study quide answers
For each of the following study guides provide answers to topics listed.
Terms: Metabolism, Catabolism, Anabolism, energetic coupling, phosphoryl-transfer potential, activated
carrier, vitamin, energy charge, Red-Ox reactions,
Need to know:
Meaning of a coupled process
Components of ATP
Factors that explain the favorable hydrolysis of ATP
ATP characteristics
Meaning of high and low energy phosphorylated compounds
Features of the ATP-ADP cycle
Relationship between the oxidation of a compound and the amount of energy released
How the energy released in an oxidation reaction is used
How the electrons released in an oxidation reaction are captured
Meaning of an activated carrier
Meaning of ATP as an activated carrier of the phosphoryl group
Structural features of the two activated carriers of electrons from fuel oxidation
The use of the hydride ion by NAD+
Structural features of the activated carrier of electrons for the synthesis of biomolecules
Structural features of the activated carrier of two-carbon fragments
Meaning of “activated carriers are kinetically stable”
General role of some vitamins in metabolism
The several ways in which metabolic processes are regulated
Energetically-Coupled reactions: 𝛥G=𝛥G°+RTlnQ
Why are physiological concentrations important?
Be comfortable using the above equation to convert between reactant/product
concentrations, Keq, 𝛥G, and 𝛥G°.
Memorize 𝛥G° for ATP-> ADP + Pi = -30.5kj/mol or -7.3kcal/mol
Why couple biochemical reactions/pathways?:
Energy can be stored (during catabolism) as high-E “activated carrier” molecules for
later use: ATP, NADH, FADH2, Acetyl-CoA.
To drive (anabolic) biochemical reactions that wouldn’t otherwise proceed (i.e. be
spontaneous): mainly NADPH, ATP, Acetyl-CoA
How do molecules store chemical potential energy?
ATP: electrostatic repulsion between phosphates, resonance, entropy of hydrolysis, and
enthalpy of water solvation.
Hydrocarbon fuels/NADH/NADPH/FADH2: reducing power of the electrons they store.
Higher energy electrons are far from nuclei and wedged in the middle of bonds
(between atoms of equal electronegativity).
Acetly-CoA: no resonance stabilization for thioesters (esters are more stable). Also S is
less electronegative than O so electrons in C-S bond store more energy than in C-O.
Be able to extrapolate these energy storage mechanisms for other high-energy
molecules (PEP, 1,3-BPG, Creatine phosphate, pyrophosphate, other thioesters, etc).
Be able to recognize oxidation and reduction reactions and understand why such reactions can
release/store lots of chemical potential energy.
How are the main energy-storage molecules structurally similar to each other? How/why are
they different? (be able to recognize ATP, ADP, NADH, NADPH, FADH2, and Acetly-CoA). Know
their names and the vitamins they’re derived from (i.e. nicotinamidenicotinate for NADH).
Enzyme Regulation mechanisms: Amounts of enzyme (transcription/translational control=> slow
to repond), Catalytic Activity (allosteric regulation=> fast to respond), substrate accessibility
(compartmentalization to separate anabolic from catabolic processes which must happen
simultaneously but with different substrates)
Need to know:
Definition of metabolism, catabolism, and anabolism
Characteristics of catabolism
Characteristics of anabolism
Digestion of proteins: where it happens, chemical reaction, and enzymes involved
Digestion of carbohydrates: where it happens, chemical reactions, and enzymes involved
Digestion of triglycerides: where it happens, chemical reactions, and enzymes involved
Role of bile salts
Zymogens: what they are, examples and how to recognize them
Overview of catabolism:
Digestion of fats, carbs, and proteins into monomers.
Partial oxidation of carbs, fats, and amino acids into Acetyl-CoA and other metabolic
intermediates, generating high-E molecules in the process.
Further oxidation in the Citric Acid Cycle followed by oxidative phosphorylation in mitochondria
to make ATP.
Protein digestion: Stomach and intestine
Pepsin (self-activating, active at low-pH where other proteins are denatured)
Secretin-function in digestion
Cholecystokinin (CCK)- function in digestion
Proteases (enteropeptidase, trypsin, elastase, carboxy-peptidase, chymotrypsin)
Zymogens (Why is this unique activation mechanism necessary?)
Absorption into intestinal cells as small peptides or amino acids
Carbohydrate digestion: Mouth/Saliva, intestine
Alpha-amylase (which glycosidic bonds does it cleave, what can’t it cleave)
Lactase (on surface of intestinal cells)
Sucrase (on surface of intestinal cells)
Active transport of sugars into cells driven by Na-Glucose symporter.
Lipids: Issue of solubility
Emulsification in the stomach
Further solubilized in the small intestine with Bile Salts (Glycocholate)
Pancreatic lipases break up fats into glycerol and fatty acids
Micelles are formed and absorbed by intestinal cells.
Lipids and repackaged into chylomicrons for further transport in the blood/lymph.
