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Summary of Metabolism 2023
Summary of Metabolism 2023
王琬菁
生化暨分子生物研究所
傳醫乙棟 R606
wangwj@nycu.edu.tw ; (02)2826-7117
Metabolism Overview
Two main processes in metabolism:
分解代谢 合成代谢
catabolism and anabolism.
Chemical energy
• ATP: energy currency.
• NADH, NADPH, or FADH2: (Coenzymes, derived from
adenine)
Pass Test Questions
(A) 29. Coenzyme A , NAD+ ,和 FAD 都利用下列何種物質作為它們的共
同成分?
A. Adenine
B. Guanine
C. Cytosine
D. Thymidine
Step 1-5
Step 6-10
Energy-investing phase
Glucose
Activation by
phosphorylation: It
requires 2 ATP.
(Hexokinase and
phosphofructokinase). Glucose-6-phosphate (G6P)
Glyceraldehyde-3-phosphate
(GAP, G3P)
Dihydroxyacetone
phosphate (DHAP)
Energy-generating phase
GAP is converted
1,3-Bisphosphoglycerate
to pyruvate. (BPG)
GAP Pyruvate
3-Phosphoglycerate (3PG)
Step 1
-High levels of
glucose-6-phosphate
Step 3
-Fatty acid
synthesis is active
Step 10
Pass Test Questions
(D) 87. 將一莫耳 (mole) 葡萄糖經由糖解作用 (glycolysis) 產生兩莫耳丙酮酸
(pyruvate) 的過程中,淨需要:
A. 四莫耳 ATP
B. 一莫耳 NAD+
C. 一莫耳磷酸根 (inogrganic phosphate)
D. 兩莫耳 ADP
UDP-glucose is the
metabolically activated
form of glucose for
glycogen synthesis.
Glycogen breakdown in muscle and liver
Glycogen degradation involves sequential phosphorolytic
cleavages of Glycosidic bonds, catalyzed by glycogen
phosphorylase.
Glucose-1-P
Phosphoglucomutase ( 葡萄糖磷酸變位酶 )
Glucose-6-P
Catabolism of sugars other than glucose
In animals, most of the carbohydrate other than glucose
(Glycogen) comes from the diet.
乳糖
麥芽糖
甘露糖
蔗糖
Lactose and galactose to glucose (Leloir pathway)
Leloir pathway: For utilizing lactose and galactose by converting it to
glucose-6-phosphate
Galactose-1-phosphate undergoes an exchange reaction with UDP-
glucose, which is catalyzed by galactose-1-phosphate uridyltransferase
and releases glucose-1-phosphate and UDP-galactose.
Enzyme defects cause galactosemia 半乳糖血症
半乳糖
乳糖
Pass Test Questions
(D) 39. UDP-glucose 參與下列那個代謝路徑?
A. 五碳糖磷酸途徑( pentose phosphate pathway )
B. 肝醣分解( glycogen degradation )
C. 糖解作用( glycolysis )
D. 半乳糖轉變為葡萄糖( epimerization of galactose to glucose )
Step 1
Step 3
Step 10
Gluconeogenesis: Bypass 1
Bypass 1: Conversion of Pyruvate to Phosphoenolpyruvate
(PEP)
The bypass of pyruvate kinase begins in the mitochondria and
involves two reactions.
Gluconeogenesis: Bypass 1
Reaction 1: Pyruvate carboxylase catalyzes the CO2, ATP,
and biotin-dependent conversion of pyruvate to oxaloacetate.
biotin
Glucagon 昇糖激素
Regulation of Glycolysis and Gluconeogenesis
+ F2, 6BP
Pass Test Questions
(A) 38. 下列何種物質無法作為葡萄糖生合成( gluconeogenesis )之前驅物?
A. 脂肪酸
B. 胺基酸 arsenate
C. 甘油( glycerol )
D. 草醯乙酸( oxaloacetate )
Ribose-5-P
Fructose-6-P
G3P
Net reaction:
The importance of pentose phosphate pathway
Energy generation: It
generates NADPH.
