biochemistry review booklet 1

7/25/2019 Biochemistry Review Booklet 1

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Biochemistry Reviewer

I. Carbohydrate Structure

Biomedical Importance of Carbohydrates:

1. Structural functional component of cell structures

2. Metabolicdietary carbohydrates mostly absorb is Glucose.

The liver converts other carbohydrates to Glucose

Glucose is a major source of energy (metabolic fuel) and the precursor in the synthesis of

all other CHO ex. Glycogen, Lactose and components of Glycolipids. Glycoproteins,

Proteoglycans

3. Diseases involving carbohydrate metabolismDiabetes mellitus, Galactosemia, Glycogen

Storage Diseases, Lactose intolerance

Structure of Carbohydrates

1. Simple

a. Monosaccharidesex. Six carbon sugars glucose, Galactose, Mannose

Classification based on number of carbons

Triose 3 carbons ex. Glyceraldehyde

Tetrose 4 carbons ex. Erythrose

Pentose5 carbons ex. Ribose

Hexose 6 carbons ex. Glucose

Classification based on functional groups

AldoseGlycerose, Erythrose, Ribose, Glucose

Ketosedihydroxy acetone, Erythrulose, Ribulose, Fructose

b. Dissacharidessucrose, lactose, maltose

2. Complex

a. Oligossacharidescondensation products of 310 monosaccharides.

b. Polyssacharidescondensation products of more than 10 monossacharides. May be

linear or branched chains. Ex. Glycogen (storage form of glucose in animals):

mostly found in liver and muscle

same structure as amylopectin, but with more branches (11 units)

provides efficient storage of glucose and prevents high osmotic pressure in cells


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one glycogen molecule may contain 1,000,000 glucose molecules but only counts as 1

particle for osmosisbest way to store glucose without affecting significantly osmotic

intracellular properties

Hexosanspolyssacharides made up of 6 carbon monossacharides

Pentosanspolyssacharides made up of 5 carbon monossacharides

Isomerssame structural formula different configuration (Glucose with 4 asymmetric carbons can

form 16 isomers

Epimersisomers differing as a result of variations in configuration of the OH and H atoms at only

one asymmetric carbon ex. Glucose and Galactose at the 4thcarbon, Glucose and Mannose at

the 2ndcarbon.

Enantiomers a pair of stereoisomers that are non-superimposable mirror images of each other

Asymmetric (chiral) carbon centers = must have a carbon atom connected to 4 different

atoms or groups of atoms bonded in a tetrahedral structure

Type of monosaccharide is based on alcohol (OH) group bonded to only or last asymmetric

carbon atom (adjacent to last alcohol carbon) D = right and L = left (mirror images)

Biomedical and clinical importance of monosaccharide:

1. Glyceraldehyde and dihydroxyacetoneimportant intermediates in glycolysis; branching points

in metabolism

2. Ribose and 2-deoxyribose are important in RNA, DNA, and nucleotide (ATP) structures. Ribose in

RNA is synthesized via the Pentose Phosphate Pathway and the deoxyribose is produced fromribonucleotide diphosphates by ribonucleotide reductase. Structural component of coenzymes,

including ATP, NAD(P), and flavin coenzymes.

3. Glucose (hexose or blood sugar) (D(+)) important in cellular energy production. Derangement in

the metabolism of glucose is the main issue in Diabetes mellitus.

4. Galactose (D(+)readily metabolized to Glucose. Precursor for the synthesis of lactose and

important in glycoproteins and lipids that are involved with nerve and brain function. Hereditary

galactosemia as a result of failure to metabolize galactose leads to cataracts

5. Fructose (laevulose or fruit sugar) is extremely sweet. Has fewer calories per gram than other

sugar. Hereditary fructose intolerance leads to fructose accumulation and hypoglycemia

Amino Sugars

D-glucosamineconstituent of hyaluronic acid

D-galactosamine(Chondrosamine) constituent of chondroitin important component of the

extracellular matrix.


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Acidic sugars

Oxidation will result to gain of oxygen and loss of Hydrogen (electrons) Oxidation of glucose (6th

carbon OH is oxidized COO- forming Glucoronic Acid). This is important in the

biosynthesis of GAG.

II. Carbohydrate Metabolism

Glucose Metabolism

Metabolic Fates of Glucose

1. Glycolysis and Citric Acid Cycle

2. Synthesis of glycogen for storage in animals

3. Synthesis of Ribose as important component for the synthesis of RNA

4. Conversion to other biological substancesex. Galactose for the synthesis of Lactose

5. Acidification as in Uronic acid pathwayconversion of glucose to glucorunic acid important inthe biosynthesis of GAG

A. Glycolysis

- occurs in the cytosol

- major pathway for glucose metabolism

- aerobic or anaerobicin aerobic metabolism, pyruvate is oxidized by pyruvate

dehydrogenase to produce acetyl CoA that enters the Krebs Cycle; in anaerobic,

pyruvate is reduced to lactate by lactate dehydrogenase and is shuttled to the liver for

gluconeogenesis.

- end product is pyruvate

- three regulatory steps are involved (rate limiting steps) catalyzed by the following

enzymes:

1). HexokinasePhosphorylate Glucose intracellularly. (Hexokinase is

nonspecific with high affinity and low Km for glucose) Glucokinase is an isozyme of

hexokinase with low affinity and high Km for glucose found in the liver and pancreas.

Phosphorylation of glucose is irreversible.

allosterically inhibited by its product (Glucose-6-Phosphate)

2). Phosphofructokinase 1Phosphorylate fructose-1-phosphate at C6 to

produce Fructose 1,6 bisphosphate. Reaction is irreversible under physiologic condition.

Has a major role in regulating glycolysis


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Allosterically regulated by:

Fructose 2,6 bisphosphate (strong activator)

5AMP (activator)

ATP (inhibitor)

3). Pyruvate kinasetransfers the phosphate of phosphoenolpyruvate to ADP

to form ATP. The reaction is irreversible under physiologic condition.

Cells (hepatocytes) capable of gluconeogenesis have different enzymes in the 3

regulatory steps to reverse glycolysis.

