EXAM III Material Flashcards
1
Q
Where does the TCA cycle take place?
A
Mitochondrial Matrix
2
Q
Where is the carbon source from for entry into the TCA cycle?
A
Acetyl CoA via pyruvate
Pyruvate becomes decarboxylated
3
Q
What is the overview of the TCA cycle?
A
Overall process involves the Oxidation of 2C units producing:
2 CO2 molecules
1 GTP
Electrons via NADH & FADH2
First step is condensation of OAA
4
Q
What are the enzymes involved in the PDH complex and what are their prosthetic groups?
A
E1 - TPP; catalyzes oxidative decarboxylation of pyruvate
E2 - Lipamide; transfer of acteyl group to CoA –> TCA
E3 - FAD; regeneration of the oxidized form of lipoamide from hihydrolipoamide (2 e- transferred to FAD & NAD+)
5
Q
What are the catalytic cofactors and stoichiometric cofactors during the TCA rxn of pyruvate to acetyl CoA?
A
Catalytic cofactors:
Thiamine pyrophosphate (TPP)
Lipoic acid
FAD
Stoichiometric cofactors:
CoA
NAD+
6
Q
What are the 3 steps of acteyl CoA formation from pyruvate?
A
Decarboxylation (E1)
Oxidation
Transfer of actyl group to CoA (E2)
Pyruvate dehydrogenase regeneration (E3)
D.O.T.
7
Q
What occurs during decarboxylation of pyruvate during the PDH complex?
A
Pyruvate combines with TPP which then becomes decarboxylated to hydroxyethyl-TPP (intermediate) via pyruvate dehydrogenase component E1 using TPP = prosthetic group
Carbanion (TPP) readily attacks carbonyl group of pyruvate causing decarboxylation (H+ on TPP is very acidic)
Product = CO2
8
Q
What occurs during oxidation in the PDH complex? (E2)
A
Hydroxyethyl group attached to TPP is oxidized to an acteyl group which is then transfered to lipoamide linked to a lysine residue of E1 creating an energy rich thioester bond in acteyllipoamide
(transfer of acteyl group to CoA)
9
Q
What are characteristics of the pyruvate dehydrogenase complex?
A
Complex containing 60 proteins of E1,E2,E3
LARGE protein
10
Q
What are the basic features of the mitochondria?
A
Outer membrane; permeable due to VDAC (voltage dep. anion channels
Inner membrane w/ cristae; impermeable = Oxidative Phosphorylation
Intermembrane space
Matrix - TCA & FA oxidation
Semi autonomous - own DNA
Human mito DNA = 16, 569 bp & encodes 13 respiratory chain proteins, rRNAs, tRNAs
11
Q
What are the electron carriers of oxidative phosphorylation?
A
Coenzyme Q/Ubiquinone
Transfers e- from NADH Q Oxidoreductase & Succinate Q Reductase to Q Cytochrome C Oxidoreductase
Cytochrome C
Shuttles e- from Q Cytochrome C Oxidoreductase to Cyt C Oxidase
Catalyzes reduction of O2
12
Q
What are the prosthetic groups for Complex I? (plus rxn catalyze)
A
FMN
FeS
NADH + Q + 5Hmatrix –> NAD+ + QH2 + 4H+cytoplasm
13
Q
What are the prosthetic groups for Complex II?
A
FeS
FAD
No proton pumping, less ATP synthesized from FADH2 oxidation
FADH2 enters via complex II and remains in the complex & transfers its electrons to FeS then Q –> QH2
14
Q
What are the prosthetic groups for Complex III?
A
Hemes bH, bL, c1
FeS
Passes electrons from QH2 to cyt c transporting 2H+ to cytoplasmic side
QH2 + 2Cyt cox + 2H+matrix –> Q + 2Cyt cred + 4Hcytoplasm
15
Q
What are the prosthetic groups of Complex IV?
A
CuA
CuB
Heme a
Heme a3
16
Q
What are the oxidation states of Quinones?
A
Becomes oxidized and reduced:
Q, ubiquinone (oxidized form)
QH2 ubiquinone (reduced form)
Intermediate contains semiquinone radical
17
Q
What is Friedreich’s Ataxia
A
Mutations in protein Frataxin
Loss of function of small mito protein crucial for FeS cluster synthesis
Affects CNS, PNS, heart, skeletal system = excitable cells
18
Q
Cytochrome C Oxidase
A
Complex IV
Catalyzes transfer of e- from reduced Cyt c to molecular Oxygen = H2o
Pumps H+ across
Cua is reduced to Cub and Fe in hemea end up binding O2 forming a peroxide bridge which becomes cleaved via 2 more protons releasing water
19
Q
What are the 2 pathologies that are related to free-radical injury in oxidative phos?
