Mgm Exam 2 Revised

Front 1

What is the best way to visualize individual gene deletions and/or duplication

Back 1

In situ hybridization with specific probes that are labeled with a fluorescent dye, unlike karotyping this can be done in the interphase nucleus

Front 2

How can you diagnose DiGeorge syndrome using fish

Back 2

In the metaphase chromosome utilizing FISH look at 22 chromosome with two probes one in the centermere and the other in the subtelemere region loss of sequence 22Q11 deletion

Front 3

Her-2

Back 3

can look for Her2 amplication for use for treatment with Her2

Front 4

After Glycolysis what is the fate of pyruvate under aerobic conditions

Back 4

pyruvate is oxidized in the mitochondria. It diffuses through the pores in the outer mitochondrial matrix, where it is oxidatively decarboxylated to acetyl-CoA

The net reaction is

Pyruvate + NAD+ + CoA--> Acetyl-CoA + NADH + CO2

Front 5

What enzyme catalyzes this irreversible reaction of pyruvate to acetyl CoA?

Back 5

pyruvate dehydrogenase, a multienzyme complex with three components:

1) Pyruvate dehydrogenase component E1, which contains thiamin pyrophosphate (TPP) as a prosthetic group

2) Dihydrolipoyl transacetylase component (E2), which contains lipoic acid covalentyl bound to a lysine side chain

3) Dihydrolipoyl dehydrogenase component E3, an FAD-containing flavoprotein

Front 6

with the exception of lipoic acid, the coenzymes of pyruvate dehydrogenase require what?

Back 6

vitamins like pantothenic acid (CoA), niacin (NAD), riboflavin (FAD), and thiamin (TPP). A deficiency of any of these vitamins can impair the pyruvate dehydrogenase reaction. In the case of thiamin deficiency (Beriberi) the blood levels of pyruvate, lactate, and alanine are elevated after a carbohydrate-rich meal. Pyruvate accumulates because its major reaction is blocked and most of it is either reduced to lactate or transaminated to alanine

Front 7

How is the activity of pyruvate dehydrogenase regulated?

Back 7

The activity of the pyruvate dehydrogenase complex (PDC) is controlled by the most common form of covalent modification, phosphorylation. There's an enzyme called pyruvate dehydrogenase kinase (PDH kinase, PDHK) that attaches phosphate groups to the E1 subunit of PDC. The phosphorylated form of PDC is inactive. Another enzyme called PDH phosphatase (PDP) removes the phosphate groups making the enzyme active again.
PDH kinase binds to the E2 subunits, specifically the lipoamide swinging arm

Front 8

How do specific substrates effect the activity of pyruvate dehydrogenase?

Back 8

The kinases and phosphatases are allosteric enzymes

One of the most important allosteric inhibitors is pyruvate, CoA and NAD+ When pyruvate binds to PDH kinase 2 it blocks the kinase (phosphorylation) activity by changing the shape of the protein. Since phosphorylation of PDC doesn't occur, the pyruvate dehydrogenase complex remains active. Conversely, ATP, Acetyl CoA, NADH will positively regulate the kinase thus causing more phosphorylation of the complex causing it to become inactive

Front 9

What is the overall intermediates formed during the Kreb cycle and where does it take place?

Back 9

Citrate

isocitrate

ketoglutarate

succinyl CoA

succinate

furmurate

malate

oxaloacetate

occurs in mitochondrial matrix

Front 10

Explain all the steps in the Kreb cycle leading up to the first oxidative decarboxylation

Back 10

decarboylation of the Isocitrate results in liberation of CO2 and a reduction of NAD+ to form NADPH

Citrate synthase

Aconitase (H2O)

Isocitrate dehydrogenase

Front 11

What is a potent inhibitor of Aconitase

Back 11

Flurocitrate is a potent inhibitor of aconitase it is derived from fluroacetate that is metabolically converted to fluorcitrate by the same enzymes that othersie metabolize acetate (acetyl CoA syntetase and citrate synthase

Front 12

Explain all the steps in the kreb cycle leading up to the second oxidative decarboxylation