Nucleotide synthesis: It
generates Ribose-5-
phosphate for nucleotide
biosynthesis.
Lactate
dehydrogenase
Cytosol
Cytosol
Mitochondria
Lactate pathway and ethanol pathway
Pyruvate to lactate: When tissues are insufficiently aerobic
to oxidize all of the NADH formed in glycolysis.
Lactate
dehydrogenase
Acetyl-CoA
Human
Pyruvate oxidation and respiration
1. Pyruvate oxidation
Pyruvate converts to acetyl-CoA
3. Electron transport
4. Oxidative phosphorylation
The reduced electron carriers
are reoxidized for ATP
synthesis.
Pyruvate oxidation
If the oxygen is present, pyruvate molecules are transported
from cytosol to mitochondria matrix to form acetyl-CoA.
Pyruvate oxidation is catalyzed by pyruvate dehydrogenase
complex (PDH complex)
It involves three enzymes and five coenzymes.
Pyruvate Dehydrogenase Complex
Three enzymes:
E1: pyruvate dehydrogenase: It removes CO2
Five coenzymes:
Pass Test Questions
(B) 87. 在動物細胞內,下列何者為葡萄糖進行無氧糖解( anaerobic
glycolysis )之淨產物?
A. ATP 和 pyruvate
B. ATP 和 lactate
C. NAD+ 和 ethanol
D. ATP 和 acetyl-CoA
It requires cofactor
CoA-SH
Regulation of TCA Cycle
In the complete
degradation of
pyruvate, pyruvate,
pyruvate is converted
to CO2.
Isocitrate
dehydrogenase at
step 3 of the TCA C6
cycle: The rate
Step 3
limiting step of the
cycle. C5
C4
The link between TCA cycle intermediates
and other metabolic pathway
Pass Test Questions
(A) 88. 下列關於克式循環( Krebs cycle ,亦稱 citric acid cycle 或 TCA
cycle )的敘述,何者正確?
A. 在克式循環過程中, oxaloacetate 淨消耗 (net consumption) 為零
B. 在克式循環過程中,不涉及受質階層磷酸化( substrate-level
phosphorylation )
C. 一次的克式循環會產生一個分子的二氧化碳
D. 一次的克式循環會產生四個分子的 FADH2
(C) 38. 下列何種分子不會直接參與克式循環( Krebs cycle ,亦稱 citric acid
cycle 或 TCA cycle )中的化學反應?
A. coenzyme A ( CoA )
B. ADP (或 GDP )
C. glutathione
D. NAD+
(B) 29. 下列何種輔酶( coenzyme )不參與 α-ketoglutarate 轉換成 succinyl-
CoA 之氧化脫羧反應( oxidative decarboxylation )?
A.Thiamine pyrophosphate
B.Tetrahydrofolate
C.FAD
D.Coenzyme A
(C) 38. 克氏循環( TCA cycle )中那種酵素的受質為一個四碳化合物?
A. 異檸檬酸脫氫酶( isocitrate dehydrogenase )
B. 烏頭酸酶( aconitase )
C. 檸檬酸合成酶( citrate synthase )
D. 乳酸脫氫酶( lactate dehydrogenase )
(A) 95. 下列那一種克式循環( Krebs cycle ,亦稱 citric acid cycle 或 TCA
cycle )的中間產物可以不經由 NADH 的產生,而將其電子直接傳遞給電子
傳遞鏈中的複合體 II ( complex II )進行氧化?
A. succinate
B.citrate
C.α-ketoglutarate
D.malate
Electron Transport Chain (ETC)
Four complexes (I-IV)
together with associated
electron carriers
(ubiquinone and
cytochrome C) is called
the ETC.
They are embedded in the
inner mitochondrial
membrane that shuttle
electrons carried by
NADH and FADH2.
