AP Bio Metabolism Test

metabolism

the totality of chemical reactions occurring within an organism; the metabolism of a cell manages the material & energy resources of the cell

anabolic pathway

invest energy to build large molecules from smaller molecules (Ex. Photosynthesis)
-gaining free energy because its becoming larger and less stable, surrounding area loses free energy for use and decreasing entropy

catabolic pathway

break large molecules down into smaller molecules and release energy. (Ex. Cellular respiration; glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water)
-so losing free energy because it's smaller molecules with more stability, but the surrounding area gains free energy which means more entropy

energy coupling

when the energy released from catabolic pathway can be stored and used to drive catabolic pathways
-can help metabolism from reaching equilibrium, although it is mostly because things are always moving in and out of cell and being recycled

energy

capacity to cause change or do work; Ability to move and/or rearrange matter

kinetic energy

Energy of movement; Moving objects impart movement on other matter

Thermal energy

KE associated w/ random movement of atoms & molecules

Electromagnetic energy

KE associated w/ photons traveling from sun

potential energy

stored energy w/ the capacity to do work; energy resulting from position or structure

Chemical energy

potential energy that can be released by chemical reactions (energy from food released as it is broken down)
-Complex molecules have more chem energy

heat

the transfer of this energy from one molecule/object to another

system

the matter under study

surroundings

anything outside of the system

open systems

Energy and matter can be transferred between the system and its surroundings

closed system

unable to exchange energy and matter with its surroundings

First Law of Thermodynamics

energy in the universe in constant; energy can’t be created or destroyed but it can be transferred and transformed

Second Law of Thermodynamics

when transferred or transformed usable energy decrease, because some is converted to thermal energy and released as heat, which is unable to do work; thus, the entropy increases

entropy

quantity that measures disorder or randomness; the more randomly arranged a collection of matter is, the greater its entropy
Heat energy has the most entropy because it is
random molecular motion

spontaneous process

a process that occurs without any outside input of energy or outside help
rarely happen and when they happen, takes years to happen though, which is why enzymes are preferred

non-spontaneous process

a process that cannot occur without an input of energy or outside help

free energy

Portion of a system's energy that can perform work when temperature is uniform throughout the system. (G)

Know Gibbs Free energy formula and what each variable means

enthalpy: total energy in a biological system

What does it mean when the change in free energy is positive?

it means that there is an absorption of free energy
anabolic, endergonic
ex: photosynthesis (takes solar energy and invests into bonds of glucose molecule)

What does it mean when the change in free energy is negative?

it means that there is a release of free energy
catabolic, exergonic
ex: cellular respiration (breaks glucose bonds and energy stored becomes ATP)

Be able to relate the amount of free energy in a system to the stability and work capacity of the system

the more free energy in the bonds the less stable because it’s bigger, more organized, lower entropy
less free energy in bonds, more in external factors, more stable because smaller, less organized, higher entropy

Endergonic reactions

intake of free energy, positive change in G

Exergonic reactions

release of free energy, negative change in G

What is the change in free energy when a cell has reached equilibrium?

no change in free energy

How do cells keep from reaching equilibrium?

cells are constantly moving and recycling things in and out of the cell; energy coupling
also na/k pumps

Chemical Work

The pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers

Transport Work

The pumping of substances across membrane against the direction of spontaneous movement

Mechanical Work

Beating of cilia, Contraction of muscle cells, and Movement of chromosomes during reproduction

energy coupling

The use of energy released by an exergonic process to drive an endergonic one; Mediated by ATP

structure of ATP

How much energy is released when ATP is hydrolyzed?

-7.3 kcal/mol (standard conditions)
-13 kcal/mol (cellular conditions)

Why is ATP such an unstable molecule?

The 3 phosphate groups all have an equal negative charge, and like charges repel. The phosphates want to break off so they are very unstable.

Explain how ATP drives cellular work through phosphorylation.

When ATP phosphorylates the phosphorylated intermediate (recipient of the terminal phosphate) the molecule becomes less stable with more free energy to do work
Transport work: The transfer of a phosphate to a transport protein changes its shape and.or its ability to bind with another molecule
Mechanical work involving motor proteins: ATP bonds to the motor protein, hydrolyzes, causes the motor protein to move, another ATP binds

Describe the ATP cycle

Catabolic reactions fuel the phosphorylation of ADP to form ATP
energy comes from cellular respiration or photosynthesis
ATP is hydrolyzed and releases energy to do work in the cell

Why don’t most spontaneous processes happen spontaneously?

They take a very long time to actually happen, usually years

enzyme

A macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed

activation energy

the energy needed to reach the transition state, the point where the bonds can break

transition state

the state where the bonds of the reactants start to break

What do enzymes do to catalyze reactions?

lower their activation energy

substrate

The reactant(s) an enzyme acts on

Explain why there is such high specificity for an enzyme and its substrate.

