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Biochem 406 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

Energy

A

Chemical energy stored in the sugar is converted to chemical energy of ATp

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2
Q

Stepwise conversion

A

Each step catalyzed by individual enzymes:: Each step generates distinct metabolic intermediates.

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3
Q

Metabolites

A

Can also be used for other pathway and biosynthesis

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4
Q

Key enzymes are regulated:

A

control of metabolic flux

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5
Q

Metabolite concentrations

A

also control metabolic flux, especially when G is around 1

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6
Q

A metabolic pathway must be

A

exergonic (ΔG < 0)

May require the input of ATP/NADH

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7
Q

Catabolic vs. Anabolic Pathways:

A

NOT simply the reverse of each other

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8
Q

Compartmentation

A

Increased organization and control

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9
Q

Coordinated Regulation of Anabolic and Catabolic pathways

A

• HormonalRegulation
(eg. Insulin/ Glucagon)
• Allostericcontrolofenzymeactivity
• Committedstepsinapathwayare often tightly regulated
• PreventFutileCycles ADP+Pi
• Long-termregulationbygene ATP expression

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10
Q

Most metabolic reactions are…

A

The chemistry of carbonyls, They are electrophilic and Carbonyl carbon can enhance the acidity of adjacent carbon-bound protons

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11
Q

What are the 5 main types of metabolic reactions?

A

Nucleophilic additions, Nucleophilic substitutions, Elimination reactions, Carbonyl condensation reaction, Oxidation and reduction.

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12
Q

Nucleophilic addition

A

when the nucleophile is a carbon anion -get a new CC bond

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13
Q

nucleophilic substitution

A

Replace one nucleophile with another. Need good leaving group. Ester and anhydrides, nucleophilic acyl sub reactions, tetrahedral intermediates.

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14
Q

Elimination reactions

A

need good leaving group

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15
Q

Carbonyl condensation

A

important for synthesizing CC bonds, can run in reverse

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16
Q

oxidation and reduction

A

Reversible, EX: hydride transfer from alcohol to form a ketone. Dehydrogenation reaction catalyzed by a dehydrogenase.

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17
Q

overview of metabolic flow

A
  1. Lipid Metabolism
  2. Amino Acid Metabolism
    • Integration of Metabolism
  3. Nucleic Acid Metabolism
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18
Q

Nucleophiles

A

Alkoxide, carboxylate, thiolate, carbanion, amine

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19
Q

electrophiles

A

Carbonyl, imine, phosphorus atome of phosphate

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20
Q

What are the uses of lipids?

A

membrane constituents, hormones, fat- soluble vitamins, thermal insulators, signaling molecules

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21
Q

What are used for energy reserves and why?

A

Fat-
• Fats are an efficient form of stored energy- can be stored without water
• Fats are more reduced than sugars or amino acids, yielding more energy
- Fats have more energy per gm

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22
Q

What are triacylglycerols?

A

Energy reserves in Adipose and other tissues. Excludes water.

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23
Q

What are lipid droplets?

A

dynamic organelles filled with Triacylglycerols (TAGs)

and Cholesterol-Esters (CEs). Surrounded by a phospholipid monolayer and associated proteins.

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24
Q

What are the components of triacylglycerols?

A

Phosopholipid monolayer, storage enzymes, lipid mobilization enzymes, Peripilins (regulatory proteins).

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25
Q

Problem with fats

A
  • Fats are insoluble in an aqueous environment

* Humans can’t directly transport triacylglycerides across the intestinal lumen

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26
Q

How do you digest and transport insoluble molecules? (fats)

A
  1. Emulsify fats (with the help of amphipathic bile salts)

2. Digestion of Triglycerides by Pancreatic Lipase

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27
Q

What are bile salts?

A

amphipathic lipid secreted by liver and gallbladder that help digestion and transfer of fats.

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28
Q

What feature of amphipathic lipids is beneficial in the aid in digestion and transfer of Fats?

A

They can self-assemble in aqueous environment around hydrophobic molecules to form mixed micelles, polar side towards the solvent and hydrophobic surface buried away from solvent.

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29
Q

How do Bile salts an phospholipids help emulsify fat globules?

A

Increases accessible surface area available to digestive enzymes.

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30
Q

What enzyme digests fat globules?

A

Human pancreatic lipase.

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31
Q

Besides phospholipids, what else is found in mixed micelles?

A
  • Fat Soluble Vitamins

* Dietary Cholesterol

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32
Q

What can be transported into intestinal Epithelial cells?

A

-free fatty acids, 2-mono-acyl glycerol, and free glycerol.

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33
Q

How does pancreatic lipase works?

A

It is a water soluble enzyme. works at the water lipid interface.
Hydrophobic Substrate – FAT
Hydrophilic Substrate – H2O

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34
Q

What is the catalytic triad of pancreatic lipase?

A

Ser, His, Asp

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35
Q

What is require for pancreatic lipase to go into active conformation.

A

Co-lipase and interfacial interaction (contact with mixed micelle)

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36
Q

What does Fatty Acid binding Protein (I-FABP) do?

A

solubilize fatty acids (sometimes other lipids) within a protein shell Transport of insoluble molecules within a cell

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37
Q

What are FABP bound FA used for inside epithileal cells?

A

Lipid droplet, Signaling or membrane synthesis in ER, enzyme activity, Transcription promotion, oxidation in mito, oxidation by peroxisome.

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38
Q

What is orlistat?

A

Binds to Pancreatic Lipase

Forms a Covalent Bond with the Catalytic Serine Inhibits Lipase Activity. (Basically it reduces absorption of fat).