Back 12

alpha keto glutarate _ CoA--> Succinyl CoA + CO2 + NADH + H

the alpha ketogluturate dehydrogenase complex is similar to pyruvate dehydrogenase

Front 13

Explain the steps leading up to the only substrate level phosphophylation that occurs in the Kreb cycle

Back 13

succinyl CoA + GDP + P --> Succinate + GTP + CoA

Front 14

Explain the step that involves the only reaction with the net reduction of FAD to FADH2

Back 14

Front 15

Where does the third and final NADH formed in the Kreb cycle

Back 15

Front 16

What is the net reaction of the Kreb cycle

Back 16

Starting from acetyl-CoA, the stoichiometry of the citric acid cycle is as follows:

Acetyl-CoA + 2H2O + 3NAD+ + FAD + GDP + Pi <=> 2 CO2 + 3 NADH + FADH2 + CoASH + GTP + 2H+

Starting from glucose (via glycolysis), the stoichiometry is as follows, through the citric acid cycle:

Glucose + 2H2O + 10 NAD+ + 2 FAD + 4 ADP + 4 Pi <=> 6 CO2 + 10 NADH + 6 H+ + 2 FADH2 + 4 ATP

Front 17

How is the Kreb cycle regulated

Back 17

Front 18

How do the cell compensate for competing reactions that use the intermediates in the TCA cycle

Back 18

Cells need only one or two major anaplerotic reactions. The most common reaction in animals is the one catalyzed by pyruvate carboxylase (located in mitochondria), which converts pyruvate to oxaloacetate, using bicarbonate and ATP. This reaction, which is also a part of the gluconeogenesis pathway, is allosterically activated by acetyl-CoA. Since acetyl-CoA is also the molecule with which oxaloacetate reacts in the reaction catalyzed by citrate synthase, the pathway has a way of jump-starting itself when oxaloacetate concentrations fall too low

Front 19

mutations in isocitrate dehydrogenase 1 and 2 result in what

Back 19

result in the formation of 2-hydroxyglutarate (2HG) instead of alpha-ketoglutarate. 2HG is a competitive inhibitor of alpha ketoglutarate dependent dioxygenases which are important in demethylation reactions for histones

Front 20

Warburg effect

Back 20

low activities of fumarate hydratase (fumarase) drives metabolic shift to aerobic glycolysis

Front 21

glycerol phosphate shuttle

Back 21

the glycerol phosphate shuttle transfers the hydrogen first to dihydroxyacetone phosphate forming glycerol phosphate and then to the FAD of the mitochondrial glycerol phosphate dehydrogenase

Front 22

malate aspartate shuttle

Back 22

the malate aspartate shuttle transfers hydrogen from cytoplasmic NASH to oxaloacetate forming malate. malate is transported into the mitochondrion where it donates its hydrogen to NAD+ forming NADH.

Front 23

Electron transport chain

Back 23

Metabolic processes use NADH and [FADH2] to transport electrons in the form of hydride ions (H-). These electrons are passed from NADH or [FADH2] to membrane bound electron carriers which are then passed on to other electron carriers until they are finally given to oxygen resulting in the production of water. As electrons are passed from one electron carrier to another hydrogen ions are transported into the intermembrane space at three specific points (1, 3, 4) in the chain. The transportation of hydrogen ions creates a greater concentration of hydrogen ions in the intermembrane space than in the matrix which can then be used to drive ATP Synthase and produce ATP (a high energy molecule)

Front 24

What are some of the inhibitors of oxidative phosphorylation

Back 24

cyanide blocks the electron transport chain by binding to ferric iron in cytochrome oxidase causing hyperventilation because of lactic acidosis

Front 25

Uncoupling agents

Back 25

they do not inhibit electron transport but the protons are shuttled across the membrane at site other than complex 5 and heat will be released

2,4 dinitrophenol and uncoupling proton thermogenin for example

valinomycin transport k across inner membrane

arsenate substitutes phosphate during atp synthesis

atractyloside-inhibits ATP-ADP translocation

Front 26

lebers heriditary optic neuropathy and Leigh syndrome

Back 26

LHON single base substitution that replaces arginine residue in one of the subunits of NADH-Q reductase with histidine mutations in mtDNA that result

leigh lactate acidosis

Front 27

A radical is a cluster of atoms one of which contains an unpaired electron what are the most common radicals