B. Tricarboxylic Acid Cycle (TCA, Citric Acid Cycle, Krebs Cycle)

- Occurs in the mitochondria

- Oxidize the acetate of acetyl CoA

- Reduce the coenzymes NAD, FAD to be used as electron carriers to the Electron

Transport Chain for ATP synthesis. 3 NADH + H and 1 FADH2are produced per turn of

the cycle. One ATP is produced by substrate level phosphorylation per turn of the cycle

- Common final pathway for the oxidation of

o glucose (acetyl CoA produced from the oxidation of the final product of

glycolysis which is Pyruvate),

o fatty acids (acetyl CoA produced in beta oxidation) and

o amino acids (acetyl CoA from pyruvate the degradation product of glucogenic

amino acids and acetyl CoA the degradation product of ketogenic amino acids).

- It has central roles in Gluconeogenesis, Lipogenesis, Amino acid synthesis. It has

anaplerotic reactionsit provides substrates for other reactions/pathways like

gluconeogenesis (Phosphoenolpyruvate decarboxylase forms Pyruvate from

decarboxylation of oxaloacetate). When concentration of acetyl CoA is high, it inhibits

Pyruvate dehydrogenase and activates Pyruvate carboxylase. Increase activity of

Pyruvate carboxylase increases the concentration of oxaloacetate.

o GluconeogenesisTCA cycle provides substrates for gluconeogenesis ex.

Oxaloacetate converted to Phosphenolpyruvate by Phosphoenolpyruvate

decarboxylase


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o Fatty acid synthesisacetyl CoA a substrate of TCA cycle is a precursor for fatty

acid synthesis. Pyruvate dehydrogenase is a mitochondrial enzyme thus acetyl

CoA is formed in the mitochondria. Fatty acid synthesis occurs in the cytosol so

the acetyl CoA formed in the mitochondria should be available in the cytosol.

Acetyl CoA is provided for fatty acid synthesis when citrate (a product produced

from the condensation of axaloacetate and acetyl CoA) is transported to the

cytosol. In the cytosol citrate is cleaved to acetyl CoA and Oxaloacetate by ATP-

citrate lyase. Citrate is transported out of the inner mitochondrial membrane

when aconitase is saturated with acetyl CoA.

o Amino acid synthesis-ketoglutarate a substrate of TCA cycle is a keto acid of

glutamate, oxaloacetate a ketoacid of aspartate. The ketoacid is converted to

an amino acid by transamination and back by deamination.- TCA has functions of both oxidative (degradative) and synthetic processes thus, it is

amphibolic.

- Aconitase isomerizes citrate to isocitrate is inhibited by Fluoroacetate causing

accumulation of citrate.

- -ketoglutarate dehydrogenase complex converts -ketoglurate to succinyl CoA. It has

the same cofactors with that of Pyruvate dehydrogenase which are thiamine

diphosphates, lipoate, NAD+, FAD, and CoA. It is inhibited by Arsenite causing

accumulation of -ketoglutarate.

- The reaction catalyzed by succinate thiokinase (synthetase) is the only reaction in TCA

that has phosphate level phosphorylation. It has 2 isozymes in gluconeogenic and non-

gluconeogenic tissues:

o Gluconeogenic tissues (liver and kidney)has to isozymes, one is specific with

GDP and the other is ADP. The GTP formed is used in the decarboxylation of

oxaloacetate (phosphoenolpyruvate carboxykinase) to phosphoenolpyruvate. It

provides a regulatory link between citric acid cycle activity and the withdrawal

of oxaloacetate for gluconeogenesis.

o Non-gluconeogenic tissuesthe isozyme is specific for ADP

- Malate dehydrogenase produces oxaloacetate and NADH from malate. Oxaloacetate is

consumed by:

o Coupling with acetyl CoA to form citrate


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o Decarboxylation to form phosphoenolpyruvate

o Transamination to aspartate

- Ten ATPs are formed per turn of the cycle (3 NADH ~2.5 ATPs , 1 FADH2 ~ 1.5 ATPs, 1

ATP in substrate level phosphorylation)

- Vitamins that play a role in TCA:

o (1)riboflavin,in the form of flavin adenine dinucleotide (FAD), a cofactor for

succinate dehydrogenase;

o (2) niacin,in the form of nicotinamide adenine dinucleotide (NAD), the electron

acceptor for isocitrate dehydrogenase, -ketoglutarate dehydrogenase, and

malate dehydrogenase;

o (3) thiamin (vitamin B1),as thiamin diphosphates, the coenzyme for

decarboxylation in the -ketoglutarate dehydrogenase reaction; ando (4) pantothenic acid,as part of coenzyme A, the cofactor attached to "active"

carboxylic acid residues such as acetyl-CoA and succinyl-CoA.

- Regulation of TCA is dependent on the:

o availability of NAD that is dependent on the concentration of ADP (due to tight

coupling of oxidation and phosphorylation.

o rate of utilization of ATP

o enzymes of the cycleSites of regulation are the nonequilibrium reactions

catalyzed by; Pyruvate dehydrogenase, citrate synthase, isocitrate

dehydrogenase, and -ketoglutarate dehydrogenase.

Dehydrogenases are activated by calciumCalcium concentration

increase during muscle contraction requiring energy

In the brain the control is in pyruvated dehydrogenase. The brain is

largely dependent glucose to supply acetyl CoA

Some enzymes are regulated by the energy status; [ATP]/[ADP] and

[NADH]/[NAD+] ratios

allosteric inhibition of citrate synthase by ATP and long-chain

fatty acyl-CoA

Allosteric activation of mitochondrial NAD-dependent isocitrate

dehydrogenase by ADP is counteracted by ATP and NADH


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-ketoglutarate dehydrogenase complex is regulated in the same way as

is pyruvate dehydrogenase

Succinate dehydrogenase is inhibited by oxaloacetate, and the

availability of oxaloacetate, as controlled by malate dehydrogenase,

depends on the [NADH]/[NAD+] ratio

the Kmfor oxaloacetate of citrate synthase is of the same order of

magnitude as the intramitochondrial concentration, it is likely that the

concentration of oxaloacetate controls the rate of citrate formation

C. Glycogen metabolism

- Glycogen is the major carbohydrate storage in man

- Liver contains higher glycogen content by weight, however total glycogen is of thetotal glycogen is in muscles (muscle mass is greater than that of the liver).

o Liver (from glycogen or gluconeogenesis) exports glucose to maintain blood

glucose level, provides glucose for the other tissues of the body,

o Muscle glycogen provides fuel for ATP synthesis. Muscle lacks glucose-6-

phosphatase so it cant produce glucose from glucose 6 phosphate a product of

the isomerization of Glucose-1-phosphate (G1P) from glycogenolysis.

