Biochem 406 Exam 2

Front 1

What are the functions of bile salts?

Back 1

-activate pancreatic lipase to hydrolyze dietary TAG's
-make dietary fat more soluble
-aid absorption of vitamins

Front 2

Where are bile salts made? Where are they stored? Where are they active?

Back 2

made in liver
stored in gallbladder
active in small intestine

Front 3

What is the function of glucocorticoids?

Back 3

made by adrenal cortex to increase protein degradation to provide substrates for GNG

Front 4

How is glucocorticoid synthesis regulated?

Back 4

Anterior pituitary secretes ACTH (adrenocorticotropic hormone)

ACTH binds 7-TM receptor on adrenal cortex --> g protein cascade/cAMP --> + hydroxylases, + cholesterol transport into matrix, + hyrolysis of cholesterol esters.

Front 5

What is the function of mineralicorticoids?

Back 5

secreted by adrenal cortex; increase blood pressure and volume by manipulating salt uptake

Front 6

What types of rxns convert cholesterol into its steroid hormone derivatives?

Back 6

mainly HYDROXYLATION by hydroxylases, aka monooxygenases

ex. Cytochrome p450

different hydroxylase for every carbon on the molecule.

Front 7

What is the common precursor to most steroid hormones?

Back 7

pregnenelone (acetyl group on C20)

synthesized in mitochondrial matrix

Front 8

Where do the initial hydroxylation reactions in steroid synthesis occur?

Back 8

mitochondrial matrix (until pregnenelone). Cholesterol esters hydrolyzed, freed cholesterol moved to matrix, then hydroxylated.

pregnenelone --> cytosol for further modification.

Front 9

How is the nitrogen in amino acids eliminated when converting them into TCA intermediates?

Back 9

transferred to α-ketoglutarate by AMINOTRANSFERASE. PLP cofactor

AA (1) + α-KG (2) --> α-keto acid (1) + glutamate (2)

Front 10

How is the nitrogen in glutamate eliminated?

Back 10

Glutamate Dehydrogenase: oxidative deamination; releases N as NH4+

Front 11

How does the body rid itself of excess NH4+ from the glutamate dehydrogenase reaction?

Back 11

UREA cycle in liver mitochondria

N enters through carbamoyl phosphate and aspartate, leaves as urea

Front 12

What is the first step in the urea cycle?

Back 12

Carbamoyl Phosphate Synthase

CO2 + NH4+ + 2 ATP --> carbamoyl-P + 2 ADP + Pi + 3H+

stimulated by N-acetylglutamine

Front 13

What is the second step in the urea cycle?

Back 13

Ornithine Transcarbamylase

carbamoyl-P + ornithine --> citrulline

Cm-P forms amide linkage with amino grp on ornithine's side chain

Front 14

What is the third step in the urea cycle? (what happens to citrulline)

Back 14

citrulline + asp + ATP --> arginosuccinate + AMP + PPi

asp's amino grp forms ~guanidino grp w/carboxyl on what used to be carbamoyl-P

Front 15

What is the 4th step in the urea cycle (what happens to arginosuccinate)?

Back 15

arginosuccinate --> fumarate + arginine

asp's carbon backbone is released as fumarate, which enters TCA cycle.

Front 16

What is the 5th step in the urea cycle (what happens to arginine)?

Back 16

arg + H2O --> ornithine + urea

arg's guanidino grp is hydrolyzed and released as urea.

Front 17

How is the urea cycle regulated?

Back 17

-liver upregulates urea cycle genes in times of starvation
-N-acetyl glutamate made from acetyl-coA to activate carbamoyl phosphate synthase

Front 18

Fates of amino acids: Alanine

Back 18

converted to pyruvate --> acetyl coA via PDH

carries amino grps from muscle to liver: glu (from aminotransferase rxn) + pyruvate --> *alanine* + α-KG

in liver: ala --> pyruvate + NH4+ --> GNG

Front 19

Fates of amino acids: Aspartate, Glutamate

Back 19

asp: converted to fumarate in urea cycle

glu: converted to α-KG by glutamate DHase; α-KG --> GNG

Front 20

Fates of amino acids: Methionine, Isoleucine

Back 20

conversion to propionyl-coA by propionyl-coA Carboxylase (biotin cofactor)

pro-coA carboxylated --> d-methylmalonyl-coA --> succinyl-coA

Front 21

Fates of amino acids: valine

Back 21

Val --> d-methylmalonyl-coA --> succinyl coA --> GNG

Front 22

Fates of amino acids: phenylalanine

Back 22

Phe --> tyr by Phenylalanine Monooxygenase

Tetrahydrobiopterin cofactor (BH4)

Front 23

Which amino acids are only ketogenic?

