Exam 3 Review Flashcards
In what organelle does glycosylation occur?
Glycosylation begins in the endoplasmic reticulum and continues in the Golgi apparatus
Which type of glycoproteins are more frequent: O-linked or N-linked?
N-linked are more frequent than O-linked
What is the consensus sequence?
Asn - X - Ser
where X is any AA except proline
This is the site of carbohydrate attachment to N-linked glycoproteins
Why is the oligosaccaride stem the same in many glycoproteins?
They are all generated from the same process in the endoplasmic reticulum
What is erythropoietin (EPO)?
A renal hormone that is stimulated by hypoxia
Stimulates red blood cell production (used for blood doping)
Has three major sugar moieties, which, if removed, decrease red blood cell production
In proteoglycans, which part is the functional part?
The sugar is the functional part unlike in glycoproteins
Describe the structure of proteoglycans in cartilage
proteoglycans bind to a central stem structure
G1 binds to the carbohydrate stem, hyaluronan
Disacharide structures (between G2 and G3) interact with H2O to form a gel like structure
After exiting the ER, where do vesicles transport proteins to?
The golgi aparatus
Describe the different components of the Golgi apparatus
- cis* Golgi network (from ER)
- cis* cisterna
medial cisterna
- trans* cisterna
- trans* Golgi network (towards plasma membrane)
What molecule addresses proteins to the lysosome?
Mann-6 P
What is the function of glycosyltransferases?
They catalyze the formation of glycosidic bonds
What is aglutination?
Red blood cells are clumping up
Which blood type is the universal receptor and which is the universal donor?
AB positive is the universal receptor
O negative is the universal donor
In A-type blood, what antigens are found?
anti-B antigens
What are Lectins?
Sugar binding proteins
Usually have a Ca2+ cofactor
What are the membrane glycoproteins associated with influenza virus?
Hemagglutinin (H) recognizes carbohydrates on the cell surface; useful for getting in
Neuraminidase (N): cuts glycosydic bonds with RNA release; useful for getting out
What do neuraminidase inhibitors do?
They trap the influenza virus within the cell that it infects
Do lipids form polymers?
No, lipids do not form polymers, they form together via hydrophobic interactions
What are the biological roles of lipids?
- Fuel
- Building blocks
- Thermal insulator
- Special tasks
Describe the difference between saturated and unsaturated fatty acids
Saturated have no double bonds, unsaturated have one or more double bonds
Describe the general structure of fats
fatty acid chains attach to a glycerol molecule
Phospholipids have 2 fatty acid chains and a phophate group attached to a glycerol
On which sides of membranes are glycolipids found?
They are only found on the extracellular side of the membrane
What are the functions of glycolipids?
Help protect membrane from harsh conditions
Charged glycolipids can influence electric field across membranes and ion concentration
Cell-cell recognition
Which membranes contain cholesterol?
All membranes except the inner mitochondrial membrane.
What role does cholesterol play in membranes?
It keeps fatty acids apart and prevents crystalization in low temperatures
How does saturation change how membrane lipids pack?
Saturated fatty acids are able to pack tighter into solids
Unsaturated fatty acids have lower melting points, are more fluid
What is a sphingosine?
An amino alcohol with a long hydrocarbon chain
What are the structural differences between triacylglycerol and sphingophospholipids?
The sphingophospholipid comes with a lipid chain as part of the sphingosine molecule
What type of bond is present in phosphoglycerides?
An ester bond between the phosphate group and the hydroxyl group of the alcohol
What molecule are glycolipids derived from?
Sphingosine
Explain how cholesterol fits into the membrane
The hydroxyl interacts with the phospholipid head groups and the nonpolar hydrocarbon tail fits between the lipid hydrocarbon tails
Describe the structure of a micelle
The hydrophobic tails all interact forming a sperical molecule with the polar heads all facing out interacting with water.
Describe the structure of a lipid bilayer
It has a hydrophobic interior that acts as a permeability barrier
It is formed spontaneusly because of hydrophobic interactions and can develop into cells w/ a large diameter
This conformation is favored over micelle
Which molecules are able to pass through the membrane and which cannot?
