Biochem 2 Exam 4 Study Guide

Study Guide Question: How does increasing temperature affect membrane lipid organization?

Increasing temperature increases lipid motion and disrupts acyl-chain packing, favoring a more fluid, liquid-disordered membrane.

Why does increasing temperature increase membrane fluidity?

Higher temperature increases thermal motion, allowing more rotation around acyl-chain single bonds and greater lateral movement of lipids. Ordered packing becomes less favorable.

What happens to a lipid bilayer as it passes through its melting temperature?

Ordered, tightly packed acyl chains → increased thermal motion → disrupted packing → a more fluid, liquid-disordered bilayer. The bilayer remains intact while its molecular organization changes.

What is the main structural change tested when a membrane is heated through its phase transition?

Disruption of lipid packing and increased molecular motion. The relevant change is in noncovalent organization; phospholipid covalent bonds remain intact.

Study Guide Question: What are the structural and functional characteristics of membrane proteins?

Membrane proteins associate with the bilayer through embedded hydrophobic regions, surface interactions, or lipid anchors and function in transport, signaling, adhesion, and catalysis.

How do integral, peripheral, and amphitropic membrane proteins differ?

Integral proteins are firmly embedded in the membrane; peripheral proteins associate through noncovalent surface interactions; amphitropic proteins reversibly associate with membranes and also occur in the cytosol.

How does a transmembrane protein accommodate both the membrane interior and aqueous surroundings?

Hydrophobic side chains face the lipid core → polar regions face water or line an internal transport pathway. Transmembrane α-helices internally hydrogen-bond their backbones; β-barrels also satisfy backbone hydrogen bonding within their folded structures.

What is the main defining feature of an integral membrane protein?

Firm insertion into the lipid bilayer through hydrophobic interactions. Many integral proteins span the membrane, but monotopic proteins insert into just one leaflet.

Study Guide Question: What type of transport is involved in glucose uptake by erythrocytes?

GLUT1-mediated facilitated diffusion, a passive glucose uniport process.

Why is glucose uptake through GLUT1 classified as facilitated diffusion?

GLUT1 provides a specific protein-mediated route for glucose to move down its concentration gradient without directly consuming ATP. Glucose is too polar to cross the lipid core rapidly on its own.

How does GLUT1 transport glucose across the erythrocyte membrane?

Outward-facing GLUT1 binds extracellular D-glucose → an occluded intermediate forms → GLUT1 becomes inward-facing → glucose is released into the cytosol → the empty transporter returns outward. The cycle is reversible and does not chemically modify glucose.

What is the most likely exam distinction between erythrocyte GLUT1, GLUT4, and SGLT?

GLUT1 provides basal, insulin-independent facilitated diffusion. GLUT4 undergoes insulin-regulated membrane recruitment; SGLT couples glucose uptake to downhill Na⁺ movement.

Study Guide Question: How do membrane compositions differ between inner and outer mitochondrial membranes?

The inner membrane is more protein-rich and enriched in cardiolipin; the outer membrane contains porins and relatively more lipid. Both contain little sterol.

Why does the inner mitochondrial membrane have a high protein content?

It contains respiratory-chain complexes, ATP synthase, and numerous selective transporters. Its composition supports energy conversion and maintenance of an electrochemical proton gradient.

The ETC proteins!

How do mitochondrial membrane compositions support different permeability properties?

Outer-membrane porins permit passage of many small solutes → the intermembrane space exchanges readily with the cytosol. Inner-membrane lipids and selective transport proteins restrict passage → proton and metabolite gradients can be maintained.

Which mitochondrial membrane contains the respiratory chain and most mitochondrial cardiolipin?

The inner mitochondrial membrane. Cardiolipin is strongly enriched there and supports respiratory-complex organization; it is not a major outer-membrane lipid.

Study Guide Question: How can integral membrane proteins be extracted from membranes?

By disrupting hydrophobic interactions with detergents; organic solvents can also extract them but often denature the proteins.

Why are detergents needed to solubilize integral membrane proteins?