1. Glycogenesis

- Occurs mainly in the liver and muscle

- One of the pathways in glucose metabolism that utilize glucose 6 phosphate (G6P). G6P

is isomerized to G1P by phosphoglucomutase the starting substrate for glycogenesis.

- Uridine diphosphates glucose phosphorylase catalyszes the reaction of G1P and uridine

triphosphate (UTP) to uridine diphosphate glucose (UDPGlc) theactive nucleotide and

pyrophosphate.

- UDPGlc is the substrate of glycogen synthase which catalyzes the formation of a

glycoside bond between C-1 of the glucose of UDPGlc and C-4 of a terminal glucose

residue of glycogen. It is the source of glucose in the glycosylation of a tyrosine residue

of glycogenin.

o In the muscle the glycogenin remains attached in the center of the glycogen

molecule


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o In the liver the number of glycogen molecules is more than the number of

glycogenin molecules

- Synthesis of glycogen requires a primer called glycogenin

- When an elongated chain of glucose reaches about 11 moieties, a branching enzyme

promotes the transfer of a part of the chain (at least 6 moieties of glucose) to a

neighboring chain to form a 1-6 linkage.

2. Glycogenolysis

- Degradation of glycogen to yield G1P the isomerized to G6P (in the liver G6P is

dephosphorylated by glucose 6 phosphatase releasing glucose to the circulation; in

the muscle G6P is metabolized in glycolysis).

- Glycogen phosphorylasecatalyzes the the phosphoroylytic cleavage

(phosphorolysis; of hydrolysis) of the 1- 4 linkages of glycogen to yield glucose 1-phosphaterate-limiting step in glycogenolysis

- glucan transferasetransfers a trisaccharide unit from one branch to the other,

exposing the 1-6 branch point for the debranching enzme to act. The glucan

transferase and the debranching enzme is a characteristic of one complex enzyme.

- Glucose 6 Phosphatase (deficiency can cause Von Gierkes disease)is in the lumen

of the smooth endoplasmic reticulum. Genetic defects involving Glucose 6

Phosphate transporterscan cause a variant of type I glycogen storage disease.

- Regulation of Glycogenolysis and Glycogenesis is integrated by cAMP. Cyclic AMP

activates adenyl cyclase that will activate cAMP dependent protein kinase which will

in turn phosphorylate proteins. One of the proteins phosphorylated is glycogen

phosphorylase b converting it to glycogen phosphorylase a, an active phosphorylase

that will favor glycogenolysis. Another protein that is phosphorylated (enzyme) is

the glycogen synthase (phosphorylation of glycogen synthase promotes the b

conformation) resulting to inactivation of the enzyme thus will favor glycogenolysis

instead of glycogenesis.

In-born error of glycogen metabolism:

- Genetic defect in the isoform of glycogen synthase will have the following

manifestations;

Post prandial state (after eating a carbohydrate meal)it will cause

high blood glucose, lactate and fatty acids. Excess glucose absorb in the


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gut cannot be utilized for glycogenesis. It will be converted to lactate

(product of reduction of Pyruvate) and fatty acids (acetyl CoA produced

from oxidation of Pyruvate).

Fasting statemanifestations include hypoglycemia (no available

stored glycogen in the liver to supply the circulation with glucose),

increased ketone bodies (an alternative fuel when blood glucose is low

produced during Beta oxidation). Beta oxidation produces acetyl CoA

which is a precursor for the synthesis of ketone bodies. Three enzymes

are responsible for ketone bodies formation; b Ketothiolase, HMG CoA

synthase, HMC CoA lyase.

- Glycogen Storage Disease (Ex. Von Gierkes disease)genetic enzyme deficiencies

leading to accumulation of glycogen intracellularly with the following manifestations; Hypoglycemia - liver enzymes Glycogen 6 phosphatase is defective

Weaknessmuscle enzymes for glycogenolysis is defective (decrease

utilization of glycogen during exercise or during physical activity)

Manifestations may also be dependent on the enzyme that is defective.

D. Pentose Phosphate Pathway or Hexose Monophosphate Shunt (HMS)

- Two major functions

(1) formation of NADPHfor synthesis of fatty acids and steroids, and

(2) synthesis of ribose(from ribose 5-phosphate) for nucleotide and nucleic acid

formation.

- Glucose 6 phosphate is the substrate of the first enzyme (glucose 6 phosphate

dehydrogenase or G6PD) in the Pentose Phosphate Pathway

- G6PD deficiencya genetic deficiency is a major cause of RBC hemolysis resulting to

anemia

- Reaction occurs in the cytosol

- Dehydrogenation reaction catalyzed by G6PD and 6-Phosphogluconate dehydrogenases

utilizes NADP as hydrogen acceptor.

- The first phase (oxidative nonreversible phase) of the pathway reactions involve

dehydrogenation and decarboxylation to yield a pentose (ribulose 5 phosphate and

ribose 5 phosphate)


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- The 2ndphase (non-oxidative reversible phase) involves two enzymes, transketolaseand

transaldolase that convert ribulose 5-phosphate back to glucose 6-phosphate by series

of reactions

III. Lipid Metabolism

A. Fatty Acid Oxidation

- Fatty acids are oxidized to Acetyl CoA and generates ATP

- An aerobic process (requires Oxygen)

- Occurs in the mitochondria

- Each step in the oxidation process involves an acyl CoA derivative, a separate

enzyme, coenzymes NAD & FAD

- Increased fatty acid oxidation leading to ketone body formation by the liver is a

characteristic of starvation and Diabetes mellitus- Free fatty acids are transported in the blood (long fatty acids bind with albumin and

short fatty acids are more water-soluble and exist in the unionized form or as an

anion

- Oxidation of fatty acids require initially ATP and Coenzyme A for the activation of

the fatty acid catalyzed by Acyl-CoA synthetase(thiokinase)

- Free Fatty Acids (FFA) cannot penetrate the inner mitochondrial membrane so it has

to undergo the following transformations;

o Fatty acid converted to an active intermediate Acyl CoA

(FFA + ATP + CoA= Acyl CoA)

Acyl CoAdiffuses through the outer mitochondrial membrane

Acyl CoA condenses with carnitine to produce Acylcarnitine + CoA by carnitine

palmitoyl-tranferase 1

Acylcarnitineis transported across the inner mitochondrial membrane by

carnitine acylcarnitine translocase

Acylcarnitine is converted back to carnitine+ Acyl CoA by carnitine palmitoyl-

tranferase 1

- Acyl CoA is oxidized producing acetyl CoA (2 carbons is cleaved from the acyl CoA at

a time). The chain is broken between the alpha and the beta bond (beta oxidation).

