M4 - The Cell Flashcards
What is the first law of thermodynamics?
The total energy of a system and its surroundings is constant.
How can we quantify the energy in a system?
Change in Esystem = E2 – E1
Change in Esystem = Q + W
E1: Energy of system before process
E2: Energy of system after
Q: Energy lost as heat
W: Work carried out
What is enthalpy?
The heat of the system. Change in energy is approximately the same as change in enthalpy for a biochemical reaction
DH = DE + pDV
In biological systems pressure does not change and volume change is small
Exothermic reaction: Energy/Enthalpy is released by the system DH<0
Endothermic reaction: Energy/Enthalpy is taken up by the system DH>0
Describe the relation between the first and second laws of thermodynamics.
Energy accountancy
(no energy created or disappeared in reactions)
Second law of thermodynamics…..
Tells you which reactions will happen
(Entropy of system and surroundings has increased)
Describe Gibbs Free Energy.
DG = DH – TDS
D = Delta
Negative DG means change in system provides energy available for work.
Chemical reactions that provide such energy are spontaneous.
Positive DG means system takes up free energy from surroundings.
Chemical reactions need free energy supplied to run, i.e., not spontaneous
What are exergonic and endergonic reactions?
IF DG is negative a reaction proceeds spontaneously and with a loss of free energy.
the reaction is EXERGONIC
IF DG is positive
reaction is unfavourable or not spontaneous
i.e. the reaction is ENDERGONIC.
The reverse reaction is spontaneous.
If DG = 0 then no free energy change takes place, this is a dynamic equilibrium.
What is Standard Free Energy?
DG = DG0 +RT lnq units J/mol or kcal/mol
R: gas constant T: absolute temperature q: mass action ratio
Who discovered Co-enzyme A?
Friz Lippman 1953: Nobel Prize in Medicine for discovery of Co-enzyme A.
Also discovered that ATP is the main energy carrier in the cell coined the term ’energy rich phosphate bonds’
Describe ATP concentration.
ATP concentration is 2.5g/kg wet muscle.
What is the meaning of redox potential?
It describes the propensity to accept electrons.
What was the significance of Buchner’s yeast experiment?
It demonstrated that fermentation can occur in cell-free extracts, disproving vitalism and marking the birth of biochemistry.
What is glycolysis and why is it important?
Glycolysis is a 10-step metabolic pathway that breaks glucose into 2 pyruvate molecules, producing a net gain of 2 ATP. It’s central to energy metabolism and provides intermediates for biosynthetic pathways.
What are the two stages of glycolysis?
Investment Stage: 2 ATP are consumed to phosphorylate glucose.
Payoff Stage: Produces 4 ATP (net gain of 2 ATP) and 2 NADH.
Where does glycolysis occur and what are its end products?
Glycolysis occurs in the cytosol. Its main end products are 2 pyruvate, 2 ATP (net), and 2 NADH per glucose molecule.
How is glycolysis regulated?
Step 1: Hexokinase (feedback inhibition by glucose-6-phosphate).
Step 3: Phosphofructokinase (activated by AMP, inhibited by ATP).
Step 10: Pyruvate kinase (feedforward activation by fructose-1,6-bisphosphate).
Why do we need metabolic pathways?
They allow controlled energy release, create building blocks for anabolism, and generate intermediates that integrate different metabolic processes.
What role do cofactors play in metabolism?
Cofactors (e.g., NAD⁺, FAD) are non-protein molecules required for enzymatic activity, often functioning as electron carriers or stabilizing reactions.
What are the three stages of energy metabolism?
Stage I: Breakdown of large molecules into smaller ones (no ATP gain).
Stage II: Conversion of smaller molecules into Acetyl-CoA (small ATP gain).
Stage III: Oxidation of Acetyl-CoA in the citric acid cycle (major ATP gain).
What are the irreversible steps in glycolysis, and why are they important?
Steps 1, 3, and 10 have large negative ΔG, making them key control points and ensuring the pathway progresses in the forward direction.
How do dietary sugars like fructose and galactose enter glycolysis?
Fructose: Enters glycolysis after the main regulatory step (Step 3).
Galactose: Is converted into glucose-1-phosphate, then enters glycolysis.
What is the Harden and Young effect in glycolysis?
Harden and Young showed that glycolysis requires both large molecules (enzymes, heat-sensitive) and small molecules (cofactors, heat-stable) for activity.
Why is glycolysis anaerobic, and how does it adapt to low oxygen environments?
Glycolysis evolved before oxygen was abundant. In low oxygen, it couples with fermentation pathways to regenerate NAD⁺ and allow ATP production to continue.
What happens to pyruvate after glycolysis?