A
Parkinson disease
Ischemia; reperfusion injury
20
Q
What free radicals form from oxidative phosphorylation and how
A
Due to partial reduction of oxygen
Single electron transfer to O2 = superoxide anion
2e- transfer to O2 = hydrogen peroxide
Both can form hydroxyl radical
21
Q
What defense mechanism occurs in response to free radicals?
A
Antioxidants;
Superoxide dismutase (SOD)
Catalase
22
Q
What is the major storage form of lipids?
A
TAGs - triacylglycerols
TG
Glycerol backbone and 3 FA chains
23
Q
Short and Medium chain FAs in TAGs are digested via what enzymes?
A
Lingual Lipase
Gastric Lipase
<12Cs i.e. TAGs in milk
24
Q
Define emulsification
A
Suspension into small molecules in the aqueous environment caused by bile salts
Which are released by the gall bladder stimulated by cholecystokinin
Bile salts = amphipathic
Increases SA for absorption
25
How are bile salts released from the gall bladder?
Via **Contractions of the gall bladder** stimulated by gut hormone **cholecystokinin**
## Footnote
**Bile salts = amphipathic**
26
Which digestive enzyme is the major one that digests FAs? Short, Medium, and Long
**Pancreatic Lipase**
The **emulsification of FAs becomes the substrate of pancreatic lipase**
27
What is the role of secretin?
**Hormone**
Released in the stomach in response to acidic material in the stomach causing the release of **bicarbonate** which increases the pH (6) to establish an optimal environment for intestinal enzymes
28
What are the 3 steps required to utilize FA as a fuel?
**Mobilization -** TAGs in adipose tissue _released & transported_
**Activation** - FA activated and transported into _mito._
**Degradation -** FA breakdown into _acetyl-CoA_ -\> TCA cycle
29
What is the major source of carbone for fatty acid synthesis?
**Dietary carbohydrates**
30
List characteristics of the mitochondrial genome
DNA contains 16, 569 bp and encodes 13 respiratory chain proteins, rRNAs, tRNAs
31
Which step of the TCA cycle is the only step that directly yields a high energy phosphotransfer compound?
**Succinyl CoA synthetase**
Converts succinyl CoA to Succinate - **The cleavage of succinyl-CoA is a high energy bond; which causes the creation of GTP**
Yields GTP
32
Define anaplerotic pathways and explain their significance
Metabolic pathways that create intermediates; can be used for other pathways
These are required during low states of energy
**OAA can form glucose, alpha-ketoglutarate forms purines and amino acids**
33
During oxidative phosphorylation, where are the protons pumped from the 3 complexes?
From the matrix into the **inter-membrane space**
Protons are returned to the matrix via ATP synthase **powering the synthesis of ATP**
34
What are the components of iron sulfur clusters and their importance?
Tetrahedrally coordinated to SH groups of 4 Cys residues of protein, 2Fe ions, 2inorganic sulfides and 4 Cys residues
4Fe ions, 2 inorganic sulfides, 4 Cys residues
35
What is the Chemiosmotic Hypothesis?
The **pH gradient** and **membrane potential** is generated via **ETC** with the **transport of proteins** from matrix to cytoplasmic side of inner membrane.
This constitutes a **proton motive force** which is used to **drive ATP synthesis**
36
What evidence was used for the Chemiosmotic hypothesis?
**Bacteriorhodopsin in synthetic vesicle**
The vesicle was incubated with ADP + Pi and exposed to light and ATP was generated
37
What are the characeristics of ATP Synthase?
Complex V
Embedded in inner membrane
Ball (**F1 subunit, protrudes into matrix; proton channel)** and Stick **(F0 subunit, membrane; proton channel)** model
38
What are the characteristics of the F1 subunit of ATP Synthase?
Made up of 5 polypeptide chains with diff. stoichiometries
**Alpha3, beta3, gamma, delta, epsilon**
Alpha + Beta = **hexameric ring**, only **beta is catalytically active**
A stalk above the alpha & beta is made up of **gamma and epsilon proteins**
39
What are the 2 ways in which both F0 and F1 subunits are connected to one another in ATP Synthase?
Central gamma and epsilon stalk
Exterior column - 1 a su, 2 b su, and delta su
40
What is the role of the proton gradient in the ETC cycle?
**Release of the ATP from the synthase**
41
Which protein subunit is the active site of ATP synthase?
3 beta su
42
What are the 3 steps in ATP synthesis?
1. **Binding of ADP and Pi (L)**
2. **ATP synthesis (T)**
3. **Release of ATP (O)**
the BAR
Conformations change via **gamma su rotation**
43
What are the characteristics of the proton conducting unit of ATP synthase?