Fatty acids with an even number of carbon atoms produce acetyl CoA. Those with

odd number carbon atoms produce acetyl CoA and Propionyl CoA. Propionyl CoA is


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the glucogenic substrate derived from oxidation of odd numbered carbon fatty

acids.

- Enzymes that catalyze the reactions and their coenzymes in Beta oxidation

1. Acyl Co A SynthetaseCoA, ATP, Mg

2. Acyl CoA dehydrogenaseFAD

3. delta2-enoyl-CoA hydratase

4. L-(+)-3-hydroxyacyl-CoA dehydrogenaseNAD

5. ThiolaseCoA

Reactions 2-5 are repeated until completion of the oxidation process

- Palmitate with 16 carbons will yield 8 acetyl CoA requiring 7 rounds of the Beta

oxidation cycle

o

4 mol of ATP is produced /cycle x 7 cycles = 28 mol ATPo 10 mol of ATP/ TCA cycle x 8 cycles = 80

o 28 + 80 = 1082 ATP (ATP used in the activation of the fatty acid in the first

reaction) = 106 mol of net ATP produced by 1 mol of palmitate.

NADH + H = 2.5 ATP; FADH2 = 1.5 ATP

- Peroxisomes oxidize very long chain fatty acids and produce acetyl CoA and

Hydrogen peroxide (broken down by catalase). Dehydrogenation (NADH, FADH

produced) is not linked directly to phosphorylation (ATP production).

- Oxidation of unsaturated fatty acids is modified. Same enzymes are utilized as in

saturated fatty acids except in that some enzymes are used like isomerases and

reductases.

B. Ketogenesis

- Occurs in conditions causing high rate oxidation of fatty acids (ex. Uncontrolled

diabetes mellitus, starvation. Ketone bodies in normal well-fed mammals do not

exceed 0.2 mmol/L.

- acetone bodies are acetoacetate, -hydroxybutyrate, acetone(acetone is produced

due to the spontaneous decarboxylation of acetoacetate)

- acetoacetate and -hydroxybutyrate are inter-converted by a mitochondrial

enzyme, D()-3-hydroxybutyrate dehydrogenase (conversion is controlled by the

ratio of mitochondrial NAD/NADH)

- the process of ketogenesis is as follows;


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o Two (2) acetyl CoA condenses (catalyzed by thiolase) to form acetoacetyl CoA.

The reaction is reversible.

o Acetoacetyl CoA condenses with acetyl CoA (by HMG CoA synthase) to form

HMG CoA

o HMG CoA is split into Acetyl CoA and acetoacetateby HMG CoA lyase

o Acetoacetate is reduced (utilizing NADH) to 3-hydroxybutyrate: 3-

hydroxybutyrate is oxidized (using NAD) to acetoacetate. Both reactions are

catalyzed by 3-hydroxybutyrate dehydrogenase

o Acetoacetyl CoA and 3Bhydroxybutyrate is readily oxidized by extrahepatic

tissues, acetone is not (volatile)

o Increased production of ketone bodies results to ketonemia. Determination of

ketonemia is preferably done by determining ketone bodies in the blood ratherthan in the urine. Renal threshold-like effects for excreting ketone bodies vary

from individuals.

o Regulation of ketogenesis

1. Factors that regulate mobilization of fatty acids from adipose tissue (Fatty

acids are precursors of ketone bodies in the liver. The liver extracts 30% of

the fatty acids that pass through it).

2. CPT I activity(found in the outer mitochondrial membrane) catalyze the

condensation of Acyl CoA and carnitine

a. in the fed state, CPT I activity is low thus reducing -oxidation

(Malonyl-CoA,the initial intermediate in fatty acid biosynthesis

formed by acetyl-CoA carboxylase in the fed state, is a potent

inhibitor of CPT-I)

b. during starvation, the CPT I activity is increased (when

concentration of free fatty acids increases with the onset of

starvation, acetyl-CoA carboxylase is inhibited directly by acyl-CoA,

and [malonyl-CoA] decreases, releasing the inhibition of CPT-I and

allowing more acyl-CoA to be -oxidized

3. Acetyl CoA produced by -oxidation may either be oxidized in the TCA or is

utilized to form ketone bodies. The partition of acetyl-CoA between the

ketogenic pathway and the pathway of oxidation to CO2is regulated so that


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the total free energy captured in ATP which results from the oxidation of

free fatty acids remains constant as their concentration in the serum

changes. This may be appreciated when it is realized that complete

oxidation of 1 mol of Palmitate involves a net production of 106 mol of ATP

via -oxidation and CO2production in the citric acid cycle (see above),

whereas only 26 mol of ATP are produced when acetoacetate is the end

product and only 21 mol when 3-hydroxybutyrate is the end product. Thus,

ketogenesis may be regarded as a mechanism that allows the liver to oxidize

increasing quantities of fatty acids within the constraints of a tightly coupled

system of oxidative phosphorylation.

a. Fall in Oxaloacetate can be caused byincreased NADH/NAD ratio

due to -oxidation of fatty acidsb. Decreased NAD will reduce the activity of Malate dehydrogenase

(NAD is a coenzyme) thus lowering Oxaloacetate.

c. Oxaloacetate is needed in the oxidation of acetyl CoAoxidation of

acetyl CoA in the TCA will decrease with low Oxaloacetate

d. Pyruvate carboxylase is activated by increased levels of acetyl CoA

which in turn increases Oxaloacetate for gluconeogenesis (a

condition that occurs in starvation and uncontrolled Diabetes

mellitus).

o Clinical Importance of fatty acid oxidation:

Carnitine deficiencymay be due to:

a. impaired biosynthesis or increased renal clearance in the newborn

especially in premature infants.

b. loss of carnitine through hemodialysis

Symptoms of deficiency include hypoglycemia, which is a consequence of

impaired fatty acid oxidation and lipid accumulation with muscular weakness.

