Bioenergetics
Section Topics:
1. Introduction, Life's beginning from Space Grease!
2. Life's building blocks
3. Life’s Energy
4. Enzymes Pathways and Glycolysis
5. The Citric Acid cycle (CAC), Kreb's 2nd cycle
6. The Electron Transport System: the spark of life
7. ATP synthesis: the search for Squiggle (~)
8. Catching starlight, Photosynthesis I
9. Making sugar, Photosynthesis II
10. Glucose: store it, or make
11. Blood glucose levels during the fed and fasting states
12. Exercise and diabetes
Lecture 1:
Percentage of elements in a human body wet mass
1. Oxygen
2. Carbon
3. Hydrogen
4. Nitrogen
5. Calcium
6. All others
Water (H2O)
● We are made up of about 80% water
● Most important compound within us is water - its charge allows it to stick together
and create tension
● 1 & 3 most abundant element
● H2O has the 2nd highest specific heat capacity (after ammonia, 4181 J/(kg·K).
● This buffers Earth's climate by buffering large fluctuations in temperature.
● Water is a powerful solvent
● Polarity attracts positive and negative ions
● Forms barriers with hydrophobic molecules (lipids membranes)
● Allows/drives structure and shape of molecules proteins, base pairing of DNA...
● Transports substrates...
●
Things that are important to life
● Oxygen.
● Food.
● Water.
● right temperature.
,The Goldilocks zone and water gives us that right temperature.
There's a lot of carbon in space which can be found in ring like structures which we are
made up of
Stanley Miller 1952 Miller-Urey Experiment
● Created an "ocean" of heated and cooled water, with NH3 , H2, CH4 atmosphere.
● 7-days later (i.e. only 1 week) water became deep red and turbid.
● Amino acids (found in humans) and metabolites (found in glycolysis and parts of the
citric acid cycle) formed…
● Building blocks of life can form quite readily
Summary of how life formed
● Life likely formed from abundant organic molecules and elements
● Life’s chemistry may have started from interactions on the surface of rocks and
clays and silicates
● Some compounds form that can even promote electrochemical reactions
Evolution from metabolism
● Only ~10 compounds are required to make all the molecules of life, they come from
● Central metabolism is very important not just to build stuff but to make life
Lecture 2:
Polymers
Key Concepts
● Life requires macromolecules
● Polymers form through the removal of water –dehydration
● Polymers break through addition of water –hydrolysis (cut water)
● This could tell us where life started
What are polymers
● Life needs structure and therefore polymers
● polymers constructed of identical/similar building blocks called monomers
● 80% of a cell’s components are polymers, 20% of a cell are monomers and other
small molecules (things that help buffer or sugars)
Types of polymers
● Lipids (kind of, similar concept, they are not a biopolymer from the fact that they are
very small and they auto assemble whereas biompolymers are joined by machines.)
● Polysaccharides (Carbohydrate)
● Proteins
● Nucleic acids
,Where life might have started
● At hydrothermal vents
○ There's lots of organic material can be present there,
○ There's lots of carbon and things being bellowed out through these
smokestacks.
○ The other is that there's energy,
○ there's temperature and there's also ion gradients
○ At the edge of these pools dehydration and hydration cycles, and heating
and cooling
1.2 Lipids (not a proper polymer)
● A simple compound acetate, is an initial building block of many compounds,
including lipids.
● Lipids can grow, to form hydrophobic fatty acid (acyl) chains
● Addition of phosphate (and often other bits) makes fatty acids amphipathic
(hydrophobic & hydrophilic parts)
● Phospholipids form membranes
● Membranes form vesicles – the first cell, or protocell?
● Acyl chains can be saturated or unsaturated
We call them different names depending on what solution they're in and how charged they
are.
