Module 09:Introduction to Metabolism (Part 01 - Stoker) Flashcards
This is entailed for cellular processes such as protein synthesis, DNA replication, RNA transcription and transport across the membrane, etc.
Energy
This pertains to the process by which all metabolic reactions in which large biochemical molecules are broken down to smaller ones
Catabolism
Explain the nature of catabolism.
(1) Usually energy is released in these reactions (Exergonic)
(2) Example: Oxidation of glucose
This pertains to the process by which all metabolic reactions in which small biochemical molecules are joined to form larger ones
Anabolism
Explain the nature of anabolism. .
(1) Usually require energy (Endergonic)
(2) Example: The synthesis of proteins
This is the chemical reactions of biomolecules. It is the biochemical basis of life processes
Metabolism
This is the breakdown of larger molecules into smaller ones; an oxidative process that releases energy,
Catabolism
What does catabolism use?
It uses OA like NAD+ and FAD
This is the synthesis of larger molecules from smaller ones; a reductive process that requires energy,
Anabolism
What does anabolism use?
It uses RA like NADPH.
This is a series of consecutive biochemical reactions used to convert a starting material into an end product. It may classified as linear or cyclic.
Metabolic Pathway
What are the two types of metabolic pathway?
(1) Linear eg. glycolysis
(2) Cyclic eg. Krebs, Fatty acid oxidation, urea cycle
This is a single compartment organism. It has no nucleus (found only in bacteria). The singular circular DNA molecule present near center of the cell called nucleoid
Prokaryotic Cell
This is where the single circular DNA molecular is present.
Nucleoid
This is a multi-compartment cell. The DNA is present in the membrane enclosed nucleus. Cell is compartmentalized into cellular organelles. This is 1000 times larger than bacterial cells and found in higher forms of organisms
Eukaryotic Cell
This cellular organelle is entailed for the process of DNA replication and RNA synthesis
Nucleus
This cellular organelle is known cellular boundary
Plasma membrane
This is the cellular water-based organelle material of a eukaryotic cell
Cytoplasm
This cellular organelle generates most of the energy needed for cell.
Mitochondria
This cellular organelle contain hydrolytic enzymes needed for cell rebuilding, repair and degradation
Lysosome
This cellular organelle is entailed for protein synthesis.
Ribosomes
This is an organelle that is responsible for the generation of most of the energy for a cell
Mitochondria
Explain the cellular structure of the mitochondria
(1) Outer membrane: Permeable to small molecules: 50% lipid, 50% protein
(2) Inner membrane: Highly impermeable to most substances: 20% lipid, 80% protein
(3) Inner membrane folded to increase surface area
What phenomenon occurs in the mitochondria?
Synthesis of ATP occurs, (ATP synthase enzymes)
This part of the mitochondria is freely permeable to small molecules and ions
Outer Membrane
Explain the structure of the inner membrane
(1) Impermeable to small molecules & ions, H+
(2) Contains ATP/ADP translocase,
(3) Contains ATP synthase,
(4) Contains the RC e- carriers
What are the important intermediate compounds in metabolic pathways?
(1) Nucleotide containing intermediates
(2) Adenosine Phosphates (AMP, ADP, ATP, cAMP)
(3) Monophosphate (AMP): one phosphate group
(4) Diphosphate (ADP): Two phosphate groups
(5) Triphosphate (ATP): Three phosphate groups
(6) Cyclic monophosphate (cAMP): Cyclic structure of phosphate
Explain the phenomenon of ATP Hydrolysis
(1) In Adenosine Triphosphate (ATP), there are two high energy bonds (phosphoanhydride bonds)
(2) Hydrolysis occurs on the terminal phosphate group by ATPase releases of 30.5 Kj/mol-1 of free energy
(3) to generate an inorganic phosphate and adenosine diphosphate (ADP)
What happens during ATP Hydrolysis?
Marked decrease in electrostatic repulsion of beta phosphate of ADP upon hydrolysis of ATP to ADP
Why is ATP less stable charge wise than ADP?
Energy must be expended to put on additional negative charge on ADP to make ATP
Phosphate groups are connected to AMP by ____________ which require less than normal energy to hydrolyze them
strained bonds
What is the formula for the ATP Hydrolysis
(1) ATP + H2O –> ADP + PO4^3- + Energy
(2) ADP + H2O –> AMP + PO4^3- + Energy
Overall Reaction: ATP + 2H2O -> AMP + 2 PO43- + Energy
The net energy produced in these reactions is used for cellular reactions
In cellular reactions ATP functions as both a source of what?
a phosphate group and a source of energy
How is glucose converted to glucose-6 phosphate?
Glucose + ATP —hexokinase— ADP + Glucose-6-Phosphate where the product contains PO3^2- unit.
How is NAD+ (oxidized) reduced to NADH?