Under aerobic conditions: Pyruvate enters the citric acid cycle.
Under anaerobic conditions: Pyruvate is converted into lactate or ethanol, depending on the organism.
What happens to pyruvate under aerobic and anaerobic conditions?
Aerobic: Pyruvate enters the citric acid cycle for complete oxidation.
Anaerobic: Pyruvate undergoes fermentation, forming lactate in animals or ethanol in yeast.
Why is regeneration of NAD⁺ crucial in glycolysis?
NAD⁺ is required for the oxidation of glyceraldehyde-3-phosphate. Without it, glycolysis would stop.
What is the pyruvate dehydrogenase complex, and what reaction does it catalyze?
It is a multi-enzyme complex that converts pyruvate to acetyl-CoA, producing NADH and CO₂. This step is irreversible and crucial for linking glycolysis to the citric acid cycle.
What cofactors are required by the pyruvate dehydrogenase complex?
TPP (from vitamin B1) – Used in decarboxylation.
Lipoamide – Transfers acetyl groups.
FAD and NAD⁺ – Electron carriers.
Coenzyme A – Acetyl group carrier.
How is the pyruvate dehydrogenase complex regulated?
Activated by low energy signals: ADP and NAD⁺.
Inhibited by high energy signals: ATP, NADH, and acetyl-CoA.
Activated by dephosphorylation and inhibited by phosphorylation.
Why can’t acetyl-CoA be used to make glucose in humans?
The conversion of pyruvate to acetyl-CoA is irreversible. Only plants and bacteria have workarounds to convert acetyl-CoA back to glucose.
What is the “sparker effect” in the citric acid cycle?
Adding trace organic acids (e.g., citrate or fumarate) to pyruvate enhances oxygen consumption. This revealed the catalytic, cyclic nature of the citric acid cycle.
What are the main products of the citric acid cycle per acetyl-CoA?
2 CO₂
3 NADH
1 FADH₂
1 GTP (or ATP)
What are anaplerotic reactions, and why are they important?
These reactions replenish citric acid cycle intermediates when they are withdrawn for biosynthesis. For example, pyruvate carboxylase converts pyruvate to oxaloacetate.
What roles do glucogenic and ketogenic amino acids play in metabolism?
Glucogenic: Can be converted to citric acid cycle intermediates for glucose production.
Ketogenic: Cannot contribute to glucose production; they form ketone bodies.
How does fermentation differ between animals and yeast?
Animals: Pyruvate is reduced to lactate (e.g., in muscles during exercise).
Yeast: Pyruvate is converted to ethanol and CO₂.
Why is the citric acid cycle considered central to metabolism?
It integrates the breakdown of carbohydrates, fats, and proteins while providing intermediates for biosynthesis and generating reduced cofactors for ATP production.
What is the role of Coenzyme A in metabolism?
It acts as a carrier of acyl groups, enabling their transfer to other molecules, which is essential for reactions in the citric acid cycle and fatty acid metabolism.
What is gluconeogenesis, and why is it important?
Gluconeogenesis is the anabolic process of synthesizing glucose from non-carbohydrate precursors like pyruvate, lactate, and glycerol. It helps maintain blood glucose levels during fasting or intense exercise.
Why doesn’t gluconeogenesis simply reverse glycolysis?
Glycolysis has three irreversible steps with large negative ΔG, which cannot be reversed under physiological conditions. These steps are bypassed in gluconeogenesis using different enzymes.
What are the unique steps in gluconeogenesis?
Pyruvate to phosphoenolpyruvate (via pyruvate carboxylase and PEP carboxykinase).
Fructose-1,6-bisphosphate to fructose-6-phosphate (via fructose-1,6-bisphosphatase).
Glucose-6-phosphate to glucose (via glucose-6-phosphatase).
What regulates gluconeogenesis?
Gluconeogenesis is activated when energy levels are high (e.g., high ATP) and inhibited when energy is low (e.g., high ADP or AMP). It is oppositely regulated compared to glycolysis.
What is the pentose phosphate pathway (PPP), and what are its functions?
PPP is a metabolic pathway parallel to glycolysis. It generates NADPH for reductive biosynthesis (e.g., fatty acids) and ribose-5-phosphate for nucleotide synthesis.
What are the two phases of the PPP?
Oxidative phase: Produces NADPH and ribulose-5-phosphate.
Non-oxidative phase: Converts ribulose-5-phosphate into ribose-5-phosphate or glycolytic intermediates.
What enzyme controls the entry of glucose-6-phosphate into the PPP?
Glucose-6-phosphate dehydrogenase (G6PD), which is regulated by the availability of NADP⁺.
