Lecture 8 - Bioenergetics & Enzymes

Question 1

def: no net fixation of carbon into organic compounds

Answer 1

chemoheterotrophs

Question 2

def: a subset of thermodynamics, the quantitative analysis of how the biological world gains and uses energy

Answer 2

bioenergetics

Question 3

where do chemotrophs get their energy from?

Answer 3

oxidizing metabolic fuels

Question 4

what are catabolic metabolic pathways?

Answer 4

oxidative reaction sequences that result tin the transfer of electrons away from carbon

Question 5

how many oxidation states does carbon have?

Answer 5

5

Question 6

what is the most highly oxidized form of carbon found in living organisms?

Answer 6

carbon dioxide

Question 7

in carbon hydrogen bonds, how are the electrons shared?

Answer 7

the more electronegative carbon owns the two electrons shared with hydrogen

Question 8

in carbon oxygen bonds, how are the electrons shared?

Answer 8

electron sharing is unequal in favour of oxygen

Question 9

T or F: entropy decreases when monomers are ordered into more complex molecules

Answer 9

true

Question 10

what relates changes in enthalpy and changes in entropy?

Answer 10

Gibbs Free Energy

Question 11

a reaction can occur spontaneously only if deltaG is ________, thus the process is _______-

Answer 11

negative, exergonic

Question 12

a reaction cannot occur spontaneously if deltaG is ________, thus the process is _________

Answer 12

positive, endergonic

Question 13

what is deltaG when the system is at equilibrium?

Answer 13

0

Question 14

what is the deltaG of the cellular environment?

Answer 14

-11.5 kcal/mol

Question 15

def: the ratio of product concentration to reactant concentration at equilibrium

Answer 15

equilibrium constant

Question 16

is homeostasis equivalent to equilibrium?

Answer 16

No!

Question 17

what is a better term for the steady state in which a cell holds itself?

Answer 17

dynamic steady state

Question 18

def: the maintenance of dynamic steady state by regulatory mechanisms that compensate for external changes

Answer 18

homeostasis

Question 19

______ and ________ catalyze virtually all cellular processes and reactions

Answer 19

enzyme and ribozymes

Question 20

what are the 7 properties of catalysts?

Answer 20

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

Question 21

def: state in which reactants are thermodynamically unstable but do not have enough energy to exceed the activation energy barrier

Answer 21

metastable state

Question 22

def: the minimum amount of energy required by reactants before collisions between them will lead to product formation

Answer 22

activation energy (Ea)

Question 23

def: the precise 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

Answer 23

transition state

Question 24

T or F: if reactants can be bound on a surface and brought closer together, their interaction will be favoured and the required Ea will be reduced

Answer 24

treu

Question 25

a _______ enhances the rate of a reaction by providing a binding surface and effectively lowering Ea

Answer 25

catalyst

Question 26

what are 3 ways enzymes reduce the activation energy?

Answer 26

1. maintain precise substrate orientation 2. change the substrate reactivity (influence the distribution of electrons) 3. exert physical stress (conformational change = destabilizing bonds)

Question 27

def: characteristic cluster of amino acids on every enzyme, region of the enzyme that binds substrate (and cofactor)

Answer 27

active site

Question 28

the active site is usually a __________ _______ ___ ________ that accommodates the substrates with high affinity

Answer 28

complimentary groove or pocket

Question 29

what does the active site contain?

Answer 29

residues that directly participate in the making and breaking of bonds

Question 30

which amino acids comprise the active site?

Answer 30

Cysteine (C) Serine (S) Aspartate (D) Glutamate (E) Histidine (H) Lysine (K)

Question 31

def: organic, participate in catalysis, but not a substate, derived from vitamins, bind loosely

Answer 31

co-enzymes

Question 32

def: inorganic, help increase the rate of catalysis, often electron carriers, bind tightly

Answer 32

metals

Question 33

def: enzyme not bound to its co-factor

Answer 33

apoenzyme

Question 34

def: enzyme found bound to its co-factor

Answer 34

holoenyzme

Question 35

what are the 4 other purposes of the rest of the enzyme structure?

Answer 35

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

Question 36

what characterizes enzymes?

Answer 36

their sensitive to temperature and pH

Question 37

at low temperatures, how does the rate of enzyme activity change with temperature?

Answer 37

it increases with temperature due to increased kinetic activity of enzyme and substrate molecules

Question 38

beyond a certain point of temperature increase, what happens to enzymes?

Answer 38

they denature and lose enzyme activity

Question 39

most enzymes are active within a pH range of about ____ units

Answer 39

3-4

Question 40

pH dependence is usually due to the presence of ________ _____ ____ __ _____ ____ or on the substrate

Answer 40

charged amino acids at the active site

Question 41

pH changes affect the charge of such residues, and can disrupt ______ and _______ bonds

Answer 41

ionic and hydrogen bonds

Question 42

what are two other factors that enzymes are sensitive to?

Answer 42

1. molecules and ions that act as inhibitors or activators 2. ionic strength of the environment which affects hydrogen bonding and ionic interactions needed to maintain tertiary conformation

Question 43

what kind of bonding does substrate bonding involve?

Answer 43

usually hydrogen, ionic or both

Question 44

def: the quantitative aspects of enzyme catalysis and the rate of substrate conversion into products

Answer 44

enzyme kinetics

Question 45

def: discrete locally folded unit of the overall tertiary structure, usually with a specific function

Answer 45

domain

Question 46

T or F: proteins will similar functions often have completely different domains

Answer 46

false, they often share common domains

Question 47

proteins will multiple functions usually have a separate ________ for each function

Answer 47

domain

Question 48

what processes regulate enzyme concentrations in a cell?

Answer 48

synthesis and degradation

Question 49

how can cells regulate protein activity?

Answer 49

- inhibition - allosteric regulation - cleavage - phosphorylation - kinase localization - Ca2+ sequesteration - receptor internalization

Question 50

what are enzymes most influenced/inhibited by?

Answer 50

products, alternative substrates, substrate analogues, drugs, toxins, and allosteric effectors

Question 51

def: regulation of an enzyme by binding an effector molecule at a site other than the enzymes active site

Answer 51

allosteric regualtion

Question 52

what does binding of a regulatory ligand do?

Answer 52

change of a proteins conformation

Question 53

T or F: all covalent modification can be reversed

Answer 53

False, some can be reversed

Question 54

Phosphorylation/Dephosphorylation: Kinases _______ Phosphatases ________

Answer 54

Kinases phosphorylate Phosphatases dephosphorylate