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energy

ability to promote change or do work

what are the two forms of energy?

kinetic and potential

potential energy

energy that a substance possesses due to its structure or location

chemical energy

the potential energy contained within covalent bonds in molecules

thermodynamics

the study of energy interconversions

first law of thermodynamics

energy can't be created or destroyed

second law of thermodynamics

transfer of energy from one form to another increases entropy

entropy

a measure of the randomness of molecules in a system

what happens to entropy when a physical system becomes more disordered?

entropy increases

enthalpy

the total energy of a system

free energy

the amount of available energy that can be used to do work

exergonic reaction

negative free energy, is spontaneous, and favors the formation of products

endergonic reaction

positive free energy, not spontaneous and favors the formation of the reactants

what is ATP broken down into?

adenosine diphosphate (ADP) and inorganic phosphate (Pi)

chemical equilibrium

the rate of formation of products equals the rate of formation of reactants

phosphorylation

the attachment of a phosphate to a molecule

catalyst

an agent that speeds up the rate of a chemical reaction without being permanently changed or consumed

activation energy

an initial input of energy in a chemical reaction that allows the molecule to get close enough to cause a rearrangement of bonds

transition state

in a chemical reaction, a change in which the original bonds have stretched to their limit. ONce this state is reached, the reaction can proceed to the formation of products

what are two ways to overcome the barrier of the activation energy slowing down the rate of chemical reactions?

reactants can be exposed to large amount of heat and to lower the activation energy by having the enzymes bind to small reactant and having chemical reactions that involve more than one reactant

active site

the location in an enzyme where the chemical reaction takes place

substrates

the reactant molecules that bind to an enzyme at the active site and participate in the chemical reaction

enzyme-substrate complex

...

specificity

refers tot he concept that enzymes recognize specific substrates

induced fit

occurs when a substrate binds to an enzyme and the enzyme undergoes a conformational change that causes the substrate to bind more tightly to the enzyme

Km

Michaelis constant- the substrate concentration at which the velocity is half its maximal value

high Km

higher substrate concentration to achieve a particular reaction velocity

affinity

degree of attraction between enzyme and substrate

high Km has high or low affinity for their substrates?

low affinity and binds weakly

low Km has high or low affinity for their substrates?

high affinity and binds tightly

competitive inhibitors

molecules that bind to the active site of an enzyme and inhibit the ability of the substance of the substrate to bind

noncompetitive inhibitor

a molecule that binds to an enzyme at a location that is outside the active site and inhibits the enzyme's function

allosteric site

a site on an enzyme where a molecule can bind noncovalently and affect the function of the active site

steps of an enzyme catalyzed?

1) ATP and glucose bind to enzyme
2) Enzyme undergoes conformational change that binds the substrates more tightly. The induced fit strains chemical bonds within the substrates chemical bonds within the substrates and/or brings them closer together
3) Substrates are converted to products
4) Products are released. Enzyme is released

prosthetic groups

small molecules that are permanently attached to the surface of an enzyme and aid in catalysis

cofactors

inorganic ions Fe3+ or Zn2+ temporarily bind to the surface of an enzyme and promote a chemical reaction

coenzymes

organic molecules that temporarily bind to an enzyme and participate in the chemical reaction but are left unchanged after the reaction is completed

what surrounding conditions affect enzymes?

temperature, pH, ionic conditions

does high or low temperature denature a protein?

high temperature

denature a protein

unfold

metabolic pathways

a series of chemical reactions in which each step is catalyzed by a specific enzyme

catabolic reactions

a metabolic pathway in which a molecule is broken down into smaller components, usually releasing energy

anabolic reactions

a metabolic pathway that involves the synthesis of larger molecules from smaller precursor molecules. Such reactions usually require an input of energy

energy intermediates

a molecule such as ATP or NADH that stores energy and is used to drive endergonic reactions in the cells

substrate-level phosphorylation

a method of synthesizing ATP that occurs when an enzyme direectly transfers a phosphate from an organic molecule to ADP

chemiosmosis

a process for making ATP in which energy stored in an ion electrochemical gradient is used to make ATP from ADP and Pi

oxidation

the removal of one or more electrons from an atom or molecule

reduction

the addition of electrons to an atom or molecule

does an oxidized or reduced substance have more energy?

reduced

NAD+

(nicotinamide adenine dinucleotide) a dinucleotide that functions as an energy intermediate molecule. It combines with two electrons and H+ to form NADH

biosynthetic reactions

also called an anabolic reaction; a chemical reaction in which small molecules are used to synthesize larger molecules

what are the three ways metabolic pathways are regulated?

gene regulation, biochemical regulation, and cellular regulation

cellular regulation

cells integrate signals from their environments and adjust chemical reactions to adapt to those signals

biochemical regulation

binding of a molecule to an enzyme directly regulates its function

feedback inhibition

the product of a metabolic pathway inhibits an enzyme that acts early in the pathway

gene regulation

cell controls chemical reactions

half-life

the time it takes for 50% of the molecule to be broken down and recycled

what is the functions of degradation?

cell conserve energy when proteins are no longer necessary, mRNA may be faulty and the degradation is beneficial to the cell to prevent the harmful effects of aberrant proteins

exonuclease

enzyme that cleaves off nucleotides, one at a time, from the end of the RNA

exosome

a multiprotein complex that degrades mRNA

proteases

enzymes that cleave the bonds between adjacent amino acids

proteasome

a molecular machine that is the primary pathway for protein degradation in Archaea and eukaryotic cells

ubiquitin

a small protein in eukaryotic cells that directs unwanted proteins in a proteasome by its covalent attachment

what is the advantages of ubiquitin targets?

enzymes that attach to its target recognize improperly folded proteins and allow the cell to identify and degrade nonfunctional proteins, change some cellular conditions may warrant the rapid breakdown of particular proteins

steps of protein degradation in eukaryotic cells

1) string of ubiquitins are attached to a target proteins
2) protein with attached ubiquitins is directed to the proteasome
3) protein I unfolded by enzymes in the cap and injected into the core proteasome. Ubiqutin is released back into the cytosol
4) protein is degraded to small peptides and amino acids
5) small peptides and amino acids are recycled back to the cytosol

process of autophagy

1) membrane tubule beings to enclose an organelle
2) double membrane completely encloses an organelle to form an autophagosome
3) autophagosome fuses with a lysosome. Contents are degraded and recycled back to the cytosol

autophagy

a process whereby cellular material, such as worn-out organelle, becomes enclosed in a double membrane and is degraded

what does the cell use to convert all exogenic reactions to endogenic reactions?

ATP

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