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39
Q

Side affects of orlistat

A
  • More dietary fat can reach your large intestine.
  • Reduced Absorption of other important dietary lipids
  • long list of more
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40
Q

What does pancreatic lipase do?

A

Hydrolyzes triacylglyceride esters.

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41
Q

What happens to dietary leftover?

A

It goes to FA biosynthesis.

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42
Q

How are FA synthesized?

A

From Acetyl-CoA In liver and adipose tissue.

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43
Q

What is palmitate?

A

16 carbon FA, saturated

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44
Q

Why do most fatty acyl chains have and even number of carbons?

A

They are made from the successful addition of two-carbon unit, it is how they are made.

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45
Q

What is the purpose of the citrate shuttle?

A

it provides metabolic control and NADPH. is and antiporter for Citrate using Pi.

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46
Q

What is biotin?

A

Water soluble B-vitamin (B7). In ACC creates a swinging arm that carries reactive CO2 from one site to another.

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47
Q

ACC (acetyl-CoA carboxylase), what are its three domains.

A

Biotin carboxylase BC, Biotin carboxyl carrier protein BCCP, Carboxyl-transferase CT.

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48
Q

Which domain is the swinging arm on ACC located?

A

BCCP

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49
Q

how many enzymes are used in FA synthesis?

A

6-MAY, KS, KR, DH, ER, TE( engages only when fatty acyl chain reaches 16-18 carbons in length and releases chain from FAS complex)

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50
Q

What si ACP?

A

Acyl carrier protein has a covalently attached pantothenate cofactor that carries the growing fatty-acyl group
(Protein version of Coenzyme-A). forms thioester bonds. attached to SER.

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51
Q

What does 4’-phosphopantetheine on ACP provide?

A

the thiol group of Coenzyme A Derived from pantothenate (Vitamin B5) and cysteine
Thiol group forms high energy thioesters.

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52
Q

What does ACC do?

A

makes Malonyl-CoA from Acetyl-CoA and HCO3

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53
Q

What is the difference in FAS in humans and E. Coli?

A

Humans have evolved to have all the enzymes in one single protein, while E. coli is broken up into 6 enzymes. They form a dimer in an active form.

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54
Q

How is ACP domain linked to FAS complex?

A

by a long flexible polypeptide segment on the KR domain.

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55
Q

What does MAT do on ACP?

A

it primes FA synthase, only used in the first step. Acetyl-CoA first charges enzyme (acyl group on KS active site) then uses Malonyl-CoA for the rest of reaction.

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56
Q

What two substrates get out of order in the FAS complex?

A

The Malonyl/Acetyl Transferase Reaction is Reversible. Need CoA-SH in the Reaction Mixture
Depletion of CoA brings Fatty Acid synthesis to a halt Process is very rapid compared subsequent catalytic steps.

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57
Q

What is the second reaction in FAS complex?

A

Condensation. Formation of C-C bond in the KS domain, release of CO2 generates carbanion that reacts with KS thioester. Driving off CO2 makes the step committed.

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58
Q

What is reaction 3 of FAS?

A

Reduction by KR forming an alcohol. Requires NADPH

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59
Q

What is reaction 4 of FAS?

A

Dehydration, does an elimination. requires H2O

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60
Q

What is the 5th reaction of FAS?

A

Reduction, Saturates the double bond. Requires NADPH. makes Butyryl ACP.

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61
Q

What happens after the 5th reaction of FAS?

A

Butyryl-ACP goes back to KS, transfers it to active site, ACP free to pick up another Malonyl-Coa. IT repeats the steps until 16 carbons long and releases it.

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62
Q

How does FAS know it is finished?

A

Thioesterase has pockets that test chain length. Binding C16-pocket not favorable until reaches 16 carbons. Then its ester-linkage is properly positioned for hydrolysis.

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63
Q

What controls FAS?

A

Pathways converge to control flux. Glycolysis, Pentose-Phosphate Pathway, TCA cycle, and shuttles that transport metabolites between compartments contribute to Fatty Acid synthesis.

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64
Q

How are longer FAs made?

A

Elongation in the ER, some in Mito. Chemistry is the same as FAS.

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65
Q

Difference elongation has from FAS?

A
  • Separate Enzymes instead of a single complex
  • Uses Fatty Acyl-CoA and Malonyl- CoA instead of Malonyl-ACP
  • ER system can extend both saturated and unsaturated fatty acids
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66
Q

How are FAs desaturated?

A

Desaturases in the ER. Humans have 4 (4,5,6,9) but cannot make past 9. Plants can desaturate 12 and 15. Rest obtained.

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67
Q

What are two essential FA form plants?

A

-Linoleate 18:2(Δ9,12)
ω6 Fatty Acid
- α-Linolenate 18:3(Δ9,12,15)

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68
Q

What are Arachidonates?

A

FA stored in membranes as phosphoglyceride. Released by Phospholipase A2.

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69
Q

What are Eicosanoids?

A

Very potent hormones that act locally because they breakdown quickly. Derived from Arachidonate.

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70
Q

What are the types of Eicosanoids?

A

Prostaglandins, thromoxanes, Leukotrienes.

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71
Q

What are prostaglandins?

A

Stimulate smooth muscle contraction, affect blood flow, elevate body temperature (fever), or cause inflammation & pain

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72
Q

What are thromoxanes?

A

Produced by platelets - formation of blood clots & reduce blood flow clot site

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73
Q

What are Leukotrienes?

A

Signaling molecules in immunes responses.

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74
Q

How does Aspirin work?

