necessary information for a protein to fold into its correct three-dimensional structure.

Flashcard #45
Term: Why does protein folding follow a distinct path rather than random sampling?
Definition: If proteins folded by random sampling, it would take an astronomically long time to explore all possible conformations (Levinthal's paradox). Instead, folding follows a 'folding funnel' model, where the protein rapidly collapses into an ensemble of intermediates with decreasing free energy, guiding it towards the native state.

Flashcard #46
Term: What are the consequences of protein misfolding?
Definition: Loss of protein function, gain of toxic function (e.g., aggregation leading to amyloid deposits), and development of various diseases (e.g., Alzheimer's, Parkinson's, prion diseases).

Flashcard #47
Term: What are prions and how do they act?
Definition: Prions: Misfolded proteins that can induce normally folded proteins of the same type to also misfold into the abnormal, pathogenic conformation. Mechanism: The misfolded prion protein (PrPSc) acts as a template, converting the normal cellular prion protein (PrPC) into the abnormal form, leading to a chain reaction of misfolding and aggregation, causing neurodegenerative diseases.

Flashcard #48
Term: What are some key functions of globular proteins?
Definition: Enzymatic catalysis, transport and storage of molecules (e.g., oxygen), immune defense (antibodies), signal transduction, and gene regulation.

Flashcard #49
Term: Why is reversible binding of ligands important for protein function?
Definition: Reversible binding allows proteins to perform their functions dynamically, such as transporting molecules, sensing signals, and regulating pathways, without being permanently occupied or inactivated, enabling cellular responses to changing conditions.

Flashcard #50
Term: What interactions facilitate ligand binding to proteins?
Definition: Mainly noncovalent interactions: hydrogen bonds, ionic interactions (salt bridges), hydrophobic interactions, and van der Waals forces. These interactions, individually weak, become strong and specific when accumulated.

Flashcard #51
Term: Define kaka, kdkd, KaKa, and KdKd in the context of ligand binding.
Definition: kaka (association rate constant): Rate at which a ligand binds to a protein. kdkd (dissociation rate constant): Rate at which a ligand dissociates from a protein. KaKa (association constant): Equilibrium constant for association (Ka=ka/kdKa=ka/kd), indicating affinity. High KaKa means strong binding. KdKd (dissociation constant): Equilibrium constant for dissociation (Kd=kd/kaKd=kd/ka), also indicating affinity. Low KdKd means strong binding.

Flashcard #52
Term: How are KaKa and KdKd related?
Definition: KaKa and KdKd are reciprocals of each other: Ka=1/KdKa=1/Kd.

Flashcard #53
Term: How are KaKa and KdKd calculated from rate constants?
Definition: Ka=ka/kdKa=ka/kd and Kd=kd/kaKd=kd/ka.

Flashcard #54
Term: How is extthetaexttheta (fraction of occupied binding sites) calculated and related to KdKd? Definition: exttheta=[extL]/([extL]+Kd)exttheta=[extL]/([extL]+Kd), where [extL][extL] is the free ligand concentration. This indicates the proportion of binding sites occupied by ligand at a given equilibrium concentration. When [extL]=Kd[extL]=Kd​, exttheta=0.5exttheta=0.5, meaning half of the binding sites are occupied.

Flashcard #55
Term: How is the fraction of oxygen bound to myoglobin represented?
Definition: Similar to general ligand binding, it's represented by exttheta=extpO2/(extpO2+P50)exttheta=extpO2/(extpO2+P50), where extpO2extpO2 is the partial pressure of oxygen and P50P50 is the partial pressure of oxygen at which half of the myoglobin sites are occupied (analogous to KdKd).

Flashcard #56
Term: What type of binding curve is observed for a single protein-single ligand interaction?
Definition: A hyperbolic binding curve, indicating that as ligand concentration increases, binding sites become saturated until a maximum is reached.

