Final Flashcards
What are the functions of a membrane?
- compartmentalization
- transport
- communication
- intercellular interactions
- energy transduction
Describe lipids
Non polar, hydrophobic compounds, soluble inorganic solvents
Most at amphipathic with a nonpolar and a polar end
What is a fatty acid?
Lipid consisting of a hydrocarbon chain with a carboxylic acid at one end
Generally have cis configurations around double bonds and even number of carbons
What are the three membrane lipids?
Phospholipids
Glycolipids
Sterols
What are glycerophospholipids?
Common constitutes of cellular membranes
Have glycerol backbone
Hydroxyls at C1 and C2 are estérified to fatty acids
Include polar region (glycerol, carbonyl, Pi, and polar head group (x)), and 2 non-polar hydrocarbon tails of fatty acids (R1,R2)
What are sphingolipids?
Derivatives of lipid sphingosine, which has a long hydrocarbon tail, and a polar domain that includes and amino group
What creates a ceramide?
Amino group of sphingosine can form an amide bond with a fatty acid carboxyl to yield a ceramide
Usually include a polar head group, esterified to the terminal OH of the sphingosine
Describe cholesterol
Largely hydrophobic but has one polar group, A hydroxyl, making it amphipathic
How are membranes dynamic?
- They can move
- Components are continuously synthesized and degraded
- The primary event in cell death may be damaged to the cell membrane
What is the chemical composition of the membrane?
Lipid assemblies held together by non-covalent bonds with proteins of specific functions
Also contains carbohydrates such as glycolipids
What are the different phases lipids can exist in?
Crystal, gel, and fluid
What prevents phase changes of membrane lipids?
Cholesterol is abundant in many membrane
Double bonds in the lipid lower melting point to below physiological temperature
What is membrane fluidity influenced by?
Fatty acid: chain length and saturation
Presence of sterols
Less fluid if longer carbon chain and fewer double bonds
What are integral proteins?
Span membrane
Cannot be removed with salt, must be solubilises with detergent
Integral proteins typically have alpha helices spanning membrane
What are the three different types of membrane proteins?
Peripheral: on membrane surface
Integral
Having a lipid anchor
Why are transporters important?
About 10% of all protein function is transport
2/3 of cellular energy at rest is used to transport ions
200 families of transporters are recognized
What are the two major modes of membrane transport?
- Simple (passive) diffusion: no carriers are involved, includes organic molecules and small uncharged molecules
- Mediated diffusion: carried out by proteins, peptides, and small molecular weight carriers, includes ions, uncharged organic compounds, peptides, and proteins. Two types: passive and active
What are he three types of integral membrane proteins that provide transport function?
- Channels and pores: can be regulated
- Passive transporters: move down gradient, no energy required
- Active transporters: move against gradient
What are the three types of passive transport?
Diffusion, osmosis, and facilitated diffusion
Define diffusion
The tendency for molecules to spread out into available space
Describe pores and channels
Transmember proteins with a central passage for ions and small molecules
Solutes of appropriate size, charge, and molecular structure can diffuse down a concentration gradient
Describe passive transport
Does not require an energy source
Protein binds solutes and transports them down a concentration gradient
What are the different types of passive transport systems?
Uniport: carry only a single type of solute
Symport: two solutes, same direction
Antiport: two solutes, opposite directions
Describe the kinetics of passive transport
Initial rate of transport increases until a maximum is reached (site is saturated)
What is aquaporin?
Hole with specific properties
Molecule that moves water using transmembrane proteins
What is active transport?
Pumping of solutes against their gradient
Non-spontaneous
Requires energy
What are the types of active transport?
- Primary: powered by a direct source of energy as ATP, light, or electron transport
- Secondary: driven by an ion concentration gradient
How does the secondary active transport function?
Coupled to the primary transporters
Utilizes gradient generated by primary transporter
Either symporters, uniporters, or antiporters
What is gradient energy?
Composed of two components: concentration and electrical
Both must be considered but may be opposing forces
What are the functions of Na+, K+ -ATPase functions?
Maintenance of osmotic stability and cell volume
Maintenance of high intracellular K+
Maintenance of membrane potential
In excitable cells, restoration of potentials
Energy for transport
Generation of heat
Describe Na+, K+ -ATPase
Results in 1 ATP, per influx of 2 K+ and 3 Na+
Pump activity is electrogenic
Not physiologically reversible
Describe the mechanism of Na+, K+ -ATPase
- 3 Na+ bind
- ATP phosphorylates active site
- conformational change releases Na+
- 2 K+ bind
- Mg2+ catalyzes dephosphorylation of enzyme
- conformational change releases K+
What are the 3 types of large molecule transport?