Back 23

Leucine
Lysine

all others can be made into TCA intermediates --> oxaloacetate; therefore glucogenic

Front 24

What are two ways for aspartate to enter the TCA cycle?

Back 24

asp + glu --> OAA + α-KG

OR

asp --> fumarate in Urea Cycle

Front 25

How can glutamate enter the TCA cycle?

Back 25

glutamate dehydrogenase

glu --> α-ketoglutarate + NH4+

Front 26

What three AA's can be converted to succinyl coA?

Back 26

Ile, Met --> propionyl coA

carboxylated to methylmalonyl-coA

val --> methylmalonyl-coA

mm-coA MUTASE coverts to succinyl-coA.

Front 27

What enzymatic cofactor is required for the rearrangement of AA's into succinyl coA?

Back 27

Methylmalonyl-coA Mutase

5' deoxyadenosyl cobalamin

heme group w/Co 2+ instead of Fe2+

Front 28

What is the role of Intrinsic Factor?

Back 28

secreted by stomach
required for absorption of dietary cobalamin in intestines

Front 29

What are the causes of PKU?

Back 29

-Phenylalanine Hydroxylase deficiency
-Tetrahydrobiopterin deficiency

Front 30

Which neurotransmitters are derived from phenylalanine?

Back 30

Catecholamines:
Epinephrine
Norepinephrine
Dopamine/L-Dopa

phe --> tyr --> catecholamines

Front 31

What is the major enzymatic cofactor (reducing agent) in most hydroxylation reactions?

Back 31

tetrahydrobiopterin

BH4

must regenerate using NADH to "re-reduce" BH4

Front 32

What is the basis of Parkinson's Disease?

Back 32

substantia nigra in the brain dies --> no dopamine production

--> muscle tremors, trouble initiating movements

remedy w/oral L-dopa, carbidopa

Front 33

Why is L-dopa administered to Parkinson's patients rather than dopamine?

Back 33

L-dopa net charge = 0

--> can cross blood brain barrier, converted to dopamine by Dopa Decarboxylase/PLP.

dopamine net charge is +

Front 34

What AA is serotonin derived from?

Back 34

Tryptophan

use BH4 to hydroxylate to 5-HTP
decarboxylate w/PLP to form serotonin.

Front 35

What is the second step in heme synthesis (after making ALA)?

Back 35

2 ALA --> porphobilinogen (has pyrrole ring)

occurs in cytoplasm!

Front 36

What is the first committed step in heme synthesis?

Back 36

ALA Synthase/PLP (in mitochondria)

glycine + succinyl-coA --> aminolevulinic acid (ALA) + CO2 + CoA-SH

glycine decarboxylates/attaches to succinyl-coA, displaces coA

Front 37

How is heme synthesis regulated?

Back 37

-heme allosterically represses ALA Synthase
-heme represses synthesis of ALA synthase
-drugs (barbiturates, etc.) requiring body to detox itself induce synthesis of ALA synthase

Front 38

What is the third step in heme synthesis (what do we do w/the pyrrole)?

Back 38

4 porphobilinogens --> linear tetrapyrrole

also in cytoplasm

Front 39

What is the fourth step in heme synthesis (after linear tetrapyrrole formation)?

Back 39

cyclization of tetrapyrrole by SYNTHASE --> Uroporphyrinogen I

side chains get moved around by COSYNTHASE --> Uroporphyrinogen III

decarboxylation to Coproporphyrinogen III

Front 40

What is the final step in heme synthesis?

Back 40

returns to mitochondrion

ferrochetalase inserts Fe2+ ion in center of ring.

Front 41

Where are the two main sites of heme synthesis?

Back 41

liver (for detoxification, cytochrome p450's)
bone marrow (for hemoglobin)

Front 42

How do Cytochrome P450 type enzymes work to detoxify the system?

Back 42

Uses NADPH to hydroxylate toxins to make them more hydrophilic --> can be flushed out of system.