Flashcard #57
Term: Explain the relationship between extthetaexttheta, extpO2extpO2, and P50P50 for oxygen binding.
Definition: exttheta=extpO2/(extpO2+P50)exttheta=extpO2/(extpO2+P50). extthetaexttheta represents the fraction of occupied sites. extpO2extpO2 is the partial pressure of oxygen. P50P50 is the partial pressure of oxygen at which half of the binding sites are saturated, serving as a measure of oxygen affinity (lower P50P50 means higher affinity).

Flashcard #58
Term: What is the thermodynamic relationship between standard free energy change (extDeltaGextdegreeextDeltaGextdegree) and the equilibrium constants (KaKa or KdKd)?
Definition: extDeltaGextdegree=−extRTextlnKa=extRTextlnKdextDeltaGextdegree=−extRTextlnKa=extRTextlnKd. This equation connects the intrinsic binding affinity (equilibrium constant) to the standard free energy change of the binding process.

Flashcard #59
Term: How do KdKd values indicate strong versus weak binding? Definition: A low KdKd value (e.g., nanomolar or picomolar range) indicates strong binding and high affinity. A high KdKd​ value (e.g., micromolar or millimolar range) indicates weak binding and low affinity.

Flashcard #60
Term: Describe the lock-and-key and induced-fit models of ligand binding specificity.
Definition: Lock-and-key: Proposed by Emil Fischer, suggests that the enzyme (or protein) active site is perfectly pre-shaped to fit its substrate (or ligand) like a lock and key. Induced-fit: Proposed by Daniel Koshland, suggests that both the enzyme/protein and substrate/ligand undergo conformational changes upon binding, optimizing the fit and interactions. This model is more widely accepted for many biological interactions.

Flashcard #61
Term: Why is the heme prosthetic group necessary for oxygen binding by globins?
Definition: Amino acid side chains in proteins lack the ability to reversibly bind oxygen. Heme, with its central iron ion, provides the specific chemical environment and coordination sites required for the reversible, noncovalent binding of oxygen molecules.

Flashcard #62
Term: Why would 'free' heme be detrimental for cells even if it binds oxygen?
Definition: Free heme, outside of globin proteins, can readily oxidize its central iron from extFe2+extFe2+ to extFe3+extFe3+ (which doesn't bind oxygen) and also produce reactive oxygen species (ROS), leading to cellular damage. The globin protein protects the heme, maintains the ferrous state, and controls oxygen binding.

Flashcard #63
Term: What are key features of a porphyrin ring and how does it coordinate extFe2+extFe2+?
Definition: Porphyrin is a planar, heterocyclic macrocycle composed of four pyrrole rings linked by methine bridges. In heme, it coordinates extFe2+extFe2+ through four nitrogen atoms, providing a stable, square planar environment for the iron.

Flashcard #64
Term: How many potential coordinating groups can extFe2+extFe2+ in heme have?
Definition: The central extFe2+extFe2+ in heme has six coordination sites: four are bound to the porphyrin nitrogens, one is bound to a proximal histidine from the globin protein, and the sixth is available for oxygen binding (or other ligands like CO/NO).

Flashcard #65
Term: Why doesn't heme bind to two oxygen molecules?
Definition: Heme has only one available coordination site for oxygen (the sixth coordination site of the ferrous iron). The other five sites are already occupied by the four porphyrin nitrogens and the proximal histidine residue of the globin protein.

Flashcard #66
Term: Which helices and residues are important for heme-protein association and heme-oxygen binding in globins?
Definition: The F helix contains the proximal histidine (F8), which directly coordinates the extFe2+extFe2+ from one side. The E helix contains the distal histidine (E7), which does not directly bind extFe2+extFe2+ or extO2extO2​, but helps stabilize bound oxygen through hydrogen bonding and reduces binding of other ligands like CO.

