Unit 3: Cellular Energetics

metabolism

The Totality of an organism’s chemical reaction

Where does metabolism arise from

orderly interactions between molecules

Metabolic pathway

a series of chemical reactions that either builds a complex molecule or breaks down a complex molecule to simpler molecules.

In a metabolic pathway…

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

catabolic pathways

energy is released by breaking down complex molecules to simpler compounds

major example of a catabolic pathway

cellular respiration

anabolic pathways

energy is consumed to build complicated molecules from simpler ones

biosynthetic pathways

another name for anabolic pathways

examples of anabolism

synthesis of an amino acid from simpler molecules and synthesis of a protein from amino acids.

bioenergeticss

study of how energy flows through living organisms

energyc

capacity to cause change

energy is important to

move matter against opposing forces, such as gravity and friction

thermal energy

kinetic energy associated with the random movement of atoms or molecules

heat

thermal energy in transfer from one object to another

potential energy

energy that mater possesses because of its location or structure.

chemical energy

the potential energy available for releases in chemical reactions.

thermodynamics

study of energy transformations that occur in a collection of matter

an isolated system is unable to

exchange either energy or matter with its surroundings outside the thermos.

in an open system…

energy and matter can be transferred between the system and its surroundings.

are organisms open or closed systems?

open systems

First Law of Thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed.

Second Law of Thermodynamics

Every energy transfer or transformation increases the entropy of the universe.

A consequence of the loss of usable energy as heat to the surroundings

each energy or transformation makes the universe more disordered.

entropy

a measure of molecular disorder or randomness

Spontaneous process

A process that occurs without an overall input of energy

nonspontaneous process

a process that, on its own, leads to a decrease in entropy

Free energy 

the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system

change in free energy

the difference between the free energy of the final state and the free energy of the initial state

reactions with a value of negative change in free energy occur

with no input of energy

the change in free energy tells us…e

whether a particular reaction in a spontaneous one.

For a reaction to have a negative change in free energy,

the system must lose free energy during the change from initial state to final state

What happens to the stability of a system in its final state with less free energy

the system is less likely to change and is therefore more stable than it was previously.

chemical equilibrium

describes a state of maximum stability

exergonic reaction

a spontaneous chemical reactions, in which there is a net release of free energy.

does an exergonic reaction have positive or negative change in free energy

negative

the magnitude of change in free energy for an exergonic reaction represents.

the maximum amount of work the reaction can perform

endergonic reaction

a non-spontaneous chemical reaction in which free energy is absorbed from the surroundings.

is endergonic negative or positive change in free energy

positive

is exergonic uphill or downhill

downhill

is endergonic downhill or uphill

uphill

is exergonic cellular respiration or photosynthesis

cellular respiration

is endergonic cellular respiration or photosynthesis

photosynthesis

chemical work

the physical and chemical processes cells perform, driven by energy from chemical sources like ATP or ion gradients.

examples of chemical work

synthesis of polymers from monomers

transport work

movement of substances across a cell membrane, requiring energy for active transport and not for passive transport.

examples of transport work

sodium-potassium pump

mechanical work

energy transferred when a biological force causes a displacement

examples of mechanical work

beating of cilia or contraction of muscle cells.

energy coupling

in cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction.

what is responsible for mediating most energy coupling in cells

ATP

ATP

an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed.

ATP structure

sugar ribose, nitrogenous base adenine, and a chain of three phosphate groups bonded to it

what process can the bonds between phosphate groups of ATP be broken

hydrolysis

when does ATP become ADP

when the terminal phosphate bond is broken by the addition of a water molecule, a molecule of inorganic phosphate leaves the ATP.

is ATP hydrolysis endergonic or exergonic

exergonic

why is ATP useful to the cell

the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver.

phosphorylated intermediate

a molecule with a phosphate group covalently bound to it, making it more reactive than the unphosphorylated molecule.

transport and mechanical work in the cell are nearly always powered by

the hydrolysis of ATP

what powers the phosphorylation of ADP to make ATP

exergonic breakdown reactions in the cell.

enzyme

a macromolecule serving as a catalyst

catalyst

a chemical agent that speeds up a reaction without being consumed by the reaction.

activation energy

the energy required to contort the reactant molecules so the bonds can break.

how do enzymes function as catalysts with respect to activation energy

the activation energy is lowered, decreasing the amount of energy needed to start a reaction.

do enzymes alter the change in free energy of a reaction

no

substrate

the reactant an enzyme acts on.

how does the active site contribute to the specificity of enzymes for their substrate

the specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate.

induced fit

a model where the active site of an enzyme changes shape to better bind with a substrate, enhancing the enzyme’s catalytic efficiency.

how does temp affect enzyme activity

higher temps increase reaction rate, which being above or below the optimum temp will slow the reaction rate.

How does pH affect enzyme activity

enzymes have optimal pHs, and being above or below will decrease reaction rate.

cofactor

inorganic molecules that help enzymes function.

coenzyme

carbon-based molecule that helps enzymes function.

renaturation

refolding of proteins / regain of biological activity

saturation

maximum rate of reaction

inhibitors

molecules that block enzyme function

reversible inhibitors

can be removed from the enzyme

irreversible inhibitorsc

can’t be removed from covalently bound enzymes

competitive inhibitors

a substance that reduces the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics.

noncompetitive inhibitors

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme’s shape so that the active site no longer effectively catalyzes the conversion of substrate to product.

examples of irreversible enzyme inhibitors

toxins and poisons.

Allosteric regulation

the binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.

where are allosteric sites often located

where subunits join

effect of the binding of an activator to a regulatory site

stabilizes the shape that has functional active sites

effect of binding of an inhibitor to a regulatory site

stabilizes the inactive form of the enzyme.

cooperativity

a kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the other subunits.

what does cooperatively facilitate

the binding of additional substrate molecules to subunits

feedback inhibition

a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

as isoleucine accumulates

it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the pathway.

chloroplasts

an organelle found in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organism compounds from carbon dioxide and water.

photosynthesis

the conversion of light energy to chemical energy that is stored in sugars or other organic compounds

Autotrophs

organisms that obtain organic food molecules without eating other organisms or substances derived from other organisms.

Heterotrophs

an organism that obtains organic food molecules by eating other organisms or substances derived from them.

decomposers

heterotrophs that decompose and feed on the remains of other organisms and organic litter such as feces and fallen leaves.

stomata

A microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allows gas exchange between the environment and the interior of the plant.

stroma

the dense fluid within the chloroplast surrounding the thylakoid membrane and containing ribosomes and DNA

thylakoids

a membranous sac inside a chloroplast that often exist in stacks called granum

chlorophyll

the green pigment located in membranes within the chloroplasts of plants and algae and in the membranes of certain prokaryotes.

light reactions

the first stage in photosynthesis that occur in the thylakoid membrane of the choroplast.

calvin cycle

the second major stage in photosynthesis involving fixation of atmospheric carbon dioxide and reduction of the fixed carbon into carbohydrate.

photophosphorylation

the process of generating ATP from ADP and phosphate by means of chemiosmosis, using a proton-motive force generated across the thylakoid membrane of the chloroplast during the light reactions of photosynthesis.

carbon fixation

the initial incorporation of carbon from carbon dioxide into an organic compound by an autotrophic organism