A

NSAID. Is a COX inhibiter (PGH2 synthase), blocks binding of arachidonate to cyclo-oxygensase active site, preventing production of PGH2.

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75
Q

How are FA incorporated into fats?

A

2 Acyl-CoA + Glycerol-P to make phosphatidic acid. Which can be a precursor for phospholipids, or fats (addition of one more acyl group from Co-A.

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76
Q

How are FA incorporated into phospholipids?

A

CTP used to generate a good leaving group, causing phosphr group susceptible to nucleophilic attack (serine, sugars, choline, ethanol amine etc.) .

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77
Q

What is the purpose of chylomicrons?

A

Assembles in golgi of intestinal cells to to transport TAGs and cholesterol by exocytosis into the lymph system than bloodstream. (basically transport of dietary fats).

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78
Q

What are lipoproteins?

A

like a soluble lipid droplet for transport. .

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79
Q

What do VLDLs do?

A

Carry endongenous/recycled cholesterol and TAGs from liver to other tissues (muscle, adipose, heart) using lipoprotein lipase. `

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80
Q

What happens to VLDL remnants?

A

Mature to LDLs in bloodstream or go back to liver.

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81
Q

What are HDLs used for?

A

Reverse cholesterol transport to liver from muscles and organs to liver.

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82
Q

What is a chylomicron?

A

Amphiphilic monolayer coat of phospholipids, cholesterol, and apolipoproteins. Core of TAGs and Cholesterol ester.

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83
Q

What do LDLs do?

A

Cholesterol transport.

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84
Q

What are IDLs

A

LDL precursor.

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85
Q

What are the 5 classes of Lipoproteins?

A

LDL,HDL,IDL,Chylomicron, VLDL`

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86
Q

What are apolipoproteins?

A

Proteins associated with lipids (about 10), important for binding to receptors on cell surface, allowing to lipoproteins to target tissue.

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87
Q

What is the structure of Apoliprotein?

A

predominantly alpha-helical.

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88
Q

How are Chylomicrons and VLDLs bound to cells and what happens when it binds to the cell?

A

They bind in the caveolae on the surface of the cell, to a GPI-anchored receptor. LPL on the receptor is activated by ApoCII on the chylomicron. This causes the FFA to be released and transported to adipose or muscle cells. Then it remnants are released to circulate back to the liver.

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89
Q

How are stored fats mobilize?

A

Glucagon (peptide hormone) bind to GPCR–stimulated cAMP production–cAMP binds to PKA, activating it–PKA phosphorylates Perilipins and HSL–activates breakdown of TAG Droplets–Mobilized Fatty acyl chain are bound to serum albumin and goes to blood.

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90
Q

What are the three lipases required for FFA in fats stored in lipid droplets?

A

ATGL, HSL, MGL

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91
Q

What is humans serum albumin (HSA)?

A

6molecules of palmitate. Produces in liver. Most common blood protein. Transports FFA, steroid/thyroid hormones, non-polar drugs, biribubin and more. Helps regulate oncotic pressure.

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92
Q

How are Long FA transported into mitochondria?

A

Long chain Acyl-CoA synthase activates it and binds it to CoA– Carintine Acyl transferase I binds acyl group to carntine past the outer mem–carnotine-acyl moves through anitporter (using carnitine) to go into inner membrane where CoA takes away the acyl group and Carnitine goes back. (look at notes) .

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93
Q

How are FA oxidized in the mito?

A

B-oxidation

-Oxidation (Makes FADH2), hydration, Oxidation (NADH made), thiolysis (acyl-SCoA)–sent to TCA, NADH/FADH2 used in ETC

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94
Q

How is FA synthysis similiar to B-oxidation?

A

it is a revers reaction of each other.

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95
Q

How many ATP is formed from B-oxidation of palmitate?

A

108 - 2 (palmitate- palmitoyl-CoA) = 106

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96
Q

How does FA oxidation compare to glycolysis?

A 
FA=(106/16) = 6.6 ATP/Carbon
Gluc= (32/6) = 5.3 ATP/carbon
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97
Q

Why do unsaturated FA require more Enzymes?

A

Just in case double bond is in the wrong place or conformation (cis-trans use something like Enoyl-CoA isomerase)

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98
Q

What odd chain FA requires additional enzymes for oxidation?

A

Biotin (proprionyl-CoA carboxylase) and B12 cofacters (methylmalonyl-Coa mutase)

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99
Q

When does FA degradation occur in the liver?

A

Low blood sugar, B-oxidation exceed energy requirements for liver or not enough carbs.

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100
Q

What happens in response to FA degradation in the liver?

A

excess acetyl-CoA is used to synthesize ketone bodies. It occurs in mito, and KB are used as alternate source of fuel by tissues.

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101
Q

What are two KB mades by the mito?

A

Acetoacetate and 3-hydroxyl-butyrate.

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102
Q

What are KB?

A

water soluble transportable acyl units. Liver can’t use (no transferase), but muscles (skeletal, heart) and brain can use.

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103
Q

How is FA metabolism regulated?

A
  • Allosteric regulation (ligand binding and covalent mod)
  • compartmentalization
  • regulation of enzyme levels
  • organ specialization,
  • response to hormones (insulin, glucagon)
  • coordinated with other pathways
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104
Q

What is a key regulator in FA metabolism?

A

ACC, Acetyl-CoA carboxylase

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105
Q

How does insulin affect FA metabolism?

A

High blood glucose–insulin–De-phosphorylates ACC–Makes malonyl-CoA–FA synthesis in cytosol/ inhibit CAT-1 transport (FA transport into mito).