Treatment is by oral supplementation with carnitine.


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1. Inherited CPT-I deficiency - affects only the liver; cause reduced fatty acid

oxidation and ketogenesis (because fatty acid will not be available in the

mitochondria for -oxidation), with hypoglycemia.

2. CPT-II deficiencyacylcarnitine that was transported by the carnitine

acylcarnitine translocase to the mitochondrial matrix will not be converted

back to carnitine and acyl- CoA (precursor of -oxidation). It affects

primarily skeletal muscle and in severe cases the liver.

Treatment is by usingsulfonylurea drugs (glyburide [glibenclamide] and

tolbutamide) which willreduce fatty acid oxidation and, therefore,

hyperglycemia by inhibiting CPT-I.

3. Inherited defects in the enzymes of -oxidation and ketogenesis also lead to

nonketotic hypoglycemia, coma, and fatty liver. Defects are known in long-and short-chain 3-hydroxyacyl-CoA dehydrogenase (deficiency of the long-

chain en-zyme may be a cause of acute fatty liver of pregnancy). 3-

Ketoacyl-CoA thiolaseand HMG-CoA lyase deficiencyalso affect the

degradation of leucine, a ketogenic amino acid

4. Jamaican vomiting sicknessis caused by ingesting the toxin hypoglycin

(from the unripe fruit of the akee tree) toxin. This inactivates medium- and

short-chain acyl-CoA dehydrogenase, inhibiting -oxidation and causing

hypoglycemia.

5. Dicarboxylic aciduriais characterized by the excretion of C6C10-

dicarboxylic acids and by nonketotic hypoglycemia, and is caused by a lack

of mitochondrial medium-chain acyl-CoA dehydrogenase.

6. Refsum's diseaseis a rare neurologic disorder due to a metabolic defect

that results in the accumulation of phytanic acid, which is found in dairy

products and ruminant fat and meat. Phytanic acid is thought to have

pathological effects on membrane function, protein prenylation, and gene

expres-sion.

7. Zellweger's (cerebrohepatorenal) syndromeoccurs in individuals with a

rare inherited absence of per-oxisomes in all tissues. They accumulate C26

C38polyenoic acids in brain tissue and also exhibit a generalized loss of


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b. It is transported into the cytosol as citrate(product of

condensation of acetyl CoA and Oxaloacetate) by a tricarboxylic

transporter. Citrate in the cytosol is cleaved back to acetyl Co A

and Oxaloacetate in the presence of CoA and ATP by ATP-

Citrate lyase (activity is increased in the well-fed state). Acetyl

CoA will be available for lipogenesis.

7. Oxaloacetate in the cytosol is reduced (using NADH as cofactor) to malate

by cytoplasmic malate dehydrogenase (sMDH-soluble malate

dehydrogenase).

a. Malate is transported inside the mitochondrion by tricarboxylic

transporter.

b. Malate is oxidized to Oxaloacetate (using NAD as cofactor) bymalate dehydrogenase (mMDH - mitochondrial MDH).

Oxaloacetate is replenished in the mitochondria as substrate for

TCA cycle.

c. Malate can also be oxidized (NADP as cofactor) by malic enzyme

resulting to decarboxylation. This will produce CO2, Pyruvate

and NADPH.

8. Fatty acid synthesis is catalyzed by a homodimer complex enzymefatty acid

synthase.

9. Each polypeptide monomer contains 7 enzymes and an acyl carrier protein

(ACL). Each monomer can synthesize a fatty acid, thus one enzyme complex

can produce two fatty acids simultaneously.

10.Elongation of fatty acid synthesis occurs in endoplasmic reticulum catalyzed

by the enzyme fatty acid elongase. Malonyl CoAis the acetyl donor utilizing

NADPH as the reductant.

11.Malonyl CoAis formed from Carboxylation of Acetyl CoA by acetyl CoA

carboxylase. This is the most important reaction in the regulation of fatty

acid synthesis.

12.Nutritional stateregulates lipogenesis

13.Excess glucose(after a fed state) and its derivatives are converted to fatty

acids. The rate of lipogenesis is high in the fed state.


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14. In state of starvation(caloric deficiency), fatty acids are utilized to supply

acetyl CoA for energy (ATP) production. The rate of synthesis is low in

restricted caloric intake, high-fat diet, or a deficiency of insulin (in DM).

15.Short term regulation of long-chain fatty acid synthesis is due to allosteric

and covalent modification

16.Long term regulation is due to changes in gene expression of enzymes

involved

17.Regulation of Acetyl CoA carboxylase

a. allosterically activated by Citrateand by long chain acyl

molecules (negative feedback);

Long chain acyl molecules may accumulate due to

1) Increased lipogenesiswill cause accumulation of long acylmolecules due to decrease in the esterification of fatty acid

synthesized.

2) Increased lipolysis (breakdown of esterified FA)results to

increase in the production of fatty acids or its influx into the cell

b. covalently activated by dephosphorylationand inactivated by

phosphorylation

1) insulin triggers dephosphorylationacetyl carboxylase

is active in the dephosphorylated form. Also Inhibits

lipolysis and is important in gene expression and is

antagonized by glucacon.

a) Insulin also increases glucose uptake thus increasing

glycolysis. Glycolysis produces Glycerol-3-phosphate

and Pyruvate.

b) Glycerol-3-phosphateused substrate for esterification

of fatty acids

c) Pyruvateis the precursor for acetyl CoA

2) glucagon triggers phosphorylationacetyl carboxylase

is inactive in the phosphorylated form


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3) epinephrine inactivates acetyl CoA carboxylase with

mechanism similar to the inactivation caused by

glucagon

18.some polyunsaturated fatty acidsare nutritionally essentials like

Linoleic and -linolenic acids. Arachidonic acids are formed from

Linoleic FA.

a. Double bonds cannot be introduced beyond 9 position. Plants

can produce nutritionally essential fatty acids by their capability

to introduce double bonds at 12 and 15 positions.

b. The liver and some tissues can produce monounsaturated FA

from saturated FA by introducing (mostly) double bonds at 9

position by a

9

desaturase.19.Essential fatty acids are required for the formation of prostaglandin,

thromboxane, leukotriene, and lipoxin

a. Deficiency of essential FA acids can have decreased growth

rates and reproductive deficiency in rats

o Patients with retinitis pigmentosaare reported to have low blood

levels of DHA (Docosahexaenoic acid (DHA; 3, 22:6), which is

synthesized to a limited extent from -linolenic acid or obtained

directly from fish oils, is present in high concentrations in retina,

cerebral cortex, testis, and sperm. DHA is particularly needed for

development of the brain and retina and is supplied via the placenta

and milk.

