Cycle 3: Energy & Membranes

Question 1

Meaning of potential, kinetic, chemical energy and examples of each.

Answer 1

Potential Energy:
- Energy that is stored and has the potential to be converted into other forms of energy
- e.g. energy stored in the bonds of molecules, such as ATP (adenosine triphosphate), which can be used for cellular work.

Kinetic Energy:
- Energy of motion, associated with the movement of objects or particles.
- e.g. movement of molecules within a cell, such as the kinetic energy of water molecules during osmosis or the movement of proteins within the cell.

Chemical Energy:
- Energy stored in the bonds of chemical compounds; released during chemical reactions.
- e.g. energy stored in the chemical bonds of glucose molecules, which is released through cellular respiration to produce ATP and power cellular activities.

Question 2

Distinction between Open, Closed and Isolated systems,

Answer 2

Open - exchanges energy AND matter (e.g. ocean)
Closed - exchanges energy BUT NOT matter (e.g. earth with heat eenrgy)
Isolated - exchanges NEITHER energy NOR matter (e.g. thermos)

Question 3

Definition and examples of: First Law of Thermodynamics, Second Law of Thermodynamics.

Answer 3

1st Law of Thermodynamics - Energy cannot be created or destroyed; it can only be transformed from one form to another OR transferred from one place to another

2nd Law of Thermodynamics - The total disorder of a system and its surroundings always increase (systems spontaneously move towards arrangements with greater disorder/entropy)

Question 4

The Four levels of protein structure. What bonding arrangements / chemical bonds and structures define each level?

Answer 4

• Primary structure: Exact sequence of amino acids forming polypeptide (held together by peptide bonds).
• Secondary structure: Polypeptide chain conformation into an α-helix (hydrogen bond and peptide bond), β-pleated sheet (hydrogen bond), or random coil.
• Tertiary structure: 3D shape of a single folded protein molecule. (formed through ionic bonding, hydrogen bonding, hydrophobic interacts, and disulfide bridges)
• Quaternary structure: 3D arrangement of protein-protein and protein-non-protein assemblies

Question 5

Why we need to eat.

Answer 5

Living things are always dying, always increasing the entropy of their surroundings. To maintain low entropy within the cell, food must be consumed as a huge source of energy to the cell, helping it fight decay and breakdown.

Question 6

Flow of energy through the biosphere….concept of carbon compounds being reduced or oxidized….link to autotroph vs heterotrophs…define each of these.

Answer 6

Most reduced carbon compounds (mostly C-H bonds) have the highest free energy, while most oxidized carbon compounds (mostly C-O bonds) have the lowest free energy. (Ravishing Heroes Hunted Old Oranges Loudly)

Energy enters the biosphere through photosynthesis. Autotrophs reduces CO2 (oxidized carbon) through photosynthesis. Heterotrophs oxidize reduced carbon to liberate energy.

Question 7

With regard to life the concept of: work and breakdown….use of energy brought in from the environment; maintaining low entropy, how the 2nd law applies to living systems , entropy as energy spreading or disorder.

Answer 7

Work needs to be done to synthesize biological compounds. Energy is required to stave off breakdown to mainting cell functioning.

Energy and matter brought in from the environment enters autotrophs separately, but as together for heterotrophs.

Energy is required to fight the 2nd law!! in biological organisms.*

Entropy can be conceptualized as a natural tendency towards disorder and energy spreading.

Question 8

Definition of free energy and delta G, spontaneous…basic understanding of enthalpy and entropy.

Answer 8

(Gibbs) Free Energy is the energy available to do work.

• Negative ΔG indicates a spontaneous reaction EXERGONIC (Gproducts &laquo_space;Greactants)
• Positive ΔG indicates a non-spontaneous reaction ENDERGONIC (Gproducts&raquo_space; Greactants)

ΔG = ΔH - TΔS

Question 9

Distinction among the terms: exothermic, endothermic, exergonic, endergonic.

Answer 9

Exothermic: -ΔH
Endothermic: +ΔH
Exergonic: -ΔG
Endergonic: +ΔG

Question 10

The role enzymes play in increasing the rate of a spontaneous reaction and their role in non-spontanous reactions.

Answer 10

Many biological processes require a ridiculously long rate of reaction w/o enzymes (even if they are spontaneous), however, upon the introduction of the appropriate enzyme, the rate of reaction drastically increases!

Enzymes DO NOT give a reaction more free energy! They cannot make a non-spontaneous reaction occur w/o the aid of an energy source like light or ATP.

Question 11

The features of the “exergonic reaction energy profile”: delta G, transition state, activation energy. WHAT’S AN ENDERGONIC REACTION ENERGY PROFILE

Answer 11

Exergonic reaction energy profile is plotted as free energy as a function of reaction progress. The reactants are plotted with higher free energy than the products, and achieve a transtion state with an even higher free energy (requires activation energy).

Question 12

What an enzyme does to the “exergonic reaction energy profile”

Answer 12

The enzyme lowers the activation energy required to react the transition state, resulting in a lower free energy bump.