Back 27

H2O2 OCL OH and O

Front 28

phagocytes form radicals

Back 28

NADPH Oxidase in both neutrophils and macrophages

2 O2 + NADPH --> 2 O2* + NADP+ + H+

MPO

H2O2 + Cl--> OCl* H2O

Front 29

3 enzymes that quench radicals

Back 29

Front 30

how are some of the free radicals produced

Back 30

Oxygen radicals can be formed by hypoxanthine reaction, complex 1 and 3

this can be converted to hydrogen peroxide by SOD which can react with iron in the fenton reaction

Fe2+ + h2o2--> 2OH-

Front 31

what is the structure of glutathione

Back 31

must be reduced back by NADPH

Front 32

chronic granulomatous disease

Back 32

rare x-linked genetic disorder that causes a defective gene for one of the subunits of NADPH and can not rid themselves of an infection caused by bacteria that produce catalase to protect themselves from hydrogen peroxide this results in the development of a persisting nest of infected cells known as a granuloma

Front 33

what is the function of the pentose phosphate pathway

Back 33

provide reduced NADP for synthetic reactions

provide pentose phosphate for nucleic acids

forms of alternative mechanism for the oxidation of glucose (hexose monophosphate shunt)

Front 34

what are the oxidative reactions in the hexose monophosphate pathway

Back 34

1) glucose 6 phosphate dehydrogenase and 6-phosphogluconolactone hydrolyase

2) 6-phosphogluconate dehydrogenase

Front 35

what are the non oxidative reactions (reversible)

Back 35

3) ribose 5 phosphate isomerase

4) phosphopentose epimerase

5) 7) transketolase

6) transaldolase

net reaction 3 G6P --> 3CO2 + 2 F6P + 1 Glyceraldehyde 3-phosphate

Front 36

glucose 6 phosphate dehydrogenase deficiency

Back 36

in RBC sole source of NADPH keeps glutathione in reduced state resulting in hemolytic anemia gene is on the x chromosome and gives some degree resistance to malaria

Front 37

pathways of glucose 6 phosphate metabolism in the erythrocyte

Back 37

Front 38

fructose metabolism and its consequence of high injestion of fructose

Back 38

in cases of high fructose instead of using hexokinase you use fructose kinase which is not regulated you will have rapid metabolism of fructose phosphate gets tied up

Front 39

defiency in fructose metabolism

Back 39

essential fructosuria defect in fructokinase

hereditary fructose intolerance- lack of aldolase B trapping of fructose 1 P causes hypoglycemoa vomiting jaundice causes hepatic failure treated by removing fructose and sucrose from the diet

Front 40

what is lactose

Back 40

disaccharide consisting of galactose and glucose with a beta 1-4 glycosidic link

Front 41

What are the enzymes involved in galactose

Back 41

Galactose + ATP--> Galactose-1-P via galactose 1-P

Galactose-1-P + UDP GLucose--> UDP-Galactose + Glucose-1-P via Galactose1-phosphate uridyltransferase

UDP-galactose can be used to make lactose as well as glycolipids and glycoaminoglycans

when galactose levels are elevated aldose reductase forms galactitol and can cause cataracts

uridyltransferase defect is more common and causes accumulation of galactose-1P and galactose and will also develop cataracts

Front 42

glycogen structure

Back 42

GLycogen is a polysaccharide in which glucosyl residues are joined by glycosidic links. the major links are 1-->4 with branch points in the chain that are 1--6 and occur at an average spacing of 8 to 12 alpha 1--> links

glycogen is stored at the highest concentration in the liver and more total glycogen in the muscle however less depleted in muscle though

Front 43

how is glycogen synthesized

Back 43

Glucose-6-phosphate is converted to glucose-2-phosphate catalyzed by phosphoglucomutase

glucose 1- phosphate + UTP --> UDP-glucose + pyrophosphate catalyzed by UDP-glucose pyrophosphorylase

glycogen synthase catalyzes the transfer of glucose from UDP-glucose to glycogen with the formation of an alpha 1--> 4 link must be primed by glycogenin

branch points are formed by glycogen branching enzyme (amylo 1--4 --> 1-6 transglucosylase

Front 44

how is glycogen broken down

Back 44

the alpha 1-->4 links in glycogen are broken down by phosphorolytic cleavage that requires inorganic phosphate. The reaction is catalyzed by the enzyme glycogen phosphorylase

Branch points are cleaved by a hydrolytic reaction that produces free glucose and is catalyzed by glycogen debranching enzyme.