Front 43

What is the cause of erythropoietic porphyria?

Back 43

-deficiency in cosynthase that switches substituents on Uroporphyrinogen I to make UPP III

--> UPP I accumulates

vampires??? red urine, fluorescent teeth, light sensitive skin etc.

Front 44

What is the cause of acute intermittent porphyria?

Back 44

synthase defective --> can't make uroporphyrinogen I.

porphobilinogen + toxic byproducts accumulate in liver. --> toxic --> mania, abdominal pain, agitation

Front 45

What is the function of S-adenosyl methionine (SAM)?

Back 45

Donor of activated methyl groups (ex. methylates Norepinephrine to form Epinephrine)

Involved in regeneration of tetrahydrofolate: takes methyl grp away from "spent" FH4: Activated Methyl Cycle

Front 46

Describe synthesis of S-Adenosym Methionine (SAM).

Back 46

Methionine + ATP --> Met-S-Adenosyl + PPP

PPP --> Pi + PPi

PPi --> 2P

costs 3 ATP! 3 high E phosphate bonds hydrolyzed.

Front 47

How does SAM aid in regeneration of Tetrahydrofolate?

Back 47

SAM + R --> R-CH3 + S-adenosyl homocysteine

S-adenosyl Homocysteine --> Homocysteine + Adenine

Homocysteine + N-5-Methyl THF --(COBALAMIN/METHYL TRANSFERASE)--> Met + FH4

SAM loses methyl, then Adenine, then accepts methyl from N-5-Me-THF

Front 48

At which N position are purines attached to ribose/deoxyribose?

Back 48

N-9

Front 49

At which N position are pyrimidines attached to ribose/deoxyribose?

Back 49

N-1

Front 50

What is the difference between a nucleoTIDE and a nucleoSIDE?

Back 50

nucleotide = has phosphate ester groups

nucleoside = just sugar + nitrogenous base.

Front 51

Which amino acid is synthesized by a an amiDOtransferase reaction?

Back 51

asparagine:

glutamine + aspartate --> glutamate + asparagine

AMIDE, not amino group N is transferred.

Front 52

How does the body synthesize alanine?

Back 52

aminotransferase rxn

pyruvate + glutamate --> alanine + α-ketoglutarate

Front 53

How does the body synthesize aspartate?

Back 53

aminotransferase rxn

oxaloacetate + glutamate --> aspartate + α-ketoglutarate

Front 54

How does the body synthesize proline?

Back 54

cyclization of glutamate

glu + NADH + ATP --> glutamate 5-semialdehyde + NAD+ + ADP + Pi
reduction of side chain carboxyl --> aldehyde

cyclization (amino grp attacks aldehyde) then reduction w/NADPH to proline.

http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/AminoAcid/Pro.html

Front 55

How does the body synthesize asparagine?

Back 55

admiDOtransferase rxn

glutamine + aspartate --> glutamate + asparagine

gln gives side chain amide N to asp's side chain

Front 56

How does the body synthesize serine?

Back 56

3-phosphoglycerate (glycolysis) + NAD+ --> 3-phosphopyruvate
(oxidize C2's -OH to keto grp)

3-phosphopyruvate + glutamate --> phosphoserine + α-ketoglutarate
aminotransferase rxn

phosphoserine --> ser + Pi
phosphatase rxn

Front 57

How does the body synthesize glycine?

Back 57

serine + tetrahydrofolate --(PLP)--> glycine + N5,N10 methylene-THF

N5,N10 methylene-THF + NADH --> N5 methyl-THF goes thru activated methyl cycle to generate SAM

Front 58

How does the body synthesize arginine?

Back 58

in the urea cycle

arginosuccinate --> arginine + fumarate

rather than losing its guanidino grp to form ornithine and urea, arg can be used elsewhere.

Front 59

How does the body synthesize tyrosine?

Back 59

hydroxylation rxn

phenylalanine --> tyrosine using Phe hydroxylase + tetrahydrobiopterin

Front 60

What is the sugar building block for all nucleotides?

Back 60

5-phosphoribosylamine

ribose-5-P (from PPP) + ATP --> 5-phosphoribosyl pyrophosphate ( = PRPP) + AMP

glutamine + PRPP --> glutamate + 5-P ribosylamine
amidotransferase rxn

Front 61

Where does nucleotide synthesis occur?