Very slow
Translocases or
flippasese: enzymes that
facilitate transverse
diffusion of lipids in
biological membrane
Rapid
The properties of the biological membranes
Membrane fluidity
-A functioning biological membrane is not a rigid, frozen
structure.
The membrane fluidity is depend on the temperature and lipid
composition, and the presence of cholesterol.
Bacteriorhodopsin
Seven helices
細菌視紫蛋白
a-helical
Hydrophobicity plot
Amino acids of transmembrane protein in lipid-
water interface
Transmembrane protein domains often contain interfacial
aromatic residues.
It may play a role in the insertion and stability of membrane
helices.
Trp and Tyr are often found situated at the lipid-water interface .
Lipid-anchored membrane proteins
Many proteins involved in signal
transduction are modified in this
way.
(3) Glycosylphosphatidylinositol-
linked proteins (GPI-anchored
proteins).
Glycosylphosphatidylinositol-linked proteins
(GPI-anchored proteins)
Gramicidin A
Valinomycin
Two features of ion channels
1. Ion selectivity
-Selectivity for a particular ion
2. Ion gating
-In response to gating stimulus (like pH, membrane potential, or
ligand), the switching between conductive and nonconductive
conformation is called ion gating.
Lys
Arg
Selectivity
filter Closed Opened
Na+/Leu transporter A model for voltage-gating in the K+ channel
Permeases
For transporting big molecules are called permeases (such
as amino acids, glucose and etc…).
E2 conformation (P)
E1 conformation
(D) 5. 下列何種運送方式需要能量?
A. simple diffusion
B. facilitated diffusion.
C. osmosis
D. secondary active transport
Emulsification
脂肪小球
脂肪球
Lipoproteins
Lipoproteins are lipid–protein complexes.
Familial hypercholesterolemia
( 家族性高膽固醇血症 ).
Lysosome
Endosome
Chylomicron VLDL LDL HDL
Density Lowest Highest
Size Biggest smallest
origin Intestine Most from VLDL-IDL Liver,
liver intestine, and
plasma
Apoprotein ApoB-48, ApoB-100, ApoB-100
Apo-C Apo-C, Apo-E
Protein Lowest Highest
amount
Lipid amount Highest Lowest
Cholesterol metabolism
Steroids
&
Ketogenesis Vitamin D
Fatty Acid metabolism
Carnitine serves as a carrier to transport fatty acyl-CoA from
cytosol to mitochondrion for fatty acid oxidation.
Citrate serves as a carrier to transport acetyl-CoA from
mitochondria to the cytosol for fatty acid synthesis.
Steps in b-oxidation of fatty acids
Step 1
Activation of fatty acids
(in cytosol)
Step 2
Transport of fatty acids
into mitochondria
Step 3
b-xidation
(in mitochondria matrix)
Transport of Fatty acyl-CoA into the mitochondria
matrix
Step 1: Carnitine interacts with fatty acyl-CoA yield fatty acyl-
carnitine via Carntine acyltransferase I.
Step 2: Fatty acyl-carnitine transverses the inner membrane through
translocase.
Step 3: Carnitine acyltransferase II exchanges fatty acyl-carnitine
for free carnitine and fatty acyl-CoA in the mitochondrial matrix
Translocase
The importance of movement of fatty acyl-CoA
through the inner mitochondrial membrane
(C3)
(C4)
Ketogenesis
It happens when carbohydrate intake is too low (fasting or
starvation). It causes acetyl-CoA accumulation.
The “extra” acetyl-CoA is 2 Acetyl-CoA
converted to ketone bodies.
It takes places in the liver
Acetoacetyl-CoA
mitochondria.
Acetyl-CoA
Ketone bodies are
transported from liver to other HMG-CoA
tissues as an energy source
for tissues. Acetyl-CoA
Acetone b-hydroxybutyrate
ketone bodies
Mobilization of the store fat (Lipolysis)
The release of fats from adipose tissue is controlled hormonally to
met the needs of organism for energy generation.
