Bio Exam 2 Study Guide Questions

How is cholesterol positioned in the lipid bilayer? What function does it serve?

***Decreases membrane fluidity at high temperature*** Acts as a glue between phospholipids bc it interrupts van der waals forces between lipids and instead interacts w/ lipids on its own ***Increases membrane fluidity at low temperatures*** Keeps phospholipids away from each other bc if it wasn't there, phospholipids would just get closer together and become more solid and have a hard time moving around ***Decreases membrane permeability to small molecules*** Acts as a plug in membrane and blocks small molecules from sneaking in through membrane pores

What membrane transport processes are involved in glucose uptake by gut epithelial cells? How do these transport mechanisms "work together" to accomplish glucose absorption from the gut?

*Active transport required to move glucose from outside of cell into cell* --> Secondary active transport → Sodium/glucose symport allows for inward movement of Na+ into cell and encourages binding affinity for glucose (occurs in apical domain) Primary active transport → Sodium-potassium antiport pumps maintain gradient by removing Na+ from inside of cell (occurs in basolateral domain) *Passive transport required for facilitated diffusion → carrier proteins carry glucose molecules from inside of cell to blood* Gradient is maintained by secondary active transport transferring glucose into cell and glucose then being moving away from cell when it exits cell and gets into bloodstream Removal of glucose via glucose uniport (occurs in basolateral domain) as soon as it enters cell helps keep the concentration gradient alive is an example of facilitated diffusion

What are the main differences between smooth and rough endoplasmic reticulum in terms of both structure and function?

*Rough ER - contains ribosomes embedded in membrane* Membrane synthesis Biosynthesis and processing of proteins Proteins get into ER itself and are deposited in ER lumen *Smooth ER - doesn't have ribosomes embedded in membrane* Membrane synthesis Drug detoxification Carbohydrate metabolism Calcium storage Steroid biosynthesis

*How does a soluble protein make it inside the ER lumen during co-translational import? What about membrane-spanning proteins - how do they become incorporated into the ER membrane?* What are start and stop signals and how do they work?

*process of co-translational import* SRP binds to ER signal sequence and blocks translation SRP binds to SRP receptor; ribosome docks to membrane GTP binds to SRP and SRP receptor (1 GTP for each); pore opens and polypeptide is inserted → process of binding causes amino terminus of polypeptide to be inserted into translocon which is open GTP hydrolyzed and SRP is released, allowing polypeptide to be directed into pore protein of translocon; protein synthesis continues and polypeptide is driven through pore Signal sequence is cleaved by signal peptidase as polypeptide elongates and translocates into ER lumen Completed polypeptide is released into ER lumen, ribosome is released and translocon pore closes Soluble proteins delivered to ER lumen Many of these proteins are destined for secretion -*membrane-spanning proteins will be embedded in ER membrane* - Stop-transfer sequence → as protein synthesis continues, there is a certain sequence that is detected by pore protein that stops driving polypeptide through pore protein into ER lumen; translation continues until polypeptide is fully formed and then translocon opens up and allows hydrophobic part of polypeptide to be attached to membrane; amino side is in ER lumen while carboxyl side is in cytosol - Internal start-transfer sequence → pore protein recognizes sequence and allows translation to continue until polypeptide is elongated; carboxyl side is located in lumen and amino side is located in cytosol

What happens to a protein or a lipid as it makes its way through the Golgi complex?

- "Compartments" contain specific enzymes (regional specialization) - Modifications sequential - Both proteins and lipids modified are sorted

Cytochrome oxidase is the final protein complex in the electron transport chain. What does this protein complex do? How is oxygen used by this complex? How do metal ions play a role in the function of this complex? What does this protein complex do to prevent the release of damaging superoxide radicals into the cytoplasm?

- 4e- enter cytochrome c and O2 is bound here to heme group; superoxide radical is confined inside cytochrome c so that it can't damage surrounding proteins by taking their e-

What is the "cost" of forming ATP from ADP? How much energy is "released" by the hydrolysis of ATP? What is the relevance of these conversions in catabolic and anabolic metabolism?

- ATP is more unstable while ADP is more stable which is why ATP synthesis requires energy input but ATP hydrolysis involves energy release and is energetically favorable - ATP hydrolysis releases enough energy to power reverse reaction of ATP synthesis - Reactions above ATP hydrolysis are high energy bc they can power reactions below them - ATP hydrolysis is intermediate bc it can only power it's own reverse reaction and nothing above or below it

Understand the alternating conformation model of carrier protein action.