Need to know:
Glycolysis
Characteristics
Meaning of investment or preparatory phase
Meaning of pay-off phase
Forms in which energy is extracted and stored
Role of first step
Regulatory (i.e. irreversible) control point steps (1, 3, 10)
Meaning of “committed” step
Regulatory enzymes
The high-energy compounds and intermediates and their role
The fates of pyruvate
Alcoholic fermentation reactions
Lactic fermentation reaction
Meaning of “The redox balance is maintained in alcoholic/lactic fermentation”
Allosteric effectors of PFK
Role of ATP/ADP ratio (energy charge) in the regulation of glycolysis
Role of fructose-2,6-bisphosphate
Regulation of PK
Role of kinases, isomerases, dehydrogenases, and mutases in main pathway.
Glycolysis: Glucose partial oxidation into pyruvate. Get 2 ATP, 2 NADH, and 2 3C pyruvates per 6C glucose.
Stage 1: Investment/preparatory phase:
• Step 1: Hexokinase/Glucokinase: Negative dG. Control point 1 (inhibited by product). Uses ATP
hydrolysis to add first phosphate. Muscle and liver isozymes. Traps glucose inside cell. Induced fit
mechanism to prevent premature ATP hydrolysis.
• Step 2: Phosphoglucose isomerase: pyranose ring-opening, acid-base catalyzed keto-enol tautomerism,
furanose ring closure.
• Step 3: Phospho-fructokinase: Negative dG. First “Committed Step” of Glycolysis. Control point 2
(allosterically inhibited by its own substrate ATP [feedback inhibition by the end product of the
metabolic pathway], activated by F2,6-BP an indicator of F6P levels [feedforward activation]). Uses ATP
hydrolysis to add second phosphate.
• Step 4: Aldolase: Cleaves the 6-carbon sugar into 2 3-carbon sugars
Stage 2: Pay-off phase
• Step 5: Triose-phosphate isomerase: acid-base catalyzed keto-enol tautomerism. DHAP to G3P.
• Step 6: G3P dehydrogenase: Step 1… Enzyme sucks high energy electrons from G3P and stores them in
NADH while making a covalent thioester bond with the substrate. Aldehyde of G3P is only partially
oxidized to a thioester intermediate (thus storing some energy as an enzyme-bound intermediate). Next
the second stage of the oxidation occurs with the conversion of the thioester to a fully-oxidized but
phosphorylated carboxylic acid which stores the chemical potential released during the second stage of
the oxidation as phosphoryl-transfer potential. 1,3-BFG is formed.
• Step 7: Phosphoglycerate kinase: Transfers Pi from 1,3-BFG onto ADP to make ATP. Substrate level
phosphorylation.
• Step 8: Phosphoglycerate mutase: moves the remaining phosphate to the middle carbon.
• Step 9: Enolase: dehydrates 2PG to generate high-energy PEP (locked into an unstable enol form).
• Step 10: Pyruvate kinase: Negative dG. Control point 3 (in the liver its inhibited by phosphorylation
when glucose is low). Pi from PEP is transferred to ADP to make ATP and pyruvate.
• Net reaction: from 1 Glucose to 2 pyruvate you get 2 NADHs and 2 ATPs.
Fate of Pyruvate (how to regenerate NAD from NADH so glycolysis can continue)
• Anaerobic Fermentation
o Alcoholic
o Lactic Acid
• Aerobic metabolism (Citric Acid Cycle + Oxidative Phosphorylation)
Entry of other sugars (not a major focus of our course):
•
•
Galactose: enters glycolysis at the stage of Glucose-6-phosphate (same branch-point as for glycogen
synthesis).
Fructose: Enters either as F6P or as DHAP and GAP (in the liver).
Need to know:
Gluconeogenesis: Definition, where it occurs, how it differs from Glycolysis and why.
1st regulatory step of gluconeogenesis and where it occurs
Structural features of pyruvate carboxylase
Coenzyme of pyruvate carboxylase (biotin: CO2 grabbing co-enzyme)
Allosteric activator of pyruvate carboxylase (Acetyl-CoA)
2nd regulatory step (PEP carboxykinase)…. Link to insulin and type-2-diabetes
3rd regulatory step and location (Fructose 1,6-bisphosphatase)
Cost of making glucose from 2 pyruvates via gluconeogenesis (6 ATPs)
Meaning of “glycolysis and gluconeogenesis are reciprocally regulated”
Need to know:
Glycogen structure
Glycogen phosphorylase activity/reaction
Debranching enzyme activities/reactions
Phosphoglucomutase reaction
Some of the components (and their roles) of the regulatory cascade for glycogen breakdown
Activated glucose donor (UDP glucose)for glycogen synthesis
Glycogen synthase activity or reaction
Branching enzyme activity or reaction
The pentose phosphate pathway
What it provides (NADPH and 5C sugars for nucleotide synthesis)
2 major phases
Oxidative (makes NADPH by oxidative decarboxylation)
Non-oxidative (enables linkage to Glycolysis: 2x6C + 3C 3x5C) enabling fuel to be
easily turned into anabolic reducing power and nucleic acid building blocks.
Is PPP older than Glycolysis?…perhaps
