Chapter 8 Flashcards
what is metabolism?
is the totality of an organisms chemical reactions
what is a metabolic pathway?
begins with a specific molecule and ends with a product
- each step is catalyzed by a specific enzyme
what is a catabolic pathway?
release energy by breaking down complex molecules into simpler compounds
- cellular respiration the breakdown of glucose in the presence of oxygen is an example of catabolic pathway
what is an anabolic pathway?
consumes energy to build complex molecules from simpler ones
- the synthesis of a protein from amino acids is an example of anabolism
what is bioenergetics?
is the study of how organisms manage their energy resources
what is energy?
the capacity to cause change
- energy exist in various forms, some which can perform work
what is kinetic energy?
is energy associated with motion
what is thermal energy (heat)?
is kinetic energy associated with random movement of atoms or molecules
what is potential energy?
is energy that matter possesses because of its location or structure
what is chemical energy?
is potential energy available or released in a chemical reaction
what is thermodynamics?
is the study of energy transformations
- in a closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings
- in an open system, energy and matter can be transferred between the system and its surroundings
- ORGANISMS ARE OPEN SYSTEMS
what is 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
what is the second law of thermodynamics?
every energy transfer or transformation increases the entropy (disorder) of the universe
- for a process to occur without energy input, it must increase the entropy of the universe
what is biological order and disorder?
- cells create ordered structures from less ordered materials
- energy flows into an ecosystem in the form of light and leaves in the form of heat
what is entropy (disorder)?
may decrease in an organism, but he universe’s total entropy increase
what is free energy?
is energy that can do work when temperature and pressure are uniform, as in a living cell
- is the measure of a systems inability, its tendency to change to a more stable state
- the change in free energy (ΔG) during a process is related to the change in enthalpy, or change in total energy (ΔH), change in entropy (ΔS), and temperature in kelvin (T)
ΔG = ΔH -TΔS
what is a spontaneous process?
- only process with a negative ΔG are spontaneous
- spontaneous processes can be harnessed to perform work
- during a spontaneous free energy decreases and the stability of a system increases (Gfinal smaller than Ginitial)
what is an exergonic reaction?
proceeds with a net release of free energy and is spontaneous
what is an endergonic reaction?
absorbs free energy from its surroundings and is non-spontaneous; its net free energy is positive
equilibrium and metabolism?
- reactions in a closed system eventually reach equilibrium and then do work
- cells are not in equilibrium, they are open systems experience a constant flow of materials
- a defining feature of life is that metabolism is never at equilibrium
A catabolic pathway in a cell does what?
A catabolic pathway in a cell releases free energy in a series of reactions
A cell does three main kinds of work what are they?
- chemical - pushes endergonic reactions
- transport - pumps substances across membranes
- mechanical - movement of cilia
what is energy coupling?
the use of an exergonic process to drives and endergonic one
- most coupling in cells is mediated by ATP- as in immediate source of energy
what is ATP?
adenosine triphosphate is the cell’s energy shuttle
- ATP is composed of ribose (a sugar), adenine ( a nitrogen base) and three phosphate groups
how does the hydrolysis of ATP work?
- the bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
- energy is released when the terminal phosphate bond is broken
when the terminal phosphate bond is broken in ATP why does this release energy?
- this release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves (by hydrolysis the three negative phosphate groups is eliminated)
The hydrolysis of ATP is what type of reaction?
- the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
- OVERALL, the coupled reactions are exergonic
what is phosphorylation?
transferring a phosphate group to some other molecule, such as a reactant
- ATP drives endergonic reactions by phosphorylation
- the phosphorylated intermediate is more reactive (less stable) than the original
what is a catalyst?
is a chemical agent that speeds up a reaction without being consumed by the reaction
what is an enzyme?
an enzyme is a catalytic protein
- hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction
- most reactions are reversible to enzymes can catalyze both forwards and backwards reactions
what is free energy of activation, or activation energy (Ea)?
the initial energy needed to start a chemical reaction is called the activation energy
- activation energy is usually supplied in the form of heat from the surroundings
what is a substrate?
the reactant that an enzyme acts on is called the enzyme’s substrate
what is an enzyme-substrate complex?
the enzyme binds to its substrate, forming an enzyme-substrate complex
what is an active site?
is the region on the enzyme where the substrate binds
what does specificity mean?
the specificity of an enzyme results from its shape and its amino acid sequence
what does induced fit mean?
induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
The active site can lower an Ea barrier by?
- orienting substrates correctly
- straining substrate bonds
- providing a favourable microenvironment
- covalently boding to the substrate
what does substrate orientation mean?
it means enzymes hold substrates in the optimal position of the reaction
what are come characteristics of R groups on enzymes?
- acidic or basic R groups on the enzyme may change the charge of the enzyme
- Charged R groups may attract the substrate
- Cofactors of the enzyme increase the reactivity of the substrate by removing or donating electrons
Inducing strain in the substrate does what?
- shifts in the conformation after binding cause an induced fit between the enzyme and the substrate
- covalent bonds of the substrate are strained
what is the Michaelis Constant (Km)?
is the substrate concentration at one half of Vmax
- units of Km are concentration units
- the Km reflect the affinity of the enzyme for the substrate
what is the Michaelis-Menten equation?
maximum velocity of an enzymatic equation results from the formation of the enzyme-substrate complex
v = Vmax [S]/ [S] + Km
what are the predictions one can assume from the Michaelis-Menten equation?
- At low substrate concentration the velocity is proportional to the substrate concentration
- At intermediate substrate concentration the velocity depends on substrate as indicated by graph
- At high substrate concentration, reaction velocity independent of substrate concentration
An enzymes activity can be affected by?
- general environmental changes such as temperature and pH
- Chemicals that specifically influence the enzyme
what are Cofactors?
are non-protein enzyme helpers; cofactors can be inorganic (such as a metal in ionic form) or organic
What is a Coenzyme?
an organic cofactor is called a coenzyme; it plays a crucial role in catalysis
- coenzymes include vitamins
what is reversible inhibition?
weak interactions (Enzyme inhibitor)
what is irreversible inhibition?
covalent bonding (Enzyme inhibitor)
what are competitive inhibitors?
bind to the active site of an enzyme, competing with the substrate
- to overcome this type of inhibition, increase the concentration of substrate which will increase the availability of active sites
what are non-competitive inhibitors?
bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective
- ie: toxins, poisons, pesticides, and antibiotics
what is an effector?
any molecule or ion that changes the activity of an enzyme
what is an allosteric effector?
if an effector binds to a different site than the active site it is called an allosteric effector
what is allosteric regulation?
occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another site
- may either inhibit or stimulate an enzymes activity
what is cooperativity?
is a form of allosteric regulation that can amplify enzyme activity
- in cooperativity, binding y a substrate to one active site stabilizes favourable conformational changes at all other subunits
what is feedback inhibition?
the end product of a metabolic pathway shuts down the pathway
- feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed
