Topic 1 : Carbohydrate Biosynthesis and Metabolism Flashcards
Metabolism is the sum of these 2 processes
Catabolism (breakdown)
Anabolism (synthesis)
Energy release of ATP hydrolysis
γ-β bond - 30.5 kJ / mol
β-α bond - 32.8 kJ / mol
Function of glycolysis
energy production
function of gluconeogenesis
glucose resynthesis
function of citric acid cycle
building blocks and energy
function of pentose phosphate pathway
NADPH and pentose synthysis
Brain uses this in well - fed state
glucose
storage of glycogen in this organ
liver
methods of enzyme regulation (general)
enzyme activity modification (short term ie hours, minutes) enzyme concentration (long term ie days, hours)
WHAT ARE THE ADVANTAGES OF USING A SINGLE ENERGY CURRENCY?
Easy to distribute energy. Reduces the number of necessary pathways to use energy
Can stock up on ATP without having to worry about converting to other forms
WHY DO CELLS LIKE MYOCYTES & NEURONS USE PHOSPHOCREATINE AS WELL AS ATP FOR ENERGY?
Phosphocreatine allows rapid regeneration of ATP from ADP. Cells like myocytes and neurons have to rapidly fire, and benefit from speedy recovery
IF ENZYMATIC STEPS ARE REVERSIBLE: WHY USE TWO PATHWAYS TO SYNTHESIZE AND BREAKDOWN COMMON CELLULAR COMPONENTS?
It makes it easier to regulate.
There are some steps that are virtually irreversible, the regulation of which aid in preventing the pathway from gong in both directions.
Sugar isomer used by mammals
D-isomers
Common aldoses (3)
D-glucose
D-galactose
D-mannose
Aldose
contains multiple alcohol groups and one carbonyl as an aldehyde
Ketose
contains multiple alcohol groups with one carbonyl as a ketone
Common Ketoses (2)
Fructose
Ribulose
anomeric carbon
hemiketal / hemiacetal carbon in a sugar
can be OH down (α)
or OH up (β)
What is unusual about the linkage between glucose and fructose in sucrose ?
They are both attached on the reducing end Therefore: Fru(2β-α1)Glc is the same as Glc (2β-α1) Fru
Reducing end
Hemiketal or hemiacetal end of a sugar (carbon 1)
or sugar chain
bonds of glycogen and amylopectin
α 1-6 linkages to create branches
α 1-4 linkages within branches
bonds between cellulose sugars
β 1-4 linkages
forms straight chains
n-linked glycoproteins use what aa for linkage to sugar ?
Asn
ARE DIGESTIVE ENZYMES GENERAL OR SPECIFIC FOR CERTAIN POLYSACCHARIDES OR GLYCOSIDIC LINKAGES?
Specific.
Amylases in the mouth are general
WHY DO ERYTHROCYTES (RED-BLOOD CELLS) DEPEND HEAVILY ON GLUCOSE FOR THEIR ENERGY?
There are no organelles,
most energy producing processes take place in the mitochondria
WHY DO WE NEED GLYCOPROTEINS, PROTEOGLYCANS AND MUCOPOLYSACCHARIDES ?
Glycoproteins are used as cell markers
Proteoglycans are used for shock absorbing in cartilage
mucopolysaccharides are slippery (mucus)
3 main sources of sugars
Diet (plant / animal)
Glycogen storage
Individual sugars
1st step of glycolysis
Hexokinase is considered the first step, but is not always done
product of glycogen breakdown
glucose 1 phosphate (G1P)
later transformed into g6p
glucose transporter in liver
GLUT2
glucose transporter in muscle
GLUT4
insulin dependent glucose transporter
GLUT4
Difference between GLUT2 and GLUT4
GLUT2 (liver) has a high Km so it can absorb glucose when in excess
GLUT2(muscle) has lower Km, so it can take in glucose at physiological concentration
ATP producing steps of glycolysis
7 (phosphoglycerate kinase)
10 (pyruvate kinase)
Substrate level phosphorylation
Irreversible steps of glycolysis
1 (glucose -> G6P by hexokinase)
3 (fructose 6-phosphate -> fructose 1,6-biphosphate by phosphofurctokinase-1)
10 (phosphoenolpyruvate -> pyruvate by pyruvate kinase)
2 phases of glycolysis
preparatory
payoff
Purpose of lactate cycle
Remove pyruvate
and
revert NADH back to NAD+
WHY CAN’T HUMANS METABOLIZE CELLULOSE?
Do not have the proper enzymes to break linkages (β-1,4)
WHY DO WE NEED GLUTs?
