Cahill Exam #2 (Cellular Respiration)

Cytoskeleton is made up of three different filaments:

- Microfilaments (twist-like)
 Functions:
1. Maintenance of cell shape
2. Changes in cell shape
3. Muscle Contraction
4. Cytoplasmic Streaming
5. Cell Motility
6. Cell Division
 THINK: MCD “Money can’t dance” Maintenance, Commented [SL1]: Microfilaments: “Money can’t dance”
- Maintain
Changes & Division - Change
 Main Protein: Actin - Divide
 Myosin  motor protein that works with actin to create movement:
myosin pulls on actin to create movement.
 Note: Actin filaments start to pinch the cell in and helps divide the
cytoplasm creating a cleavage furrow.
 Actin builds up & breaks down using an extending pseudopodium to
create movement: movement similar to an amoeba.
 Form a contractile unit with striations: found in muscles. Each
striation is made up of sarcomeres (these are only associated with
actin and myosin)
NOTE: striations are covered by smooth
ER, which is known as the sarcoplasmic
reticulum.
 Sarcomere  thick filaments of myosin.
 Path of movement: a motor neuron
triggers the muscle to move. Actin
attaches to myosin sites, ATP binds and
removes myosin head.
- Microtubules (tube-like)
 Functions:
1. Maintenance of cell shape
2. Cell Motility (via cilia & flagella)
 3. Chromosome movement in cell
division
4. Organelle movement
 THINK: 3M’s: Commented [SL2]: Microtubules: 3M’s
- Maintain
Maintenance, Motility - Mobility
(c&f) & Movement - Movement
 Main Protein: Tubulin
 Dynein  motor protein that generates
movement with microtubules. This is how to get a wave motion and
help vary vesicles along.
 Centrosome  microtubule organizing center.
- Intermediate Filaments
 Not as large as microtubules or as small as microfilaments, they
are the median size.
 Functions:
1. Maintenance of cell shape
2. Anchorage of nucleus + some organelles
3. Formation of nuclear lamina.
 THINK: “fishing”: maintain, anchor, form Commented [SL3]: Intermediate Filaments: THINK
- “fishing”
- Energy is the result of breaking down food. - Maintain, Anchor, Form
- NOTE: the channels for communication are plasmodesmata, fibronectin
& gab junctions. Each of these are found in different places. Either cell
wall (for plants), extracellular matrix (for animals) or intercellular
junctions. Commented [SL4]: Where are intercellular junctions
found?

- (Most) Cells produce structures that create:

 Cell walls (plants)

 Extracellular Matrix (animals)

 In animal cells
 Mostly made of proteins
 Fibronectin  a protein that can connect to other parts creating
a communication channel.
 Proteoglycan complex  the “filler” substance existing between
cells in an organism. It is used at connective tissue

 Intercellular Junctions
 Plasmodesmata (?)
o Definition  channel for communication between 2 plant
cells.
 o Identify: plasmodesmata, secondary
cell wall, primary cell wall and
middle lamina.
o Note: middle lamina is made of
sticky sugars.
 Tight junctions
o Definitions  proteins that create a
tight seal between two cells. Note:
this isn’t very strong, it is just used as a seal; to seal up
the space.
o A tight junction is used to keep bacteria out of our cells.
 Desmosomes
o Made of intermediate filaments.
o These anchor to the cell via keratin. Note: these are very
strong, tightly held together.
 Gap Junctions
o Purpose: link one cell to another for communication
through various compounds.

Energy
- Metabolism  all of the organisms chemical reactions.
- Thermodynamics  study of energy transformations

- Catabolic Pathways  release energy to build complex molecules into

simpler ones
 “breaking down”
 THINK: the cat breaks things down

- Anabolic Pathways  consume energy to build complex molecules

from simpler ones.
 “building”
 THINK: anabolic steroids  building up, trying to get bigger.

- First Law of Thermodynamics

 Energy can be transferred and transferred, but it cannot be
created nor destroyed.
 Can’t released energy, just change shape.

- Second Law of thermodynamics

 Every energy transfer or transformation increases the entropy
(disorder) of the universe.
  Heat  faster movement of air molecules
 THINK: a cheetah releases heat.