Small molecules can freely pass through the membrane, but large molecules and ions cannot
What type of amino acids make up transmembrane regions of membrane proteins?
Mostly nonpolar amino acid residues
Describe the structure of a pore
The outside surface is nonpolar and the inside surface is polar.
They have a hydrophilic channel through the middle, allowing for substrates to pass through
How are integral membrane classified?
Type I through VI are distringuished by which end sticks out and in which direction
Type III: one protein with many transmembrane domains
Type IV: many proteins grouped together each with a transmembrane domains
What is Prostaglandin H2 synthase-1?
I membrane protein with a hydrophobic channel.
This channel is blocked by aspirin to aleviate headaches
How many amino acid residues does it take for an alpha helix to span the membrane?
About 20 amino acid residues will span the membrane
What is a hydrophobicity plot?
A plot of the free energy of transfer to water in a shifting window along the primary sequence of a protein.
Peaks with values greater than +84 kJ/mol have a high chance of being part of an alpha helix, and thus in a transmembrane domain
How does the viscosity of the membrane compare to that of H2O?
It is ~100x higher
What are the three ways that lipids can move throughout a membrane?
They can rotate in place or diffuse laterally
Can also flip-flop (but very rare)
What enzyme catalyzes the flip-flop movement of lipids?
flipases
What is the function of a scramblase enzyme?
They allow the bilayer to grow evenly by translocating lipids from the inner membrane to the outer membrane (or vice versa)
What factors increase membrane fluidity?
More cis double bonds
Shorter hydrocarbon chains
Less cholesterol
Higher temperature
How does cholesterol help with temperature regulation?
The amount of cholesterol in the membrane changes to help deal with temperature changes
How do charged ions usually get through the membrane?
Through channels or transporters
Describe the relative concentrations of Na+ and K+ inside and outside of the cell
The ICF has low Na+ and high K+ compared to the ECF
Describe the electrochemical gradient
The difference in the concentration of the solute between the two sides of the membrane
The charge or valence of the solute molecule
The difference in voltage between the two sides of the membrane
**Membrane potential can be opposite direction of chemical gradient.
What is the equation for diffusion of ions across the cell membrane?
ΔG = RT ln(c2/c1) + zFΔV
How are primary and secondary active transport related?
Secondary active transport requires gradients created by primary active transporters
What are the three types of ATP pumps?
P-type
F-type
ABC transporter
What is a P-type ATP pump?
The actual protein is phosphorylated
Couples free energy of ATP hydrolyses to an interconversion between two conformations, allowing a substrate to pass through
What is an F-type proton pump?
The pump is phosphorylated, but it uses ATP
ex: in lysosomes
What is an ABC transporter?
ABC = ATP binding casettes
Plays an important role in resistance to antibiotics
When cells are exposed to a drug, these pumps remove the drug out before the drug can exert its effect
What type of pump is the Ca2+ pump in the sacroplasmic reticulum?
A P-type pump
The conformational change creates/destroys the binding site
What are E1 and E2 of the sarcoplasmic Ca2+ pump ?
They are the two distinct enzyme conformations (Eversion States)
What is the effect of digitalis?
It inhibits the Na+/K+ pump by preventing dephosphorylation
Describe the mechanism for ABC Transporters
1) No ATP or substrate bound
2) Substrate enters central cavity which causes a conformational change that increases ATP affinity
3) ATP binds to ABCs
4) Conformational change
5) Hydrolysis of ATP resets the protein
What is the major difference in tertiary structure between the Na channel and the K channel?
The Na channel is made up of 4 repetitive domains all from the same protein whereas the K channel is a homotetramer made from 4 identical proteins
Why isn’t Na able to pass through the K channel?
The channel maximizes its interactions with the K+ ion. Because the Na+ ion has a smaller ionic radius, it is not large enough to be properly stabilized, so it cannot pass through.