Glucose does not diffuse fast enough through the membrane
WHAT HAPPENS TO EXCESS BLOOD GLUCOSE?
Insulin is released and it is absorbed into the tissues.
It is converted to glycogen in the liver
It may also be turned into fats
What is glucuconeogenesis ?
synthesis of glucose from non carbohydrate precursors
What non carbohydrate precursors can be used to make glucose ?
Lactate, glucogenic amino acids (alanine, etc), glycerol
Where does gluconeogenesis happen ?
Liver
Kidney (to a lesser extent)
Normal HbA1c ?
3.5 - 5.5 mM
What happens when HbA1c drops below normal ?
hypoglycaemic shock / coma
Gluconeogenesis
Catabolic or anabolic ?
Anabolic
Requires energy
Irreversible steps of glucolysis (enzymes)
hexokinase,
phosphofructokinase-1,
pyruvate kinase
irreversible steps in gluconeogenesis (enzymes)
glucose-6-phosphatase
fructose-1,6-bisphosphatase-1
pyruvate carboxylase
Hexokinase in muscle
Hexokinase I and II
Hexokinase in liver
Hexokinase IV (Glucokinase)
Difference between hexokinase I and IV
Hexokinase IV / Gluclkinase (liver) has a higher Km so it will operate at a higher [glucose]
This is to process glucose more efficiently when in excess
Which hexokinase is upregulated by insulin ?
Muscle (I)
effect of G6P on hexokinase I?
Inhibition
(end product inhibition)
NB that Glucokinase is not inhibited by G6P
Reaction catalyzed by PFK1
Phosphofructokinase - 1 catalyzes
Fructose 6-phosphate -> Fructose 1,6-biphosphate
Activators and inhibitors of PFK1
Phosphofructokinase 1
Activators:
ADP, AMP, Fructose 1,6 bisP
Inhibitors:
ATP, citrate
reaction catalysed by pyruvate carboxylase
pyruvate + bicarbonate -> oxaloacetate
explain the role of fructose 2,6-bisphosphate in glucose control
In the presence of insulin, PFK-2 activates and creates fructose 2,6-BP, stimulating glycolysis
In the presence of glucagon, FBPase activates and creates fructose 6-phosphate, stimulating gluconeogenesis
Why can liver and kidney export glucose from glycogen ?
Glycogen breakdown results in G6P.
Only the liver and kidneys have G6Pase to create glucose for transport
WHAT HAPPENS IF YOUR BLOOD GLUCOSE FALLS <3.5 mM?
Hypoglycaemic shock / coma / death
WHY DO WE NEED TWO SEPARATE PATHWAYS IN GLYCOLYSIS AND GLUCONEOGENESIS TO BREAKDOWN & RESYNTHESIZE GLUCOSE?
These two pathways are opposing, so only one should be happening at a time.
Having separate pathways allows for regulation
WHAT IS THE CONSEQUENCE OF TISSUES (eg MUSCLE) LACKING THE ENZYME, GLUCOSE-6-PHOSPHATASE?
G6P cannot be dephosphorylated to glucose, and therefore cannot be transported outside the cell
Difference between glycogen and amylopectin
Amylopectin has a α1-6 branch every 24-30 residues
Glycogen has α1-6 branches every 12-14 residues
what is glycogenenin ?
glycogenin is the core around which glycogen is fomed
Amino acid glycogenin uses to attach to glucose
Tyr 194
Compare glycogen and fat
Glycogen is stored with water (hydrated), which makes it less dense, but easier to access
Type of chemical reaction used in glycogen breakdown
phorylysis (NOT hydrolysis)
results in G6P
enzyme that converts G1P to G6P
phosphoglucomutase
HOW DOES AMYLASE DIFFER FROM GLYCOGEN PHOSPHORYLASE? (BOTH HYDROLYZE GLUCOSE POLYMERS SUCH AS GLYCOGEN)
Amylase is hydrolytic and acts in the gut,
whereas glycogen phosphorylase is phospholytic to maintain the high energy phosphate bond and acts in the cell
Both cleave at the alpha 1-4 link
WHY IS TRIGLYCERIDE A BETTER LONG-TERM STORAGE FORM?
It is more energy dense (more energy per bond), and is kept in an anaqueous environment.