Phagocytosis: extension of cytoplasm to encompassing food creating vacuole
Pinocytosis: infolding of plasma membrane, creating vesicle
Receptor mediated endocytosis
Describe receptor mediated endocytosis
Receptors bind to molecules and plasma membrane folds in forming a coated pit then pinches of creating vesicle
Describe exocytosis
Vesicles fuse to the plasma membrane and release contents
Define anabolic and catabolic reactions
Catabolic: degrade large molecules to liberate smaller molecules and energy
Anabolic: responsible for the synthesis of all compounds
What is metabolism?
Concerned with the management of material and energy resources within the cell
Almost all enzyme catalyzed
Define aerobes, obligate aerobes, anaerobes, facultative anaerobes, and obligate anaerobes
Aerobes: use O2 as electron acceptor in energy producing pathways
Obligate aerobes: have to use O2
Anaerobes: don’t use O2
Facultative anaerobes: can do either
Obligate anaerobes: cannot use O2 or may even be poisoned by it
What are the five rules of metabolism?
- Living systems are able to conserve energy
- Heat is wasted energy, energy that cannot be conserved
- Living system will do their utmost to prevent loss of free energy as heat
- In biochemical transformations a large part of the energy is channeled into chemical bonds of the product
- Catabolic reactions drive anabolic reactions
Describe catabolism
The phase of intermediary metabolism that encompasses the degradation and energy yielding reactions
Generally oxidative and produce reducing potential
Cellular respiration
Describe anabolism
The phase of intermediary metabolism that encompasses the biosynthetic and energy requiring reactions
Reductive and consume reducing potential
Photosynthesis
What are amphibolic intermediates?
Central pathway that have dual purposes: serve in both catabolism and anabolism
May differ for anabolism and catabolism, although some steps may be the same
What is ATP?
Energy molecule used to couple exergonic reactions to endergonic
Currency of the cell
Nucleotide with three phosphate groups attached to the ribose sugar
High 🔺G
Energy is released though loss of phosphate group
How does ATP work?
Hydrolysis of ATP produces inorganic phosphate that is attached to a molecule involved in an endergonic process
Phosphorylation is the process of ATP transferring phosphate to a molecule
Results in a phosphorylated intermediate
Why is ATP a good source?
It can participate in many different kinds of reactions within the cell
Usually is directly involved in reactions
Little wasted energy during phosphorylation of an intermediate
What is the overall free energy change of a coupled reaction?
Negative
Endergonic reaction is driven by exergonic reaction
Occur simultaneously and share common intermediate which cancels out in the final sum
What is nicotine adenine dinucleotide?
NAD
NAD: collects electrons in catabolism
NADH: powers some anabolic reactions + ETC in mitochondria
NADPH: used in reductive biosynthetic reactions
In general participates in reactions where alcohols are converted to jetons/aldéhydes and organic acids
What is flavin adenine dinucleotide?
FAD
Generally participates in reactions where double bonds are involved
Describe the hydrolysis of acetyl CoA
Results in acetate, CoA and protons
Thermodynamically favourable
Acetyl CoA has a high acetyl group transfer potential
Carries and activated acetyl group
What are the different types of chemical reactions seen in metabolism?
Oxidation reduction: electron transfer
Ligation requiring ATP cleavage: formation of covalent bonds
Isomerization: rrearragement of atoms to form isomers
Group transfer: transfer of functional group
Hydrolytic: cleavage of bonds by water
Addition or removal of functional groups
What are the different types of metabolism control?
Allosteric regulation
Feedback inhibition
Cooperativity
What is allosteric regulation?
Enzyme function may be stimulated or inhibited by attachement of molecules to allosteric site
What is feedback inhibition?
End product of metabolic pathway may serve as allosteric inhibitor
What is cooperativity?
Single substrate molecule primes multiple active sites increasing activity
What is intrinsic regulation?
Molecules such as NAD, NADH, ATP, ADP, AMP, etc are intrinsic regulators
Concentration of these molecules mirror energy charge of the cell and act as allosteric regulators of cell metabolism
What is extrinsic regulation?
Hormones
Some Interact with cell surface and set of cascade of molecular events which
- stimulate or repress activity of key enzymes
- stimulate or repress the transcription of specific genes
What is feedback and feed-forward inhibition?
Feedback: product of a pathway controls the rate of its own synthesis by inhibiting an early step
Feed-forward: metabolite early in pathway activates an enzyme further down the pathway
What are the general functions of glycolysis?
Provide ATP energy
Generate intermediates for other pathways
What is the preparatory phase of glycolysis?
First 5 steps
Converts glucose to 2 molecules of glyceraldehyde-3-P
Requires investment of 2 ATP
No oxidations take place so no energy has been extracted from the original molecule
What is the payoff phase of glycolysis?