Explain how the K+ ions pass through the K+ channel
They enter the vestibule and align into ‘single file’
Repulsion between individual ions push them through the channel and out the other side.
Explain how the voltage gated potassium channel works
The S4 region acts like a valve, turning to open the channel when it is depolarized
Important for propagation of action potentials
What is the ball-and-chain model?
Explains the inactivation of the K+ channel
There is an inactivation domain that acts as a stopper. It is rapidly pulled up into the channel to block it once the channel is open.
Three distinct phases of channel: closed, open, inactivated
What are the differences between gap junctions and other membrane channels?
They traverse two membranes rather than one
They connect cytoplasm to cytoplasm, instead of to ECF or lumen of an organelle
The connexons forming them are synthesized by different cells
What are the two general types of pathways involved with metabolism?
Catabolic pathways (breakdown of food)
Anabolic pathways (building new molecules)
What is the only ATP producing pathway that can occur in the absesnce of O2?
Glycolysis
What cells in the body rely exclusively on glycolysis for energy?
Red blood cells and neurons
What are Coupling Reactions?
Using ATP to drive anabolic reactions that are energetically unfavorable
The overall free energy change for a chemically coupled series of reactions is equal to the sum of the free energy changes of the individual steps.
Fill in the blank:
_______ drives ________ in a process we call metabolism
Catabolism drives anabolism in the process we call metabolism
What factors cause the high transfer potential of ATP?
Resonance stabilization
Electrostatic repulsion
Stabilization due to hydration
What energy charge is maintained throughout the body?
About 0.8-0.9
Is ATP hydrolysis exergonic or endergonic?
Exergonic
What is the importance of a combined intermediate?
It physically connects the 2 reactions, allowing for the reaction to occur using energy of hydrolysis (for example)
Is substrate level phosphorylation dependent on oxygen levels?
No. It is independent of O2
Why is it important that ATP have a intermediate phosphoryl transfer potential?
It enables ATP to function efficiently as a carrier of phosphoryl groups.
Allows ADP to be phosphorylated by other groups with higher phosphoryl transfer potential to form ATP
When ATP reacts with hexokinase, is ATP hydrolyzed?
No. In many metabolic reactions, ATP is not hydrolyzed because it reacts with enzymes that prevent H2O from entering the active site.
This allows the energy to be used for coupled reactions
What are the 2 ways that ATP can be formed?
Substrate level phosphorylation
Oxidative phosphorylation
What percent of the ATP is produced by oxidative phosphorylation?
90%
Describe the sources of ATP during exercise.
Available ATP is immediately used up
Then Creatine phosphate can combine with ADP to make useable ATP
Anaerobic metabolism begins to produce ATP after minutes, and aerobic metabolism begins after ~1 hour
Describe the mechanism of Glyceraldehyde 3-phosphate dehydrogenase
A thioester bond is formed between glyceraldehyde 3-phosphate and the active site of the enzyme.
NAD+ is protonated to NADH during the formation of the thioester bond.
The molecule is then phosphorylated by an inorganic phosphate, crerating 1,3 BPG
What are the three types of activated carriers of electrons?
- Activated carriers of electrons for fuel (NAD+, FAD)
- Activated carriers of electrons for reductive biosynthesis (NADPH)
- Activated carrier of two carbon fragments (AcetylCoA)
What is the significance of adding a second phosphoryl group to G3P in glycolysis?
The product, 1,3 BPG has a very high transfer potential, which allows it to donate a phosphoryl group to ADP to produce ATP in the next step.
Describe the pH in the mitochondria, and its significance for ATP generation.
There is a higher pH in the matrix, which means that there is a proton gradient. This gradient is used in order to form ATP molecules in the mitochondria.
Does regulation occur by modifying the reactants, the enzymes, or the products in the glycolysis pathway?
Pathways are regulated by controlling the enzyme activities
What type of pathway can NAD+ be found in? What about NADP?
NAD+ is found in catabolic pathways
NADP is found in anabolic pathways
What type of high energy bond is found in Acetyl CoA?
A high energy thioester bond is found in Acetyl CoA
How are most activated carriers produced in the body?