- Alternating conformation ("flip-flop") model - Selective to certain molecules - It can release molecules in either direction (outside or inside of cell) so long as it follows concentration gradient - Open to region where concentration gradient is higher bc it wants more opportunities to bind w/ solute and move it to area of lower concentration

In what ways can the fluidity of a cell membrane be altered?

- As the number of carbon atoms increases, the melting point increases - As the number of double bonds increases, the melting point decreases

How does facilitated diffusion through an ion channel differ from facilitated diffusion through a carrier protein?

- Both concentration gradients and electrical forces determine rate of passive transport through an ion channel bc ion channels transport ions - only concentration gradient determines movement through a carrier protein bc carrier proteins transport solutes

Where is most protein synthesis initiated? How does a newly synthesized protein "decide" where to go?

- Common pool of ribosomes in cytosol → where synthesis of proteins occurs These proteins are used in different locations - Cotranslational import - importation of ribosome and it's polypeptide into ER lumen -Posttranslational import - importation of ribosomes and proteins where it stays in cytoplasm - "Signal" sequences direct proteins to the correct compartment

What is the structure of the Golgi complex? Why is this organelle described as being polarized? What is the significance of this polarization?

- Components of Golgi are functionally biochemically distinct Cis face is where vesicles enter while trans face is where vesicles exit and are transported There is transport in both directions and get further modified - Golgi complex highly polarized bc membranes at one end of the stack differ in both composition and in thickness from those at the other end

What is the difference between constitutive and regulated secretion?

- Constitutive - secretion of molc w/ no specific signal - Regulated - secretion of molc w/ specific signal

What is NAD+? NADH? What is the relationship between the two? How are the two used during glycolysis?

- Difference between NAD+ and NADH is that NADH is more reduced and at a higher energy state bc it contains e- and will readily donate them while NAD+ is more oxidized, at a lower energy state and will readily accept e- - NADH donates e- to e- carriers in ETC; used indirectly to make more ATP

Indirect transport is always linked ("coupled") to a direct transport mechanism. Explain.

- Direct active transport of proteins occurs to create a concentration gradient - Indirect active transport of solute molecules occurs after concentration gradient is created

What is the difference between endocytosis and exocytosis?

- Endocytosis - when membrane fuses to release molc to inside of cell - Exocytosis - when membrane fuses to release molc to outside of cell

What happens when a cell membrane is torn? Why does this happen and why is it crucial to cell function?

- Everything that's needed for cell function is contained in a protect environment - Lipid bilayer membrane will self-repair bc bilayer is formed in a very thermodynamically stable way

What is the biological significance of asymmetric distributions of proteins within the cell membrane?

- Extracellular and cytosolic ends of integral proteins are different structurally and functionally - The way proteins are oriented in membrane makes a difference in their function - allows the membrane to be rigid and allows the cell to have a different intracellular environment from the existing extracellular environment; helps allow for signal transduction and maintain cell homeostasis

In step 6, glyceraldehyde-3-phosphate is oxidized and a phosphate is added, producing 1,3-bisphosphoglycerate via glyceraldehyde-3-phosphate dehydrogenase. What happens during the oxidation? What, exactly, is being oxidized and what is being reduced in this coupled reaction? Where does the new phosphate come from?

- Glyceraldehyde 3-phosphate is oxidized NAD+ is reduced Carrier of two electrons May be used later to produce ATP indirectly via oxidative phosphorylation -phosphate comes from a free phosphate group

What is the difference between anterograde and retrograde transport in the endomembrane system? Why must these two types of transport be "balanced"?

- Go from inside to outside → anterograde movement - Go from outside to inside → retrograde movement - Balanced flow of membrane → ability to have outward and inward transport of molc so that cell doesn't change overall in shape

What are the characteristics of simple diffusion, what are the main factors that control the rate of diffusion, and how can these be described mathematically?

- Higher free energy state → lower free energy state movement from more "ordered" state (lower entropy) to less "ordered" state (higher entropy) - Spontaneous and passive event - Unassisted - "Driven" by concentration gradient -solubility increases at a faster rate as molc become smaller and more hydrophobic

What is a hydrophobicity plot, how is it generated, and what can it tell you about protein structure? How is this relevant to the cell membrane?