Flashcard #67
Term: Why are we not all susceptible to lethal CO poisoning, despite its high affinity for heme?
Definition: The distal histidine (E7) in globins sterically hinders the linear binding of CO to heme, forcing it into an angled conformation, which significantly reduces CO's effective binding affinity compared to the ideal linear binding. This preferential stabilization of oxygen binding over CO helps mitigate CO toxicity.

Flashcard #68
Term: What residue helps position oxygen in the binding pocket of globins and how?
Definition: The distal histidine (E7) helps position the oxygen molecule in the binding pocket through hydrogen bonding to one of oxygen's atoms. This interaction stabilizes bound oxygen and helps prevent the oxidation of extFe2+extFe2+ to extFe3+extFe3+.

Flashcard #69
Term: How can oxygen binding to heme (or globins) be measured?
Definition: Oxygenated heme has a distinct red color and absorption spectrum compared to deoxygenated heme. This change can be measured spectrophotometrically by observing changes in absorbance at specific wavelengths as oxygen partial pressure is varied.

Flashcard #70
Term: Why is myoglobin unsuitable for oxygen release to tissues, unlike hemoglobin?
Definition: Myoglobin has a very high affinity for oxygen and exhibits hyperbolic binding. It releases oxygen only at very low extpO2extpO2 values, conditions typically found only in severely oxygen-deprived tissues. Hemoglobin, conversely, exhibits cooperative binding and allosteric regulation, allowing it to efficiently load oxygen in the lungs and release a significant proportion in tissues where extpO2extpO2 is higher than myoglobin's P50P50​ but still relatively low.

Flashcard #71
Term: Define positive and negative cooperativity in ligand binding.
Definition: Positive cooperativity: Binding of one ligand molecule increases the affinity of subsequent binding sites for the same ligand. Negative cooperativity: Binding of one ligand molecule decreases the affinity of subsequent binding sites for the same ligand.

Flashcard #72
Term: What is the Hill coefficient and how does it indicate cooperativity?
Definition: The Hill coefficient (nHnH) measures the degree of cooperativity in ligand binding. 1. nH=1nH=1: Non-cooperative binding (e.g., myoglobin). 2. nH>1nH>1: Positive cooperativity (e.g., hemoglobin binding oxygen). 3. nH<1nH<1: Negative cooperativity.

Flashcard #73
Term: Describe the shape of a Hill plot for non-cooperative and cooperative binders.
Definition: Non-cooperative (e.g., myoglobin): A straight line with a slope of 1 (when plotted as log(extthetaexttheta / (1 - extthetaexttheta)) vs. log[L]). Cooperative (e.g., hemoglobin): An S-shaped curve (on a standard fractional saturation plot) or a straight line with a slope greater than 1 (on a Hill plot), reflecting the changing affinity as ligands bind.

Flashcard #74
Term: Define allosteric regulation, distinguishing between homotropic and heterotropic.
Definition: Allosteric regulation: Binding of a ligand at one site on a protein affects the binding properties at another site. Homotropic: The ligand that causes the allosteric change is the same as the one whose binding is affected (e.g., oxygen binding to hemoglobin). Heterotropic: The allosteric ligand is different from the ligand whose binding is affected (e.g., extCO2extCO2​ or 2,3-BPG binding to hemoglobin affects oxygen affinity).

Flashcard #75
Term: Describe the general structure of hemoglobin (subunits and complex).
Definition: Hemoglobin is a tetramer composed of four polypeptide subunits (typically two alpha and two beta subunits, forming two extalphaextbetaextalphaextbeta dimers), each binding one heme group. The complex has a quaternary structure.

Flashcard #76
Term: How do hemoglobin subunits interact, and how does pH affect these interactions?
Definition: Subunits interact primarily through noncovalent interactions between extalphaextalpha and extbetaextbeta chains. Changes in pH (the Bohr effect) alter the protonation state of certain residues, affecting salt bridges and H-bonds between subunits, shifting hemoglobin between its T (tense, low oxygen affinity) and R (relaxed, high oxygen affinity) states.

