Chapter 6: An Introduction to Energy, Enzymes, and Metabolism

2 types of chemical reaction

1. Catabolic reactions

2. Anabolic reactions

Anabolic reactions

Synthesis of molecules.

Energy is stores

Catabolic reactions

Broken down or degradation of molecules

Energy is released

Metabolism

total of chemical reaction or anabolic and catabolic reactions

First law of Thermodynamics = law of conservation of energy

Energy cannot be created or destroyed

Energy can be transfered from one place to another and can be transformed from one type to another

Second law of Thermodynamics

When Energy is transferred from one place to another, the level of disorder (entropy) is increase.

2 forms of Energy

Kinetic and Potential

Important types of Energy in Biology

light

heat

mechanical

chemical

electrical/ ion gradient

Entropy

measurement of disorder in the system

Why energy is unusable?

because of entropy, the degree of disorder cannot be used in an useful way

Spontaneous reaction

reaction that does not require energy.

ΔG = Δ H - T Δ S

ΔG is the free energy change

Exergonic reaction

spontaneous reaction

ΔG<0 or negative free energy change

Endergonic reaction

it requires additional energy.

ΔG>0 or positive free energy change

Hydrolysis of ATP

Reaction favors formation of products because of

ΔG = -7.3 kcal/mole

Energy liberated can drive a variety of cellular processes

Cells use ATP hydrolysis

to drive endergonic reactions

An endergonic reaction and an exergonic reaction are coupled together to proceed spontaneously

Endergonic reaction will be spontaneous if net free energy change for both processes is negative

Phosphrylation

a phosphate is directly TRANSFERRED from ATP to glucose

ATP cycle

To use ATP the bond breaks by hydrolysis between the 2nd and 3rd phosphate releasing energy (exergonic) to synthesize ADP. To go back to ATP a free phosphate must attach to ADP. This requires energy input.

Proteomes

all the proteins that cells make

Enzymes

protein catalyst in living cells.

May change the local environment of reactants.

Sometimes they participate in the chemical reaction

Importance of enzymes

lowers the activation energy to overcome the bonding and achieve the transition state

2 ways of enzyme have to lower activation energy

Straining the reactants

Bringing them close together

Active site

location in an enzyme where the reaction takes place

Substrate

reactant that binds to enzyme at the active site, and are part of chemical reaction

Enzyme-substrate complex

binding between an enzyme and substrate

Key features of enzymes

Ability to bind the substrates with a high degree of specificity.

Induced fit.

Enzymes are reusables.

Induced fit

interaction between enzymes and substrates involve conformational changes that causes the substrate to bind tightly to enzyme. It lowers the activation energy

Conformational change

alteration in the shape usually the tertiary structure of a protein as a result of alteration in the environment ph, temperature, ionic strength) or the binding of a ligand (to a receptor) or binding of substrate (to an enzyme)

Affinity

degree of attraction between an enzyme and its substrate

Enzyme-catalyzed reaction

Step 1:

substrate binds to enzyme

Step 2:

enzyme undergoes conformational change that binds the substrates more tightly. This induced fit strains

chemical bonds within the substrates and/or brings closer together

Step 3:

substrates are converted to products.

Step 4:

Products are releases. Enzyme is ready to be reused.

V max

maximal rate or velocity of a chemical reaction

Concentration reaches a plateau

It means most of the active site are occupied with substrate. Further the line the effect is negligible

K m

substrate concentration at which velocity is half its maximal value

Reversible inhibitors

cells use them to modulate the enzyme function.

It allows enzyme to be reusables when inhibitor concentration is lowered

Competitive inhibitors

compete with substrate for the ability to bind to enzyme

Characteristics of competitive inhibitors

Non covalently bond

Its structure is like the enzyme's substrate.

It increases K m

It requires higher K m to achieve the same rate of chemical reaction.

Adding more substrate, increases the chances to create real substrate and overcome inhibitor.

Characteristics of noncompetitive inhibitor

Non covalently bond

It lowers the V max, so K m is the same.

It binds outside of the enzyme, allosteric site.

It never reaches the velocity of original reaction.

At the beginning the slope are the same because the system is still open.

V max is different because the substrate will never accommodate well.

Allosteric site

The place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme and influencing its ability to be active

Irreversible inhibitors

Permanently inactive an enzyme to further use.

Covalently bond

Factors that influence Enzyme function

Reversible and irreversible Inhibitors.

Prosthetic groups.

Cofactors.

Coenzymes.

They are affected by environment.

Only function in a narrow range of pH

Why enzyme function changes when pH is changed?

because:

- Enzyme cannot maintain 3 dimensional shape

- The ezyme becomes unstable because the proton amount wil be altered by the change in pH

Prosthetic groups

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

Cofactors

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

Coenzyme

Organic molecule that is a necessary participant in some enzymatic reactions; helps catalysis by donating or accepting electrons or functional groups; e.g., a vitamin, ATP, NAD+.

Metabolic pathways

A series of chemical reactions that either builds a complex molecule or breaks down a complex molecule into simpler compounds when it's needed

Energy intermediates

released energy of the broken covalent bonds is stored in them, which are directly used to drive endergonic reactions

E.g: ATP, NADH

Substrate-level phosphorylation

enzyme transfers a phosphate from organic molecule to ADP, thereby making ATP

Chemiosmosis

energy is stored in an ion electrochemical gradient is used to make ATP from ADP and Pi

2 ways to make ATP

Substrate-level phosphorylation

Chemiosmosis

Redox reaction

are important in the metabolism of small organic molecules

Oxidation

loose electron (less energy)

Reducing agent

Reduction

Gain electron (has more energy)

Oxidizing agent

NAD+

nicotinamide adenine dinucleotide.

It's composed by two nucleotide; one with adenine base and other one with nicotinamide base.

Function of NADH

it's use to make ATP.

It can donate electrons to other organic molecules and thereby energize them to form covalent bonds

NAD+ bonding to NADH

redox reaction

two electrons and H+ are incorporated to ring

Regulation of metabolic pathways

Gene regulation

Cellular regulation

Biochemical regulation

Characteristics of metabolic pathways

Regulations ensure that cell synthesizes molecules when they're needed.

Each step is catalyzed by a specific enzyme

Feedback inhibitors

ability of the cell to use the end product of metabolic pathway to react/inhibit with the initial step through the allosteric site , making a conformation change in the enzyme that shuts down pathway.

In order to prevents the over accumulation of the product in the cell

Recycling of organic molecules

saves a great deal of energy for living organisms

mRNA degradation

they're are degraded by 5' to 3' exonucleases or by exosomes

Exonuclease

enzyme that cuts a nucleic acid chain at the end

Exosome

multiprotein complex that degrades mRNA

Proteasome

degrades proteins in ekaryotes and archea

Autophagy

lysosomes digest intracellular material

Difference between competitive and noncompetitive inhibitor on effects of enzyme function

- competitive inhibitor bind to active site, while noncompetitive inhibitor binds to allosteric site

- only the effects of competitive inhibitor can be overcome by increasing substrate concentration

Function of catabolic pathways

Two functions:

- recycle macromolecules

- produce energy intermediate e.g: ATP, which is use to drive endergonic reactions

Direction and rate of chemical reaction

Thermodynamics govern the direction but not he rate of ____

The change in free energy determines the direction of the ____

Catalyst influence in the rate of ____

Chemical reactions depend on

rate and direction