48 terms

Bio 4

Catabolic Pathways
- exergonic
-release energy by breaking down complex molecules into simpler molecules
Catabolic Pathways Example
ex. Cellular respiration
C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP
Anabolic Pathways
- endergonic
-use energy to build complex molecules from simpler molecules
Anabolic Pathways Example
ex. Synthesis of proteins from amino acids
First law of Thermodynamics
-energy can be transferred and transformed but not created or destroyed
-also called principle of conversion of energy
Second law of Thermodynamics
-every energy transfer of transformation increases the disorder (entropy) of the universe
~~much of the usable energy is converted to heat energy by cells
~~if there is a temp difference, heat flows from warmer location to cooler location
~~if no temp difference, heat will warm organism
~~loss of usable energy during energy transformation is entropy in universe
~~universe becomes more disordered because of random movement of molecules or atoms as a result of heat
the quantitative measure of disorder in a system.
free energy
-measures portion of a systems energy that can perform work when temp and pressure are uniform throughout the system, as in a living cell.
Equation: calculate change in free energy
^G = ^H - T ^S
~ ^G =change in free energy
~ ^H = change in total energy (enthalpy)
~ ^S = change in systems entropy
~~ T = absolute temp in Kelvins
spontaneous energy change reaction
only negative ^G
Exergonic Reactions
-net release of energy
~~ ^G positive, ^H positive, ^S negative
~~spontaneous reactions
~~the greater the decrease in free energy, the greater the amount of work that can be done
Exergonic Reaction Example
~~ex.- cellular respiration; polymers → monomers
C6H12O6 + O2 → 6CO2 + 6H2O + Energy (ATP)
Endergonic reactions
-absorbs free energy
~~ ^G positive, ^H positive, ^S negative
~~not spontaneous
Endergonic reaction Example
~~ex- photosynthesis; monomers linked → polymers
6CO2 + 6H2O →(sunlight) → C6H12O6 +O2
Adenosine Triphosphate
ATP 3 parts
-ribose (sugar)
-adenine (nitrogen base)
-3 phosphate groups bonded to ribose
bonds between_______
____phosphate groups broken by hydrolysis
~ one molecule of P leaves ATP → ADP +P
~ ATP + H2O → ADP + P
~ exergonic reaction, energy released
Regeneration of ATP
ATP regenerated by addition of P to ADP
~energy to regenerate ATP comes from exergonic breakdown reactions (catabolism) in the cell
~called ATP
~~~ couples exergonic to endergonic processes
~~~ working muscles recycles its entire pod of ATP in less than one minute
~~~~~ This turnover represents 10 million molecules of ATP consumed and regenerated per second per cell
~~~ ADP + P → ATP + H2O (endergonic)
~ chemical energy stored in ATP drives most cellular work
How ATP performs work
~when ATP hydrolyzed in test tube, release of free energy heats surrounding H2O
~shivering uses ATP hydrolysis during muscle contraction to generate heat and warm the body
~cell's work is powered by hydrolysis of ATP
~~ phosphate group transferred from ATP to some other molecule
~~~ this molecule is said to be phosphorylated
~~~phosphorylated molecule undergoes change and performs work
~ATP drives chemical work
~~ phosphorlyates glutamic acid that is converted to glutamine
~~ as work is done, phosphorylated molecules lose phosphate groups, which leaves ADP and P as products
~~ cellular respiration that replenishes the supply of ATP by powering the phosphorylation of ADP
activation energy
—energy required to change reactant (Ea) molecule so bonds can be reformed

~supplied in form of heat from surroundings
~~ bonds break when enough energy has been lost has been absorbed
~~ absorption of energy increases speed of molecules so they can collide more often
~~ thermal agitation of atoms make bond more like to break
How enzymes lower activation barrier (Ea)
-enzymes enable reactant molecules to absorb enough energy to reach transition state
-- enzyme cannot change ^G
-- enzyme cannot make endergonic reaction exergonic
-- enzymes can only speed up a reaction that would occur anyway
-- enzymes are selective in which reactions they catalyze
- reactant that enzymes acts on
~ enzyme binds to substrate to form an enzyme-substrate complex
~ enzyme converts substrate to product of reaction
enzyme + substrate →← enzyme substrate complex →← enzyme + product
Substrate Specificity of Enzymes
-reaction catalyzed by enzyme is very specific
-- specificity results from shape of enzyme
-- ex. Sucrase will only act on sucrose and will not bind to any other monosaccharides

