Ch 6 : how cells Utilize Energy

Mitochondria play key role in

the production of ATP

Used to power a variety of processes including muscle contraction

chemical Reaction

processes in which one or more substances are changed into other substances 

Every living cell continuously performs thousands of chemical reactions to sustain life

Metabolism

 the sum total of all chemical reactions that occur within an organism. Also a specific set of chemical reactions occurring at the cellular level

Two general factors govern the fate of a given chemical reaction in living cells, what are they?

Direction 

Rate

Energy

the ability to cause change or do work

two general forms of engery

kinetic

potential

Kinetic energy

associated with movement

Potential energy

the energy that a substance or an object possesses due to its structure or location

Chemical potential energy

energy that is stored in the bonds between atoms

how is energy released

By the breaking of bonds

Used by living cells to perform various functions

Energy types

Light

Heat

Mechanical

Chemical Potential

Electrical/Ion Gradient

Light energy

Form of electromagnetic radiation that is visible to the eye ; packaged in photons

Heat Energy

The transfer of kinetic energy from one object to another or from an energy source to an object

Mechanical Energy

The Energy possessed by an object due to its motion to its position relative to other objects

Chemical Potential Energy

Is potential energy stored in the electrons of molecules ; bonds are broken or

electrical/ion gradient

The movement of charge or separation of changes can provide energy. Also a difference in ion concentration across a membrane creates an electrochemical gradient which is a source of potential energy

Thermodynamics

the study of energy transfers and transformation

Two most common laws that govern thermodynamics

 energy cannot be created or destroyed

any energy transferred from one form to another increases the degree of disorder of a system(entropy)

Entropy

Is a measure of the randomness of molecules in a system 

As energy becomes more evenly distributed that energy is less able to promote change or do work

The Change in what energy Determines the Direction of a Chemical Reaction

free energy

Total energy =

 usable energy  +  usable energy 

free energy

Total energy of a system is termed enthalpy (H) and the usable energy

If a chemical reaction has a negative free-energy change (ΔG < 0), the products have less or more free energy?

the products have less free energy than the reactants, and therefore free energy is released during product formation

Exergonic

 a type of chemical reaction that releases free energy and occurs spontaneously

Endergonic

not a spontaneous reaction 

If ΔG (change in free energy) for a chemical reaction is (-) the reaction favors

the conversion of reactions to products 

If ΔG for a chemical reaction is (+) the reaction favors

the conversion of formation of reactants

Cells Use ATP to Drive

 Endergonic Reactions 

Phosphorylation

the attachment of a phosphate to a molecule 

Exergonic reaction, such as the breakdown of ATP, are commonly coupled to

chemical reactions and other cellular processes that would otherwise be endergonic

Catalyst

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

In cells most common catalysts are

enzymes ; proteins 

Activation energy

an initial input in a chemical reaction that allows the molecules to get close enough to cause a rearrangement of bond s

(E_A) allows the molecules to get close enough to cause a rearrangement of bonds

Transition state

 in a chemical reaction a state in which the original bonds have stretched to their limit; once this state is reached the reaction can proceed to the formation of products 

Enzymes lower the activation energy barrier by?

straining reactions

positioning reactants closer together

Straining reactants

Enzymes are large proteins that bind relatively small reactants. When bound to an enzyme, the bonds in the reactants can be strained, thereby making it easier for them to achieve the transition state

Positioning reactants closer together

When a chemical reaction involves two or more reactants, the enzyme provides sites in which the reactants are positioned very close to each other in an orientation that facilitates the formation of new covalent bonds

Active site

 the location in an enzyme where the chemical reaction takes place

Substrates

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

Enzyme-substrate complex

he binding between enzyme and substrate(s) produces

A key features of nearly all enzymes is their ability to bind their substrates with a ____ degree of specificity

high, Only the correct shaped key will fit (substrate) wil fit into the keyhole (active site) of the lock (enzyme)

Induced fit

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

Only after the induced fit has occurred does the enzyme catalyze the conversion of reactant to products

Affinity

the degree of attraction between an enzyme and its substrate(s)

Some enzymes have a very high affinity meaning?

They bind to their substrate even when the substrate concentration are relatively low

Some enzymes have a lower affinity rate meaning?

