BIO OUTLINE Essay, Research Paper
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. Jagendorf experiments -a. Knew of existence of pH differences within chloroplast
b. Review experiment with overhead
c. Experiment shows connection between H+ gradient, H+ flow, and phosphorylation of ADP to ATP.
4. Latest information on ATP Synthase
a. Still unknowns
(1) how it works so fast
(2) how it couples proton flow to ATP production
b. Background information on structure
(1) Figure 13-14
(2) 3 parts
(3) F0 – subunit – channel for protons
(4) F1 – subunit – catalytic subunit ?ATP production
(a) called ATPase
(b) uses ATP to pump protons
(5) Stalk – connects F0 to F1.
c. Latest info on structure of F1
(1) made of 6 subunits + ? subunit
(a) 3 ? subunits
(b) 3 ? subunits
(c) arranged in alternating fashion
(d) ? subunit contains catalytic activity
(e) ? subunit extends into stalk region
i) knife shaped protein.
d. Current theory of how it works
(1) H+ moving through F0 causes ? subunit to rotate
(2) knife edge contacts ? subunit
(3) ? subunit is deformed allowing for ADP & P binding,separately, to active site
(4) ? subunit releases contact
(5) ? subunit reformation brings ADP + P in contact and reaction takes place.
VII. PHOTOSYNTHESIS (Chapter 13 – p.430- 438)
A. Overview – Use ?Energy Flow through Living Systems? OH to put things in perspective.
B. Overall reaction
1. Radiant Energy + H2 O + CO2 ??O2 + Glucose
2. Balanced equation:
a. 6CO2 + 6H2 O + Radiant Energy ?? C6 H12 O6 + 6O2
3. Leaf structure
a. Epidermis
b. Spongy and Palisade Mesophyll
(1) Where photosynthesis takes place
c. Stomates.
4. Chloroplast structure ? EMPHASIZE ORGANIZATION
a. Outer membrane
b. Inner membrane
c. Stroma – Glucose production enzymes
d. Thylakoid membrane
(1) Light absorbing molecules or Photosystems
(2) Electron transport chain/Proton pumps
(3) NADP reductase
(4) ATP synthase
e. Thylakoid space or lumen ? proton reservoir.
C. Photosynthesis as a REDOX 2-step
1. REVIEW STRUCTURE
2. Energy capturing ? LIGHT DEPENDENT REACTIONS
a. Capture energy in the form of ATP and NADPH
b. Use electrons from oxidation of water
3. Energy storage ? LIGHT INDEPENDENT REACTIONS
a. Take energy from ATP and NADPH and use it to reduce carbon dioxide.
D. Light Dependent Reactions
1. Occur on thylakoid membrane
2. Discuss electromagnetic spectrum
a. Gamma, X, UV, Visible (380nm-750nm), IR, Micro, Radio
b. Violet, Indigo, Blue, Green, Yellow, Orange, Red
c. High energy, Short wavelength, High freq — Low, Long, Low.
3. Pigments
a. Imbedded in the thylakoid membrane
b. All have hydrophobic tails anchored in thylakoid membrane
c. Chlorophylls (a & b) ? Mg 2+ Center ?Figure 13-30
d. Carotenes – pure hydrocarbons ?aromatics rings linked by polyunsat?d chain
e. Xanthophylls – as above w/ alcohols on rings
f. Draw absorption spectrum on board.
4. Light Energy Absorption
a. achieved by pigment molecules
b. Excitation event & excitation energy (see Figure 13-32)
(1)electrons at ground state (inner orbital) ?excited? by photon of light to
excited state (outer orbital)
(2) can remain in this state for only a billionth of a second
c. Possible fates of excitation energy
(1) If excited electron returns to ground state ? FLUORESCENCE + heat
(2) Excited electron is picked up by stable acceptor molecules. excited electron is transferred to stable orbital of the same energy level (Figure 13-32)
(a) Light energy converted to chemical energy.
(3) Inductive transference
(a) energy is transferred to adjacent pigment molecule
i) vibration of excited e – sets up electromagnetic field.
ii) adjacent e – in equivalent orbitals begin to vibrate in resonance
iii) energy is transferred.
(b) little or no loss of energy.
5. Capturing and Converting Light Energy to Chemical Energy
a. Photosystems (see Figure 13-31 for general diagram)
(1) Photosystem I
(a) 110 chlorophyll a + 16 – bcarotenes = CORE ANTENNA
(b) Reaction Center = special chlorophyll a molecule: P700 (700 refers to light absorbing properties @ 700nm)
(c) Energy is absorbed by Core Antenna and passed by inductive resonance to P700 then to 1? acceptor.
(2) Photosystem II
(a) 40 Chlorophyll a + ** b carotenes = CORE ANTENNA
(b) Reaction Center = special chlorophyll a molecule: P680
(3) Energy is absorbed by Core Antenna and passed by inductive resonance to P680 then to 1? acceptor
b. Light Harvesting Complexes (Not shown in Alberts diagrams)
(1) One associated with each PS
(2) Designated LHC I and LHC II
(3) Collections of pigment molecules imbedded in thylakoid membrane
(4) In close physical proximity if not physically attached to PS?s
(5) Funnel excitation energy to reaction centers via inductive resonance.
USE PHOTO REVIEW HANDOUT W/ EXPLANATION BELOW
6. Non-Cyclic electron Photophosphorylation (Figure13-34 = Z Scheme with electron volt ratings)
a. The players
(1) Mn -center – Water Oxidizing Enzyme
(2) LHC II & PS II
(3) Plastoquinone ? e- carrier ?aromatic ring w/ long chair hydrocarbon ?not attached to PS II
(4) Cytochrome b6 – e- carrier ?Heme (Fe) containing protein Fe2+ ? Fe 3+
(5) Cytochrome f.
(6) PROTON PUMPING IN PS II
(a) b6+f complex = H+ pump
(b) Sets up H+ gradient between Stroma and Thylakoid lumen
(c) H+ pumped from stroma into lumen
(d) Flow out through CF0CF1 ? ATPase imbedded in thylakoid lumen.
(e) Make ATP in Stroma
(7) PC = e- carrier – plastocyanin ?
(a) Cu containing protein: Cu+ ? Cu2+
(8) electrons are passed to PS I
(9) Ferrodoxin – Fe/S center ?mobile – not attached to PS I
(10) NADP+ Reductase ? use electrons to reduce NADP+ to NADPH.
7. Cyclic Photophosphorylation
a. electrons pass from Ferrodoxin to cytochrome b6
b. only produces ATP
c. may be used to produce the additional ATP needed to drive glucose production (~3:2 ATP:NADPH).