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Biochemistry > Biochem 2 M1 > Flashcards

Biochem 2 M1 Flashcards

1
Q

Non-essential Amino Acids

A

Can be produced in the body by precursors

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2
Q

Essential Amino Acids

A

Can not be produced in the body

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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

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4
Q

Energy content in Vegetarian vs Mixed diet

A

30 - 50 cal/100g
150 - 300 cal/100g (mixed)

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5
Q

Protein content in Vegetarian vs Mixed diet

A

1 - 2g / 100g
15 - 20g / 100g (mixed)

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6
Q

Minimum iron requirement of Liver vs Spinach

A

300g of Cooked Liver
2.4Kg of Spinach

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7
Q

Where are most a.a Absorbed

A

Jejunum

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8
Q

Aspartic Protease + Domains + Active site?

A

Endopeptidases
Pepsin + 2 HIV protease
2 Asp side chains in Active Site
(One protonated, One deprotonated)

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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

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10
Q

pH in Duodenum

A

6 - 7.5

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11
Q

Importance of Trypsinogen

A

Key regulator
Only enzyme that activates the rest of the proteases once activated to Trypsin

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12
Q

What activates Trypsinogen?

A

Enteropeptidase
Produced by intestinal mucosal epithelia

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13
Q

ACE2 function

A

Breaks down peptides into free amino acids in the intestine

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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

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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

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16
Q

LAT2 function

A

Neutral amino acid transporter, out of cell.
Adapter proteins direct transport towards a preferred direction (apical/basolateral)

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17
Q

EAAT3 function

A

Negative amino acid transporter (Asp & Glu)
Uses Na+ and K+ as a cotransporter

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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

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19
Q

Glutamate Dehydrogenase reaction
(+ known as)

A

Glutamate <—> a-Ketogluterate + NH4
(NAD+ to NADH)
OXIDATIVE DEAMINATION

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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

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21
Q

Why is Glutathione important? How is it maintained?

A

Crucial Antioxidant in the Liver.
Maintained by liver y-Glutamyl cycle

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22
Q

Where is y-glutamyl transpeptidase found?

A

Plasma membrane of Hepatocytes

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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

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24
Q

LAT1 function

A

Exchange of long neutral amino acids
(Antiporter)

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25
Q

2 Types of Tissue Proteases

A
  • Intracellular (Lysosomal, Proteasomal, Autophagosomal)
  • Extracellular (Matrix Metalloproteases, Elastase)
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26
Q

26S Proteasome Structure

A

Threonine protease
Acts in Neutral pH
4 rings, 7 ubunits

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27
Q

26S Proteasome Function

A

Protein degrades sequentially as it enters central canal as peptide bonds are cleaved
Similar to serine protease

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28
Q

26S Proteasome Ubiquitin and E subunits

A

Proteins marked by ubiquitin are recognized and further degraded
E1- Ubiquitin activating Enzyme
E2- Ubiquitin conjugating Enzyme
E3- Ubiquitin ligase

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29
Q

Autophagy steps

A

1) Isolation membrane engulfs the target forming Autophagosome
2) Autophagosome fuses with lysosome
3) Autolysosome

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30
Q

What is the marker of the Autophagosome and how do they attach?

A

LC3 - II
Attaches by adapter proteins
(p62) to Ubiquitin

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31
Q

mTORC1 funtion in Fed state

A

Inhibits the break down of muscle proteins

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32
Q

mTORC1 funtion in Fasting state

A

High AMP levels activate AMP-Kinase which inhibits mTORC1, allowing for autophagy and breakdown of muscle proteins for gluconeogenesis

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33
Q

What happens after long-term amino acid starvation?

