Chapter 10 Study

10.1 How do biological molecules ca

rry energy?
• Context: Molecules that perform work carry energy brought to them
by other molecules and produce waste products.
• Major themes: Time-dependent processes regulate biological
systems; life requires organization, which is energy dependent; and a
biological system’s size and environment influences how it addresses
physical and chemical challenges.
• Bottom line: Paired electrons within covalent bonds of molecules are
the source of molecular energy that powers your cells, although some
of the energy is unused.
Energy
• Showing different types of energy
and the work that is being produced.
• A and B are chemical energies
requiring combustion.
• C is representing generation of
electron flow which creates energy
Laws of theormodynamics
• 1st law- energy cannot be created or destroyed but can be
transformed
• 2nd law- states that entropy or disorder increases over time unless
energy is used to decrease entropy.
• Entropy- Measure of degree of randomness of matter. Increase in
number of states in which something can exist.

• These are laws and are proven. No exception

• H= total energy of system
• G= free energy available to do work (primary focus when looking at
molecules)
• S= entropy or disorder.

• as: ΔG = ΔH – ΔS × T
A molecule of ATP
• 3 phosphates

• Energy is in covalent bonds between

phosphorus molecules.
Bomb calorimeter
• Is a way to measure Delta H and
Delta G
Redox
• OIL RIG
• If you add hydrogens, you’re reducing. If you take away hydrogens you
are oxidizing.
• Ex. NADH is reduced form NAD+

• Oxidizing agent is being reduced itself. Giving away hydrogen

• Reducing agent is being oxidized itself. Accepting hydrogen
Homeostasis
• Keeping something within a specific range of acceptable extremes.

• Cells require energy to maintain homeostasis. Each chemical reaction

loses some energy to entropy; so without an investment of more
energy, the breakdown of food to ATP gradually reduces the amount
of ΔG and ΔH at each step
Converting ATP to
ADP
• When covalent bond between 2nd and
3rd phosphate is broken, energy is
released
Delta G is -32 Kj/Mol

If delta G has negative value, it is good

creating spontaneous reaction.
10.2 How does food get converted t
o molecular energy?
• Context: Lipids, proteins, and carbohydrates are complex foods that
you eat frequently, but they need to be broken down to smaller
molecules for energy to reach your cells.
• Major themes: Biological systems use feedback mechanisms to
regulate and maintain optimal conditions; and life requires
organization, which is energy dependent.
• Bottom line: Organisms use enzymatic pathways to produces simple,
2-carbon fuels from complex molecules, and this digestive process is
regulated by feedback mechanisms.
• Casein has highest free energy (huge protein.)

• Enzymes- proteins that catalyze(speeds up) chemical

reactions
• Redox- Reactions involving either oxidation or
reduction of a molecule.
• Cofactors- small, inorganic molecules, that are
required for enzymatic reactions. Ex. Mg2+ Ca2+
• Coenzymes- are organic molecules that are reuired
for enzymatic reactions. Ex. NAD+, NADH
• A= protein
• B= sugar
• C= fat
Lipid Metabolism
• Guy feeds dogs with nonnatural
lipids.
• Lipids either contain even number of
carbons or odd number of carbons.
• He noticed in their eurine that if they
were fed even number, then
phenylacetic acid was present but if
they were fed and odd number of
carbons then benzoic acid was
present.
• LIPIDS BROKEN DOWN 2 CARBONS AT
A TIME
Beta Oxidation
• Process of breaking down fatty acids into 2 carbon bits.

• 2 carbons then bond to CoA and then becomes acetyl-CoA then

Acetyl-Coa is used in Krebs.
• Realized it was 2 carbin fragments
and wanted to know how.
• Started by grinding up liver cells and
incubating them with different
extracts.
• 4 different types of extracts with 2
different variables ATP and octanoic
acid (lipid with 8 carbons)
• Realized you need ATP and lipid in
order to consume most amount of
oxygen.
• Most effective when you have both
ATP and octanoic acid.
Reactants and products of
beta oxidation.

• Reaction input is lipid, CoA, Fad,

NAD+ and ATP
• Output: Acetyl-CoA (goes to Krebs),
FDH2(electron transport chain),
NADH (electron transport chain), and
ADP
four different enzymes that metabolize
fatty acids of particular length

• A Shows different proteins are

better at metabolizing different
lipids at certain lengths

• B. not crucial
Limiting factors
• Cellular respiration- processes that take place in the cells of organisms
to convert biochemical energy from nutrients into adenosine
triphosphate (ATP)

• Beta oxidation is regulated by amount of CoA available.

