Biochem 2 M1 Flashcards
(149 cards)
1
Q
Non-essential Amino Acids
A
Can be produced in the body by precursors
2
Q
Essential Amino Acids
A
Can not be produced in the body
3
Q
Semi-essential Amino Acids
A
Synthesized by the body at inadequate rates
May be dependent on intake of other essential amino acids
e.g: Cyt is Met dependent
4
Q
Energy content in Vegetarian vs Mixed diet
A
30 - 50 cal/100g
150 - 300 cal/100g (mixed)
5
Q
Protein content in Vegetarian vs Mixed diet
A
1 - 2g / 100g
15 - 20g / 100g (mixed)
6
Q
Minimum iron requirement of Liver vs Spinach
A
300g of Cooked Liver
2.4Kg of Spinach
7
Q
Where are most a.a Absorbed
A
Jejunum
8
Q
Aspartic Protease + Domains + Active site?
A
Endopeptidases
Pepsin + 2 HIV protease
2 Asp side chains in Active Site
(One protonated, One deprotonated)
9
Q
Activation of Pepsinogen
A
1) One Asp protonated & one deprotonated for catalysis
2) Attacking water oriented at peptide bond
3) Attacking water activated
4) Tetrahedral intermediate (Enzyme + Sub. + Water)
5) Peptide bond split and products released
6) H+ is shuttled back to Asp
10
Q
pH in Duodenum
A
6 - 7.5
11
Q
Importance of Trypsinogen
A
Key regulator
Only enzyme that activates the rest of the proteases once activated to Trypsin
12
Q
What activates Trypsinogen?
A
Enteropeptidase
Produced by intestinal mucosal epithelia
13
Q
ACE2 function
A
Breaks down peptides into free amino acids in the intestine
14
Q
B0AT1 function + where is it found?
A
Transport of free (neutral) amino acids into the cell long with Na+ (cotransport)
Found on the apical side of Enterocytes
Low in duodenum, increases towards ileum
15
Q
What allows B0AT1 to function continuously?
A
Na+ / K+ ATPase on the Basal side
Maintains the proper Na+ conc to allow the entrance of amino acids
16
Q
LAT2 function
A
Neutral amino acid transporter, out of cell.
Adapter proteins direct transport towards a preferred direction (apical/basolateral)
17
Q
EAAT3 function
A
Negative amino acid transporter (Asp & Glu)
Uses Na+ and K+ as a cotransporter
18
Q
B0+AT function
A
Positive amino acid transporter
Absorbs a positive a.a in exchange for a neutral one which can be later absorbed by BOAT-1
19
Q
Glutamate Dehydrogenase reaction
(+ known as)
A
Glutamate <—> a-Ketogluterate + NH4
(NAD+ to NADH)
OXIDATIVE DEAMINATION
20
Q
Why do Proline, Glycine, and B -a.a need special transporters + what are they?
A
SIT1
PAT1
TauT
Due to short side chains and distance bw a-amino & a-carboxyl group
21
Q
Why is Glutathione important? How is it maintained?
A
Crucial Antioxidant in the Liver.
Maintained by liver y-Glutamyl cycle
22
Q
Where is y-glutamyl transpeptidase found?
A
Plasma membrane of Hepatocytes
23
Q
LNAA function
A
Uptake of Tryptophan and branched chain a.a (Na+ dependent)
Branched chain a.a are broken down in muscle during exercise elevating tryptophan, which is converted to Serotonin in Brain
24
Q
LAT1 function
A
Exchange of long neutral amino acids
(Antiporter)
25
2 Types of Tissue Proteases
- Intracellular (Lysosomal, Proteasomal, Autophagosomal)
- Extracellular (Matrix Metalloproteases, Elastase)
26
26S Proteasome Structure
Threonine protease
Acts in Neutral pH
4 rings, 7 ubunits
27
26S Proteasome Function
Protein degrades sequentially as it enters central canal as peptide bonds are cleaved
Similar to serine protease
28
26S Proteasome Ubiquitin and E subunits
Proteins marked by ubiquitin are recognized and further degraded
E1- Ubiquitin activating Enzyme
E2- Ubiquitin conjugating Enzyme
E3- Ubiquitin ligase
29
Autophagy steps
1) Isolation membrane engulfs the target forming Autophagosome
2) Autophagosome fuses with lysosome
3) Autolysosome
30
What is the marker of the Autophagosome and how do they attach?
