BICH 411 Exam 1

What are the 4 functions of metabolism?

1. Obtain free energy for the cell

2. Degrade macromolecules as required for biological function

3. convert nutrients into macromolecules

4. Assemble macromolecules into cellular structures

What is catabolism? function? oxidative or reductive?

degradative pathways

produce free energy

oxidative

What is anabolism? function? oxidative or reductive?

biosynthetic pathways

consuming free energy

reductive

ATP is formed via ________ in phototrophic cells or __________ in heterotrophic cells

photosynthesis

catabolism

Draw the structure of ATP, ADP and AMP

Why is ATP a "high energy" compound?

hydrolysis --> increased resonance stabilization, decreased electrostatic interaction, increased energy of solvation

Draw the structure of NADH and NADPH

What is the function of NAD+? NADH?

collects electrons released in catabolism

NADH is the most common e- carrier, always transfers two e- at a time

Draw the structure of oxidized and reduced NADH

LEO the lion says GER

Loss of electrons is oxidation, gain of electrons is reduction.

What is the function of NADPH?

provides the reducing power for anabolic processes

oxidative precursor - reductive biosynthetic reactions - reduced biosynthetic product

NADPH --> NADP+

NADPH can be viewed as the carrier of electrons from catabolic reactions to anabolic reaction

How do the pathways of catabolism converge to a few end products?

catabolism converges to three principal end products: water, carbon dioxide and ammonia

What are the three stages of catabolism?

1. proteins, polysacch and lipids broken into building blocks

2. building blocks are degraded into common products: acetyl groups of acetyl-CoA

3. catabolism converges to three principal end products: water, carbon dioxide and ammonia

What are the two ways to manage catabolism and anabolism?

1. cells maintain tight and separate regulation of catabolism and anabolism so metabolic needs can be met

2. metabolic pathways are localized within different cellular compartments (COMPARTAMENTALIZATION)

Describe bonds in an endothermic reaction?

head is absorbed

new bonds are less stable

Describe bonds in an exothermic reaction?

heat is evolved by the system

new bonds are more stable

What are the three thermodynamic equations?

1) ∆G = ∆H -T∆S

2) ∆G = ∆G°+ RT ln([P]/[R])

3.) ∆G° = -RT lnKeq

What are biosynthetic enzymes?

operate as part of anabolic pathways (reductive biosynthesis)

What are degradative enzymes?

operate as part of catabolic pathways (oxidative degradation)

What are vitamins?

organic molecules acquired through diet that assist metabolic reactions

What are the water soluble vitamins?

almost always converted to coenzymes

What are fat soluble vitamins?

ADEK and are stored for longer periods of time

How are metabolic pathways controlled? (3)

thermodynamics, compartamentalization, metabolic flux

What is metabolic flux? What are 4 types?

regulation of key enzymes

1. allosteric control

2. covalent modification

3. substrate cycles

4. genetic control

What are the 2 phases of glycolysis?

1. Energy investment phase (2 ATP)

2. Energy payback phase (4 ATP)

Why is PEP such a high energy intermediate?

enol phosphate

large -ΔG° ́, potent phosphorylating agent

1. Hydrolysis of a phosphate group (PEP--> pyruvate)

2. tautomerization (PEP enol --> keto)

What are three high energy intermediates?

PEP

1,3-BPG

PC

Define Glycolysis

a pathway for glucose breakdown that consists of 10 enzymes that facilitate conversion to pyruvate

What is the Pentose Phosphate Pathway (PPP)?

an alternative pathway that allows for NADPH production and provides biosynthetic precursors

What is Gluconeogenesis?

a pathway in the liver and kidneys that allows for biosynthesis of glucose from pyruvate, lactate and amino acids

7 of the enzymes are also glycolytic enzymes that function near eq. and are reversible

How are glycolysis and gluconeogenesis related?

glycolysis and GNG are reciprocally regulated by allosteric effects, covalent modification and changes in enzyme synthesis rates

How is glucose transported in epithelial cells?

secondary active transport- fueled by Na+

sodium pumped from low to high conc. (high extracellular)

glucose catches ride from sodium passive transport back in

How is glucose transported in other cells?

driven by concentration and hormones- independent of Na+

What is the difference between GLUT2 and GLUT4 transporters?

GLUT2- low affinity transporter in hepatocytes and pancreatic cells

-higher Km, 1st order kinetics- based on glucose conc., sensor for insulin release

GLUT4- high affinity transporter in adipose tissue and muscle cells

-lower Km, 0th order, rate is constant, increased production of GLUT4

Where does glycolysis occur? Does it require oxygen?

cytoplasm

no

Draw the overall strategy of glycolysis (powerpoint)

Glucose (2ATP->2ADP) 2 GA3P (2NAD+-> 2NADH, 2ADP->2ATP) 2 3PG

What do the two phases of glycolysis produce?