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106
Q

How does glucagon affect FA metabolism?

A

low blood glucose–glucagon–PKA (inhibits ACC and PDH, AMPK), Turns of FA synthesis and increases B-ox.

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107
Q

What is the central metabolic intermediate?

A

Acetyl-CoA

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108
Q

In what metabolic processes is Acetyl-CoA an intermediate?

A

CO2 int TCA, KB in liver, FA in liver adipose muscle, and cholesterol in liver .

109
Q

What is and allosteric regulator of ACC?

A

Citrate. ACC normally a dimer (less active). It stimulates polymerization of ACC dimers into filaments (very active).

110
Q

Why doe metabolic assemblies form filaments?

A
  • metabolic organization
  • Regulation of metabolic activity (inhibitor)
  • coordination of cellular activity through large distances.
111
Q

How is FA synthesis regulated by feedback inhibition.

A 
Palmitoyl-Coa is a negative regulator:
-Promotes disassembly of ACC filaments. 
 -Inhibits Citrate Translocase.
Inhibits 
-Inibits G6DPH form PPP
*product accumulation feeds back to inhibit FA synthesis
112
Q

In the case with the little girl with hypoglycemia, what was wrong with her?

A

She had hypoketonic hypoglycemia, could not generate KB. CAT-1 required for transport of FA into mito was missing in the liver. This affected B-oxidation, generation of acetyl-CoA, and of KB in liver.

113
Q

How did they cure the little girl with hypoketonic hypoglycemia?

A

Realized MCTs did not require CAT-1. Not all FA uses CAT-1. She ate a lot of this frequently.

114
Q

List the FA B-Oxidation disorders.

A
  • Carnitine deficiency,
  • Acyl-CoA deficiency
  • CAT-1 an CAT-2 deficiencies
115
Q

What are the functions of cholesterol?

A
  • essential in eukaryotic membranes
  • Stored as cholesterol esters in lipid droplets
  • Precursor to: Bile acids, Steroid hormones, Vitamin D
116
Q

What are the sources of hepatic cholesterol?

A
  1. Dietary cholesterol
  2. From extra-hepatic tissues
  3. De novo synthesis
117
Q

What are the fates of hepatic cholesterol?

A
  1. Small amount incorporated into hepatic membranes.
  2. Synthesis of cholesterol esters by ACAT.
  3. Synthesis of bile salts to aid lipid digestion.a
  4. direct secretion of cholesterol into bile. (only route to remove from body).
118
Q

Where is the primary site for cholesterol biosynthesis?

A

The liver

119
Q

What are the three stages of Cholesterol DE Novo synthesis?

A

Stage:
1a- synthesis of HMG-CoA in cytosol
1b- synthesis of isoprenoid units - in cytosol
2. six isoprenoid units condense into squalene
3. Squaline,O2, NADPH = cholesterol . - in ER
*reference slide to see process.

120
Q

How many carbons are in squalene?

A

30

121
Q

In cholesterol, what stage is like KB synthesis?

A

stage 1a

122
Q

In cholesterol synthesis, which stage is the committed step?

A

1b- Synthesis of isoprenoid units- HMG-CoA reductase

123
Q

How is squalene converted into a 4-ring sterol?

A

A. Squalene epoxidase
B. Cyclase (lanosterol synthase)
C. 19 different enzymes located in the ER membrane.

124
Q

Cholesterol is energetically..

A

expensive. Not degraded or used for energy, must be tightly regulated.

125
Q

What are some uses for cholesterol intermediates?

A
  • isopentyl pyrophosphate– ubiquinone.
  • Farnesyl (15) used in post-translational modification, targets certain proteins to anchor into membranes.
  • Vitamin D
126
Q

What is vitamin D important for?

A
  • Hormone involved in calcium and phosphorus homeostasis, -Regulate synthesis of intestinal Ca2+ binding protein.
  • Rickets- Vitamin D deficiency causes softness in bones.
127
Q

What are some steroid hormones derived from cholesterol?

A

Aldosterone, Glucocorticoids, Testosterone and estradiol, Steroids regulate gene expression.

128
Q

What is Aldosterone?

A

From adrenal gland, regulates reabsorption of NA+, Cl-, HCO3- in the kidney.

129
Q

What is Glucocorticoid?

A

Cortisol (adrenal gland). Affects protein, fat, and carbohydrate metabolism; suppresses immune response, inflammation, and allergic responses.

130
Q

How do steroids regulate gene expression?

A

Steroid enters because lipid soluble-Bind to steroid receptor–Receptor migrates to nucleus—Bind hormone response element (HRE) on DNA—-Activates target gene expression .

131
Q

How is the steroid receptor structured for signaling?

A

domains. AD (activater domain. ZF (zinc finger) domain binds DNA. SB (steroid binding) domain. Ligand-binding leads to dimerization and binding to DNA.

132
Q

How do cells take in LDLs?

A

Receptor-mediated endocytosis.

133
Q

What is Apo-B100?

A

LDL surface protein. One of the larges singe polypeptide chains known. It is sensed by receptors on the cells and the cells taking in the LDL.

134
Q

What is Clathrin Triskelion?

A

Also know as jsut clathrin, it is a hexamer that forms coated pits when LDLs or large cargo is sensed outside the cell. IT forms and internalized cage inside the cell.

135
Q

What is Dynamin?

A

GTpase involved in receptor-mediated endocytosis. Oligomerizes around the neck of the budding vesicle. Catalyzes scission of the vesicle from parent membrane.

136
Q

What is Auxilin and HSC70?