LC3 - II
Attaches by adapter proteins
(p62) to Ubiquitin
31
mTORC1 funtion in Fed state
Inhibits the break down of muscle proteins
32
mTORC1 funtion in Fasting state
High AMP levels activate AMP-Kinase which inhibits mTORC1, allowing for autophagy and breakdown of muscle proteins for gluconeogenesis
33
What happens after long-term amino acid starvation?
ATF4 triggers Sestrin expression to inhibit mTORC
34
Sestrin2 functions
1) Sestrin ubiquitination and binding to GATOR2 to inhibit mTORC1 signaling. --> skeletal mm breakdown.
2) Sestrin binds to Leu not GATOR2, so mTORC1 is free to be active
35
Fasting state effect on mTORC
1) AMP rises as ATP drops
2) AMP-Kinase activated
3) AMPK inhibits mTORC, independently from Sestrin2
(Aldolase inhibits AMPK)
36
Role of Insulin on mTORC1
Insulin phosphorylates PKB that inhibits the Autophagy genes (proteosome & ubiquitin), and activates mTORC1
37
Matrix Metalloprotease (MMP) Structure / maintained by what
Made up of catalytic domain (Zn2+) and Hemopexin domain which has high processivity.
Maintained by Propeptide
38
2 ways to activate MMP
1) Serine Proteases: Removed propeptide from ProMMP
2) Chemical Agents: Hg salts or NO + O2- (peroxinitrite)
39
MMP use
Activated in sites of inflammation / wounds to break down damaged collagen to allow for new collagen formation
40
2 Ways to regulate serine proteases
1) Pseudo-substrate Inhibitor
2) SERPINS (irreversible)
41
Prosthetic group in the Transamination reaction
Pyridoxal-phsophate in Transaminase enzyme.
Bound by Schiff-base linkage to Lys.
Functions in both directions with PP or Pyridoxamine phosphate which dontes NH3+ to a-KG
42
What is the use of the Purine nucleotide cylcle?
Indirect deamination of a.a using aspartate
43
Direct deamination of Serine
Serine ------> Pyruvate
Serine Dehydratase
(PLP cofactor B6)
44
Where does Direct deamination of Serine occur?
Liver
45
Direct deamination of Glycine
Glycine ---> N5,N10-methylene THF
Glycine Oxidase
(NAD+ to NADH)
46
Importance of Direct deamination of Glycine
Metabolism of Purines and Pyrimidines
Source of Methyl group
47
Amino Acid Oxidases
Uses FMN cofactor
Forms Keto Acid
Eliminate D-amino acids
48
Byproduct of Amino acid oxidase activity + Importance
H2O2
Hydrogen Peroxide
Destroys any infectious agents in GI
49
Why are D-amino acids potentially toxic
They bind to L-amino acid enzymes and inhibit them
50
Sources of ammonia in Liver
1) Intestinal Glutaminase & Urease
2) Hepatic transdeamination
3) Hepatic Purine nucleotide cycle
51
What is the rate limiting step of the ornithine cycle?
CPS1 (carbamoyl ph. synthase)
Regulated by NAG (N-acetyl-glutamate)
52
Where is NAG produced
Mitochondria
53
What A.A can stimulate NAG production?
Arginine (Arg)
Signals a.a absorption to increase CPS-1 activation
54
Role of Glucagon on CPS1 in fasting state
- Glucagon inhibits NAG from leaving the mitochondria (by transporter to cytosol), so it stays bound to CPS1 to activate it for more Urea
55
SIRT3 & SIRT5 activate:
SIRT3: OTC
SIRT5: CPS1
(need NAD+)
56
What activates NAG synthase?
(well fed state)
Arginine
57
What is the signal of Deacetylation of urea cycle?
Tryptophan
By raising NAD+ levels
58
What compensated for ammonia elimination in Acidosis
The kidney
Glutamine to Glutamate by Glutaminase (amm. released)
Glutamate converted to a-KG by Glutamate D.H. (amm. released)
59
What is the major source of Glutamine?