- only a restricted area of enzyme binds to substrate called the active site
-- sometimes shape is changed slightly to allow enzyme to fit better to substrate: induced fit
Active Site of Enzyme's
-substrate held in active site by hydrogen and ionic bonds
-- once reaction is finished the product leaves active site
-- enzyme is unchanged and is available to catalyze another reaction
--enzymes can catalyze both forward and reverse reactions
-- enzyme always catalyzes reaction in direction of equilibrium
mechanisms used to lower activation energy
-. orient substrates correctly so reaction can occur
-. stress bonds so they can be broken
-. provide a microenvironment that is more conducive to reaction
-. enzyme may covalently bond with substrate
How certain conditions affect enzyme activity
- up to a point, rate of reaction increases with increasing temperature because substrates collide with active sites more frequently
-- above certain temp, bonds are disrupted and protein denatures
-- optimum temp for most human enzymes is 35-40 degrees C

~ PH
- optimal pH is 6-8 normally
- too acidic or too basic will denature enzyme
- exceptions
-- pepsin - pH 2; trypsin - pH 8

- non-protein helpers for enzymes during reactions
- if cofactor is an organic molecule - called coenzyme
- vitamins are coenzymes

~Enzyme inhibitors
- competitive inhibitors
-- chemicals that selectively inhibit action of enzyme by blocking substrates from entering active sites
--- reversible by increasing concentration of substrate so active sites become available
- non-competitive inhibitors
-- impede interaction by causing enzyme to change shape so substrate cannot bind to active site
-- toxins and poisons, such as Sarin, a nerve gas, or DDT, an insecticide
-- antibiotics, such as penicillin, which blocks active sites on the enzyme that bacteria use to make their cell walls
-- non-reversible
Allosteric regulation of Enzymes
Allosteric Regulation
1. change in enzyme shape due to non-competitive inhibition is example of allosteric regulation

2. allosteric regulation occurs when an effector molecule binds to a site other than the active site and this induces the enzyme to change shape

3. change in shape alters affinity of active site for substrate so rate of reaction is changed

4. effectors can influence form an enzyme takes
- binding of an inhibitor to a site other than active site can stabilize inactive form of an enzyme, making it less likely to convert to active form
- active form can be stabilized by the binding of an activator to another site on the enzyme

5. allosteric enzymes control metabolism
- ex - ATP binds to allosteric enzymes, which lowers their affinity for a substrate and inhibits their activity
- ex - ADP functions as an activator of the same enzyme
* allosteric reactions either activate or inhibit a reaction

6. Feedback Regulation
a. metabolic pathways is switched off by inhibitory binding of its end product to an enzyme that acts early in pathway
- ex. - ATP alloaterically inhibits an enzyme in an ATP-generating pathway
Redox Reactions=
(oxidation and reduction)
- transfer of electrons from one reactant to another which releases energy stored in organic molecules
- loss of electrons
- addition of electrons
Redox example
ex. Na + Cl → Na+ + Cl-
(Na) Becomes oxidized, loses electrons
(Cl) Gains electrons, becomes reduced
-Na is electron donor = reducing agent (loses energy)
- Cl is electron acceptor = oxidizing agent
not all redox reactions involve complete transfer of electrons from one substance to another, such as in reactions involving covalent bonds
ex. - CH4 and O2
- covalent bonds of CH4 are shared equally because electronegatvity is equal
- when CH4 reacts with O2 , CO2 is produced
- electrons end up further away from C and closer to O2 which is highly electronegative
- in effect, C has partially "lost" its shared electrons and CH4 has become oxidized; O2 has become reduced
- chemical energy released to do work