Final five steps
Each molecule of glyceraldehyde-3-P is oxidized to pyruvate
Yields 4 ATP and 2 NADH
What occurs during stage 1 of glycolysis?
Glucose goes to glucose 6 phosphate using hexokinase and ATP
G6P goes to fructose 6 phosphate using phosphoglucose isomerase
F6P goes to fructose 1,6-bisphosphate using phosphofructokinase and ATP
What occurs on stage 2 of glycolysis?
F-1,6-B goes to G3P and DHAP
One 6-carbon sugar makes 2 3-carbon compounds
What occurs in stage 3 of glycolysis?
G3P goes to 1,3-bisphosphoglucerate using G3P dehydrogenase creating NADH
Goes to 3-phosphoglycerate creating ATP
Goes to 2-phosphoglucerate
Goes to phosphoenolpyruvate creating water
Goes to pyruvate using pyruvate kinase creating ATP
What happens when oxygen is not present during glycolysis?
Pyruvate become lactate or acetaldehyde than ethanol both using NADH
What are some feature of glycolysis?
- All enzymes are soluble
- All there is in anaerobes, red blood cells, tissues like muscles in absence of O2, facultative organisms in abcense of O2
- End product depends on organism
- No NET change in oxidation state
- Many side reactions
- Energy yield: 2 lactate + 2ATP
What does hexokinase do?
Transfer of a phosphoryl group from ATP to glucose
Low affinity
Ensures a supply of glucose even under low blood glucose concentrations
Found in all cells
Irreversible under physiological conditions
🔺G = -27.2
What is glucokinase?
Special hexokinase
Low affinity, high Km
Functions to remove glucose from blood
Found in liver and pancreas
How does hexokinase work?
Glucose Induces a large conformational change in hexokinase
Brings catalytic groups close to the substrate and positions the ATP in close proximity to the -C6H2OH of glucose (and excludes water from active site)
Allow reaction to occur
What does phosphofructokinase do?
Transfers a second phosphoryl group from ATP to fructose 6-phosphate
First commited step in glycolysis: rate limiting step
Allosteric and inducible
Considered functionally irreversible under physiological conditions
🔺G = -25.9
What does pyruvate kinase do?
Transfers a high energy phosphoryl group to ADP, yielding ATP
Second site of ATP production
Phosphorylation at substrate level
Regarded as physiologically irreversible
🔺G = 13.9
What is the total pathway of glycolysis?
Glucose + 2NAD+ + 2ADP + 2Pi –> 2 pyruvate + 2NADH + 2 ATP
What is the total yield of fermentation?
Glucose + 2ADP + 2Pi –> 2 lactate + 2 ATP
What are the mechanisms that can alter the flux through rate-determining steps?
- Allosteric control
- Covalent modifications
- Substrate cycles - futile cycles
- Genetic control - enzyme concentrations
What is local control?
Involves dépendance of enzyme catalyzed reactions on concentrations of pathway substrates or intermediates within a cell
What is global control?
Involves hormone activated production of second messengers that regulate cellular reactions for the benefit of the organism as a whole
What are regulatory enzymes?
Some enzymes are regulated by the activity of the enzyme (reaction is enzyme limited)
Enzyme limited steps are generally the rate limiting steps in a pathway and tend to catalyse very exergonic reactions that are essentially irreversible
Often located at branch points, where the substrate could enter multiple pathways
What are the sites for controlling glycolysis?
Hexokinase, phosphofructokinase, and pyruvate kinase
How is hexokinase inhibited?
Allosterically inhibited by its product, G6P
Binds to the enzyme at high concentrations and causes inhibition
Ensures that cells will not accumulate glucose from the blood if G6P within cell is ample
How is glucokinase inhibited?
Requires insulin as an inducer
Not allosterically inhibited by G6P
Opposed by enzyme glucose-6-phosphatase
Inhibited by regulatory protein which binds to GK in present of high F6P
Reversed by F1P in a competitive manner
Subject to inhibition by glucokinase regulatory protein
What regulates phosphofructokinase-1?
Complex combination of factors regulate the activity of PFK-1
ATP inhibits by binding to an allosteric site and decreasing its affinity for F6P
ADP and AMP relieve inhibition by ATP though allosteric activation
High citrate levels accentuate inhibitory effect of ATP
Fructose 26-bisphosphate strings activated the enzyme
What inhibits pyruvate kinase?
High concentrations of ATP allosterically inhibit pyruvate kinase by decreasing its affinity for phosphoenolpyruvate using feedback inhibition
What is gluconeogenesis?
Occurs mainly in liver
To a lesser extent in kidney and small intestine under some conditions
Hexokinase, phosphofructokinase, and pyruvate kinase steps must be bypassed in gluconeogenesis
How is hexokinase bypassed in gluconeogenesis?
Hydrolysis catalyzed by glucose 6 phosphatase to yield glucose
How is phosphofructokinase bypassed in gluconeogenesis?
Hydrolysis by fructose 1,6 bisphosphatase to yield fructose 6 phosphate
How is psyruvate kinase bypassed in gluconeogenesis?
Cleavage of 2 P bonds is required
Uses pyruvate carboxylate to create oxaloacetate then PEP carboxykinase to create GDP and PEP
How is pyruvate carboxylase activated?
Allosterically activated by acetyl coA
Ocaloacetate tends to be limiting for kerbs cycle
How many P does glycolysis yield? Gluconeogenesis?
2
6
What does the opposite effect of adenine nucleotides ensure?
Insures that when cellular ATP is high, glucose is not degraded to make ATP
When ATP is high it is more useful to the cell to store glucose as glycogen
When ATP is low the cell does not expend energy synthesizing glucose
What does phosphorylation of enzyme and proteins in liver by protein kinase A result in?
Results in inhibition of glycolysis and stimulation of gluconeogenesis to make glucose available for release to the blood
What is the reciprocal regulation of fructose-2,6-bisphosphate?
F26B stimulate glycolysis by allosterically activating phosphofructokinase as well as activating transcription of the gene for glucokinase
Allosterically inhibits gluconeogenesis enzyme fructose-1,6-bisphosphate
Promotes relaxed state, activating PFK at high ATP therefore superseding local control
What does cAMP dependent phosphorylation do?
Activated FBPase2 and inhibits PFK2
Thus F26B decreases in liver cells in response to a cAMP signal cascade, activated by glucagon when blood glucose is low
What are the downstream effects of the cAMP cascade?
Glycolysis slows because F2,6B is not available to activate PFK
Gluconeogenesis increases because of the decreased concentration of F2,6B which would otherwise inhibit F16B
What are the effects of glucagon-cAMP cascade in the liver?
Gluconeogenesis is stimulated Glycolysis is inhibited Glycogen breakdown is stimulated Glycogen synthesis is inhibited Free glucose is formed for release to the blood
What is the Cori cycle?
Operates during exercise
Muscle cells utilize P stored as phosphocreatine
Once gone, lactate produced from pyruvate passes via the blood to the liver, where it may be converted to glucose
Glucose may travel back to the muscle to fuel glycolysis
Costs 6 P for every 2P made
What is the pentode phosphate pathway?
Begins with glycolysis intermediate glucose 6-P
Reconnects with glycolysis because two of the end products of the pathway are glyceraldehyde 3-P and fructose 6-P
Often referred to as a shunt
What is the point to the pentose phosphate pathway?
Yields reducing potential in the form of NADPH to be used in anabolic reactions during electrons
Yields ribose 5-phosphate
What is NADPH used for?
Synthesis and detoxification
What regulates the pentose pathway?
Glucose 6-phosphate DH
NADPH is a potent competive inhibitor of the enzyme
Usually NADPH/NADP+ is high so enzyme is inhibited
With increased demand for NADPH, the ratio decreases and enzyme activity is stimulated
What is G6PD deficiency?
Can not produce sufficient GSH to cope with the ROS
Proteins become cross linked leading to Heinz body formation and cell lysis
Inherently X linked recessive disorder
Generally are not anemic and display no evidence of disease until red blood cells are exposed to oxidant or stress
What is glycogen?
A high molecular weight glucose polysaccharide
Comprised of alpha-1,4 glucose lineages and alpha-1,6 banches every 8-12 residues
Found mainly in muscle and liver
What is the function of glycogen?
Stored by liver for use in regulating blood glucose levels; acts as a glucose buffer
Stored by muscle as a rapidly available form of glucose to fuel muscle work
Epinephrine, glucagon stimulate breakdown
Insulin stimulates glycogen synthesis
Glycogen granules contain glycogen, synthetic and degradative enzymes and regulatory proteins
Why is glucose stored as glycogen rather than just metabolizing fats?
1) muscles cannot use data as rapidly as they can glycogen
2) fatty acids can not be catabolized in the absence of oxygen
3) animals can not convert fatty acids to glucose so metabolism of fats can not supply circulating glucose levels for peripheral tissues
What is glycogenolysis?
A catabolic process
The breakdown of glycogen to glucose units
In liver: synthesis and breakdown used to regulate blood glucose levels
In muscles: the synthesis and breakdown regulated to meet the energy requirements of working muscle cells
What is phosphorolysis?