How does the PPP adapt to different cellular needs?
If cells need ribose-5-phosphate: The non-oxidative phase runs in reverse.
If cells need NADPH: The oxidative phase runs cyclically, producing maximum NADPH.
If cells need both: Both phases operate together.
What are the starting materials and end products of gluconeogenesis?
Starting materials: Pyruvate, oxaloacetate, glycerol, some amino acids.
End product: Glucose.
How does gluconeogenesis interact with the citric acid cycle?
Oxaloacetate, a citric acid cycle intermediate, is a key precursor in gluconeogenesis, linking the two pathways.
What is the significance of NADPH generated by the PPP?
NADPH is essential for:
Reductive biosynthesis (e.g., fatty acid synthesis).
Protecting cells from oxidative stress by regenerating reduced glutathione.
What is Favism, and how is it related to the PPP?
Favism is caused by a deficiency in glucose-6-phosphate dehydrogenase, impairing NADPH production. This reduces the ability of red blood cells to handle oxidative stress, leading to hemolysis.
How is futile cycling avoided between glycolysis and gluconeogenesis?
Opposing enzymes, like PFK and fructose-1,6-bisphosphatase, are tightly regulated to ensure one pathway is active while the other is suppressed, preventing energy wastage.
Describe briefly what oxidative phosphorylation is.
The process in which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O2 by a series of electron carriers
What are NADH shuttles?
The inner mitochondrial membrane is impermeable to NADH. Two shuttles transport e- from NADH:
glycerol phosphate shuttle
malate shuttle.
Describe the glycerol-phosphate shuttle.
e- carried by FADH2 onto Q
So, complex I is bypassed therefore only 6H+ pumped instead of 10
And less ATP is made from cytoplasmic NADH
Describe the malate shuttle.
Used in heart and liver only when energy must be conserved.
Complex redox shuttle
Net reaction is NADH moved to
mitochondria
Enter via complex I
Describe what nucleotide carriers are.
It’s the method that ADP and Pi uses to get into the matrix, it’s what ATP uses to get to the cytoplasm. This is done via two antiporters:
Pi-OH- antiporter
ATP-ADP antiporter
1 H+ is spent to import ADP+Pi and export ATP from the matrix.
Describe Complex IV: Cytochrome C oxidase
Cyt C delivers electrons
Again mini electron transport chain inside Cpx III
Carriers iron cytochromes and cupper
Delivered to oxygen: the final acceptor, reduced to water
Result: 2 protons pumped across membrane
Describe Complex II: Succinate - Q reductase.
Directly linked to TCA cycle: Succinate is oxidised to fumerate delivering e- to FAD
FADH2 starts mini electron transport chain
Chain of iron sulphur clusters
Delivered to ubiquinone
Result: NO protons pumped across membrane
Describe the chemiosomotic theory.
In 1961 Peter Mitchell proposed that:
The primary energy-conserving event induced by e- transport is the generation of a proton-motive force across the inner mitochondrial membrane.
What is chemiosmotic coupling?
Chemiosmotic coupling is the process that links the movement of electrons through the electron transport chain to the production of ATP.
What is the proton-motive force?
Pumping of protons in the intermembrane space generates:
A concentration gradient : ΔpH ~ -1.4
A transmembrane potential: Em ~ 0.14 V
Both contribute to the proton-motive force, Δp
Describe the natural uncoupling to generate heat.
Thermogenin in animals
Found in mitochondria of brown fat cells
natural uncoupler
maintains body temperature e.g., in babies and during wake up from hibernation
Alternative oxidase in plants
Oxidises QH2 and generates heat
used by some species to increase temperature of specific organs i.e., flowers or to germinate early.
What is photosynthesis, and why is it important?
Photosynthesis captures solar energy to produce reducing power (NADPH), ATP, and carbohydrates, storing about
10^18kJ of free energy annually. Oxygen is released as a waste product.
What are the two main stages of photosynthesis?
Light-dependent reactions: Capture light energy to produce NADPH and ATP.
Light-independent reactions (Calvin cycle): Use NADPH and ATP to fix CO₂ into carbohydrates.
Where do the light-dependent reactions occur?
In the thylakoid membranes of the chloroplast. These reactions generate a proton gradient and produce NADPH and ATP.
What is the role of chlorophyll in photosynthesis?
Chlorophyll absorbs light energy, exciting electrons. The excited electrons are transferred through reaction centers in Photosystem I and II.
What is the Hill reaction?
It demonstrated that light drives the transfer of electrons from water to electron acceptors, evolving oxygen in the process.
What is the Z-scheme in photosynthesis?