Flashcard #77
Term: Explain the T and R states of hemoglobin: their cause, effect, and regulation.
Definition: T (Tense) state: Deoxyhemoglobin, stabilized by more salt bridges, lower affinity for oxygen. Favored in tissues with lower pH and higher extCO2extCO2 concentration. R (Relaxed) state: Oxyhemoglobin, fewer salt bridges, higher affinity for oxygen. Favored in the lungs with higher extpO2extpO2 and pH. Regulation: Allosteric effectors like oxygen (homotropic), extH+extH+ (pH), extCO2extCO2​, and 2,3-bisphosphoglycerate (heterotropic) modulate the equilibrium between T and R states.

Flashcard #78
Term: How is carbon dioxide removed from tissues?
Definition: Carbon dioxide is removed from tissues in two main ways: 1. Bicarbonate buffer system: Most extCO2extCO2 is converted to bicarbonate (extHCO3−extHCO3−) in red blood cells by carbonic anhydrase and transported in the plasma. 2. Carbamate formation with hemoglobin: Some extCO2extCO2​ binds directly to the N-terminal amino groups of hemoglobin chains, forming carbaminohemoglobin (releasing extH+extH+ and stabilizing the T state), which is transported to the lungs.

Flashcard #79
Term: What type of regulator is 2,3-bisphosphoglycerate (2,3-BPG) for hemoglobin, and why?
Definition: 2,3-BPG is a heterotropic allosteric regulator of hemoglobin. It binds to a central pocket in the T state of deoxyhemoglobin, stabilizing this low-affinity state and promoting oxygen release to tissues. Its negative charge interacts with positively charged residues in the central cavity.

Flashcard #80
Term: How does 2,3-bisphosphoglycerate (2,3-BPG) affect oxygen binding to hemoglobin?
Definition: 2,3-BPG decreases hemoglobin's affinity for oxygen. By preferentially binding to and stabilizing the T (deoxy) state, it shifts the oxygen binding curve to the right, meaning more oxygen is released to the tissues at a given extpO2extpO2​.

Flashcard #81
Term: Explain sickle cell anemia: its cause, effects, and selective advantage in some populations.
Definition: Cause: A single point mutation in the extbetaextbeta-globin gene (glutamate to valine at position 6), leading to sickle hemoglobin (HbS). Effects: HbS aggregates and polymerizes under low oxygen conditions, causing red blood cells to become rigid and sickle-shaped, leading to blockages, anemia, and organ damage. Selective advantage: Heterozygous individuals (carrying one copy of the HbS gene) have increased resistance to malaria because the presence of HbS makes their red blood cells less hospitable to the parasite and leads to premature destruction of infected cells.

Flashcard #82
Term: What are the two types of human immune systems?
Definition: Innate immunity (non-specific, first line of defense, rapid) and Adaptive/Acquired immunity (specific, involves memory, slower development).

Flashcard #83
Term: Describe the composition, structure, and domain function/interaction of an antibody (immunoglobulin).
Definition: Composition: Two identical heavy chains and two identical light chains, joined by disulfide bonds. Structure: Y-shaped molecule, with each chain having variable (V) and constant (C) domains. Domains: 1. Fab region (V domains): Antigen-binding fragment, provides specificity for antigen. 2. Fc region (C domains of heavy chain): Constant fragment, mediates effector functions (e.g., binding to immune cells, complement activation).

Flashcard #84
Term: Define antibody, antigen, and epitope.
Definition: Antibody (immunoglobulin): A Y-shaped protein produced by B cells that recognizes and neutralizes specific pathogens, acting as a key component of the adaptive immune system. Antigen: Any molecule (often foreign) that can induce an immune response and be recognized by an antibody or T-cell receptor. Epitope: The specific part of an antigen that is recognized and bound by an antibody or T-cell receptor.

Flashcard #85
Term: Differentiate between monoclonal and polyclonal antibodies.
Definition: Monoclonal antibodies: Homogeneous antibodies produced by a single B cell clone, recognizing a single specific epitope on an antigen. Polyclonal antibodies: Heterogeneous antibodies produced by multiple B cell clones, recognizing multiple different epitopes on the same antigen.

Flashcard #86
Term: What is ELISA (Enzyme-Linked Immunosorbent Assay), its process, and common uses?
Definition: ELISA: A plate-based assay technique used to detect and quantify substances such as peptides, proteins, antibodies, and hormones. Process: Typically involves coating a plate with antigen/antibody, washing, adding samples, adding enzyme-linked secondary antibody, and detecting signal via a substrate causing a color change. Uses: Diagnosing diseases (e.g., HIV, Lyme disease), detecting allergens, pregnancy tests, measuring protein levels.

Flashcard #87
Term: Describe Western blotting of proteins separated by SDS-PAGE: its purpose and general steps.
Definition: Purpose: To detect specific proteins in a complex mixture and determine their molecular weight. Process: 1. SDS-PAGE: Proteins are separated by size via gel electrophoresis. 2. Transfer: Separated proteins are transferred from the gel to a membrane. 3. Blocking: Membrane is blocked to prevent non-specific antibody binding. 4. Primary antibody: Incubated with an antibody specific to the target protein. 5. Secondary antibody: Incubated with an enzyme-linked antibody that binds to the primary antibody. 6. Detection: Addition of substrate to the enzyme, producing a detectable signal.

Flashcard #88
Term: Describe the structure of myosin.
Definition: Myosin is a motor protein composed of six subunits: two heavy chains (each with a globular 'head' domain, a neck region, and a long alpha-helical coiled-coil 'tail') and four light chains associated with the neck regions. The heads contain ATPase activity and bind to actin.

Flashcard #89
Term: How does myosin interact with actin?
Definition: Myosin globular heads bind to actin filaments in a cycle involving ATP hydrolysis. This binding and release, coupled with conformational changes (power stroke), causes the actin filament to slide relative to myosin.

Flashcard #90
Term: Describe the components of muscle fibers: thick/thin filaments, Z disk, M line, A band, and I band.
Definition: Muscle fibers: Individual muscle cells. Sarcomere: The basic contractile unit, defined by Z disks. Thick filaments: Composed primarily of myosin. Thin filaments: Composed primarily of actin, tropomyosin, and troponins. Z disk: Anchors thin filaments; separates sarcomeres. M line: Center of the H zone; anchors thick filaments. A band: Dark band, spans the length of thick filaments (may overlap with thin). I band: Light band, contains only thin filaments.

Flashcard #91
Term: Explain the molecular process of muscle contraction (sliding filament model).
Definition: Muscle contraction occurs when myosin heads, powered by ATP hydrolysis, bind to actin, pivot (power stroke), and pull the thin filaments towards the M line, shortening the sarcomere. ATP binding causes myosin to detach, and hydrolysis 're-cocks' the myosin head for another cycle.

Flashcard #92
Term: What are the roles of troponins and tropomyosin in muscle contraction?
Definition: Tropomyosin: A filamentous protein that wraps around actin, blocking myosin-binding sites on actin in relaxed muscle. Troponins: A complex of three proteins (troponin C, I, T) associated with tropomyosin. When calcium (extCa2+extCa2+) binds to troponin C, it causes a conformational change that moves tropomyosin, unblocking the myosin-binding sites on actin, allowing contraction to occur.

Flashcard #93
Term: How does myosin function as both a structural protein and an enzyme?
Definition: Myosin acts as a structural protein as it forms the thick filaments of muscle fibers, providing the scaffolding for contraction. It also functions as an enzyme due to its ATPase activity located in its globular head, which hydrolyzes ATP to ADP and inorganic phosphate, providing the energy for the power stroke and movement along actin filaments.