C subunit made up of **2 alpha helices** that **span membrane**
Contains an **Asp** in the center of membrane
**a subunit** has **2 half channels** which allows proton to enter and pass partway, but not completely
44
Define respiratory control
Regulation of cellular respiration via ADP levels
Electrons flow thru ETC only when **ADP is phosphorylated to ATP**
45
What does Inhibitory factor regulate?
ATP synthase; **inhibits hydrolytic activity of ATP synthase**
**Prevents the reverse reaction** (ATP breakdown)
46
Is Inhibitory factor I upregulated or downregulated during ischemia or oxygen deprivation?
**Upregulated**; you do not want ATP synthase pumping due to no oxygen being present as final electron acceptor
IF1 inhibits ATP synthase hydrolytic activity
47
What is the Warburg effect? (ATP synthase regulation)
In cancers where inhibitory factor 1 facilitates the switch from aerobic to anaerobic respiration
48
Define UCP 1 and explains its usage and mechanism of action, what is it activated by?
**Uncoupling protein in the IMM** = **_thermogenin_**
**Uncouples oxphos from ATP synthesis** where **energy is converted to heat rather than ATP**
Used to generate heart and maintain body temp.
**Brown adipose tissue**
rich in mitochondria; reddish brown due to cytochromes & Hb
**Activated by fatty acids!!!**
49
Name the 3 proteins that are involved in uncoupling oxphos and ATP synthesis
**UCP 1**
**UCP 2**
**UCP 3**
Energy homeostasis
50
What is the mechanism of action of 2,4-DNP (dinitrophenol) in OxPhos?
Uncouples ETC from ATP
Dissipates the proton gradient
51
What is the antibiotic and antifungal agent used to inhibit influx of protons into ATP synthase? How does it do this?
**Oligomycin**
Binds to **c su (F0 = proton channel)**
52
What are the methods of actions of atractyloside and bongkrekic acid on OxPhos?
**Atractyloside - inhibits ATP export**
**Bongkrekic acid - inhibits ATP-ADP translocase**
53
Define reperfusion
the action of restoring the flow of blood to an organ or tissue, typically after a heart attack or stroke.
54
What is ATP/energy used for primarily in the brain?
**Signaling (75%)**
Maintaining essential cellular activity (25%)
Metabolic rates higher in gray matter than in white matter
55
How do energy rich substrates enter the brain for cerebral energy metabolism?
Via the blood brain barrier
**Transporters** in the endothelial cells that uptake glucose and monocarboxylic acids
Cerebral metabolic rate increases during early development and plateaus after maturation
56
What are the nutrients that the brain utilizes for energy? (4)
Glucose - primary
Monocarboxylic acids - lactate
Ketone bodies - acetoacetate and beta hydroxy butyrate (used during suckling due to high fat content of milk)
57
What is the significance of compartmentalization of metabolism in the brain?
During hypoxia, glucose is transported into astrocytes for the formation of lactate that can be utilized by neurons
58
What metabolic pathways does the brain utilize?
Glycolysis
Glycogenolysis
Pentose Phosphate Shunt
Malate Aspartate shuttle
TCA cycle
59
What are some experimental methods utilized for studying metabolism of the brain?
Surgical methods - **focal ischemia** (middle cerebral artery occlusion); **global ischemia** (cartid artery occlusion)
In vivi imaging techniques - **MRIs, CTs, CAT scans**
60
What experimental method is useful for local rates of glucose and O2 utilization? How does this work?
**PET Imaging** (positron emission tomography)
Uses analogs of glucose (2-deoxy glucose; experimental animals) and 2-fluoro-deoxy glucose (humans)
Rely on **quantitative intracellular trapping** of DG-6P
61
How does Magnetic Resonance Spectroscopy (MRS) work?
**Utilizes glucose labeled with radioactive (3H, 14C, 11C) or stable isotope (13C)**
Allows assessment of glucose metabolites as they're formed in diff. pathways
**NMR spectra is obtained**
Determines **metabolism of precursors** via specific neuronal and glial pathways
62
What are the two types of ischemia?
**Focal cerebral ischemia -** focal disruption of blood flow to a part of the brain (i.e. due to occlusion of an artery by an embolus)
**Global cerebral ischemia -** transient impairment of blood flow to whole brain (i.e. during cardiac arrest)
63
List some characteristics of a focal ischemia and what happens, how does it occur, etc.