1-4 linkages are cleaved by glycogen
Energetically favourable
Prevents glucose from diffusing out of cell
What occurs during phosphorolysis?
Phosphorylase cleaves down to a branch in the sugar chain
Transferase of glycogen debranching enzyme moves 3 in branch to main chain
1-6 glucosidase activity of debranching enzyme hydrolyzes branching sugar
ATP must be invested to phosphorylated glucose
What does phosphoglucomutase do?
Interconverts G-1-P and G-6-P by donating phosphate from enzyme
What does the glycogen synthesis pathway consist of?
Glucose transporters Hexokinase and/or glucokinase to produce G6P Phosphoglucomutase to convert to G1P UDP glucose pyrophosphorylase Glycogen synthase
What would occur if synthesis and breakdown of glycogen were activated simultaneously?
Would be a futile cycle with cleavage of one P bond per cycle
To prevent this glycogen synthase and glycogen phosphorylase are reciprocally regulated by allosteric effectors and by protein phosphorylation
How is glycogen metabolism regulated?
Allosteric regulation of glycogen synthase and glycogen phosphorylase
Glycogen synthase: activated by G6P
Glygogen phosphorylase: activated by AMP and inactivated by G6P and ATP
Describe glycogen phosphorylase in the muscles
Phosphorylase b predominates
In testing muscle is in subscribe state
With exercise, increase AMP shift equilibrium to the active site
Stimulates epinephrine which triggers phosphorylation to convert phosphorylase b to a
As a result glycogen breakdown increases massively
Describe glycogen phosphorylase in liver
High glucose shifts phosphorylase to the T state, deactivating the enzyme
Glucose is a negative regulator of liver phosphorylase, not mobilized when abundant
Liver phosphorylase is insensitive to AMP
What can oversize glycogen synthesis?
Phosphorylation has opposite effects on synthesis and degradation
Activated glycogen phosphorylase
Inactivates glycogen synthase
What are glycogen storage diseases?
Genetic enzyme deficiencies associated with excessive glycogen accumulation in cells
What is Von gierke disease?
Hereditary metabolism disorder with autosomal recessive inheritance Lack of glucose 6 phosphatase Glycolysis increases Glycogen levels increase Causes inlarged liver
What is mcardle disease?
Defect in the muscle isoemzyme of glycogen phosphorylase
Can be cause by more than 30 mutations
O2 cannot be transported to muscle cells fast enough so use glycogen stores as fuel
Lactate does not build up
Experience severe muscle pain probably from increased ADP
What is pompe disease?
Autosomal recessive inheritance
Due to an inborn lack of 1-4 glucosidase, enzyme that cleaves glycosidic linkages
Leads to accumulation of glycogen in lysosomes
Leads to bulky muscle, hypotonia (loss of muscle tone), and muscle weakness
Where does the citric acid cycle occur?
Mitochondria
What occurs in the TCA cycle?
Pyruvate from glycolysis is degraded to CO2
Some ATP is produced
More NADH is made
NADH goes on to make more ATP in electron transport and oxidative phosphorylation
What are the reaction in the TCA cycle?
Citrate synthase Aconitase Isocitrate dehydrogenase Alpha-ketoglutarate dehydrogenase Succinyl-coenzyme A synthétase Succinate dehydrogenase Fumarase Malays dehydrogenase
What is acetyl CoA?
High energy compound
Hydrolysis of thioester
Bind more exergonic than ATP
What is pyruvate dehydrogenase?
Multi enzyme complex E1= pyruvate dehydrogenase E2= dihydrolipoyl transacetylase E3= dihydrolipoyl dehydrogenase Converts pyruvate to acetyl coA
What are the cofactors of PDH?
TPP: bound to E1: decarboxylation of pyruvate Lipoid acid: covalently bound to E2 Coenzyme À: A substrate for E2 FAD: bound to E3 NAD+: A substrate for E3
Where are citric acid cycle enzymes found?
Matrix of the mitochondria
What are the compartments of the mitochondria?
Matrix: contains pyruvate dehydrogenase, enzymes of kerbs cycle, and other pathways
Outer membrane: contains large VDAC channels
Inner membrane: infoldings, called cristae, contain constituants of the respiratory chain and ATP synthase
What regulates the pyruvate dehydrogenase complex?
NADH competes with NAD+ for binding to E3
Acetyl CoA competes with CoA for binding to E2
What are the different uses for acetyl CoA?
Ketone bodies
Critic acid (kerbs cycle)
Fatty acids (triacylglycerol and phospholipids)
Cholesterol (bile acids and steroids)
What occurs with citrate synthase?
Acetyl CoA becomes citrate
Irreversible
What occurs with aconitase?
Rearrangement of citrate to isocitrate
What occurs with isocitrate dehydrogenase?
Isocitrate becomes alpha-ketoglutarate
NAD becomes NADH and CO2 is released
Oxidative decarboxylation
What occurs with alpha-ketoglutarate dehydrogenase complex?
Alpha ketoglutarate becomes succinyl CoA
HS-CoA and NAD becomes NADH and CO2
Oxidation decarboxylation
What occurs with succinyl CoA synthétase?
Succinyl CoA becomes succinate
Substrate level phosphorylation
GDP(or ADP) become GTP(or ATP)
Also releases SH-CoA
What occurs with succinate dehydrogenase?
Succinate becomes fumarase
Oxidation
FAD becomes FADH2
Enzyme is bound to inner mitochondrial membrane
What occurs with fumarase?
Fumarase becomes L-malate
Hydration
What occurs with Malate dehydrogenase?
L-malate becomes oxaloacetate
Oxidation
NAD becomes NADH and H
Pulled forward by citrate synthase
What inhibits and activated the E2 complex of PDH?
HS-CoA activates and acetyl CoA inhibits
What activate and inhibits the E3 complex of PDH?
NAD activated and NADH inhibits
What inhibits and activates the phosphorylation of the E1 complex of PDH?
NADH and acetyl CoA activates and NAD, HS-CoA, ADP, and pyruvate inhibit
What activates the dephosphorylation of the E1 complex of PDH?
Calcium 2+ ion
How is the citric acid cycle in anaerobic bacteria different?
Incomplete for production of biosynthetic precursors
Do not have alpha keyoglutarate dehydrogenase
What are the intermediates of the citric acid cycle used for?
Precursors of carbohydrates, lipids, and amino acids
Reactions feeding into the cycle replenish the pool of cycle intermediates
What are some intermediates of the TCA cycle?
Ketoglutarate is transaminated to make glutamate, used to make purine nucleotides
Succinyl CoA used to make porphyrins
Fumarase and oxaloacetate are used to make amino acids and pyramidine nucleotides
Citrate is exported from the motochondria and then broken down by ATP-citrate lyase to yield oxaloacetate and acetyl CoA for fatty acid synthesis
What are the rate controlling enzymes of the kerbs cycle?
Citrate synthase
Isocitrate dehydrogenase
Alpha ketoglutarate dehydrogenase
What regulates the activity of the TCA cycle?
Substrate availability
Product inhibition
Allosteric inhibition or activation by other intermediates
What inhibits and activates citrate synthase?
Inhibited by citrate, NADH, succinyl CoA, ATP
Activated by ADP
What activates and inhibits isocitrate dehydrogenase?
Inhibited by ATP
Activated by Ca2+, ADP
What activates and inhibits alpha ketoglutarate dehydrogenase?
Inhibited by succinyl CoA, NADH
Activated by Ca2+
What is the glyoxylate pathway?
Plants and fungi can convert acetyl CoA to oxaloacetate
Occurs in glyoxosomes, a membrane bound organelle specific to plants
Allows acetyl CoA from stored data to be converted to sugars and other biochemicals
Where does the TCA cycle occur in eukaryotes and prokaryotes?
Eukaryotes: mitochondrial matrix
Prokaryotes: cytoplasm
Where is the ETC?
Built into the inner mitochondrial membrane along cristae
What does the ETC do?
Transports electrons down ETC land pumps H+ to create gradient
Yields 34 ATP from 1 glucose
Only occurs in presence of oxygen
What are the two mobile carriers of the ETC?
Coenzyme Q across complexes 1,2,and 3
Cyt C from 3 to 4
What occurs in the ETC?
NADH passes electrons to ETC
H cleaved off NADH and FADH2
Electrons stripped from H atoms -> Protons
Electrons passed from one electron carrier to next in motochondrial membrane
Transport proteins in membrane pump H+ across inner membrane to intermembrane space
How do electrons follow in the ETC?
Electrons move in steps from carrier to carrier downhill to oxygen
Each carrier is more electronegative
Controlled oxidation
Controlled release of energy
What is chemiosmosis?
The diffusion of ions across a membrane
Build up of proton gradient just so H+ could flow through ATP synthase enzyme to build ATP
How many protons are pumped out in the ETC?
10
What are the steps to the ETC?
- Electrons are harvested and carried to the transport system
- Electrons provide energy to pump protons across the membrane
- Oxygen joins with protons to form water
- Protons diffuse back in down their concentration gradient, driving the synthesis of ATP
What is the malate aspartate shuttle?
NADH produced by glycolysis cannot cross inner mitochondrial membrane
Oxaloacetate receives electrons from NADH, reducing it to malade which can be carrier in by the malate/alpha ketoglutarate transporter
Once inside it is reoxidized to regenerate NADH
Occurs in liver, heart and kidney
What is the G3P dehydrogenase shuttle?