A model describing the flow of electrons through Photosystem II (P680) and Photosystem I (P700), resulting in the production of NADPH and ATP.
How does Photosystem II split water?
Using its high redox potential, PSII oxidizes water, releasing oxygen, protons, and electrons. This step contributes to the proton gradient.
What is cyclic photophosphorylation, and why is it used?
It recycles electrons through Photosystem I to produce additional ATP without generating NADPH, balancing the energy requirements of the Calvin cycle.
What is the Calvin cycle, and where does it occur?
The Calvin cycle, occurring in the chloroplast stroma, fixes CO₂ into organic molecules using ATP and NADPH to form G-3-P, which can be converted into glucose.
What are the three main stages of the Calvin cycle?
Carbon fixation: CO₂ reacts with ribulose-1,5-bisphosphate (RuBP) to form 3-phosphoglycerate (3PG).
Reduction: 3PG is converted into G-3-P using ATP and NADPH.
Regeneration: RuBP is regenerated for the cycle to continue.
What is photorespiration, and why is it wasteful?
Photorespiration occurs when Rubisco fixes O₂ instead of CO₂, producing glycolate. This process consumes ATP and releases CO₂, reducing photosynthetic efficiency.
How do C4 plants avoid photorespiration?
They spatially separate CO₂ fixation and the Calvin cycle. CO₂ is first fixed into a 4-carbon compound (malate) in mesophyll cells and then transported to bundle sheath cells where the Calvin cycle occurs.
What is the efficiency of photosynthesis?
About 30% of the absorbed light energy is converted into stored chemical energy, a higher efficiency compared to average solar panels (15%).
What is glycogen, and what are its main roles?
Glycogen is a highly branched polymer of glucose stored in the liver (for blood glucose maintenance) and muscles (for energy). It allows anaerobic metabolism and supports brain function, unlike fats.
Why can’t animals convert fatty acids to glucose?
Animals lack the glyoxylate pathway found in plants and bacteria, which enables conversion of acetyl-CoA to glucose.
What are the key steps in glycogen breakdown?
Glycogen phosphorylase cleaves α-1,4 glycosidic bonds, releasing glucose-1-phosphate.
A debranching enzyme removes α-1,6 linkages.
Phosphoglucomutase converts glucose-1-phosphate to glucose-6-phosphate.
In the liver, glucose-6-phosphatase converts it to free glucose for export.
What is the energy-saving advantage of glycogen breakdown?
Phosphorolysis saves one ATP by directly producing glucose-1-phosphate instead of free glucose.
How is glycogen synthesized?
UDP-glucose is formed using UTP and glucose-1-phosphate.
Glycogen synthase adds glucose residues via α-1,4 bonds.
A branching enzyme creates α-1,6 bonds for branching.
What happens in Andersen’s disease?
Patients lack the branching enzyme, resulting in abnormal glycogen structure and early liver failure.
How are glycogen synthesis and breakdown reciprocally regulated?
Glycogen synthase is active when dephosphorylated and promotes synthesis.
Glycogen phosphorylase is active when phosphorylated and promotes breakdown.
Hormones like insulin, glucagon, and adrenaline regulate these processes.
What is the role of insulin in glycogen metabolism?
Insulin activates glycogen synthase and inhibits glycogen phosphorylase, promoting glycogen synthesis during high blood glucose levels.
How does adrenaline affect glycogen metabolism?
Adrenaline promotes glycogen breakdown by activating phosphorylase and inhibiting glycogen synthase, especially during stress or exercise.
What are isozymes, and how do liver and muscle glycogen phosphorylases differ?
Isozymes are enzyme variants catalyzing the same reaction but with different regulation. Muscle phosphorylase is activated by AMP (low energy), while liver phosphorylase is inactivated by glucose.
What is the Cori cycle?
It describes the recycling of lactate produced by muscles during anaerobic respiration back to glucose in the liver, supporting energy supply during intense exercise.
How do hormones regulate blood glucose levels?
High glucose: Insulin from the pancreas promotes glycogen synthesis and glucose uptake.
Low glucose: Glucagon and adrenaline promote glycogen breakdown and gluconeogenesis.
Why is glycogen metabolism crucial for glucose homeostasis?
It maintains blood glucose levels, prevents futile cycles between synthesis and breakdown, and supports coordinated responses by organs like the liver and muscles to energy demands.
What are the main functions of cellular membranes?
They act as semipermeable barriers, detect changes in the extracellular environment, provide anchorage for proteins, and create compartments within cells.
What is the Fluid Mosaic Model?
A model that describes membranes as semi-fluid structures composed of a phospholipid bilayer with proteins embedded within it, allowing lateral movement of components.
