Cycle 3:

Thermodynamics
and Membranes
Presented by the BMP
iClicker Workshop Slides
In-workshop questions will be Sides can be found in OWL,
polled through iClicker. under the “Biology Mentorship
Program” tab.
Lecture 5: Energy and Enzymes
- Thermodynamics
- Enzymes
- Proteins
Energy and systems
Types of energy

Kinetic: energy from motion

Potential: stored energy from position or chemical structure
Chemical: energy released during a chemical reaction

Types of systems

Open: can exchange both energy and matter with surroundings

Closed: can exchange energy but not matter with surroundings
Isolated: no matter or energy exchange with surroundings
Thermodynamics
- Energy can be transferred between one form and another but never
created or destroyed - first law of thermodynamics

- Entropy can be thought as disorder - second law of thermodynamics

- there is a natural tendency of any isolated system to degenerate into
a more disordered state - entropy increasing

- Entropy of living cells is kept low - energy is always being taken in, to
replace the things that are breaking down
- Cells are “islands” of low entropy
- Surroundings are disordered
Thermodynamics
Enthalpy
ΔH > 0 is endothermic
ΔH < 0 is exothermic
Free energy
ΔG = Gproducts - Greactants
ΔG = ΔH - TΔS
ΔG > 0 is endergonic
(requires energy)
Entropy
ΔG < 0 is exergonic ΔS > 0 is more spread out (less order)
(spontaneous) ΔS < 0 is less spread out (more order)
Thermodynamics
- Enzymes can only increase the
rate of reaction for exergonic
reactions
- Enzymes do not change ΔG for any
reaction!
- Reduces energy required to get
to transition state (activation
energy)
- This is done by driving substrate molecules to the transition state
conformation (e.g. through precise orientation of two substrates,
charge interactions, conformational strain
Can you use an enzyme to speed up the rate?

- NO! Endergonic reaction! Enzymes only work for exergonic reactions

* Enzymes do not provide energy to a reaction.

Protein Structure
Primary
● Sequence of amino acids in polypeptide chain

Secondary
● Due to interactions between the polypeptide backbone

Tertiary
● Due to interactions between R groups (side chains)

Quaternary
● Protein interactions between polypeptides
Proteins Folding
- Anfinsen's Dogma
- Protein folding is spontaneous, happens by itself
- The final conformation is ONLY dictated by the primary sequence

Protein folding is extremely quick

(occurs in milliseconds)
- Secondary structure
(intramolecular hydrogen
bonding)
- Hydrophobic effect (non-polar
aa are buried) Native conformation
(lowest energy state)
Catalysis
Enzyme flexibility
(tertiary structure) allows
for induced fit

A mutation here
Active Site will likely not affect
- Binding site on function (neutral)
the enzyme
- Where catalysis
occurs
- a mutation here
could cause a
deleterious effect Catalytic Cycle:

- Enzyme can bind to more substrates upon release of products

- Different enzymes have varying speeds
- The cycle is temperature dependent
Enzyme Rates
- Different enzymes have different optimum environments (ex.
pH/Temperature)
- Based on the organism’s environment
Practice Question
Lecture 6: Membrane Structure & Function
Textbook topics: Lecture topics:

- Phospholipid structure - Steps of the secretory pathway

- Domains of integral proteins
- Membrane permeability
(prior knowledge)
- Types of membrane transport
- Membrane-bound proteins
- Hydropathy Plot
- CFTR
- Practice questions
Phospholipids and Integral Proteins
Hydrophilic domain
Glycerol (hydrophilic)

Phospholipid bilayer
Hydrophobic

Membrane
Integral
domain

Fatty acid tails (hydrophobic)

Membrane Permeability

* Integral proteins needed

(spans the bilayer)

 The Hydropathy Plot (New Lecture Material for 2022-23)
A graph where…
● X-axis: amino acid number
● Y-axis: relative hydrophobicity index

Integral membranes have hydrophobic parts (likely hydrophobic domain)

SAMPLE PROTEIN

Hydrophilic AAs

Hydrophobic AAs

*not to scale
What is the Secretory Pathway? Transmembrane
proteins
Extracellular
proteins

● How proteins get on the

plasma membrane or
Vesicles
secreted out of cell
● ER → Golgi → plasma
membrane via vesicles
○ Examples:
Channelrhodopsin,
nutrient transporters, CFTR
(as we will see!)