This makes it good for storing lots of energy in a small space, but its hard for the enzymes to access
WHAT IS THE CONSEQUENCE IF THERE IS A GENETIC DEFECT IN GLYCOGEN STORAGE
Mostly death
Steps to glycogen synthesis
- 1) GLYCOGENIN FORMS 8-Glu CORE OF THE GLYCOGEN PARTICLE
- 2) GLYCOGEN BRANCHING ENZYME INSERTS (α1->6) LINKAGES
- 3) GLYCOGEN SYNTHASE USING UDP-GLUCOSE COUPLES GLUCOSE UNITS JOINED BY (α1->4) LINKAGES
- 4) REPEATS OF STEPS 2) AND 3) TO PRODUCE MULTIPLE (12) TIERS FOUND IN HIGHLY BRANCHED GLYCOGEN STRUCTURE
INSULIN IS A GLUCOSE-ABUNDANCE HORMONE? GLUCAGON IS A GLUCOSE-SHORTAGE HORMONE? WHAT TYPE OF BIO-MOLECULES ARE THEY?
Yes
Yes
Protein
Prof’s answer:
Peptide hormones (Lectures 25,27,29) that work through completely different signal
transduction processes: insulin via receptor-tyrosine kinase-mediated pathway
(Lecture 27); glucagon via cAMP and protein kinase A mediated pathway (Lecture 29)
WHAT IS GLYCOGENIN AND WHAT DOES IT DO?
It is a protein that acts as the core in glycogen synthesis
It makes the 8-glucose primer before glycogen synthase takes over
WHAT ARE THE ANSWERS TO THE FOLLOWING FACTUAL QUESTIONS REGARDING GLYCOGENIN?
a) HOW MANY GLUCOSE UNITS COMPRISE THE PRIMER ON GLYCOGENIN?
b) HOW BIG IS GLYCOGENIN?
c) WHICH AMINO ACID RESIDUE IS ATTACHED TO THE PRIMER?
d) TO WHICH END OF THE PRIMER CHAIN ARE NEW GLU RESIDUES ADDED?
a) 8
b) 37K
c) Tyr
d) non-reducing
Overall purpose of the citric acid cycle
- convert acetyl coA into CO2
- Trap reducing power as NADH, FADH2, GTP
- generate useful building blocks
Where does the TCA cycle take place ?
Inside the mitochondrial matrix
How many subunits does the pyruvate dehydrogenase complex have ?
3
E1, E2, E3
3 parts of pyruvate dehydrogenase (names)
E1 : Pyruvate dehydrogenase
E2 : Dihydrolipoyl transacetylase Dihydrolipoyl dehydrogenase
Citric acid cycle intermediates
citrate isocitrate α-ketogluterate succinyl-CoA succinate fumerate malate
of steps in TCA cycle
8
enzymes in TCA cycle that give reducing agents
NADH:
- isocitrate dehydrogenase
- α-ketogluterate dehydrogenase complex
- malate dehydrogenase
FADH2:
-succinate dehydrogenase
GTP:
-succinyl coA synthetase
H+ to ATP generation ration
~4H+ to make 1 ATP
ATP generated from NADH
gives 10H+ (2.5 ATP)
ATP generated from FADH2
gives 6H+ (1.5ATP)
Net total ATP produced from 1 glucose
30 - 32
Citric acid cycle regulation molecules
Activators:
AMP, CoA, ADP, Ca2+
Inhibitors:
ATP, NADH, fatty acids, succinyl CoA
Anapleurotic steps
PEP to Oxaloacetate
Pyruvate to malate
WHY DO EITHER THIAMIN DEFICIENCY OR LOSS-OF-FUNCTION MUTATIONS
OF PYRUVATE DEHYDROGENASE PRIMARILY AFFECT BRAIN?
The brain uses glucose and ketones exclusively
WHY ARE MAMMALS UNABLE TO CONVERT FATTY ACIDS OR ACETYL CoA TO
GLUCOSE? WHAT DOES THIS TELL US ABOUT PYRUVATE DEHYDROGENASE?
1) TCA does not occur at the same time as gluconeogenesis in the liver
2) Acetyl CoA (product of fatty acid breakdown) is not converted totally to oxaloacetate
3) Pyruvate dehydrogenase is irreversible and inhibited by Acetyl CoA
IF GLYCOLYSIS ENDS IN PYRUVATE & IS CYTOSOLIC AND PYRUVATE
DEHYDROGENASE OCCURS IN MITOCHONDRION THEN HOW DOES PYRUVATE
GET INTO THE MITOCHONDRION.
Pyruvate translocase transports it across inner mitochondrial membrane
steps of Glyoxylate cycle
citrate isocitrate succinate malate oxaloacetate
Glyoxylate cycle differences compared to TCA (4)
5 steps (vs 8)
2 acetyl coA added
glyoxylate
2 new enzymes (isocytrate lyase and malate synthase)
Glyoxosome found in what type of cell ?