Question 13

How do enzymes actually lower the Ea.

Answer 13

Enzymes lower the activation energy of a reaction by mimicking the transtion state confromation of the substrates by using charge interactions to produce the correct conformational strain.

Question 14

The importance of enzymes in the evolution of life

Answer 14

Many reactions required for biological function have rates of reaction that are too slow to occur without enzymes AND these reactions cannot have significantly increased rate of reaction without altering T and P beyond biologically conducive conditions.

Question 15

Basics of protein folding: What is required for a protein to fold correctly (Anfinsen’s Dogma)

Answer 15

Protein folding occurs naturally and spontaneously and does not require any additional substances to occur.

Anfinsen proved that this was true by denaturing (altering tertiary structure) of a protein using urea (polar molecule) and then got rid of the urea and the protein spontaneously refolded.

Question 16

Properties of urea that enable it to denature proteins

Answer 16

Urea is a polar molecule with N which forms hydrogen bonds with the protein and causes the protein-protein hydrogen bonding holding the tertiary structure together to break.

Question 17

Free energy and the Energy funnelling model of protein folding…role of chaperones

Answer 17

Nascent or unfolded proteins are in the highest energy state, while native folded progeins are in the lowest energy state. Transtional state complexes have an intermediate energy state.

Chaperones (e.g. HSP) use energy to get proteins to unfold and refold correctly.

Question 18

Basics of enzyme structure and the catalytic cycle.

Answer 18

Substrates binds to the active site and forms an enzyme-substrate complex, before producing a product and freeing the enzyme to repeat its role in the catalytic cycle.

Question 19

Link between active site and protein folding and the primary structure.

Answer 19

The primary strucure of the protein is not enough information to determine the location of the active site. Only the tertiary structure (folded protein) can enable you to hypothesize the location of the active site.

Question 20

What processes explain the shape of a Growth vs Temperature curve in E. coli

Answer 20

The rate at which E. coli divide is highly temperature dependent, due to the ENZYME ACTIVITY involved, or the rate at which the enzyme goes through substrate to produce a product.

On a growth vs. temperature curve, growth rate starts at zero at the minimum temperature before slowly increasing up to the maximum growth rate at the optimum growth temperature (for E. coli and many other bacteria this is about 37deg). This slow rise can be attributed to the increased number of collisions occuring between enzymes and substrates due to increasing temperature (and so, kinetic energy of particles).

From optimum temperature onwards, there is a steep decline in growth rate, due to the denaturation of the enzyme, which renders the active site less and less useful. So, enzyme activity and growth levels decrease.

Question 21

How is the tertiary structure of the enzyme Hexokinase different between organisms adapted to extreme cold versus extreme heat.

Answer 21

Extremophiles are adapted to different temperatures.

Extreme cold (psychrophiles): increased FLEXIBILITY in tertiary structure (more alpha helices) of hexokinase to remain enzymatically active and catalytically efficient.

Extreme heat (hyperthermophiles): increased STABILITY in tertiary structure (more beta-pleated sheets) of hexokinase to maintain structure and not denature.

Question 22

Basic structure of a phospholipid (what is hydrophobic and what is hydrophilic) consequences of introducing a C-C double bond.

Answer 22

A phospholipid is fomed of a hydrophilic (substance attracted to water) phosphate head and hydrophobic (substance repelled by water) fatty acid tails. Introducing a C-C double bond desaturates the hydrocarbon tails and introduces a kink.

Question 23

Basic characteristics of molecules that can easily diffuse across a membrane and those that cannot (Figure 4.13)

Answer 23

Membranes are selectively permeable:
- Non-polar molecules (soluble in the lipid bilayer) and small, uncharged polar molecules can pass through the diffuse through a membrane
- Large, uncharged polar molecules and ions cannot

Charge and size impede transfer across membrane.

Question 24

The secretory pathway (components of it…and what goes through it)

Answer 24

The secretory pathway refers to the endoplasmic reticulum, Golgi apparatus, and vesicles that travel between them AND the cell membrane and lysosomes. This pathway processes proteins that will be membrane-bound and other proteins that live their lives in the secretory pathway.*

Question 25

Protein targeting to the ER and the role of the signal sequence and signal recognition particle SRP.

Answer 25

Proteins are targeted to the ER. Ribosomes are free floating in the cytosol. 1) The ribosome starts to **translate** and a **signal peptide is produced**. 2) **Translation** is then **arrested**. 3) The **SRP** (signal recognition particle) recognises the signal pepide and **pulls the signal peptide and ribosome** to a translocation complex on the **ER**. 4) The **signal peptide** is **removed** and **translation resumes**. 5) Once the protein is produced, the **ribosome detaches** again and returns to free floating in the cytosol.

Question 26

Basics of simple and facilitated diffusion. (Textbook outcome....what is the property of molecules that can move by simple diffusion).

Answer 26

Simple diffusion - for molecules that **pass right through the membrane** (**small and uncharged**) thanks to a difference in the concentration gradient. Facilitated diffusion - for molecules that need a **pore/channel to shield** the transported molecule from the hydrophobic fatty-acid core of the membrane. The property of molecules that can move by simple diffusion: **ENTROPY**.