What are the three main types of lipids found in membranes?
Phospholipids (phosphoglycerides and sphingolipids), glycolipids, and cholesterol.
What defines a lipid’s structure?
Lipids are defined by their hydrophobic nature, not a specific structure, and are soluble in organic solvents like chloroform.
What does amphipathic mean in relation to lipids?
Amphipathic molecules have both hydrophobic (water-fearing) and hydrophilic (water-loving) regions, allowing them to form bilayers.
What is the role of cholesterol in membranes?
Cholesterol modulates membrane fluidity and stability by fitting between phospholipids.
How do saturated and unsaturated fatty acids differ?
Saturated fatty acids have no double bonds and are straight, while unsaturated fatty acids have double bonds that introduce kinks, increasing membrane fluidity.
What are essential fatty acids?
Fatty acids that the body cannot synthesize and must be obtained from the diet, such as linoleic acid (omega-6) and linolenic acid (omega-3).
What is arachidonic acid, and why is it important?
A polyunsaturated fatty acid derived from linoleic acid, it serves as a precursor for eicosanoids, which are involved in inflammation and signaling.
What are glycolipids, and what is their function?
Sugar-containing lipids involved in cell-cell recognition, immune responses, and attachment, typically found on the extracellular side of membranes.
What is sphingomyelin?
A type of sphingolipid that forms a major component of the myelin sheath, essential for insulating nerve axons and speeding up electrical impulses.
How does the myelin sheath contribute to nerve function?
It insulates nerve fibers, increasing the speed of electrical signal transmission and preventing signal loss.
What is the role of phosphatidylinositol in cell signaling?
It participates in intracellular signaling pathways by generating secondary messengers when cleaved by phospholipase C (PLC).
How do lipids contribute to membrane asymmetry?
Different lipids are distributed unevenly between the inner and outer layers of the bilayer, affecting membrane curvature and cell signaling.
What happens during the process of lipid flipping?
Certain enzymes, such as flippases, transfer phospholipids from one leaflet of the bilayer to the other, maintaining membrane asymmetry.
What is membrane fluidity, and why is it important?
Membrane fluidity refers to the flexible, dynamic nature of the lipid bilayer, allowing lateral movement of lipids and proteins. It is essential for cell signaling, diffusion, membrane transport, and vesicle fusion.
What factors affect membrane fluidity?
Temperature, lipid composition (saturation and chain length), and cholesterol content.
How does temperature influence membrane fluidity?
Higher temperatures increase fluidity, while lower temperatures decrease it, potentially making the membrane too rigid.
How do unsaturated fatty acids affect membrane fluidity?
Unsaturated fatty acids introduce kinks in the lipid tails, preventing tight packing and increasing membrane fluidity.
What is the role of cholesterol in membrane fluidity?
Cholesterol increases fluidity in the membrane’s interior but decreases fluidity near the edges by stabilizing the phospholipids.
What is lateral diffusion in membranes?
The movement of lipids and proteins within the same layer of the bilayer; occurs at a rate of ~2 μm per second.
What is transverse diffusion (flip-flop)?
The rare movement of phospholipids between membrane layers, typically occurring once every three days, facilitated by flippases.
What are integral membrane proteins?
Proteins embedded within the lipid bilayer that can span the membrane once or multiple times, involved in transport and signaling.
What are peripheral membrane proteins?
Proteins attached to the membrane surface via non-covalent interactions, involved in structural support and signaling.
What role do glycans play on cell membranes?
Glycans are involved in cell recognition, signaling, and immune responses, forming a protective glycocalyx on the cell’s surface.
How do plants regulate membrane fluidity?
Plants adjust their lipid composition—favoring unsaturated fats at low temperatures and saturated fats at high temperatures—to maintain fluidity.
What happens to membrane fluidity with chronic alcohol exposure?
Alcohol increases membrane fluidity, but chronic exposure leads cells to compensate by increasing membrane cholesterol, reducing fluidity over time.
What is the glycocalyx, and what are its functions?
A carbohydrate-rich layer covering the cell surface, providing protection, aiding in cell recognition, and functioning in mechanosensing.
Why are β-barrel proteins important in membranes?
They form pores across membranes, allowing selective transport of molecules, commonly found in bacterial outer membranes.
What is ICAM, and what is its role in cell communication?
Intercellular Adhesion Molecule (ICAM) is a membrane protein involved in immune responses and inflammation by facilitating cell-cell adhesion.
What are the main types of membrane transport?
Simple diffusion, facilitated diffusion, passive transport, and active transport (primary and secondary).
What molecules can cross lipid bilayers by simple diffusion?
Small, non-polar molecules such as gases (O₂, CO₂) and hydrophobic molecules.