First phase converts glucose to two glyceraldehyde-3-P

Second phase produces two pyruvates

Why does glycolysis start by "investing" ATP?

investing ATP allows glucose uptake to be controlled

glucose can either move in or out of cells via transport proteins

glucose-P is trapped inside the cell

Using ATP to irreversibly convert G--> G6P allows regulation of glucose uptake

What is the first reaction of glycolysis?

priming reaction- hexokinase or glucokinase

Gluc --> G6P

Why are there two different enzymes for G--> G6P?

Typical Cell- Hexokinase - takes only as much glucose as needed

Liver Cell- Glucokinase - stores excess glucose, but doesn't compete with other tissues

What are the differences between Hexokinase and Glucokinase?

Hexokinase- gluc, fruct or mannose, low capacity, low Km-high affinity, direct feedback regulation by G6P

Glucokinase- gluc only, high capacity, high Km-low affinity, diff regulatory mechanism

Where is G6P common to several metabolic pathways?

gluc-> G6P

two F6P for glycolysis, Glucose-1-P for glycogen synthesis or to PPP

Draw the mechanism of hexokinase and glucokinase

What is the 2nd reaction of glycolysis? Is it reversible?

Phosphoglucoisomerase

G6P -> F6P

reversible

Draw the mechanism for phosphoglucoisomerase reaction ** note carbon #s**

What is the intermediate?

cis-enediolate intermediate

Why does PGI reaction occur?

next step is 2nd phosphorylation at C-1, tough for a hemiacetal, easy for primary alcohol

isomerization to fructose puts the carbonyl at C2 position which activates the C3 for an aldolytic cleavage rxn

What is the 3rd reaction of glycolysis?

F6P --> F-1,6-BP

phosphofructokinase

What is the importance of PFK?

KEY REGULATORY STEP

FIRST COMMITTED STEP IN GLYCOLYSIS

CONTROLS GLYCOLYSIS VS GLUCONEOGENESIS

LARGE -DELTAG

Draw the reaction with PFK

What are the allosteric affecters of PFK?

inhibited by ATP and citrate

activated by AMP and Fructose 2,6 BP

What is the function of fructose 2,6 BP as an allosteric affector?

potent allosteric activator that increases affinity of PFK for F6P for various levels of response- cell needs more energy, can override effects of ATP

Draw the mechanism of PFK

What is the 4th reaction of glycolysis?

FBP-> DHAP and G3P

Aldolase

Draw the Aldolase reaction

PAY ATTENTION TO CARBONS

What are the two classes of aldolase enzymes?

Class I- animal tissues

-formation of covalent Schiff base E-S intermediate

Class II- bacteria and fungi

- active site metal to shield oxyanion int.

What is the importance of the Schiff's base in the aldolase reaction?

resonance stabilization - electron sink

What is the 5th reaction of glycolysis?

DHAP --> G3P

Triose Phosphate Isomerase

Draw the mechanism for TPI

what is the important intermediate??

track carbons

What are the general acids and bases in the TPI mechanism?

glutamate and histidine

What are the two high energy intermediates of the second phase? What is the yield of the second phase?

1,3-Bisphosphoglycerate

Phosphoenolpyruvate

yields 4 ATP, 2 net

What is the 6th reaction of glycolysis?

G3P -> 1,3 BPG

Glyceraldehyde 3-phosphate dehydrogenase

What is important about the reaction with Gly-3-Dehydrogenase? what's important about it's mechanism?

Gly-3P is oxidized to 1,3-BPG

energy yield from converting aldehyde to carboxylic acid used to make 1,3 BPH and NADH

mechanism involves covalent catalysis and nicotinamide coenzyme

What is the 7th reaction of glycolysis?

1,3-BPG --> 3-PG

Phosphoglycerate Kinase

Why is the reaction with phosphoglycerate kinase important?

ATP synthesis from high-energy phosphate

substrate level phosphorylation

transfer of a phosphoryl group form 1,3-BPG to ADP to form ATP

How is 2,3-BPG made? back to 3-PG?

made by reactions that detour around phosphoglycerate kinase reaction

formed from 1,3-BPG by biphosphoglycerate mutase; 3-PG fromed form 2,3-bisphosphoglycerate phosphatase

What is important about 2,3-BPG?

regulator of hemoglobin

made from circumventing the PGK reaction

What is the 8th reaction of glycolysis?

3-PG --> 2-PG

phosphoglycerate mutase

What is a mutase?

an enzyme that catalyzes the migration of a functional group within the substrate molecule

What is required for the enzymatic activity of phosphoglycerate mutase?