The enzyme-substrate complex is likely to form only when the substrate concentration are higher

V_max 

the enzyme is saturated with substrate, and the velocity of the chemical reaction is near its maximal rate

K_M

the substrate concentration at which the velocity is half its maximal value

is a measure of the substrate concentration required for a chemical reaction to occur

Enzyme with a high K_M

have a low affinity for their substrate -they bind them more weakly 

Enzyme with a low K_M

have a high affinity for their substrate -they bind them more strongly 

Competitive Inhibitors

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

• Compete with substrate in binding to the enzyme

• Usually have a structure or a portion of their structure that mimics the structure of the enzyme’s substrate

Noncompetitive inhibitor

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

Lowers V_max  for the reaction without affecting the K_M

Allosteric site

A site on an enzyme or a regulatory protein where a molecule can bind noncovalently and affect the function at a second site, such as the active site on an enzyme or a DNA-binding site on a repressor protein.

At a location outside the active site

Irreversible inhibitor

Usually bind to covalently to an enzyme to inhibit its function 

Not a common way for cells to control enzymes function 

Permanently inactivate an enzyme, preventing its further use

Prosthetic groups

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

Cofactors

usually inorganic ions that temporarily bind to the surface of an enzyme and promote a chemical reaction 

Coenzymes

an organic molecule that participates in a chemical reaction with an enzyme but is left unchanged after the reaction is completed

Some are synthesized by cells, but many of them are taken in as dietary vitamins by animal cells

Enzymes ability to increase the rate of a chemical reaction is also addicted by their environment

Temperature

pH

Ionic conditions

Most enzymes function in a maximally in a narrow range of temp. and pH meaning?

Very high temps. may denature a protein causing it to unfold and lose its 3D shape , inhibiting its function 

Metabolic pathway

each step is catalyzed by a different enzyme

Catabolic reaction

result in a breakdown of larger molecules into smaller ones

Often exergonic

Anabolic reaction

the synthesis of larger molecules from smaller precursor molecules

Usually endergonic and in living cells ; must be coupled to an exergonic reaction 

Catabolic reactions result in the breakdown of larger molecules into smaller ones,Have two advantages which are?

Recycling of Organic Building Blocks

Breakdown of Organic Molecules to Obtain Energy

proteases 

When a protein is improperly folded or is no longer needed by cell the peptide bonds between the amino acids in the protein are broken by enzymes

energy intermediates

 are directly used to drive endergonic reaction in cells 

Molecules such as ATP

The phosphate can be transferred from phosphoenolpyruvate to ADP which is used to what?

to synthesize ATP

During the breakdown of small organic molecules, the removal of

one or more electrons from atoms or molecules may occur 

Oxidation ; oxygen is frequently involved in chemical reactions that remove electrons from another atom or a molecule 

Reduction

 a process that involves the addition of electrons to an atom or a molecule 

Named because the addition of a negatively charged electron reduces the net charge of an atom or a molecule

When an atom or a molecule is oxidized, the electron that is removed must be

transferred to another atom or molecule, which becomes reduced 

reduction-oxidation reaction or redox reaction

Cells use NADH in 2 common ways

(1)The oxidation of NADH is highly exergonic reaction can be used to make ATP

(2)NADH can donate electrons to other organic molecules and thereby energize them

Energized molecules can more readily from

covalent bonds

NADH is often needed in anabolic reactions that involve the synthesis of larger molecules through the formation of covalent bonds between smaller molecules

Catabolic pathways are regulated so that organic molecules are broken down only when

they are no longer needed or when the cell requires energy

Gene Regulation

Enzymes are proteins that are coded by genes 

One way they control metabolic pathways is through gene regulation

Regulation via Cell-Signaling Pathways

Metabolic reactions are also coordinated at the cellular level 

Cells integrate signals from the environment and adjust their metabolic pathways at adapt to those signals 

Epinephrine is sometimes called the fight-or-flight hormone becases the assed energy prepares an individual to either stay and fight or run away quickly

Biochemical Regulation

The noncovalent binding of a molecule to an enzyme directly regulates the enzyme’s function

Feedback Inhibition

a form or regulation in which the product of a metabolic pathway inhibits an enzyme that acts early in the pathway, thus preventing the overaccumulation of the product

This form is reversible ; inhibition will occur only when the concentration of the product is high

Allosteric site

a site on an enzyme or a regulatory protein where a molecule can bind noncovalently and affect the function at a second site, such as the active site on an enzyme or a DNA-binding site on a repressor protein

are often found in the enzyme that catalyzes the early steps in a metabolic pathway

The 3 levels or regulation are not not mutually exclusive are?