Majority of strokes
Occurs when an **artery** supplying a brain region is **occluded** by an **embolus, thrombus**, or **platelet plug**
Injury grows over time, **necrosis** occurs extending to penumbra (area of reversible damage) = surrounds core
64
Define penumbra
During focal ischemia, the rim/area that is surrounding the core
Area of reduced cerebral flow, impaired protein synthesis, preserved energy metabolism
Prompt restoration = **thrombolytic agents**
During acute phase, want to save the penumbra bc the core is done
Necrosis to penumbra occurs within 3 hours
65
List some characteristics of a global ischemia and what happens, how does it occur, etc.
Transient loss of blood flow to **entire brain** as in cardiac arrest followed by resuscitation
Neurons more sensitive than glial cells
**Selective loss of vulnerable neuronal populations** i.e. pyramidal cells, purkinje cells, striatal neurons
66
List some problems that occur in terms of biochemistry of ischemia
Disruption of blood flow
Reduction/absence of O2 & glucose supply to brain
Impaired energy metabolism
Reduction in ATP levels
Ion pump dysfunction
Disruption of ion gradients
Membrane depolarization
Opening of v.g. channels
Cascade of subsequent signaling events
Cell death in a given brain region
67
What are the events that occur during an ischemic episode in terms of lactate
Fall in PO2 = greater lactate production (Paseur effect)
Cells switch to **glycolysis** = lactic acidosis
K efflux thru K channels
Cellular depolarization/spreading depression propagates in brain tissue
Na+ and Ca2+ gradients collapse
v.g. Ca2+ channels open allowing Ca2+ influx
Release of NT
68
Explain the significance of glutamate in relation to excitotoxic injury
Loss of ion gradients leads to **build up of ECM glutamate**
Glutamate receptor activation = Ca2+ influx = greater ICM Ca2+ = NT release (greater ECM NTs)
Impaired glutamate uptake & excess release
**Glutamate receptor activation causes Ca2+ & Zn2+ influx**
**Activates cytotoxic intracellular pathways**
Mito. damage, NOS activation; NO & ROS, lipid free radicals; membrane damage
69
Which ion causes neuronal death in ischemia when accumulated intracellularly? What harmful substances are released? What degrades the cytoskeleton
Ca2+
**NO and ROS which activate phospholipase A2**
**Damage to mitochondria, membranes, cytoskeleton = calpain**
70
How are ROS formed and what do they do during brain damage
Reactive Oxygen Species (H2O2, superoxide, hydroxyl free radicals) are formed when **mito. donate electrons to O2 forming reactive unpaired e-**
React w/ **proteins, lipids, DNA**
Structural/functional changes in biomolecules
Cellular dysfunction and eventually cell death
71
What are some major characteristics that occur after microvascular injury and edema in the brain? What are the acute and secondary effects?
BBB damaged; greater permeability
**Acute** = Endothelial cells die
Promotoes leukocyte adhesion causing vessel plugging
Hemorrhagic transformation
Entry of cytokines and pro-inflammatory factors
**Edema** = further secondary injury
72
What is ischemic apoptosis and what does it cause?
Programmed cell death
Deprivation of growth factor support
Oxidative stress
Exposure to inflammatory cytokines
Mito. damage
Induced by factors **FAS and TNF-alpha** = apoptosis
73
What are some multi-prong approaches for neuroprotective strategies against ischemia of the brain?
Thrombolytics
**Omega 3 FAs (DHA)**
Heat shock resposne
Antioxidants
Growth Factors
GABA agonists
Protein synthesis inhibitors
Caspase inhibitors
74
Define thrombolytics and state what it is used for
Thrombolysis/Embolectomy
Breakdown (lysis) of blood clots by pharmacological means, and commonly called clot busting
Infusion of tissue plasminogen activator (TPA)
Reperfusion reestablishes circulation; high risk; may cause fatal edema or intracranial hemorrhage
75
What is the pentose phosphate pathway? What is its purpose?
An alternate pathway for glucose oxidation
Begins at **G6P** via glycolysis
Primary role is to create **NADPH and Ribose-5-Phosphate (sugars)**
76
What are the products of the pentose phosphate pathway?
**Ribose-5-phosphate --\> pentoses (ribose, deoxyribose)**
**NADPH (reductive biosynthesis i.e. cholesterol synthesis)**
77
What are the two phases of the pentose phosphate pathway?
**Oxidative Phase I**
**Non Oxidative Phase**
78
What happens during the oxidative phase I of the pentose phosphate pathway?
**G6P --\> Ribulose-5-Phosphate**
**Defective enzyme causes hemolytic anemia**
**Forms 2NADPH + CO2**
**\*\*Rate Limiting**
Enzyme = **G6P Dehydrogenase**
79
What are the fates of the 2NADPH from the first step of the pentose phosphate pathway?
