METABOLISM Flashcards
CATABOLISM
degradative/biosynthetic?
oxidative/reductive?
energy released/needed?
converging/diverging?
degradative
oxidative
energy released [though there are some reactions that don’t]
converging
ANABOLISM
degradative/biosynthetic?
oxidative/reductive?
energy released/needed?
converging/diverging?
biosynthetic
reductive
energy needed
diverging
what CONVERGING means in terms of CATABOLISM?
all sugars can be catalysed to CO2 and H2O [final products the same]
what DIVERGING means in terms of ANABOLISM?
same building blocks, different products
in ideal conditions ____ ATP molecules can be obtained from 1 glucose molecule
94 ATP molecules
Chemotrophs are… [def.]
organisms that obtain energy by the oxidation of electron donors in their environments
NAD+ and 2H+ is reduced to
NADH and H+
FAD and 2H+ is reduced to
FADH2
naming of the enzymes is regulated by
NC-IUBMB
NC-IUBMB is an acronym for
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
enzyme class: Oxidoreductases
function: _______
example: ______
enzyme class: Oxidoreductases
function: enzymes catalysing oxido-reductions
example: Alcohol dehydrogenase
enzyme class: ______
function: Transfer a group onto a substrate
example: ______
enzyme class: Transferases
function: Transfer a group onto a substrate
example: UMP kinase
enzyme class: _____
function: ______
example: aminoacyl-tRNA hydrolase
enzyme class: Hydrolases
function: Catalyse the hydrolysis of various bond
example: aminoacyl-tRNA hydrolase
enzyme class: Lyases
function: _____
example: _____
enzyme class: Lyases
function: Cleave C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation
example: pyruvate decarboxylase
enzyme class: ______
function: Catalyse changes within one molecule
example: _______
enzyme class: Isomerases
function: Catalyse changes within one molecule
example: DNA topoisomerase
enzyme class: _______
function: ______
example: DNA ligase (ATP)
enzyme class: Ligases
function: Catalyse the joining of two molecules with accessory hydrolysis of the diphosphate bond in ATP or a similar triphosphate
example: DNA ligase (ATP)
enzyme name: Kinase
action: _____
example: _____
enzyme name: Kinase
action: Transfer of phosphate group
example: Phosphofructokinase
enzyme name: ____
action: Rearrangement of the molecule
example: ____
enzyme name: Isomerase
action: Rearrangement of the molecule
example: Isomerase
enzyme name: ____
action: _____
example: ATP synthase
enzyme name: Synthase
action: Makes a molecule from parts
example: ATP synthase
enzyme name: Dehydrogenase
action: _____
example: _____
enzyme name: Dehydrogenase
action: Removes hydrogen
example: Isocitrate dehydrogenase
enzyme name: ______
action: Removes phosphate from protein
example: _______
enzyme name: Phosphatase
action: Removes phosphate from protein
example: Dual specificity phosphatase
list 4 active consumers of glucose (think high metabolism):
RBCs
retina
renal medulla
brain
brain consumes _____% of glucose (in a resting person), weights _____% of body mass
brain consumes 20% of glucose (in a resting person), weights 2% of body mass
hydroxyl group in a glucose is in the alpha position when…
-OH facing downwards
hydroxyl group in a glucose is in the beta position when…
-OH facing upwards
monosaccharides include (3)
3 C sugars
5 C sugars
6 C sugars
all C 6 sugars have two forms
alpha and beta
in fructose it’s not the hydroxyl group that changes the position but …
H2OH
list disaccharides (they don’t want lactose here)
sucrose
maltose
cellobiose
sucrose - composition & linkage [imagine drawing them]
⍺-D-glu + fru (in alpha position )
⍺-1,2 glycosidic linkage
maltose - composition & linkage [imagine drawing them]
⍺-D-glu + β-D-glu
⍺-1,4 glycosidic linkage
cellobiose - composition & linkage [imagine drawing them]
β-D-glu + β-D-glu
β-1,4 glycosidic linkage
list polysaccharides + say if linear (L) or branched (B) structure
cellulose (L)
starch (B)
glycogen (B)
orientation of hydroxyl group in cellulose
in turns, i.e. up, down, up, down…. [can start/end with either of the two]
starch and glycogen are both _____ polysaccharides
they form _____ and _____ bonds
the bonds require _____ (same/different) enzyme to break them
branched
C1-C6 and C1-C4
the bonds require different enzyme to break them, i.e. one for C1-C6 and another one for C1-C4
how is glucose transported into the cell? (2)
ACTIVELY via Na+/glucose symporters
PASSIVELY via passive facilitated diffusion through glucose transporters aka GLUTs 🤧🤧🤧
symport [def.]
channel in a membrane that transports 2 different molecules in the same direction across the membrane; does NOT require energy
antiport [def.]