A

Proteins involved with receptor-mediated endocytosis, bind at the vertices where 3 triskelia meet and promotes disassembly of the clathrin cage.

137
Q

Acyl-CoA cholesterol Acyl transferase (ACAT) is used for what purpose?

A

Esterfies cholesterol with a fatty acid for transfer or storage. Activity important in intestine and liver for cholesterol incorporation into lipoproteins. Esterfication promotes storage into lipid droplets.

138
Q

LCAT is associated with circulating…?

A

LDL and HDL

139
Q

High levels of cholesterol affects cells intracellularly by..?

A

Fed state

  • activates ACAT for storage
  • Stimulates degradation of HMGR
  • Reduces synthesis of LDL receptors
140
Q

Low levels of cholesterol affects cells intracellularly by..?

A

Low energy

  • Stimulates HMGR synthesis
  • Stimulates synthesis of LDL receptors
141
Q

In rapid regulation of HMG-CoA Reductase activity, insulin..?

A

Fed state

-Synthesized and store cholesterol. Promotes HMGR dephosphorylation.

142
Q

In rapid regulation of HMG-CoA reductase activity, AMPK…?

A

Low energy state

-Turns off an expensive synthetic pathway, promotes phosphorylation.

143
Q

HMGR is what type of protein and what organelle is it associated with?

A

It is and integral protein associated with the ER.

144
Q

What it the long term regulation of HMG-CoA reductase Activity?

A

control of enzyme levels through gene expression. When cholesterol levels are high, it binds to SCAP preventing gene expression of HMG-CoA reductase and LDL receptors.

145
Q

In low cholesterol levels, how is HMGR gene expression promoted?

A
  1. INISIG dissociates from complex SREBP/SCAP migrates form ER to golgi.
  2. In golgi, S1P cleaves SREBP
  3. S2P Zn2+ - Metaloprotease releases bHLH transcription activation domain from the golgi membrane, where it begins to form a dimer
  4. it moves to the nucleus and binds to the specific DNA sequence (SRE)
146
Q

SREBP

A

Regulates expression of genes for HMG-CoA reductase, LDL receptors.

147
Q

How do high levels of cholesterol directly affect HMG-CoA reductase?

A

Promotes HMGR degradation by binding to HMGR sterol sensing domain. Promotes complex formation between INSIG and HMGR/ . Leads to destruction of HMGR by proteases.

148
Q

Individuals with defective LDL receptors have..?

A

Exceptionally high plasma cholesterol (Familial Hypercholesterolemia).

149
Q

Tangier Disease is when-

A

Lack ABC-A1 transporter, flips cholesterol from inner to outer leaflet of the plasma membrane where it can be captured by apolipoprotein A-1 and incorporated into HDL. Deposition of cholesterol in cells and tissues.

150
Q

What are the ways to treat high cholesterol?

A
  • Bile acid binding Resins (limits absorption increases elimination)
  • Statins - target HMG-CoA reductase
  • Inhibitors of cholesterol absorption - Inhibit the protein for transport into intestine
  • combination therapies
151
Q

Statins

A

-Reduces circulating LDL-cholesterol levels. Increases in HDL and decreases in Triglycerides. Inhibition of cholesterol synthesis reduces intracellular cholesterol pool and up-regulates LDL-receptors.

152
Q

Why does HMG-reductase have such a more higher affinity for statins than actual HMG?

A

Hydrophobic rings of the statins. Exploits the conformational HMGR for higher affinity binding.

153
Q

Adapter proteins do what?

A

Bind receptors loaded with protein and Clathrin, sorting and concentrating at the membrane.

154
Q

What makes amino acids valuable in energy metabolism?

A

The Nitrogen.

155
Q

What happens to Amino acids?

A
  • new protein synthesis
  • nucleic acids
  • neurotransmitters
  • Basically amino acids are recycled.
156
Q

Proteases and peptidases are secreted by?

A

The stomach and the pancreas.

157
Q

What is the problem with digestive enzymes?

A

Should degrade dietary proteins, but not the proteins of you own body.

158
Q

What is the solution to prevent digestive enzymes from affecting body cells?

A

Synthesize them as inactive zymogens. Secretion of inhibitors. Localization.

159
Q

What is pepsin?

A

An aspartic protease secreted as pesinogen by the stomach. It is optimal at pH of 2 and cleaves N-terminal of phe, Trp, Tyr

160
Q

What are serine proteases?

A

Secreted by pancreas, consists of trypsin-ogen, chymotrypsin-ogen, and carboxypeptidases optimal at ph of 7 in the small intestine.

161
Q

What is Aminopeptidase N?

A

Located in the intestinal wall, it is a membrane-associated metalloprotease.

162
Q

How are aa transported from the intestine to the blood stream.

A

Na +-dependent amino acid symporters. AA are relatively soluble.

163
Q

What is a lysosome?

A

Membrane organelle, originating from golgi. Contains digestive enzymes. Breaks down components through vesicular fusion and cross-membrane transport.

164
Q

What is lysosome autophagy vs endo- and phagocytosis?

A

Autophagy is breaking down and recycling cellular components. Phago and endo is degrading extracellular components.

165
Q

How are lysosome enzymes controlled?

A

It is optimal at pH of 5, transport proteins bring proteins in and products out. Vesicles can fuse with the lysosome. Membrane proteins are glycosylated to prevent digestion.

166
Q

How is the pH maintained in a lysosome?

A

Lysosomal ATP-dependent proton pump.

167
Q

What is the Ubiquitin-PRoteosome System (UPS)?