• Limiting factor- resources are environmental conditions that limit the

growth, abundance
Protein
metabolism
• A. Shows that certain enzymes are most
effective when at their particular optimal pH.
Ex. Pepsin super acidic and found in stomach.
• B. Is showing substrates that are digested by
pepsin. Digested enzymes have substrate
specifity.
• Not all enzymes can digest all proteins
• Ex. Pepsin digest hemoglobin best compared
to other two
Deamination
• GDH takes an amino acid, NAD+, and water and converts it to a 2
carbon molecule NADH and ammonia.
• Then two carbon molecule binds to CoA, NADH goes to electron
transport change, and the ammonia is changed and becomes waste
• Formation of NADH combinded with NAD+ provides a large Delta G.
Lots of energy stored in this bond. Not a spontaneous reaction

• SEE A BELOW
Deamination
• B. Shows how GDH activity is
modulated by the amount of ATP
and ADP. Shows that if you ADP
then the GDH activity increases.
And if you add ATP then GDH
activity decreases.
• C. Shows GTP and ATP have
different effect on GDH activity.
GTP is stronger
GDH is allosterically modulated by
these 4 points…
• ATP-inactivate
• GTP-inactivate
• ADP-activates
• NADH-inactivates

• If there are any of these things it decreases the amount of GDH

activity. If there is ADP this increases amount of GDH Activity
Carbohydrate
metabolism
• A and B is just showing an individual who is
lactose tolerant vs an individual who is lactose
intolerant.

• C shows how lactose is digested into galactose

and glucose and then galactose becomes
glucose. Glucose eventually goes through
glycolosis

• Lactose is 12 carbon
• Galactose is 6 carbon
• Glucose is 6 carbon
Glycolysis
• Get a net gain of 2 ATP molecues from one
round of glycolysis.
• The glucose becomes 2 pyruvate
molecules with 3 carbons each
• Also get 4 NADH molecules from this
process.
• Pyruvates. Take 1 pyruvate molecule and
NAD+ and then get out acetyl-CoA and
CO2
• Glycolysis- the breakdown of glucose by
enzymes, releasing energy and pyruvic
acid.
Glycolysis
• YOU GET OUT WHAT YOU PUT IN
BB
Regulation of
Glycolysis
• Overview of a multi-enzyme pathway modeled on
glycolysis plus the production of CO2 and acetyl-CoA
from Figure 10.14
• Each state in glycolysis there is an enzyme. The
slowest of these enzymes is what regulates
glycolysis. PFK is slowest therefore it is the
regulator.
• In Figure 10.15, you can tell that enzyme 2,
phosphofructokinase (PFK), must be the
slowest enzyme because its
substrate has accumulated behind it
Regulation of PFK
• A. Shows how the comparison of effects of
citrate and AMP. If lots of citrate, then PFK
activity is low. If you have AMP, it overpowers
any citrate and increases PFK activity.
• B. Shows that as ATP increases then PFK
activity decreases. If you already have energy?
Why make more. Yo body is amrt
• C. Shows PFK activity can be affected by health
of said cells.
Negative Feedback Loop
• Atp is an example.

• Def: Occurs when product of process results in a decrease in the

production of that product.
• Starts at Citric Acid
• Ends at Oxaloacetic acid
• Initially thought this was a linear
process
• Get out NADH, GTP, FADH2.
• A. Injected Acid 8, inhibitor,
oxaloacetic acid, and nothing for
control.
• When adds acid 8 there is
accumulation of acid 1 and 4. This
showed it was cyclic.
• When oxaloacetic acid was added,
there was a build up of citric acid.
• B. Thought there was linear
relationship between amount of
acid and the oxygen uptake
(products) In reality, they found out
the proportions were not linear.
Just extra evidence that this a cyclic
process.
Cyclic cycle
• Inputs: start with citric acid(6
carbon), acetyl-CoA, 3 NAD+,
Fad, GDP
• Outputs: oxaloacetic acid (4
carbon), CoA, 3 NADH, 1 FADH2,
1 GTP.

• Cycle occurs 2x so double

numbers^^^
• 1. Oxygen is used within
mitochondria. Basically
discovered within charts.

• 2. Shows what inhibits and

activates Krebs
• Reducing agent- a chemical that has potential
to reduce other chemicals and become oxidized
in process. Ex. NADH and FADH2
• Mitochondrial matrix- The lumen that is in both
membranes.

• Glowing stuff is matrix.

• pH of matrix is higher than that of cytoplasm.
Check chart b on how.

• B. Added protein channels to membrane and let

hydrogen diffuse. Balanced out through
diffusion.
• C. When adding NADH, pH decreases. H+ are
leaving the cell. When you add inhibitor, protein
complex functions decreases. If you add ion
channel, then H= can diffuse freely meaning no
change.
Electron transport chain.
• A. Only Complexes 1,3,4 can transport protons out
of the matrix.
• NADH is oxidized in complex 1, FADH is oxidized in
complex 2 only. Complex 4 is in charge of reducing
oxygen.
• Electrons from NADH travel directly from Complex 1
to 3, then to 4
• Electrons from FADH2 travel from Complexes 2, to
3, to 4.
• B. Specificity in substrates.

• C. The effect of CO2 on different complexes. CO2

attaches to complex 4 inhibiting oxygen
ATP synthase spins like a
turbine to produce ATP

• A/B Spins due to H+ ions

reentering into the matrix.
• Spins synthase and that
generates enough energy to
covalently bond phosphate to
ADP which in turn creates ATP.
• C. In lab video proof of Atp
synthase rotating.
• D. Shows rate of spinning is
effected by length of actin rod.
Red=Inhibits
Green=
Activating
• Energy rich molecules inhibit
• Energy deficient molecules are
acitivators.