Chapter 10.
1 ● Nucleoside triphosphate ATP - most
● Metabolism is central to all life
Metabolism that are common to all
organisms
● Life obeys the law of
thermodynamics
● The energy cells obtain from their
environment is most often conserved
as a molecule called ATP
ATP is used to supply energy
● Oxidation-reduction(redox) reactions
play a critical role in energy
conservation
● Chemical reactions that occur in
cells are organized in pathways
● Each reaction of a pathway is
catalyzed by an enzyme or a
ribozyme
Enzyme and ribozyme speedup the
reaction
● The functioning of biochemical
pathways is regulated
Cellular work and Energy Transfers
● Do work in order to survive and
reproduce
● Chemical work - synthesis of
biological molecules, energy is
needed to increase the molecular
complexity of cell
● Transport work - take up nutrients,
eliminates waste, maintain ion
balances, ions must be transported
across cell membranes against an
electrochemical gradient
● Mechanical work - energy is required
for cell motility, movement of
structures such as partitioning
chromosomes
● Energy - capacity to do work
● Physical and chemical processes
are results of the application or
movement of energy
commonly used form of cellular
energy
● Thermodynamics - energy changes
in collection of matter called system
● All other matter in the universe is
called system
Law of Thermodynamics
● 1st Law - energy can be neither
created nor destroyed. Total energy
of the universe remains
constant,redistributed
● 2nd Law - physical and chemical
processes proceed in such a way
that the randomness or disorder of
the universe increases
● Entropy - Measure of Randomness
● Calorie - amt. Of heat energy
needed to raise 1 gram of H20 from
14.5 to 15.5 degrees celsius
● Joules - units of work capable of
being done
Free Energy Change predicts the nature
of a chemical reaction
● ^G = ^H - T^S
● ^G is the change in free energy
● ^H is the change in enthalpy
● T is the temperature in Kelvin
(Celsius + 273)
10.2
● ATP - Cells energy currency, high
energy molecule
● ATP serves as link between
exergonic and endergonic reactions
● Adenosine diphosphate and
orthophosphate (P1)
● Energy released is used to power
endergonic reactions
● The very negative ^G’ of hydrolysis
of ATP: ability to transfer a
phosphoryl group to another
molecule
● ATP is high phosphate transfer
potential, it readily donates a
 phosphoryl group to another
molecule
● ATP can easily be made by cells
from ADP using molecules such
as phosphoenolpyruvate(PEP).
This mechanism is called substrate-
level phosphorylation
● Guanosine 5’ - triphosphate (GTP)
supplies energy used during protein
synthesis
● Uridine 5’ - triphosphate - used for
synthesis of peptidoglycan and other
polysaccharides.
10.3 Redox Reactions
● Free energy changes are related to
equilibria of all chemical reactions,
including equilibria of oxidation-
reduction
● Redox - electrons move from an
electron donor to an electron
acceptor
● Electrons - packets of energy
● The more electrons the more
energy rich the molecule is
● Glucose can donate up to 24
electrons in redox reactions
● Each redox reaction consists of two
half reactions. functions as the
electron-donating(oxidation) and
electron-accepting(reduction)
● The acceptor and donor of a half
reaction = conjugate redox pairs
● Standard reduction potential (E0)
- equilibrium constant for a redox
half reaction, measure of the
tendency of the donor of a half
reaction to lose electron
● E0 are measured in volts, unit of
electrical potential or electromotive
force
● Conjugate redox pairs area potential
source of energy
● Nicotinamide adenine dinucleotide
(NAD+) - electron acceptor. The
NAD+/NADH conjugate redox pair
has a very negative E0 and NADH
can therefore give electrons to many
acceptors, including 02
10.4 ETC: Sets of sequential redox
reactions
● Reduction of 02 by NADH
● As glucose is catabolized, it is
oxidized. Many of electrons released
from glucose are accepted by
NAD+, reducing it to NADH, which
transfers the electrons to 02
● Electrons are transferred to 02 via a
series of electron carriers that are
organized into a system called
electron transport chain
● The 1st electron carrier has the most
negative E’0 each successive carrier
is slightly less negative
● Carriers direct the electrons to the
terminal electron acceptor (02)
● This protects the cells, from random
nonproductive reductions of other
molecules in the cell
● ETC are associated in the plasma
membranes / intracytoplasmic
membranes of bacterial and
archeal cells
● In eukaryotes they are localized to
the internal membranes of
mitochondria and chloroplasts
● The electron carriers associated with
ETC differ in terms of their chemical
nature
● Nicotinamide adenine dinucleotide
phosphate (NADPH), which donates
electrons to ETC, contain
nicotinamide ring that accepts 2
electrons and one proton from donor
and a second proton is released
● Flavin adenine dinucleotide (FAD)
and Flavin mononucleotide (FMN)
bears two electrons and two protons
on the complex ring
 ● Proteins bearing FAD and FMn are
often called flavoproteins
● Coenzyme Q (CoQ) / ubiquinone is
a quinone that transports 2 electrons
and 2 protons
● Cytochromes and several other
carriers use iron atoms to transport
one electron at a time
● There are several different
Cytochromes, each consisting of a
protein and an iron-porphyrin ring.
