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374 Cards in this Set

  • Front
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Anabolic Pathway

synthesizes macromolecules


aka biosynthetic pathway


an energy-requiring or energy-consuming


pathway


use energy derived from catabolic pathways


endergonic rxn (delta G > 0)


ex: glycogenesis, gluconeogenesis



delta G = +ve

Catabolic pathway

aka degradative pathway


breaking down of complex molecules to simpler ones that results in energy release captured by formation of high energy compounds such as ATP


energy-generating or energy-releasing pathway


exergonic rxn (delta G < 0)


example: glycolysis, complete oxidation of glucose to CO2 and H20



delta G = -ve

metabolism

the sum of all of the chemical reactions that occur within an organism in order to maintain life

the metabolic activities of cells are dictated by two major goals:

1) the cell has to synthesize it macromolecules: proteins have to be made from amino acids, carbs from monosaccharides, membrane lipids form fatty acids, nucleic acids from nucleotides


2) the cell has to generate metabolic energy: nutrients must be oxidized to supply the energy for biosynthesis, active membrane transport, cell motility, and muscle contraction.

intermediary/ energy metabolim

reactions concerned with generating or storing energy; using that energy for biosynthesis of small molecules (maintenance of cellular ATP and blood glucose levels)



combined activities of all the metabolic pathways that inter-convert precursors, metabolites etc



these processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments

most amino acids can be converted to

glucose

glucose can be converted to

amino acids and fatty acids

2 alternative fates of a nutrient molecule entering a cell:

it is either used for the synthesis of a macromolecule or



it is oxidized to CO2 and H2O for the generation of ATP through various metabolic pathways

the direction in which the pathway proceeds depends on...

the sum of the free energy changes of the individual reactions

a metabolic pathway is a :

series of chemical reactions occurring within a cell

metabolic pathways are:

compartmentalized



driven by the net free energy change of the sum of individual reactions



regulated

cytosol/ cytoplasm

contains both anabolic and catabolic pathways such as glycolysis, glycogen metabolism, pentose phosphate pathway, and it is also the place where glycogen and fat are stored as energy reserves

ER and golgi apparatus

concerned with the synthesis and processing of proteins and membrane lipids

mitochondria

the powerhouse of the cell, generating >90% of ATP synthesis by oxidate phosphorylation

lysosomes

are hydrolytic enzymes for the degradation of macromolecules. they hydrolyze cellular macromolecules

peroxisomes

specialized organelles for oxidative reactions such as reactions forming hydrogen peroxide as a byproduct

Nucleolus

synthesis of ribosomal RNA, assembly of ribosomal subunits

nucleus

central databank,


DNA and RNA synthesis

Free energy

the component of the total energy of a system that can do woe at constant temperature and pressure

free energy change

the amount of free energy released or absorbed in a rxn at constant temperature and pressure

exergonic reaction

when delta G is negative (the product has lower free energy than the substrate), process or chemical run proceeds spontaneously in the forward direction

endergonic reaction

when delta G is positive (the reaction does not go spontaneously), the process proceeds spontaneously in the reverse

delta G = zero

the process is in equilibrium, with no net change taking place over time

under aerobic conditions, [NAD+] is ...

always higher than [NADH]

in the cell, [GTP] concentration is ...

almost 100 times higher than [GMP]


Cells respond to signals from _____ to adjust their metabolism

nutrients

cells have 3 options for the regulation of their metabolic pathways

1) long term at the DNA level: the amt of enzyme is adjusted by a change in its synthesis or degradation... SLOW


2) short term at protein level: some enzymes are modified covalently by phosphorylation. this requires a protein kinase and protein phosphatase... FAST


3) allosteric effectors: VERY FAST

phosphorylation

formation of a phosphate derivative

dephosphorylation

removal of phosphate groups from a biomolecule

the protein kinases and protein pho sphatases are regulated by:

metabolites or hormones

metabolic enzymes are also subject to competitive inhibition in the form of :

product inhibition - meaning the product of the reaction competes with the substrate for the active site of the enzyme.

hormones can regulate both the synthesis and degradation of metabolic enzyme and their phosphorylation by :

protein kinase

most biosynthetic pathways are inhibited by :

high concentrations of their end product (feedback inhibition)

regulation of anabolic pathway

regulation by feedback inhibition

regulation of catabolic pathway

regulation by ATP and ADP, Pi

regulation of catabolic pathway

regulation by feedforward stimulation

in energy-producing catabolic pathways, the important product is :

ATP

the ATP level is inversely related to:

the concentrations of ADP and AMP.


ADP and /or AMP act opposite to ATP in the regulation of many catabolic pathways

feedback inhibition

the regulated enzyme is inhibited by a product of the pathway

feedforward stimulation

a substrate stimulates the pathway by which it is utilized

a regulated enzyme must be present in:

lower activity than the other enzymes in the pathway

the regulated enzyme should serve :

an essential function in only one metabolic pathway

the regulated enzyme should catalyze:

the first irreversible reaction ( the committed step) in the pathway

regulation of the committed step ensures:

that only the substrate of the pathway accumulates when the regulated enzyme is inhibited.


if a later reaction would be inhibited, metabolic intermediates would accumulate causing possible toxic effects.

inherited enzyme deficiencies cause

metabolic diseases

when an enzyme is missing as a result of a genetic defect, the immediate effects are always:

the accumulation of the substrate in blood and the lack of the product

deficiency of an enzyme in a catabolic pathway, ATP producing pathway causes:

a serious problem

if the intracellular degradation of a macromolecule by hydrolytic enzymes is blocked...

