Topic 9

How Does Life Use Energy?

Dr. George Lapennas

Dept. of Biology

Nature of science:

Search for mechanistic explanations – ones that predict events based on underlying rules and structures, rather than attributing events to the whims of god(s).

Explanations for behavior of non-living matter

Scientists have developed theories that successfully explain natural phenomena such as motion, gravity, energy, and chemical reactions

Explanations for behavior of non-living matter were …

- developed on relatively simple systems

- but also apply to more complex non-living systems, such as the mechanism of a clock

Clock face

Behavior of man-made mechanisms involves laws of physics and chemistry, together with their structure (shapes and arrangement of their parts)

Can life also be understood mechanistically (vs vitalistically)?

Quick review of special characteristics of living things (organisms)

1. Growth

2. Development (changes other than growth during individual lifetime)

3. Reproduction (involves inheritance)

4. Ordered, complex structure; adaptation

5. Movement (esp. animals)

6. Sensitivity/Responsiveness

7. Consciousness/Rationality

8. Evolution (change over generations)

9. Use of energy

An early mechanistic success:

Harvey’s partial explanation of the pumping and circulation of the blood

Some 19th century steps from a vitalistic toward a mechanistic

understanding of life

1. The cell theoryLiving things are made up of large numbers of tiny units called “cells” that come from previous cells

Prerequisite technical advance: Invention of the microscope (early 1600’s)

Structure of an animal cell

Structure of a plant cell

2. In vitro (in glass) synthesis of organic molecules

Wohler’s 1828 in vitro synthesis of urea, etc.

Eventually, chemists learned to synthesize everything in vitro that organisms synthesize in vivo.

General conclusion: There are no unique laws of chemistry operating within living organisms.

3. The fermentation controversy

“Fermentation” – chemical transformations that had only been observed in association with living things, including …

- souring of milk

- fermentation of fruit/grain, producing alcohol and carbon dioxide

- putrification and decay of dead animals and plants

Do fermentations require presence of living organisms?

Buchner (1897) observed fermentation of fruit juice by cell-free extract of yeast, yielding alcohol and carbon dioxide (CO2)

Conclusion: Living cells are not required for fermentation – only need some materials that were present within the cells (now known to be enzymes - proteins that act as catalysts to speed up reactions).

4. Cryptobiosis

Does life irreversibly end when life processes cease?

or …

Can life processes be stopped and later re-started, so long as necessary structures have been preserved intact?

Can the “clock” of life be stopped and then re-started?

Conclusion: Life processes only depend upon the presence of certain matter in a certain structural arrangement.

That matter and structure can persist during drying or freezing when all processes cease.

Life processes can resume upon restoration of water or thawing.

Why did mechanistic explanations take so long to develop in biology?

- Because living things are much more complex than anything else that scientists study

- Many other discoveries had to be made before the mechanisms of biological structures and processes could be effectively investigated.

Machinery of life: 4 classes of organic “macro-molecules” assembled from

building blocks

1. Proteins (structural; catalytic “enzymes”)

2. Nucleic acids (DNA, RNA; instructions for inheritance as the structure of proteins)

3. Polysaccharides (energy storage; structure)

4. Complex lipids (energy storage; cell membranes)

Protein building blocks – amino acids

Protein structure – primary structure

Protein structure – secondary structure

Protein structure – tertiary structure

Protein function

DNA (molecule of inheritance)

Living matter seems to obey the same laws of physics and

chemistry as non-living matter

Conservation of mass

Conservation of momentum

Gravitation

Chemical properties of elements

Laws of thermodynamics

Laws of thermodynamicsIn any isolated system (no matter or energy can enter or leave the system), including the entire universe:

First Law – the total amount of energy is constant, though it can change form.

Laws of thermodynamicsIn any isolated system (no matter or energy can enter or leave), including the entire universe:

First Law –total amount of energy is constant, though it can change form.