**Reductive Biosynthesis Reactions:**
**Cholesterol synthesis**
**FA synthesis**
80
What steps occur during the Non-Oxidative phase of the pentose phosphate pathway?
**Ri**_bulose_**-5-Phosphate --\> Ribose-5-Phosphate --\> Nucleotide Biosynthesis**
81
What are the 2 fates of ribose-5-phosphate during the pentose phosphate pathway?
**Nucleotide Biosynthesis**
**OR**
**Fructose-6-Phosphate --\> G3P --\> Pyruvate**
82
What enzyme is involved in the rate limiting step of the pentose phosphate pathway?
**G6P Dehydrogenase**
From G6P --\> Ribulose-5-Phosphate
In the Oxidative Phase
83
What occurs when there is a defect in G6P Dehydrogenase of the pentose phosphate pathway?
**Hemolytic anemia**
Causes less NADPH which causes **reduced Glutathione** in RBCs - **Needed for healthy membranes**
**Glutathione reductase - reduces RBCs membranes**
84
What is Mode 1 is the pentose phosphate pathway?
**R5P \> NADPH**
F6P, G3P are forming ribose-5-p
85
What occurs in Mode 2 of the pentose phosphate pathway?
**Balanced**
**Ribose-5-P = NADPH**
Oxidative phase is forming ribose-5-p
86
What occurs in Mode 3 of the pentose phophate pathway?
**NADPH \> Ribose-5-P**
**Reverse glycolysis to go through oxidative phase**
**Ribose-5-p switches to glycolysis**
87
What occurs during Mode 4 of the pentose phosphate pathway?
**Both ATP + NADPH is required**
Complete glycolysis occurs, ribose-5-p reverses arrows
88
What is the key modulator in maintenance of protein homeostasis? (involved w/ protein folding disorders)
**Molecular Chaperons**
Eliminates misfolded, malfunctional proteins
89
What are the 3 components of the cellular quality control system for protein folding disorders?
**Proteosomes -** eliminates proteins
## Footnote
**Autophagy**
**ERAD - ER-Associated Degradation**
90
What is the first known protein-misfolding disease?
Alzheimer's disease
ALS
Sickle cell anemia
Parkinson's disease
Cystic fibrosis
**Sickle cell anemia**
91
What are the 5 types of protein-folding related problems?
**Improper degradation**
**Improper localization**
**Dominant-negative mutations**
**Gain-of-toxic function**
**Amyloid Accumulation**
92
What chaperones are involved in the detection of mutant CTFR and beta-glucosidase? (protein misfolding)
**HSP90**
**AHA 1**
Inhibition of AHA1 allows for a partially funtional mutant CTFR = therapeutic options
93
What degradation systems can be involved with protein misfolding?
**Autophagy**
**ERAD - ER Associated Degradation**
Overactivity that can contribute to accumulation of mutant, misfolded, incomplete degraded proteins and can contribute to more severe diseases
94
What is the cause of improper localization during protein diseases?
**Misfolding of proteins, doesn't allow them to reach their final destination**
**Improper subcellular localization**
**= loss-of-function**
**gain-of-function**
95
What causes AAT deficiency? How can it be treated? Which protein folding disorder is involed?
**Misfolding of AAT, causing it to stay in the liver where it is synthesized**
AAT never gets delivered to the lungs, causing pulmonary emphysema and liver disease
Treatment via enzyme replacement therapy
**Causes Loss of Function and Gain of Function**
96
What occurs during dominant negative mutations? (protein misfolding) Give an example
**A mutant protein antagonizes the function of the WT protein**
Loss of protein activity, mutant interferes w/ function of WT at cellular and structural levels
**Normal conditions, keratin assembles to form intermediate filaments.**
**With a mutant keratin, interacts w/ WT to form a weak filament that fragments upon mechanical stress = Epidemolysis bullosa** (i.e. weak cytoskeleton)
97
What occurs during a gain-of-toxic function in protein misfolding? Describe the 2 examples
**Protein conformation changes that can cause dominant phenotypes**
**ApoE in Alzheimer's Disease** - polymorphism in allele (C112R) forms a salt bridge b/w aa that prevents helix for extending. This causes **altered lipid binding, mito. dysfunction, inhibition of neurite outgrowth**
**SRC Kinase in Cancer -** mutant v-SRC is active and oncogenic due to loss of autoinhibitory region that's regulated by phosphorylation by WT
v-SRC is dependent on chaperones (i.e. HSP 90) so if that's not present, v-SRC is tagged for degradation
98
What occurs during amyloid accumulation of protein misfolding, what are the examples of the problems that it causes? What is the amino acid sequence?