Plant cells only
Regulation of TCA vs Glyoxylate is controlled by (enzyme):
isocitrate dehydrogenase
Glyoxylate cycle is preferred over TCA under in circumstance ?
Well - fed state.
TCA produces more NADH and FADH2
Glyoxylate allows for gluconeogenesis
2 options of the pentose phosphate pathway
Oxidative and non-oxidative phase
Difference between 2 pathways of pentose phosphate pathway
Oxidative:
Irreversible
produces NADPH from NADP
Non oxidative:
The opposite of that
purpose of pentose phosphate pathway:
changes G6P to ribulose 5-phosphate, then to ribose 5-phosphate for use in DNA, nucleotides, conezymes, RNA
Things that cause free radicals
Electron transport chain
Chemotherapy
Key points of the nonoxidative pentose phosphate pathway (3)
- six 5C sugars converted to five 6C sugars (or the other way)
- Enzymes involved are transketolase (2x) and transaldolase
- Energy supplied by thiamine pyrophosphate at transketolase steps
Regulating factor of pentose phosphate pathway
NADPH
PENTOSE PHOSPHATE PATHWAY PROVIDES: NADPH & RIBOSE-5-P WHAT IF A CELL HAS SUFFICIENT NADPH & A HIGH [NADPH]/[NADP] RATIO BUT STILL NEEDS RIBOSE-5-P FOR NUCLEOTIDE SYNTHESIS?
HOW DOES A CELL MAKE RIBOSE-5-P IF G-6-P-D IS INHIBITED?
It will use the nonoxidative pathway, (which is reversible)
WHAT IS NAPDH USED FOR? WHICH TISSUES NEED A RICH SUPPLY?
All tissues involved in fat production (liver, adipose, mammary gland)
or steroid production (adrenal)
IT IS ESTIMATED THAT 400 MILLION PEOPLE HAVE G-6-P-D DEFICIENCY. HOW WOULD YOU EXPECT THESE INDIVIDUALS TO BE AFFECTED?
Antioxidant pathways require NADPH.
Drugs and other dietary methods are used to regulate this
The cell most vulnerable is the RBC, and this condition may induce haemolysis.
Definition of vitamin
Essential substance not synthesized, and must be ingested in diet
(Sometimes converted a bit, but the important part is that its not created de novo)
When are vitamins converted to active form and why ?
They are converted near the time of use because it improves specificity and regulates
(“You dont want coenzymes floating around and fucking shit up”)
Biotin is a prosthetic group of what 4 enzymes ?
Pyruvate carboxylase
Acetyl-CoA carboxylase
Propionyl-CoA carboxlase
3-methylcrotonyl-CoA carboxylase
Starred enzymes important to know
Biotin containing enzymes have these three parts :
1) biotin carrying protein
2) biotin carbozylase
3) Transcarboxylase
How carboxylases work (details of the 3 parts)
1) Biotin carrying protein
carries biotin and moves it between parts 2 and 3
2) Biotin carboxylase
Adds COO- group to biotin (activates biotin, requires ATP)
3) Transcarboxylase
Transfers carboxyl group to substrate
Substance blocks biotin absorption
Avidin (found in egg white)
(Biotin and avidin are used in antibody studies because it binds so tightly
Reasons for biotin deficiency (or any vitamin deficiency, really) (3)
Biotin supply
dietary, gut flora, absorption issues
Biotin enzyme error
If the enzyme is not properly handling biotin, its effects will present as a deficiency
Biotin recycling efficiency (biotinidase)
If it is not properly being reused, it will run out
WHAT WOULD BE THE CLINICAL OUTCOME IF THERE WAS A MUTATION OF THE
BIOTIN CARRIER PROTEIN (1) SUBUNIT?
Death
The patient would not be able to add biotin to the enzyme, non-functional enzyme
WHAT WOULD BE THE CLINICAL OUTCOME IF THERE WAS A MUTATION OF THE BIOTIN CARBOXYLASE (2) SUBUNIT?
Death
The patient would not be able to carboxylate the biotin and therefore the enzyme would be non-functional
WHAT WOULD BE THE CLINICAL OUTCOME IF THERE WAS A MUTATION OF THE
TRANSCARBOXYLASE (3) SUBUNIT OF ANY ONE OF THE CARBOXYLASES?
That particular pathway would be inhibited, but the patient may be able to survive if the pathway blocked is non-critical and the diet is changed to accommodate.
