biochem exam 1 - from review sheet :) Flashcards
___ is formed by an essentially irreversible process and is the “glucose donor” in the synthesis of glycogen.
A
Glucose-1-phosphate
B
Glucose-6-phosphate
C
ADP-glucose
D
UDP-glucose
D
UDP-glucose
The primer and enzyme that begins the synthesis of glycogen is…
A
Glycogen phosphatase
B
Glycogen phosphorylase
C
Glycogen synthase
D
Glycogenin
E
Glycogen kinase
D
Glycogenin
- this is the seed for glycogenin
Metabolic pathways (converging metabolism, diverging metabolism, cyclic), metabolites, catabolism (degradation, yielding energy), anabolism (synthesis, requiring energy)
- 1st and 2nd laws of thermodynamics (FYI)
- Know: Keq = [C]c[D]d/[A]a[B]b; know how to use ΔG’º = -RTlnK’eq;
- Remember: ΔG = ΔH – TΔS
Know how to use: ΔG = ΔG’º + RTln[C]c[D]d/[A]a[B]b (the term [C]c[D]d/[A]a[B]b is Q, the mass-reaction ratio)
+ Will a reaction occur spontaneously?
+ Depends on ΔG, not just ΔG’º
+ Enzymes change rates, not equilibria
+ Standard ΔG’s are additive;
+ Overall ΔG is independent of pathway
- Special role of ATP: link between catabolism and anabolism; large ΔG of hydrolysis, but process is slow
- Actual ΔG depends on concentration; though ΔG’º is –30.5 kJ/mol, ΔG is typically –50 to –65 kJ/mol; it varies from cell to cell and over time
- Other molecules w/large ΔG of hydrolysis: PEP, 1,3-BPG, Phosphocreatine, thioesters (e.g., Acetyl-CoA)
- Reaction is often not simply hydrolysis, but a group transfer (phosphate or adenylate)
- Part of the reason for ATP’s importance is due to the fact that it a moderately high-energy molecule: it can transfer energy from very-high-energy compounds to low-energy compounds
- ATP can undergo several different hydrolysis reactions, yielding diff. products & energies
- Adenylylation reactions have a high ΔG’º and are part of Fatty Acid activation, Amino Acid activation and DNA and RNA synthesis
- Phosphoryl group transfer reactions: ATP to other NDP’s (ΔG’º ~0), to reduce [ADP] when it accumulates (to ATP + AMP, ΔG’º ~0), from Creatine to ADP (ΔG’º =-12.5kJ/mol)
- Biological oxidation-reduction reactions (flow of electrons does work; electromotive force [emf]); usually have coupled oxidation-reduction pairs; in bio-reactions, Carbon can be reduced or oxidized
- C6H12O6 + 6O2 → CO2 + 6H2O ΔG’º =-2,840 kJ/mol … but in cells, this is released a little bit at a time
- Electron/Energy carriers: NAD, NADP, FMN, FAD
- Mobile carriers: NAD, NADP; electrons transferred in pairs
- NAD/NADP: coenzymes are loosely bound and serve as e- shuttles (‘trucks’)
- FMN/FAD: coenzymes that are tightly bound to flavoproteins (FMN/FAD not usually mobile: ‘warehouses’)
- FMN/FAD derived from riboflavin
- Glucose: the major fuel of most organisms (ΔG’º =-2,840 kJ/mol)
- Possible fates of glucose: can be (1) stored, (2) oxidized to 3-C compounds, (3) oxidized to pentoses
- Glycolysis: an almost-universal central catabolic pathway; energy is stored in ATP and NADH; a part of fermentation (anaerobic break-down of glucose; 2-phases [Preparatory and Payoff])
Fate of pyruvate:
I. Aerobic conditions:
Pyruvate → Acetate → CO2 + H2O + NADH + O2 + 2H+ → NAD+ + H2O
II. Anaerobic/Hypoxic conditions:
See below
- How much of the energy stored in glucose is released during glycolysis? 146 kJ/mol, which is only 5% of the stored energy (2,840 kJ/mol)
- Some important features of the phosphorylated intermediates of the glycolytic pathway: (a) ionized (charged) at physiological pH, so they can’t pass through the hydrophobic membranes of cells; (b) conserve energy released by oxidations; (c) binding of phosphate to Mg++ to enzymes lowers activation energy
- See “Glycolysis Summary” spreadsheet with notes on the 10 steps of the pathway
Overview of Glycolysis:
Total reaction:
Glucose + 2ATP + 2NAD+ + 4ADP + 2Pi → 2 Pyruvate + 2ADP + 2NADH + 2H+ + 4ATP + 2H2O
Net reaction:
Glucose + 2NAD+ + 2ADP + 2Pi → 2 Pyruvate + 2NADH + 2H+ + 2ATP + 2H2O
- Know what Channeling is.
