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23: Biochemical Production metabolic pathway
- a series of consecutive biochemical reactions used to
Outline: convert a starting material into an end product
I. Metabolism - major metabolic pathways for all life forms are similar which
II. Metabolism and Cell Structure enables scientists to study metabolic reactions in simpler life
III. Important Intermediate Compounds in Metabolic Pathways forms and use the results to help understand the
A. Adenosine Phosphates (ATP, ADP, AMP) corresponding metabolic reactions in more complex
B. Flavin Adenine Dinucleotide (FAD, FADH2) organisms like humans
C. Nicotinamide Adenine Dinucleotide (NAD+, NADH) - linear: a series of reactions generates a final product
D. Coenzyme A (CoA-SH)
E. Classification of Metabolic Intermediate Compounds
IV. High-Energy Phosphate Compounds
- cyclic: a series of reactions regenerates the first reactant
V. An Overview of Biochemical Energy Production
VI. The Citric Acid Cycle
A. Reactions of the Citric Acid Cycle
B. Summary of the Citric Acid Cycle
C. Regulation of the Citric Acid Cycle
VII. The Electron Transport Chain
II. METABOLISM AND CELL STRUCTURE
A. Complex I: NADH-Coenzyme Q Reductase
B. Complex II: Succinate-Coenzyme Q Reductase
C. Complex III: Coenzyme Q-Cytochrome c Reductase Two Types of Cell:
D. Complex IV: Cytochrome c Oxidase A. prokaryotic cell
VIII. Oxidative Phosphorylation - has no nucleus
IX. ATP Production for the Common Metabolic Pathway - found only in bacteria
X. The Importance of ATP - DNA is governed by usually a single circular molecule found
XI. Non-ETC Oxygen-Consuming Reactions near the center of the cell in a region called the nucleoid
B. eukaryotic cell
I. METABOLISM
- cell in which the DNA is found in a membrane-enclosed
nucleus
metabolism - found in all higher organism
- sum total of all the biochemical reactions that take place in - about 1000 times larger than bacterial cells
a living organism - key components:
- an average human adult whose weight remains the same for • outer membrane
40 years processes about 6 tons of solid food and 10,000 • nucleus
gallons of water
• cytosol
• ribosomes
Two Subtypes of Metabolic Reaction:
• lysosomes
A. catabolism
• mitochondria
- all metabolic reactions in which large biochemical molecules
are broken down to smaller ones
- usually release energy
- involved in the oxidation of glucose
B. anabolism
- all metabolic reaction in which small biochemical molecules
are joined together to form larger ones
- usually require energy
- ex. Synthesis of proteins from amino acids
cytoplasm
- water-based material of a eukaryotic cell
- lies between the nucleus and the outer membrane of the cell
- within in are several kind of small structures called
organelles
organelles
- minute structure within the cytoplasm of a cell
- carries out a specific cellular function
- surrounded by the cytosol
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cytosol
III. IMPORTANT INTERMEDIATE COMPOUNDS IN METABOLIC
- water-based fluid part of the cytoplasm of a cell
PATHWAYS
Three Important Types of Organelles:
A. ribosome - all have nucleotides
- site of protein synthesis
ADENOSINE PHOSPHATES (ATP, ADP, AND AMP)
B. lysosome
- contains hydrolytic enzymes needed for cellular rebuilding,
repair, and degradation
- some hydrolyze proteins to amino acids
- others hydrolyze polysaccharides to monosaccharides
- enzymes from it degrades and destroys bacteria and viruses
trapped by the body’s immune system AMP
- one of the nucleotides present in RNA molecules
mitochondrion
- responsible for the generation of most of the energy for a - ATP and ADP differ structurally from AMP only in the
cell number of phosphate groups present
- sausage-shaped
- containing both: ATP
• outer membrane - a phosphoester bond joins the first phosphoryl group to the
• inner membrane pentose sugar ribose
- the other two phosphoryl groups are joined to one another
by phosphoanhydride bonds
outer membrane of the mitochondrion
- about 50% lipid and 50% protein
- freely permeable to small molecules
inner membrane of the mitochondrion phosphoryl group
- multi-folded - functional group derived from a phosphate ion that is part
- 20% lipid and 80% protein of another molecule
- highly impermeable to most substances - ATP: 3; ADP: 2; AMP: 1
- nonpermeable nature dives a mitochondrion into two
separate components: phosphoanhydride bond
• matrix - chemical bond formed when two phosphate groups react
- interior region with each other and a water molecule is produces
• intermembrane space - when two phosphate groups react with one another, a water
- region between the inner and outer membranes molecule is produced hence “anhydride”
cristae
- folds of the inner membrane that protrude into the matrix
ATP synthase complexes - ATP and ADP molecules readily undergo hydrolysis
- small spherical knobs attached to the cristae reactions in which phosphate groups (Pi, inorganic
- located on the matric side of the inner membrane phosphate) are released