- Spontaneous, Exergonic & Entropy

 Eventually, without any help, it will occur on its own. Occurs
without any energy input
 less disorder (more structure/order) less stability
 greater work capacity
 more spread out more stable
 Examples:
o When a man is standing on top of the ledge, he has a high
amount of G. High potential energy.
o When a group of chemicals are bundled together, orderly
and tightly bound.
o When the concentration gradient
o Jumping off diving board

- Nonspontaneous, Endogenic & Enthalpy

 Cannot occur unless energy is added.
 More disorder, more stability
 MORE FAVORABLE
 Increased entropy
 Examples:
o Man that jumps off the ledge, transforms the potential
energy into kinetic energy.
o When chemicals are all spread out, break down food for
energy.
o When the reaction is equally spread out after diffusion.
o Bouncy balls being held in the corner and then let go.
o Walking to diving board
- NOTE: PE  orderly  kinetic energy  disorderly
- What type of reaction would increase entropy? Increase entropy?
 Decreasing entropy would create less disorder, a more
structured reaction. An example of this would be a dehydration
reaction. An increase in entropy would require more disorder,
reactions like hydrolysis, digestion and catabolism.

- Three types of energy movement

 Gravitational motion
 Chemical reaction
 Diffusion

- Negative Delta G
  Catabolic pathways
 Spontaneous
 Less stable  more stable
 Increase entropy
 Releases energy
 Exergonic

- Positive Delta G
 Anabolic pathways
 Nonspontaneous
 More stable  less stable
 Decreases entropy in the system
 Requires energy (consumes)
 Endergonic

- Exergonic Reaction  net release of free energy (energy released)

- Endergonic Reaction  absorbs free energy from its surroundings
(energy consumed)

- Energy Coupling  use of exergonic process to drive an endergonic

one
 When do we use energy coupling?
 NOTE: one ATP is -7.3 kCal/mol
 Ex) If I only have +5 kCal/mol, energy coupling would work
because we have enough ATP to cover that.
 Ex) If I have +10 kCal/mol, energy coupling would fail. There is
not enough ATP.
 NOTE: Because energy gets lost into the universe, if you are only
given 1 ATP (+7.3 kCal/mol) and you need 7.3 kCal/mol or
higher energy coupling wouldn’t work. However, +7.29
kCal/mol or below would work.
 To find the net, kCal/mol, take the delta G that is given and
subtract that from the amount of ATP you have.

- Types of Work the cell does:

- NOTE: these all require energy!! Associate the examples with
something that requires energy
 Chemical Work
o Building up polymers from monomers
o Monomers  polymers
o Ex) combining amino acids to make a polypeptide,
combining glucose to form starch.
 Mechanical Work
 o Movement within a cell
o Ex) moving cilia & flagella, moving actin and myosin in
muscle cells, moving vesicles or other organelle along a
microtubule.
 Transport Work
o Movement of substances against its gradient
o Ex) sodium-potassium pump, proton pump

- Enzymes
 Spontaneous reactions occur on their own (eventually), an
enzyme aids in the
acceleration of a
spontaneous reaction.
 Induced fit  the idea that
an enzyme will change
shape when substrates bind
to the active site.
 Activation Energy (Ea) 
the energy that must be
added top start any
reaction.
 Enzymes are able to get over the hurdle more quickly and the
delta G is unaffected.
 How can an enzyme lower activation energy?
o COPS
o C
o O  orienting substrates correctly
 Twisting for the shape enables the correct side for
binding
o P  providing a favorable microenvironment
 This includes making sure there are balanced charges
or acidity/basicity
o S  straining substrate bonds
NOTE: An enzyme lowers Ea by disrupting and destabilizing bonds by
changing charges, concentration or acidity making it favorable.
- Understand that enzymes selectively accelerate reactions and
inhibitors are necessary.
- Types of inhibitors:
 Competitive Inhibitor  binds to the active site of an enzyme.
o Who gets there first mentality
 Noncompetitive Inhibitor  binds to an another part of the
enzyme
 - Practice Problem:
 If you’re unsure of the type of inhibitor that is present and you
add a lot of substrate and the reaction still works pretty well,
what type of inhibitor is most likely present?
o Competitive because the reaction is still working pretty
well. This means that enough substrate is being it to the
spot and it will work as a result.
o Note: this is dependent on substrate: competitive = still
working.
 If you are unsure of the type of inhibitor present and either low
or high amounts of substrate do not affect enzyme function,
what inhibitor is present?
o Noncompetitive because a noncompetitive inhibitor binds
at different site, the substrate wouldn’t be affected
(because its binding site is somewhere else)