- Note: in cancer cells, glucose-uptake and glycolysis are accelerated to compensate for limited O2 supply (for aerobic oxidation)
Other pathways feeding into the Glycolytic Pathway:
+ Degradation of polysaccharides (glycogen, starch) – using phosphorylase
1. Phosphorylase acts repetitively on non-reducing ends, forming glucose 1-phosphate
- A specialized enzyme removes branches (FYI – don’t need to remember this detail)
- Glucose 1-phosphate is converted (isomerized) to glucose 6-phosphate, which feeds into glycolysis
Degradation of polysaccharides – using amylase – forms maltose + Dextrins
(Dextrins are then broken down into glucose monomers)
Disaccharides:
Maltose → 2 glucose
Lactose → galactose + glucose (Lactose intolerance: absence of lactase → GI distress)
Sucrose → fructose + glucose
Trehalose → 2 glucose
Other monosaccharides are converted into intermediates of the glycolytic pathway:
Galactose →→ Glucose 1-phosphate → Glucose 6-phosphate
Fructose → Fructose 6-phosphate (muscle & kidney)
Fructose →→→ Glyceraldeyde 3-phosphate (liver)
Mannose →→ Fructose 6-phosphate
Fate of pyruvate, part II:
II. Anaerobic/Hypoxic conditions: Need to regenerate NAD+ by some other pathway:
Pyruvate + NADH + H+ → Lactate + NAD+ (lactate: accumulates during rigorous exercise)
Or, in yeast: Pyruvate → Ethanol + NAD+ (TPP required [removal of carboxyl]; CO2 evolved)
- Carbohydrate biosynthesis: gluconeogenesis, etc.
Organizing principles of biosynthesis:
“Antiparallel pathways:” degradative and synthesis pathways may share reversible reactions, but each must have at least 1 unique reaction.
There is some form of regulation at at least one reaction – coordinate, reciprocal – usually early in the chain.
The biosynthetic processes are usually coupled to ATP breakdown, which usually makes the process irreversible (large, negative ΔG).
- Central pathway for carbohydrate biosynthesis is gluconeogenesis (precursors → glucose). This is very important for animals, which need much glucose.
- Note antiparallel paths of gluconeogenesis and glycolysis. 7 common reactions, 3 different reactions or groups of reactions (bypasses).
- Bypass #1 (antiparallel to glycolysis step #10): Complex and costly (1 ATP + 1 GTP); overall exergonic; NADH consumed in mitochondria and re-formed in cytosol.
- An alternate bypass predominates when lactate is available but mitochondrial NADH is not – i.e., under conditions of anaerobic metabolism, when muscle tissue produces lactate, lactate is transported to the liver, where it is converted to pyruvate and converts NAD+ to NADH in the cytosol.
- Bypass #2 ( reversal of glycolysis step #3): no involvement of ADP/ATP
- Bypass #3 (reversal of glycolysis step #1): no involvement of ADP/ATP; enzymes present in hepatocytes and renal cells (where glucose is formed), but not muscle or brain (where glucose is used)
- Gluconeogenesis is expensive (4 ATP, 2 GTP and 2 NADH) relative to the amount of energy stored through glycolysis (2 ATP and 2 NADH); the ‘payoff’ of this “cost” is that it is essentially irreversible.
- Also feeding into carbohydrate biosynthesis are: glucogenic amino acids, and fatty acids (in plants).
- In animals, fatty acids cannot be net-converted to glucose.