Integral proteins expose hydrophobic surfaces to membrane lipids. Detergents surround these surfaces with their hydrophobic portions while presenting hydrophilic groups to water.

What is the mechanism of detergent extraction of an integral membrane protein?

Detergent partitions into the bilayer → lipid–protein interactions are disrupted → mixed lipid–detergent aggregates form → detergent coats the protein’s hydrophobic surfaces → the protein becomes dispersed in aqueous solution. Mild nonionic detergents are often used to preserve function.

What is the main extraction-method distinction between integral and peripheral membrane proteins?

Integral proteins generally require detergents; peripheral proteins can often be released with high salt or altered pH. The distinction reflects hydrophobic insertion versus surface noncovalent interactions.

Study Guide Question: What determines the potassium channel's selectivity for K⁺ over Na⁺?

Selectivity-filter carbonyl oxygens coordinate dehydrated K⁺ optimally, compensating for its dehydration; smaller Na⁺ is not stabilized equivalently.

Why can a potassium channel exclude Na⁺ even though Na⁺ is smaller than K⁺?

The main factor is favorable coordination of dehydrated K⁺ by the selectivity filter. Na⁺ is too small to interact optimally with the filter’s oxygen ligands, so its dehydration is not adequately compensated.

How does the potassium-channel selectivity filter distinguish K⁺ from Na⁺?

Hydrated ion enters the aqueous vestibule → ion loses its hydration shell at the narrow filter → backbone carbonyl oxygens replace water ligands. K⁺ receives favorable coordination that offsets dehydration; Na⁺ receives insufficient stabilization and faces a larger energetic barrier.

Which chemical groups are the main determinants of K⁺ coordination in the potassium-channel selectivity filter?

Peptide-backbone carbonyl oxygens. Their arrangement mimics the hydration environment of K⁺; other pore features support conduction, but this coordination is the main selectivity concept.

Study Guide Question: How do bacteria adapt their membrane composition to colder temperatures?

They increase unsaturated fatty acids and may increase shorter or branched chains, preventing tight packing and maintaining fluidity.

What is homeoviscous adaptation?

Adjustment of membrane lipid composition to maintain a suitable membrane viscosity as environmental conditions change. Cooling commonly favors lipids with lower melting temperatures.

How does increased fatty acid unsaturation help a bacterium tolerate cooling?

Temperature falls → acyl-chain motion decreases → the cell increases cis-unsaturated membrane fatty acids → double-bond kinks disrupt close packing → the membrane remains functional at the lower temperature.

What is the most likely exam answer for how bacteria preserve membrane fluidity in the cold?

Increase cis-unsaturated fatty acids. Shorter or branched chains can also help, whereas longer saturated chains generally promote rigidity.

Study Guide Question: What is the transport kinetics of GLUT1 in erythrocytes?

GLUT1 exhibits saturable, Michaelis–Menten-like kinetics: v₀ = Vmax[glucose]out/(Kt + [glucose]out).

What do Vmax and Kt mean for GLUT1-mediated glucose uptake?

Vmax is the maximum initial transport rate; Kt is the external glucose concentration producing half-maximal initial transport. Kt is analogous to an enzyme’s Km.

Why does GLUT1-mediated transport approach a maximum rate?

Increasing extracellular glucose increases transporter occupancy → more transport cycles occur → available binding sites and conformational cycling become limiting → uptake approaches Vmax. The initial-rate equation assumes intracellular glucose is initially negligible.

What distinguishes GLUT1 uptake kinetics from simple diffusion through a lipid bilayer?

GLUT1 transport is saturable and stereospecific. Simple diffusion does not show a transporter-limited Vmax and increases approximately with the concentration difference under otherwise fixed conditions.

Study Guide Question: What type of transport systems moves Ca²⁺ into the endoplasmic reticulum against its gradient?

Primary active transport by the P-type Ca²⁺ ATPase SERCA, powered directly by ATP hydrolysis.

Why is SERCA a primary active transporter and a P-type ATPase?

