Transcript Slide 1

Concepts of Metabolism
Chapter 8
Energy Needs
• Organisms need constant supply of
energy
• Plants supply themselves and almost all
other living organisms with basic
molecules needed for life
• Use energy stored in new molecules to
drive life-sustaining processes
• Chemical reactions make up complex
process of metabolism
Chemical Reactions
• Rearrangement of atoms from initial
positions to new positions in other
molecules
• Biochemical reactions
– Reactions in living organisms
• Plant cells synthesize complex
compounds from carbon, hydrogen,
oxygen, nitrogen, and smaller amounts of
sulfur and phosphorus
Basic molecules used for
production of other
Function
molecules in cell
Water (H2O)
Primarily a solvent
Source of most of the hydrogen atoms and some of
the oxygen atoms in organic molecules
Carbon dioxide (CO2)
Primary source of carbon
Major source of oxygen
Ammonium (NH4+)
Primary source of nitrogen in proteins and nucleic
acids
Nitrate (NO3-)
Primary source of nitrogen in proteins and nucleic
acids
Sulfate (SO42-)
Source of sulfur found in some amino acids
Phosphate (PO43-)
Incorporated in nucleotides
Chemical Reactions
• Involve rearrangement of atoms
• Breaking and re-forming of covalent bonds
– Breaking requires stretching or bending of
bonds
• Potential energy
– Stored energy that can be used to stretch or
break bonds
Chemical Reactions
• Kinetic energy
– Energy of motion
– Average kinetic energy of mixture depends on
temperature
– The greater the temperature, the faster the
molecules are moving
• Activation energy
– Energy barrier that must be overcome so
reaction can proceed
Chemical Reactions
A+BC+D
Substrates
or reactants
Have potential energy
in respective bonds
Collisions of A and B
increase potential
energy
High energy state
called activated
complex
Products
Catalysts
• Rate of chemical reaction is important
• Ways to speed a reaction
– Increase concentrations of substrates
• Increases probability that pairs of substrate molecules will
meet
– Increase temperature
• Increases probability that substrate molecules will have
enough kinetic energy to form activated complex
• Not practical in living cells
• Denatures proteins
Catalysts
• Catalysts
– Better strategy than increased temperature
• Increased heat harms cellular components
– Not used up or formed as reaction proceeds
– Work by forming temporary complex with one
or more substrates
• Attaches to substrate with reversible bonds
• Formation distorts bonds of complex so further
bond bending or stretching requires less energy
Enzymes
•
•
•
•
•
•
Biological catalysts
Work only on one set of substrates
Catalyze one type of reaction
Primarily made of protein molecules
3-D shape
Has active site into which substrate
molecule fits
Enzymes
• H bonds hold substrate in active site
• While in active site, bonds of substrate
become distorted
• Distortion of substrate makes it
susceptible to reaction catalyzed by
enzyme
Enzymes
• Ways substrate bonds become distorted in
active site
– Pulling substrate into misfitting groove distorts
substrate’s shape
– Active site may change shape once substrate is
present
– Electrical charges in active site push and pull
electrons of substrate
– Functional groups (side chains of amino acids) in
active site react (temporarily) with substrate
Enzymes
• Enzyme activity
– May depend entirely on protein structure
– Some enzymes cannot function without
nonprotein cofactors (coenzymes)
• Examples of cofactors
– Metal ions such as Fe2+, Fe3+
– Organic molecules without metal ions
Enzymes
– Ways cofactors attach to enzymes
• Covalent bonds
• Loosely bound and easily removed from enzyme
protein
– Cofactors often able to accept or donate
electrons in oxidation-reduction reactions
– Trace elements that serve as cofactors in
plants
• Iron, copper, molybdenum
Enzymes
– Bio-organic cofactors common in plants
• Riboflavin, thiamin, niacin, pantothenic acid
• Cannot be synthesized by humans
• Humans must obtain these from plants that we
consume
Plant Enzyme Activities
• Easy to detect examples
• Darkening of apple fruit after cutting or biting
– Action of enzyme polyphenol oxidase on chemicals
released from cells
• Softening of tomato fruit as it ripens
– Action of enzymes on polysaccharides in cell wall
– Cellulase – acts on cellulose
– Polygalacturonase – acts on pectin
Plant Enzyme Activities
• Papain
– Enzyme from papaya
– Digest protein in fruit as it ripens
– Can be extracted from fruit and used to
tenderize meat before cooking
Control of Reaction Rates
• Synthesis of enzyme catalyzing particular
reaction when and only when reaction is
needed
– Slow and crude method of control
– Example
• Formation and germination of seeds
Control of Reaction Rates
• Regulation of catalytic activity of already