"undegraded" macromolecules accumulates mostly within the cells. the result is a "storage disease"

vitamin deficiencies

can affect multiple metabolic pathways.


a vitamin deficiency can prevent a metabolic react by depriving it of an essential coenzyme. most vitaim derived coenzymes (NAD, FAD, CoA), participate in multiple metabolic pathways. al of these pathways are impaired when vitamin deficient

toxins

act by inhibiting metabolic enzymes



lead: causes the accumulation of toxic intermediates by inhibiting enzymes of heme biosynthesis



cyanide: blocks cell respiration by inhibiting the mitochondrial cytrochrome oxidase

endocrine disorders

the most complex metabolic diseases because each hormone controls a whole set of metabolic pathways.



diabetes mellitus: insufficient insulin action disrupts a host of pathways in carbohydrate and fat metabolism

bioenergetics

the quantitative study of every relationships and energy utilization, and conversions in biological systems, or energy transformations in living organisms

metabolism

the sum of all chemical reactions that occur within an organism in order to maintain life or the entire set of enzyme-catalyzed transformations of organic molecules in living cells (the sum of anabolism and catabolism)

autotrophs

aka producers


can use CO2 from the atmosphere as their major source of carbon, from which they construct all their carbon-containing biomolecules, such as photosynthetic bacteria, green algae, and plants

heterotrophs

aka consumers



can not use CO2 from the atmosphere and must obtain carbon from their environment in the form of complex organic molecules such as glucose. Multi cellular animals an most micro-organisms are heterotrophic

free energy source

cells are isothermal systems - function at constant temp and pressure. autotrophic cells acquire free energy form solar radiation, and heterotrophic cells acquire it from nutrient molecules

autotrophic organisms are ____ and obtain their energy from ____

photosynthetic



sunlight

heterotrophic organisms obtain their energy from ....

the degradation of organic nutrients produced by autotorphs

Carbon, oxygen, nitrogen, and water are constantly cycled between the ____ and _____

autotrophic producers and heterotrophic consumers

oxidation-reduction

reactions involving the loss or gain of electrons - one reactant gains electrons and is reduced while the other loses electrons and is oxidized

oxidation reactions generally ______ energy and are important in _____

release



catabolism

in many organisms, the oxidation of ____ supplies energy for the production of ____

glucose



ATP

NAD+ and FAD

are a prosthetic group covalently bound in some enzymes



NAD+ or NADP+

soluble co-factors free to diffuse from one enzyme to another.


Both accept two electrons and one proton

FAD or FMN

coenzymes derived from the vitamin riboflavin, often tightly bound to specific enzyme called flavoproteins

great majority of NAD+/NADH is located in

the mitochondria

most of the NADP+/NADPH is

in the cytosol

electron carrier

a biomolecule that can reversibly gain and lose electrons

NAD+ and NADP+ undergo

reduction to NADH and NADPH by accepting a hydride ion from an oxidizable substrate



the hydride ion is added to either the front or back of the nicotinamide ring

Reduction of nicotinamide ring produces

a new broad ring



NADH at 340 nm

NAD+ or NADP+ move readily fro one enzyme to another, acting as a water-soluble electron carriers, derived from

vitamin niacin which is synthesized from tryptophan

Niacin deficiency causes a disease called

pellagra (rough skin)

Rossmann fold

most dehydrogenates that use NAD or NADP bid the cofactor in a conserved protein domain



it is an NAD-binding site, consisting of : six stranded parallel beta pleated sheets and four alpha helices

FAD/FADH2

flavoproteins are enzymes that catalyze oxidation-reduction reactions using either FMN or FAD as coenzyme

FAD or FMN are coenzyme derived from

vitamin B2, riboflavin

in a healthy cell: [NAD+]/[NADH]

>> 1


due to continuous ATP production (rapid utilization of NADH in the mitochondria)

in a healthy cell: [NADP+]/[NADPH]

= 0.05



maintains reductive environment in the cytosol (NADPH)

ATP is the chemical link between:

catabolism and anabolism


and is the energy currency of the living cell

NAD and NADP, both are the freely diffusible coenzymes of

dehydrogenases



total concentration of NAD+ + NADH in tissues is

10^ -5 M

total concentration of NADP+ + NADPH in tissues is

10^ -6 M

all major nutrients are degraded to

acetyl coenzyme A



"activated acetic acid"

in the mitochondria, the two carbons of the acetyl group become oxidized to CO2 and produce reduced coenzymes in the

tricarboxylic acid (TCA) cycle

the deoxidation of the reduced coenzymes produces the bulk of the cellular ATP in the process of

oxidative phosphorylation

glucose is not only the most abundant monosaccharide in food, but is

also produced from other monosaccharides by the breakdown of the storage polysaccharide glycogen



from amino acids and other non-carbohydrate substrates

dietary sources of glucose

starch- a glucose polymer


sugar (dimer of glucose and fructose)


milk (lactose, dimer of galactose and glucose)


fruit/ vegetables (a source of glucose and fructose)

glucose is the principal

transported carbohydrate in humans and most abundant monosaccharide in dietary carbohydrates

glucose can be transported by the

blood

glucose cannot be stored in

the cells

glucose storage

to be stored, it has to be converted to the polysaccharide glycogen

glucose is relatively rich in

potential energy, and thus a good fuel

in many organisms, the oxidation of glucose supplies energy for the production of

ATP

is glucose lipid soluble

glucose is not sufficiently lipid soluble to enter in cells by diffusion across the plasma membrane

dietary glucose enters the intestinal mucosal cells mainly by

sodium co-transport, but the uptake of glucose from blood or interstitial fluid into the cells occurs by so-called "facilitate diffusion"

GLUT 4

express in muscle, adipose tissue, heart



function: insulin-dependent glucose uptake

GLUT 4 deposition in the plasma membrane is enhanced by

insulin

during the well-fed state

decreased levels of glucagon and elevated levels of insulin



muscle and adipose tissue take up glucose



muscle and adipose do not depend on glucose, but can subsist on fatty acids and other nutrients if needed

durgin starvation

elevated levels of glucagon and low levels of insulin develops during fasting. this results in a decrease in the overall rate of glycolysis and an increase in gluconeogenesis



glucose is redirected from muscle and adipose tissue to tissues that depend on glucose - brain, RBCs

insulin-independent tissues

utilize glucose independently of the dietary/nutritional status



includes tissues that depend on glucose as a sole source of energy



RBCs, brain, beta cells of the pancreas

insulin - dependent tissues

can take up glucose only during the fed state (high insulin) levels



do not depend on glucose as a sole source of energy



muscle, fat

glucose metabolism by the liver depends on

the insulin/glucagon but insulin is NOT required for the entry of glucose into the liver cell

glucose absorption from diet leads to

increase in blood glucose concentrations

rising blood glucose levels will

increase liver-mediated glucose consumption by the liver (insulin-independent) - GLUT 2 transporters

rising glucose triggers the release of

insulin by the beta cells of the pancreas, which leads to a rapid removal of excess glucose from blood by tissues expressing GLUT 4 transporters (fat and muscle) Insulin-dependent

blood glucose levels never fall below

4-5 mM

falling glucose leads to

decreased insulin, increased glucagon and cessation of glucose uptake by most tissues

carbohydrate

a major source of energy

glucose

the major product of carbohydrate digestion

some cells depend exclusively on

glucose for energy

glucose is stored in cells as

glycogen (animal starch)

glucose can be synthesized by cells from

other metabolites

the brain always depends on

glucose supply.

blood glucose level must be maintained at

4-5.5 mmol/liter (70-100 mg/dL)

the main site for glucose metabolism is

the liver

glucose degradation begins in the _____ and ends in the _____

cytoplasm



mitochondria

glucose oxidation:

when glucose is oxidized completely to CO2 and H2O, 36 or 38 ATP molecules are generated

glycerol phosphate shuttle

the transfer of electrons from cytoplasmic NADH to the respiratory chain of mitochondria

malate- aspartate shuttle

the reversible shuttling of hydrogen, in the form of malate, across the inner mitochondrial membrane

glycolysis

the catabolic pathway by which a molecule of glucose (6 carbons) is broken down into 2 molecules of 3 carbon compound pyruvate

All cells of the body are capable of

GLYCOLSIS

glycolysis produces

ATP without consuming oxygen

glycolysis functions under

aerobic or anaerobic conditoins

many microorganisms are entirely dependent on

glycolysis

where does glycolysis take place

in the cytoplasm of the cells

glycolysis is an essential step for :

aerobic metabolism of glucose

in the liver _____ is the first step in the conversion of carbohydrate to fat

glycolysis

during glycolysis, some of the free energy released from glucose is conserved in the form:

of ATP and NADH

step 1 of glycolysis

glucose is phosphorylated to glucose 6 phosphate catalyzed by glucokinase in the liver or by hexokinase in muslce/ fat

glycolysis produces a net yield of

2 molecules of pyruvate, 2 molecules of ATP, and 2 molecules of NADH per molecule of glucose (aerobic)



2 molecules of lactate, 2 molecules of ATP, and no net product of NADH per molecule of glucose (anaerobic glycolysis)

2 phases of glycolysis

1) energy investment phase (steps 1-5)


phosphorylation of glucose and its conversion to glyceraldehyde 3-phosphate



2) energy generation phase (steps 6-10): oxidative conversion of glyceraldehyde 3-phosphate to pyruvate

glucokinase

(liver and pancreas)


highly specific for glucose


high but variable Km for glucose (10mM)


not saturated at physiological blood glucose [] (4-5mM


inhibited by fructose 6 P, but not glucose- 6- phosphate


induced by insulin (transcriptionally)

hexokinase

(peripheral tissues)


-low specificity - phosporylates most relevant hexoses


-soluble and cytoplasmic protein


-low Km (0.1mM); saturated at all plasma glucose concentrations


-inhibited by glucose 6 phosphate


-activated by fructose 1 phosphate and glucose


-insulin has no effect on expression


during glycolysis, some of the energy of the glucose is conserved in ___ while much remains the product ___

ATP



pyruvate

each molecule of glucose is degraded to :

2 molecules of pyruvate


2 molecules of ATP


and 2 molecules of NADH

conversion of glucose to pyruvate is

exergonic (neg G)

formation of ATP from ADP and Pi is

endergonic (positive G)

what is the most important regulated enzyme of glycolysis

phosphofrutokinase (PFK)

PFK is stimulated by ____ and inhibited by _____

insulin


AMP and ADP




glucagon (in the liver)


citrate


low pH


ATP

what inhibits pyruvate kinase

ATP

in RBCs, rates of glycolysis are regulated by

ATP / (AMP + ADP) only

hexokinase, phosphofructokinase, and pyruvate kinase reactions are

irreversible

aldolase and triose phosphate isomerase have very

unfavorable equilibria (G>0)



but can still proceed, since fructose 1,6 bisP forms irreversibly, and glyceraldehyde 3P is rapidly consumed in the next react of the pathway bc NAD+ is in excess compared to NADH

committed step of glycolysis

Phosphofructokinase - commits conversion of glucose to pyruvate

fate of 1,3 BPG

converted to 3-phosphoglycrerate by phophoglycerate kinase



converted to 2,3- BPG by bisphophoglycerate mutase



2,3 bisphosphoglycerate is converted to 3-phosphoglycerate by bisphophoglycerate phosphatase

pyruvate kinase is more active in

the fed state than in the fasting state

pyruvate kinase is inhibited by

ATP


acetyl CoA


alanine

pyruvate kinase is activated by

fructose 1,6-bisphosphate

pyruvate formed by glycolysis, is only the first stage in

the complete degradation of glucose

acetyl - CoA is formed from

carbohydrates through glycolysis and pyruvate dehydrogenase

the major fate of acetyl CoA is

oxidation in the TCA cycle

pasteur effect

the stimulation of glycolysis under anaerobic conditions



this is due to a much higher energy yield from glucose metabolism in the presence of oxygen



pasteur effect NOT observed in red blood cells

flux of glucose through the glycolytic pathway is dramatically reduced uner

aerobic conditions



oxygen appears to "inhibit" glucose metabolism

lactate is produced under

anaerobic conditions

anaerobic glycolysis is only useful under what circumstances:

mature RBCs



vigorously contracting skeletal muscle in which oxygen supply becomes a limiting factor



ischemic tissue

warburg effect

most cancer cells rely on aerobic glycolysis

fructose metabolism occurs primarily in

the liver, kidneys, and small intestine

in the liver, fructose is converted to

fructose 1 phosphate by fructokinase and activates glucokinase

essential fructosuria

a deficiency of fructokinase

hereditary fructose intolerance

a deficiency of fructose 1-phosphate metabolism by aldolase B

pyruvate

produced by glycolysis and further oxidized in the mitochondria under aerobic conditions

cellular respiration

the aerobic phase of catabolism when cells consume O2 and produce CO2 (and H2O)

transport of pyruvate

must be transported into the mitochondria,


it diffuses through the pores in the outer mitochondrial membrane into the mitochondria matrix to reach the multi-enzyme complex pyruvate dehydrogenase

The TCA cycle is ____ in metabolism

"hub"

first step of TCA

conversion of pyruvate to acetyl groups, then acetyl groups are carried into the TCA cylce

3 stages of cellular respiration

1) oxidation of fatty acids, glucose, and some amino acids yields acetyl COA


2)oxidation of acetyl groups in TCA cycle includes 4 steps in which electrons are transferred ( 4 pairs of electrons are transferred during one turn of the cycle)


3) electrons carried by NADH and FADH2 enter the respiratory chain - ultimately reducing O2 to H2O and the production of ATP

Oxidative Decarboxylation

the conversion of pyruvate to Acetyl CoA


Exergonic reaction


catalyzed by pyruvate dehyrogenase complex


NAD+ and CoA-SH are needed as co-substrates


-vitamins: niacin (NAD) and panthotenic acid (CoA)



co-enzymes are lipoid acid and the vitamins thiamin pyrophosphate and riboflavin

3 enzymes that make up the PDH complex

1) pyruvate dehydrogenase


2) dihydrolipoyl transacetylase


3)dihydrolipoyl dehydrogenase

pyruvate dehydrogenase

-inhibited by its product NADH and acetyl CoA


-stimulated by AMP


-Inactivated but the phosphorylation


-reactivated by dephosphorylation

dihydrolipoyl transacetylase

catalyzes the transfer of the acetyl group to coenzyme A, forming Acetyl - CoA

dihydrolipoyl dehydrogenase

catalyzes the regeneration of the disulfide form of lipoate

regualtory enzymes of PDH

phosphorylate/dephosphorylate E1 (a kinase and a phophatase)

5 cofactors required for PDH

-Thiamin pyrophosphate (TPP)


-Lipoic acid (lipase)


-Flavin adenine dinuclueotide, FAD (Riboflavin)


-Nicotinamide adenine dinucleotide, NAD+ (Niacin)


-Coenzyme A, CoA (Pantothenic acid)

4 different vitamins required in human nutrition are vital components of PDH complex

thiamine (in TPP)


riboflavin (in FAD)


niacin (in NAD)


pantothenate (in CoA)

thiamine pyrophosphate (TPP)

a coenzyme important in respiration in the TCA cycle, and often plays a role in the removal of carboxyl groups from organic acids



a vitamin B1 derivative produced by the enzyme thiamine

thiamine deficiency leads to

inability to oxidize pyruvate and thus has a major neurological impact - Beriberi

lipoamide

lipoate, a prosthetic group of pyruvate dehydrogenase, has two thiol groups that can undergo reversible oxidation to a disulfide bond. because of its capacity to undergo oxidation-reduction reactions, lipase can serve both as an electron carrier and as an acyl carrier.

Coenzyme A

has a reactive thiol (-SH) group that is critical to the role of CoA as an acyl carrier in metabolic reactions



formed from pantothenic acid and ATP, is necessary for carb, fatty acid synthesis and metabolism, and the oxidation of pyruvate in the TCA cylce

PDH complex carries out __________ in the decarboxylation and dehydrogenation of pyruvate

five consecutive reactions

sources of acetyl - Co A

in aerobic organisms, glucose and other sugars, fatty acids, and most amino acids are ultimately oxidized to CO2 and H2O via TCA cycle and respiratory chain



pyruvate, the product of glycolysis is converted to acetyl CoA, the starting material for the TCA cycle, by the PDH complex

Regulation of PDH

Allosteric: inhibition by ATP, acetyl-CoA and NADH


Activation by AMP, CoA and NAD+



Covalent: Inhibition by phosphorylation of E1 (pyruvate dehydrogenase). A specific kinase (co-substrate: ATP) catalyzes this phosphorylation (PDH kinase)


Activation by dephospho rylation


pyruvate is a potent inhibitor of

pyruvate dehydrogenase kinase

TCA/Krebs cylce

the final common pathway for the oxidation of all major nutrients, and plays several roles in metabolism

where do TCA and oxidative phosphorylation take place

in all cells that contain mitochondria

TCA cycle and oxidative phosphorylation are the

final common pathway for the oxidation of all major nutrients

degradation of acetyl CoA derived form carbs, fatty acids, and amino acids:

-produces most of the CO2 generated in tissues


-is the major source of NADH


-allows excess energy to be used for fatty acid biosynthesis


-provides precursors for many metabolites

most TCA cycle enzymes are in the

mitochondrial matrix, some are in the inner mitochondrial matrix

one complete turn of the TCA cycle generates

only one GTP, 3 molecules of NADH and one molecule of FADH2 from one acetyl residue

TCA: in a series of 7 reactions 2 carbons are released as

CO2, regenerating oxaloacetate

how many pairs of electrons are transferred during one turn of the TCA cycle

4 paris


3 pairs of electrons reducing 3 NAD+ to NADH, and one pair reducing FAD to FADH2

one complete turn of the TCA cycle generates ____ ATP


____ NADH


____ FADH2


1 ATP in the conversion of succinyl CoA to succinate


3 NADH


1 FADH2


oxidation of one NADH leads to formation of ___ ATP

3

Oxidation fo FADH2 yields ____ ATP

2

Total ATP generated by one round of TCA cycle from one acetyl residue

12ATP

Total ATP yield from one molecule of glucose (through glycolysis and TCA)

38 ATP

The TCA cycle activity is responsive to:

energy state of the cell


-redox state of the cell, through flux rate limitation caused when intramitochondrial NAD+ decreses


- availability of energy - rich compounds, through inhibition of relevant enzymes by acetyl CoA or succinyl CoA

TCA cycle is an ______ pathway, that serves in ...

amphibolic pathway that serves in both catabolic and anabolic processes

PDH complex is allosterically inhibited when

[ATP]/[ADP], [NADH]/[NAD+] and [acetylCoA]/[CoA] ratios are high, indicating an energy sufficient metabolic state



when these ratios decrease, allosteric activation of pyruvate oxidation results

the overall rate of the TCA cycle is controlled by

the rate of conversion o pyruvate to acetyl CoA

In TCA cycle: Citrate synthase is inhibited by

ATP


citrate


NADH


succinyl CoA

in TCA: isocitrate dehydrogenase is inhibited by

ATP and NADH

in TCA: alpha keto glutarate dehydrogenase is inhibited by

succinyl CoA and NADH

TCA cycle intermediates are also used in

biosynthetic (anabolic) pathways

Anaplertoic reactions

biosynthetic reactions tat consume TCA cycle intermediates, must be balanced by reactions that produce them

example of anplerotic reactions

synthesis of oxaloacetate from pyruvate by pyruvate carboxylase... this is ATP dependent carboxlation reaction, activated by acetyl CoA bound biotin



synthesis of malate form pyruvate by malic enzyme - pro and eukaryotes



synthesis of oxaloacetate from PEP by PEP-CK


- heart and skeletal muscle


pyruvate carboxylase defficiency

a rare recessively inherited condition



pyruvate accumulates because pyruvate carboxylase is a major consumer of pyruvate



acculated pyruvate is converted to lactate and alanine



hypoglycemia

caused by the inability to convert pyruvate to glucose

neurological deficits and mental retardation can be caused by

dysfunction of TCA cycle due to insufficient oxaloacetate

Antiporters

transport metabolites across the inner mitochondrial membrane



ex: ADP, ATP, pyruvate, phosphate, alanine, aspartate, glutamate, substrates, intermediates, and products of the TCA cycle : except acetyl CoA, oxaloacetate, fumarate, NAD, NADH

the mitochondrial translocases are

antiporters



they do not hydrolyze ATP, but energy is consumed whenever active maintained ion gradient or the membrane potential is dissipated

Can TCA function in anaerobic conditions?

NO, unlike glycolysis, TCA cycle cannot function under anaerobic condition


TCA cycles is an aerobic pathway

under aerobic conditions, pyruvate is transported to...

into the mitochondria, where it is turned into the 2 carbon compound acetyl coenzyme A (CoA)

how does Acetyl CoA enter the TCA cycle

by reacting with the 4 carbon compound oxaloacetate to form the 6 carbon compound citrate



citrate is converted back to oxaloacetate in the reactions of the TCA cylcw

in aerobic organisms, glucose and other sugars, fatty acids and most amino acids are ultimately oxidized to

CO2 and H2O via TCA and respiratory chain.

what converts pyruvate to acetyl CoA

pyruvate dehydrogenase complex

FADH2

is not free in solution like NAD+ and NADH;


it is tightly bound to enzymes

TCA cycle produces ___ molecules of CO2 for each acetyl residue

2

succinate dehyrogenase

is the only membrane bound enzyme in the TCA cycle

lipoate (lipoid acid)

a prosthetic group of pyruvate dehyrdogenase

prosthetic group

a metal ion or an organic compound that is covalently bound to a protein an dis essential for its activity

pantothenic acid (pantothenate)

an essential constituent of coenzyme A, also called vitamin B5, a water soluble vitamin required to sustain life (essential nutrient)

TPP

thiamine pyrophosphate, a prosthetic group that transfers carboxyla

acyl carrier

part of the fatty acid synthesizing enzyme complex, which carries acyl groups, including the acetyl group


election carriers

a protein such as flavoprotein or a cytochrome that can reversibly gain and lose electrons

lyase reaction

an enzymatic reaction that removes a group non hydrolytic ally from its substrate

isomerization

convert form one isomer to another

condensation

a chemical reaction in which two molecules or moieties combine to form one single molecule, with the loss of a small molecule

decarboxylation

a chemical reaction in which a carboxyl group is split off from a compound as CO2

deydration

a chemical reaction that involves the loss of water from the reacting moleculeh

hydration

a chemical reaction involving the loss of water from the reacting molecule

dehyrogenation

chemical reaction that involves the elimination of H2

the respiratory chain is present in

the mitochondrial membrane

the respiratory chain and oxidative phosphorylation are

tightly couple processesin

inhibition of the electron transport chain also results in

inhibition of ATP synthesis

oxidative phosphorylation

means ATP synthesis, its the culmination of energy yielding metabolism in aerobic organisms

what is the principal source of ATP

oxidative phosphorylation

where do TCA cycle and oxidative phosphorylation take place?

in all cells that contain mitochondria

TCA cycle and oxidative phosphorylation are the final..