Cofactor:
-Biotin
-NADH
1. Condensation of the
growing chain with
actived acetate
2. Reduction
3. Dehydration
4. Reduction.
Rate-limiting step for fatty acid synthesis
acetyl-CoA carboxylase
(ACC)
Pass Test Questions
(C) 90. 脂肪酸生合成之速率決定步驟( rate-limiting step )為:
A. 從 acetate 合成 acetyl-CoA
B. acetyl-CoA 與 malonyl-CoA 的縮合反應( condensation )
C. acetyl-CoA carboxylase 所催化合成 malonyl-CoA 的反應步驟
D. 使 malonate 轉變為 malonyl-CoA 的反應步驟
HMG-CoA reductase is
an ER membrane
Committed reaction
protein with catalytic
unit hanging in the
cytosol.
Control of cholesterol
amount
1. Through controlling de
novo cholesterol
biosynthesis : the major
target for regulation of the
overall pathways (HMG-
CoA reductase).
(3) (1, major)
2. Through storing excess
cholesterol in the form of
cholesterol ester.
Low cholesterol
Express HMG-CoA
reductase and
LDL receptor
Regulation of HMG-CoA reductase
- through ubiquitin-mediated proteolysis
Sterol binding leads to rapid ubiquitin-proteasome degradation of
the HMG-CoA reductase.
Uniquitination complex
1 3
Sterol
2 4
Statin
(1) They act by competitivelysinhibiting HMG-CoA reductase.
(2) It also leads to the increase production of LDL receptors and allows
more rapid clearance of extracellular cholesterol from the blood.
Thus, it decreases blood cholesterol level.
The biological functions of cholesterol
Cholesterol
desmolase
1, 25-dihydroxyvitamin D3 is the
active form of vitamin D.
Pass Test Questions
(B) 40. 下列關於固醇調節區域結合蛋白質( sterol regulatory element-binding
protein ; SREBP )之敘述,何者錯誤?
A. 位於內質網
B. 經由切斷連結的脂肪酸而活化
C. 活化後進入細胞核
D. 做為轉錄因子增加合成膽固醇( cholesterol )的基因表現
4 1
3 2
low-molecular-
weight precursors
Overview of nucleotide metabolism
Salvage pathways: The reutilization of nucleosides and nucleobases
b-Alanine
5-phospho-a-D-ribosyl-1-pyrophosphate (PRPP) is the
central metabolite in de novo and salvage pathway
PPi
Nucleotide Nucleotide
The synthesis of PRPP
It requires ATP
1
5 1 5
Pass Test Questions
(D) 80. 下列何者為核苷酸( nucleotide )重新合成路徑( de novo synthesis )
及補救合成路徑( salvage pathway )皆會使用的重要代謝物?
A. glycinamide ribonucleotide ( GAR )
B. 5-phosphoribosylamine ( PRA )
C. formylglycinamide ribonucleotide ( FGAR )
D. 5-phospho-α-D-ribosyl-1-pyrophosphate ( PRPP )
Purine Metabolism
Generation of IMP
Inosinic acid (Inosine-5’-monophosphate; IMP): The first fully
formed purine nucleotide (11 step reaction).
Hypoxanthine
11 step
reaction
Generation of IMP
The atoms of purine ring are contributed by a number of compounds
including amino acids (aspartate, glycine and glutamine), CO2, and
tetrahydrofolate (10-Formyl-tetrahydrofolate).
Regulatory step
-It requires PRPP amidotransferase
-High amount of AMP, GMP, ADP, and GDP amount inhibit the
reaction
Purine ring
IMP
IMP GMP
Gln, ATP
GMP
IMP synthetase
dehydrogenase
AMP
IMP
Asp, GTP
Adenylosuccinat
e synthetase
Regulatory control of IMP to GMP and AMP
-The reciprocal control of production
De Novo biosynthesis of purine nucleotides
Nucleoside diphosphate
kinase
Salvage pathway of purine nucleotides
A phosphoribosyl transferase reaction catalyzes the
transfer of a free base to the ribose of PRPP, displacing
pyrophosphate and producing a nucleoside
monophosphate (nucleotide).
Phosphoribosyl
transferase
HGPRT: hypoxanthine-guanine
phosphoribosyltransferase.
APRTase: adenine
phosphoribosyltransferase
Purine degradation
Purine degradation leads to form of xanthine and uric acid.
Strategy
Nucleotides
Nucleotidase
Nucleosides
Purine
nucleoside
phosphorylase
(PNP)
Free nucleobases
Uric acids
Xanthine to Uric acid
Xanthine is the point of convergence for the metabolism of the purine
bases (Xanthine Uric acid)
Allopurinol
Pass Test Questions
A) 32. 5-phosphoribosyl-1-pyrophosphate ( PRPP )合成 inosine 5'-
monophosphate ( IMP )的核苷酸生合成途徑中, PRPP amidotransferase 反
應速率可受到下列那一個產物的直接負調控?
A. AMP
B. CMP
C. FAD
D. Malonyl-CoA
Glutamine
CO2
Glutamine and CO2 Sources of carbon atoms
in pyrimidine rings
Control of pyrimidine synthesis
1. Aspartate transcarbamoylase
(ATCase): The enzyme is
inhibited by CTP and activated
by ATP.
CTP synthetase
Thymidylate
synthase
dUMP
(2) salvage
From
Thymidine 5, 10-Methyle-THF
kinase
5-Fluorouracil (FUra)
A target enzyme for chemotherapy because cancer cells requires
dTTP for their proliferation.
Those compounds form dUMP analog that can function as an
irreversible inhibitor of TS.
Some of chemotherapeutic drugs are indicated by
blocking the conversion of DHF to THF.
Pass Test Questions
(C) 30.RNA 降解後, CMP 與 UMP 主要會被代謝成下列那一個中間產物?
A.β-aminoisobutyrate
B.thymine
C.uracil
D.hypoxanthine
Precursors of
Nucleotides and
Heme
Source of energy
(TCA cycle)
The degradation and recovery of amino acid
Degradation of Carbon skeletons
Glucogenic amino acids are amino acids whose carbon skeletons
are degraded to one of these five intermediates.
• Pyruvate
• a-Ketoglutarate
• Succinyl-CoA TCA cycle (Glucogenesis)
• Fumarate
• Oxaloacetate
Ketogenic (Lipogenic) amino acids are amino acids whose
carbon skeletons are degraded to: ketone bodies
• Acetoacetate
Ketone body(ketogenesis)
• Acetyl-CoA
Aminotransferase
PLP
Coenzymes
(amino acid1) (α-keto acid1) (Vitamin B6) (α-keto acid2) (amino acid2)
Pyridoxal phosphate (PLP)
Vitamin B6
Vitamin B6 is also called pyridoxine.
PLP
Amino acids that produce pyruvate
Serine: transamination.
Transamination
Amino acids that produce a-ketoglutarate
Glutamine to a-ketoglutarate via Glutamate
glutaminase
Deamination
Or
Transamination
Amino acids that produce a-ketoglutarate
Glutamate
Amino acids that produce Succinate
Succinyl-CoA
Nitrogen disposal
Protein Synthesis of
Amino acid
synthesis N-compound
a-ketoglutarate
Transamination
Glutamate
Deamination
NH3
Keto acids
Urea
Energy Glucose Fat Non-essential
Amino acids
Pass Test Questions
(C) 44. 胺基酸代謝須進行轉氨反應,此反應最常需要那一種維生素參與?
A. Vitamin B1 ( Thiamine )
B. Vitamin B2 ( Riboflavine )
C. Vitamin B6 ( Pyridoxine )
D. Vitamin B12 ( Cobalamin )