A

ATF4 triggers Sestrin expression to inhibit mTORC

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34
Q

Sestrin2 functions

A

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

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35
Q

Fasting state effect on mTORC

A

1) AMP rises as ATP drops
2) AMP-Kinase activated
3) AMPK inhibits mTORC, independently from Sestrin2
(Aldolase inhibits AMPK)

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36
Q

Role of Insulin on mTORC1

A

Insulin phosphorylates PKB that inhibits the Autophagy genes (proteosome & ubiquitin), and activates mTORC1

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37
Q

Matrix Metalloprotease (MMP) Structure / maintained by what

A

Made up of catalytic domain (Zn2+) and Hemopexin domain which has high processivity.
Maintained by Propeptide

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38
Q

2 ways to activate MMP

A

1) Serine Proteases: Removed propeptide from ProMMP
2) Chemical Agents: Hg salts or NO + O2- (peroxinitrite)

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39
Q

MMP use

A

Activated in sites of inflammation / wounds to break down damaged collagen to allow for new collagen formation

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40
Q

2 Ways to regulate serine proteases

A

1) Pseudo-substrate Inhibitor
2) SERPINS (irreversible)

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41
Q

Prosthetic group in the Transamination reaction

A

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

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42
Q

What is the use of the Purine nucleotide cylcle?

A

Indirect deamination of a.a using aspartate

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43
Q

Direct deamination of Serine

A

Serine ——> Pyruvate
Serine Dehydratase
(PLP cofactor B6)

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44
Q

Where does Direct deamination of Serine occur?

A

Liver

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45
Q

Direct deamination of Glycine

A

Glycine —> N5,N10-methylene THF
Glycine Oxidase
(NAD+ to NADH)

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46
Q

Importance of Direct deamination of Glycine

A

Metabolism of Purines and Pyrimidines
Source of Methyl group

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47
Q

Amino Acid Oxidases

A

Uses FMN cofactor
Forms Keto Acid
Eliminate D-amino acids

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48
Q

Byproduct of Amino acid oxidase activity + Importance

A

H2O2
Hydrogen Peroxide
Destroys any infectious agents in GI

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49
Q

Why are D-amino acids potentially toxic

A

They bind to L-amino acid enzymes and inhibit them

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50
Q

Sources of ammonia in Liver

A

1) Intestinal Glutaminase & Urease
2) Hepatic transdeamination
3) Hepatic Purine nucleotide cycle

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51
Q

What is the rate limiting step of the ornithine cycle?

A

CPS1 (carbamoyl ph. synthase)
Regulated by NAG (N-acetyl-glutamate)

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52
Q

Where is NAG produced

A

Mitochondria

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53
Q

What A.A can stimulate NAG production?

A

Arginine (Arg)
Signals a.a absorption to increase CPS-1 activation

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54
Q

Role of Glucagon on CPS1 in fasting state

A
  • Glucagon inhibits NAG from leaving the mitochondria (by transporter to cytosol), so it stays bound to CPS1 to activate it for more Urea
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55
Q

SIRT3 & SIRT5 activate:

A

SIRT3: OTC
SIRT5: CPS1
(need NAD+)

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56
Q

What activates NAG synthase?
(well fed state)

A

Arginine

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57
Q

What is the signal of Deacetylation of urea cycle?

A

Tryptophan
By raising NAD+ levels

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58
Q

What compensated for ammonia elimination in Acidosis

A

The kidney
Glutamine to Glutamate by Glutaminase (amm. released)
Glutamate converted to a-KG by Glutamate D.H. (amm. released)

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59
Q

What is the major source of Glutamine?

A

Skeletal muscle

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60
Q

Which hepatocytes produce Glutamine?

A

Pericentral hepatocytes

61
Q

What hepatocytes utilize Glutamine?

A

Periportal hepatocytes
In Urea cycle

62
Q

Importance of Glutamine in Kidneys

A

Bicarbonate (HCO3-) production
Used for pH balance

63
Q

Where are Glutamate DH and Glutaminase found?

