from molecules to organisms: life and the laws of energy...

Structure & Function (LS1A) Life and the Laws of Energy

Copyright © Rebecca Rehder Wingerden

From Molecules to Organisms: Structure & Processes

LIFE SCIENCE DISCIPLINARY CORE IDEAS

Ch 5 Intro, 5.1-5-5.9, 5.21

Life and the Laws of Energy• All the chemical processes of life obey the laws of thermodynamics which state that:

- energy cannot be created or destroyed, and - entropy (disorder) is increasing in the universe.

Copyright © 2014 Rebecca Rehder Wingerden

ENTROPY downhill

LIFE uphill

Order

Disorder

• If the universe is dispersing its energy (heading towards disorder), then how is life creating order?

• Life can resist entropy, for a time, due to the Earth’s - steady stream of usable energy from the Sun, - stable molecules with which to build (carbon) - and the assembly of information chains (macromolecules).


ENTROPY downhill

LIFE uphill

Order

Disorder

ENERGY

mon

omer

pol

ymer


• The Earth is not a closed system, the second law of thermodynamics only applies to a closed system.

• Life involves an increasing in order (growth, reproduction evolution), at the expense of a much greater increase in disorder somewhere else (heat, sweat, waste products).

Ask a Mathematician

Sunlight is a bunch of high-energy photons coming from one direction, which involves relatively little entropy. A little later that energy is re-radiated from the Earth as heat, which is the same amount of energy spread over substantially more photons and involves a lot more entropy (relatively). The huge increase in entropy, between the incoming sunlight and the outgoing heat, is the “entropy sink” that make all life on Earth possible (with just a hand full of exceptions). In particular, green plants take a tiny amount of sunlight that hits the Earth and turns some of the energy into sugars (chemical energy) and other useful plant materials.

It all eventual turns into heat and radiates away, but instead of doing it all at once it does it through a few links in the food chain.

You can think of this huge sunlight-to-re-radiated-heat increase in entropy like water going over a waterfall, and life as being a hydro-electric dam. All of the water ends up at the bottom of the falls, but sometimes it can do some interesting stuff (life and other useful mechanical work) on the way down.

• Life is a series of chemical reactions which are carried out at a cellular level.

• In chemical reactions, reactants are converted to products until equilibrium* is reached.

• Cellular metabolism is the sum of endergonic and exergonic reactions in an organism.


Reactants

Pote

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of m

olec

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Products

Amount of energy INPUT

Endergonic reactions absorb energy yielding products right in potential energy (photosynthesis).

Reactants

Pote

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Products

Amount of energy

OUTPUT

Exergonic reactions release energy and yield products that contain less potential energy than their reactants (cellular respiration).

*Equilibrium is a state of balance. In cells atoms continue to collide converting reactants to products, but at equilibrium equal number of collision convert products back to reactants. Life generally abhors equilibrium, so products are continually removed and reactants are continually added and which prevents equilibrium.


• Life can’t get by on energy alone, it needs a way of making chemical events happen more surely and rapidly.

• Getting molecules into the correct orientation and then pushing them to react is the job of enzymes.

• The energy needed to push these reactions comes from ATP (adenosine triphosphate).

Protein phosphorylation is a reversible process and occurs with many enzymes and receptors. It activates and deactivates the function of enzymes. It is a regulatory mechanisms which can occur in both prokaryotic an d eukaryotic organisms.

ATP ADP

P

P

Enzyme

Phosphorylation

Dephosphorylation

reactants

product

Enzyme


• ATP shuttles chemical energy within the cell and energizes other molecules by phosphorylation (the transfer of a phosphate group to a molecule).

Reactants

Pote

ntia

l ene

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of m

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Products

Protein Work

• ATP molecules are the key to energy coupling. • Energy coupling uses energy release from exergonic reaction to drive essential endergonic reactions.


When a cell uses chemical energy to perform work, it couples an exergonic reaction with an endergonic one. The ATP Cycle is also an example of energy coupling. The energy released from a glucose molecule in cellular respiration, an exergonic reaction, is used to phosphorylate the ADP molecule, creating ATP. The energy, now stored in the ATP molecule, can be used to drive endergonic reactions throughout the organisms, such as the contraction of a muscle cell.