Skeletal muscle
60
Which hepatocytes produce Glutamine?
Pericentral hepatocytes
61
What hepatocytes utilize Glutamine?
Periportal hepatocytes
In Urea cycle
62
Importance of Glutamine in Kidneys
Bicarbonate (HCO3-) production
Used for pH balance
63
Where are Glutamate DH and Glutaminase found?
Mitochondria
64
Importance of Protonation of Ammonia in Urine
- Rids blood of H+
- Ensures constant gradient of NH3 in blood to NH4 in Urine for constant diffusion
65
Urea salvage process
Aided by intestinal bacteria
1) Urea enters intestine, converted to ammonia by Urease.
2) Ammonia used by bacteria to synth a.a even essential ones.
3) A.A absorbed by gut
66
Ketoplastic amino acids
Amino acids converted to Ketone bodies
67
Glucoplastic amino acids
Amino acids converted to glucose (gluconeogenesis)
68
What and how much AA is released from skeletal muscle in fasting state?
60% of total aa from skeletal m is Alanine and Glutamate
69
Daily consumption of Gln and sources
100g
- Skeletal muscle (80g)
- Dietary (only 50% abs.)
70
Glutaminolysis and uses
Using Glutamine to generate Aspartate and ATP
ATP from TCA
Asp used for P nucleotide cycle
71
What a.a used for synthesis of Glutamine in Muscle
Leucine & Valine
72
Vitamin B12 deficiency issues
Affects conversion of Homocysteine to Methionine, so it interacts with water forming Homocysteine Thiolactone which leads to atherosclerosis
73
Degradation of Phenylalanine
Phe ---> Tyrosine
Phenylalanine hydroxylase
74
What can a defect in the breakdown of Phe cause?
Phenylketoneuria
PKU
75
Daily requirement of Fe and diet and storage
20 - 25mg / Day
Diet: 1 - 2mg / Day = loss
Liver store: 100mg
76
What forms H2O2 used in Fenton reaction
Superoxide forming H2O2 using SOD (SO Dismutase)
Can be harmless if Glutathione dismutase converts to H2O and O2
77
Fenton reaction
H2O2 forms OH and Radicle OH-
Leads to Ferroptosis
In cells with excess Fe
(Iron dependent form of cell death)
78
Absorption and transport of Iron
1) Fe(III) reduced to Fe(II) by DcytB + VitC
2) Fe(II) enters duodenal enterocytes via DMT-1
3) Ferroportin releases Fe(II) from basal part of cell.
4) Fe(II) Oxidised for transport in Blood to Fe(III) by Hephaestin/ceruloplasmin (liver)
5) Binds to Transferrin for T.
79
Normal saturation of Transferrin in Blood
30%
(FeIII)
80
Fate of Iron in cells
1) Transferrin carrying 2 ferric ions
2) Binds to TfR1 (primary)
3) Complex enters a Lysosome where Fe is released and reduced to Fe(II) by STEAP
4) Fe(II) exits via DMT1 to be used in mitochondria or stored as Ferritin
81
Ferritin function
Protein (24 subiunits)
Oxidises Fe(II) to Fe(III) and stores it as Ferrihydrite
82
How much Fe found in Ferrihydrite
4500 Fe(III) in one Ferrihydrite
83
Ferritinophagy
Release of Fe from Ferritin by fusion with a lysosome (via NCOA4)
84
Role of Hepcidin
Blocks Ferroportin causing its endocytosis and degredation
So Fe abs. is reduced
Found in Hepatocytes
85
3 ways to regulate hepcidin level
- Plasma Iron (TFR-2 & HFE-prot)
- Intensity of Erythropoiesis
- Inflammation (against bacteria)
86
What happens in Low Iron
IRP binds to IRE, increasing TFR1 production to bring more iron in
87
What happens in High Iron
Iron activates aconitase, and IRP2 is degraded (destroyed), reducing iron uptake.