Gene, cell-signaling, and biochemical regulation 

Cell signaling and biochemical regulation are important rapid ways to ?

control chemical reactions in a cell

Rate-limiting step

the slowest step in a pathway 

If inhibited or enhanced such changes will have the greatest influence on the formation of the final product of the metabolic pathway

Cellular respiration

a process by which living cell obtain energy from organic molecules and release waste products

Comprises the metabolic reaction that a cell uses to get energy from organic molecules and release waste products 

A primary aim of cellular respiration is to make

adenosine triphosphate (ATP)

During aerobic respiration ___ is used and ____ is released via

o2 , co2, the oxidation of organic molecules 

what is the  energy source for cellular respiration 

glucose, C6H12O6 + 6 O2 → 6 CO2 + 6 H2O      ∆G=-686 kacl/mol (Glucose)

Certain covalent bonds within glucose store

a large amount of energy 

When glucose is broken down via oxidation , ultimately to CO2 and water , a tremendous amount of free energy is released meaning?

Some energy is lost in heat but much of it make 3 energy intermediates : ATP , NADH, and FADH

The breakdown of glucose involves what 4 metabolic pathways?

 (1) GLYCOLYSIS

(2) THE BREAKDOWN OR PYRUVATE

(3) THE CITRIC ACID CYCLE

(4) OXIDATIVE PHOSPHORYLATION

Glycolysis

Glucose is broken down to two pyruvate molecules producing a net energy yield of two ATP molecules and two NADH molecules 

The two molecules are synthesized via substrate-level phosphorylation which occurs when an enzyme directly transfers a phosphate from on organic molecule to ADP

In eukaryotes,  glycolysis occurs in the cytosol

substrate-level phosphorylation

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

Breakdown of pyruvate to an acetyl group

In eukaryotes the two pyruvate molecules enter the mitochondrial matrix where each one is broken down to acetyl group and one CO2 molecule 

For each pyruvate broken down via oxidation one NADH molecule is made by the reduction of NAD+

citric acid cycle

Each acetyl group is incorporated into an organic molecule, which is later oxidized to liberate two CO₂ molecules. 

One ATP, three NADH, and one FADH₂ are made in this process

Because there are two acetyl groups (one from each pyruvate), the total yield is four CO₂, two ATP via substrate-level phosphorylation, six NADH, and two FADH₂. This process occurs in the mitochondrial matrix

Oxidative phosphorylation

The overall process of electron transport and ATP synthesis is called oxidative phosphorylation because NADH or FADH₂ has been oxidized and ADP has become phosphorylated to make ATP.

 The theoretical yield of ATP via oxidative phosphorylation is 30–34 ATP molecules; the actual yield is less, perhaps 25 ATP molecules, because some of the NADH and FADH₂ are used for other types of chemical processes.

Chemiosmosis

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

Oxidative phosphorylation

a process during which NADH and FADH2 are oxidized to make more ATP via the phosphorylation of ADP

In eukaryotes occurs along the criste

Cristae

projections of the highly invaginated membrane of  mitochondrion 

Greatly increases the surface area of the inner membrane ; increasing the amount of ATP that can be made

In bacteria and archaea, oxidative phosphorylation occurs along

the plasma membrane because the proteins that carry out this process are located there

Glycolysis

a metabolic pathway that breaks down glucose to pyruvate

Breakdown of glucose into two molecules of a compound called pyruvate

Occurs when oxygen is present  under aerobic conditions and can occur in the absence of oxygen 

Biochemistry

study of the chemistry of living things

there are how many steps in catalyzing different enzymes

10 steps

Energy investment phase

The first phase (steps 1–3) involves an energy investment. Two ATP molecules are hydrolyzed, and the phosphates from those ATP molecules are transferred to glucose, which is converted to fructose-1,6-bisphosphate

The energy investment phase raises the free energy of glucose, thereby allowing later reactions to be exergonic

Cleavage phase

During steps 4 and 5, a six-carbon molecule is cleaved into two molecules of glyceraldehyde-3-phosphate