Energy from exergonic reactions

Deh

ydra

tion

synt

hesi

s

Hydrolysis

Energy for endergonic reactions

The ATP Cycle

• Enzymes are proteins which serve as biological catalyst, they increase the rate of a reaction without being consumed in the reaction.

• Enzymes facilitate chemical reactions by lowering EA barrier.

• The energy of activation (EA) prevents molecules from breaking down spontaneously.


This graph shows the effect of an enzyme on the reaction it catalyzes. The black curve represents the course of the reaction without an enzyme; the EA barrier is higher than in the reaction with an enzyme (red curve). In catalyzing metabolic reaction in cells, enzymes are essential to life. One way enzymes lower the energy of activation is by holding reactant molecule is a particular position.

EA with enzymeReactants

Products

EA without enzyme

Net change in energy

• Enzymes are very specific, each enzyme recognizes only one specific substrate.


Active site

1

Enzyme (sucrase)

Enzyme available with empty active site

Substrate (sucrose)

2

Substrate binds to enzyme with

induced fit

3

Substrate is converted

to products

4

Products are released

Glucose Fructose

The figure illustrates how an enzyme works. Its specific substrate is table sugar (sucrose), and the reaction it catalyzes is the hydrolysis of sucrose to glucose and fructose. 1) Sucrase enzyme) starts with an empty active site. 2) sucrose enters the active site, attaching by weak bonds. The interaction with sucrose induces the enzyme to change shape slightly so that the active site fits even more snugly around the sucrose. This “induced fit” is like a clasping handshake. It holds the substrate in a position that facilitates the reaction, and 3) the substrate is converted to the products of glucose and fructose. 4) The enzyme releases the products and emerges unchanged from the reaction. Its active site is how available for another substrate molecule, and another round of the cycle can begin. A single enzyme molecule may act on thousand or even millions of substrate molecules per second.


Enzyme

SubstrateActive site

NORMAL BINDING OF SUBSTRATE

Competitive inhibitor

Noncompetitive inhibitor

ENZYME INHIBITION

When an inhibitor prevents an enzyme from catalyzing a crucial metabolic reaction, an organisms can be poisoned. Certain pesticides are toxic to insects because they irreversible inhibit key enzymes in the nervous systems. Malathion inhibits a nervous system enzyme called acetylcholinesterase, preventing nerve cells from transmitting signals and kills the insect.

• Inhibitors can interfere with enzyme function by:

• Enzyme inhibitors, especially reversible ones, are important regulatory of metabolic pathways in cells (negative feedback).

- taking the place of the substrate (competitive),

- or altering the shape of the enzyme active site (noncompetitive)


Hemoglobin, the protein inside red blood cells that carries oxygen from the lungs to body tissues and carbon dioxide from the tissues back to the lungs, is made up of four subunits bound together by weak bonds. Each subunit contains a heme-iron complex, a molecule of heme with an iron atom at its center. When oxygen concentration is low, it is relatively rare for an oxygen molecule to bind to a heme-iron complex When an oxygen does bind to one of the heme-iron complexes, this induces a change in shape in the hemoglobin molecule which increases the affinity of the other three heme-iron complexes for oxygen. Therefore, hemoglobin binds with its substrate oxygen more efficiently when that substrate is present at higher concentration. Conversely, as oxygen concentration decreases, the affinity of hemoglobin for oxygen falls off, resulting in oxygen release. !As hemoglobin give up oxygen, its affinity for carbon dioxide increases. It binds with carbon dioxide molecules and carries them back to the lungs. Deoxygenated hemoglobin also binds with hydrogen ions (acid) making the blood more alkaline. Alkaline blood more readily absorbs carbon dioxide, which is then transported to the lungs and breathed out into the atmosphere. All this finely tuned regulation is the result of tiny changes in the relative positioning of the four protein subunits of hemoglobin.

• Regulatory enzymes change shape in response to a signal, switching on and off in response to chemical information which allows them to control and coordinate cellular processes (allosteric enzymes).

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