channel in a membrane that exchanges ions
DOES requires energy
tissue: brain
GLUT name: _______
characteristics: _______
tissue: brain
GLUT name: GLUT1 and GLUT3
characteristics: low Km [affinity]
tissue: ______
GLUT name: GLUT2
characteristics: __________
tissue: liver (pancreatic β cells)
GLUT name: GLUT2
characteristics: high Km [affinity], insulin independent
tissue: _________
GLUT name: ______
characteristics: insulin dependent
tissue: adipose tissue, muscles
GLUT name: GLUT4
characteristics: insulin dependent
tissue: gut
GLUT name: ______
characteristics: _______
tissue: gut
GLUT name: GLUT5
characteristics: fructose transport
explain transport of glucose via GLUT1
- Binding of glucose to the outside triggers a conformational change so that the binding site faces inwards.
- Glucose can be released in the inside.
- Conformational change regenerates the binding site on the outside.
draw glycolysis pathway
:) refer to printed materials
if both needs (_________ and _________) are met we shouldn’t produce more of pyruvate, so to monitor a reaction, an irreversible step should be chosen as a control point (so you can’t go back)
if both needs (production of ATP and provision of building blocks for synthetic reactions) are met we shouldn’t produce more of pyruvate to monitor a reaction, an irreversible step should be chosen as a control point (so you can’t go back)
how many control points are there?
3
first control point (reaction + enzyme)
you MUST know the enzymes
glucose + ATP —> glucose 6-phosphate + ADP + H+
HEXOKINASE
second control point (reaction + enzyme)
you MUST know the enzymes
fructose 6-phosphate + ATP —> fructose 1,6-bisphosphate + ADP + H+
PHOSPHOFRUCTOKINASE
third control point (reaction + enzyme)
you MUST know the enzymes
phosphoenolpyruvate + ADP + H+ —> pyruvate + ATP
PYRUVATE KINASE
which enzyme is key in the control of glycolysis?
PHOSPHOFRUCTOKINASE (2nd control point)
what happens to ΔG as glycolysis progresses?
ΔG 🔽
PHOSPHOFRUCTOKINASE can be modulated by several factors
list and briefly explain (where appropriate) the NEGATIVE MODULATORS:
- ATP
- citrate – early intermediate in citric acid cycle, biosynthetic precursors are abundant
- H+ – prevents excessive formation of lactic acid
PHOSPHOFRUCTOKINASE can be modulated by several factors
list the POSITIVE MODULATORS:
- AMP
* fructose 2,6-bisphosphate
energy charge is…
the ratio of ATP/AMP
the cell is fully charged when…
all adenylate nucleotides are in the shape of ATP
the cell is discharged when…
it only contains AMP and Pi
the AMP and not ADP is the positive regulator because…
- if ATP is rapidly used up …
- adenylate kinase can rescue some of the energy in the form of…
if ATP is rapidly used up … ATP -> ADP + Pi
… adenylate kinase can rescue some of the energy in the form of ADP
2 ADP -> ATP + AMP
2 ADP ->
2 ADP -> ATP + AMP
Anaerobic respiration (2):
alcoholic fermentation
lactic acid fermentation
alcoholic fermentation =
yeast and some microorganisms can form ethanol from pyruvate
lactic acid fermentation =
+who?
some microorganisms and humans can convert pyruvate to lactate
Aerobic respiration = pyruvate is…
further oxidised, and much more energy is released
what is the lactic acid fermentation equation?
C6H12O6 + 2 ADP + 2 Pi —> 2 lactic acid + 2 ATP
2 pyruvate are converted into 2 lactic acid molecules by [enzyme]
lactate dehydrogenase
ADP and Pi are (okay/toxic)
toxic
where is lactic acid fermentation used…
cheese production!
muscles sore after anaerobic respiration due to…
low pH
training at the gym gives 3 benefits:
- Diminishes lactate production
- Increases lactate clearance
- Endurance runners have completely different threshold than sprint runners and non-athletes
Plasma lactate during exercise predicts….
endurance performance
what is the alcoholic fermentation equation?
what enzyme?
C6H12O6 + 2 ADP + 2 Pi —> 2 ethanol + 2 CO2 + 2 ATP
alcohol dehydrogenase
how is pyruvate converted into acetyl-CoA?
pyruvate enters _________ via a specific transporter
there, the _______ complex (___) catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA
pyruvate enters mitochondria via a specific transporter
there, the pyruvate dehydrogenase complex (PDC) catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA
PDC consists of:
3 enzymes involved in the actual reaction mechanism …
plus 2 enzymes involved in the control of PDC…
… plus 5 coenzymes
E1, E2 and E3
a kinase and a phosphatase in a single polypeptide
thiamine, lipoic acid, coenzyme A, FAD, NAD+
the activity of the PDC is the major determinant of glucose oxidation in well oxygenated tissues in vivo
The reaction is _____ (reversible/irreversible) aka Acetyl-CoA _______ (can/cannot) be converted to pyruvate
IRREVERSIBLE
CANNOT!
one molecule of glucose undergoes how many TCA cycles?