Front 45

allosteric regulation of glycogen synthesis and degradation

Back 45

Front 46

what hormones effect glycogen synthesis

Back 46

epinephrine and glucagon can stimulate a cAMP-pka dependent inhibition of glycogen synthase by phosphorylation

also when the receptors are activated glycogen phosphorylase kinase is activated by phosphorylation that act on glycogen phosphorylase which result in glycogen breakdown

insulin stimulates glycogen synthesis by activating protein phosphatases

Front 47

type one glycogen disease

Back 47

Front 48

type 2 glycogen disease

Back 48

Front 49

type 3 glycogen disease

Back 49

Front 50

type 4 glycogen disease

Back 50

Front 51

type 5 glycogen disease

Back 51

Front 52

type 6 glycogen disease

Back 52

Front 53

I cell disease

Back 53

results from an enzyme deficiency so that lysosomal enzymes do not acquire the targeting signal mannose 6-phosphate

fibroblasts in this disease have dense inclusion bodies and are deficient in many lysosomal enzymes

Front 54

structure of glycoproteins

Back 54

there may be one or more carbohydrate chains covalently linked to a protein. The chain may be neutral or negatively charged. They are frequently branched

O glycosidic link-in collagen there is an O-glycosidic link between galactose or glucose and the hydroxyl group of hydroxylysine

N glycosidic link between N acetylglucosamine and asparagine high mannose or complex

Front 55

structure of proteoglycans

Back 55

consist of a long polysaccharide chain with a repeating disaccharide motif

glycoaminoglycans are polyanionic. The negative charge comes from the presence of carboxyl and sulfate groups. The carboxyl group is either D-glucuronic acid or L-iduronic acid

Front 56

what are the glycosaminoglycans

Back 56

hyaluronic acid

chondroitin sulfate

dermatan sulfate

heparan sulfate

haparin

karatan sulfate

polysaccharide chains

repeating disaccharide motifs

amino groups

polyanionic charater

Front 57

synthesis of glycoproteins and proteoglycans

Back 57

the units in the saccharide chains are added from nucleoside diphosphate derivatives

UDP-glucuronic acid

UDP-N-acetylgalactosamine

GDP-mannose

Sialic acid in glycoproteins is added from CMP-NANA

Front 58

Mucopolysaccharidoses (MPS)

Back 58

a series of hereditary disease resulting from mutations in genes coding for degradative enzymes acting on glycoaminoglycans

enzymes are mostly hydrolases and defiency leads to mental retardation and or structural deformities

Front 59

MPS 1

Back 59

Hurler syndrome

deficiency of L-iduronidase leads to mental retardation and structural changes due to the accumulation of dermatan sulfate and heparan sulfate

Front 60

MPS 2

Back 60

Hunters syndrome X linked disease due to defieciency of iduronate sulfatase acculmulation of dermatan sulfate and heparan sulfate

Front 61

MPS 3

Back 61

Sanfilippo syndrome

defieciency in one of four degradative enzymes leads to severe mental retardation but little structural change accumulation in heparan sulfate

Front 62

MPS 4

Back 62

Morquio syndrome deficient in galactose-6-sulfatase or beta galactosidase to accumulation of keratan sulfate with normal intelligence

Front 63

How is fat ingested

Back 63

2-monoacylglycerol and free fatty acids after they are absorbed they fatty acids are activated by acyl-co-enzyme A in the ER of the intestinal mucosal cell by the hydrolysis of inorganic pyrophosphate making this reaction essentially irreversible. The acyl-CoA then reacts with 2-monoacylglycerol to from triglyceride

