Topic 6 Flashcards
Living cells are
miniature chemical factories
Cellular respiration extracts energy stored in
sugars and other fuels
* Cells apply this energy to perform work
Metabolism:
the sum of all chemical reactions in an organism
* Transforms matter and energy
* Subject to Laws of Thermodynamics
Metabolism is an emergent property of life that arises from
orderly interactions between molecules
- A metabolic pathway begins with
a specific molecule and ends with a product
* Each step is catalyzed by a specific enzyme
* Cascade effect drives conversion from A to D
Two types of metabolic pathways
Catabolic pathways:
* Release energy by breaking down complex molecules into simpler compounds
* Ie) Cellular respiration, the breakdown of glucose in the presence of oxygen
Anabolic pathways:
* Consume energy to build complex molecules from simpler ones
* Ie) The synthesis of protein from amino acids
Bioenergetics:
the study of how energy flows through living organisms
- Energy:
- Capacity to cause change
- Exists in various forms, some of which can perform work
Can be converted from one form to another
- Types of Energy:
- kinetic
- thermal
- potential
- chemical
- Kinetic energy:
energy associated with motion
thermal energy
the kinetic energy associated with random movement of atoms or molecules
heat- thermal enery transferred between objects
potential energy
energy that matter possesses becuase of its location or structure
chemical energy
potential energy avaliable for release in a chemical reaction
Thermodynamics
is the study of energy transformations
Isolated vs open systems:
isolated
unable to exchnage energy or matter with its surroundings
open systems
able to exchnage energy or matter with surroundings
- organisms are open systems
The First Law of Thermodynamics:
- The principle of conservation of energy
- The energy of the universe is constant
- Energy can be transferred and transformed, but it cannot be created or destroyed
The Second Law of Thermodynamics
- During every energy transfer or transformation, some energy is unusable and is often lost as heat
- Every energy transfer or transformation increases the entropy of the universe
- Entropy is a measure of molecular disorder, or randomness
- Entropy
a measure of molecular disorder, or randomness
Biological Order vs Disorder 1
- Living cells convert organized forms of energy to heat
- Heat is a more disordered form of energy
- But, in Topic 01, Order was a Unifying Theme in Biology
Biological Order vs Disorder 2
- Organisms create ordered structures from less organized forms of energy and matter
- Organisms also replace ordered forms of matter and energy in their surroundings with less ordered forms
- Ie) animals consume complex molecules in their food and release smaller, lower energy molecules and heat into the surroundings
Biological Order vs Disorder 3
- The evolution of more complex organisms does not violate the second law of thermodynamics
- Entropy (disorder) may decrease in a particular system, such as an organism, so long as the total entropy of the system and surroundings increases
Conversion of Energy
- Living cells convert organized forms of energy to heat (a more disordered form of energy)
- Spontaneous processes:
- occur without energy input
- can happen quickly or slowly
- for a proccess to occur spontaneously, it must increase the entropy of the universe
non spontaneous process
decrease entropy, need energy to occur
- Free Energy
energy that can do work when temperature and pressure are uniform, as in a living cell
represented as: G
- Free Energy change indicates whether reaction occurs spontaneously or not
Free energy is a measure of
a system’s instability - its tendency to change to a more stable state
- During a spontaneous change, free energy decreases, and the stability of a system increases
- Equilibrium is a state of
maximum stability
* A process is spontaneous and can perform work only when it is moving toward equilibrium
exergonic reaction:
- Proceeds with a net release
of free energy * Spontaneous * G < 0
endergonic reaction:
- Absorbs free energy from its
surroundings - Nonspontaneous * G > 0
Equilibrium and Metabolism
Reactions in a closed system eventually reach equilibrium and can then do no work
Cells are not in
equilibrium
* A defining feature of life is that
metabolism is never at equilibrium
* A catabolic pathway in a cell releases free energy in a series of reactions
- A cell does 3 main kinds of work:
Chemical work: pushing
endergonic reactions
* Transport work: pumping substances against the direction of spontaneous movement
* Mechanical work: such as contraction of muscle cells
- To perform work, cells use
energy coupling
Energy coupling:
the use of exergonic processes to drive endergonic processes
* Most energy coupling in cells is mediated by ATP and ATP hydrolysis
