Chapter 3- biochem basics CLASS 1 Flashcards
(59 cards)
1
Q
kinetic energy
A
- energy for the movement of molecules
2
Q
potential energy
A
- energy stored in chemical bonds
3
Q
1st law of thermodynamics
A
- law of conservation of energy
- states energy in the universe is constant
ex. if energy in system decreases, them energy in universe increases
4
Q
2nd law of thermodynamics
A
- disorder (entropy) in the universe tends to increase
- therefore, we want spontaneous rxn bc they increase the disorder in the universe
- entropy= S
5
Q
Change G<0
A
- spontaneous rxn; energetically favourable
- more kinetic energy, than potential energy (change H)
- what we want (for 2nd law)
6
Q
Change G>0
A
- non spontaneous rxn
- more potential than kinetic
- needs an energy input
7
Q
Change G= 0
A
- equilibrium
- Potential and kinetic are equal
8
Q
Gibbs free energy(change in G) determines_________
A
- if reactants will stay or be converted into products
- tells us if the rxn will go
- does not tell the rate/ how long the rxn will go
- does not tell the pathway a rxn will take
9
Q
Exergonic
A
- negative change in G
- energy exits the system
- occur without the input of energy
10
Q
Endergonic
A
- Positive change in G
- only happens when there is an input of energy into the system
11
Q
Exothermic
A
- Negative change in H/ enthalpy
- release heat
12
Q
Endothermic
A
- Positive change in H/ enthalpy
- require an input of heat
13
Q
system always moves towards___________
A
- lower free energy state
- negative change in G
14
Q
endergonic and exergonic pairing (reaction coupling)
A
- pair exer with ender rxn, in order to have a negative change in G, and therefore for rxn to go
- so thermodynamically unfavourable reactions in the cell can be driven forward
- possible bc free energy changes are additive
15
Q
ATP hydrolysis
A
ATP>< ADP+P
- inputting water in order to break the polymer into it’s monomers
- exergonic ^ negative change in G
(-)57kJ/mol or (-)12kCal/mole
- veru favourable, often used in rxn coupling bc it is favourable
16
Q
Kinematics
A
- study of reaction rates
17
Q
Transition State
A
- intermediate bw the the reactants and the products
- short/ transient
- high energy needed to produce TS
- unstable state where molecule is deformed/ bent
18
Q
Energy of activation (Ea)
A
- energy to produce the transition state
- allows molecules to reach the TS
- prevents many rxn from proceeding even if Change in G is negative
- difference bw the TS and R/P= Ea
19
Q
Ea and rate
A
- increase in Ea, causes a decrease in rate of rxn (bc molecule has to climb a higher hill)
- Decrease in Ea. causes an increase in rate of rxn
- (+) value
20
Q
Catalysts
A
- speed up the reaction by lowering the Ea ^ lowering the TS
- stabilizes TS
- ex. enzymes
- does not affect the change in G (equilibrium)
- only changes the rate of rxn
21
Q
3 defining characteristics of enzymes
A
- must increase the rate of reaction
- must no be used up the in reaction (recycled)
- specific for a particular reaction
22
Q
Phosphorylation
A
- used to regulate enz activity
- binding phosphate to the enzyme and causes a conformational change in the active site in order to bind or not bind the S
- turns the enzyme on or off
23
Q
Allosteric Site
A
- used to regulate enz activity
- allosteric regulators bind to a site (that is not the active site)
- turns enz on or off
- allosteric inhibitors and allosteric activators
- causes conformational change in the active site
24
Q
Negative feedback
A
- used if have to much of something
- last product of the pathway (too much), will inhibit the first unique and committed step ( the first enzyme)
- therefore that last product will be produced less
- acts as an allosteric inhibitor for the first enz
25
Positive feedback
- used if have not enough of something
- last product (not enough) will go to the firsy unique and committed step (the fist enzyme)
- therefore the last product will be produced more
- acts as an allosteric activator for the first enz
MUST HAVE AN EXTERNAL REGULATOR BC IT CANNOT STOP ITSELF AND WILL CONTINUE TO MAKE THE PRODUCT
26
27
what does Vmax depend on
- constant
- depends on...