In skeletal muscle or brain, alternative to malate aspartate shuttle
Directly enter complex III obviating the need for any membrane transport systems
Fewer protons are pumped so less ATP per electron pair
What are the dietary fatty acids?
Triacylglyderol, phospholipids, sterol esters
Where does digestion of dietary triacylglycerol occur?
Occurs in duodenum
Facilitated by bike sales and alkaline medium (pancreatic juice)
How is fat stored?
Mainly as triacylglycerols in adipose cells
What are the steps to processing lipid reserves?
- Lipid mobilization: TAGs in adipose tissue are hydrolyses to fatty acid plus glycerol
- Transport of fatty acids in blood to tissues
- Activation of fatty acids as CoA esters
- Transport in mitochondria
- Metabolism to acetyl-CoA
What occurs to glycerol after lipolyses?
Becomes dihydroxyacetone phosphate then pyruvate through glycolysis or glucose through gluconeogenesis
What is beta oxidation?
Cleavage of fatty acids to acetate tissues
Occurs in mitochondria
What are the steps in beta oxidation?
Fatty acid activation by estérification with CoASH
Membrane transport of fatty acyl-CoA esters
Carbon backbone reaction sequence
What is the carbon backbone reaction sequence of beta oxidation?
Dehydrogenation
Hydration
Dehydrogenation
Carbon-carbon cleavage
What occurs in the first step of beta oxidation?
Fatty acid is activated by estérification with CoASH releasing 1AMP and 2Pi via pyrophosphatase
Occurs in outer mitochondrial membrane for long chain fatty acids
What occurs in the second step of beta oxidation?
RSCOCoA loses CoA-SH and then binds to carnitine
Transported across both mitochondrial membranes into matrix via a transporter on inner matrix
Once in matrix carnitine is removed and CoA-SH reattaches, regenerating carnitine
Helped along by carnitine acyltransferase I and II
What is the reaction sequence of beta oxidation?
Palmitoyl CoA goes to trans 🔺^2 enoyl-CoA through dehydrogenation
Trans🔺^2enoyl-CoA goes to L-B-hydroxy-acyl-CoA through hydration
L-B-hydroxy-acyl-CoA goes to B-ketoacyl-CoA through dehydrogenation
B-ketoacyl-CoA goes to myristoyl Co and Acetyl CoA
Repeated once for every 2 carbons -2
What does each reaction sequence of beta oxidation produce?
1 CH3COSCoA
1 FADH2
1 NADH
1 H+
What regulates beta oxidation?
Low blood glucose activates fatty acid oxidation
High blood glucose activates fatty acid synthesis
Malonyl CoA inhibits transference of acyl-CoA across mitochondrial membrane
What are the biochemical consequences of decreased insulting production?
Glucose not taken up by liver results in decreased oxaloacetate to combine with acetyl CoA to enter TCA
Adipocytes release fatty acids into blood resulting in increased production of ketone bodies in liver
Describe fatty acid biosynthesis
Occurs in cytosol
Starts with acetyl-CoA
Problem is most acetyl-CoA is produce in mitochondria and cannot travserse membrane
What are the three processes of fatty acid biosynthesis?
- Transport of mitochondrial acetyl CoA from matrix to cytosol through citrate transport system
- Carboxylation of acetyl CoA from malonyl CoA, the substrate for elongation by acetyl-coa carboxylase (regulated step)
- Assemble of FA by fatty acid synthase
Describe the formation of Malonyl CoA in fatty acid biosynthesis
First commited step Irreversible Acetyl CoA carboxylase inhibited by palmitoyl CoA and epinephrine and glucagon Activated by citrate and insulin Inhibited carnitine acyl transferase
What are the steps to fatty acid synthase?
- Loading
- Condensation
- Réduction (of keto group)
- Dehydration
- Reduction (of enoyl)
What are the sources of NADPH in fatty acid biosynthesis?
Pentose phosphate shunt and malic enzyme
What are lipoproteins?
Protein lipid complexes
Hydrophobic lipids in core and hydrophilic lipids on surface
What do lipoproteins do?
Serve to transport lipid soluble compounds between tissues
What is apolipoproteins?
Proteins that bind to fats (lipids)
Form lipoproteins which transport dietary fats through blood stream
What is chylomicron metabolism?
Long chain fatty acids are reesterified into triacylglycerol in the gut and transferred
What is endogenous lipid transport?
VLDL is transported in capillaries as lipoprotein lipase
Become IDL which then goes to receptors in liver of become LDL
LDL goes to receptor on liver or on extrahepatic cell
How is cholesterol metabolized?