The Pentose Phosphate Pathway relatively minor compared to glycolysis
- major products:
NADPH (a universal reductant in anabolic pathways)
Ribose 5-phosphate (may be needed for the biosynthesis DNA/RNA)
- In tissues that need NADPH, but not ribose 5-phosphate, the latter compound is recycled into glucose 6-phosphate
- Understand: the Dynamic Steady State and Homeostasis (in relation to metabolic regulation)
- Key role of AMP in regulating ATP consumption and synthesis
- ΔG depends on the concentrations of the reactants and products (metabolites) – one way to regulate reactions
- Ways to control enzyme activity: change no. of molecules, covalent modification, allosteric effectors
(Reciprocal) Regulation of Glycolysis and Gluconeogenesis
- For some steps of glycolysis, concentrations and activities of enzymes are high, so substrates and products are almost instantaneously in equilibrium; for reactions that are far from equilibrium these are the points at which the process is controlled (rate-limiting steps); these steps are usually exergonic (ΔG<0), and the enzymes are controlled by allosteric regulators and/or hormones
- Paired anabolic and catabolic pathways: the pathways often use common enzymes, but have different enzymes at points of regulation, to catalyze reactions in two different directions; for 3 highly-exergonic reactions (Steps 1, 3 and 10 of glycolysis) the pathways use different enzymes; these 3 steps are also key regulation points for glycolysis
Step #1: in muscle, feedback inhibition by product; in liver, regulation by controlling [substrate]
* Step #3: regulation by [substrate], ATP, ADP, AMP, etc.
* Step #10: inhibited if cell is energy-rich (ATP, acetyl-CoA, fatty acids)
- Beginning of gluconeogenesis: control fate of pyruvate: (a) if energy is abundant (acetyl-CoA), synthesize OA and then glucose; (b) if not, break down pyruvate to acetyl-CoA (on to CAC)
- Coordinate reciprocal regulation of Step #3 of glycolysis and its gluconeogenesis counterpart:
Allosteric regulation:
1. If the cell has stored excess energy as ATP or by activating the citric acid cycle, ATP or Citrate reduces PFK-1 activity
2. If the cell has used much energy, its ADP and AMP concentrations will be higher, which will activate PFK-1.
Hormonal regulation:
1. Low blood sugar → Glucagon synthesis → decreases level of Fructose 2,6-bisphosphate (F26BP)
2. Decreased conc. of F26BP inactivates PFK-1, and re-activates FBPase-1. This prevents the breakdown of glucose and favors its synthesis through gluconeogenesis.
- Regulation of Step #10 (Pyr. Kinase); allosteric, by ‘indicators of abundant energy;’ in the liver, by phosphorylation/dephosphorylation (role of glucagon)
- Regulation of gluconeogenesis by controlling the fate of pyruvate (by acetyl-CoA)
- Glycogen catabolism (breakdown)
- Glycogen biosynthesis: key precursor/intermediate is UDP-glucose (a sugar nucleotide), which is synthesized from glucose and UTP, with energy from ATP
- Steps in glycogen synthesis: (1) Make UDP-glucose (requires 1 ATP + 1 UTP). (2) Form a primer, beginning with glycogenin. (3) Add glucose monomers to non-reducing end of growing chain (α1→4). (4) Remove short chain segments and ‘graft’ them onto the chain to form branches (α1→6; branching enzyme).
(Reciprocal) Regulation of glycogen breakdown and synthesis
- Glycogen breakdown is regulated by controlling the enzyme glycogen phosphorylase (Recall the feeder pathway into glycolysis: Glycogen → glucose 1-phosphate)
- The fully-active form of the enzyme is phosphorylase a; the less-active form is phosphorylase b. The enzyme phosphorylase b kinase catalyzes the transformation of the b form to the a form; the enzyme phosphorylase a phosphatase catalyzes the transformation of the a form to the b form.
Regulation of carbohydrate metabolism
Generally: (1) When there is a high blood glucose level, glycolysis is activated (to break down some of the glucose), glycogen synthesis is activated (to store some of the glucose), and glycogen breakdown is inhibited. (2) When there is a low blood glucose level, glycolysis is inhibited (so as not to further lower the glucose level), glycogen synthesis is inhibited (so as not to further lower the glucose level), and glycogen breakdown is activated (to supply glucose)