It directly couples ATP hydrolysis to uphill Ca²⁺ transport and forms a transient phosphorylated Asp residue during its catalytic cycle.

What is the ATP-driven transport cycle of SERCA?

E1 binds 2 cytosolic Ca²⁺ → MgATP binds → ATP transfers its terminal phosphate to Asp-351, producing ADP and an occluded phosphoenzyme → conversion to E2-P lowers Ca²⁺ affinity and exposes the sites to the ER lumen → 2 Ca²⁺ are released → hydrolysis of the Asp-phosphate releases Pi → E1 is regenerated. One ATP is consumed per two Ca²⁺ transported; H⁺ countertransport accompanies the cycle.

What transport direction is the main exam association for SERCA?

Cytosol → ER or sarcoplasmic-reticulum lumen. SERCA lowers cytosolic Ca²⁺ and replenishes intracellular Ca²⁺ stores.

Study Guide Question: Which choline-containing lipids are found in the outer leaflet of plasma membranes?

Phosphatidylcholine and sphingomyelin.

How do phosphatidylcholine and sphingomyelin differ structurally despite both containing choline?

Phosphatidylcholine is a glycerophospholipid with a glycerol backbone; sphingomyelin is a sphingolipid with a ceramide backbone. Both have phosphocholine head groups.

How do lipid translocators help maintain plasma-membrane leaflet asymmetry?

Selective ATP-dependent flippases move aminophospholipids inward → floppases move selected lipids outward → slow spontaneous phospholipid flip-flop preserves unequal leaflet compositions. Scramblase activation can dissipate this asymmetry.

Which phospholipids are generally enriched in the cytosolic leaflet rather than the outer leaflet?

Phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol and its phosphorylated derivatives. Phosphatidylcholine and sphingomyelin are generally enriched outside.

Study Guide Question: Which membrane transport processes do not require protein facilitators?

Simple diffusion through the lipid bilayer, including diffusion of small nonpolar molecules and some water.

Why can O₂ and CO₂ cross membranes without transport proteins?

They are small, uncharged molecules that can dissolve in the hydrophobic membrane interior. Their movement down a concentration gradient does not require a protein pathway.

How does a molecule cross a membrane by simple diffusion?

Molecule leaves the aqueous phase → partitions into the lipid bilayer → diffuses through its hydrophobic interior → emerges into the opposite aqueous phase. Net movement follows the concentration gradient and requires no ATP or transporter.

What is the main exam association for rapid water transport across cell membranes?

Aquaporins provide rapid, selective water transport. Water can also diffuse directly through the lipid bilayer, so osmosis itself does not require an aquaporin.

Study Guide Question: Are flippases and floppases considered facilitated transport systems?

They facilitate lipid translocation broadly, but are ATP-dependent active transporters, not passive facilitated-diffusion systems.

Why is “protein-mediated transport” not equivalent to “facilitated diffusion”?

Protein-mediated transport includes both passive and active processes. Facilitated diffusion specifically moves a substance downhill without direct energy input; flippases and floppases consume ATP.

How do flippases, floppases, and scramblases differ mechanistically?

Flippases: selected phospholipids, especially PS and PE, move toward the cytosolic leaflet using ATP. Floppases: selected lipids move toward the outer leaflet using ATP. Scramblases: lipids move bidirectionally down their leaflet concentration gradients without ATP, reducing asymmetry.

Which lipid-translocating proteins are most directly associated with passive loss of leaflet asymmetry?

Scramblases. Some are activated by Ca²⁺, whereas apoptotic scramblases can be activated through caspase-dependent mechanisms.

Study Guide Question: What are the common components of biological membranes?

Lipids and proteins, with carbohydrates attached to lipids or proteins in many membranes.

What are the main structural roles of membrane lipids, proteins, and carbohydrates?

Lipids form the permeability barrier; proteins provide transport, signaling, adhesion, and catalytic functions; carbohydrates contribute recognition and surface protection.

How do amphipathic membrane lipids assemble into a bilayer?