88
Lead (Pb) on Heme synth
Inhibits at 2 sites:
1) ALA - Dehydratase (Cytosol)
2) Ferrochelatase (Mitochondria)
89
2 Types of ALA Synthase
ALAS1: 'Housekeeping' in many tissues. (PGC1-a transcriptional coactivator)
ALAS2: In RBCs
90
Pyrimidine enter the Enterocyte?
CNT1
or CNT3
Apical side
(Use of Na+ gradient)
91
Purine enter the Enterocyte?
CNT2
or CNT3
Apical side
(Use of Na+ gradient)
92
How is Uracil taken up to Enterocyte?
ENT transporter
Basal Side
93
Hyperuricaemia
1.5% in General Population
7% above 75 y/o
Higher risk of Gout
94
Gout
Deposition of Uric Acid crystals due to high amount in blood, in tissues where pH is less than pKa of UA
95
Uric Acid as an Antioxidant
Can donate H+ to ONOO (Peroxide Nitrite) formed by NO + O2-
Uric acid radicle is excreted by conversion to Allantoin by Uricase
96
Uric Acid as Pro-Oxidant
Can induce the synthesis of NADPH+ Oxidase
Creates ROS
97
Uric acid in Proximal convoluted tubule
Uric acid is Secreted with help of Na+ cotransporters (URAT1)
98
Uric acid in Distal convoluted tubule
Reabsorption of Uric acid by Lactate antiporter (UA exchanged for lactate)
99
Thiazide diuretics
Act on Distal convoluted tubules
Inhibit reabsorption of 3-5% of Sodium
Help treat hypertension and edema
100
Salvage of Purine bases
Ribose-5-phosphate ---> 5-PRPP
by PRPP synthase (Mg2+ cofactor & ATP)
101
Importance of 5-PRPP
Primary method of maintaining purines
Used in De Novo Synthesis of Purines
102
HGPRT enzyme
Phosphorylates:-
- Hypoxanthine to IMP
- Guanine to GMP
(using purine nucleotide cycle)
IMP can also form GMP
103
Treatment of Hyperuricaemia (3)
1) Uricolytic = Lysis of UA to allantoin by Uricase
2) Uricosuric = Secretion of UA in urine (inh. URAT1, OAT4, OAT10)
3) Uricostatic = Inhibits UA formation
104
Amino acids associated with Pyrimidine ring synthases (De Novo)
- Aspartate (C-N)
- Glutamine (N)
- HCO3 (C)
105
Amino acids associated with Purine ring synthases (De Novo)
Glycine (C-N)
Aspartate (N)
Glutamine (N)
HCO3 (C)
106
Limiting step of Purine ring synthesis
PRPP amidotransferase
(Inactive in dimer form)
107
Degradation of Pyrimidine bases
- Uracil --> B-alanine --> Acetyl-CoA
- Thymine --> B-aminoisobutyrate --> propionyl-CoA
108
Salvage reactions of Pyrimidine bases
- Uracil --> UMP
- Thymine --> TMP
(using PRPP and pyrimidine phosphoribosyl transferase)
109
dTMP synthesis
dUMP --> dTMP
Thymidylate synthase + H4 folate
110
How can we inhibit DNA synthesis
Inhibition of H4 folate using MTX
111
How does macrophage recognize cell for Apoptosis
Phosphatidylserine exposure to the outer leaflet (usually inside)
112
How to prevent ROS in Hemolysis
1) Hb binds Hp (Haptoglobin) forming a complex. (or hypoxanthine)
2) Transported by CD163
3) Degraded in Macrophages forming Bilirubin (CO + Fe)
113
Carbohydrate metabolism in the Kidney
Medulla: Glycolytic Part
Cortex: Gluconeogenic Part
114
Lipid metabolism in the Kidney
FA synth is Low
- FA ox. M>C
- Ketone body ox. C>M
- Mitochondria density C>M
115
Gluconeogenesis Stimuli in order
Glucagon
Adrenaline/Noradrenaline
Glucocorticoids
116
How / Where can we form creatine
Arginine + Glycine ---> GAC (guanidinoacetate)
GAC to Creatine in Liver or Kidney
117
Glucose transporter in Liver
GLUT2
118
Glucagon receptors in Liver
Alpha 1 & Beta Receptors
119
Glucagon receptors in Striated Muscle
No glucagon receptors
Rather, E/NE receptors
120
Pentose Phosphate Pathway functions
NADPH increase
Ribose-5-phosphate for nucleotide synthesis
121
Alanine function Liver
Carries ammonia from muscles to the Liver
122
Roles of Valine, Leucine, and Isoleucine in muscles
Valine: Glucoplastic --> succinyl-CoA
Leucine: Ketoplastic --> acetyl-CoA
Isoleucine: Both --> succ/acet CoA
123
Role of Malonyl-CoA in muscle well fed state
Malonyl-CoA blocks CAT-1 transporter from taking FA-CoA into the mitochondria
Signaling that fat is being synthesized so stop B-ox
124
Muscle intense exercise metabolism
1) ATP dec, AMP increases
2) AMPK activated and phosphorylates ACC
3) ACC inactive and does not form Malonyl-CoA from Acetyl-CoA
4) CAT-1 transport active FA-CoA enters
5) LPL active to bring FA in
125
What is preferred in muscles when both glucose and FA available?