A

provides a means of degradation of cellular proteins. Highly selective and efficient degradation (within minutes). Proteins are tagged with Ubiquitin as a signal and 26s Proteasome degrades it. UB is reused.

168
Q

Where is the 26s Proteasome found?

A

In the nucleus and cytosol. Both free and associated with the ER (for the ER-associated degradation. ERAD)

169
Q

What consists of the 20s core particle of 26s Proteasome?

A
  • 4 heptameric rings
  • inner B-rings form the proteolytic chamber. Different ones with different specificities. Outer a-rings form an entry gate.
170
Q

What makes up the 19s part of the 26s Proteasome?

A

Lid - removes Ub from captured substrates

Base- ATPase subunits unfolds substrates and opens a-rings.

171
Q

Proteasome participates in the control of critical processes such as?

A
  • Inflammatory response
  • Cell-cycle progression
  • Gene transcription
  • Organ formation
  • Circadian rhythms
  • Cholesterol metabolism
  • Tumor suppression
  • Protein Quality Control
  • Antigen processing and presentation
172
Q

How do cells let the immune system know that they have been invaded by a pathogen?

A

Pathogen proteins get destroyed by proteasome. Peptide are displayed on cel surface bound to MHC complex. It helps recognize self versus non-self.

173
Q

What are some key features of Ubiquitin?

A

Highly conserved, found in all eukaryotes. Can be post-translationally attached to lysine residue. Can form polymers. requires enzymatic cascade for attachment. Can be reversible cleaved off.

174
Q

What are the three classes of enzymes involved with ubiquitin?

A
  • E1 Ubiquitin Activating Enzymes (~2)
  • E2 Ubiquitin Conjugating Enzymes (~40)
  • E3 Ubiquitin Ligases (>700, more than kinases)
175
Q

What does E1 of the Ub cascade do?

A

• ATP-dependent activate the Ub C-terminus

176
Q

What does E2 of the Ub cascade do

?

A
  • carry activated Ub as a covalent thioester conjugate
  • in most cases, transfer Ub to the substrate protein
  • share a conserved core domain of ~150 amino acid residues
177
Q

What does E# of the Ub cascade do?

A

• catalyze efficient and specific transfer of Ub to a Lys residue on a substrate protein • level of regulation

178
Q

How can the different linkage type of multi ub affect the function of Ub?

A

Poly Ub can cause Proteasomal degradation, signal transduction. Mono ub causes DNA repair or Endocytosis. Multi ub causes endocytosis.

179
Q

Other than degradation, what can Ub signal for?

A

change in protein localization, conformation, activity, binding partners etc.

180
Q

In the Ub code, what is the difference between lys48 versus lys63?

A

Lys 63 is elongated structurally, it used for signaling, trafficking, and DNA damage response. Lys 48 is more compacted and used for proteasomal degradation.

181
Q

Is there a way to reverse Ubiquitylation?

A

Yes by deubiquitinases (DUBs)it is similar to phos/dephos. IT hydrolyzes at the c-terminus of Ubs. That can have specificities for certain chain types. They are often bound to a respective E3. It breaks them down into polyprotein precursors.

182
Q

What are Ubls?

A

Ubiquitin-like proteins. Each Ubl has its own dedicated E1, E2, and E3 system.

183
Q

What is Nedd8?

A

An Ubl used for covalent activator of cullin Ubiquitin E3 ligases.

184
Q

What is Atg8/12?

A

An Ubl essential for the growth and expansion of autophagosome membranes.

185
Q

What is SUMO?

A

And Ub like molecule, (smal-ub-related-modifier). It is important for protein interactions like nuclear transport, transcription, DNA repair, and more.

186
Q

How does HIF1a use UPS for regulation/

A

In normoxia, an E3 ligase complex recognizes Pro564-OH and degrades it.

187
Q

What are some of the things AA are used for?

A

New protein synthesis, nucleic acids, neurotransmitters, etc.

188
Q

How is excess NH4 excreted from the body?

A

It is converted into Urea by the Urea cycle in the liver.

189
Q

What are some key AA for nitrogen transport and amino acid metabolism?

A

Glu, Gln, Ala, Asp. Used for moving amino groups between molecules. Easily converted to glycolytic and TCA cycle intermediates.

190
Q

What are reactions that use ammonia?

A
  • Glutamine synthetase
  • Carbamoyl-Phosphate synthetase I
  • Glycine synthase (glycine cleavage enzyme)
191
Q

What are reactions that generate or release ammonia?

A
  • Glutamate dehydrogenase

- glutaminase (Release for synthesis or excretion)

192
Q

What is PLP (Pyridoxal Phosphate)?

A

a versatile cofactor used throughout Amino acid metabolism. (vitamin B6)

193
Q

Aside from AA metabolism, what else is PLP used for?

A

Glycogen phosphorylase (carb metabolism), Sphingolipids (Serine + palmitoyl-CoA) in lipid metabolism.

194
Q

What does PLP-dependent Aminotransferase reactions do?

A

α-amino groups are transferred to α-ketoglutarate to form Glutamate. Lys at end.

195
Q

What are the mechanism for PLP-dependent Aminotransferase reactions?

A
  1. Aspartate + PLP = oxaloacetate + PMP
  2. α-ketoglutarate + PMP = Glutamate + PLP

Ping pong reaction

196
Q

What are some medically useful markers for tissue damage?

A
  • Alanine transaminase
  • Aspartate Amino Transaminase (most active enzyme in liver)
  • SGPT and SGOT tests

Appear in serum after heart attack, drug toxicity, or infection released form injured cells. For Heat attacks and liver damage.

197
Q

How does nitrogen get from Muscles to the liver?