20.Trans Fatty Acids

a. Small amounts of trans-unsaturated fatty acids are found in

ruminant fat (eg, butter fat has 27%),

b. The main source is in the human diet from partially

hydrogenated vegetable oils (eg, margarine).

c. Trans fatty acids compete with essential fatty acids and may

exacerbate essential fatty acid deficiency.


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2015 REVIEWER

Enzymes, Water & Iron

1. Lysosomes- Referred to as suicide bags of the cell, containing a variety of hydrolytic anddegradative enzyme

2. High specific heat - The ability of water to absorb and store a large amount of heat3. Nucleus - The most prominent feature of the eukaryotic cell, serving as its

information center

4. Water as hydrophilic colloid system maintains body temperature for its main function5. Iron in the body is absorbed in the ileum.6. Transferrin is the glycoprotein involved in the transport or iron.

7. Ferritin is the major protein involved n the storage or iron.8. Lactoferrin is the Iron that has anti-microbial effects thus can protect the newborn9. Low ph is necessary in the absorption of iron10. Protein digestion starts in the stomach where the acidic environment favors denaturation.11. Excess NH4 from the breakdown of amino acids are converted into urea and excreted

12. Five carbon amino acids enter the citric acid cycle as Ketoglutarate13. Example of a non-competitive inhibition - lead combines with the sulfhydryl group of enzymes.14. Apoprotein is the protein, heat labile, non dialyzable portion a complex enzyme system.15. Activity of enzymes is expressed in terms of velocity.16. In an enzyme-substrate reaction, a large Km means a low affinity of enzyme for the substrate17. Vitamin C as co-enzyme can act alternately as an oxidizing and reducing agent18. The enzyme Lyase can bring about the cleavage of C-C, C-O, and C-N bonds in a substrate.

19. Km and Vmax are the two constants that are always measured whenever enzymes arecharacterized.

20. Lyases are enzymes that catalyze the addition or removal of water, ammonia or carbon dioxide todouble bonds.

21. Alkaline phosphataseis the nonfunctional serum enzyme that is diagnostic of obstructive liverdiseases

22. Carbonic anhydraserequires zinc as cofactor.23. ALA dehydrataseis a zinc containing enzyme that is sensitive to the inhibition of lead.24. Cyclooxygenase (COX1 and COX2) or Prostaglandin H synthaseis inhibited by NSAIDS (ex.

Aspirin). COX2 is selectively inhibited by coxibs (ex. Celecoxib).25. Anti-inflammatory corticosteroids inhibit transcription of COX2 but not COX1.26. The quantitative value of the Michaelis constant or Km, is a measure oftherelative affinity between

the substrate and enzyme27. Acid phosphatase is valuable in the diagnosis of metastatic carcinoma of the prostate gland. 28. Ligasesjoin two molecules along with breakdown of a pyrophosphate (P-P) bond29. Oxygen is the H+ acceptor of oxidases30. Acetylcholine stimulates the secretion of the following saliva, pancreatic enzymes, and gastric juices


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BIOENERGETICS and BIOLOGICAL OXIDATION

1. The net ATP generated in the complete oxidation of beta-hydroxybutyrate is 26 ATPs2. Twelve NADPH are required for complete synthesis of one (1) mole of

palmitic acid

3. Oxidative phosphorylationis the major source of ATP in aerobic organisms.4. Embden Myerhoff pathwayis the primary pathway for the oxidation of glucose5. Complete oxidation of one (1) mole of palmitic acidto CO2 and H2O, generates 131ATP6. Anaerobic glycolysis produces 2 moles of ATP per mole of glucose?7. Phosphofructokinase is the Rate limiting enzyme and the major regulatory enzyme in glycolysis 8. Pyruvate dehydrogenaselinks glycolysis and the citric acid cycle 9. Oxidative phosphorylation is carried out by respiratory assembly located in theinner mitochondrial

membrane

10. Anon-spontaneous endergonic cellular reaction be driven to completion by Coupling with an exergonicreaction

PROTEIN AND AMINO ACID CHEMISTRY/ METABOLISM

1. Primary structure of proteinsdetermined by the sequence of amino acids in the polypeptide chainand sulhydril bridges

2. Secondary - the folding of short (3- to 30-residue), contiguous segments of polypeptide intogeometrically ordered units. Ex. Helix structure

3. Tertiary - the assembly of secondary structural units into larger functional units such as the maturepolypeptide and its component domains

4. Quaternary - the number and types of polypeptide units of oligomeric proteins and their spatialarrangement

5. Glutamine is the amino acid that serves as the major mode for disposing ammonia from the brain

6. Transamination of pyruvate will produce alanine

7. Tyrosine is the amino acid precursor of catecholamines.


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8. Tryptophan is theprecursor of serotonin9. Leucineis purely ketogenic.10. Urea is synthesized in the liver and the major pathway for nitrogen excretion in humans.11. Fumaratelinks the urea cycle and the citric acid cycle.12. The functional group of tryptophan is the indole grp.13. Glutamate dehydrogenase funnels amino nitrogen from glutamate to urea. The most active enzyme

involved in oxidative deamination14. The metabolism of tryptophanleads to the production of small amounts of nicotinic acid in humans.15. Lysine, threonine, proline and hydroxyproline do not participate in transamination reactions.16. The coenzyme pyridoxal phosphate (PLP) a derivative of vit. B6 is present at the catalytic site of all

Aminotransferases.17. Glutamine formation is the major means by which the brain detoxifies ammonia. 18. Carbamoyl phosphate synthetase requires N-acetylglutamate as positive modulator.