- responsible for ATP synthesis, and their association with - in metabolic pathways in which they are involved, the
inner membrane is critically important for this task adenosine phosphates continually change back and forth
among the various forms
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- these hydrolyses are energy-producing reactions that are
used to drive cellular processes that require energy input
- phosphoanhydride bonds in ATP and ADP are very reactive
bonds that are require less energy than normal to break
strained bonds
- reactive bonds
- presence of such is the basis for the net energy production
that accompanies hydrolysis
- cause: greater than normal electron-electron repulsive
forces at specific locations because of highly ribitol
electronegative atom and/or highly charged atoms - reduced form of ribose
occurring together in a molecule - —CH2OH in place of —OH GROUP
- ATP and ADP: highly electronegative oxygen atoms in the
additional phosphate groups
Example:
conversion of glucose to glucose-6-phosphate:
- typical cellular reaction in which ATP functions as:
• source of a phosphate group and
• a source of energy flavin
- first step in the process of glycolysis - active portion of FAD in metabolic redox reactions
- reduced, converting FAD to FADH2
Other Triphosphates Present in Cells: FAD
A. uridine triphosphate (UTP) - oxidized form
- involved in carbohydrate metabolism
FADH2
B. guanosine triphosphate (GTP) - reduced form
- participates in protein and carbohydrate metabolism
(oxidation = loss of hydrogen; reduction=gain of hydrogen)
C. cytidine triphosphate
- involved in lipid metabolism Example:
- a typical cellular reaction in which FAD serves as the
oxidizing agent involves —CH2—CH2— portion of a
FLAVIN ADENINE DINUCLEOTIDE (FAD, FADH2)
substrate being oxidized to produce a carbon-carbon double
bond
flavin adenine dinucleotide (FAD)
- coenzyme required in numerous metabolic redox reactions
- can be visualized as containing either three or six subunits
- six block diagram shows basis for its name
(saturated = single bonds)
- for enzyme-catalyzed redox reaction involving removal of 2 H
atoms, each removed hydrogen atom is equivalent to a
* Flavin and ribitol together constitute riboflavin (vitamin B). hydrogen ion, H+, pluas an electron, e-
summary equation relating oxidized and reduced forms of FAD:
- continually changes back and forth between its oxidized
form and its reduced form
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- both electrons lost by the alcohol go to the nicotinamide
NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD+, NADH)
ring in the NADH (two electrons are required, rather one,
because of the original positive charge on NAD+)
parallels between NAD+ and FAD:
- have coenzyme functions in metabolic redox patheays
- have a B vitamin as a structural component (nicotinamide in
NAD+)
- both can be represented structurally by using 3 or 6 subunits
COENZYME A (CoA-SH)
- general metabolic function: transfer of acetyl groups in
metabolic pathways
structural formula: acetyl group
- portion of an acetic acid molecule (CH3—COOH) that
remains after the —OH group is removed from the carboxyl
carbon atom
- bonds to CoA-SH through a thioester bond to give acetyl
CoA
Three- and Six-Subunit Block Diagram:
source of + sign:
- refers to the positive charge on the nitrogen atom in the
nicotinamide
- nitrogen has four bonds instead of the usual 3
- 3 subunit diagram: ADP unit is phosphorylated at C3
nicotinamide
Structural Formula:
- active portion of NAD+ in metabolic redox reactions
- reduced, converting NAD+ to NADH
NAD+
- oxidized form
NADH
- reduced form
- with one additional hydrogen atoms and two additional sulfhydryl group (—SH)
electrons - active portion of coenzyme A
- in the ethanethiol subunit of the enzyme thus coA-SH
CLASSIFICATION OF METABOLIC
INTERMEDIATE COMPOUNDS
Example:
oxidation of secondary alcohol to give a ketone:
- NAD+ serves as the oxidizing agent
- one H atom of the alcohol substrate is directly transferred
to NAD+
- one H atom appears in solution as H+ ion
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IV. HIGH-ENERGY PHOSPHATE COMPOUNDS
high-energy compound
- compound that has a greater free energy of hydrolysis than
that of a typical compound
- contain one or more very reactive bonds, strained bonds
- the balance between the energy needed to break bonds in
the reactants and that released by bond formation in the
products > typical amount of free energy released during
hydrolysis
free energy
- amount of energy released by a chemical reaction that is
actually available for further use (unlike heat)
In chemical reaction, the energy balance between the bond breaking
among reactants (energy input) and new bond formation among
products (energy release) determines whether there is a net loss or a
net gain of energy.
H3PO4
- weak triprotic inorganic acid
- parent molecule for phosphate groups
- exists in aqueous solution in several forms
- dominnat form
