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BIOLOGY 220 OUTLINE SECTION II Text: Essential Cell Biology I. Opening
Comments (Chapter 3) A. Life creates order out of disorder through a
never-ending series of chemical reactions B. This is Metabolism and the ability
to Metabolize C. Most of the chemical reactions required by the cell would not
occur at physiological conditions D. Control of these reactions is achieved by
specialized protein, ENZYMES. II. Basic Principles of Energy A. Energy - Basics
Principles 1. Define Energy - ability to do work 2. Define Work - the ability to
change the way matter is arranged 3. Define Kinetic Energy 4. Define Potential
energy - energy of position 5. FIRST LAW of THERMODYNAMICS Energy can be
transferred or transformed by never created or destroyed. 6. Explain transferred
or transformed Different kinds of energy a. Radiant (solar) b. Chemical (e.g.
gasoline, carbohydrates, fats) c.
Mechanical (involves movement) d. Atomic. 7.
SECOND LAW of THERMODYNAMICS - In any energy transformation or transfer some
energy is lost to the surrounding environment as heat. a. Define Entropy b. 2nd
Law says - ENTROPY IS INCREASING c. ADD HEAT LOSS TO ENERGY DIAGRAM ABOVE. B.
The Concept of Free Energy 1. Free energy - the portion of a systems energy that
can perform work given constant T throughout system (e.g., living cell) 2. Total
free energy of a system (G) is define by this equation G = H - TS a. H = total
energy of system = ENTHALPY b. T = absolute temp in K (KELVINS) ( C + 273) c. S
= entropy d. Note that T increases value of S since as Heat increases, molecular
motion increases, and disorder increases. 3. Spontaneous Processes a.
Definition
- occur w/o outside help (energy) - energy of system is sufficient to carry out
reaction or process b. Is not concerned with rate or time, so spontaneous
processes will not necessarily occur in a useful time frame 4. Determining when
a system can undergo spontaneous change a. Stability b. The change in Free
Energy is negative for spontaneous systems . G = Gfinal state - Ginitial state
or .DG = DH - TDS III. Basics of Chemical Reactions A.All reactions require an
input of energy to get them started 1. ENERGY OF ACTIVATION or ACTIVATION ENERGY
a. Define Activation Energy with overhead b. For some reactions the activation
energy can be provided by the reacting molecules themselves. c. For others, the
activation is very high since the reacting molecules must be brought together in
exactly the right orientation in order for the reaction to take place
(effective collision).. B.Enzymes reduce activation energy (Chap5. p. 167-69)
1. Define Catalyst 2. Define Substrate 3. Random interactions lead to
Enzyme-Substrate Complex formation (effective collision) 4. Enzymes reduce
activation energy by a. Increasing the number of effective collisions between
substrates 5. Enzymes are proteins a. review structure of proteins. 6. Define
Active Site a. Active Site can function by (1) shape similarities (2) chemical
attraction (3) both b. Example: Ribonuclease c. Review steps of RNAse active
site d.Another example: Lysozyme: pg.170 Figure 5-28 7. Discuss how enzymes are
named a. See Table 5-2 p.169 for list of common enzyme group names and
functions.. IV. Factors effecting Reactions (in general, including enzyme-mediated)(Back
to Chapter 3) A. Free energy considerations (as discussed earlier) 1. Free
energy change must be negative B. Concentration of the molecules in the system
also determines whether a reaction will occur. 1. As the concentration of one
molecule increases the reaction will move toward the production of the other
molecule (Le Chatlier's Principle).
C. BIG QUESTION - how much of a
concentration difference is required to overcome a .G that might be unfavorable.
1. Rewrite .G to reflect concentration component 2. .G = .G o + 0.616ln[B]/[A]
a. 0.616 is a constant b. .G o is the Standard Free Energy change (1M @ pH=7) in
kcal/mole c. @37 o C d. Note that when [A] = [B], concentration effects are
negated and .G=.G o (ln 1 = 0). D. For a reversible reaction A B (see Figure.
3-20 p.92) 1. One direction is energetically favored (-.G) over the other 2. For
example A to B is favored 3. As A converts to B, the concentration effect of
greater amounts of B begins to overcome the + G (for B A), to a point
where B A is equal to A B. 4. In Table 3-1 some calculations were done to
determine when .G=0 (equilibrium), that is when .G o = -0.616ln[B]/[A] (con't on
next page). 5. It is important to note that it requires significant excess of
the favored product (B) to push the reaction back to unfavored product (A). 6.
Enzymes do not change the equilibrium point.. V.Factors Affecting
Enzyme-Mediated Reactions A. Physical Parameters affecting Enzyme Activity (use
graphs) 1. Temperature 2. pH B. Concentration effects 1. Unlimited substrate in
the presence of limited enzyme a. Saturation kinetics b. where did we see this
before -answer: membrane transporters 2. Unlimited enzyme in the presence of
unlimited substrate. VI. Regulating Enzyme Reactions A. Competitive inhibition
1. Reaction rate is [substrate] dependent B. Non-competitive inhibition 1.
reaction rate is [substrate concentration] independent 2. Inhibitor binds at a
site other than active site 3. causes conformational change in enzyme - makes
active site unavailable C. Allosteric Control 1. allo = other steric = structure
or state 2. Like noncompetitive - Control Molecule binds at alternate site 3.
alternate site = allosteric site 4. Control Molecule called a REGULATORY
SUBSTANCE a. may increase or decrease activity.