- Hydropathy index: calculated based on known hydrophobicity values for amino acids (average for 10 AA window) - Hydrophobic peaks of around 20 AA suggest a transmembrane segment - Hydrophobic amino acids will be coiled up between phospholipid tails while hydrophilic amino acids will be hanging out uncoiled exposed to water

How can a synthetic membrane be used effectively to study membrane characteristics and function?

- In synthetic lipid bilayers, phospholipid molc tumble from one half of bilayer to other - w/o proteins to facilitate the process, this event is called flip-flop

What is the citric acid cycle? What is its main "purpose"? What is the starting material for this series of linked metabolic reactions? What are the major products of this reaction sequence? How much of each of these products are produced per "turn" of the cycle. Why is this series of reactions considered a "cycle"?

- Main function: to capture a portion of energy in chemical bonds of acetyl CoA and store in energy-rich "shuttles" that are used in ETC - Pyruvate comes in and is converted to acetyl CoA, 1 NADH and CO2 is produced in process, 1 acetyl CoA enters and is converted to citrate which is then reduced and energy from intermediates is redirected towards high-energy carriers NADH and FADH2 - each turn forms 1 GTP (ATP), 3 NADH, 1 FADH2, and 2 CO2 (there are 2 turns)

Why is the ability to move materials across membranes such an important problem for cells to solve?

- Materials differentially distributed within cells - All cells and organelles must Obtain needed materials - Eliminate other materials This requires controlled exchange w/ environment

What are the two main ways in which carbohydrates are linked to proteins?

- N-linked to amino group of asparagine - O-linked to hydroxyl group of serine or threonine

What is oxidation? What is reduction? How are they related? Is it possible to have one without the other? Explain.

- Oxidation is loss of e- while reduction is gain of e- - energy released during oxidation while energy is consumed during reduction - oxidation is always accompanies by a reduction

How are lipids found in the lipid bilayer similar and how are they different? How does each contribute to membrane function?

- Phospholipid contains phosphate group while cholesterol and glycolipids contain hydroxyl groups - All are amphipathic tho - they all contribute to membrane function tho bc they regulate movement of molc through the way they allow both hydrophobic and hydrophilic interactions

What is the significance of the asymmetrical distribution of lipids within the lipid bilayer? How does this asymmetry arise?

- Phospholipid synthesis adds to cytosolic half of bilayer - Flippase catalyzes transfer of phospholipid molecules and flips/transfer it to other side of bilayer which causes asymmetry - Symmetric growth of both halves of bilayer - When vesicle fuses w/ plasma membrane, phospholipids that were on outside of vesicle were flipped and are now facing inside vesicle

What is meant when it is said that a trans-membrane-spanning protein "melts" into the lipid bilayer? What molecular interactions between the protein and the bilayer can account for this?

- Protein interacts w/ interior of bilayer → interacts w/ hydrophobic tails - All the hydrophobic AA residues of alpha helix interact w/ hydrophobic tails which is very thermodynamically stable

What are the main transport mechanisms that move solutes across cell membranes?

- Simple diffusion - Facilitated diffusion → protein-protein assisted diffusion - Active transport Primary (direct) Secondary (indirect)

What is the significance of the protein to lipid ratio in different cells?

- Some membranes have higher protein to lipid ratio bc they need more proteins - Ex: mitochondrial inner membrane have higher ratio bc they need more protein channels during cell respiration whereas myelin sheath of nerve cell has a lower ratio bc it doesn't need proteins to carry out nerve signals

In step 7, 1,3-bisphosphoglycerate is converted to 3-phosphoglycerate by the removal of a phosphate (it is combined with ADP to produce a molecule of ATP.....hey, that makes it even.......2 ATPs produced at this step......remember there are 2 molecules of 1,3-bisphosphoglycerate being worked on here, due to the molecular splitting that occurred in step 4. This is an example of substrate-level phosphorylation. What does this mean?

- Substrate-level phosphorylation → Phosphoglycerate kinase uses ADP and adds phosphate group to 1,3-bisphospho-glycerate to create ATP, releasing enough energy to create 3-phosphoglycerate - Direct transfer to ADP of a high-energy phosphate group from a phosphorylated substrate

Why don't planar lipid bilayers occur in nature? Why is this important to a cell?

- always form into sealed compartments - Hydrogen bonds are maximized when phospholipids form a sealed compartment and hydrophobic tails minimize contact w/ water; if phospholipid bilayer was planar, hydrophobic tails would be forced to make contact w/ water - process happens spontaneously

In the glycolytic pathway, which are the energy consuming steps and which are the energy producing steps? How many ATPs are consumed overall and how many produced per glucose molecule? What is the net ATP production per glucose molecule?