-Allosteric Reactions
 NOTE: small molecules can bind to make sure molecules are
stabilized in position.
 Allosteric Regulation  occurs when a regulatory molecule
binds to a protein at one site and affects protein function at
another side.
 Types of Allosteric Regulators:
o Activators
o Inhibitors
o Cooperativity
 This when a substrate binds to one active site,
stabilizing the other.
 Stabilizes an enzyme in its active form.

 Feedback Inhibition  the end product of a metabolic pathways

shut down the pathways
o Products block the active site, shutting down the pathway
that made it.
o Examples:
 The heat in your house: when you turn up the
thermostat and the house heat up & heats up until it
reaches the desired temperature.

- Aerobic  requires oxygen

- Anaerobic  doesn’t require oxygen
- Cellular Respiration  includes both aero & anaerobic respiration.
- C6H12O6 + 6O2  6CO2 + 6H2O + Energy (ATP + Heat)
 Blue  oxidation
 Pink  Reduction
 There is an increasing entropy
- Redox Reactions  chemical reactions that transfer electrons (also
called oxidation-reduction reactions)
- LEO GER or OIL RIG
 Oxidation  substances loses electrons
 Reductions  substances gain electrons
 L – Loses
 E – Electrons
 O – Oxidation
 --------------------
 G – Gain
 E - Electrons
 R – Reduction
- Na + Cl  Na+ + Cl- Commented [SL5]: Check oxidation and reduction.
 Use code from above
 Note: the opposite is the agent
o Reduced – is the oxidizing agent
o Oxidized – is the reducing agent
 NOTE: If it gains H+ then it is being reduced
 Whatever has more electrons has more energy.

- Potential Energy
 Depended on the hold on oxygen for example, C6H12O6 vs C6H12,
the Carbon creates a double bond with oxygen creating less
potential energy. C6H12 has less of a hold on oxygen and we are
able to get energy from this.
 Stronger hold via Oxygen = less PE
 Weaker hold via Oxygen = more PE (can break to get energy)
 NOTE: electronegative atoms hold more strongly to the
electrons making them harder to be broken down and used.
 Electron Carriers
o NADH (reduced form) *this has 2 more e- than NAD+*
o NAD+ (unoxidized form) Commented [SL6]: ???
o FAD+
o FADH2
o NOTE: think of NADH + FADH2 as trucks, just dropping
things off.

- Dehydrogenase  removes hydrogens Commented [SL7]: What about them?

  Responsible for removing hydrogens to great a molecule that is
harder to break, having more PE.

- Cellular Respiration
 Glycolysis
o Initial breakdown of sugar: starting molecule – glucose
o Steps 1-5
 Step 5:
 Dihydroxyacetone Phosphate (DHAP)
 Glyceraldehyde 3-Phosphate (G3P)
 Explains what happens at the end of G3P. How
does the system deal with G3P moving on?
 The system deals with G3P moving on by
converting DHAP into its isomer (G3P) and
creating the balance to enable G3P to move
on.
 Generally, it converted DHAP to G3P (its
isomer) so it can be used.
 2 G3P for one glucose moves on.
 NOTE:
1000 glucose

1000 Carbon Sugars

500 DHAP +
500 G3P

500 DHAP + 0 G3P

(Using an isomer)
250 DHAP + 250 G3P

250 DHAP + 0 G3P

(etc.)