1. enzyme concentration
2. the specific enzyme you are using
28
Km
- substrate concentration to reach 1/2 Vmax
29
when increase affinity what happens to Km?
- Km decreases bc if the enz has a higher affinity for S, won't need as much S to get to 1/2 V max
- enz will take up more S
30
Enzyme Inhibition
- Lowers product formation
- is reversible
31
Competitive Inhibition
- bind to the active site
- Vmax= the same
- Km= increased bc affinity for the S has decreased
- overcome by increasing substrate concentration
32
Uncompetitive Inhibition
- binds to allosteric site of ES complex
- V max= decreased
- Km= decreased
- Km has decreased bc affinity for S has increased, in order to make more ES complex
33
Non competitive inhibition
- binds to E alone at allosteric site. does not change shape of active site
- Vmax= decreased
- Km= same
34
Mixed inhibition
- binds to: 1. allosteric site of E alone (which changes the shape of the active site)
2. ES complex
Vmax= decreases
effect on Km= decreased (ES complex)
or increased (E alone)
35
which Inhibitor is each
black- no I
purple- Competitive I
red- Uncomp I
green non comp I
36
On the Lineweaver Burk plot, which inhibitor is each line
black- no I
purple- comp I
green- non comp I
red- umcomp I
- double reciprocal plot
- increase in Km towards the origin
- decrease in Vmax away from origin
37
entropy vs enthalpy
entropy (S) and has to do with disorder, randomness
enthalpy (H) and has to do with bond energy and heat
38
value of change in G depends on
- concentration of products and reactants
39
equilibrium
- point where the rate of rxn in the forward direction equals the rate of rxn in the reverse direction
- concentrations of products and reactants are constant, but not necessarily equal
- use Keq for ratio at equilibrium
40
equilibrium goes towards the_________
- lower energy state
- look at Keq. for ex. if Keq is large, therefore have higher concentration of products, and the equilibrium is towards the products. Which also tells that the products have the lower energy state
41
photosynthesis
- process which plants store energy from the sun in the bond energy of carbohydrates
42
photoautotrophs
- plants
- use energy from the sun (photo) to make their own food (auto)
43
Chemoautotrophs
- humans
- use energy of chemicals (chemo) produced by other living things (hetero)
44
ATP
- energy source that drives energetically unfavourable reactions
- used to store energy or to make energy storage molecules like glycogen or fatty acids
45
Oxidation
- LEO
- loss of electrons
- loss of hydrogen atoms
- gains oxygen atoms
46
Reduction
- GER
- gains electrons
- gain of hydrogen atoms
- loss of oxygen atoms
47
one atom gets reduced and the other is oxidized=
redox pair
48
Catabolism
- breaking down molecules
49
Anabolism
- building up molecules
50
Bronsted Lowry Acids are proton________
- donors
- proton= H+
51
Bronsted Lowry Bases are proton_________
- acceptors
- proton= H+
52
Lewis acids are_________
- electron pair acceptors
53
Lewis Bases are__________
- electron pair donors
54
Conjugate base
- when an bronsted lowry acid donates a H+, the remaining structure is a conjugate base
- diff bw the acid and conjugate base is that the base is missing an H+
55
Conjugate acids
- when a bronsted lowry base accepts a H= the remaining structure is a conjugate acid
- diff bw the base and conjugate acid is that the acid has an extra H+
56
Amphoteric
- substance can act like either an acid or base
57
pH scale measures__________ concentration
H+ (or H3O+) ions in solution
58
buffer
- solution that resists changing pH when a small amount of acid or base is added
- comes from presence of weak acid and its conjugate base ( or weak base and its conjugate acids) in roughly equal concentrations
- important bc biological processes in the human body are pH dependent
59
Bicarbonate buffering system
- imp buffer system in our blood plasma