In the ER of the intestinal celll they are assembled into small fat droplets known a chylomicrons which travel through the lymph

to target cells

tissue that utilizes the triglycerides like adipose and skeletal muscle poesses LPL an enzyme that is attached to heparan sulfate that bind chylomicrons and the triglycerides are hydrolyzed to free fatty acids and 2 monoacylglycerol and these products are taken up by the cell

Front 64

Orlistat

Back 64

inhibits pancreatic lipase preventing the absorption of lipids

Front 65

Lovaza

Back 65

promotes lowering of plasma triglycerides

fatty acid ethyl esters of EPA and DHA

inhibit acyl Co

Front 66

how does acetyl CoA get from the mitochondria to cytosol for fatty acid synthesis

Back 66

Front 67

how does one convert acetyl CoQ to fatty acid

Back 67

Acetyl CoA + Malonyl Co + NADPH--> fatty acids

Front 68

what is the rate limiting enzyme in fatty acid synthesis

Back 68

conversion of acetyl coa to malonyl coa

ACC Acteyl CoA Carboxylase

1. BCCP no enzymatic function carries biotin carries CO2

2. Biotin carboxylase take bicarbonate onto to BCCP (BCCP+ HCO3- + ATP--> BCCP-CO2 +ADP + P)

3. Transcarboxylase puts Co2 on methyl group on acetyl CoA

Front 69

Net reaction of fatty acid synthesis

Back 69

Front 70

how is FAS regulated

Back 70

Citrate is an allosterically activation of ACC by polymerization

Front 71

How is ACC inactivated

Back 71

AMP-activated protein kinase phosphorylates ACC inactive in the presence of glucagon thereby resucing malonyl-CoA level stimulating beta oxidation

Front 72

how are triacylglycerols that are stored in adipocytes cells mobilized

Back 72

Front 73

Once mobilized how does fatty acids get in the cell

Back 73

Front 74

how does Acyl CoA get into the mitochondrian matrix

Back 74

CAT1 is the rate limiting enzyme in fatty acid oxidation

Front 75

steps in beta oxidation

Back 75

number of cycles is # of C -2/2

# of acetly coa=# C/2

# FADH2= #C-2/2

#NADH= #C-2/2

for every double bond you subtract a FADH2

Front 76

how are odd chain fatty acids oxidized

Back 76

forms Acetyl CoA + Propionyl CoA which can form succinyl CoA an intermediate in citric acid cycle

Front 77

Excessive fatty acid oxidation in mitochondria

Back 77

Acetyl CoA + Acetyl CoA will form acetoacetate to form Acetone + CO2 and B-hydorxybutyrate

Front 78

How is CPT1 the rate limiting enzyme in fatty acid oxidation

Back 78

Malonyl CoA

Front 79

Fatty acid oxidation deficiency

Back 79

carnitine-add carnitine

fattyacryl CoA synthetase-add medium chain to diet can be metabolized directly

medium chain (MCAD)-

acyl carntine- short and medium chain

Front 80

synthesis of triglycerides

Back 80

Front 81

phopholipid synthesis

Back 81

activation of Diacylglycerol or an alcohol by linkage to a nucleoside diphosphate CDP

Front 82

phospholipases

Back 82

selectively hydrolyze specific ester linkages on phosphatidyl compounds

phospholipase A2 acting on phosphotidylinositol releases arachidonic acid, phospholipase 2 is inhibited by glucocorticoids

phospholipase C is found in liver lysosomes activated by PIP2 system

Front 83

spingolipids

Back 83

spingosine is synthesized from palmitoyl coenzyme A and the amino acid serine. Acylation with a fatty acid transferred from a fatty acyl coenzyme A results in the formation of a ceramide. Addition of choline phosphate yields spingomyelin

They are important molecules within the cell membrane and are particularly rich in nerve tissue