**Amyloid fibers = insoluble protein**
**Amyloidogenic proteins = _VQIVY_ sequence** (amyloid-related diseases; Alzheimer's, Parkinsons, cataracts)
Common in elderly, natural aging, if young individuals have ApoE allele from parents, more likely to develop disease w/ mutations early in life
**Diseases occur from toxic oligomers** (in which amyloid plaques can possibly be a defense mechanism) **or membrane-solubilizing pores that distrupts membrane integrity**
99
What are some ways in which researchers/pharmaceuticals can remediate protein misfoldings?
**TTR = Transthyretin protein = amyloidogenic, primary carrier of hormone thyroxine and a retinol transporter**
**Block aggregate formation**
small molecules that act as a stabilizer
site-specific antibodies that recognize conformational changes, sequence specific = **_VQIVY_**
**Intrinsic induction of stress defence programs & resulting adaptation can increase life expectancy**
**Caloric restriction (Hormetic stress** - adaptive response to stress)
100
Define proteostasis, what steps are required of proteins during this process? What pathways ensure proteostasis in the cytosol, ER, and mito.?
**The maintenance of protein homeostasis**
**Protein production, folding, degradation**
**UPR - unfolding protein response**
**Cytosol = HSP**
**ER = UPRER**
**Mito. = UPRmt**
101
What are the ways in which PDH is regulated?
**Allosterically via Acetyl CoA which _directly inhibits E2_**
**Phosphoylation via Phosphatase and Kinase**
**Pyruvate, Ca2+** (muscle contraction)**, Insulin** (FA synthesis)**, and ADP** activate Phosphatase to make dephosphorylate and make PDH active = **_low energy states_**
While **Acetyl-CoA, ATP, & NADH** activate kinase = **_high energy states_**
102
Describe the unique features of alpha-ketoglutarate dehydrogenase and explain why it's important
**Complex is similar to _pyruvate dehydrogenase_**
In PDH ---\> Acetyl**-CoA**, **NADH, CO2**
In alpha-keto. ---\> Succinyl**-CoA**, **NADH, CO2**
**Both catalyze an alpha-ketoacid and create a thioester linkage with CoA**
103
What 3 enzymes/steps are highly regulated in the TCA cycle?
Pyruvate ---\> Acetyl-CoA (irreversible)
**_Isocitrate dehydrogenase_;** Isocitrate ---\> alpha-ketoglutarate
**alpha-ketoglutarate dehydrogenase;** alpha-ketoglutarate ---\> Succinyl-CoA
104
Explain the regulation of isocitrate dehydrogenase in the TCA cycle; what are the substrates, products, and inhibitors/stimulators?
Isocitrate ---\> alpha-ketoglutarate
Allosterically Stimulated = **ADP** (low energy)
Inhibitor = **NADH, ATP** (high energy)
Integration of this step can involve citrate build up which can go back and stop glycolysis if in high energy states
105
Explain the regulation of alpha-ketoglutarate dehydrogenase in the TCA cycle; what are the substrates, products, and inhibitors/stimulators?
alpha-ketoglutarate ---\> Succinyl-CoA
Allosterically inhibited = **Succinyl-CoA, NADH, ATP** (high energy)
Integration of this step with other cycles occurs during inhibition with a buildup of alpha-ketoglutarate which can be used for amino acid and purine bases synthesis
106
What is the cause of hemolytic anemia? (pentose phosphate)
**Reduced levels of NADPH in RBCs**
**Low NADPH levels inhibit G6P-dehydrogenase = reduced glutathione in RBCs; affects their membrane integrity**
107
What is the function of leptin? What does it act on?
**Signals the hypothalamus that you are full**
Released from fat
108
What is a possible link in the mechanism between obesity and leptin?
Leptin may use a similar mechanism that insulin uses during leptin signaling and obesity (possible leptin resistance)
Pathway is inhibited by suppressors of cytokine signaling SOCS = inhibit inside of the cell even with insulin bound
109
How is overall energy balance regulated in cells?
via **AMP-activated protein kinase (AMPK)**
## Footnote
**receives input from metabolic inputs to determine if PK activity should occur**
110
What determines whether AMPK is active or inactive?
**ATP levels; competition b/w ATP/AMP for binding to AMPK allosteric sites**
**High = Inactive** (does not phosphorylate)
**Low ATP levels = Allosterically Activated**
Phosphorylates targets controlling cellular energy production and consumption
111
What enzyme is involved in the rate limiting step of the urea cycle? Where is it located?
**Carbamoyl Phosphate Synthetase CPS**
**Mitochondria**
Orange Colored Cats Always Ask For Awesome Umbrellas
112
What two amino acids transport ammonia (NH3+) in the blood? (via transamination rxns)
**Alanine**
**Glutamine**
113
What are the digestive hormones involved in lipid metabolism?