What is facilitated diffusion?
The passive transport of molecules across a membrane via specific transport proteins or channels, without using energy.
What are the three main types of transporters?
Uniporters (single solute movement), symporters (co-transport of two solutes in the same direction), and antiporters (exchange of two solutes in opposite directions).
How does membrane potential affect charged molecule transport?
The electrochemical gradient, which combines membrane potential and concentration gradient, drives the movement of charged solutes.
What is the role of the GLUT family of transporters?
They facilitate glucose transport across membranes, with specific GLUT isoforms expressed in different tissues.
What is GLUT4, and where is it found?
GLUT4 is an insulin-regulated glucose transporter found in adipose tissue and muscle cells, enabling glucose storage.
What is active transport?
The movement of molecules against their concentration gradient using energy, typically from ATP hydrolysis or ion gradients.
What is the Na⁺/K⁺ pump, and how does it function?
A P-type ATPase that exchanges 3 Na⁺ ions out of the cell for 2 K⁺ ions into the cell, maintaining membrane potential.
How does secondary active transport work?
It uses the energy from ion gradients (often Na⁺) to drive the uphill transport of another molecule against its concentration gradient.
What is the role of V-type ATPases?
They pump protons into organelles like lysosomes to acidify their internal environment, necessary for enzymatic activity.
How is stomach pH maintained?
A P-type proton pump transports H⁺ into the stomach lumen, while Cl⁻ ions enter via facilitated diffusion to form hydrochloric acid (HCl).
What is the function of ABC transporters?
They use ATP hydrolysis to transport various molecules across membranes, including drugs and metabolic products.
How does the F-type ATP synthase operate?
Located in the mitochondria, it uses the proton gradient across the inner membrane to synthesize ATP from ADP and inorganic phosphate.
How does transcellular glucose transport occur in intestinal epithelial cells?
Glucose enters via a Na⁺-driven symporter, exits through a passive glucose transporter, and Na⁺/K⁺ pumps maintain ion gradients.
What is protein trafficking in cells?
Protein trafficking refers to the movement of proteins within the cell, directing them to their correct compartments based on sorting signals.
What are the three main modes of protein transport?
Gated transport (nucleus), protein translocation (e.g., ER import), and vesicular transport (e.g., secretion along the secretory pathway).
What is a sorting signal in protein transport?
A sequence within the protein (short peptides or 3D structures) that directs the protein to its proper cellular destination.
What are Nuclear Localization Signals (NLS)?
Signals rich in lysine and arginine that guide proteins into the nucleus via importins.
What is the role of importins in nuclear transport?
Importins are cytosolic receptors that recognize NLS and facilitate the transport of proteins into the nucleus.
What are nuclear pore complexes (NPCs)?
Large protein structures that allow gated transport of macromolecules between the cytoplasm and nucleus.
How does molecular size affect nuclear transport?
Small molecules (<5 kDa) diffuse freely, while larger proteins (>40 kDa) require active transport through NPCs.
What is the role of Ran-GTPase in nuclear import?
Ran-GTPase regulates active nuclear import by providing energy and directionality for transport.
How does Ran-GTP facilitate nuclear import?
Ran-GTP binds importin in the nucleus, causing it to release its cargo protein.
What is the function of Ran-GAP and Ran-GEF?
Ran-GAP hydrolyzes GTP to GDP in the cytosol, while Ran-GEF exchanges GDP for GTP in the nucleus, maintaining the Ran gradient.
What is nuclear export?
The process of transporting proteins from the nucleus to the cytoplasm via nuclear export signals (NES) and exportins.
How do exportins function?
Exportins recognize NES and, together with Ran-GTP, mediate the export of proteins through NPCs.
Why are nuclear localization signals (NLS) not cleaved after transport?
Many nuclear proteins continuously shuttle between the cytoplasm and nucleus, requiring repeated import.
What is the role of nuclear pore complexes (NPCs) in gene regulation?
NPCs influence genome organization and gene activation, with some nucleoporins like Nup98 playing roles in diseases such as leukemia.
How can protein trafficking be visualized experimentally?
Using dyes or fluorescent proteins like GFP, mNeonGreen, or mCherry to track protein movement in live cells.
What is the secretory pathway in eukaryotic cells?
It is a process by which proteins enter the endoplasmic reticulum (ER) via translocation and are transported through vesicular trafficking to their final destinations, such as the plasma membrane or lysosomes.
What percentage of human genome-encoded proteins are secreted?
Approximately 15% of human proteins are secreted, known as the secretome.
What is the role of the endoplasmic reticulum (ER) in the secretory pathway?