Specificity of the enzyme / substrate interaction is determined by the shape of the active site.
Also R groups of amino acids on enzyme must be a complementary charge to the substrate

active site

location on the enzyme that substrates bond to

induced fit

When a substrate binds to the active site, it “grabs” the substrate in a tight fit

catalytic cycle

How do enzymes lower activation energy? (4 ways)

when an enzyme attached to substrate, the induced fit can stretch the substrate, which puts stress on the bonds and make them easier to break, thus lowering their activation energy
provide a template in which the substrate can come together, in a way that a reaction can occur between them
active site can't provide a microenvironment that is conducive to the reaction
-ex. active site can have acidic R-groups and some reactions do better in low pH environment
direct participation of the active site in the chemical reaction
-might involve brief covalent bonding between the substrate and side chains of the amino acids of the enzymes

Explain how substrate concentration influences the rate of reaction

increase in substrate concentration, increase rate of reaction until enzymes run out to convert
decrease in substrate concentration, decrease rate, less substrate to convert

Explain how temperature and pH (AND SALINITY) influence enzyme activity and reaction rates

-increase in temp: particles move around more and bump into one another more so reactions happen more frequently
too high, enzyme denatures
-decrease in temp: slows down because particles less active
-pH changes activeness and shape of the enzyme - optimal pH is best

cofactor

inorganic materials that help with enzymes catalyze reactions
-Zinc, Iron, copper

Coenzyme

organic materials that help enzymes catalyze reactions; other proteins that aren't enzymes

competitive inhibitor

inhibitor that stops enzymatic activity by binding to the active site, blocking substrate
-cell can overcome competitive inhibition by adding more substrate

noncompetitive inhibitor

inhibitor that stops enzymatic activity by binding to a different site and changing the shape of the active site so the substrate can’t bind onto it

What is allosteric regulation?

-activator locks the enzyme in its active form when the -active sites are exposed so more substrate can be made into product
inhibitor locks the enzyme in an inactive form when the active site is not exposed
Changes by a conformational change of shape

What is the structural level of most proteins that are regulated allosterically?

Quaternary since there are multiple units

Explain how ATP and ADP act as inhibitors and activators.

ATP is an inhibitor because it can’t allow the cell to do work immediately because it cannot be used as energy
ADP + P is an activator because it can be instantly used to do work (phosphorylation)

cooperativity

Substrate molecules bind to one active site and stabilize the other active sites so they remain in the active form.
Substrates bound to one active site makes it easier for more substrates to bind to the other active site.

Explain how feedback inhibition can shut off a metabolic pathway

Enzymes can be turned off by feedback inhibition.
Metabolic pathways consist of a chain of reactions.
Enzyme 1 makes the first molecule in the chain.(intermediate A)
The final product (isoleucine)
Once enough product is made it diffuses back to the 1st enzyme.
Isoleucine binds to enzymes as a noncompetitive inhibitor because no more needs to be made.

Enzyme structure/specificity essay

-EXPLAIN the enzymes active site and the substrate are similar in shape and charge
-the active site is the most important region
-substrate has to be complementary in shape and charge of the R-groups of amino acids in enzyme
-Enzymes are proteins, have levels of structure
-primary structure: dictates R-groups which determines charge, imwhat substrates its gonna react
-tertiary structure; determines shape of active site
-conformational change in shape
-EXPLAIN catalytic cycle: substrate binds to active site of enzyme; enzyme catalyzed reaction; does so by decreasing the activation energy needed to get to transition phase; products are released from the enzyme
enzyme active sites open for more substrates

Explain the graph

-There is a certain amount of active sites for the increasing amount of substrate
-at first there's a lot of production because of the high enzyme to substrate ratio
-as substrate is added, there’s not enough enzymes to keep up with the inc in substrate so the rate slows
-Explain how would you increase the reaction rate: increase enzyme concentration to make more active sites available for substrate

Explain the graph

-each enzyme has a certain optimal temperature
-as temp increases the particles move faster and bump into one another much more
-more reactions happen and as a result the rate of reaction increases exponentially
-the top of the curve is the max rate and the optimal temp
-as the temp goes over the optimal temp the protein starts to denature and can’t catalyze anymore
-optimal temp: the maximum point on the graph, the temp where the rate of reaction is highest

Explain the graph

-This graph shows the rate of product synthesis as a reaction progresses (with time). The first increase in rate shows the amount of product increasing and production occurs. The sudden plateau is when all the substrate is used and no more product can be produced.
-How would you calculate the rate for a given time interval: always y/x; product/time in this case