- consume ATP step 1: glucose is phosphorylated by ATP to form glucose 6-phosphate step 3: hydroxyl group on fructose 6-phosphate is phosphorylated by ATP to produce fructose 1,6 bisphosphate - produce ATP step 7: transfer of phosphate from 1,3 bisphosphoglycerate to ADP via phosphoglycerate kinase step 10: transfer of phosphate from phosphoenolpyruvate to ADP via pyruvate kinase - 1 glucose molc split into 2 pyruvate molc; 2 ATP are consumed while producing 4 ATP and 2 NADH so there is a NET GAIN of 2 ATP and 2 NADH per glucose molc

What is fermentation? What is the difference between lactate fermentation and alcohol fermentation? Where does lactate fermentation commonly occur in the human body (or that of other mammals)?

- fermentation - replenishing the NAD+ supply to keep glycolysis going - lactic acid fermentation occurs in muscles while alcohol fermentation occurs in bacteria

What is a beta-barrel?

- formation of multiple beta sheets that can create a cylindrical shape and act as pores/channels

*What are some of the advantages conferred on a cell by membrane-bound organelles and what are some of the challenges they pose to the cell?*

- increases surface area-volume ratio - they involve more regulation

What types of molecules make up the lipid bilayer? What structural features of each make them amphipathic?

- made up of proteins, lipids and carbohydrates - phospholipids make structure amphipathic bc of hydrophobic tail and hydrophilic tail

What, exactly, is metabolism? What is catabolism? What is anabolism? What is the relationship between the three? Which is energy demanding? Which is energy providing?

- metabolism - sum total of all chemical reactions that occur in an organism - Catabolic pathways (energy providing) involve break down of molc via oxidation reactions; much of energy is lost as heat and is energetically favorable - Anabolic pathways (energy demanding) involve putting together small molecules into bigger molc using energy produced from catabolic pathways bc it is energetically unfavorable

*How does the sodium/glucose symport work?* Where does the energy for glucose transport against a large concentration gradient come from? In this system, what is actively transported and what is passively transported and in which directions (assume glucose moved into the cell)?

- no phosphorylation is happening here; instead, energy from movement of Na+ is being used to power - Na+ is moved down its concentration gradient into lumen while glucose is moved actively into lumen - binding of Na+ increases binding affinity for glucose allowing glucose to move to an area of higher concentration

What is osmosis? Does osmosis differ from simple diffusion? If so, how does it differ? Why is osmosis important to cells?

- passive, spontaneous movement of water across a semi-permeable membrane from high concentration to low concentration - different from diffusion bc instead of solute concentration reaching equilibrium, water concentration reaches equilibrium - important to cells bc it helps control cell volume and stabilize environment bc wherever water goes, solute follows

What are the main types of active transport? How is active transport distinguished from passive transport?

- primary active transport and secondary active transport - different from passive transport bc it: Requires active input of energy Moves solute against concentration gradient Protein-mediated

What is the SNARE hypothesis? How can it account for the extraordinary specificity of transport vesicles for the different organelles?

- proposal for vesicle fusion to membrane - Rab protein on vesicle interacts w/ tethering protein - v-SNARE and t-SNARE interact and dock vesicle until they cinch close enough that fusion can occur (SNAREs act like a winch to draw membranes close)

What characteristics distinguish facilitated diffusion from simple diffusion? Can either of these methods of diffusion be characterized by Michaelis-Menton kinetics? If so, what is the basis for this?

- simple is spontaneous, passive movement from high to low concentration - facilitated is spontaneous, passive movement assisted by a protein from high to low concentration - simple diffusion will have a linear line while facilitated diffusion will have a hyperbolic line bc proteins will reach their max binding potential and working as fast as possible before concentration gradient is too high relative to number of carrier proteins

Distinguish a "single pass" vs a "multi-pass" integral membrane protein.

- single pass proteins have only one polypeptide extending through membrane bc they just contain a stop transfer sequence - multipass proteins have multiple polypeptides extending through membrane and can essentially form channels bc they contain an internal start and stop transfer sequence

What is a uniport? A symport? An antiport? Can they involve both passive and active transport?