They cannot be synthesized, and therefore must be ingested through vitamins
What are the 6 types of chemical reactions that occur in metabolism?
- Oxidation-reduction
- Ligation requiring ATP cleavage
- Isomerization
- Group transfer
- Hydrolytic
- Addition or removal of functional groups
How are metabolic processes regulated?
- Controlling the amount of enzyme (transcriptional regulation)
- Controlling catalytic activity (allosteric regulation, feedback, covalent modifications)
- Controlling accessibility of substrates (Compartmentalization)
What quantity regulates every pathway in the cells?
The energy charge
= (ATP + 1/2 ADP)/ (ATP +ADP + AMP)
What is phosphorylation potential?
Phosphorylation potential of the mitochondria is the free energy storage available from ATP
= [ATP] / ([ADP] + [Pi])
How is AMP produced ?
2 ADP molecules can combine to form 1 ATP and 1 AMP
As the energy charge increases, what happens to the relative rates of the ATP generating pathway and the ATP utilizing pathway?
As Energy charge moves from 0 to 1:
ATP generating pathway slows down
ATP utilizing pathway speeds up
Describe the general process of Glycolysis
Glucose (a 6 C ring) is broken down into 2 molecules of pyruvate (a 3-C compound)
Energy must be put in in order to break apart the stable glucose ring
What is stage 1 of glycolysis?
The investment phase: glucose is trapped in the cell and is formed into a compound that can readily be cleaved into phosphorylated 3-C units
No ATP is generated
What is stage 2 of glycolysis?
Numerous small molecules are degraded to a few simple units that play a central role in metabolism
What is stage 3 of glycolysis?
ATP produced from complete oxidation of acetyl CoA (TCA cycle and oxidative phosphorylation)
What enzyme catalyzes the first reaction of glycolysis?
Hexokinase
Phosphorylates Glucose to Glucose-6-Phosphate
Describe the conformational change of hexokinase
When glucose binds to the enzyme, the environment around glucose becomes more nonpolar, which favors the reaction between the hydrophilic hydroxyl group of glucose and the terminal phosphoryl group of ATP.
The conformational change enables the kinase to discriminate agains H2O as a substrate.
What cofactor is needed for hexokinase activity?
Mg2+ (or Mn2+)
Describe the glycolytic reaction that converts an aldose into a ketose
Phosphoglucose Isomerase catalyzes the conversion of G6P into F6P
The glucose ring is broken open, the groups are moved, and then the ring is closed into a 5 membered fructose ring.
What is the key enzyme or pacemaker of glycolysis? What does it do?
Phosphofructokinase (PFK)
It uses ATP to phosphorylate F-6P to F-1,6-BP
What is the significance of breaking a 6C unit into 2 3C units?
This step allows for all downstream steps to happen two times simultaneously (in parallel)
Aldolase creates DHAP and GAP, and then DHAP is converted into GAP, resulting in 2GAP molecules
What enzyme converts DHAP into GAP?
Triose phoosphate isomerase
What 2 amino acids are found in the active site of triose phosphate isomerase?
Glutamate (H+ donor)
Histidine (Base)
What is the only oxidation reaction that occurs in glycolysis?
Glyceraldehyde 3-phosphate dehydrogenase catalyzes the oxidation reaction from GAP to 1,3 BPG
2 processes:
Oxidation of aldehyde to carboxylic acid by NAD+
Joining of carboxylic acid and orthophosphate
What glycolytic enzyme has a peroxidative cysteine in the active site?
Glyceraldehyde 3-phosphate dehydrogenase
The cysteine forms a thioester intermediate
What molecule is the limiting factor for the reactoin catalyzed by glyceraldehyde 3 phosphate dehydrogenase?
The availability of NAD+ limits this reaction
Electrons must be siphoned off for reaction to occur
What is unique about the enzyme phophoglycerate mutase?