19. -ketoglutarate depletionin severe liver disease is the immediate cause of coma.20. All of these three conditions cause Phenylketonuria - Deficiency of phenylalanine

monooxygenase, deficiency of NADPH, and deficiency of dihydrobiopterin reductase21. Homocystinuria is an inborn error of methionine metabolism which is manifested by skeletal

deformities and dislocation of the lens of the eyes

INORGANIC ELEMENTS/VITAMINS, MINERALS & TRACE ELEMENTS

Inorganic elements are needed to provide a suitable medium for protoplasmic activity, play a role inosmotic phenomena and are involved in acid-base equilibra.Miscible calcium pool is the freely moving calcium in tissue, extracellular fluid and blood.Vitamin D aids the absorption of calcium and phosphates in the GIT.Gastric acidity reduces dietary iron to ferrous form (the form that is absorb in the intestines) Extrahepatic tissues like the skeleton and heart muscle can utilize acetoacetic acid, B-hydroxybutyricacid, and Ketoacids but not acetone as source of fuel

Chylomicrons produces the milky appearance of blood following a heavy intake of fat, and can beremoved only by the action of lipoprotein lipase and heparin.Cholesterol can give rise to bile acids, steroid hormones and Vitamin D.Ascorbic acid is an important anti oxidant because it inhibits the formation of nitrosamines duringdigestion.Vit E deficiency may lead to anemia in the prematures due to red blood cell hemolysis

. Thiamineis a cofactor of transketolase an enzyme of the pentose phosphate pathway,

NUCLEIC ACIDS

1. The ability of the products in purine and pyrimidine nucleotide de novo pathways to inhibit theformation of PRPP is responsible for the concerted regulation betweenthese two pathways.

2. Small nuclear RNA has catalytic splicing activity and converts primary transcript to its matureform.

3. elongation, processivity and proofreading are the three important properties of DNA polymerases4. Adherence to the Watson-Crick base pairing rules is a common characteristic of replication and

transcription5. TATA boxis important in transcription because binding of DNA binding protein to this box

enhances transcription.


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6. Degeneracy of the genetic code is an important feature of the genetic code that may protect thecodon in the event of a single base substitution:

7. Single base insertion or deletion on the genetic code changes the reading frame and result to aframeshift mutation.

8. Tumor p53 suppresor protein plays a key role in both the G1 and G2 chekpoint control.9. Southern blot is the technique involved in the analysis of DNA.

10. Cosmids are used for cloning DNA fragment with a length of 400,000 bp11. The enzymes required for the synthesis of cDNA are, reverse transcriptase, DNA ligase,

andRnase H12. DNA chips(microarray) is the method based on the preparation of large arrays of oligonucleotides

on miniaturized solid supports for analysis of DNA sequence.13.Antibiotic resistance gene is an important feature of a cloning vector because it will allow

screening of the host (successfully transfected host)14. Dnase 1 an enzyme that does not form phosphodiester bonds.15. DNA amplification is the diagnostic technique to use in patients at with sickle cell anemia or at

risk of this disease.16. DNA methylation is the process that occurs at the 5-position of Cytidine and is often correlated

with gene inactivation

17.A specific nuclease detects damaged areas following ultraviolet damage to DNA in the skin.18. Northern Blot AnalysisDetects RNA molecules19. RNA polymerase synthesizes RNA primer to initiate DNA synthesis20. The function of a promoter site on DNA is to Initiate transcription

LIPID CHEMISTRY / LIPID METABOLISM

1. high density lipoprotein - is inversely related to the incidence of

coronary atherosclerosis ( HARPERs 25th

ch 27 pp 268-271)

2. very low density lipoproteins- The lipoprotein that serves to transport triacylglycerolfrom the liver to the different extrahepatic tissues:

(Harpers Ch 27 p 268-271)

3. apolipoprotein D - the apolipoprotein that serves as lipid transferprotein ( Harpers ch 27 p 271)

4. Chylomicronslipoproteins that have the highest total lipid content( Harpers p 268)

5. chylomicrons- the lipoproteins that have the highest triacylglycerol content- is elevated in Type I Hyperlipidemia

(Harpers Ch 27 p 268-271)

- produces the milky appearance of blood following aheavy intake of fat, and can be removed only by the action of

lipoprotein lipase and heparin


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- transports exogenous triglycerides

6. chylomicronsthe fraction of the plasma lipoproteins thatis located closest to thenegative pole when separated by electrophoresis on agarose gel (HarpersCh 27 p 268-271)

7. apolipoprotein A-IIthe apolipoprotein that serves as inhibitor oflecithin:cholesterol acyltransferase (LCAT)

( Harpers ch 27 pp 270-271)

8. Triacylglyceridesis the form of lipid that stores energy9. malate Pyruvatethe step that generates NADPH In the shuttle of mitochondrial

acetyl coenzyme A to the cytosol for fatty acid synthesis( Harpers ch 24 pp238-239)

10. Beta hydroxybutyrate acetoacetatethe steps in the metabolism of ketone bodiesthat generate NADH

( Harpers ch 24 p 244-245)

11. Cytosolwhere cholesterol and fatty acid synthesis occur( Harpers ch 28 p285)

12. Krabbe's Diseasea condition which is characterized by pathologicaccumulation of galactocerebroside in the affected tissues.