A

Mitochondria

64
Q

Importance of Protonation of Ammonia in Urine

A
  • Rids blood of H+
  • Ensures constant gradient of NH3 in blood to NH4 in Urine for constant diffusion
65
Q

Urea salvage process

A

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
Q

Ketoplastic amino acids

A

Amino acids converted to Ketone bodies

67
Q

Glucoplastic amino acids

A

Amino acids converted to glucose (gluconeogenesis)

68
Q

What and how much AA is released from skeletal muscle in fasting state?

A

60% of total aa from skeletal m is Alanine and Glutamate

69
Q

Daily consumption of Gln and sources

A

100g
- Skeletal muscle (80g)
- Dietary (only 50% abs.)

70
Q

Glutaminolysis and uses

A

Using Glutamine to generate Aspartate and ATP
ATP from TCA
Asp used for P nucleotide cycle

71
Q

What a.a used for synthesis of Glutamine in Muscle

A

Leucine & Valine

72
Q

Vitamin B12 deficiency issues

A

Affects conversion of Homocysteine to Methionine, so it interacts with water forming Homocysteine Thiolactone which leads to atherosclerosis

73
Q

Degradation of Phenylalanine

A

Phe —> Tyrosine
Phenylalanine hydroxylase

74
Q

What can a defect in the breakdown of Phe cause?

A

Phenylketoneuria
PKU

75
Q

Daily requirement of Fe and diet and storage

A

20 - 25mg / Day
Diet: 1 - 2mg / Day = loss
Liver store: 100mg

76
Q

What forms H2O2 used in Fenton reaction

A

Superoxide forming H2O2 using SOD (SO Dismutase)
Can be harmless if Glutathione dismutase converts to H2O and O2

77
Q

Fenton reaction

A

H2O2 forms OH and Radicle OH-
Leads to Ferroptosis
In cells with excess Fe
(Iron dependent form of cell death)

78
Q

Absorption and transport of Iron

A

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
Q

Normal saturation of Transferrin in Blood

A

30%
(FeIII)

80
Q

Fate of Iron in cells

A

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
Q

Ferritin function

A

Protein (24 subiunits)
Oxidises Fe(II) to Fe(III) and stores it as Ferrihydrite

82
Q

How much Fe found in Ferrihydrite

A

4500 Fe(III) in one Ferrihydrite

83
Q

Ferritinophagy

A

Release of Fe from Ferritin by fusion with a lysosome (via NCOA4)

84
Q

Role of Hepcidin

A

Blocks Ferroportin causing its endocytosis and degredation
So Fe abs. is reduced
Found in Hepatocytes

85
Q

3 ways to regulate hepcidin level

A
  • Plasma Iron (TFR-2 & HFE-prot)
  • Intensity of Erythropoiesis
  • Inflammation (against bacteria)
86
Q

What happens in Low Iron

A

IRP binds to IRE, increasing TFR1 production to bring more iron in

87
Q

What happens in High Iron

A

Iron activates aconitase, and IRP2 is degraded (destroyed), reducing iron uptake.

88
Q

Lead (Pb) on Heme synth

A

Inhibits at 2 sites:
1) ALA - Dehydratase (Cytosol)
2) Ferrochelatase (Mitochondria)

89
Q

2 Types of ALA Synthase

A

ALAS1: ‘Housekeeping’ in many tissues. (PGC1-a transcriptional coactivator)
ALAS2: In RBCs

90
Q

Pyrimidine enter the Enterocyte?

A

CNT1
or CNT3
Apical side
(Use of Na+ gradient)

91
Q

Purine enter the Enterocyte?

A

CNT2
or CNT3
Apical side
(Use of Na+ gradient)

92
Q

How is Uracil taken up to Enterocyte?