Back 61

in the cytoplasm.

lone exception: pyrimidine synthesis dehydrogenation of dihydroorotate to orotate occurs on mito. membrane.

Front 62

What is the major difference between purine and pyrimidine biosynthesis?

Back 62

purines: assemble base on 5-ribosylamine

pyrimidines: assemble base, then attach to PRPP

Front 63

What is the starting "scaffolding" for purine synthesis? Roughly how is it synthesized?

Back 63

inosine monophosphate

glycine attaches to PRPP, gets methylated by FH4, cyclizes to form 5-membered ring

carboxylation (biotin-free!) and aspartate furnish carbons for 6-membered ring

Front 64

How is inosine monophosphate converted to adenine?

Back 64

IMP + asp --> asp forms imine w/carbonyl

asp leaves as fumarate, carbonyl grp has been replaced by amino grp.

Front 65

How is inosine monophosphate converted to guanine?

Back 65

C2 oxidized to keto grp by NAD+

amidotransferase rxn: glutamine + C2 keto grp makes amino grp at C2 = guanine.

Front 66

How is purine synthesis regulated?

Back 66

IMP (allosterically), AMP, GMP all inhibit amidotransferase rxn PRPP --> 5-ribosylamine

AMP, GMP each partially inhibit IMP conversion into AMP/GMP

need to keep ~equal concentrations of all nt's in cell.

Front 67

How does pyrimidine biosynthesis begin?

Back 67

formation of carbamoyl phosphate in cytosol:

CO2 + gln + 2 ATP --> carbamoyl-P + glu + 2 ADP

amiDOtransferase, unlike in urea cycle (uses free NH4+ and CO2 instead of gln)

Front 68

What is the second step in pyrimidine biosynthesis, after formation of carbamoyl-P?

Back 68

aspartate transcarbamoylase

carbamoyl-P + aspartate --> N-carbamoyl aspartate

Front 69

What is the third step in pyrimidine biosynthesis, after formation of N-carbamoyl aspartate?

Back 69

cyclization to dihydroorotate

oxidation of DHorotate --> orotate occurs on outer surface of inner mitochondrial membrane.

Front 70

What is the foruth step in pyrimidine synthesis (what do we do with the orotate)?

Back 70

phosphoribosyl transferase attaches to PRPP to form orotidylate

orotidylate decarboxylates to URIDYLATE (UMP).

Front 71

How is pyrimidine synthesis regulated in humans?

Back 71

carbamoyl phosphate formation regulated.

Front 72

Describe the enzymes involved in pyrimidine biosynthesis.

Back 72

2 multi-enzyme complexes in the cytosol

one enzyme on the outer surface of the inner mitochondrial membrane.

Front 73

How is CTP synthesized?

Back 73

UTP (not UMP!!) undergoes amiDOtransferase rxn:

UTP + glutamine --> CTP + glutamate

keto grp on top of ring --> amino grp.

Front 74

How is TTP synthesized?

Back 74

methylation of dUMP using N5,N10 methylene tetrahydrofolate

dUMP + N5N10methyleneTHF --> dTMP + DHF

dihydrofolate converted back to THF using NADPH.

Front 75

What are the two ways of regenerating tetrahydrofolate (FH4) from N5,N10 methyleneFH4?

Back 75

use N5-N10 methyleneFH4 to donate methyl grp to dUMP

reduce N5,N10 methyleneFH4 --> N-5-methylFH4 and use in synthesis of SAM

Front 76

Of those we discussed, which two reactions require cobalamin?

Back 76

1. regeneration of tetrahydrofolate from N-5methyl FH4 through the activated methyl cycle (gives methyl to homocysteine)

2. conversion of L-methylmalonyl coA to succinyl-coA in the glucogenic pathways of val, met, and ile

Front 77

What enzyme is inhibited by methotrexate? Why is this detrimental to the cell?

Back 77

Dihydrofolate reductase

Can't methylate UTP --> TTP
can't replicate DNA properly --> mutations accumulate.

Front 78

What type of nucleotide do Ribonucleotide Reductases work on?

Back 78

NDP's

nucleotide diphosphates.

removes 2' -OH to make dNDP out of NDP

Front 79

What is the body's primary source of intrinsically synthesized glutamate?

Back 79

alpha-ketoglutarate

aminotransferase reaction, PLP?