( Harpers ch 27 p 267t)

13. Liverwhere ketone bodies are synthesized from fatty acidsmajor site of fatty acid synthesis

(Harpers ch 24 p242) (Harpers ch 23 p 230-231)

14. Brainutilizes ketone bodies as much as 75% for its energy substrate duringuncontrolled diabetes mellitus or starvation ( harpers ch 29 p 301)

15. Acetone

produced from spontaneous decarboxylation of acetoacetate( Harpers ch 24 p 242-243)

is not utilized as energy source, is a volatile substance

16. Ganglioside lipids that accumulates in tissues of patient withTay-Sachs Disease


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17. Citratethe compound that is transported out of the mitochondria that contains theacetate group needed for fatty acid biosynthesis in the cytosol

18. Carnitineferries the fatty acids (acyl CoA) through the inner mitochondrialmembrane for beta-oxidation in the matrix

19. Mitochondrial matrixwhere the activation of medium chain and short fatty acidsoccurs in the for beta-oxidation

(Harpers pp 238-239)

20. Malonyl coenzyme Ais the product formed in the committed (rate limiting) step offatty acid synthesis

( Harpers Ch 23 pp 230)

inhibitsCarnitine palmitoyl transferase Ithus inhibiting beta-oxidation in

the feed state

21. Phospholipids and Cholesterolthe fats that may still be found in the tissues after along period of starvation.

22. Cholesterol - is the precursor for the synthesis of bile acids (metabolic product),Vitamin D, and Steroid hormones

23. CardiolipinStructure is composed of three glycerol, two phosphoric acid and 4 fattyacids

24. Thromboxane- the eicosanoids that can promote platelet aggregation

25. Lecithinlipid that acts as surfactant and deficient in cases of Respiratory Distresssyndrome

26. Palmitic acidis the end-product of extra-mitochondrial lipogenesis

27. Acetyl CoAis the two carbon product released by the action of thiolase in the beta-oxidation of fatty acids

28. Carnitine transportis the committed step in beta-oxidation

29. HMG-CoA reductaseenzyme that catalyze the rate-limiting step in cholesterolsynthesis


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30. Isopentenyl pyrophosphatethe formation of which is the most expensive stage inthe biosynthesis of cholesterol

31. alpha lipoproteinfunctions in the reverse transport of cholesterol in the blood.

32. Insulinthe hormone which is antilipolytic

33. Hormone-sensitive lipasethe major regulatory enzyme in lipolysis

34. Dihydroxyacetone phosphatethe source of glycerol 3-phosphate for triglyceridesynthesis in adipose tissue

35. acetoacetic acidis produced by the reaction that is catalyzed by HMG-CoA lyase

36. Phospholipase Chydrolyzes phospholipids specificallyphosphatidylinositol-4,5-bisphosphate (PIP2) andproducessecond messengers inositol triphosphate (IP3)and diacylglycerol (DAG)

37. Ceramideprecursor of sphingolipids

38. Clyclooxygenasecatalyze the production of prostaglandins, thromboxanes, andprostacyclins

39. Polyunsaturated fatty acidsup-regulate LDL

40. HMP shuntmain source of NADPH for lipogenesis

41. Substrate level phosphorylationdirect phosphorylation of ADP to produce ATP (Anexample of substrate level phosphorylation that occurs in glycolysis is the production of

ATP when 1,3 bisphophoglycerate is converted into 3-phosphoglycerate).main source of ATP formation in brown adipose

tissue

42. Lovastatin

inhibitor of HMG CoA reductase

43. HMG CoA reductase- repressed by cholesterol

44. LDLtransports the highest proportion of cholesterol


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45. Acetyl CoA carboxylasecatalyzes the initial and controlling step in lipogenesis

46. Ascorbic acid - is needed in the rate limiting reaction of bile acid synthesis

47. [NADH]/NAD+] ratioincrease levels is the biochemical explanation for fatty liver andhyperuricemia in chronic alcoholics

48. Fatty acidsthe major source of energy for oxidative metabolism in the heart

49.Carnitine shuttletransport system that shuttles activated fatty acid molecule from the

cytoplasm to the inner mitochondrial membrane during -oxidation of fatty acids

50.Apo B-48is the apoprotein found exclusively associated with chylomicrons

B. Carbohydtrate chemistry/ Carbohydrate metabolism

1. -D glucose and -L glucose areEnantiomers. What are enantiomers?2. glycoside- is the sugar derivative produced by the reduction of the carbonyl group on a

monosaccaharide3. galactoseis the primary hexose, which is a constituent of glycolipids and

glycoproteins

4. Choindroitin sulfateis the glycosaminoglycan that is found in large amount incartilages

5. sorbitol - the compound that is the probable causative factor in the development ofcataract in patients with diabetes mellitus

6. McArdles disease- the glycogen storage disease resulting from the deficiency ofmuscle phosphorylase

7. Fructose - the major energy source for spermatozoa in seminal fluid?8. an enlarged liver is the likely manifestation of a patient with von Gierkes disease9. In humans, liver glycogen stores are adequate up to 12 hourswithout support from

gluconeogenesis

10. Lactateis the end product of anaerobic metabolism11. Peptidoglycan layeris responsible for the gram negativity or gram positivity of bacterial cell

wall

12.Muscle lacks glucose-6-phosphatase so that it cannot contribute glucose to the blood. Glycogen

in muscles is used to supply glucose 1 phosphate that is utilized for glycolysis. G1P is converted

to G6P by phosphoglucomutase.

13. Citrateis the citric acid cycle intermediate which is the source of acetyl CoA for

extramitochondrial palmitate synthesis


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14. fructose-2,6-bisphosphateis a potent activator of Phosphofructokinase 1 and an inhibitor of

fructose-1,6-bisphosphatase. It is synthesized from fructose 6 phosphate by

phosphofructokinase-2. It favors glycolysis.

15. Phosphoenolpyruvate carboxykinase is a regulatory enzyme of gluconeogenesis

16.The carbon skeletons of the following amino acids enter Krebs citric acid cycle via alpha-ketoglutarate for gluconeogenic conversion

17.Brain - The organ most vulnerable to hypoglycemia because of its utter dependence on

circulating blood glucose for energy

18. The importance of some derived monosaccharide - Phosphorylation of glucose as glucose-6-

phosphate traps the hexose for entry into carbohydrate metabolism.

19. The most important monosaccharide in man is glucose because it is the important substrate for

cellular glycolysis.

20. An important feature of the electron transport chain it provides most of the energy captured in

metabolism.

BIOCHEMISTRY

REFERENCES :

1. Biochemistry by Harper, 25thedition

2. Textbook of Biochemistry with Clinical Correlation by Thomas Devlin

3. BiochemistryCampbell 3rdedition

4. Biochemistry a Case Oriented Approach by Mosby

5. Biochemistry by Orten and Newhaus

6. Molecular Biology of the Cell by Alberts

biochemistry review booklet 1

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