Lecture 8-9

Question 1

Enzymes

Answer 1

Enzymes:
- speed up the rates of chemical reactions without need for increase in temperature
- difference between uncatalyzed rate and enzyme-catalyzed rate = removal of phosphate group
o In cell, group of enzymes called phosphatases catalyze removal of phosphate group (reversible process)
o This is a central mechanism of intracellular communication in all cells
 Without removal of phosphate takes approx. = 10 milliseconds
 In aqueous environment like cell, without enzyme, phosphate removal would take over 1 trillion years to occur
o On cold planet, evolution of enzymes = critical for evolution of life
- Key players in metabolic reactions (for characteristics of life eg. Responding to stimuli)

Question 2

Energy:

2 major types

Answer 2

Energy:
- Capacity to do work or be transferred as heat
- Exists in different forms (chemical, mechanical, electrical)
- Can be transformed from one form to another
- 2 major types of energy:
o Kinetic energy:
 Energy possessed by object b/c it is in motion
 Light, thermal
• Ex: flow of electrons, moving car
 Movement of kinetic energy: can perform work by making objects move
o Potential energy:
 Stored energy due to position or chemical structure
• Ex: dropping a rock off a cliff
 Chemical
 Molecules: potential energy = chemical energy, energy stored in bonds (interaction between negatively charged electrons vs positively charged nuclei)

Question 3

Thermodynamics:

Answer 3

Thermodynamics:

• Branch of science and how it changes during chemical and physical transformations
• System = objects being studied (atom, cell etc.)
• Outside of system = surroundings

Question 4

• 1st Law of thermodynamics

Answer 4

• 1st Law of thermodynamics
  o Energy can be transformed but not created or destroyed
  o Rock falling, possesses high potential energy but as it drops it loses EP and gains EK, EK is then transformed into heat, sound.

Question 5

• 2nd Law of thermodynamics:

Answer 5

• 2nd Law of thermodynamics:
  o Energy moved from being localized to being dispersed
  o Entropy of system and surroundings will increase, energy and matter will always become more spread out
  o Ex: heating a pan, heat is centralized to the pan but as it gets hotter, it disperses through the kitchen
  o Entropy: tendency of energy to disperse (chaos)
   Represented by S
   Measure of disorder or randomness
   Reason why machines aren’t 100 % efficient (energy loss to heat)

Question 6

Free energy:

-

Answer 6

Free energy:

- Spontaneous process: process that can occur without constant input of energy

Question 7

• Enthalpy:

Answer 7

• Enthalpy: head content of a system (deltaH)

o Molecule: enthalpy represents kinds of bonds existing between atoms

Question 8

• Endothermic:

Answer 8

• Endothermic: transformations resulting in a system taking up heat from surroundings
  o Products have more thermal energy than reactants
  o Overall change in enthalpy: Change in products H – change in reactants H

Question 9

• Exothermic: process releasing heat

Answer 9

• Exothermic: process releasing heat

o Products have less thermal energy than reactants = - change in H

Question 10

• Sources of Energy Biological Systems transform energy from:

Answer 10

-	Sources of Energy Biological Systems transform energy from: 
o	Light (photosynthesis) 
o	Catabolism (chemical breakdown) of organic and inorganic molecules

Question 11

• Change in enthalpy of a reaction

Answer 11

• Change in enthalpy of a reaction = important to evaluate likely hood of spontaneous reaction, 2 factors:
  o Reactions tend to be spontaneous if they are exothermic (products have less thermal energy than reactants)
  o Reactions tend to be spontaneous when entropy of products is greater than entropy of reactants (ex: C6H1206 + 6O2->6CO2 + 6H2O spontaneous reaction because exothermic and products have greater entropy, i.e more molecules exist on one side than the other)

Question 12

Free energy

Answer 12

portion of a systems energy that can perform work when temp is uniform through system

Question 13

• Spontaneous reaction:

Answer 13

• Spontaneous reaction: free energy of products is less than free energy of reactants.
  o Ex: diffusion of molecule across a membrane b/c of an increase in entropy

Question 14

• Exergonic process:synonym of spontaneous process

Answer 14

• Exergonic process: synonym of spontaneous process

Question 15

• Endergonic process:

Answer 15

• Endergonic process: a nonspontaneous reaction (change in G is positive)
  o Both exergonic and endergonic require activation energy (on graph seen as initial bump) (higher to lower concentration)

Question 16

sponteneity of reactions

Answer 16

reactions tend to be more spontaneous if products have less potential energy than reactants

Question 17

Equilibrium (maximum stability, ΔG=0) is reached when

Answer 17

Equilibrium (maximum stability, ΔG=0) is reached when reactants
are converted to products and products are converted back to
reactants at equal rates (not necessarily when concentrations are
equal)

Question 18

Life doesn’t go against second law of thermodynamics

- Living systems and surroundings appear to never increase in entropy

Answer 18

Life doesn’t go against second law of thermodynamics
- Living systems and surroundings appear to never increase in entropy
o due to organisms ability to maintain organized state with energy concentrated into complex molecules = this is b/c they are open systems using entropy and matter from surroundings to maintain low entropy state
o due to chemical reactions, organisms give off heat and via products of metabolism that spread out = increase in entropy or surroundings

Question 19

• Why do living systems keep consuming energy:

Answer 19

• Why do living systems keep consuming energy:
  o @ cellular level, tendency of energy to spread out = cellular components constantly break down
  o Continued synthesis of proteins acts like maintenance to cell
  o Living cells can never reach equilibrium (change in G = 0)
  o Light from sun = highly concentrated packs of energy known as photons
  o The biosphere is sustained by consumption of various forms of chemical energy produced by photosynthetic organism

Question 20

Metabolism:

-

Answer 20

Metabolism:

- Collection of all chemical reactions present within a cell

Question 21

• These reactions result in the break down of molecules that fall into 2 pathways

Answer 21

• These reactions result in the break down of molecules that fall into 2 pathways
  o Pathways requiring energy to build molecules
  o Those that release energy by breaking down molecules

Question 22

• Reactions that make up metabolism are…

Answer 22

• Reactions that make up metabolism are grouped into pathways (one reaction at a time)

Question 23

1. Catabolic pathway:

Answer 23

1. Catabolic pathway:
   a. Energy is released by breakdown of complex molecules to simpler compounds
   b. Free energy of final products in pathway is less than free energy of starting molecule
   c. Ex: cellular respiration (energy rich molecules converted into lower energy molecules

Question 24

2. Anabolic pathway:

Answer 24

2. Anabolic pathway:
   a. Consumes energy to build complicated molecules from simpler ones
   b. Results in the synthesis of larger more complex molecules from simpler molecules
   c. Also known as biosynthetic pathways
   d. These pathways require energy b/c free energy of products is greater than free energy of starting molecule
   e. Ex: photosynthesis

Question 25

- These pathways can be utilized together:

Answer 25

see word

Question 26

ATP Hydrolysis provides free energy

Answer 26

ATP Hydrolysis provides free energy | - ATP = energy currency of cell

Question 27

ATP

Answer 27

- Consists of 5 carbon sugar, ribose, linked to nitrogenous base adenine joined via three phosphate groups

Question 28

- ATP = source of free energy b/c of reaction with water (hydrolysis reaction)

Answer 28

- ATP = source of free energy b/c of reaction with water (hydrolysis reaction) o Terminal phosphate group is broken = formation of adenosine diphosphate and a molecule of inorganic phosphate o Energy is never released when bonds break = energy is required to break bonds, energy is released when new bonds form o ATP = negative G  Electrostatic repulsion between terminal phosphate and rest of molecule = small amount of energy is required to break down bond vs large amount of energy released when more stable products ADP and Pi are formed  Hydrolysis of ATP is spontaneous b/c of increase in entropy as energy is no longer localized to single molecule but two  Phosphorylation - ATP loses a Phosphate group through hydrolysis, donating the phosphate group to another molecule  All life uses ATP, evidence of common ancestor

Question 29

Energy Coupling Links the Energy of ATP breakdown to reactions -

Answer 29

Energy Coupling Links the Energy of ATP breakdown to reactions - ATP isn’t necessarily a hyperactive molecule (very low in aqueous environment)

Question 30

- If ATP = super active no be good

Answer 30

- If ATP = super active no be good o Impossible for metabolism to be controlled o Rapid hydrolysis of ATP = only release heat could result in cell death