- uniport - in one direction, passive transport (facilitated diffusion) - antiport - in opposite direction, active transport - symport - two molc in one direction, active transport

During step 4 of glycolysis, fructose-1,6-bisphosphate is split into two 3 carbon compounds, only one of which proceeds further along the glycolytic pathway. Which one is this and what happens to the other compound?

-glyceraldehyde 3-phosphate proceeds down glycolysis while dihydroxyacetone phosphate is converted to glyceraldehyde 3-phosphate by triose phosphate isomerase

The first step in glycolysis is to add a phosphate to glucose, making glucose-6-phosphate (the enzyme is hexokinase). What is the relevance of this phosphorylation event? An ATP is used in this step (down by one....and glycolysis is only just begun.....)

1) Concentration gradient of glucose is maintained bc phosphorylation of glucose requires more glucose to get into cell bc it is just constantly converted to glu 6-phosphate and is no longer glucose 2) Since glu 6-phosphate is charged, it cannot exit membrane and is trapped inside This is the sink for glucose Essentially irreversible and drives glycolysis in forward reaction

What are the five main functions membranes perform in cells?

1) Physical separation from environment and internal compartmentalization 2) Division of labor import/export 3) Diffusion Facilitated diffusion Active transport 4) Signal transduction 5) Intercellular communication and adhesion

Is there a net production of NAD+ or NADH in glycolysis? Explain.

2 NAD+ are reduced into 2 NADH and H+

Overall, approximately how many ATP molecules are produced per glucose molecule consumed as a result of aerobic respiration? How does this compare to glycolysis?

32 ATP per glucose; this is a significantly larger amount than glycolysis which only produces 2 ATP

What protein complex is involved in ATP production? How is this linked to the previous movement of protons in the electron transport chain?

ATP synthase involved in ATP production; flow of protons in counterclockwise motion through ATP synthase powers phosphorylation

What happens to misfolded proteins?

Chaperone protein has a Binding protein and through ATP process, pries apart protein and allows protein to fold back into its normal configuration and proper folding pattern Budding transport vesicle ships properly folded protein out of ER

Aerobic respiration occurs within the mitochondrion. What are the major structural features of this organelle?

Contains its own DNA and ribosomes Cristae are folds; contains two membranes, inner and outer membrane Contains ATP synthase proteins

What did I mean when I said the endomembrane system was a "continuous" single system?

Continuous in the sense that molc don't move in a single path but they move in a general direction

What is the electron transport chain? Where is it located? What is the starting material for the electron transport chain? What are its main components?

ETC - a series of proteins found in inner membrane of mitochondria; start w/ NADH and FADH2 and takes e- from these carriers; as e- flow through complexes 1, 3, 4 (interact w/ NADH) and complex 2 (interact w/ FADH2) from high energy states to low energy states, protons move through complexes from matrix to intermembrane space and form a high concentration gradient that allows them to then move back across ATP synthase and produce ATP

A hallmark of the electron transport chain is a "fall" of electrons down the chain. What does this mean? What kind of chemical reactions occur that mediate this "fall" and what are the consequences of this? What is the main "purpose" of these reactions?

Each transfer results in a loss of a little bit of energy which allows transfer of protons through protein complexes into intermembrane space where they form a gradient and form back through ATP synthase (via facilitated diffusion)

What is the endocytic pathways in a cell and why is it important?

Early endosomes become late endosomes based on changes inside vesicle as they become more acidic ; ultimately fuse w/ and become lysosomes

What are the main types of membrane proteins? How do they differ in their association with the membrane? What types of functions do membrane proteins perform? How is the structure of each main type related to its function?

Enzymes Channel ATPase Receptor Transport Adhesion Recognition Structural sensory - some are directly embedded in membrane while others are able to move away from membrane and into cytosol - structure determines function bc some allow movement from cytosol through lumen and vice versa while others need to interact w/ other proteins to be activated and cannot be physically passed through

What is the structure of ATP synthase, and in general, how does it work to produce ATP?

F0 static component - consists of one a and two b subunits A is channel that hydrogen ions flow through B is component that connects F0 component to F1 component F0 mobile component 0 consists of ring of 10 c subunits which rotate Each time a hydrogen ion moves through a is when ring rotates F1 static component - consists of delta subunit plus a catalytic ring formed by alpha beta subunits Beta subunits are site of ATP synthesis F1 mobile component - consists of epsilon and gamma subunits which form central stalk that is firmly attached to c10 ring When 10c ring rotates, gamma subunit also rotates

What is a flippase? What function does it serve and where does it act?