Endoplasmic Golgi
reticulum Plasma
(ER) membrane
 Confused
protein Protein Targeting
- Translation occurs in the
cytoplasm.

- If a protein is to be sent to the

membrane, how do we do that?

A “tag” on the protein

● Cell is able to recognize this tag

● Cell transports proteins to proper
Endoplasmic
places
reticulum
(ER)
The Secretory Pathway (1)
The Secretory Pathway (2)
Tracking the Signal Sequence
- mRNA → signal sequence is included in the
mRNA

- Initial protein → signal sequence appears as a

polypeptide

- Final/mature protein → signal sequence is

excised
Exam-Level Question:
1. The signal peptide is not encoded by the gene of the translated protein; it is added after
translation (post-translational modification)
2. A loss-of-function mutation to the signal recognition particle would prevent ribosomes from
binding to the ER
3. The final folded protein has the exact same amino acid sequence predicted from its mRNA
4. The signal recognition particle is part of the translated protein and is required for the
protein to interact with the Golgi

*Pulled from a past test

A. F, T, T, F
B. F, T, F, T
C. T, F, T, T
D. F, T, F, F
Membrane-bound Proteins and Functions
- Various types:
- Integral vs. peripheral membrane proteins
- Differences in mobility
- Many function to help with membrane transport
- Passive: Follow their concentration gradients, spontaneous, increase in entropy
- If there was no membrane, the particle would move in this way
- The membrane prevents movement of the particle
- The passive transporter acts as a hole in the membrane for the particle to pass
through
- Active: Move against concentration gradients
- You add in ATP to provide energy to make up for the fact that, without ATP, this
reaction would have been endergonic
- If there was no membrane, the particle would move in a manner opposite to this
- Not spontaneous
CFTR & Chloride Transport in Lung Epithelium
- Normal lung physiology involves a delicate balance of ions and water
- Chloride pump (CFTR) is an ABC that maintains the correct concentration gradient of
chloride within the lungs
- Concentration gradient ensures correct osmosis of water
- Water needed to keep cilia wet and mobile to prevent lung infections

- HSP90 prevents misfolded CFTR from reaching the membrane

- Useful in healthy person
- Causes problems in cystic fibrosis:
- Infections, thick mucus, troubles breathing
Practice Question
Why does the ATP-Binding Cassette need to bind ATP?

A. It actively transports ATP into/ out of the cell

B. ATP is a signal that lets the cell know other molecules need to cross
the membrane
C. ATP hydrolysis provides energy that lets molecules cross the
membrane against their concentration gradients
D. ATP hydrolysis prevents molecules from crossing the membrane
when the cell doesn’t need them to
Practice Question
The delta F508 mutation is one example of a mutation that could lead to cystic
fibrosis. Which of these examples could also cause cystic fibrosis?

1. A mutation in the transmembrane domain of CFTR protein that leads

to this region becoming hydrophilic
2. A mutation in HSP90 that causes it to assess functional CFTR proteins
as misfolded proteins
3. A mutation in the CFTR gene that prevents DNA polymerase from
recognizing it as a gene that needs to be transcribed
4. A mutation in the CFTR protein that leads to improved chloride
transport across the membrane

A = 1, 2, 3 B=1,3 C=2,4 D=4 only E=all of the above

Importance of Unsaturated Lipids:
The degree of lipid saturation affects the fluidity of the membrane.

● Increased saturation → decreased fluidity

● Decreased saturation → increased fluidity

Desaturases are enzymes that can adjust membrane fluidity by increasing

the degree of unsaturation in membrane fatty acids.

Organisms can alter their membrane fluidity at different temperatures by

changing the level of desaturase expression.
Practice Question
Which of the following mutations could inappropriately affect membrane
fluidity?

1. Mutation in a membrane transport protein

2. Mutation in an enzyme responsible for degrading fatty acids in the
membrane and replacing them with new ones
3. Mutation in a gene encoding a fatty acid
4. Mutation in a desaturase enzyme that decreases its functionality

A = 1, 2, 3 B=1,3 C=2,4 D=4 only E=all of the above

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