Second Law – Whenever anything actually happens, the entropy (disorder) of the system increases.

Laws of thermodynamicsIn any isolated system (no matter or energy can enter or leave), including the entire universe:

First Law –total amount of energy is constant, though it can change form.

Second Law – Whenever anything actually happens, the entropy (disorder) of the isolated system increases.

- “Time’s Arrow” points in the direction of increasing

entropy (disorder) of the universe.

- Changes that would reduce the entropy of the

universe cannot occur

“Spontaneous” changes= changes that can happen

= “downhill” changes

“Spontaneous” processes can happen

Two old hypotheses about animals’ use of food

1. Assimilation - food is added to the body for growth or to replace material lost through “wear and tear”

Two hypotheses about animals’use of food

1. Assimilation - food is added to body for growth or to replace material lost through “wear and tear”

2. Combustion - food is somehow “burned” within the body, like fuel in a fire, generating heat, and being consumed in the process

Reinterpretation of combustion and animal respiration by Lavoisier

Lavoisier (late 1700’s)…

- Overthrew phlogiston theory and applied new knowledge of gases to combustion

- Flames and animals do not produce phlogiston,

- Both consume oxygen (O2) and

release carbon dioxide (CO2) and heat

“Slow combustion”Lavoisier had observed a quantitative similarities between burning charcoal and a living animal.

They hypothesized that animals carry out a “slow combustion” of fuel (process now called cellular respiration).

They believed that the function of cellular respiration was to make heat.

What do we know now about the use of food?

- Blood carries digested food from intestine and oxygen from lungs throughout body, where cells take them up through walls of capillaries.

What do we know now about the use of food by animals?

- Blood carries digested food from intestine and oxygen from lungs throughout body, where cells take them up through walls of capillaries.

- Cells both ASSIMILATE food and use it as FUEL FOR CELLULAR RESPIRATION

What do we know now about the use of food?

- Blood carries digested food from intestine and oxygen from lungs throughout body, where cells take them up through walls of capillaries.

- Cells both ASSIMILATE food and use it as FUEL FOR CELLULAR RESPIRATION

- For most organisms, heat is just a by-product of cellular respiration, not the function of the process.

What is the primary function of cellular respiration?

Cellular respiration provides energy to do “cell work”.

What is the function of cellular respiration?

Cellular respiration provides energy to do “cell work”.

“Cell work” means “uphill” cellular processes that would not be spontaneous (could not occur) on their own, without being “coupled” to some other highly spontaneous process that supplies energy.

3 Types of Cell Work

Digestion of macro-molecules

When we digest food macro-molecules, we break them down into their building blocks

Examples:

proteins amino acids

polysaccharides simple sugars

Nucleic acids nucleotides

Digestion of macro-molecules

When we digest food macro-molecules, we break them down into their building blocks.

Blood carries building block to the cells, where they are taken up, and some are reassembled into new macro-molecules.

Digestion is “downhill”

Dismantling macro-molecules is a disordering process that increases the entropy of the universe.

Macro-molecule building blocks + heat

(ordered, non-random) (disordered) (random energy)

Assembly of macromolecules simply by reversing digestion?

NO! Digestion is downhill (increases the entropy of universe).

Assembly by simply reversing digestion?

NO - Digestion is downhill (increases entropy of universe)

The reverse process (assembly simply by reversing digestion) would be uphill (reduce entropy of the universe), and can’t happen

“Spontaneous” processes can happen; the reverse cannot

Question: Then how can macro-molecule assembly (and other

types of cell work) occur?

Answer: By “coupling” cell work to some very downhill process

A spontaneous process can be reversed by coupling it to a MORE spontaneous process (such as a larger weight).

Mechanical coupling

A spontaneous process can be reversed by coupling it to a MORE spontaneous process (such as a larger weight).

The COMBINED process is then downhill, and increases the entropy of the universe.

We say: “The second, highly spontaneous, process supplies energy to drive the uphill process (which could not have occurred alone).”