**Secretin = bicarbonate release (duodenum)**
**CCK = bile release**
114
What digestive enzymes are involved in lipid metabolism?
**Esterase**
**Lingual lipase -** short chain
**Gastric lipase** - short and medium
**Pancreatic lipase** - all lengths
**Phospholipase A2** - removes FA from phospholipids
115
Explain the importance of apoprotein B48
Involved with the packaging of TAG into chylomicrons with cholesterol, proteins, phospholipids to be transported though the blood by crossing the lymph via **thoracic duct**
inside mucosal cell
116
When does a mature chylomicron form? What are the important Apoproteins?
**Once HDL includes proteins within lymph and blood**
## Footnote
**ApoE and ApoC**
**_ApoCII_ - activates capillary lipoprotein lipase to digest the chylomicron**
**_ApoE_ - is recognized by _receptor_ on surface of liver cells = endocytosis**
117
What sites contain lipoprotein lipase for the digestion of chylomicrons?
**Adipose Tissue**
**Muscle cells**
Which hydrolyzes TG
118
What are the basic steps of FA mobilization from adipocytes?
Activated by glucagon + epinephrine
via G-protein
119
What is the importance of glycerol kinase? What other enzyme is utilized?
**Only used in the liver!!!**
**Breakdown of glycerol into pyruvate or glucose**
**Also uses glycerol-P-dehydrogenase**
120
What are the 3 ketone bodies that are formed from acetoacetate? Why do they form?
**D-3-Hydroxy-butyrate**
**Acetone**
**Acetoacetate**
When acetyl CoA is not being utilized (due to low levels of OAA) they can convert to ketone bodies = **fasting or diabetes**
121
What is the purpose of the carnitine shuttle? Why must this occur?
**Carries long-chain _fatty acyl CoAs_ across mitochondria via carnitine acyltransferase I, translocase, acyltransferase II**
FA synthesis occurs in the cytoplasm, beta-oxidation occurs in the mito. matrix
122
What step is required before the carnitine shuttle takes place?
FA Activation via **Acyl-CoA synthetase** so that CoA can be transferred to carnitine
123
What enzymes are involved during unsaturated and odd chain FA degradation? What vitamin is required?
**Isomerase = odd numbered double bonds = propionyl CoA + Acetyl CoA** (which is converted to succinyl CoA 4C) = **Requires B12; cobalamin**
**Reductase = even chain**
124
What is the major source of carbon for fatty acid synthesis?
Dietary carbohydrates
125
What are eicosanoids?
**Local hormones** which act upon growth, inflammation, infection, immunity via **_Arachidonic acids_**
Signaling messenger molecules
126
What organ does FA synthesis primarily occur? Where in the cell? What other organs?
Liver
Brain, Kidneys, Adipose tissue
**Cytoplasm**
127
What are the major steps of FA synthesis?
**Formation of _Acetyl CoA_**
**Conversion of Acetyl CoA to _Malongyl CoA_**
**_Elongation_**
**_Desaturation_** (introduction of double bonds)
128
What two enzymes are involved in forming acetyl-CoA and OAA from pyruvate? (FA synthesis)
**PC - pyruvate carboxylase forming OAA**
**PDH - pyruvate dehydrogenase forming acetyl CoA**
**Both OAA and Acetyl CoA form Citrate**
129
What is the rate limiting step in FA biosynthesis? What is the enzyme? What cofactor is required?
**Conversion of acetyl CoA to Malonyl CoA**
**via Acetyl CoA carboxylase (ACC)**
Carboxylation, CO2 is added to acetyl CoA
**Biotin**
130
What are the 3 types of regulation of ACC; acetyl CoA carboxylase?
**Allosteric Regulation = (+) citrate; (-) LC FAs**
**Phosphorylation (-)/Dephosphorylation(+) = (+) Insulin, (-) Epinephrine, (-) Glucagon**
**Induction/Repression = gene expression up-regulated high carb/low fat**
**down-regulated high fat/low carb**
131
What are the two steps that occur during the formation of ammonia? What is the prosthetic group and what are the enzymes?
Via transamination and oxidative deamination
**1. Aminotransferase**
**2. Glutamate Dehydrogenase**
Ammonia is taken off Asp and transferred to alpha-KG
alpha-KG is deaminated via GLDH and ammonium is released and enters urea cycle
prosthetic group = **PLP Pyridoxal Phosphate via B6**
132
What are the families of Arachidonate acid? (20C FA)
PPTL
**T**immy **L**oves **P**laying (with) **P**ussy
**Thromboxanes** - platelet
**Leukotrines**
**Prostaglandins**
**Prostacyclins**
133
What is the major transport of cholesterol?