Question 31

- Energy coupling: an endergonic reaction occurs when coupled with exergonic reaction

Answer 31

- Energy coupling: an endergonic reaction occurs when coupled with exergonic reaction o Energy is provided by exergonic breakdown of ATP o Reactions will occur so long as the combined ΔG of the two reactions is negative (will let us know its spontaneous) o Free energy from exergonic reaction not fully transferred to endergonic reaction (excess typically lost as heat) o Coupled Reactions typically require Enzyme catalysts  Facilitates movement of PE from molecule of ATP to substrate molecule through transfer of terminal phosphate group

Question 32

- Chemical reactions occur when bonds are broken and then formed

Answer 32

- Chemical reactions occur when bonds are broken and then formed o To be broken, bonds must be strained or made less stable: Activation Energy o Activation energy: initial energy required to start a reaction o Molecules that gain AE occupy transition state (where bonds are unstable)

Question 33

- Enzymes accelerate reactions by reducing AE and increase reaction rates

Answer 33

- Enzymes accelerate reactions by reducing AE and increase reaction rates o Heat is often used to speed rate of reaction = problematic high temps can result in cell death o How to do so safely?  Catalyst: Chemical agent that speeds up the rate of reaction without itself taking part in the reaction • Enzymes are catalysts o By lowering AE, more molecules would react o Enzymes don’t alter thermodynamics of a reaction o Change in free energy of a reaction isn’t altered by presence of enzyme o Enzymes don’t supply the energy, chemical energy typically supplied by ATP

Question 34

Enzymes combine with reactants and are released unchanged | -

Answer 34

Enzymes combine with reactants and are released unchanged - Enzymes combine with reacting molecules and are released unchanged - Reactant that an enzyme acts on is called enzyme’s substrate - Each type of enzyme catalyzes reaction for specific molecules - Substrate reacts with small portion of enzyme: this region is called active site (specific site on enzyme where catalysis takes place) - Enzyme folds into three-dimensional shape, flexible, changes shape so that active site can more thoroughly bind the substrate = induced fit hypothesis - B/c enzyme remains unchanged, can bind to other substrates and catalyze (known as enzyme cycle)

Question 35

Factors effecting enzyme activity: | -

Answer 35

Factors effecting enzyme activity: - Enzyme and substrate concentrations can change the rate of catalysis - Reactions proportional to enzyme concentration - Enzymes become saturated - Temperature and pH are key factors affecting enzyme activity. - Some enzymes need a cofactor (non-organic trace elements) or coenzyme (organic molecules like vitamins) to facilitate reaction. Enzyme activity can be altered by competitive and noncompetitive interactions - Metabolism is finely controlled by noncompetitive regulation - Principles of collision theory - Enzymes possess ideal states to avoid denaturing

Question 36

- Competitive Inhibition:

Answer 36

- Competitive Inhibition: molecules competes with substrate for active site o Presence of competitor decreases rate of normal substrate-dependent reaction o Molecules that have similar shape to the normal substrate. Competes to bind at the active site

Question 37

- Noncompetitive Inhibition

Answer 37

- Noncompetitive Inhibition o Inhibitor binds to the enzyme at a site AWAY from the active site, but changes the enzyme’s conformation. The active site no longer binds the substrate. o Controls how active cells are without having to produce more enzymes

Question 38

``` - Non competitive regulation • High affinity state: • Low affinity state: o Allosteric inhibitor: o Allosteric activator: ```

Answer 38

- Non competitive regulation  Decrease or increase in enzyme function  Reversible  Regulatory molecule binds with enzyme on allosteric site (location on enzyme outside active site) allosteric enzymes can have 2 states: • High affinity state: enzyme binds strongly to substrate • Low affinity state: enzyme binds to substrate weakly or not at all o Allosteric inhibitor: converts enzyme from high to low affinity state o Allosteric activator: converts enzyme from low to high affinity state

Question 39

- Feedback inhibition:

Answer 39

- Feedback inhibition: metabolic regulation that increases or decreases abundancy of product, where product of a reaction acts to inhibit own synthesis o Cellular resources are not wasted via high and low affinity states