metabolism

the totality of an organism's chemical reactions

- manages the material and energy resources of the cell

- living systems require a constant input of energy and exchange of macromolecules

metabolic pathway

a specific molecule is altered in a series of defined steps, resulting in a certain product

- each step is catalyzed by a specific enzyme

catabolic pathways

"breakdown pathways"

- metabolic pathways that lead to the release of energy by the breakdown of complex molecules to simpler compounds

ex. digestive system enzymes break down food and release energy

anabolic pathways

"biosynthetic pathways"

- consume energy to build complicated molecules from simpler ones

ex. linking of amino acids to form muscle protein in response to physical exercise

energy

the capacity to do work / cause change

- the ability to rearrange a collection of matter

note about pathways

energy released from downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways

bioenergetics

the study of how energy flows through living organisms

kinetic energy

- associated with the relative motion of objects

possessed by anything that is moving

(moving objects can perform work by imparting motion to other matter)

thermal energy

kinetic energy associated with the random movement of atoms or molecules

heat

- thermal energy in transfer from one object to another

light

also a type of energy

- can be harnessed to perform work, such as powering photosynthesis in green plants

potential energy

- energy that matter possesses due to its location or structure

chemical energy

- potential energy available for release in a chemical reaction

- stored in molecules

- amount of this energy a molecule possesses depends on its chemical bonds

biochemical pathways...

- enable cells to release chemical energy from food molecules and use the energy to power life processes

organisms are...

- energy transformers

thermodynamics

the study of energy transformations that occur in matter

first law of thermodynamics

the energy of the universe is constant

- energy can be transferred and transformed, but it cannot be created or destroyed

second law of thermodynamics

- in every energy transfer the potential energy of the final state is less than the potential energy of the initial state

- every energy transfer or transformation increases the entropy of the universe

energy cannot be recycled (some energy is converted into thermal energy and released as heat - becomes unavailable to do work)

living things must have a constant inflow of energy

each energy transfer or transformation makes...

the universe more disordered

entropy

a measure of molecular disorder or randomness

spontaneous process

- energetically favorable

- leads to an increase in entropy

- do not require energy to occur

nonspontaneous

- leads to decrease in entropy

- will only happen if energy is supplied

living systems...

increase the entropy of their surroundings

free energy

- the part of a system's energy that is able to perform work (when the temperature and pressure of a system are uniform)

- measure of a system's instability; tendency to change to a more stable state

Gibbs free energy used in biology...

to predict which kinds of change can happen without an input of energy

- such spontaneous changes can be harnessed by the cells to perform work

a process is spontaneous and can perform work only when...

it is moving toward equilibrium

exergonic reaction

energy is released

- occur spontaneously

- release free energy into the system

G <0

endergonic reaction

requires energy to proceed

- absorb free energy

- require free energy from the system

G>0

metabolism at a whole...

is never at equilibrium

(this is one of the defining features of life)

energy coupling

- a key feature in the way that cells manage their energy resources to do cell work

- the use of a rxn that releases energy to drive a reaction that requires energy (exergonic -> endergonic)

ATP

- primary source of energy in cells

- when a phosphate group is hydrolyzed, energy is released in an exergonic reaction

- mediates energy coupling in cells

ATP structure

- nitrogenous base adenine

- bonded to ribose

- chain of three phosphates

work in the cell is done by...

the release of a phosphate group from ATP

- exergonic release of the phosphate group is used to do endergonic work of the cell

When ATP transfers one phosphate group through hydrolysis, it becomes...

ADP

three types of cellular work

chemical work, transport work, and mechanical work

chemical work

the pushing of endergonic reactions that would not occur spontaneously

transport work

pumping of substances across membranes against the direction of spontaneous movement

mechanical work

such as the beating of cilia, the contraction of muscles, and the movement of chromosomes during cellular reproduction

phosphorylation

- the transfer of a phosphate group from ATP to some other molecule

how can ATP be regenerated?

- by the addition of the phosphate to ADP

catalysts

- substances that can change the rate of reaction without being altered in the process

enzymes

- macromolecules that are biological catalysts

- speed up metabolic processes by lowering energy barriers

activation energy

- the amount of energy it takes to start a reaction

- the amount of energy it takes to break the bonds of the reactant molecules

substrate

the reactant that an enzyme acts on

active site

- the part of the enzyme that binds to the substrate

enzyme-substrate complex

what the enzyme and substrate form when bonded together

- generally held together by weak interactions

products

- substrate converted into this

- released from enzyme

factors that can affect enzyme activity

-changes in pH

- changes in temperature

(any changes in the precise shape of the enzyme usually mean the enzyme will not be as effective)

denatured

- enzyme has lost its folded structure, is no longer able to function

enzymes have...

optimal temperatures and pHs in which they function best at

cofactors

- nonprotein enzyme helpers

- function in some crucial way to allow catalysis to occur

coenzymes

- organic cofactors

ie. vitamins

how are enzymes regulated?

- can be turned on and off

competitive inhibitors

- molecules that compete with the substrate for the active site on the enzyme

- may bind reversibly or irreversibly to the active site

- often very similar to the normal substrate molecule and reduce the efficiency of the enzyme as it competes for the active site

noncompetitive inhibitors

- do not directly compete with the substrate molecule to bind to the active site

- they impede enzyme activity by binding to another part of the enzyme

- causes the enzyme to change its shape, often rendering the active site nonfunctional

concentration of enzymes and substrates...

- can also affect the efficiency of an enzymatic reaction

assuming abundant substrate, an increase in enzyme concentration will lead to an increase in the production of the final product

enzymes regulate biological activities by...

- increasing the rates of their reactions

allosteric site

- a specific binding site on an enzyme that is not the active site

- enzyme regulators bind to this

- once bound, the shape of the enzyme is changed and this can either simulate or inhibit enzyme activity

feedback inhibition

- increases the efficiency of a pathway by turning it off when the end product accumulates in the cell

- the end product on an enzymatic pathway can switch off its pathway by binding to the allosteric site of an enzyme in the pathway