2
Krebs cycle can be also called (2):
the citric acid cycle
tricarboxylic acid cycle
state the mnemotechnic to remember all the intermediate products of the TCA cycle:
A Clown In (alpha)Kilimanjaro Sings Songs For Money Only
state the intermediate products of the TCA cycle:
- Acetyl CoA
- Citrate
- Isocitrate
- α Ketoglutarate
- Succinyl CoA
- Succinate
- Fumarate
- Malate
- Oxaloacetate
state the enzymes catalysing reactions of the TCA cycle:
- citrate synthase
- aconitase
- isocitrate dehydrogenase
- α-ketoglutarate dehydrogenase
- succinyl thiokinase
- succinate dehydrogenase
- fumarate
- malate dehydrogenase
each TCA cycle:
uptake of ___ [number] carbon atoms in the form of _____ [substance], and release of ___ [number] carbon atoms in the form of _____ [substance]
2, acetyl-CoA
2, CO2
each TCA cycle:
___ [number] pair(s) of electrons is/are transferred in the form of NAD+ to form NADH + H+, and
transfer of ___ [number] pair(s) of electrons to reduce FAD to FADH2,
there is also ___ [number] GTP molecule(s) formed from GDP and Pi
3, 1, 1
from each acetyl-CoA, the TCA cycle generates: 🍍\_\_x NADH + H+ 🥝\_\_x FADH2 🍊\_\_x GTP (GTP + ADP --> GDP + ATP) 🍇 \_\_x CO2
3
1
1
2
high ATP, NADH and acetyl-CoA = ? [energy]
plenty of energy
high ADP and NAD+ = ? [energy]
lack of energy
high succinyl-CoA and acetyl-CoA = ?
plenty of precursor molecules for biosynthetic reactions
chemiosmosis [def.]
movement of ions down their [ ] gradient through the selectively permeable membrane; here it’s H+
Electrons flow ____ the electron transport chain from ________ to more ______ redox potential
down
negative
positive
Big jumps in redox potential equate to ___ which can be harnessed (=take advantage of)
big changes in ΔG
Chemiosmotic hypothesis (proposed by Peter Mitchell, 1961, chemiosmotic hypothesis) consists of two stages:
electron transport (oxidative part) ATP synthesis (phosphorylation part)
details of electron transport (oxidative part)
- electrons flow from NADH and FADH2 to O2
- collectively known as respiratory chain
- energy is used to pump H+ out of the mitochondrial matrix
details of ATP synthesis (phosphorylation part)
- electrochemical gradient of H+ across mitochondrial inner membrane
- energy stored in this gradient can be used to synthesise ATP
Electron transport and ATP synthesis are catalysed by ________ (same/separate) proton pumps
separate - one set of enzymes for protons going in another for protons going out
P/O ratio is a measurement of ________
P/O ratio = the number of molecules of inorganic phosphate (Pi) incorporated into ATP per atom of _____
Depends on the substrate which is oxidised
the coupling of ATP synthesis to electron transport
oxygen reduced
if NADH is oxidised to NAD+
P/O ratio = ___
numbers are empirical and approximate measurements
2.5
if FADH2 is oxidised to FAD
P/O ratio = ____
numbers are empirical and approximate measurements
1.5
FINAL BALANCE (from 1 glucose molecule) How much ATP can be generated from the complete oxidation of one glucose molecule?
Glycolysis: _ ATP + _ NADH + H+
Pyruvate dehydrogenase: _ NADH + H+
TCA cycle: _ NADH + H+ + _ FADH2 + _ ATP
Total: 4 ATP, 10 NADH + H+, 2 FADH2
Using the P/O ratio:
10 NADH + H+ yield 25 ATP
2 FADH2 yield 3 ATP
1 glucose molecule yields 30-32 ATP molecules (uncertainty bc P/O ratio is just an approximation)
Glycolysis: 2 ATP + 2 NADH + H+
Pyruvate dehydrogenase: 2 NADH + H+
TCA cycle: 6 NADH + H+ + 2 FADH2 + 2 ATP
OXPHOS diseases
OXPHOS diseases
Involve components of oxidative phosphorylation
Common degenerative diseases (happen over time)
Mutations in mitochondrial or nuclear DNA
Pathology usually becomes worse with age
initially, a decreasing number of normal mitochondria may provide enough ATP
with age, spontaneous mutations accumulate
at some point, not enough ATP can be generated
Symptoms usually appear in tissues with highest ATP demands
nervous system, heart, skeletal muscle, kidneys