Mg2+

What is the importance of the reaction with phosphoglycerate mutase? imp. about mechanism?

catalyzes a phosphoryl group transfer from C-3 to C-2

repositions the phosphate to make PEP in the following reaction

phospho-histidine intermediates

small amount of 2,3-BPG to phosphorylate the His residue - activates the enzyme

What is the 9th reaction of glycolysis? What type of reaction is this?

2-PG --> PEP

enolase

dehydration reaction

What inhibits enolase?

strongly inhibited by flouride in presence of phosphate

What is the 10th reaction of glycolysis? What is the reaction named for?

PEP --> pyruvate

pyruvate kinase

named for the reverse reaction

What is important about the reaction with pyruvate kinase?

IRREVERSIBLE IN VIVO

two ATP are produced here- last payoff

large -deltaG

Draw the mechanism for pyruvate kinase

What are the allosteric affectors of pyruvate kinase?

inhibited by ATP, acetyl-CoA and alanine

activated by AMP and fructose 1,6 BP

What three steps of glycolysis are irreversible?

1. Hexokinase/glucokinase

2. PFK

3. Pyruvate kinase

At the end of glycolysis, what do we have?

2 ATP, 2 NADH and 2 Pyruvate

What are the three fates of pyruvate?

O2 availability/pyruvate fate in animals: TCA cycle, lactic acid fermentation

O2 availability/pyruvate fate in yeast: TCA cycle, lactic acid fermentation, alcoholic fermentation

How is ethanol an endpoint of glycolysis?

through anaerobic metabolism

fermentation

anaerobic breakdown of pyruvate produces ethanol by a two step process (1. pyruvate decarboxylase 2. alcohol dehydrogenase)

How is Lactate an endpoint of glycolysis?

anaerobic metabolism

occurs in animal tissues when oxygen has been depleted, TCA cycle no longer option

Pyruvate reduced to lactate by lactate dehydrogenase (large amounts of ATP generated)

Do humans have PDC and ADH?

Humans do not have PDC- to not create ethanol from exercise and acetaldehyde is toxic

Humans do have ADH- destroys ethanol made by intestinal bacteria (EtOH-->Acetaldehyde-->hangover)

What does Pyruvate decarboxylase require? Why?

Thiamine pyrophosphate (TPP)

allows a better reaction pathway- resonance stabilized carbanion

Draw the important part of TPP, what is it called?

Draw the reaction of lactate DH

What is the main goal of anaerobic metabolism?

generate NAD+ so glycolysis can continue

If anaerobic glycolysis generates much less ATP in one round of glucose breakdown, how is it still useful?

anaerobic glucose metabolism has a much faster rate of generates a lot more ATP in the same time period- higher max energy output

How is lactic acid recycled into glucose?

In muscle, Gluc-> G6P -> Pyruvate -> Lactate

Lactate transferred to Liver

Lactate -> Pyruvate -> Glucose

Glucose is transferred back to the muscles

What are the differences between slow vs fast twitch muscle fibers?

fast-twitch: rapid movements, anaerobic resp., fewer blood vessels, less mitochondria, less myoglobin

slow-twitch: endurance, aerobic resp., many blood vessels, more mitochondria, more myoglobin

What are three other substrates for glycolysis?

Fructose, Galactose, Mannose

How is Fructose routed into glycolysis? How many enzymes?

fructose routed into glycolysis as fructose 6-Phosphate in the muscle tissue or as Glyceraldehyde 3-Phoshpate in the liver

1 in muscle cells

7 in liver cells

How is Galactose routed into glycolysis? How many enzymes?

galactose converted into glucose 6-Phosphate via the Leloir Pathway

4 Enzymes

How is Mannose routed into glycolysis? How many enzymes?

mannose is converted into fructose 6-phosphate

2 Enzymes

Draw the Leloir Pathway

***enzymes!!

Draw the pathway Mannose takes to enter glycolysis

Draw the pathway Fructose takes in both muscle and liver cells to enter glycolysis

***powerpoint

What is an important regulation step in glycolysis as fructose as a substrate?

pyruvate kinase

What are the issues with high fructose?

HFCS

fructose only metabolized in excess amounts by the liver- excess sugars turned to fat- leads to fatty liver

How can glycerol enter glycolysis? Draw reaction

can be converted to glycerol-3-P by glycerol kinase

G3P is then oxidized to dihydroxyacetone phosphate by glycerol phosphate dehydrogenase

Why must glucose be made from non-carbohydrate precursors?

brain functions on glucose- 75% of daily consumption of glucose

muscles require glucose (Glycolysis Glu->Pyr)

Pentose Phosphate Pathway

-uses glucose catabolism to produce NADPH, 30% liver glucose oxidation via PPP