Flippase located in cytosol and catalyzes transfer of phospholipid molecules and flips/transfer it to other side of bilayer which causes asymmetry

The location of mitochondria within a cell is not random. Why is this? Provide an example of this well-known observation and, using this example, explain its functional significance.

Located within strategic locations of cell so that it can provide ATP exactly where it's needed to do work - ex: increased amount of mitochondria in muscles to allow for production of energy needed for movement

NADH and FADH2 have been described as high energy "shuttles". Explain.

NADH feeds high energy electrons on matrix side to complex 1,3,4 It can also take e- from complex 2 interacting w/ FADH2 and shuttle them to complex 2

Glycosylated lipids and proteins are found in the plasma membrane of red blood cells. What main function are they thought to serve?

Negative charges from attached sugars allow red blood cells to bump off of each other rather than clotting and sticking together

Mitochondria are dynamic structures. Explain this statement.

Often shown as a sausage shape but often can merge and split into branched structures

Both pyruvate and inorganic phosphate are utilized during aerobic respiration. Exactly where in the mitochondrion are these materials used, and how do they get there? (Both are negatively charged molecules at physiological pH).

Porin molc allow pyruvate to diffuse into cell - Pyruvate comes in and interacts w/ secondary active transport that utilizes H+ gradient to co-transport, via symport, pyruvate across inner membrane and into matrix Driven by pH gradient Phosphate gets in through antiport by utilizing opposite movement of hydroxide ion which come from water OH- neutralized by protons and becomes H2O

Mitochondria have a double membrane. In what ways do these membranes differ and what is the significance of these differences? What compartments do the membranes define and how do the contents of these compartments differ? What specific metabolic functions are associated with each membrane and each compartment?

Porin molc, beta-barrels, allow for transport of certain molc through outer membrane which is semi permeable Inner membrane is highly impermeable bc it needs to get very specific things in and for ETC - glycolysis occurs in cytosol, citric acid cycle occurs in matrix, and oxidative phosphorylation occurs in inner mitochondrial membrane

When pure phospholipids are placed in an aqueous environment, they spontaneously form liposomes that are surrounded by water and have a water-filled core. Why does this happen and why does it happen spontaneously?

Pure phospholipids form closed, spherical vesicles called liposomes - Molc of bilayer will spontaneously rearrange to eliminate free edge in the event of a tear in the membrane and exposure to water - Only way an amphipathic sheet can avoid having free edges is to bed and seal, forming a boundary around a closed space → phospholipids are capable of assembling into closed compartments ranging from vesicles to entire cells

*In what ways can a specific protein be selectively packaged into a transport vesicle on the TGN face of the Golgi complex?*

Selective packaging into vesicles at trans face where they are sorted and shipped to specific locations - Receptor molc bind to specific cargo → adaptin molc bind to cargo receptors → adaptin molc interact w/ other adaptin molc and form a complex on Golgi membrane → clathrin will bind to adaptin and is non-specific → clathrin will round out shape of complex until you get a coated vesicle that has a specific cargo → once vesicle gets to a certain point where it is almost a free-floating molc, dynamin protein (GTP-binding protein) will bind to point of contact between forming vesicle and trans-Golgi face → GTPase will hydrolyze and constrict this point of contact, allowing free-floating coated vesicle to be pinched off from trans-Golgi face and released → uncoating ATPase enzyme removes clathrin coat and results in naked transport vesicle

What is the "driving force" that induces electrons to move down the electron transport chain? If oxygen is present, this process continues, but in the absence of oxygen it stops. Why is this?

The driving force of the ETC is the fact that each electron carrier has a higher standard reduction potential than the one that it accepts electrons from; oxygen has greatest reduction potential which is why it is final e- acceptor - When no oxygen is present, the electron transport chain can't run because there is no oxygen to act as the final electron acceptor. This means that the ETC will not be accepting electrons from NADH as its source of power, so NAD+ will not be regenerated

What is the "binding change" model for ATP synthesis and how does it work? What is meant by the term rotational catalysis?

The three beta subunits are in contact w/ aspect of gamma subunit has a specific shape ( OPEN → LOOSE → TIGHT) Open - can accept and recognize ADP and P, affinity is up for ADP and P Loose - ADP and inorganic phosphate can enter into active site where it can be converted to ATP but haven't yet been converted Tight - ADP and inorganic phosphate come together to form ATP

Why can the plasma membrane in a sense be thought of as a "minor" membrane?