A

ENT transporter
Basal Side

93
Q

Hyperuricaemia

A

1.5% in General Population
7% above 75 y/o
Higher risk of Gout

94
Q

Gout

A

Deposition of Uric Acid crystals due to high amount in blood, in tissues where pH is less than pKa of UA

95
Q

Uric Acid as an Antioxidant

A

Can donate H+ to ONOO (Peroxide Nitrite) formed by NO + O2-
Uric acid radicle is excreted by conversion to Allantoin by Uricase

96
Q

Uric Acid as Pro-Oxidant

A

Can induce the synthesis of NADPH+ Oxidase
Creates ROS

97
Q

Uric acid in Proximal convoluted tubule

A

Uric acid is Secreted with help of Na+ cotransporters (URAT1)

98
Q

Uric acid in Distal convoluted tubule

A

Reabsorption of Uric acid by Lactate antiporter (UA exchanged for lactate)

99
Q

Thiazide diuretics

A

Act on Distal convoluted tubules
Inhibit reabsorption of 3-5% of Sodium
Help treat hypertension and edema

100
Q

Salvage of Purine bases

A

Ribose-5-phosphate —> 5-PRPP
by PRPP synthase (Mg2+ cofactor & ATP)

101
Q

Importance of 5-PRPP

A

Primary method of maintaining purines
Used in De Novo Synthesis of Purines

102
Q

HGPRT enzyme

A

Phosphorylates:-
- Hypoxanthine to IMP
- Guanine to GMP
(using purine nucleotide cycle)
IMP can also form GMP

103
Q

Treatment of Hyperuricaemia (3)

A

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
Q

Amino acids associated with Pyrimidine ring synthases (De Novo)

A
  • Aspartate (C-N)
  • Glutamine (N)
  • HCO3 (C)
105
Q

Amino acids associated with Purine ring synthases (De Novo)

A

Glycine (C-N)
Aspartate (N)
Glutamine (N)
HCO3 (C)

106
Q

Limiting step of Purine ring synthesis

A

PRPP amidotransferase
(Inactive in dimer form)

107
Q

Degradation of Pyrimidine bases

A
  • Uracil –> B-alanine –> Acetyl-CoA
  • Thymine –> B-aminoisobutyrate –> propionyl-CoA
108
Q

Salvage reactions of Pyrimidine bases

A
  • Uracil –> UMP
  • Thymine –> TMP
    (using PRPP and pyrimidine phosphoribosyl transferase)
109
Q

dTMP synthesis

A

dUMP –> dTMP
Thymidylate synthase + H4 folate

110
Q

How can we inhibit DNA synthesis

A

Inhibition of H4 folate using MTX

111
Q

How does macrophage recognize cell for Apoptosis

A

Phosphatidylserine exposure to the outer leaflet (usually inside)

112
Q

How to prevent ROS in Hemolysis

A

1) Hb binds Hp (Haptoglobin) forming a complex. (or hypoxanthine)
2) Transported by CD163
3) Degraded in Macrophages forming Bilirubin (CO + Fe)

113
Q

Carbohydrate metabolism in the Kidney

A

Medulla: Glycolytic Part
Cortex: Gluconeogenic Part

114
Q

Lipid metabolism in the Kidney

A

FA synth is Low
- FA ox. M>C
- Ketone body ox. C>M
- Mitochondria density C>M

115
Q

Gluconeogenesis Stimuli in order

A

Glucagon
Adrenaline/Noradrenaline
Glucocorticoids

116
Q

How / Where can we form creatine

A

Arginine + Glycine —> GAC (guanidinoacetate)
GAC to Creatine in Liver or Kidney

117
Q

Glucose transporter in Liver

A

GLUT2

118
Q

Glucagon receptors in Liver

A

Alpha 1 & Beta Receptors

119
Q

Glucagon receptors in Striated Muscle

A

No glucagon receptors
Rather, E/NE receptors

120
Q

Pentose Phosphate Pathway functions

A

NADPH increase
Ribose-5-phosphate for nucleotide synthesis

121
Q

Alanine function Liver

A

Carries ammonia from muscles to the Liver

122
Q

Roles of Valine, Leucine, and Isoleucine in muscles

A

Valine: Glucoplastic –> succinyl-CoA
Leucine: Ketoplastic –> acetyl-CoA
Isoleucine: Both –> succ/acet CoA

123
Q

Role of Malonyl-CoA in muscle well fed state

A

Malonyl-CoA blocks CAT-1 transporter from taking FA-CoA into the mitochondria
Signaling that fat is being synthesized so stop B-ox

124
Q

Muscle intense exercise metabolism

A

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
Q

What is preferred in muscles when both glucose and FA available?