Front 84

Tay Sachs disease

Back 84

accumulation of gangliosides (GM2) defieciency in hexosaminodidase A

rapid and progressive neurogeneration

blindness

cherry red macula

Front 85

Gaucher disease

Back 85

accumulation of glucocerebrosides because of glucocerebrosidase is missing completely

most common lysosomal storage disease

heptosplenomegalay

Front 86

Nnemann-pick disease

Back 86

accumulation of sphingomyelin

hepatosplenomegaly

neurodegeneration course type A

Front 87

structure of cholesterol

Back 87

27 carbons all derived from acetate

C3 hydroxyl group

C17 side chain with 8 carbons

the C3 and C17 are the common modification points

Front 88

What is the rate limiting step during cholesterol synthesis

Back 88

HMG CoA (6C) + NADPH---> Mevalonic acid (6C) catalyzed by HMG CoA reductase in ER

expend alot of cholesterol 18ATP/chol and 14 NADPH/chol

Front 89

what is the protein that regulates cholesterol synthesis

Back 89

SREBP-Sterol Regulatory Element Binding Protein

a transmembrane protein a DNA binding domain and SCAP interacting domain

SCAP-SREBP cleavage activating protein

has a sterol sensing domain and binds SREBP in the ER when er sterols are low, SCAP-SREBP move to the golgi

Protease 1 and protease 2-localized to the golgi responsible for the two step cleavage of SREBP resulting in soluble cytosolic SREBP

mature SREBP translocate to nucleus and regulates gene expression

Front 90

regulation of cholesterol synthesis

Back 90

1) cholesterol regulated gene expression

2)cholesterol regulated degradation of HMG CoA reductase (HMGR)

3)Phosphorylate of HMGR when ATP is low AMPK will phosphoylate HMGR

4) Hormone regulated HMGR expression and activity insulin stimulates HMGR expression and activity, glucagon inhibits HMGR expression

5) drug inhibition-Statins competitively inhibit HMGR they mimic the transient intermediate mevadyl CoA. Zetia (ezetimibe) inhibits absorption of cholesterol a combination of the two Vytorin (ezemtimibe + simvastatin

Front 91

lipoproteins particles general characteristics and functions

Back 91

spherical particles with varying amounts of lipid and protein

maintain solubility of constituent lipids

transport of lipids in plasma

Front 92

major classes of lipoproteins

Back 92

chylomicrons

VLDLs, LDLs and HDLs

major components are triacylglycerols cholesterol esters and phopholipids

Front 93

relative size and densities of lipoproteins

Back 93

apoB --> aquire apoCII and apoE from HDL

Front 94

chylomicron interactions with HDL

Back 94

1) nascent chylomicrons assembled in intestine released into plasma with ApoB-48

2) mature chylomicrons apoE and COO added from HDL apoCII activates lipoprotein lipase

3) lipoprotein lipase capillary walls hydrolyzes TG delivers FFA into adipose and muscle

4) chylomicron remnants-lack apoCII which transferred to HDL

5) mature HDLs reacquire apo CII also acquires cholesterol from membranes accumulates apoCII and E transferring them to VLDL and LDL functions in reverse transport of cholesterol to liver

Front 95

where are VLDL and LDL metabolism start

Back 95

1) liver containing apoB100

2) VLDL aquire apoCII and apoE from HDL

3) lipoprotein lipase hydrolyzes TGs FFA are taken up, LDL circulates

4) apoCII and apoE are transferred from VLDL to HDL resulting in LDL

5) LDL binds receptor on cells and taken up by cells increasing intracellular cholesterol

6)LDL and HDL bind specific receptors and mediate uptake in the liver

7) cholesterol is exreted as bile

Front 96

general characterisitics of HDLs

Back 96

synthesied in the liver and intestine

secreted directly into the blood from liver intestine

protein rich

express apo-AI and AII , apo-CII and apo E

nearly devoid of cholesterol and cholesterol esters

HDL transfers apoCII and apo E to VLDLS

VLDL returns apo CII and apoE to HDLs

HDL can acquire cholesterol from chylomicrons, VLDLs or membrane and convert them to cholesterol esters

cholesterol esters in HDL can be transferred to VLDLs and LDLs by cholesterol ester transfer protein CETP

Front 97

familial hypercholesterolemia

Back 97

mutations in gene encoding the LDL receptor mediates the cellular uptake of cholesterol by receptor mediated endocytosis

when functional normally increased blood chol leads to LDL uptake in cells results in inhibition of cholesterol synthesis

Front 98

classes of mutations in LDL receptor in FH

Back 98