A

Glucose-alanine cycle

198
Q

What is the Cori cycle?

A

Muscles operate anaerobically. They produce pyruvate from glycolysis and is converted to lactate where it is recycled by the liver.

199
Q

What is the glucose-alanine cycle?

A

Pyruvate from the muscles are converted to alanine where it is recycled in the liver. In the liver Ala is converted back to pyruvate, pyruvate and lactate are turned into glucose and ammonia is released and converted to urea.

200
Q

In tissues (not muscle) how his nitrogen transported via glutamine?

A

Degradation of certain AA and nucleotides generates free NH4. This transported using three components:

  • Glutamine synthase
  • glutamine -neutral and non-toxic
  • glutaminase
201
Q

Describe the mechanism for using glutamine to transport nitrogen?

A
  • Glutamine synthase-Key regulator of cellular nitrogen metabolism.
  • Glutamine- transports amino groups from extra-hepatic tissues to the liver.
  • Glutaminase -mitochondrial liver enzyme releases one NH4 from Gln.
202
Q

What is glutamate Dehydrogenase’s purpose (GDH)?

A

A Liver- specific Mitochondrial Enzyme Generates α-KG, NAD(P)H, and free NH4+. a-KG is sent to TCA, NH4 is sent to Urea cycle.

203
Q

In the Urea cycle how is NH4 converted into Urea?

A

In the mito:
-CPS-I uses ATP to turn NH4–carbamoyl phosphate–citrulline.

In the cytosol:
-ATP and Aspartate used to to make Arginine, where arginase will use H20 to make Urea.

204
Q

In the Urea cycle: where does the aspartate come from?

A

Aspartate aminostransferase in to mito.

205
Q

How is the Urea cycle regulated?

A

Allosteric Activation of Carbamoyl-Phosphate-Synthase-I (CPS-I) by N-Acetylglutamate

206
Q

How is N-Acetylglutamate produced?

A

High levels of Arg and Glu signal nitrogen levels are high and activate N-acetylglutamate synthase. To deactivate it a specific hydrolase degrades N-acetylglutamate and turns off CPS-I.

207
Q

In degradation of AA what can carbon skeletons be used for?

A

Enter TCA or be used for glucogenesis.

208
Q

What can the liver do with AA?

A

Energy, gluconeogenic precursors, ketone bodies, FA biosynthesis.

209
Q

Which AA are purely Ketogenic?

A

Leu, Lys,

210
Q

What is Phenylketonuria?

A

Genetic deficit in Phe-hydroxylase, Phe build up in body. Need to watch protein intake.

211
Q

What are some essential proteins for humans that can e synthesized, but not in adequate amounts.

A

Arg and Met.

212
Q

What are the 5 classes of PLP catalyzed reactions?

A
  • Transamination
  • racemization
  • decarboxylation,
  • B-elimination/replacement,
  • y-elimination/replacement.
213
Q

What are the purposes for the PLP catalyzed reactions?

A
  • Transamination reactions- AA synthesis and degradation
  • decarboxylation- synthesis of neurotransmitters
  • β and γ-elimination/replacement– Amino acid synthesis
214
Q

Why is PLP so versatile?

A

-Formation of a Schiff’s base
covalently links the amino acid to the cofactor
-PLP cofactor is an “electron sink” Stabilizes the carbanion by electron delocalization
-determines which bond is broken

215
Q

How are PLP reactions controlled stero-electronically?

A

The enzyme orients the σ-bond to be cleaved with the conjugated π-orbitals

216
Q

Describe the Tryptophan Synthase α2β2 multi-enzyme complex from Salmonella.

A

• linear α-β-β-α arrangement of enzymes • α-subunits catalyze the cleavage of IGP
• β-subunits synthesize L-Trp
• β-subunits are PLP-dependent enzymes
-uses substrate channeling

217
Q

How does tryptophan synthase in salmonella synchronize catalytic activity?

A

Binding of IGP at α-site increases reactivity at β-site.
E(A-A) formation at the β-
site is the allosteric trigger to increase catalytic activity of the α- subunit.

218
Q

What is carbamoyl phosphate synthase?

A

Important for:

Enyzmes of the Urea cycle & Amino Acid synthesis Nucleotide Biosynthesis (many rxns get nitrogen from Gln)

219
Q

How does Carbamoyl Phosphate Synthase substrate channel?

A

Substrate channeling

  1. covalently tethered intermediates.
  2. Enzyme Tunnels
    - NH3 released from Gln travels via a channel to a second site. `
220
Q

In FAS, what makes domains make up the condensing and modifying domain?

A

Modifying-KR, DH, ER

Condensing-KS, MAT

221
Q

In FAS, Thioesterase (TE) domain is tethered to what domain?

A

ACP

222
Q

Amino acid synthesis and degradation is closely linked to…?

A

Glycolysis and TCA

223
Q

where does Ala enter in the TCA cycle?

A

It is converted into pyruvate.

224
Q

How does Asn/Asp enter the TCA cycle?

A

Oxaloacetate.

225
Q

How does Gln/Glu enter the TCA cycle?

A

alpha-glutarate

226
Q

How is L-serine synthesized?

A

Glucose—3-phosphglycerate– It is then oxidized by NAD+, transferred an amine group from Glutamate and PLP, then it is loses a Pi, becoming L-serine.

227
Q

What can L-serine be made into

A

L-cysteine, and glycine

228
Q

What two cofacters are required to synthesize glycine from L-serine?

A

PLP and THF

229
Q

What enzyme makes glycine from Serine?

