Metabolism and Energy

Metabolism

• the totality of an organisms chemical reaction

  • sum of anabolism and catabolism

• emergent property of life that arises from interactions between molecules within the cell

  • but in a controlled manner homeostasis

Metabolic pathway

• begins with a specific molecule and ends with a specific product

• each step is catalyzed by a certain enzyme

catabolic pathways

release energy by breaking down complex molecules into simpler compounds

cellular respiration

the breakdown of glucose in the presence of oxygen

anabolic pathways

• consume energy to build complex molecules from simpler ones

• Ie- the synthesis of protein from amino acids

Bioenergetics

• the study of how organisms manage their energy resources

  • all life boils down to energy budget

Kinetic energy

energy associated with motion

heat (thermal energy)

kinetic energy associated with random movement of atoms or molecules

potential energy

energy that matter posesses because of its location or structure

chemical energy

potential energy available for release in a chemical reaction

thermodynamics

the study of energy transformations

closed system

isolated from its surrounded

• liquid in a thermos

open system

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

• organisms are open systems

First law of thermodynamics (law of conservation of energy)

The energy of the universe is constant

second law of thermodynamics

• every energy transfer or transformation increases the entropy (disorder) of the universe

• during every energy transfer or transformation

  • some energy is unusable, often lost as heat

    • increases entropy

living cells unavoidably convert organized form of energy to heat

2nd law

spontaneous processes occur without energy input ___

• can happen quickly/slowly to occur without energy input

  • must increase the entropy of the universe

• generally corresponds to breakdown

Cells

• create ordered structures from less ordered materials

  • anabolism

  • equals less entropy

  • requires the input of energy

cells also replace ordered froms of matter and energy with ___

• less order forms

• catabolism

energy flows into an ecosystem in form of ___ and exits as ___

light, heat

evolution

• yields more complex organisms

  • does not violate the second law of thermodynamics

  • entropy (disorder) may decrease in an organism

    • but the universe’s total entropy increases

enthalpy (H)

• a measure of the total energy of a thermodynamic system (including volume and pressure)

  • not actually measurable

    • instead measure how much energy is released or absorbed

Gibbs Free Energy (G)

a living system’s energy available to do work when temperature and pressure are uniform

ΔG = ΔH - TΔS

Gibbs Free Energy Change

ΔG

change in Gibbs free energy during a chemical reaction

ΔH

Change in enthalpy (total energy in biological systems)

ΔS

Change in entropy (Disorder)

T

Temperature in Kelvin

Only processes with a negative ΔG are spontaneous

• release energy 

• spontaneous processes can be harnessed to perform work

Free energy

measure of a system instability, its tendency to change to a more stable state

during spontaneous change

free energy decreases and the stability of a system increases

equilibrium

• state of maximum stability

• lowest energy

• a process is spontaneous and can perform work only when it is moving toward equilibrium 

Exergonic reaction

• proceeds with a net release of free energy and is spontaneous

• results in lower energy, more stable products

Endergonic reaction

• absorbs free energy from  its surroundings and nonspontaneous

• results in higher energy, less stable products

a cell does three main kinds of work:

• chemical

  • forced endergonic reactions

    • monomers —> polymers

• transport

  • active transport

    • across cell membrane against concentration gradients

• mechanical

  • movement

    • muscle contraction, beating of flagella or cilia

energy coupling

• cells use energy of an exergonic process to drive an endergonic one

• most energy coupling in cells is mediated by ATP

ATP (Adenosine triphosphate)

• energy currency of the cell

ATP is composed of

• ribose (sugar)

• adenine (a nitrogenous base)

• three phosphate groups

harvesting power from ATP

break high energy phosphate bonds by hyrolysis

energy released when terminal phosphate bond is broken

release of energy comes from chemical change to state of lower free energy

not from phosphate bonds themselves

phosphorylation

• transferring a phosphate group to another molecule, such as a reactant

  • performed by kinases

• drives endergonic reactions

  • the recipient molecule is now phosphorylated

  • change a hydrophobic regions to hyrophilic

catalyst

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

enzyme

catalytic protein

ex. hyrolysis of sucrose by enzyme sucrase

activation energy or free energy of activaiton

• the initial energy needed to start a chemical reaction

  • often supplied in form of heat from surroundings

enzymes catalyze reactions by lowering th E_A barrier

• do not affect the change in free energy (ΔG)

  • instead hasten reaction that would occur eventually

substrate

• the reactant that an enzyme acts on

• the enzyme binds to its substrate, forming an enzyme-substrate complex

active site

region on enzyme where substrate binds

induced fit

• enzyme substrate comple triggers conformational change in enzyme

• brings chemical groups of the active site into position that enhance their ability to catalyze the reaction by contorting and stressing bonds in substrate

active site can lower E_a barrier by

• oreinting substrate correctly

• straining substrate bonds

• providing a favorable microenvironment

• covalently bonding to susbtrate

each enzyme has

• an optimal temperature for function

• an optimal pH for function

• not necessarily the same for all enzymes

cofactors

• nonprotein enzymes helpers that may be (in)organic

coenzyme

• organic cofactor

• includes vitamin

  • ex. Vitamin c

competitive inhibitors

• bind to the active site of an enzyme, completing with the susbtrate

  • block active site

noncompetitive inhibitors

• binds to another part of an enzyme

  • cause enzyme to change

inhibitors examples

toxins, poisons, pesticides, and antibiotics

allosteric regulation

• may either inhibit or stimulate an enzymes activity

• occurs when a regulatory molecule binds to a protein at one site

  • and affects protein’s function at another site

  • can be form of non-competitive inhibition

feedack inhibition

• the end product of a metabolic pathway shuts down the pathaway

Feedback inhibition prevents a cell from

wasting chemical resources by synthesizing more product than needed.