The ER is responsible for lipid synthesis, protein folding and assembly, N-glycosylation, and quality control, degrading misfolded proteins.
What is co-translational translocation?
It is the process by which proteins are translocated into the ER as they are being synthesized by ribosomes.
What is the function of the Sec61 complex in protein translocation?
Sec61 acts as a signal-gated aqueous channel that facilitates the translocation of proteins into the ER.
How are misfolded proteins handled in the ER?
Misfolded proteins are retained in the ER and, if not properly folded after multiple attempts, are sent to the cytosol for degradation by the proteasome.
What is N-glycosylation, and why is it important?
The addition of oligosaccharides to specific asparagine residues of proteins in the ER, aiding in proper folding and stability.
What is the role of the Golgi apparatus in protein trafficking?
It modifies, packages, and sorts proteins for delivery to various destinations, such as lysosomes, the plasma membrane, or for secretion.
What is the mannose-6-phosphate (M6P) signal?
A glycan modification that targets proteins to lysosomes by binding to M6P receptors in the trans-Golgi network.
How do lysosomal enzymes get modified with M6P?
A signal patch on the enzyme is recognized by N-acetylglucosamine phosphotransferase in the Golgi, which adds the phosphate group required for targeting.
What are lysosomes, and what is their function?
Lysosomes are cellular organelles rich in hydrolytic enzymes that degrade and recycle cellular waste, old organelles, and foreign materials.
What happens if M6P signaling is defective?
Enzymes fail to reach the lysosome and are secreted instead, leading to lysosomal storage diseases due to undigested material accumulation.
What is clathrin, and what is its role in vesicle trafficking?
Clathrin is a protein that forms a coated vesicle around proteins destined for the lysosome, facilitating vesicle formation and sorting.
Name three lysosomal storage diseases and their causes.
Gaucher’s Disease: Lack of glucocerebrosidase, leading to glucocerebroside accumulation.
Tay-Sachs Disease: Deficiency of hexosaminidase A, causing ganglioside accumulation in neurons.
I-cell Disease: Absence of GlcNAc phosphotransferase, preventing proper lysosomal enzyme targeting.
What are the key steps in vesicular transport from the Golgi to lysosomes?
M6P-modified enzymes bind to receptors in the trans-Golgi, clathrin-coated vesicles bud off, vesicles uncoat and fuse with late endosomes, and cargo is delivered to lysosomes.
What is the extracellular matrix (ECM)?
The ECM is a network of proteins and polysaccharides outside cells that provides structural support, anchors the cytoskeleton, and influences cell behavior such as survival, development, migration, and proliferation.
What are the major components of the ECM?
Polysaccharides (glycosaminoglycans and proteoglycans) and proteins (collagen, elastin, and glycoproteins like fibronectin).
What role does collagen play in the ECM?
Collagen provides structural strength and is the most abundant protein in the ECM, making up about 25% of total body protein, with Type I collagen being the most common.
What is the function of elastin in the ECM?
Elastin gives tissues elasticity, allowing them to stretch and return to their original shape, especially important in arteries.
What are glycosaminoglycans (GAGs), and what is their role?
GAGs are long chains of negatively charged disaccharides that attract water and cations, creating turgor pressure and resisting compressive forces in tissues.
What are proteoglycans, and how do they function in the ECM?
Proteoglycans are proteins heavily modified with GAGs that help form hydrated gels, provide support, and regulate cell signaling.
What is hyaluronan, and what role does it play?
Hyaluronan is a large GAG that contributes to tissue hydration and turgor, playing an essential role in joint lubrication and shock absorption.
How is collagen processed before it becomes functional?
Collagen is synthesized as pre-procollagen, hydroxylated in the ER, modified in the Golgi, and secreted as tropocollagen before forming fibrils through cross-linking.
What is the function of fibronectin in the ECM?
Fibronectin is a glycoprotein that connects the ECM to integrins on cell membranes, supporting cell adhesion, migration, and tissue repair.
What is the basal lamina, and why is it important?
The basal lamina is a specialized ECM layer beneath epithelial cells that provides mechanical support and separates epithelial tissues from underlying connective tissue.
What enzymes are responsible for ECM degradation?
Matrix metalloproteinases (MMPs) and serine proteases break down ECM components for tissue remodeling and repair, with their activity tightly regulated.
What role does the ECM play in cancer progression?
Cancer cells degrade the ECM to facilitate invasion and metastasis, often down-regulating fibronectin and increasing the activity of metalloproteinases.
What is scurvy, and how is it related to collagen?
Scurvy is caused by vitamin C deficiency, which impairs collagen hydroxylation, leading to weak connective tissues, gum disease, and poor wound healing.