common pathway for the oxidation of all major nutrients

failures of oxidative phosphorylation are caused by

hypoxia and anoxia

oxidative phosphorylation involves the reduction of

O2 to H2O with electrons donated by NADH and FADH2

oxidative phosphoyrlation involves

a "flow of electrons"

oxidative phosphorylation begins with

the entry of elections into the respiratory chain

NADH

a water soluble electron carrier that associates reversibly with dehydrogenates

energy yields from cytoplasmic NADH depends on

the shuttle used

complete oxidation of glucose molecule to CO2 yields

36 or 38 ATP



only 4 of them are produced by phosphorylation during glycolysis and the TCA cycle, the rest are from oxidative phosphorylation

all major catabolic pathways form

NADH and or FAHD2



these reduced coenzymes must be re-oxidized to NAD+ and FAD, which are needed as substrates of the pathways and requires the respiratory chain in the inner mitochondria membrane

nutrient energy potential (H2) is stored in

mitchondrial NADH+, H+/FADH2

the transfer of the protons and electrons to oxygen generates the

energy required for ATP synthesis

none of the functional groups in proteins can transfer

hydrogen or electrons



the components of the respiratory chain have to employ metal and ions and coenzymes

the respiratory chain contains:

flavoproteins


iron-sulfur proteins


cytochromes


ubquinone or coenzyme Q


protein bound copper



* with the exception of Coenzyme Q, all members of this chain are proteins

FAD or flavin mononucleotide (FMN) in the flavoproteins can transfer:

either one or two electrons at a time

electron transfer occurs because:

the FAD/FMN has a higher reduction potential than the compound oxidized

FAD/FMN accepty hydrogen/electrons from :

NADH and donate it to the cytochromes

flavoproteins

proteins containing flavin adenine dinucleotide (FAD) or FMN as a prosthetic group, participate in hydrogen transfer reactions

reduction potential

delta E: the measure of tendency of a redox pair reaction


cytochromes

heme proteins that functions as electron carriers in respiration, photosynthesis, and other oxidation reduction reactions

iron-sulfur proteins

a large family of electron-transfer proteins in which the electron carrier is one or more iron ions associated with 2 or more sulfur atoms of cysteine residues



aka non-heme proteins


anchored in proteins through cysteine


both the iron sulfur proteins and flavoproteins are integral membrane proteins

iron sulfur complexes in proteins

iron in these complexes can change its oxidation state reversibly between the ferrous (Fe2+) and ferric (Fe3+) forms

cytochromes contain

red or brown heme proteins


the heme iron of the cytochrome switches back and forth between ferrous and ferric


one electron carriers


mitochondria contain 3 classes of cytochromes based on wavelengths of the spectral absorption peaks (a, b, c)


all but one are integral membrane proteins


cytochrome c

is a small and water soluble protein. after its single heme accepts an electron from complex III, cytochrome c moves to complex IV to donate electron to a binuclear copper center.

cytochromes consist of

4 five membered nitrogen containing rings in a cyclic structure, called a porphyrin



the 4 nitrogen atoms are coordinated with a central Fe ion, either Fe2+ or Fe3+

ubiquinone or coenzyme Q

a lipid soluble hydrophobic benzoquinione with a long isoprenoid side chain (a long hydrocarbon tail of 10 isoprene units makes it hydrophobic)



a component of the respiratory chain



a hydrogen carrierp

protein bound copper

participates in the last reaction of the respiratory chain, the transfer of electrons to molecular oxygen. it switches between the Cu+ and Cu 2+ forms during these electron transfers

4 components of the respiratory chain are freely diffusible:

NADH


ubiquinone


cytochrome c


molecular oxygen

the respiratory chain contains

large multi protein


four electron carrier complexes, each capable of catalyzing electron transfer: complex I, II, III, IV

Complexes I and II

catalyze electron transfer to ubiquinone from 2 different electron donors: NADH (complex I) and succinate dehydrogenase (complex II)

Complex III

carries electrons from reduced ubiquinone to cytochrome C

complex IV

transferring electrons from cytrochrome c to O2

the respiratory proteins are located in

the inner mitochondrial membrane



cells with high rates of respiration (heart muscle) have mitochondria with many densely packed cristae.



liver cells have much fewer cristae

for each pair of electrons transferred to O2, ___ protons are pumped out by Complex I, ___ by Complex III, and ___ by complex IV

4 protons by complex 1


4 protons by complex III


2 protons by complex IV

electron transport

progressive transport of electrons for NADH+H+/FADH2 through various electron acceptors with increasing reduction potentials, ultimately to O2

Complex I

aka NADH: ubiquinone oxidoreductase or NADH dehydrogenase, transfers electrons from NADH to ubiquinone, is a large enzyme composed of 42 different polypeptide chains, including FMN-containing flavoprotein and at least 6 iron sulfur centers



electrons are transferred from NADH to flavoprotein (FMN) then iron sulfur centers to ubiquinone

amytal, rotenone, and piericidin A inhibit:

electron flow from the Fe-S centers of complex I to ubiquinone, and therefore block the overall process of oxidative phosphorylation

complex II

aka succinate dehyrogenase is the only membrane-bound enzyme in the TCA cycle



contains only 5 cofactors and 4 different protein subunits (A, B, C, D)


contains 3 Fe-S centers, bound FAD


electrons from succinate pass through a flavoprotein and several Fe-S centers to ubiquinone

glycerol 3-phosphate donates electrons to

a flavoprotein on the outer face of the inner mitochondrial membrane, then pass to ubiquinone

acyl CoA dehyrogenase transfers

electrons to ETF from which they pass to ubiquinonec

complex III

(ubiquinone to cytochrome c)


aka cytochrome c oxidoreductase or cytochrome bc1 complex, couples the transfer of electrons from ubiquinol (QH2) to cytochrome c



it contains cytochrome b, an Fe-S protein, and cytochrome c1.