Properties of Lipids
● Hydrophobic: water insoluble
● Functions:
○ Energy storage (for mass, 6x energy of stored sugar-e.g. glycogen)
○ Structural molecules e.g. membranes
○ Steroid Hormones
Fats are stored as triglycerides
● This molecule consists of glycerol binded to acyl chains with ester linkages
● Acyl chains can be different lengths
Saturated and Unsaturated Fatty Acids
● In saturated fats the acyl chains are straight and are found more solid than
unsaturated fats
● Unsaturated fats have double bonds in their acyl chains which causes bending and
as a hydrogen is removed to make the double bond, it is no longer saturated with
hydrogen. The kink in the acyl chain makes it bend and therefore harder to rotate
Why the difference
, ● In saturated fats the acyl chains are straight so they take up less space whereas in
unsaturated fats the bent legs push each other apart and therefore take up more
space.
● As unsaturated fats cannot rotate so easily due to their double bonds it means that
they are less likely to come together and solidify when it gets cold meaning they stay
more liquid.
● Animals use the properties of saturated and unsaturated fats in their diets such as
squirrels who feed on unsaturated fats can drop their body temperature lower as if
they feed on saturated fats at these low body temperatures the fat might solidify
whereas with the unsaturated fats it would not.
Lipids: Phospholipids
● One fatty acid acyl chain of a TRG is replaced by a phosphate-linked group. This
phosphate is charged and therefore is hydrophilic.
Lipids: The phospholipid bilayer
● The cell membrane is formed of a phospholipid bilayer
● Phospholipids can also form micelles and liposomes which transport stuff around
the cell.
● These membranes allow us to partition things in the cell.
Replication
Phospholipids get to a certain size and they become weakened and then they form, they
bud and they become two things. And then they grow and grow and grow and then they
may become three things and so on.
● No genetic information was required
● Just physical laws of stability of vesicle size
1.3 Sugars
● Dihydroxyacetone (technically not a sugar, but tastes sweet, like glycerin)
● Glucose
Key Concepts
● Sugars form from central pathways (trioses)
● Monosaccharides are single sugars and there are different types (glucose, fructose)
● Disaccharides – Oligosaccharides form from several mixed sugar types (e.g.
sucrose)
● Polysaccharides form from many repeated units connected by glyosidic bonds
● Polysaccharides are useful for energy storage (starch and glycogen)
● Plants and animals use polysaccharides to form structures (e.g. cellulose and chitin)
and specific glycosidic bonds determine flexibility
Sugars
Section Topics:
1. Introduction, Life's beginning from Space Grease!
2. Life's building blocks
3. Life’s Energy
4. Enzymes Pathways and Glycolysis
5. The Citric Acid cycle (CAC), Kreb's 2nd cycle
6. The Electron Transport System: the spark of life
7. ATP synthesis: the search for Squiggle (~)
8. Catching starlight, Photosynthesis I
9. Making sugar, Photosynthesis II
10. Glucose: store it, or make
11. Blood glucose levels during the fed and fasting states
12. Exercise and diabetes
Lecture 1:
Percentage of elements in a human body wet mass
1. Oxygen
2. Carbon
3. Hydrogen
4. Nitrogen
5. Calcium
6. All others
Water (H2O)
● We are made up of about 80% water
● Most important compound within us is water - its charge allows it to stick together
and create tension
● 1 & 3 most abundant element
● H2O has the 2nd highest specific heat capacity (after ammonia, 4181 J/(kg·K).
● This buffers Earth's climate by buffering large fluctuations in temperature.
● Water is a powerful solvent
● Polarity attracts positive and negative ions
● Forms barriers with hydrophobic molecules (lipids membranes)
● Allows/drives structure and shape of molecules proteins, base pairing of DNA...
● Transports substrates...
●
Things that are important to life
● Oxygen.
● Food.
● Water.
● right temperature.
,The Goldilocks zone and water gives us that right temperature.
There's a lot of carbon in space which can be found in ring like structures which we are
made up of
Stanley Miller 1952 Miller-Urey Experiment
● Created an "ocean" of heated and cooled water, with NH3 , H2, CH4 atmosphere.
● 7-days later (i.e. only 1 week) water became deep red and turbid.