NAD+ and NADP+ Nicotinamide adenine dinucleotide, NAD+, and its phosphorylated analog NADP+ (the hydroxyl group is esterified with phosphate) undergo reduction to NADH and NADPH, accepting a hydride ion (two electrons and one proton) from an oxidizable substrate.
How is Flavin adenine dinucleotide (FAD) and Flavin mononucleotide (FMN) reduced?
FADH+ (FMNH-) (semiquinone) ——-> FADH2 (FMNH2) (fully reduced)
Oxidized and reduced FAD and FMN. FMN consists of the structure above the dashed line on the FAD (oxidized form). The flavin nucleotides accept two hydrogen atoms (two electrons and two protons), both of which appear in the flavin ring system. When FAD or FMN accepts only one hydrogen atom, the semiquinone, a stable free radical, forms. From this ribitol and ADP is produced.
What does the nucleotide contain?
Nucleotide = N base, sugar & phosphate
How is a semiquinone formed?
Both FAD and FMN can accept and donate 2e- in the isoalloxazine ring. The isoalloxazine ring accepts and transfers e- and protons in a stepwise manner forming a semiquinone
This is a coenzyme required in numerous metabolic redox reactions
Flavin Adenine Dinucleotide (FAD)
This is the active form – accepts and donates electrons
Flavin subunit
This is a reduced form of ribose sugar
Ribitol (Contains Flavin and Ribitol)
What does Flavin Adenine Dinucleotide contain?
(1) Flavin
(2) Ribitol
(3) Adenosine Diphosphate (ADP)
What does Nicotinamide Adenine Dinucleotide contain?
(1) Adenosine Diphosphate (ADP)
(2) Nicotinamide
(3) Ribose
(4) Adenine
Explain the cellular reaction between FAD and FADH?
A typical cellular reaction in which FAD serves as OA, oxidizing agent involves conversion of an alkane group to an alkene (dehydrogenation reaction)
(1) FAD is oxidized form
(2) FADH2 is reduced form
In enzyme reactions FAD goes back and forth (equilibrium) from oxidized to reduced form.
What is NAD in its cellular reaction?
Coenzyme (Oxidizing Agent)
What does an oxidizing agent involve?
conversion of an alkane group to an alkene (dehydrogenation reaction)
What is NADH in its cellular reaction?
Reduced Form
In the cellular reaction between NAD and NADH what is the three (3) subunit structure?
3 Subunit structure: Nicotinamide - Ribose - ADP
In the cellular reaction between NAD and NADH what is the six (6) subunit structure?
6 Subunit structure: Nicotinamide – ribose -phosphate –phosphate - ribose – adenine
A typical cellular reaction in which NAD+ serves as the OA, oxidizing agent is the what
oxidation of a secondary alcohol to give a ketone.
Explain the formula between the cellular reaction between NAD and NADH.
Lactic Acid + NAD + —-> Pyruvic Acid + NADH + H -
This is a derivative of vitamin B.
Coenzyme A
What is the three-subunit structure in the cellular reaction of Coenzyme A?
Three Subunit Structure : 2-Aminoethanethiol - pantothenic acid - phosphorylated ADP
What is the six-subunit structure in the cellular reaction of Coenzyme A?
Six Subunit structure: 2-Aminoethanethiol - pantothenic acid -phosphate - phosphate phosphorylated ribose - adenine
What is the active component of coenzyme A?
the sulfhydryl group (-SH group) in the ethanethiol subunit of the coenzyme
Explain the structure of Coenzyme A?
Acetyl-CoA (acetyl CH3CO- group is attached to -SCoA)
2-Aminoethanethiol - Pantothenic Acid (Vitamin - Phosphorylated ADP
What are the three (3) classifications of metabolic intermediate compounds?
(1) Intermediates for the storage of energy and transfer of phosphate groups (ATP - ADP - AMP)
(2) Intermediates for the transfer of electrons in metabolic redox reactions (FAD - FADH and NAD - NADH)
(3) Intermediates for the transfer of acetyl groups (H-S-CoA - acetyl-S-CoA)
This are high energy bonds in adenosine-5’-triphosphate.
Phosphoric Anhydride Bonds (2 high energy bonds)
Several phosphate containing compounds found in metabolic pathways are known as _________________. These have greater free energy of hydrolysis than a typical compound:
high energy compounds
These are the reactive bond in higher energy compounds.
Strained Bonds (at least one reactive bond)
Explain the nature of energy in high energy compounds.
Energy to break these bonds is less than a normal bond – the free energy of hydrolysis of high energy compounds is higher than normal compounds. The higher the negative the free energy of hydrolysis,G= - the greater the bond strain.
The typical free energy release is greater than what?
