APB - Unit 2 - Cell Structure and Function 4.0

APB - Unit 2 - Cell Form and Structure 4.0 #GoBioRams

Remember when we talked about enzymes a while back?

A bit of chemistry/physics

• Your textbook goes into a bit more depth, if you would like to review this but, for our purposes...

• Hopefully you understand that in order to go from point A to point B, you sometimes have to take many small steps in between.

• In other words, you need a biochemical pathway that you need to follow to get your result.

The importance of being able to read a biochemical pathway.

• 1- Don't get psyched out.

• 2- Look for either the word "start" or the beginning of the arrow.

• 3- Follow things step by step.

• You will see MANY biochemical pathways in the very near future since metabolic pathways explain a lot of what is going on inside an organism.

Ready?

BTW - My husband loves this stuff so much, in college, he had this poster on his wall and we still have it rolled up in storage. https://www.pathwayz.org/Tree/Plain/BIOCHEMICAL+PATHWAYS - Keep scrolling until you get to the bottom of the page.

What did you notice?

https://bio.libretexts.org/Bookshelves/

Biotechnology/Bio-OER_(CUNY)/09%3A_Genetics/

9.05%3A_Non-Mendelian_Genetics

This is a relative short biochem pathway.

• Even though there are only 2 steps, how can you increase the chances that these steps will happen in the order that they happen?

• What could you do?

Thermodynamics and Kinetics

• This is why we need to think about these two concepts so that we can apply them or understand how the organism tweaks so that things happen the way they should.

• For example, the organism can manipulate their body temperature.

Why do they hibernate?

What benefit does this give the animal?

Metabolism and life expectancy.

Metabolism and size

Temperature or Heat matters.
 $\Delta H\ =\ enthalpy$  

Disorder = Chaos = Entropy = Randomness

• If you don't "control" the amount of randomness, how can you guarantee a result?

• Do you really want all of your equations to be completely random?

Disorder = Chaos = Entropy

 $\Delta S\ =\ entropy$  

A spontaneous process

IF a given process occurs by itself and leads to an increase in entropy, that process can proceed without needing an input of energy.

Spontaneous process

https://chem.libretexts.org/

Bookshelves/General_Chemistry/

Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/

19%3A_Chemical_Thermodynamics/

19.1%3A_Spontaneous_Processes

Spontaneous process

https://chem.libretexts.org/

Bookshelves/General_Chemistry/

Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/

19%3A_Chemical_Thermodynamics/

19.1%3A_Spontaneous_Processes

Please watch.

Entropy = Chaos = Disorder = Randomness is not something that we usually think about but, as biologists, we have to think about it.

Note the math equation

 $\Delta G\ =\ \Delta H\ -\ T\Delta S$  

Equation will be provided.
You just substitute and calculate.

Be able to predict if a reaction is spontaneous.

 $\Delta G\ =\ \Delta H\ -\ T\Delta S$  

Equation will be provided.
You just substitute and calculate.

Entropy is a name changer.

• Why we no longer use endothermic but use endergonic.

• Why we no longer use exothermic but use exergonic.

• -thermic = heat while -gonic = energy

• Doesn't change their graphs, though, just the name.

Gibbs Free Energy

Yes, you need to watch this too just to make sure you got the concept of Gibbs Free Energy. This is how you will see this topic discussed at the college/university level.

High Energy Compound reactions

• ATP = A-P-P-P = triphosphate

• ADP = A-P-P = diphosphate

• ADP + P_i <--> ATP

• P_i = Inorganic Phosphate

• See Fig. 8.9 to 8.12 on pages 149 to 151

Look for the movement of the phosphates.

Remember

P_i = one phosphate that is ready to be attached while

P = one phosphate that is already attached.

Understanding what is going on with regards to Gibbs Free Energy and the need to move phosphates helps us understand the importance of enzymes.

• Catalysts with active sites for substrate(s)

• Induced Fit Model

• Please note that energy is not being shown in these next slides.

Look what happens to the $\Delta G$   on the next slide.

How to "control" enzymes?

• Don't forget about denaturation Fig. 8.16 on page 156.

• Some require helpers or cofactors.

• If the helper is an organic molecule, they are called coenzymes.

Cofactors

https://www.pathwayz.org/Tree/

Plain/ENZYME+COFACTORS

How to "control" enzymes?

• You could also stop its binding capabilities with inhibitors.

• Competitive inhibitors bind at the active site.

• Noncompetitive inhibitors bind somewhere other than the active site.

• Fig. 8.18 on page 156.

How to "control" enzymes?

• You could also have a group of enzymes grouped together = allosteric regulation.

• Activators

• Inhibitors

• Cooperativity

• Fig. 8.20 on page 158

How to "control" enzymes?

• Feedback inhibition

• See Fig. 8.21 on page 159

A review.

• We need to keep entropy in mind when thinking about biochemical pathways.

• Gibbs Free Energy equation - Know how to use it.

•  $\Delta G\ =\ \Delta H\ -\ T\Delta S$  

• Be able to predict, given calculations, if a reaction will be spontaneous.

A review

• Be able to "read" a biochemical pathway.

• Know how an enzyme works.

• Know about cofactors and coenzymes.

• Know about competitive inhibition vs. noncompetitive inhibition

A review

• Know about allosteric regulation.

• Know activators vs. inhibitors

• Know cooperatively

• Understand what a negative feedback loop looks like and how it works.

Next Up

Cellular Energetics - Cellular Respiration & Photosynthesis

Chapters 9 & 10