● Some iron containing electron-
carrying proteins lack a heme group
and are called nonheme iron
proteins. Often referred to as iron-
sulfur proteins because the iron is
associated with sulfur atoms. Four S
atom and 2 Fe atoms
● Ferredoxin is an FE-S Protein active
in synthesis related electron
transport. Carry one electron at a
time
10.5: Biochemical Pathway
● Organism carry out a myriad of
chemical reactions, products are
called metabolites
● Reactions are organized into
biochemical pathways
● Metabolite Flux: rate of turnover of a
metabolite. Used as a measure of
pathway activity and to understand
metabolic networks
10.6: Enzymes and Ribozymes speed up
cellular chemical reactions
● Most of these catalysts are proteins
called Enzymes
● Other catalyst are RNA molecules
termed Ribozyme
Enzyme Structure
● Catalyst: a substance that increases
the rate of a chemical reaction
● Reacting molecules are called
substrates
● Substances formed are products
● Many enzymes are composed only
of one part. But some have 2 part
● Apoenzyme the protein component
● cofactor is the non protein
component, include metal ions and
organic molecules
● Holoenzyme=Apoenzyme + cofactor
● If the cofactor is firmly attached to
the apoenzyme it is a prosthetic
group
● If the cofactor is loosely attached,
dissociate after product is formed it
is called coenzyme
How enzymes speed up reactions
● If a reaction is endergonic, presence
of enzyme will not shift its
equilibrium so that more products
are formed
● Activation Energy: required to bring
the reacting molecules together in
the correct way to reach the
transition state
● Enzymes accelerate reactions by
lowering the activation energy, more
substrate molecules will have
sufficient energy to come together
and form products
● Enzymes bring substrates together
at a specific location called
active/catalytic site to form an
enzyme-substrate complex
● Induced fit model: enzyme changes
shape when it binds the substrate so
that the active site surrounds and
precisely fits the substrate.
Hexokinase
● Enzymes binds so that it is correctly
oriented. Orientation lowers the
amount of energy that the
substrates required to reach the
transition state
Substrate concentration affects enzyme
activity
 ● Enzyme activity varies in response
to substrate concentrations
● At very low substrate concentrations,
enzyme binds substrates more often
● Michaelis constant(Km) substrate
concentrations required for the
enzyme to achieve half-maximal
velocity, is used to measure of the
apparent affinity of an enzyme for its
substrate
● The lower the Km the lower the
substrate concentration At which an
enzyme catalyzes its reaction
● Enzymes with a low Km are said
to have a high affinity for their
substrates.
● Enzymes with lower Km value are
able to function better
Enzyme denaturation destroys enzyme
activity
● Enzyme activity is also changed by
alterations in pH and temperature
● When ph Deviates too greatly from
an enzyme's optimum,activity slows
and the enzyme may be damaged
● If the temperature rises too much,
structures, enzyme structures will be
disrupted
● Bacteria and archaea grow best at
high temperature
Enzyme Inhibition
● Most potent poisons are enzyme
inhibitors
● Competitive inhibitor : directly
competes with substrate at an
enzyme’s catalytic site and prevents
the enzyme from forming a product
● Resemble normal substrates but
they cannot be converted to
substrates
● p-aminobenzoate(PABA) - molecule
used in the formation of the
coenzyme folic acid
● Noncompetitive inhibitors - affect
enzyme activity by binding to the
enzyme at some location other than
the active site
● Alters enzyme shape, rendering it
inactive or less active
● Heavy metals such as mercury
frequently are noncompetitive
inhibitors of enzyme
Ribozymes: Catalytic RNA Molecules
● RNA Molecules also can catalyze
reactions
● Ribozymes-Catalytic RNA molecules
● Ribozyme is located in ribosomes
and is responsible for catalyzing
peptide bond formation between
amino acids during protein synthesis
● Best studied ribozyme cut
themselves and then join segments
of themselves back together
10.7 Metabolism must be Regulated to
maintain homeostasis and prevent waste
Metabolic pathways can be regulated in
three major ways:
1. Metabolic Channeling
2. Regulation of Synthesis
(regulation of gene
Expression)
3. Direct stimulation or inhibition
of the activity of the critical
enzymes (posttranslational
regulation)
● Cells often use multiple regulatory
approaches to coordinate their
complex metabolic activities
● Metabolic Channeling influences
pathway activity by localizing
metabolites and enzymes into
different parts of the cell
● One of the most common metabolic
channeling mechanisms is
compartmentation
● The differential distribution of
enzymes and metabolites among
separate cell structures or
organelles. It is particularly important
in Eukaryotes
● Regulation of Gene Expression -
Transcription and translation Rates
are altered to control the amount of
an enzyme present in the cell
● Posttranslational Regulation of
Enzyme Activity - in contrast to
regulation of gene expression, the
direct stimulation or inhibition of the
activity of critical enzymes rapidly
alters pathway activity