What is the function of fibripositors in collagen secretion?
Fibripositors are cellular structures that align and secrete collagen fibrils in an organized manner for proper ECM formation.
How do cells interact mechanically with the ECM?
Cells use integrins to connect their cytoskeleton to ECM components, allowing them to exert forces, organize ECM fibers, and influence cell migration.
What are the three main components of the cytoskeleton?
Microtubules, actin filaments, and intermediate filaments.
What are the main functions of the cytoskeleton?
It provides mechanical strength, moves organelles, determines cell polarity, drives chromosome segregation during mitosis, enables cell movement, and serves as an anchor for cell-cell junctions.
What are microtubules made of?
Non-covalent heterodimers of α- and β-tubulin subunits, which bind GTP and GDP.
How do microtubules grow and shrink?
Growth occurs at the (+) end through GTP-bound dimers, while shrinkage happens rapidly from the same end if the cap is GDP-bound.
What are the functions of actin filaments?
They control cell shape, enable movement, and provide structural flexibility by bundling together to form strong structures.
What is the primary role of intermediate filaments?
They provide mechanical strength and flexibility without breaking, supporting cells under stress.
What are desmosomes?
Cell-cell junctions that connect intermediate filaments in adjacent cells, providing mechanical strength, especially in tissues under high stress.
What proteins are involved in adherens junctions?
Cadherins, which form homodimers and link indirectly to the actin cytoskeleton through anchor proteins like catenins.
How do cadherins enable cell-cell adhesion?
They form weak homophilic bonds with cadherins on adjacent cells, creating strong overall adhesion through numerous interactions (the “Velcro effect”).
What are focal adhesions, and what do they do?
Cell-ECM anchoring junctions that connect the internal cytoskeleton to ECM molecules via integrins, allowing cells to grip or release ECM as needed.
What proteins form tight junctions?
Claudins and occludins, which seal spaces between epithelial cells to maintain polarity and prevent leakage.
What are gap junctions, and what is their function?
Channel-forming junctions made from connexins that allow direct communication and exchange of small molecules between neighboring cells.
How do integrins function in focal adhesions?
Integrins are α/β heterodimers that bind ECM components and link to actin via talin, enabling cells to anchor to or migrate through the ECM.
What is anchorage dependence?
The requirement of many cells to adhere to the ECM via integrins for survival, proliferation, and growth.
Why are tight junctions important in epithelial cells?
They maintain cell polarity by preventing the mixing of apical and basolateral membrane proteins, ensuring directional transport, such as glucose absorption in the gut.
What are the main phases of the cell cycle?
G1 (first gap), S (synthesis), G2 (second gap), and M (mitosis).
What happens during the S phase of the cell cycle?
DNA replication occurs, doubling the genetic material to prepare for cell division.
What is mitosis, and what is its primary role?
Mitosis is the process of nuclear division where chromosomes are equally apportioned between two daughter cells.
What are the stages of mitosis?
Prophase, metaphase, anaphase, and telophase, followed by cytokinesis.
What discovery did Sir Tim Hunt make in 1983?
He discovered cyclins, proteins that regulate the cell cycle and are degraded at each cell division.
What is the role of cyclins in the cell cycle?
Cyclins regulate progression through the cell cycle by activating cyclin-dependent kinases (CDKs).
What is a cyclin-CDK complex?
A heterodimer consisting of a regulatory cyclin and a catalytic cyclin-dependent kinase (CDK) that phosphorylates target proteins.
How is the cyclin-CDK complex activated?
It becomes active after phosphorylation and removal of inhibitory signals, allowing it to regulate cell cycle transitions.
What happens to cyclins after their function is completed?
They are degraded by the proteasome, ensuring proper regulation of the cell cycle.
What are the specific cyclin-CDK complexes in mammalian cells?
G1 Phase: Cyclin D with CDK4/6
S Phase: Cyclin A with CDK2
G2/M Phase: Cyclin B with CDK1
What is the function of G1 cyclin-CDK complexes?
They prepare the cell for DNA replication by promoting the expression of S phase cyclins.
What role does the G2/M cyclin-CDK complex play?
It phosphorylates targets necessary for spindle formation and activation of mitosis.
How is cell division related to cancer?
Errors in cell cycle regulation can lead to uncontrolled cell division, a hallmark of cancer.
What is the importance of metaphase spreads in cell biology?
They allow visualization of chromosomes for diagnostic purposes, such as identifying chromosomal abnormalities in diseases like multiple myeloma.
What is the role of centrosomes during mitosis?
Centrosomes organize microtubules and help establish the mitotic spindle, ensuring accurate chromosome segregation.