Dietary and biliary cholesterol
De novo synthesis in the liver
Cholesterol from extrahepatic tissues
Where are amino acids obtained for synthesizing proteins?
Obtained by degrading other proteins
Labelled with ubiquitin if destined for degradation
Are a source of nitrogen for other biomolecules o
What are the two types of protein degradation?
Dietary: dietary proteins are hydrolyzed to amino acids and absorbed into the blood stream
Cellular: degraded at different rates
What is the first step in amino acid degradation?
Removal of nitrogen
Produces alpha keto acids which are degraded to other metabolic intermediates
What occurs to amino acids after nitrogen removal?
Alpha amino groups are converted to ammonium ions by the oxidative deamination of glutamate
Transamination
In deamination, ammonium ion is converted to urea
How can conversion to ammonium occur?
Transamination and deamination
Peridoxal phosphate
Define and threonine
How is nitrogen transported to liver?
Alanine cycle is used
What happens to the ammonium ion in the liver?
Converted to urea
What is the first step to the urea cycle?
Formation of carbamoyl phosphate
Free NH4 reacts with HCO3 to form carbamoyl phosphate
Driven by the hydrolysis of two ATP
What is the second step of the urea cycle?
Formation of citrulline
Citrulline is formed from transfer of the carbamoyl group to the y-amino group of ornithine using ornithine transcarbamoylase
What is the third step of the urea cycle?
Formation of arginosuccinate
Condensation of citrulline with aspartate to form arginossuccinate
2 ATP required
What if the fourth step of the urea cycle?
Formation of arginine and fumarate
Arginosuccinase cleaves arginosuccinate to form arginine and fumarate
What is the fifth step in the urea cycle?
Formation of urea
Using arginase, the arginine is hydrolyzed to produce the urea and to reform the ornthine
Ornithine reenters the mitochondrial matrix
What are the major metabolic intermediates formed from the degradation of the 20 amino acids?
Ketogenic: acetyl CoA, acetoacetyl coa
Glucogenic: pyruvate, ketoglutarate, succinyl CoA, fumarate,
Oxaloacetate
What are the entry points of pyruvate?
Alanine
Serine
Cysteine
Threonine to aminoacetone
What are the entry points of oxaloacetate?
Aspartate and asparagine
What are the entry points of ketoglutarate?
Glutamine, proline, arginine, and histidine to glutamate to ketoglutarate
What are the entry points of succinyl CoA?
Methionine, valine, or isoleucine to propionyl to methylmalonyl coa to succinyl CoA
What are some inborn errors of metabolism?
Alcaptonuria: absence of homogentisate oxidase activity (purple urine)
Tyrosinemia: absense of activity of fumarylacetoacetase
Albinism: absence of melanin pigment
Maple syrup urine disease: lack of branch-chain dehydrogenase activity, leads to elevation of keto branched chain acids
Phenylketonuria: absence of phenylalanine hydroxylase activity
How is the purine ring synthesized?
The purine ring is synthesized by a series of reactions that add the carbon and nitrogen atoms to a preformed ribose-5-phosphate synthesized as part of pentose phosphate pathway
Describe purine nucleotide biosynthesis
Adenine and guanine are synthesized from precursors
Each donor donates the specific C or N atom sequentially to form the purine ring
C and N atoms are added to ribose phosphate
Depends on energy
Describe purine biosynthesis
Ribose phosphate goes to phosphoribosyl pyrophosphate using PRPP synthétase
Phosphoribosyl goes to phosphoribosylamine using phosphoribosylamido transferase
Goes to ATP and GTP
Describe regulation of purine biosynthesis
ATP and GTP use feed back inhibition on PRPP synthétase and phosphoribosylamido transferase
Phosphoribosyl pyrophosphate uses feed forward activate on PRPP transferase
How are ribonucleotides converted to DNA?
Use enzyme RNA reductase
Thioredoxin and NADPH are required
Hydroxyurea is an inhibitor of RNA reductase
What is the purine salvage pathway?
Purine bases can be recycled by pathway
Bases are converted to the nucleotides
Uses less energy than de novo synthesis
HGPRT and APRT are enzymes of the purine salvage pathway
What is leach nyhan syndrome?
Absense of HGPRT
Purine bases are not reused therefore increased degradation of the purine to form Uric acid
Characterized by behavioural disturbances, self mutilation, mental retardation, orange coloured crystals,
What is Uric acid?
End product of purine break down
Normally excreted by urine
If blood levels are too high, tends to precipitate in joint fluid causing arthritis
May also cause renal stones
What are some causes of hyperuricemia?
Inderexcretion of Uric acid: renal disease, lactic acidosis
Over production of Uric acid