Question 27

Transport against a concentration gradient (active transport).

Answer 27

To transport molecules against the gradient, we must use **active transport with an ATP-binding cassette (ABC) transporter**.

Question 28

Linking transport with free energy change (delta G)....what drives transport..think about this one.

Answer 28

Simple and facilitated transport are driven by **ENTROPY**. The **difference in concentration gradient (order vs. disorder)** causes the movement of ions and molecules from one side of the membrane to the other.

Question 29

Basic structure of ABC transporter. What does each component do?

Answer 29

An ABC transporter is made up of a **transmembrane domain** (much **variety** betwen ABCs) and an **ATP-binding domain** (highly **conserved**).

Question 30

Given the primary sequence of a protein YOU CAN determine if its an Integral membrane protein...HOW?

Answer 30

You can make a prediction based off on whether the amino acids in the protein are integral membrane proteins, since the **20~ amino acids** that interact with the membrane tend to be **hydrophobic**. On a hydropathy plot, these show up as **peaks of hydrophobic activity**.

Question 30

How can a pore/channel be specific for certain molecule (e.g. aquaporin)

Answer 30

The specificity comes from the **shape and charge interactions** of the channel. The protein folds in such a specific way and has such unique charge interactions that it will only work with that specific substrate.

Question 31

Cystic fibrosis and the function of CFTR

Answer 31

CFTR, an ABC-transporter, is mutated in individuals with cystic fibrosis. The **deletion of phenylalanine at position 508** alters the entire primary structure of CFTR and causes the conformational shape (tertiary structure) of CFTR to change. CFTR **pumps Cl- out of the cell** and causes the osmotic movement of water out of the cell (through aquaporin), which is **necessary for lung function** (requires water to coat the cilia of the epithelial lining for the coughing up of mucus, debris trapping, infection prevention, and gas exchange). In people with CF, Cl- builds up inside the cell, such that **water cannot be pumped out** and **cilia dries out**. Patients experience an **increased rate of infection and difficulty breathing**.

Question 32

Fate of the ΔF508 form of CFTR

Answer 32

Using Western blotting, we see that the prevalence of CFTR in WT and ΔF508 form, we see that there's hardly any for the ΔF508 form on the plasma membrane, but the same prevalence on the ER. The **ΔF508 form of CFTR never leaves the ER** and is instead **degraded and discarded into the proteosome**. *signal peptide/secretory pathway*

Question 33

Experiment showing the deltaF508 form is actually functional.

Answer 33

With an **artificial lipid vesicle** encasing Cl- (created in Cl- solution), express a ΔF508 form of CFTR on the lipid membrane and add it to a buffer solution with a Cl- deficit. Cl- can be detected outside the cell. **ΔF508 form can pump Cl-**, maybe only 20%, but still **enough to prevent patients from having CF**.

Question 34

Role of chaperone proteins (HSP90) in folding of deltaF508 form and wildtype

Answer 34

The ΔF508 form **does not pass the ER quality control **system, where chaperone proteins, like HSP90, detect misfolding and send the ΔF508 form to be **degraded in the proteosome**.

Question 35

Relationship of fatty acid saturation levels on membrane fluidity

Answer 35

At **low** temperatures, organisms intentionally enzymatically **introduce double-bonds (kinks)** to the hydro-carbon tails to **increase fluidity** (unsaturated hydrocarbon tails). At **high** temperatures, organisms' membranes are sufficiently fluid without unsaturated fatty acid tails, so their **hydrocarbons are saturated**.

Question 36

Relationship of temperature on membrane Fluidity.

Answer 36

If membranes are **too fluid**, as a result of high temperatures, **too much ion transfer** occurs and the **membrane falls apart**. If the membrane is **not fluid enough**, as a result of low temperatures, **electron transport stops**.

Question 37

Importance of maintenance of proper fluidity for processes such as import/export, electron transport.

Answer 37

Too **high** fluidity results in **excess import/export**. Too **low** fluidity impedes **electron transport**.*

Question 38

Properties of saturated vs. unsaturated fats

Answer 38

**Saturated** fats are **linear** hydrocarbonds fully saturated with hydrogens. **Unsaturated** fats have C=C double bonds and results in **kinks**.

Question 39

Role of desaturases in fatty acid biosynthesis.

Answer 39

Desatures act on fatty acids to **introduce kinks** or double bonds to the hydrocarbon. Temperature REGULATES desaturase expression.

Question 40

Relationship of bacterial desaturase expression vs. temperature.

Answer 40

As **temperature increases**, bacterial **desaturase** expression **decreases**, since it does not need to enzymatically desaturate hydrocarbons to artificially increase fluidity.

Question 41

So given your, now extensive, understanding of the biochemical basis of cystic fibrosis....if you ran a research laboratory, what do you think would be a promising avenue of research to head down? Let's go to the Forum and chat on this.

Answer 41

Messing with the ER to allow the delta form to pass through the quality control system