its a dimer of identical monomers, each with 11 different subunits

Complex IV

(cytochrome c to O2)


the final step of the respiratory chain. aka cytochrome oxidase, carries electrons from cytochrome c to molecular oxygen, reducing it to H2O



a large enzyme of the inner mitochondrial membrane



contains 2 heme groups, each located near a copper ion



oxygen is tightly bound between heme a3, and copper to be released after its reduction to H20 by the transfer of 4 electrons



cytochrome oxidase has a very high affinity for oxygen.

complex IV inhibitoin

acute cyanide poisoning

both iron and copper has been shown

to bind cyanide

oxidative phosphorylation proceeds in 2 steps

1) protons are pumped out of the mitochondria: driven by the redox reactions in resp chain


2)protons are admitted back into the mitochondria via a proton channel: this process drives ATP synthesis

ATP is synthesized only when

protons flow, and protons can only flow when ATP is synthesized

inner mitochondrial membrane acts like a

storage battery, is charged by the proton pumps of the respiratory chain

proton pumping out of the mitochondria matrix is fueled by

the exergonic reactions in the respiratory chain

protons move back into the matrix through a proton channel. This proton channel is coupled to

an ATP- synthesizing enzyme (ATP synthase).


ATP synthesis is field by the flow of protons down their electrochemical gradient.

there is no rate limiting step in:

oxidative phosphorylation

what does the rate of oxidative phosphorylation depend on

substrates availability and an oxidizable metabolite, like NADH and or FADH2

ATP synthesis absolutely dependent on

continuous electron flow and electron transport occurs only during ATP synthesis

what produces most of the ATP

oxidative phosphorylation

in healthy cells, the level of ATP exceeds that of ADP by a factor of:

4-10

high demand for ATP, generates:

ADP, which stimulates respiration

At rest, accumulation of ATP depletes

ADP levels and suppresses respiration

uncoupler

any substance that inhibits ATP synthesis but have no effect on electron transport



means the dissociation of oxidative phosphorylation (not reduction) from ATP synthesis. wh

at is the most common uncoupler

2,4-dinitrophenol (DNP)

Valinomycin

an antibiotic that makes the inner mitochondrial membrane permeable for potassium

oxygen utilization is maintained as

electron transport (H+ pumping) continues

ATP synthesis is diminished or inhibited as

proton gradient is weak, disrupted, or non-existentt

thyroxin

a hormone produced by the thyroid glands to regulate metabolism by controlling the rate of oxidation in cells

thermogenin

a protein of the inner mitochonrial membrane that allows trans-membrane movement of protons, called uncoupling protein, a membrane-spanning protein that forms a natural channel to allow proton return



-increases heat generation


-found in specialized tissues (hairless, hibernators, cold-adapted)


-brown fat (particularly high content of cytrochromes) localized in the neck and upper back

oxidative phosphorylation is inhibited by:

by many poisons; electron flow through the respiratory chain, can be blocked by:


-rotenone


-amytal


-antimycin A


-cyanide

rotenone

an insecticide, blocks flow of electrons from Fe-S complexes in the NADH-Q reductase complex to ubiquinone through complex I. blocks transfer of electrons associated with NADH

amytal

(a barbituate), site of action same as rotenone, also inhibits electron flow through the NADH-Q redutase compile (complex I)

antimycin A

an antibiotic, that blocks electron flow from cytochrom b to c1 through the cytochrome c oxido-reductase complex (complex III)

cyanide

binds to cytochrome oxidase (complex IV) and prevents electron transfer ot oxygen. hydrogen sulfide, carbon monoxide and azide also act as cyanide.

mitochondrial genome consists of

16,569 base pairs that encode:


13 polypeptides


7 subunits of complex I


1 subunit of complex II


3 subunits of complex IV


2 subunits of ATP synthase


22 transfer RNAs


2 RNAs of the mitochondrial ribosomes

mutation in mitochondrial DNA can cause

-Lebers hereditary optic neuropathy (LHON): blindness, caused by degeneration of the optic nerve


-myoclonic epilepsy and ragged-red fiber disease (MERRF)


-mitochondrial DNA has a higher mutation rate than nuclear DNA

reactive oxygen species are formed when?

during oxidative metabolism



electrons may "leak out" of the respiratory chain

what is the most harmful radical

hydroxyl radical

enzymes evolved to destroy ROS

superoxide dismutase (SOD)



catalase - a heme containing enzyme that destroys H2O2)



peroxidases: glutathione peroxidase

examples of metabolites, vitamins, hormones,and phytochemicals that can eliminate free radicals

bilirubin


uric acid


ascorbate (vitamin C)


estrogens

heart muscle obtains nearly all its ATP from

oxidative phosphorylation

oxidative phosphorylation and photo-phosphorylation account for

most of the ATP synthesized by organisms

mitochondria have ___ membranes

2: the outer membrane is readily permeable to small molecules, which move freely through transmembrane channels. The inner membrane is impermeable to small molecules and bears the components of the respiratory chain and the ATP synthase.

can NADH and NADPH cross the inner mitochondrial membrane

NO

respiratory chain creates

a proton gradient

inhibition of ATP synthesis blocks:

electron transfer in intact mitochondria

glycolysis under anaerobic conditions yields only

2 ATP per glucose

ATP consumption increases...

the rate of electron transfer and oxidative phosphorylation increases

mitochondria of heart muscle

have much larger are of inner membrane, contain more than 3 times the electron transport systems compared to liver mitochondria

electron transport system:

movement of electrons from electron donor to electron acceptor molecules, especially from substrates to oxygen, via carriers such as components of the respiratory chain

cytochromes

heme proteins that functions as electron carriers in respiration, photosynthesis and other oxidation - reduction reactions

proton pump

proton pumps are integral membrane proteins capable of moving protons across the membrane of a cell, mitochondrion, or other sub-cellular compartment

iron-sulfur proteins

non-heme iron proteins that participate in electron transfer reactions

ATP synthase

an enzyme complex that forms ATP from ADP and phosphate during oxidative phosphorylation in the inner mitochondria membrane, and during phosphorylation in chloroplast

uncouplers

also called uncoupling agents


substances tha uncouple phosphorylatin of ADP from electron transfer,


ex; 2,4 dinitrophenol

free radicals

molecules with an unpaired electron; most of them are highly reactive

the brain alone consumes ____ of glucose

120 grams of glucose per day

what blood glucose level must be maintained at all times

4-5.5 mmol/liter

only ____ glycogen can be used to maintain the blood glucose level

liver

gluconeogenesis produces

glucose from amino acids, lactic acid, and glycerol



it is the only source of glucose during prolonged fasting

only the liver and kidneys have a ..

complete gluconeogenic pathway

liver produces ___ times more glucose than kidney, because...