energy must be added to pull an electron away
- the more electronegative the atom the more energy required
- electron loses potential energy when it moves from led electronegative to more electronegative atom
examples of redox reactions
~ burner of gas stove- methane oxidized by O2
~gasoline combustion in car engine - redox reaction
Oxidation during cellular respiration
cellular respiration
- glucose (C6H12O6) oxidized to CO2
- O2 is reduced to CO2
- electrons lose energy during their transfer from organic compounds to O2
C6H12O6 + 602 → 6CO2 + 6H20 + energy
(C6H12O6) becomes oxidized
(602) Becomes reduced
Release of energy during cellular respiration
- organic compounds broken down in series of steps
-electrons stripped from glucose and travel with proton as a H+ atom
- H+ not transferred directly from O2
~ passed first to coenzyme, NAD+ (NAO+ is a derivative of the vitamin niacin)
~ NAD+ functions as oxidizing agent during cellular respiration
~ NAD+ receives 2 electrons and 1 proton which neutralizes its charge and it becomes reduced to NADH
~ NADH passes electrons to electron transport chain, which conducts them to O2 in series of steps
~ energy that is released is used to make ATP
Cellular respiration
- uses O2 and organic molecules to produce ATP, CO2, and H2O
Cellular respiration Equation
C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (ATP + heat)

-cells produce ATP through oxidation/reduction
3 stages of Cellular respiration
(1) Glycolysis
(2) Citric Acid Cycle (Krebs Cycle)
(3) Oxidative Phosphorylation
-occurs in cytosol
-anaerobic (does not require oxygen)
-decomposes glucose into pyruvate (10 steps)
-supplies electrons to electron transport chain
-produces NADH + 2 ATPs
Citric Acid Cycle (Krebs Cycle)
-takes place in mitochodria
-aerobic (requires oxygen)
-oxidizes pyruvate to CO2 (8 steps)
-supplies electrons to electron transport chain
-produces NADH + 2ATPs + FADH2
Oxidative Phosphorylation
-takes place in mitochondria
--Electron Transport Chain
---reduces O2 to H2O
---electrons transferred from NADH to first molecule on electron transport chain
---makes no ATP directly
---function is to break energy release into steps
---drives cellular work, such as ATP
---produces 34 ATPs
Totally- each time a molecule of glucose from food is broken down in cellular respiration how many ATPs are produced?
~~ 38 ATPs produced
Number of ATPs produced are inexact
(Range and reason)
-range of 36-38 (can be less)
3 reasons
1) Oxidative phosphorylation not directly coupled to each other, so ratio of NADH to ATP not a whole number
2) ATP yield varies depending on how electrons get from cytosol to mitochondria
3) force generated by redox reactions not always used solely for production of ATP
All cells can produce ATP without O2 (anaerobic)
-generated ATP by substrate-level phosphorylation
enzyme transfers phosphate group to ATP to make ATP
requires sufficient amount of NAD+
Types of Fermentation
(1) alcohol fermentation
-pyruvate converted to ethanol (2 steps)
-carried out by bacteria and yeast
-CO2 generated; ATP produced
-brewing, winemaking, baking (CO2 allows bread to rise)

(2) lactic acid fermentation
-pyruvate reduced by NADH--> lactic acid
-CO2 not produced; NAD+ produced
-used by fungi and bacteria to make cheese and yogurt
-humans produce lactic acid during strenuous exercise
--may cause muscle fatigue and pain
--lactic acid eventually converted back to pyruvate by liver cells
Cellular Respiration vs Fermentation
(1) Cellular Respiration
(a) aerobic
(b) produces 2 ATPs by harvesting chemical energy of food by glycolysis
(c) uses glycolysis to oxidize glucose to pyruvate
(d) NAD+ is oxidizing agent
(e) harvests more energy (19 times more ATP per glucose molecule ~~38 ATPs)

(2) Fermentation
(a) anaerobic
(b) produces 2 ATPs by harvesting chemical energy of food by glycolysis
(c) uses glycolysis to oxidize glucose to pyruvate
(d) NAD+ is oxidizing agent
total harvest of energy = 2 ATPs
Other Metabolic Pathways connected to Glycolysis and the Citric Acid Cycle *pgs 184-187
A. Catabolism
1. catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration
a) carbohydrates broken down by glycolysis in digestive tract
b) fats broken down to enter citric acid cycle to make ATP for energy

B. Biosynthesis (anabolism)
1. glycolysis and citric acid cycle convert some molecules into fats to be stored

C. Feedback Mechanisms
1. cellular respiration is controlled by allosteric enzymes at key points in glycolysis and citric acid cycle
2. as end products accumulate, the process slows down