Lecture 4 - Bioenergetics

Question 1

what is bioenergetics

Answer 1

• subset of thermodynamics
• quantitative analysis of how the biological world gains and uses energy

Question 2

what do cells require energy for

Answer 2

• building macromolecules
• active transport
  -cell division
  -maintaining homeostasis

Question 3

first law of thermodynamics

Answer 3

• energy cannot be created or destroyed
• deltaE=deltaH

Question 4

is a reaction that releases heat the favored reaction for the biochemical reaction

Answer 4

• depends on deltaG value

Question 5

second law of thermodynamics

Answer 5

• in every physical or chemical change the universe always tends towards greater disorder or randomness
• entropy increases

Question 6

entropy

Answer 6

• measure of randomness or disorder
• entropy increases with less order (ice melts)
• deltaS is positive for every spontaneous process

Question 7

example of entropy in organisms

Answer 7

• entropy decreases when monomers are ordered into more complex molecules

Question 8

gibbs free energy

Answer 8

deltaG = deltaH - TdeltaS

Question 9

standard free energy change and equilibrium constant

Answer 9

deltaG = -RTlnKeq

Question 10

Hydrolysis reaction of ATP

Answer 10

• highly favorable (exergonic)
• tends toward a large ADP/ATP ratio at equilibrium

Question 11

What is homeostasis

Answer 11

• not equilibrium
• living cells are maintain themselves in states far from equilibrium
• maintain a steady state (dynamic steady state)
• the maintenance of dynamic steady state by regulatory mechanisms that compensate for external change

Question 12

how can an unfavored reaction proceed

Answer 12

• if coupled to an energetically favorable reaction

Question 13

what determines whether a reaction will go

Answer 13

• enzymes and ribozymes
• enzymes kinetics

Question 14

What are the 7 properties of enzymes

Answer 14

1. only required in small amounts
2. function at physiologically relevant temp and pH
3. aren’t irreversibly altered during the reaction - reusable
4. highly specific to their substrate
5. generate very specific product
6. can be regulated to meet the needs of the cell
7. change the rate not the thermodynamics of a reaction

Question 15

what is metastable state

Answer 15

• result of the activation barrier
• for most biologically important reaction the activation energy is high enough that the number of molecules that have enough energy to react is small
• if this wasnt the case we would all spontaneously burst into flames
• state in which reactants are thermodynamically unstable and dont have enough energy to exceed the activation barrier

Question 16

what is activation energy

Answer 16

• minimum amount of energy required by the reactants for reaction to proceed

Question 17

what is the transition state

Answer 17

• point at which weak chemical reactions between substrate and enzyme are at the stage where the reaction has an equal chance of going to product or back to substrate

Question 18

what is the role of catalysts and how do they act

Answer 18

• enhances the rate of reaction by providing a surface that allows reactants to be brought close together and lowering Ea

Question 19

how do enzymes reduce the activation energy to allow substrates to reach the transition state more efficiently

Answer 19

1. maintaining the precise substrate orientation
2. changing the substrate reactivity
   - r groups can influence the distribution of electrons within the substrate - increasing reactivity
3. exerting physical stress
   - conformational changes can exert a physical force on certain bonds destabilizing the substrate

Question 20

what is the active site of enzymes

Answer 20

• a cluster of amino acids
• region of the enzyme that binds substrate (and cofactor) and where catalysis takes place
• complimentary groove or pocket that accommodates the substrate with high affinity

Question 21

why are these amino acids common at active sites of enzymes: cysteine, serine, aspartate, glutamate, histidine, and lysine
why not ala or val

Answer 21

• they have reactive side chains
• act as acids or bases
• perform nucleophilic attacks
• ala and val side chains don’t participate in chemical reactions — they can’t donate or accept protons, or form covalent or ionic bonds.

Question 22

what is an apoenzyme

Answer 22

• enzyme not bound to its co-factor

Question 23

what is a holoenzyme

Answer 23

• enzyme found bound to its co-factor

Question 24

The active site takes up a relatively small part of the total volume of an enzyme so what’s the rest of the enzyme used for

Answer 24

1. support structure to allow the three dimensional creation of active site from primary sequence
2. regulatory sites
3. sites of interaction with other proteins
4. substrate channels

Question 25

what is the relationship between temp and enzymes

Answer 25

- at low temp the rate of enzyme activity increases with temp due to increased kinetic activity of enzyme and substrate molecule - beyond a certain point further increases in temp result in denaturation

Question 26

what is the relationship between pH and enzymes

Answer 26

- pH dependance is usually due to the presence of charged amino acids at the active site or on the substrate - pH changes affect the charge of such residues and can disrupt ionic and hydrogen bonds

Question 27

what are enzymes sensitive to

Answer 27

- factors such as molecules and ions that act as inhibitors or activators - ionic strength of the environment which affects hydrogen bonding and ionic interactions needed to maintain tertiary conformation

Question 28

what are enzyme kinetics

Answer 28

- describes the quantitative aspects of enzyme catalysis and the rate of substrate conversion into products

Question 29

what are reaction rates influenced by

Answer 29

- concentration of substrates, products and inhibitors

Question 30

what are some ways to regulate enzyme activity

Answer 30

1. the amount of enzyme (protein) in a cell can be regulated by synthesis and degradation 2. cells can regulate protein activity by turning them on and off - inhibition, allosteric regulation, cleavage, phosphorylation 3. cells can regulate protein activity via localization - kinase localization, Ca2+ sequestration, receptor internalization

Question 31

what is competitive and non competitive inhibition

Answer 31

- competitive = inhibitor binds to active site preventing substrate from binding - non competitive - inhibitor binds to some other site on enzyme and changes the shape so substrate cant bind

Question 32

what is allosteric regulation

Answer 32

- regulation of an enzyme by binding an effector molecule at a site other than the enzymes active site - common in multi-subunit proteins and enzymes

Question 33

what is allosteric inhibition

Answer 33

- enzymes is active in uncomplexed form which has high affinity for its substrate - binding of an allosteric inhibitor stabilizes the enzyme in its low-affinity form - little or no activity

Question 34

what is allosteric activation

Answer 34

- enzyme is inactive in its uncomplexed form which has low affinity for its substrate - binding of an allosteric activator stabilizes the enzyme in its high affinity form resulting in enzymes activity

Question 35

what is the relationship between binding site and ligand

Answer 35

- ligand binds to a specific binding site on an enzyme - can be reversible or irreversible

Question 36

why isnt homeostasis equilibrium

Answer 36

- equilibrium is no net change - static balance with no energy required - homeostasis requires continuous input of energy and active control mechanisms (like feedback loops). - actively maintaining balance