existing enzymes
– Lower affinity of active site for substrate or its
catalytic efficiency once substrate has been
found
• Enzyme inhibited
– Increase affinity of active site for substrate or
its catalytic efficiency
• Enzyme activated
Metabolic Pathways
• Series of linked reactions in a cell
• Making complex molecules requires a
series of steps
• Product of first reaction is substrate for
second reaction, product of second
reaction is substrate for third reaction, and
so on
• Each reaction requires a different enzyme
Metabolic Pathways
• Intermediates
– Products of reactions other than final product
of a series
• Intermediary metabolism
– Collection of all the metabolic pathways in
cells
Metabolic Pathways
Linked Reactions
• Form complex network
• Branch point
– One intermediate is used as substrate by
several separate enzymes to produce
different products
• Anabolic reactions
– Reactions that produce subunits of functional
or structural molecules
– Predominant type of reaction in meristems
Linked Reactions
• Catabolic reactions
– Reactions that break down damaged or
unwanted molecules into their component
parts
– Catabolic reactions predominate in cells of
ripening fruit
Concentration of Compound
• Often controls its production in a cell
• Feedback inhibition
• Efficient way to control formation of end product
– Shut off activity of first enzyme in pathway to restrict
formation of final product
– Branch point enzyme (1st enzyme) of pathway has
regulatory site
– Final product serves as its inhibitor
– Keeps concentration of product constant
Concentration of Compound
Role of Free Energy
• Free energy determines direction of
reversible reaction
• A+BC+D
– Overall reaction eventually reaches state of
equilibrium
• Rates of forward and reverse reactions become
equal
• Concentrations of substrates and products become
constant
Role of Free Energy
• Factors determining reaction direction
– Initial concentrations of substrates and
products in reaction’s mixture
– Relative stability of bonds in substrate and
products
– Number of substrates and products that
participate in reaction
– Temperature
Role of Free Energy
• Free energy
– Greater the concentration of substrates in a
reaction’s mixture, the greater their free
energy
– More stable the bonds of the substrate, the
lower their free energy
– More independent molecules included in the
substrates, the lower their free energy
** above statements also apply to products of a
reaction
Role of Free Energy
• Reactions that proceed forward
spontaneously
– Lose free energy
– Downhill reactions
• Reaction that shows no change in free
energy is at equilibrium
Role of Free Energy
• Reactions associated with increase in free
energy will not occur spontaneously
– Need source of free energy to proceed
– Uphill reactions
Role of Free Energy
– Examples of uphill reactions
• Combination of amino acids into a single protein
• Synthesis of RNA or DNA
• Reduction of carbon-containing molecules to form
hydrocarbon chain in lipid molecules
• Movement of flagella
• Separation of chromosomes during mitosis
Coupled Reactions
• Reactions that must occur together
• Examples
– Oxidation-reduction reactions
• One compound is oxidized
• Another compound is reduced
• Neither reaction occurs by itself
Coupled Reactions
– Transfer of phosphate group
• One compound loses phosphate group through
hydrolysis reaction (requires addition of
components of water)
• Another compound gains phosphate group through
condensation reaction (produces water)
• Change in free energy of overall reaction
equals sum of changes in free energy of
partial reactions
Reactions That Run Most of the
Cell’s Machinery
• Hydrolysis of ATP
• Oxidation of NADH and NADPH
Hydrolysis of ATP
• ATP – adenosine triphosphate
• Adenine + ribose + three phosphates
– Phosphate linkages are unstable
– Can be split apart by hydrolysis to form ADP +
phosphate
• High energy compound or energy carrier
• Hydrolysis occurs spontaneously
• Releases free energy of 7-12 kcal per
mole of ATP
Oxidation of NADH and NADPH
• NADH – nicotinamide adenine
dinucleotide
• NADPH – nicotinamide adenine
dinucleotide phosphate
• Both are coenzymes
• Reactive part of molecule is nicotinamide
functional group
– Humans obtain this from food because we
cannot synthesize nicotinamide (niacin)
Oxidation of NADH and NADPH
• Plant cells synthesize niacin
– Use it to make NADH and NADPH
• NADPH
– Reduced form of molecule
– Can donate electrons
• NAD+
– Oxidized form of molecule
Oxidation of NADH and NADPH
• Oxidation of NADH by oxygen gas
releases 52 kcal per mole of free energy
• Oxidation of NADH coupled to formation of
2 to 3 molecules of ATP
• Oxidation of NADPH used to synthesize
fatty acids and some amino acids