biochem exam 1 - from review sheet :)

Question 1

___ 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

Answer 1

D
UDP-glucose

Question 2

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

Answer 2

D
Glycogenin
- this is the seed for glycogenin

Question 3

Metabolic pathways (converging metabolism, diverging metabolism, cyclic), metabolites, catabolism (degradation, yielding energy), anabolism (synthesis, requiring energy)

Question 4

• 1st and 2nd laws of thermodynamics (FYI)

Question 5

• Know: Keq = [C]c[D]d/[A]a[B]b; know how to use ΔG’º = -RTlnK’eq;

Question 6

• Remember: ΔG = ΔH – TΔS

Question 7

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)

Question 8

+ 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

Question 9

• Special role of ATP: link between catabolism and anabolism; large ΔG of hydrolysis, but process is slow

Question 10

• 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

Question 11

• Other molecules w/large ΔG of hydrolysis: PEP, 1,3-BPG, Phosphocreatine, thioesters (e.g., Acetyl-CoA)

Question 12

• Reaction is often not simply hydrolysis, but a group transfer (phosphate or adenylate)

Question 13

• 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

Question 14

• ATP can undergo several different hydrolysis reactions, yielding diff. products & energies

Question 15

• Adenylylation reactions have a high ΔG’º and are part of Fatty Acid activation, Amino Acid activation and DNA and RNA synthesis

Question 16

• 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)

Question 17

• 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

Question 18

• C6H12O6 + 6O2 → CO2 + 6H2O ΔG’º =-2,840 kJ/mol … but in cells, this is released a little bit at a time

Question 19

• Electron/Energy carriers: NAD, NADP, FMN, FAD

Question 20

• Mobile carriers: NAD, NADP; electrons transferred in pairs

Question 21

• NAD/NADP: coenzymes are loosely bound and serve as e- shuttles (‘trucks’)

Question 22

• FMN/FAD: coenzymes that are tightly bound to flavoproteins (FMN/FAD not usually mobile: ‘warehouses’)

Question 23

• FMN/FAD derived from riboflavin

Question 24

• Glucose: the major fuel of most organisms (ΔG’º =-2,840 kJ/mol)

Question 25

• Possible fates of glucose: can be (1) stored, (2) oxidized to 3-C compounds, (3) oxidized to pentoses

Question 26

• 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])

Question 27

Fate of pyruvate:
I. Aerobic conditions:
Pyruvate → Acetate → CO2 + H2O + NADH + O2 + 2H+ → NAD+ + H2O
II. Anaerobic/Hypoxic conditions:
See below

Question 28

• 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)

Question 29

• 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

Question 30

• See “Glycolysis Summary” spreadsheet with notes on the 10 steps of the pathway

Question 31

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

Question 32

• Know what Channeling is.

Question 33

• Note: in cancer cells, glucose-uptake and glycolysis are accelerated to compensate for limited O2 supply (for aerobic oxidation)

Question 34

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

2. A specialized enzyme removes branches (FYI – don’t need to remember this detail)
3. Glucose 1-phosphate is converted (isomerized) to glucose 6-phosphate, which feeds into glycolysis

Question 35

Degradation of polysaccharides – using amylase – forms maltose + Dextrins
(Dextrins are then broken down into glucose monomers)

Question 36

Disaccharides:
Maltose → 2 glucose
Lactose → galactose + glucose (Lactose intolerance: absence of lactase → GI distress)
Sucrose → fructose + glucose
Trehalose → 2 glucose

Question 37

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

Question 38

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)

Question 39

• Carbohydrate biosynthesis: gluconeogenesis, etc.

Question 40

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).

Question 41

• Central pathway for carbohydrate biosynthesis is gluconeogenesis (precursors → glucose). This is very important for animals, which need much glucose.

Question 42

• Note antiparallel paths of gluconeogenesis and glycolysis. 7 common reactions, 3 different reactions or groups of reactions (bypasses).

Question 43

• 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.

Question 44

• 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.

Question 45

• Bypass #2 ( reversal of glycolysis step #3): no involvement of ADP/ATP

Question 46

• 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)

Question 47

• 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.

Question 48

• Also feeding into carbohydrate biosynthesis are: glucogenic amino acids, and fatty acids (in plants).

Question 49

• In animals, fatty acids cannot be net-converted to glucose.

Question 50

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

Question 51

• Understand: the Dynamic Steady State and Homeostasis (in relation to metabolic regulation)

Question 52

• Key role of AMP in regulating ATP consumption and synthesis

Question 53

• ΔG depends on the concentrations of the reactants and products (metabolites) – one way to regulate reactions

Question 54

• Ways to control enzyme activity: change no. of molecules, covalent modification, allosteric effectors

Question 55

(Reciprocal) Regulation of Glycolysis and Gluconeogenesis

Question 56

• 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

Question 57

• 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

Question 58

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)

Question 59

• 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)

Question 60

• Coordinate reciprocal regulation of Step #3 of glycolysis and its gluconeogenesis counterpart:

Question 61

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.

Question 62

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.

Question 63

• Regulation of Step #10 (Pyr. Kinase); allosteric, by ‘indicators of abundant energy;’ in the liver, by phosphorylation/dephosphorylation (role of glucagon)

Question 64

• Regulation of gluconeogenesis by controlling the fate of pyruvate (by acetyl-CoA)

Question 65

• Glycogen catabolism (breakdown)

Question 66

• Glycogen biosynthesis: key precursor/intermediate is UDP-glucose (a sugar nucleotide), which is synthesized from glucose and UTP, with energy from ATP

Question 67

• 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).

Question 68

(Reciprocal) Regulation of glycogen breakdown and synthesis

Question 69

• Glycogen breakdown is regulated by controlling the enzyme glycogen phosphorylase (Recall the feeder pathway into glycolysis: Glycogen → glucose 1-phosphate)

Question 70

• 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.

Question 71

Regulation of carbohydrate metabolism

Answer 71

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)