A different phosphate molecule is on the enzyme after each reaction occurs
Explain why phosphoenolpyruvate (PEP) has a large phosphoryl transfer potential
There is a large driving force for the subsequent enol-ketone conversion of pyruvate
The enol form of pyruvate is energetically unstable, but the ketone form is stable
What are the possible fates of pyruvate?
1) Ethanol: alcoholic fermentation
2) Lactate: lactic acid fermentation
3) TCA cycle: aerobic respiration ending with electron transport chain
How many molecules of pyruvate are formed from each glucose molecule?
2 pyruvate for each glucose
Why is hexokinase not a major enzyme for regulation of glycolysis?
It is involved in too many other bodily functions to regulate, so we regulate glycolysis using PFK
Is ATP a substrate or a regulator of PFK?
BOTH
ATP binds to 2 different sites on PFK: the active site and the regulatory site
Does PFK show a sigmoidal reaction kinetic curve?
Yes. At low [ATP] it appears nearly hyperbolic, but at high [ATP] the sigmoidal shape is apparent
What is the primary control of glycolysis in the muscles?
The energy charge
PFK activity increases when the ATP/AMP ratio is lowered
Describe the role of negative feedback in glycolysis in relaxed muscle fibers
If G6P accumulates, hexokinase is inhibited, lowering the rate of G6P production
High energy charge (high ATP/AMP) will downregulate the action of PFK and Pyruvate kinase in order to prevent accumulation of toxic intermediates
What molecule activates PFK in the liver?
Fructose 2,6-biphosphate activates PFK in the liver
What effect does citrate have on PFK function?
citrate inhibits the action of PFK
What is unique about PFK-2?
PFK-2 is both a kinase and a phosphatase
If it is phophorylated, it acts as a phosphatase
If it is dephosphorylated, it acts as a kinase
What is the last enzyme in the glycolytic pathway?
Pyruvate kinase converts phosphoenolpyruvate into pyruvate
Many of the glycolytic steps have ΔGo close to zero. Why is this relevant?
These are the steps that can occur in either direction based on concentrations of products and reactants, and are therefore involved in both glycolysis and gluconeogenesis
What is the general conversion that takes place in gluconeogenesis?
Pyruvate is converted into Glucose
What are the major noncarbohydrate precursors of gluconeogenesis?
Lactate, amino acids, and glycerol
What is the purpose of gluconeogenesis?
It maintains the glucose level in the blood so that the brain and muscle can extract sufficient glucose from it to meet their metabolic demands
What organs does gluconeogenesis take place in?
The liver and the kidney
How many steps are in glycolysis? What about gluconeogenesis?
Glycolysis has 10
Gluconeogenesis has 11
Which steps differ between glycolysis and gluconeogenesis?
The irreversible steps (1, 3, and 10) of glycolysis are different in gluconeogenesis
Phosphatases perform reverse role of kinases
The pyruvate to PEP step is 2 reactions in gluconeogenesis, catalyzed by Pyruvate Carboxylase and then PEP carboxykinase
In gluconeogenesis, what molecule is pyruvate first converted into before it is converted to PEP?
Oxaloacetate is formed in the mitochondrial matrix
How does oxaloacetate exit the mitochondria?
It is reduced to malate by the oxidation of NADH. Upon exiting the mitochondria, it is oxidized back to oxaloacetate before the next step of gluconeogenesis
Describe reciprocal regulation of glycolysis and gluconeogenesis
Both pathways are not active at the same time in the same cells.
They are regulated in order to prevent the accumulation of toxic intermediates.
If glucose concentrations are high, what hormone responds?
Insulin acts via cAMP to increase the rate of glycolysis
What hormone has the opposite effect on metabolism as insulin?
Glucagon
What is the cori cycle?
In contracting skeletal muscle, the formation and release of lactate lets the muscle generate ATP in the absence of oxygen and shifts the burden of metabolizing lactate from muscle to other organs
lactate produced by anaerobic glycolysis in the muscles moves to the liver and is converted to glucose, which then returns to the muscles and is converted back to lactate
What molecule does the Alanine cycle function to get rid of?
The alanine cycle gets rid of NH2 by excreting urea