Lipids enter water → hydrophobic tails aggregate to reduce exposure to water → polar head groups remain exposed → two leaflets assemble tail-to-tail → exposed edges close, often producing a sealed vesicle. Assembly is driven largely by the hydrophobic effect.

What is the main form and location of carbohydrates in the plasma membrane?

Oligosaccharides attached to proteins and lipids on the extracellular surface. These form glycoproteins and glycolipids rather than a free carbohydrate layer within the hydrophobic core.

This is known as the glycocalyx (Ex. Zona Pellucida)

Study Guide Question: What are the general features of lipid bilayers in biological membranes?

They are thin, fluid, asymmetric, self-sealing barriers with hydrophilic surfaces and a hydrophobic interior that selectively restricts solute passage.

Why is a lipid bilayer selectively permeable?

Its hydrophobic interior favors passage of small nonpolar molecules but creates a large energetic barrier for ions and most polar solutes. Transport proteins provide selective routes for otherwise poorly permeant substances.

Why does a damaged lipid bilayer tend to reseal small openings?

An opening exposes hydrophobic acyl chains to water → this exposure is energetically unfavorable → nearby lipids rearrange to bury the tails → the opening closes. Extensive damage can exceed this self-sealing capacity.

Which lipid movements occur readily within a bilayer, and which are usually slow?

Lateral diffusion, rotation, and acyl-chain flexing occur readily. Spontaneous phospholipid movement between leaflets is usually slow because the polar head group must cross the hydrophobic core.

Study Guide Question: What are the key features of the fluid mosaic model of membranes?

A fluid lipid bilayer contains a mosaic of associated proteins, with lateral mobility, structural asymmetry, and locally specialized domains.

What do “fluid” and “mosaic” mean in the fluid mosaic model?

Fluid refers to molecular motion within the bilayer; mosaic refers to the varied proteins and lipids distributed within it. The membrane is a dynamic, heterogeneous structure.

How does lateral diffusion occur without destroying the membrane barrier?

Lipids and mobile proteins exchange positions within the membrane plane → hydrophobic regions remain buried and polar regions remain exposed → the bilayer retains continuity while its components redistribute.

Think of people in a crowd moving past each other

What is the main mobility concept tested by the fluid mosaic model?

Many lipids and proteins can diffuse laterally within the bilayer. Cytoskeletal attachments, protein complexes, and membrane domains can restrict particular proteins’ movement.

Study Guide Question: What are integrins and what is their role in membranes?

Integrins are α/β heterodimeric transmembrane adhesion receptors that connect cells to extracellular ligands and transmit signals across the membrane.

What structural organization allows integrins to link extracellular and intracellular environments?

Each integrin contains an α subunit and a β subunit, each with a single transmembrane helix. Their extracellular domains bind ligands, while cytoplasmic regions associate with intracellular signaling and cytoskeletal proteins.

How do integrins mediate bidirectional signaling?

Inside-out signaling: intracellular regulators alter integrin conformation and ligand affinity. Outside-in signaling: extracellular ligand binding and integrin clustering recruit intracellular proteins → cytoskeletal and signaling responses. Divalent cations support ligand binding.

What integrin-binding sequence is a likely exam target?

RGD, or Arg–Gly–Asp, a recognition motif in several extracellular-matrix ligands, including fibronectin. Some integrins recognize other motifs, but RGD is the key sequence to associate with integrin binding.

Study Guide Question: How do ligand-gated ion channels function in membranes?

Ligand binding changes channel conformation and opens or closes an ion-selective pore, allowing passive ion movement down an electrochemical gradient.

What mainly determines ion direction after a ligand-gated channel opens?

The ion’s electrochemical gradient. Ligand binding controls gating; concentration differences and membrane voltage determine whether net movement is inward or outward.

What is the mechanism of a ligand-gated ion channel?

Ligand binds a regulatory site → channel conformation changes → the gate opens or closes → permitted ions move through the pore according to their electrochemical gradients → ligand dissociation or desensitization terminates the response. Ion passage itself does not require ATP hydrolysis.

How do ligand-gated channels differ from voltage-gated channels?