5. Allosteric enzymes exist in 2
different states a. R(elaxed) state = high affinity for substrate b. T(ense)
state = low affinity for substrate 6. Binding of regulatory substance can induce
either state. a. Allosteric Inhibitor - binding causes T state b. Allosteric
activator - binding causes R state. 7. Allosteric enzymes and Reaction rate a.
Regulatory substances may have multiple binding sites. Leads to sigmoidal graph
of reaction rate b. For T to R state...enzyme activity is low until sufficient
regulator binds to convert enzyme completely to R state c. For R to T
state...enzyme activity is high until sufficient regulator binds to convert
enzyme completely to T state d. Regulator may be substrate or product. D.
Allosteric Feedback Inhibition 1. end product acts as regulator of 1st enzyme in
pathway 2. Discuss Threonine to Isoleucine pathway a. enzyme #1 = threonine
deaminase. E. Regulation by Covalent Modification 1. additions may include a. Ca
2+ b. PO4 - phosphorylation (1) Added by protein kinases (2) Removed by protein
phosphotases c. CH3 - methylation d. COCH3 - acetylation 3. binding can up or
down regulate enzyme. F. GTP-binding Proteins 1. Binding of GTP or GDP can cause
major conformational changes 2. Phosphorylation of bonded GDP and
Dephosphorylation of bonded GTP can also cause changes 3. Mode of action a.
Exchange of GTP and GDP b. Dephosphorylation of bound GTP 4. Exchange and
phosphorylation can have different rates a.
Control achieved by different rates
for different reactions b. See Figure 5-37 pg. 176. G. Ribozymes 1. RNA based
catalysts 2. Self splicing RNA molecules c. also show activity with some
proteins (1) removal of proteins from ribosomes (2) separation of amino acids
from tRNAs. H. Coenzymes 1. vitamins 2. minerals 3. Carriers a. Discuss coupled
reaction diagrams b. Electron Carriers (1) NAD (Figure 13-8) , & NADP (2) FAD
(Figure 4-12) (3) oxidized and reduced forms (4) show chemistry (5)
Dehydrogenase oxidizing enzymes (6) Reductase - reducing enzymes c. Function
as cofactors in redox reactions d. required by enzymes that are involved in
oxidations or reductions electron donors or receivers. I. ATP - universal
energy currency of the cell 1. Describe molecular structure a. nucleoside
triphosphate 2. Describe cycle ATP ADP + P a. .G 0 = -7.3 kcal/mole b.
Phosphorylation and its relationship to Redox 3. Energy required to make ATP or
Energy released from ATP hydrolysis depends on .G 0 and the relative
concentrations in the cell a. For some cells the ATP/ADP ratio approaches 1000
b. Under these conditions, the .
G for the hydrolysis of ATP to ADP can approach
11-13 kcal/mole (remember G equation includes a concentration factor). J.
Coupling Reactions to the Hydrolysis of ATP 1. The hydrolysis of ATP can be
linked to reactions with + G o Overall reaction: Glu +NH3 Gln .G 0 =
+3.4kcal/mole Step 1: Glu + ATP Glu-P + ADP .G 0 = -7.3kcal/mole Step 2: Glu-P
+ NH3 Gln .G 0 = +3.4kcal/mole NET .G 0 = - 3.9 kcal/mole. 2. Can also be
coupled to Dehydration reactions or almost any synthesis reaction that has a
+ G 0 3. If the desired product has a .G 0 * +7.3 kcal then the reaction
is broken down into steps.. K. ATP Production (Some coverage in Chap 13 p.409 -
410) 1. Substrate-level phosphorylation a. Direct enzymatic transfer of
phosphate group & energy to ADP from a high energy substrate b. low efficiency.
2. Chemiosmotic Phosphorylation MITCHELL THEORY a. Transfer indirectly through
proton gradient (1) electrochemical gradient (2) stored charge = ENERGY (3) high
efficiency achieved through step-wise transfer = ELECTRON TRANSPORT CHAIN b. 3
requirements for Chemiosimosis (1) Selectively Permeable membrane (2) H+ pumping
Enzymes (Active Transport) (3) ATP Synthase c.Introduce ATP synthase - enzyme
that captures energy from proton gradient and transfers it to ATP production -
Figure 13-3 & 13-13. c. Discuss charge separation and release of energy (1)
separate charges across insulator - Battery Analogy: Figure 13-11 (2) Create a
charge gradient across an insulator (3) CHARGE SEPARATION REPRESENTS STORED
ENERGY (4) Release Energy by allowing gradient to dissipate (5) In living cells,
charge separation achieved with different ion concentrations across membranes
(ION GRADIENTS) (6) ex. H+ gradient (7) Figure 13-15. 3.
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