o Energy Investment Phase

 Adding 2 ATP (to eventually get it back)
 Catabolic
 What we put in:
 1 glucose
 2 ATP
o Energy Payoff Phase
 Steps 6-10
  What we get out:
 4 ATP
 2 NADH
 2 Pyruvate
o Net Gain in both these steps: 2 ATP, 2 NADH, 2 Pyruvate
o What is the molecule that connects the energy investment
and the energy payoff phase? Commented [SL8]: ???
o Glycolysis  Pyruvate
o At the end of glycolysis:
 2 pyruvates
 2 ATP
 2 NADH
 Pyruvate Oxidation
o Does NOT involve ATP
o In the matrix of the mitochondria
o Pyruvate Oxidation  Acetyl CoA
o Steps:
 CO2 gets released
 NAD+ gets reduced and forms NADH
 Coenzyme A attaches
o How much NADH do we get? From the beginning?
 2 NADH

o Citric Acid Cycle

 Acetyl CoA/Oxaloacetate  Citrate
 3 NAD+  3 NADH
 1 ATP out
 1 FAD+  1 FADH2
 Back to Oxaloacetate
 NOTE: this needs to be cycled around twice, located
in the matrix of the mitochondria.
 How many electron carriers do we have from on
initial glucose to the end of the citric acid cycle?
 12 electron carriers (2 NADH from glycolysis, 2
NADH from pyruvate oxidation, 6 NADH from
the citric acid cycle, 2 FADH2 : 10 NADH + 2
FADH2.
 How many ATP from one glucose to the end of the
citric acid cycle?
 4 ATP

 Oxidative Phosphorylation
o Steps: Electron transport Chain (exergonic) &
Chemiosmosis
o NADH + FADH2 account for most of the energy extracted
from food.
o Routes:
 NADH  I  Q  III  Cyt. C  IV  Oxygen
 NADH: Route starts @ I, can aid in protons
being pumped up = more ATP later.
 FADH2  II  Q  III  Cyt. C  IV  Oxygen
 FADH2: Route starts @ II, fewer protons being
generated, less ATP generated.
 Q  ubiquinone
o Drawing of Ox. phos:
 o Explain what happens to in the electron transport chain.
 NADH  I  Q  III  Cyt. C  IV  Oxygen, as the
electrons move through, the protons are pumped
into the intramembrane space, high [], and moves
passively through ATP synthase, FADH2 adds
electrons later in the chain getting fewer protons
pumps into ATP intermembrane space and generated
energy used for ATP, fewer ATP.
 As it goes to the right, there is a change in potential
energy.
 During ox. phos, chemiosmosis couple electron
transport chain to ATP synthesis (energy coupling)

 Cellular Respiration Vocab:

o Substrate-level phosphorylation  when an enzyme
transfers phosphate from a substrate from a substrate to
ADP to form ATP.
o Kinase  an enzyme that transfers phosphates from one
substance from another.
o Hexokinase  move phosphate + sugar
o Isomerase  enzyme that converts one isomer into
another. Rearrange the same thing so it has a different
arrangement.
o Proton Motive Force  refers to the high concentration of
protons in the intermembrane space that can be used to do
work.
o Chemiosmosis  the use of energy in a H+ gradient to
make ATP.
o Cytochromes  proteins that are found in the inner
membrane of the mitochondria that are involved in the
electron transport change.
o Fermentation  consists of glycolysis plus reactions that
regenerate NAD+, which can be reused to glycolysis.

- 30-32 ATP MAX per glucose

- Practice Problems:
 2 Acetyl CoA going through the CAC, how many FADH2?
o 3 FAHD2
 Are there other pathways like cellular respiration for molecules
other than glucose, such as fats and proteins? Commented [SL9]: ???
o No(?)
  NOTE: if a cell has a lot of AMP, the cellular respiration should
increase because the situations is more dire due to AMP being
involved (only one phosphate).
 NOTE: if the cell has a lot of ATP, the cellular respiration
should decrease because it is less needed. In fact, it may need
to stop production via feedback inhibition.
 NOTE: AMP is used as an allosteric regulator to get cellular
respiration working really well.

High PE
• ATP (3 phosphates)

Lower PE
• ADP (2 phosphates)

Low PE
• AMP (1 phosphate)

- Fermentation
 Alcohol Fermentation
o Pyruvate  (CO2) Acetaldehyde  (NADH  NAD+) 
Ethanol
 Lactic Acid Fermentation
o Pyruvate is reduced by NADH
o Pyruvate  (NADH  NAD+)  lactate
 The purpose of fermentation is to get more NAD+ to be able to
continue with glycolysis. (oxidized NADH to get NAD+)
 Obligate Anaerobic  carry out fermentation, can’t survive
without the presence of CO2. Ex) Botulism
 Facilitative anaerobic can survive using either fermentation or
aerobic respiration.