A

FA breakdown
Glucose taken to other organs with higher glucose dependency

126
Q

FA-CoA action in Muscles

A

Inhibits GLUT4
Inhibits PFK
Inhibits citrate leaving mitochondria
Phosphorylates ACC, no Malonyl-CoA

127
Q

Energy sources of Normal heart

A

FA ox: 40 - 60%
Glucose ox: 20 - 40%
Ketone & Lactate ox: 10 - 15%
Glycolysis: 2 - 8%
BCAA ox: 1 - 2%

128
Q

PPARs

A

Nuclear receptors binding FA
PGC-1a cofactor
Binds to DNA via PPRE which initiate transcription

129
Q

Lactate importance brain

A

Lactate produced in Astrocytes
Utilized by Neuron for ATP through Pyruvate
(Lactate D.H)

130
Q

Glucose transporter Astrocyte vs Neuron

A

Astrocyte: GLUT 1
Neuron: GLUT 3

131
Q

What percentage of body cholesterol is in the Brain?

A

25%

132
Q

Brain metabolism in starving condition

A

FFA can not pass BBB
Ketone bodies can pass
Ketones provide energy source instead of glucose

133
Q

Role of Acetyl-CoA and Asp in Brain

A

Interact and form N-acetyl-aspartate
Used in Oligodendrocytes for myelin sheaths

134
Q

2 Benefits of Keto diet

A

1) Suppress malignant tumors
2) Helps decrease seizures in Epilepsy

135
Q

What transports glucose into adipocytes

A

GLUT 4

136
Q

How do we sense that we have enough precursor for protein synthesis?

A

Leucine will signal
Activates mTORC = less muscle breakdown

137
Q

PPAR-a

A

Targets Liver
Stimulates FA oxidation

138
Q

PPAR-y

A

Stimulates storage of lipids in adipose tissue

139
Q

PPAR-d

A

Fatty acid oxidation and Thermogenesis in Muscles

140
Q

Leptin and Adiponectin

A

Leptin: Decreases appetite and increases metabolic rate
Adiponectin: Increases insulin sensitivity and clearance

141
Q

What enzymes have Vitamin B12

A
  • Homocysteine methyltransferase
  • Methyl-malonyl CoA Mutase
  • Methionine Synthase
142
Q

What enzyme uses Biotin?

A

Propionyl-CoA Carboxylase

143
Q

Where is non-conjugated (indirect) bilirubin produced?

A

Spleen
Issues with Hemolysis
Fat-soluble (albumin)

144
Q

Where is conjugated (direct) bilirubin produced?

A

Liver
Issues with Bile Obstruction
Water-soluble

145
Q

What does Allopurinol Inhibit?

A

Xanthine Oxidase
(increase in hypoxanthine)
Prevents formation of Uric acid
= Less gout

146
Q

How can we form Ornithine from Glutamate?

A

1) Pyrroline-5-carboxylate synthetase (ATP) to Glutamate-Semialdehyde
2) Glutamate-Semialdehyde to Ornithine with Aminotransferase

147
Q

Role of R-Proteins and Vit. B12

A

Produced in Salivary glands and stomach to protect Vitamin B12 from degradation by stomach acid

148
Q

Role of Intrinsic Factor and Vit. B12

A

Secreted by Parietal cells in Stomach, binds VB12 in duodenum and gets absorbed in the terminal ileum

149
Q

What carries Vitamin B12 in the blood plasma?

A

Transcobalamin (TC)

Biochemistry (3 decks)

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