There is more membrane inside cell than there is outside

Transport vesicles are used to move components (both membrane-bound and soluble) from one part of the endomembrane system to another. What is the general process by which transport vesicles are formed?

Transport vesicle formation at the TGN is mediated by clathrin

Membrane fluidity can be demonstrated using a technique called fluorescence recovery after photobleaching (FRAP). How does this work?

Unlabeled cell surface Cell surface molc labeled w/ fluorescent dye Laser beam bleaches an area of cell surface Fluorescent-labeled molc diffused into bleached area Measure rate of diffusion of fluorescence into bleached area

Signal sequences are both necessary and sufficient to direct a protein to a specific organelle. Explain. What might be the consequence of an abnormal signal sequence?

a misplaced signal could result in the wrong protein being inserted in a certain location while the correct protein is sent somewhere else

Step 2 in glycolysis involves converting glucose-6-phosphate (an aldose) to fructose-6-phosphate (a ketose) via the enzyme phosphoglucosisomerase. Why is this step "necessary"?

bc CH2OH is easy to phosphorylate

What is clathrin? How is it involved in selective packaging of proteins/lipids into transport vesicles? With what other molecules does it associate to accomplish this goal?

clathrin is special protein that interacts w/ adaptin molc which recognize certain cargo receptors carrying specific cargo; this interaction forms a vesicle

What is the glycocalyx? On what side (extracellular or cytosolic face) of the cell membrane is it found? What function(s) is it thought to serve?

coating of carbohydrates found on exterior of membrane; serves purpose of cell signaling and physically protecting plasma membrane

Phospholipid molecules are amphipathic. What does this mean?

contain hydrophobic tail and hydrophilic tail

What, exactly, is pyruvate dehydrogenase? What role does it play in aerobic respiration? What is the substrate for this enzyme complex? What are the products formed by this complex?

converts pyruvate to acetyl CoA for citric acid cycle - acetyl CoA is oxidized throughout citric acid cycle and reduces NADH and produces CO2 in process

What are lysosomes and how are they involved in intracellular digestion?

degrade worn-out organelles

What does the "fluid mosaic model", with respect to the cell membrane, mean? Why fluid? Why a mosaic?

describes the cell membrane as a tapestry of several types of molecules (phospholipids, cholesterols, and proteins) that are constantly moving. This movement helps the cell membrane maintain its role as a barrier between the inside and outside of the cell environments.

*What is the first step that must be overcome to utilize the endomembrane system?*

destination of vesicle must be determined

The technique of freeze-fracture, in combination with electron microscopy, have provided evidence for the fluid mosaic model of membrane structure. Explain.

freeze fracture shows proteins embedded in protoplasmic face of cell, indicating that membrane is composed of multiple different components and not just proteins

What is meant by the term membrane "domain"?

functionally specialized regions of cell membrane; Help keep proteins anchored in place

How might a newly synthesized protein be modified once it is imported into the ER?

glycosylation (addition of sugars to proteins and lipids); purpose: Protect from degradation "Holding" signal Vesicle transport signal

The lateral mobility of membrane proteins may be restricted. Why might this be important?

helps make sure proteins do their job in the correct location and don't just move away from membrane and onto different cell

Proton movement during the production of ATP is driven by both chemical and electrical forces. Explain.

inside of matrix has negative membrane potential and there is a lower concentration of protons inside matrix; both work in tandem to encourage protons to move down it's concentration and electrical gradients

How is the sodium/potassium ATPase thought to function? Why is this protein so important to cells?

it dephosphorylates ATP which allows movement of Na+ into lumen and K+ into cytosol and thus creates an electrochemical gradient - this gradient can result in cooperative binding of glucose

What is the potential fate of pyruvate at the end of the glycolytic pathway? What happens to it if oxygen is present? If oxygen is absent?

it has two potential routes: citric acid cycle or anaerobic respiration - if oxygen is present, it will proceed through citric acid cycle and ETC - if oxygen is not present, it will go through fermentation

Glucose-6-phosphate acts as an allosteric inhibitor of hexokinase. Why do you suppose this is the case and when do you think it happens?

it is an example of negative feedback bc whenever the level of glucose 6-phosphate rises above its normal level, hexokinase is temporarily and reversibly inhibited, bringing the rate of glucose-6phosphate formation into balance with the rate of its utilization and reestablishing the steady state