Ligand-gated channels respond directly to ligand binding; voltage-gated channels respond to membrane potential changes. Both can conduct ions passively when open.

Study Guide Question: What does a hydropathy plot reveal about membrane proteins?

It identifies hydrophobic sequence regions that may form membrane-spanning segments and helps predict membrane topology.

Why does a long hydrophobic sequence suggest a transmembrane α-helix?

A stretch of roughly 20 predominantly hydrophobic residues can form an α-helix long enough to cross the bilayer’s nonpolar core. Its side chains can interact favorably with lipid tails.

How is a hydropathy plot constructed and interpreted?

Assign a hydropathy value to each residue → average values over a sliding sequence window → plot average hydropathy against residue position → identify extended hydrophobic regions → evaluate them as candidate membrane-spanning segments. The direction of “hydrophobic” on the vertical axis depends on the scale used.

What is the main exam interpretation of a long hydrophobic region on a hydropathy plot?

A likely membrane-spanning α-helix, especially when the region is about 20 residues long. Signal peptides and buried hydrophobic regions can produce similar signals, so the plot is predictive rather than definitive.

Study Guide Question: Which molecules are typically enriched in lipid rafts?

Cholesterol, sphingolipids, and selected proteins, especially GPI-anchored and some acylated signaling proteins.

Why do sphingolipids and cholesterol favor raft formation?

Long, relatively saturated sphingolipid chains pack tightly with cholesterol, creating more ordered and often thicker membrane regions than neighboring unsaturated phospholipid-rich regions.

A lipid raft is a cholestrol/Sphingomyelin rich area of the membrane that is more ordered than the rest of the membrane

How can lipid rafts organize membrane signaling?

Preferential lipid interactions generate local ordered domains → selected anchored proteins and receptors partition into these regions → signaling components become concentrated or segregated → the likelihood of specific molecular interactions changes. Rafts are dynamic rather than permanent rigid platforms.

Which lipid pair is the most likely exam answer for lipid-raft enrichment?

Cholesterol and sphingolipids. Selected proteins, especially GPI-anchored proteins, also concentrate in rafts, but this lipid pair is the central compositional association.

Study Guide Question: What is the mechanism of facilitated diffusion across membranes?

A specific carrier or channel lowers the barrier to solute passage, allowing movement down its concentration or electrochemical gradient without direct energy input.

How does facilitated diffusion differ from active transport?

Facilitated diffusion is downhill and cannot independently accumulate a solute against its gradient. Active transport couples uphill movement to ATP hydrolysis or another energy source.

How does carrier-mediated facilitated diffusion work?

Solute binds one side of a carrier → the carrier undergoes an alternating-access conformational change → solute is released on the opposite side → the carrier resets. Net movement is downhill; the carrier does not remain simultaneously open to both sides.

What mechanism is most likely tested for GLUT-mediated facilitated diffusion?

Alternating access: substrate binding → carrier conformational change → substrate release on the opposite side. Channels also mediate passive transport, but GLUT proteins are carriers.

Study Guide Question: What enzyme class does the F-type ATPase belong to?

An ATP-driven proton translocase, functioning as a rotary ATPase or, in reverse, an ATP synthase; older classifications group it among ATP-hydrolyzing hydrolases.

Why can F-type ATPase be described as both an ATPase and an ATP synthase?

Its energy coupling is reversible. ATP hydrolysis can drive uphill proton transport, while downhill proton flow can drive ATP synthesis.

How does the F₀F₁ complex couple proton movement to ATP metabolism?

ATP-synthesis direction: H⁺ flows downhill through membrane-embedded F₀ → rotor and central stalk rotate → conformations of F₁ catalytic sites change → ADP and Pi form ATP, which is released. Reverse direction: MgATP hydrolysis in F₁ drives rotation that pumps H⁺ uphill through F₀.

What is the main mechanistic distinction between F-type and P-type ATPases?

F-type ATPases use rotary energy coupling; P-type ATPases form a transient phosphorylated Asp intermediate. Associate F-type with F₀F₁ and reversible ATP synthesis/proton pumping.