What highly spontaneous process drives cell work?

The highly spontaneous process that drives cell work is “splitting ATP”

ATP = Adenosine Tri-Phosphate

Splitting ATP

ATP ADP + Phosphate + heat

(one larger (two smaller (random

molecule) molecules) energy)

Splitting ATP

ATP ADP + Phosphate + heat

Splitting ATP is very downhill, and so can drive uphill cell work.

Example of coupling: ATP-driven assembly of a protein

spontaneous?

1) Amino acids + heat protein no

2) ATP ADP + Phosphate + heat YES

----------------------------------------------------------------------------

1+2) Amino acids + ATP protein + ADP yes

+ Phosphate + heat

ATP splitting

also drives

the other

types of cell

work

Regeneration of ATP

Human cells contain only enough ATP to last about 30 seconds.

Regeneration of ATP

Human cells contain only enough ATP to last 30 seconds.

We must constantly regenerate ATP by putting 3rd phosphate back on ADP to “make ATP” again (= ATP synthesis)

What process is downhill enough to drive uphill ATP

synthesis? Since ATP splitting is downhill, putting the third phosphate back on must be uphill.

How can we drive ATP synthesis?

What process is downhill enough to drive uphill ATP

synthesis? Since ATP hydrolysis (splitting) is downhill, putting the third Phosphate back on must be uphill.

How can we drive ATP synthesis?

Couple it to something even more downhill – something highly spontaneous - but what?

What process is downhill enough to drive uphill ATP

synthesis?Since ATP hydrolysis (splitting) is downhill, putting the third Phosphate back on must be uphill.

How can we drive ATP synthesis?

Couple it to something even more downhill – something highly spontaneous - but what?

The “slow combustion” of food = cellular respiration.

Coupling cell respiration and ATP synthesis

spontaneous?

ADP + Phosphate + heat ATP no

Food + O2 CO2 + H20 + heat YES

----------------------------------------------------------------------------

Food + O2 + ADP ATP + CO2 + heat yes

Coupling cell respiration and ATP synthesis

spontaneous?

ADP + Phosphate + heat ATP no

Food + O2 CO2 + H20 + heat YES

----------------------------------------------------------------------------

Food + O2 + ADP ATP + CO2 yes

The COMBINED process makes ATP and increases the entropy of the universe.

The ATP Cycle

“Metabolic pathways”Metabolism = all the chemical processes of

cells

Metabolic pathway = sequence of reactions by which chemical changes such as cell respiration are carried out in many small steps, each catalyzed by an enzyme

Metabolic pathwaysMetabolism = the chemical processes of cells

Metabolic Pathway = sequence of reactions by which chemical changes such as cell respiration are carried out in many small steps.

Cellular respiration using the sugar glucose as fuel takes place in three phases, involving 20 separate reactions, and 20 different enzymes.

3 Stages of glucose “burning”

The ten steps of Stage 1

(glycolysis)

Stage 1 (glycolysis) occurs in the cytosol (“cell juice”); Stages 2 & 3 in mitochondria

Mitochondrion

Enzymes = protein catalysts

Enzymes are proteins that act as catalysts – enzymes speed up chemical reactions.

Structure of an enzyme

Where does the food come from that is used as fuel in cellular

respiration?

Animals eat plants, or they eat animals that have eaten plants.

Where does the food come from that is used as fuel in

cellular respiration?

Animals eat plants, or they eat animals that have eaten plants.

Plants make their own food by photosynthesis

Photosynthesis

spontaneous?

CO2 + H2O Glucose + O2 no

Photons of light heat YES

(ordered energy) (random energy)

------------------------------------------------------------------------------

CO2 + H2O + Photons Glucose + O2 + heat yes

Light supplies the energy to drive synthesis of glucose in photosynthesis

Where photosynthesis occurs

NOTE WELL: Plant cells use the food they make in the same way that animal cells do - by cellular

respiration