Typically the free energy release is G= - greater than 6.0 kcal/mole (indicative of bond strain)
Strained bonds are represented by what?
Strained bonds are represented by sign ~ (squiggle bond)
What is the free energy of hydrolysis of enol phosphates like phosphoenolpyruvate (PEP)?
-14.8 kcal/mole
What is the free energy of hydrolysis of 1-3 biphosphoglycerate and acetyl phosphate (1-3 BPG)?
-11.8 kcal/mole
-11.3 kcal/mole
What is the free energy of hydrolysis of guanidine phosphates like creatinine phosphate and arginine phosphates?
-10.3 kcal/mole
- 9.1 kcal/mole
What is the free energy of hydrolysis of triphosphates namely:
(1) ATP - AMP - PP
(2) ATP - ADP + P
-7.7 kcal/mole
-7.5 kcal/mole
What is the free energy of hydrolysis of diphosphates namely
(1) PPi (pyrophosphate) - 2P
(2) ADP - AMP + Pi
-7.8 kcal/mole
-7.5 kcal/mole
What is the free energy of hydrolysis of sugar phosphates namely:
(1) glucose 1 phosphate
(2) fructose 6 phosphate
(3) AMP - adenosine + Pi
(4) Glucose 6 phosphate
(5) glycerol 3 phosphate
-5.0 kcal/mole
-3.8 kcal/mole
-3.4 kcal/mole
-3.3 kcal/mole
-2.2 kcal/mole
This is used as a general designation for any free monophosphate species present in cellular fluid. Free diphosphate ions are designated as PP where i means inorganic.
PPi
This is needed to run human body is obtained from food
Energy
What are the four (4) general stages in the biochemical energy production process?
(1) Stage 1: Digestion
(2) Stage 2: Acetyl CoA formation
(3) Stage 3: Citric Acid Cycle
(4) Stage 4: Electron transport chain, ETC and oxidative phosphorylation
Explain the stages of catabolism.
(1) Bulk food is hydrolyzed in the stomach and small intestine to give small molecules
(2) Fatty acids, monosaccharides and amino acids are degraded in the cells to yield acetyl CoA
(3) Acetyl CoA is oxidized in the citric acid cycle to give CO2
(4) The energy is released in the citric acid cycle and is used by the electron transport chain to oxidatively phosphorylate ADP and produce ATP
This stage in the biochemical energy production process begins in mouth (saliva contains starch digesting enzymes), continues in the stomach (gastric juice), completed in small intestine:
Digestion (Results in small molecules that can cross intestinal membrane into the blood)
What are the end products of digestion?
(1) Glucose and monosaccharides from carbohydrates
(2) Amino acids from proteins
(3) Fatty acids and glycerol from fats and oils
What happens after digestion?
The digestion products are absorbed into the blood and transported to body’s cells
This stage in the biochemical energy production occurs when the small molecules from stage 1 are further oxidized.
Acetyl Group Formation
What is the end product of Acetyl Group Formation?
Acetyl CoA
Where does Acetyl Group Formation occur?
Reactions occur both in cytosol (glucose metabolism) as well as mitochondria (fatty acid metabolism) of the cells.
This stage in the biochemical energy production takes place in the mitochondria. In this stage the acetyl group is oxidized to produce CO2 and reduced coenzymes NADH and FADH2.
Citric Acid Cycle (CAC) or Krebs Cycle
Which cycle does the carbon dioxide that we exhale primarily comes from?
Citric Acid Cycle (CAC) or Krebs Cycle
What is the first intermediate of the cycle?
First intermediate of the cycle is citric acid, a tricarboxylic acid – therefore designated as Citric acid cycle or TCA
Most energy from the Citric Acid Cycle (CAC) or Krebs Cycle is trapped in what?
Most energy is trapped in reduced coenzymes NADH and FADH2
Some energy produced from the CAC is lost in the form of what?
Heat
This stage in the biochemical energy production also takes place in the mitochondria. In this, NADH and FADH2 produced in the CAC cycle are passed down to this.
Electron Transport Chain and Oxidative Phosphorylation
Explain the process of Electron Transport Chain and Oxidative Phosphorylation
(1) H+ and e- from NADH and FADH2 are passed to ETC carriers and ultimately to O2.
(2) NADH and FADH2 are re-oxidized in the ETC
(3) The ETC is a series of reactions where H+ and e- from NADH & FADH2 are transferred to O2 which is reduced to H2O
(4) During e- transfer H+ are pumped into the IMS by e- carriers
(5) H+ ions reenter the mitochondrial matrix and drive ATP-synthase reaction to produce ATP
In the Electron Transport Chain and Oxidative Phosphorylation, where are e carriers located?
The e- carriers in ETC are located along the inner mitochondrial membrane
This is the primary energy carrier in metabolic pathways. This is also the energy currency of the cell.
ATP