ATP Hydrolysis
- Bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
- Energy is released from ATP when the terminal phosphate bond is broken
- This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
- Cellular work (mechanical, transport, and chemical) is powered by
the hydrolysis of ATP
Energy from the exergonic reaction of ATP hydrolysis can be used to drive an
endergonic reaction
ATP drives endergonic reactions by
phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
The recipient molecule is now called a phosphorylated intermediate
* Overall, the coupled reactions are exergonic and occur spontaneously
Transport and mechanical work in the cell are also powered by
ATP hydrolysis
* ATP hydrolysis leads to a change in protein shape and binding ability
what needs to be regenerated
- ATP hydrolysis is an exergonic reaction, so it occurs spontaneously
- ATP levels become depleted and need to be regenerated by adding a phosphate group to adenosine diphosphate (ADP)
ATP regeneration
- The energy to phosphorylate ADP comes from catabolic reactions in the cell
- Ie) cellular respiration, photosynthesis
- The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways
- Enzymes are
proteins that speed up chemical reactions
* Catalysts:
- Catalysts:
they speed up reaction without being consumed
* Often have name that ends in ‘ase’
Every chemical reaction between molecules involves
bond breaking and bond forming
How enzymes speed up reactions
- Enzymes speed up specific reactions by lowering the EA barrier
- Enzymes do not affect the change in free energy (ΔG)
- Enzymes allow reactions that would eventually occur to occur faster
- The enzyme binds to its substrate, forming an
enzyme-substrate complex
* While bound, the activity of the enzyme converts substrate to product
- The active site is the
region on the enzyme where the substrate binds
- Induced fit of a substrate:
- Brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
- Lock and Key Model
- Induced fit of a substrate:
- Brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
- Lock and Key Model
- Enzymes are:
- Extremely fast acting
- Catalysts: Emerge from reactions in their original form
- Very small amounts of enzyme can have huge metabolic effects
- Used repeatedly in catalytic cycles
- The active site can lower activation energy by 4
- Orienting substrates correctly
- Straining substrate bonds
- Providing a favorable microenvironment
- Covalently bonding to the substrate
- The rate of an enzyme-catalyzed reaction can be sped up by
increasing substrate concentration
* When all enzyme molecules have their active sites engaged, the enzyme is saturated
* If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme
- An enzyme’s activity can be affected by:
- Environmental factors, such as temperature & pH
- Chemicals tha tspecifically influence the enzyme
- Each enzyme has optimal temperature and pH for its function
- Optimal conditions – favor most active shape for enzyme molecule
- Cofactors
are non-protein enzyme helpers
* Cofactors may be inorganic (a metal in ionic form) or organic
* An organic cofactor is called a coenzyme
* Coenzymes include vitamins
- Competitive inhibitors:
- Bind to the active site of an enzyme
- Compete with the substrate
- Noncompetitive inhibitors:
- Bind to another part of an enzyme, causing the enzyme to
change shape - Makes the active sitel ess effective
- Examples of inhibitors: toxins, poisons, pesticides, and antibiotics
- Not all inhibitors are bad, allows for regulation of enzymatic activity
- A cell’s metabolic pathways need to be tightly regulated A cell does this by:
- Switching on or off the genes that encode specific enzymes
- Regulating the activity of enzymes
Allosteric regulation:
- May either inhibit or stimulate an enzyme’s activity
- A regulatory molecule binds to a protein at one site, and affects the protein’s function at another site
- Most allosterically regulated enzymes are made from
polypeptide subunits, each with its own active site
* The enzyme complex has active and inactive forms
- The binding of an activator stabilizes
the active form of the enzyme
- Cooperativity:
a form of allosteric regulation that can amplify enzyme activity
* One substrate molecule primes an enzyme to more easily act on additional substrate molecules
* Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site
- Feedback inhibition:
- The end-product of a metabolic
pathway shuts down the pathway - Prevents a cell from wasting chemical resources by synthesizing more product than is needed
- Compartmentalization within the cell help bring
order to metabolic pathways
* In eukaryotic cells, some enzymes reside in specific organelles
* Ie) Enzymes for cellular respiration are in mitochondria
* Ie) Acid hydrolases in lysosome