● Amino acids (found in humans) and metabolites (found in glycolysis and parts of the
citric acid cycle) formed…
● Building blocks of life can form quite readily
Summary of how life formed
● Life likely formed from abundant organic molecules and elements
● Life’s chemistry may have started from interactions on the surface of rocks and
clays and silicates
● Some compounds form that can even promote electrochemical reactions
Evolution from metabolism
● Only ~10 compounds are required to make all the molecules of life, they come from
● Central metabolism is very important not just to build stuff but to make life
Lecture 2:
Polymers
Key Concepts
● Life requires macromolecules
● Polymers form through the removal of water –dehydration
● Polymers break through addition of water –hydrolysis (cut water)
● This could tell us where life started
What are polymers
● Life needs structure and therefore polymers
● polymers constructed of identical/similar building blocks called monomers
● 80% of a cell’s components are polymers, 20% of a cell are monomers and other
small molecules (things that help buffer or sugars)
Types of polymers
● Lipids (kind of, similar concept, they are not a biopolymer from the fact that they are
very small and they auto assemble whereas biompolymers are joined by machines.)
● Polysaccharides (Carbohydrate)
● Proteins
● Nucleic acids
,Where life might have started
● At hydrothermal vents
○ There's lots of organic material can be present there,
○ There's lots of carbon and things being bellowed out through these
smokestacks.
○ The other is that there's energy,
○ there's temperature and there's also ion gradients
○ At the edge of these pools dehydration and hydration cycles, and heating
and cooling
1.2 Lipids (not a proper polymer)
● A simple compound acetate, is an initial building block of many compounds,
including lipids.
● Lipids can grow, to form hydrophobic fatty acid (acyl) chains
● Addition of phosphate (and often other bits) makes fatty acids amphipathic
(hydrophobic & hydrophilic parts)
● Phospholipids form membranes
● Membranes form vesicles – the first cell, or protocell?
● Acyl chains can be saturated or unsaturated
We call them different names depending on what solution they're in and how charged they
are.
Properties of Lipids
● Hydrophobic: water insoluble
● Functions:
○ Energy storage (for mass, 6x energy of stored sugar-e.g. glycogen)
○ Structural molecules e.g. membranes
○ Steroid Hormones
Fats are stored as triglycerides
● This molecule consists of glycerol binded to acyl chains with ester linkages
● Acyl chains can be different lengths
Saturated and Unsaturated Fatty Acids
● In saturated fats the acyl chains are straight and are found more solid than
unsaturated fats
● Unsaturated fats have double bonds in their acyl chains which causes bending and
as a hydrogen is removed to make the double bond, it is no longer saturated with
hydrogen. The kink in the acyl chain makes it bend and therefore harder to rotate
Why the difference
, ● In saturated fats the acyl chains are straight so they take up less space whereas in
unsaturated fats the bent legs push each other apart and therefore take up more
space.
● As unsaturated fats cannot rotate so easily due to their double bonds it means that
they are less likely to come together and solidify when it gets cold meaning they stay
more liquid.
● Animals use the properties of saturated and unsaturated fats in their diets such as
squirrels who feed on unsaturated fats can drop their body temperature lower as if
they feed on saturated fats at these low body temperatures the fat might solidify
whereas with the unsaturated fats it would not.
Lipids: Phospholipids
● One fatty acid acyl chain of a TRG is replaced by a phosphate-linked group. This
phosphate is charged and therefore is hydrophilic.
Lipids: The phospholipid bilayer
● The cell membrane is formed of a phospholipid bilayer
● Phospholipids can also form micelles and liposomes which transport stuff around
the cell.
● These membranes allow us to partition things in the cell.
Replication
Phospholipids get to a certain size and they become weakened and then they form, they
bud and they become two things. And then they grow and grow and grow and then they
may become three things and so on.
● No genetic information was required
● Just physical laws of stability of vesicle size
1.3 Sugars
● Dihydroxyacetone (technically not a sugar, but tastes sweet, like glycerin)
● Glucose
Key Concepts
● Sugars form from central pathways (trioses)
● Monosaccharides are single sugars and there are different types (glucose, fructose)
● Disaccharides – Oligosaccharides form from several mixed sugar types (e.g.
sucrose)
● Polysaccharides form from many repeated units connected by glyosidic bonds
● Polysaccharides are useful for energy storage (starch and glycogen)
● Plants and animals use polysaccharides to form structures (e.g. cellulose and chitin)
and specific glycosidic bonds determine flexibility
Sugars