What experimental evidence indicates that like lipids, proteins can move laterally within a cell membrane?

mouse and human cells, when fuse together, form a chimera in which membrane proteins from both cells move laterally across to other side of cell

At the end of glycolysis, then, how many extra ATPs? Extra NADHs?

only 2 ATP and 2 NADH produced

*What is the relationship between chemical gradients and electrical gradients with respect to their effects on uncharged solutes? Effects on charged solutes?*

only concentration gradient affects uncharged solutes whereas both concentration gradient and electrical gradient affects charged solute bc charged solutes will move towards membrane potential that has opposite charge of solute

What are the major starting materials that "feed" aerobic respiration? Into what common substrate must these molecules be converted before aerobic respiration can take place?

oxygen and glucose are starting materials - pyruvate must be converted into acetyl CoA

In the overall chemical reaction describing aerobic respiration, which uses molecular oxygen to "burn" glucose, resulting in the production of carbon dioxide, water, useable energy (in the form of ATP) and heat (lost to the environment), exactly where in the process is the oxygen utilized, and where is the carbon dioxide produced?

oxygen is burned in mitochondria; oxygen is used by ETC and carbon dioxide is produced by krebs cycle

What is the main factor that determines whether aerobic respiration will proceed? What is the main advantage of aerobic respiration over glycolysis for supplying the energy needs of a cell?

oxygen is main factor that determines whether aerobic respiration will happen; main advantage is that oxygen acts as final e- acceptor in ETC, if oxygen isn't present, ETC can't happen and ETC produces a large amount of ATP

*How does glucose initially get into cells?*

primary active transport antiport establishes Na+ gradient by removing Na+ from inside of cell; secondary active transport symport uses gradient to allow Na+ to flow into cell along w/ glucose

What is the difference between primary (direct) and secondary (indirect) active transport?

primary active transport store energy, which can be released as the ions move back down their gradients. Secondary active transport uses the energy stored in these gradients to move other substances against their own gradients

The complement of proteins in a cell membrane in a sense gives the cell its unique "character". Explain this sentence.

proteins in a cell often determine cell's overall function

How is electron transport down the electron transport chain tied to proton movement within the mitochondrion? From what compartment are protons removed? To what compartment are they added? Where do the protons come from? What is the functional significance of this movement?

protons move across membrane into ATP synthase - they are removed from matrix and are added to intermembrane compartment - the protons come from water - ETC forms proton gradient and this gradient powers phosphorylation of ATP

*How is cell volume regulated?*

regulated by gain or loss of osmotically active solutes which are mediated by membrane transport processes such as ion channels

What are the major characteristics of a solute that determine what mode of transport is required to move it across a cell membrane?

size and polarity determine how easy or difficult it is for solutes to move across membrane - Small hydrophobic molecules and small uncharged polar molecules can get across via simple diffusion w/o that much difficulty - Larger uncharged polar molecules and ions are too polar to get across membrane easily so they require transport and protein --> Some of them can get across but their rate of diffusion is very slow

What is a chaperone protein? What function does it serve within the ER?

special proteins that prevent improperly folded or partially assembled proteins from leaving the ER

*What are the main steps involved in transport vesicle recognition and fusion with the correct target membrane?*

tethering, docking and fusion

How are catabolic and anabolic processes linked within the cell? What is the common currency for these two processes?

they are linked within cell bc energy provided by catabolism (oxidation) is used to power anabolism (reduction); currency is e-

Membranes are very "dynamic" in nature. What does this mean?

they participate in exo and endocytosis

In step 3 of glycolysis, fructose-6-phosphate is converted to fructose-1,6-bisphos-phate by the enzyme phosphofructokinase-1, using up another ATP (down by two.....). What does this step accomplish?

this step accomplishes phosphorylation of CH2OH

How do protein channels facilitate diffusion of ions across the cell membrane?

usage of ion channels -ligand-gated channels require binding of ligand to open -voltage-gated channels require high membrane potential

In both glycolysis and the citric acid cycle, the metabolic sequence utilizes substrates, but also provides substrates for other distinct metabolic pathways. Explain what this means and why it is important to the cell. Given this, why is it important not to think of metabolic reactions as being strictly linear in form?

you don't necessarily need to start w/ glucose to carry out glycolysis and CAC; other sugars can be used for glycolysis and CAC can end up producing intermediates that are used for AAs and nucleotides