**LDL - low density lipoprotein**
**Contributes to plaque formation**
134
Define ketogenic and glucogenic. What two amino acids are strongly ketogenic?
**Leucine**
**Lysine**
Ketogenic = amino acids that can be converted to ketone bodies or FAs (acetoacetyl CoA)
Glucogenic = amino acids that can be converted to glucose
135
What is ammonium toxic to?
**The CNS; neural tissue**
136
What two enzymes are involved in eliminating free radicals?
**Superoxide dismutase**
**Catalase**
Antioxidants
Oxygen radical -\> Hydrogen peroxide -\> Water
137
What is the role of the proton gradient during ETC?
To release ATP from ATP synthase
138
Which amino acid is involved with the ATP synthase channel?
Asp
Center of subunit c of the proton channel
139
What is the active site of ATP synthase?
3 beta su
140
What is the function of ATP translocase during ETC?
Allows ATP to leave the mito matrix and ADP enters mito matrix during the formation of ATP due to it being impermeable to mito. membrane
141
Conjugated bilirubin
vs.
Unconjugated bilirubin
Conjugated - **soluble/direct** - contains diglucoronide
Unconjugated - **insoluble, bound to albumin**
142
What are the biogenic amines that are derived from amino acids?
HS4T(aday) HSN.S.ET
**H**e **S**hits **4T**imes/day
**H**e **S**hits **N**on**S**top **E**liminating **T**rauma
Histidine - Histamine
Serine - Sghingosine
Tryptophan - Nicotiamide of NAD+
Tryptophan - Serotonin
Tyrosine - Epinephrine
Tyrosin - Thyroxine
143
What is nitric oxide? Which amino acid is it derived from? What enzyme is involved in the formation of NO and what's the required cofactor?
**Short-lived signaling molecule via Arginine**
**NO synthase**
**BH4 - tetrahydrobiopterin**
144
What are the 4 types of NO?
**nNOS = neurotransmitter**
**iNOS = killer compound**
**eNOS = endothial = vasodilator**
145
What is the importance of the glutathione system and what chemical element/antioxidant is involved with it?
**Cytoprotective mechanism, antioxidant, sulfhydryl buffer**
**Selenium** - protects against tissue damage during inflammation and oxidized lipids & hydrogen peroxides (from free radicals)
146
What is the function of AMPK? Under what conditions is it active/inactive?
**Cellular energy sensor**
**_Phosphorylates_ targets controlling cellular energy production and consumption**
Active = low ATP (high AMP)
Inactive = high ATP
147
What is the function of SIR2 gene? What human gene is it analogous to? What enzyme is utilized?
**Deacteylases Lysine making a free Nicotiamide**
Changes metabolic activity when you restrict caloric intake therefore increasing your life span
**Longevity; SIRT1**
**Enhanced by NAD+**
**Inhibited by NADH and Nicotinamide**
***_Enzyme = NAMPT_***
148
Define Long Term Potentiation (LTP), what induces it? Explain the characteristics of this receptor (learning and memory)
**High frequency, sustained stimulation/signals**
**AMPA**
Ca2+ channel with **Glutamate signals**
149
What are the relative percentages of oxygen and glucose utilized by brain cells?
Oxygen is utilized more than glucose
Oxygen **50-70%**
Glucose **10%**
150
What is focal ischemia?
**Middle cerebral artery occlusion**
Certain region of the brain is blocked from receiving blood
151
What is global occlusion?
**Carotid artery occlusion**
Entire brain is blocked from receiving blood
152
What nutrients are used during brain imaging and spectroscopy? (ischemia)
**Glucose and Oxygen**
Cannot detect at cellular level, only detects across various brain structures
153
What reaction does PET imaging detect
Glucose analogs?
**Hexokinase reaction**
2-deoxy glucose (animals)
2-fluoro-deoxy glucose (humans)
154
Define the Pasteur effect (ischemia)
When a fall in PO2 leads to enhanced lactate production
155
What is the protective strategy of NR2B during ischemia?
Injected intravenously 2 hours after stroke
Protected against brain damage and improved neurological functions
156
What death receptors are involved in the extrinsic pathway of ischemic apoptosis?
Outside factors activate:
**FAS**
**TNF-alpha**
157
Which ion is involved in the intrinsic pathway and which organelles do they affect? What does mito. release that causes apoptosis?
**Ca2+**
**Mito. and ER**
Mito. = Cytochrome c - caspase-3 activation via apoptosome complex
ER = ER stress caspase 3,9,12
158
What is DHA and what is their importance?
omega 3 FA that protects against apoptosis