FA breakdown
Glucose taken to other organs with higher glucose dependency
126
FA-CoA action in Muscles
Inhibits GLUT4
Inhibits PFK
Inhibits citrate leaving mitochondria
Phosphorylates ACC, no Malonyl-CoA
127
Energy sources of Normal heart
FA ox: 40 - 60%
Glucose ox: 20 - 40%
Ketone & Lactate ox: 10 - 15%
Glycolysis: 2 - 8%
BCAA ox: 1 - 2%
128
PPARs
Nuclear receptors binding FA
PGC-1a cofactor
Binds to DNA via PPRE which initiate transcription
129
Lactate importance brain
Lactate produced in Astrocytes
Utilized by Neuron for ATP through Pyruvate
(Lactate D.H)
130
Glucose transporter Astrocyte vs Neuron
Astrocyte: GLUT 1
Neuron: GLUT 3
131
What percentage of body cholesterol is in the Brain?
25%
132
Brain metabolism in starving condition
FFA can not pass BBB
Ketone bodies can pass
Ketones provide energy source instead of glucose
133
Role of Acetyl-CoA and Asp in Brain
Interact and form N-acetyl-aspartate
Used in Oligodendrocytes for myelin sheaths
134
2 Benefits of Keto diet
1) Suppress malignant tumors
2) Helps decrease seizures in Epilepsy
135
What transports glucose into adipocytes
GLUT 4
136
How do we sense that we have enough precursor for protein synthesis?
Leucine will signal
Activates mTORC = less muscle breakdown
137
PPAR-a
Targets Liver
Stimulates FA oxidation
138
PPAR-y
Stimulates storage of lipids in adipose tissue
139
PPAR-d
Fatty acid oxidation and Thermogenesis in Muscles
140
Leptin and Adiponectin
Leptin: Decreases appetite and increases metabolic rate
Adiponectin: Increases insulin sensitivity and clearance
141
What enzymes have Vitamin B12
- Homocysteine methyltransferase
- Methyl-malonyl CoA Mutase
- Methionine Synthase
142
What enzyme uses Biotin?
Propionyl-CoA Carboxylase
143
Where is non-conjugated (indirect) bilirubin produced?
Spleen
Issues with Hemolysis
Fat-soluble (albumin)
144
Where is conjugated (direct) bilirubin produced?
Liver
Issues with Bile Obstruction
Water-soluble
145
What does Allopurinol Inhibit?
Xanthine Oxidase
(increase in hypoxanthine)
Prevents formation of Uric acid
= Less gout
146
How can we form Ornithine from Glutamate?
1) Pyrroline-5-carboxylate synthetase (ATP) to Glutamate-Semialdehyde
2) Glutamate-Semialdehyde to Ornithine with Aminotransferase
147
Role of R-Proteins and Vit. B12
Produced in Salivary glands and stomach to protect Vitamin B12 from degradation by stomach acid
148
Role of Intrinsic Factor and Vit. B12
Secreted by Parietal cells in Stomach, binds VB12 in duodenum and gets absorbed in the terminal ileum
149
What carries Vitamin B12 in the blood plasma?
Transcobalamin (TC)