A

SHMT-PLP dependent cleavage of an α-β C-C bond

230
Q

What is THF derived from?

A

Folate, which is obtained form diet.

231
Q

How is Folate converted to THF?

A

It oxidized by NADPH to make DHF, the it is oxidized by NADPH again to make THF.

232
Q

Sulfonamides are antibiotics that do what?

A

They inhibit folate synthesis in bacteria. IT mimics p-aminobenzoate, inhibiting pathway.

233
Q

What can a folate deficiency cause?

A

Critical for nervous system development. can cause neural tube deficits.

234
Q

What makes up the THF structure?

A
  • PTeridine,
  • p-aminobenzoate,
  • glutamate (0-4)
235
Q

What can THF do?

A

Carry 1-carrbon units in different oxidation states. Enzymes can interconvert most form except N5-Methyl-THF

236
Q

What is the main source of 1-carbon units for THF

A

Ser to Glyc

237
Q

What are the cofactors involved in 1-carbon metabolism?

A
  • biotin
  • tetrahydrofolate (THF)
  • S-adenosyl Methionine (SAM)
238
Q

Biotin is involved with what reactions?

A

-FAS (ACC)
-Gluconeogenesis (Pyruvate Carboxylase)
Carries MOST oxidzed carbon

239
Q

What reactions are THF involved in?

A
  • AA degradation
  • AA synthesis (MET biosynthesis)
  • Purine, Pyrimidine biosynthesis
240
Q

What is the purpose of SAM?

A

> 40

  • Methylate (modify) proteins, Nucleic acids, lipids, and, secondary metabolites
  • note sulfonium ion
241
Q

What drives SAM carbon metabolism?

A

Conversion of homocysteine to Methionine.

242
Q

How is homocysteine converted to Methionine?

A

Mehtionine Synthase

  • N5-methyl THF
  • Coenzyme B12
243
Q

coenzyme b12 is also know as?

A

Cobalamin

244
Q

Cobalamin is required for what two reactions?

A
  1. conversion of Homocysteine to methionine

2. rearrangement of methyl-malonyl-CoA to Succinyl CoA

245
Q

Methylmalonyl-CoA is formed from?

A

Propionyl-CoA, carboxylation using biotin.

246
Q

What are the components of Methyl-Cobalamin?

A
  • corrin Ring (cobalt)
  • Ribose-P
  • benzimidazole
247
Q

B12 deficiency due to loss of intrinsic factor is called?

A

Pernicious anemia.
Causes reduced production of Hb, erythrocytes, and progressive impairment of the central nervous system. Can be cause by intestinal surgery.

248
Q

Proprionyl-CoA is formed from?

A
  • Catabolism of Val, Ile, Met.

- Degradation of odd-chain lipids.

249
Q

Porphyrins are derived from?

A

Glycine and Succinyl-CoA. Synthesized in the liver and erythroid cells.
Synthesized by δ-aminolevulinate synthase

250
Q

Porphyrins are key for..?

A
  • Hemoglobin
  • Myoglobin
  • cytochromes
  • Detox enzymes
251
Q

What are the precursors for Creatine?

A

Gly, Arg, using SAM cofactor

252
Q

What are the three precursors for Glutathione?

A

Gly, Cys, γGlu

253
Q

What is phospho-creatine used for?

A

Important energy buffer in muscles.

254
Q

What can glutathione be used for?

A

GSH- act as a redox buffer

GST- detoxification of xenobiotics.

255
Q

Tyrosine is a precursor for what bioactive amines?

A

Dopamine, and epinephrine

256
Q

What is the precursor AA of GABA?

A

Glutamate

257
Q

What is the precursor for histamine?

A

Histidine

258
Q

What key enzyme helps create bioactive amines from AA?

A

Decarboxylases

259
Q

What are catecholamines (Epinephrine, dopamine)?

A

regulate blood pressure. Parkinson’s associated with reduced levels
of dopamine

260
Q

What is GABA?

A

Neurotransmitter

261
Q

What is histamine?

A

Vasodilator, allergic response.

262
Q

What is the precursor for serotonin?

A

Tryptophan

263
Q

What are some functions of serotonin?

A

• intestine (regulate gut-movements)
• platelets (released at the site of blood clots -vasoconstrictor - helps stop bleeding)
• Central Nervious System - serotonergic neurons - affects mood, appetite, and
sleep

264
Q

What is Nitric oxide (NO) derived from?

A

Arginine

265
Q

What is NO and its function?

A

hormone, acts locally,
Functions:
neurotranmission, blood clotting, vasodilation (blood pressure regulator, nitroglycerin & amylnitrate)

266
Q

What is the function of dopamine?

A
  • In CNS: Motor Control Reward-motivated behavior Hormone Release
  • Outside the CNS:
  • Affects blood pressure, kidney function, intestinal motility, insulin release, etc.
267
Q

What are PLP-dependent enzymes for which there are available drugs?

A
  • GABA aminotransferase
  • Serine hydroxymethyltransferase
  • Ornithine Decarboxylase
  • Dopa Decarboxylase
268
Q

Why are Parkinson’s patients given L-Dopa and Carbidopa?

A
  • L-dopa is inert and can cross blood/brain barrier

- Carbidopa inhibits the PLP enzyme

269
Q

Why inhibit the enzyme to convert L-dopa to Dopamine in Parkinson’s patients?

A

-L-dopa is highly decarboxylated in the intetstine and other sites outside the CNS, causing nausea and side affects, Carbidopa cannot cross blood brain barrier so it inhibits activity outside the CNS, causing less side affects.

Biochem 406 (3 decks)

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