10 x


bc the liver is this much larger than the kidney

where is glucose stored

in the liver and muscle, in the form of glycogen

where does gluconeogenesis occur

primarily in the cytosol, although some precursors are generated in the mitochondria

glucose is a universal

fuel and building block in humans, some tissues depend almost completely on glucose for their metabolic energy

what is the major gluconeogenic organ of the body

LIVER

does muscle contribute to gluconeogenesis

muscle does NOT contribute, because it has no glucose-6-phospatase and no glucagon receptors

gluconeogenesis

synthesis of carbohydrate from non carbohydrates such as oxaloacetate or pyruvate

gluconeogenesis and glycolysis run in

oposite directions

3 reactions of glycolysis are irreversible and cannot be used in gluconeogenesis:

1. conversion of glucose to glucose 6 phosphate (hexokinase/glucokinase)



2. phosphorylation of fructose 6 phosphate to fructose 1,6 bisphosphate (PFK-1)



3. Conversion of PEP to pyruvate (pyruvate kinase)

3 reactions bypassing irreversible reactions of glycolysis in gluconeogenesis

1) bypass from pyruvate to PEP. Pyruvate is carboxylated to oxaloacetate by pyruvate carboxylase.


2) the PFK rxn is bypassed by fructose 1,6 bisphosphate which hydrolyzes the phosphate from carbon 1


3) hexokinase reaction is bypassed by glucose 6 phosphate

where is glucose 6 phosphate

located in the ER and present only i the liver.

glucose

is an important metabolic substrate for most tissues, and is required fuel for brain and RBCs. normal blood glucose level: 70 to 100 mg/dL

in the fasting state, the liver...

has to produce glucose by gluconeogenesis and glycogen degradation

for each molecule of glucose formed by pyruvate, ___ high-energy phosphate groups are required, ___ from ATP and ___ from GTP

6


4


2

___ molecules of NADH is required for the reduction of 2 molecules of 1,3 bisphosphoglycerate to glyceraldehyde 3 phosphate

2

gluconeogenic substrates

glucogenic amino acids - all except leucine and lysine



lactate - cori cycle



glycerol



all TCA intermediates except Acetyl CoA

Acetyl CoA cannot be converted to glucose, because

the PDH reaction is irreversible

gluconeogenesis depends on

amino acids, lactate, and glycerol

fatty acids that are released from adipose tissue during fasting cannot

be turned into glucose

most important substrates of gluconeogenesis

lactate and alanine bc they are readily converted to pyruvate by lactate dehydrogenase and by transamination

cori cycle

shuttling of glucose and lactate between muscle/ RBC and liver during physical exercise

after vigorous exercise, lactate produced by anaerobic glycolysis returns to

the liver and is converted to glucose, which moves back to muscle and is converted to glycogen (core cycle)

regulation of gluconeogenesis

insulin and glucagon


epinephrine and norepinephrine


glucocorticoids


pyruvate kinase


phosphofructokinase and fructose 1,6 bisphosphate

insulin

released from pancreatic Beta cells in response to hyperglycemia



insulin lower blood glucose level



insulin is needed to convert sugar, starches, and other food into glucose or regulates storage of glycogen in the liver and accelerates oxidation of sugar in cells

glucagon

a polypeptide hormone from the alpha cells of the pancreas that stimulates the glucose producing pathways of the liver. it is released in response to hyperglycemia



glucagon raises blood glucose level

the release of glucagon and insulin is inhibited by

somatostatin that is secreted by the pan created delta cells

epinephrine and norepinephrine

stress hormones that released during physical exertion and cold exposure. in the liver, they promote gluconeogenesis over glycolysis by inducing cAMP

glucocorticoids

also stress hormones that affect gene transcription.


stimulate gluconeogenesis by inducing gluconeogenic enzymes

pyruvate kinase

the most important regulated enzyme in the PEP-pyruvate cycle. it is inhibited by ATP and activated by fructose 1,6 bisphosphate

phosphofructokinase and fructose 1,6 bisphosphatase

in the liver are oppositely regulated. ATP and citrate stimulate fructose 1,6 bisphosphatase but inhibit phosphofructokinase

glucose-phosphorylating enzymes in the liver are:

hexokinase and glucokinase

fructose 2,6 bisphosphate

the most potent modulator of phosphofructokinase and fructose 1,6 bisphosphatase

fatty acid oxidation is less controlled by _______ _______ than is glucose oxidation

feedback inhibition



therefore, levels of ATP and acetyl CoA in the liver are actually elevated during fasting

fatty acid oxidation provides the necessary energy required by

gluconeogenesis

feedback inhibition

inhibition of a metabolic pathway by its end product

fatty acid oxidation

the burning of stored fat

gluconeogenesis is inhibited by:


and stimulated by:

inhibited by fructose 2,6 bisphospate



stimulated by acetyl CoA

liver consumes _____ to maintain _____

glucose to maintain blood glucose level

muscle consumes

glucose for energy production

lactate is transported from muscle to...

liver for the re-synthesis of glucose in the Cori cycle

glycolysis

conversion of glucose to pyruvate

gluconeogenesis

conversation of 2 molecules of pyruvate to one molecule of glucose

glycogenesis

synthesis of glycogen

glycogenolysis

breakdown of stored glycogen