Study Guide Question: What proteins mediate fusion of vesicular membrane during neurotransmitter release?

SNARE proteins, particularly vesicular synaptobrevin and plasma-membrane syntaxin and SNAP-25.

What are the respective roles of synaptobrevin, syntaxin, and SNAP-25?

Synaptobrevin is the vesicular SNARE; syntaxin and SNAP-25 are target-membrane SNARE components. Together they assemble a four-helix bundle that promotes fusion.

What is the mechanism of Ca²⁺-triggered synaptic vesicle fusion?

Vesicle docking and priming → partial assembly of synaptobrevin, syntaxin, and SNAP-25 → action potential opens voltage-gated Ca²⁺ channels → Ca²⁺ binds synaptotagmin → final SNARE-driven membrane apposition and fusion-pore opening → neurotransmitter release. After fusion, α-SNAP and the ATPase NSF help disassemble SNARE complexes for reuse.

Which proteins provide the four helices of the neuronal SNARE bundle?

Synaptobrevin contributes one helix, syntaxin contributes one, and SNAP-25 contributes two. SNAP-25 is distinct from α-SNAP, which participates in SNARE recycling.

Study Guide Question: What types of molecules are transported by ABC transporters?

A broad range, including lipids, sterols, bile salts, drugs, peptides, amino acids, proteins, and certain ions.

What does ABC stand for, and what is the basic architecture of an ABC transporter?

ATP-binding cassette. A typical functional transporter has two transmembrane domains and two cytosolic nucleotide-binding domains, which may occur in one or multiple polypeptides.

How does a typical ABC transporter couple ATP to substrate movement?

Substrate binds the transporter → ATP binds the nucleotide-binding domains and promotes their association → transmembrane domains rearrange to expose substrate to the opposite side → substrate is released → ATP hydrolysis and product release reset the transporter. ATPase activity generally requires Mg²⁺.

What is the main exam association for ABC transporters, and what important exception should be recognized?

Most are ATP-driven transporters that move substrates across membranes. The major exception is CFTR, an ATP-regulated Cl⁻ channel whose ions move down their electrochemical gradient.

Study Guide Question: What is the role of caveolin in membrane structure and function?

Caveolin organizes cholesterol-rich caveolae and promotes membrane curvature, contributing to membrane trafficking and signaling.

What are caveolae?

Small, flask-shaped plasma-membrane invaginations enriched in cholesterol and associated with caveolin. They participate in membrane organization, trafficking, and signaling.

How does caveolin help curve a membrane?

Its hydrophobic region inserts into the cytoplasmic leaflet → palmitoyl groups strengthen membrane association → caveolin molecules oligomerize and interact with cholesterol → unequal organization of the leaflets favors inward membrane curvature and caveolar organization.

What membrane orientation is the main structural association for caveolin?

A membrane-associated hairpin with both amino and carboxyl termini facing the cytoplasm. Its hydrophobic region associates with the cytoplasmic leaflet and helps organize caveolae.

Study Guide Question: What structural features contribute to potassium channel selectivity?

A narrow, conserved selectivity filter formed by four subunits positions backbone carbonyl oxygens to coordinate dehydrated K⁺ precisely.

How does the tetrameric structure of a potassium channel create a selective pore?

Four subunits contribute equivalent pore-loop regions around a central axis, producing a symmetric filter with multiple K⁺ coordination sites.

How does the potassium-channel pore support rapid K⁺ conduction?

Hydrated K⁺ enters the wide aqueous vestibule → pore-helix dipoles help stabilize the cation → K⁺ dehydrates at the filter → successive oxygen-lined binding sites stabilize it → occupancy by additional K⁺ ions favors onward movement → K⁺ exits and is rehydrated. Transport is driven by the electrochemical gradient.

Which conserved sequence is associated with the selectivity filter of many K⁺ channels?

TVGYG is a characteristic conserved filter sequence. Its backbone geometry helps create the oxygen-lined K⁺-binding sites.