AP Bio Ch 8, 9, 40, 10 (Unit 7)

Metabolism

totality of an organism’s chemical reactions is called metabolism; is an emergent property of life that arises from orderly interactions between molecules

metabolic pathway

begins w/ a specific molecule and ends w/ a product; each step catalyzed by a diff enzyme

Catabolic pathways

metabolic pathways that release energy by breaking down complex molecules to simpler compounds (ex: cellular respiration, digestion)

Anabolic pathways

consume energy to build complicated molecules from simpler ones (ex: photosynthesis)

Energy

capacity to cause change

Kinetic energy

energy associated w/ motion of objects

Thermal Energy

kinetic energy associated w/ random movement of atoms or molecules

Potential energy

energy that matter possesses bc of its location or structure; stored energy gravitationally

Chemical energy

potential energy available for release in a chem rxn; stored energy in a bond that can be released

Thermodynamics

tudy of the energy transformations that occur in a collection of matter

Bioenergetics

study of how energy flows through living organisms; system is the matter under study; rest of the universe, everything outside the system, are the surroundings

isolated & Open Systems

An isolated system is unable to exchange either energy or matter with its surroundings. In an open system, energy and matter can be transferred between the system and its surroundings.

1st Law of Thermodynamics

energy of the universe is constant; energy can be transferred and transformed, but never created or destroyed; AKA principle of conservation of energy

Entropy

a measure of molecular disorder, or randomness, as a result of lost heat during every energy transfer or transformation; there is a tendency to disorder, need energy to counteract

2nd Law of thermodynamics

during every energy transfer/transformation, some energy is unusable and is often lost as heat, increasing the entropy of the universe

Spontaneous process

leads to an increase in entropy, no energy needed (energetically favorable); can be fast or slow

Nonspontaneous processes

leads to a decrease in entropy; requires energy input

Free energy of a system

portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

Change in free energy

△G during a process is related to change in enthalpy - change in total energy △H - change in entropy △S, and temperature in Kelvin; △G is negative for spontaneous processes; processes w/ 0 or positve △G are never spontaneous

Exergonic Reaction

proceeds with a net release of free energy and is spontaneous (“energy outward”, downhill reaction);

Endergonic

absorbs free energy from its surroundings (uses E); stores free energy in molecules (G increases), △G is positive; are nonspontaneous reactions (uphill reactions)

Rxn Equilibrium

rxns in a closed environment eventually reach equilibrium and can no longer do work; cells are open systems that have a constant flow of materials, never reach equilibrium

Chemical, Transport, and Mechanical Work

Chem: pushed endergonic rxns (building up molec); Transport: pumping substances against the direction of spotaneous movement (active transport); Mechanical: muscle contraction moving things in a cell or cell movement itself

Energy Coupluing

use of an exergonic process to drive an endergonic one, mediated by ATP; overall, the coupled rxn is exergonic; ATP drives rxns by phosphorylation, adding a P group to other molec

ATP

adenosine triphosphate; cell’s energy shuttle, short term exogenoic to endergonic; composed of ribose sugar, adenine, & 3 phosphate groups; E relased by hydrolyzing high E bonds at terminal phosphate; high E becuase its a cloud of negative P groups, chem change from high to low E state, forms ADP & inorganic phosphate

Phosphorylation

addition of a phosphate group

Phosphorylated Intermediate

recipient molecule of inorganic P from the breakdown of ATP to ADP & inorganic P; in transport & mechanical work, it changes protein shape

ATP Cycle

renewable resourcer that is regenerated by addition of a P group to adenosine disphosphate (ADP); E to phosphorylate ADP comes from catabolic rxns; ATP + water to ADP + inorganic P, constant cycle

Catalysts & Enzymes

chem agent that speeds up a rxn w/out being consumed by the rxn; enzymes are catalytic proteins

Activation Energy

initial investment of energy for starting a reaction—the energy required to contort the reactant molecules so the bonds can break; used to control rxns; heat used in rxns but not in an organism

Catalysis

enzymes or other catalysts that speed up specific rxns by lowering the activation E; do not affect change in free E, instead they hasten rxns that would occur eventually

Enzyme-Substrate Comples

substrate is the reactant that an enzyme acts on, active site is region on enzyme where substrate binds; enzyme binds to its substrate and forms enzyme-substrate complex; while bound, the enzyme activity converts the substrate to a product; specificity is due to complementary fit & shape

Induced Fit Model

substrate enters active site, enzyme changes shape slightly due to interactions between the substrate’s chem groups & chem groups on the side chains of the amino acids that form the active site

How Active Site lowers Activation Energy

orienting substrates correctly, straining substrate bonds, providing a favorable microenvironment, and covalently bonding to the substrate

Saturated Enzyme

rate of enzyme-catalyzed rxn is sped up by increasing substrate concentration; concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged, only way to speed it up more is adding more enzymes

Enzyme Conditions

temp, pH, chemicals

Cofactors

adjuncts that are nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins; general (zinc, iron, and copper in ionic form)

Coenzyme

an organic cofactor; specific (vitamins)

Competitive inhibitors

reversible inhibitors that resemble the normal substrate molecule and compete for binding into the active site with the substrate

Noncompetitive inhibitors

do not directly compete with the substrate to bind to the enzyme at the active site, they impede enzymatic reactions by binding to another part of the enzyme and changing the shape, making the active site less effective

Allosteric Regulation

term used to describe any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site; can inhibit or stimulate enzymes activity, has inactive & active forms that are stabilized

Cooperativity

form of allosteric regulation taht amplfiiers enzyme activity; a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites (ex: oxygen attached to hemoglobin increases O affinity)

Feedback Inhibition

end product of a metabolic pathway shuts down the pathway; prevents cellfrom wasting chem resouerces by syhnthesizing more product than needed

Cellular Respiration & Equation

Organic compounds + Oxygen → Carbon Dioxide + Water + Energy

organic comp. can be carbs, fats, & proteins; includes aerobic and anaeorbic respiration, up to 32 ATP made

Energy Flow in an Ecosystem

enters as sunlight, exits as heat

Catabolic Pathways

release stored E in bonds (exergonix rxn); electrons in a high energy state to low energy state release energy

Fermentation

partial degradation of sugars that does not use oxygen; used by animals temporarily

Aerobic Respiration

consumes organic molec and uses oxygen to yield ATP

Anaeorbic Respiration

consumption of compounds instead of oxygen

Oxidation-Reduction reactions (redox rxn)

trasnfer of electrons during chem rxns taht releases energy stored in organic molecukles; released energy is used to make ATP; OIL RIG (oxidation is lost, reduction is gain)

Oxidation

substances loses electrons, or is oxidized; named after oxygen bc it is very electronegative

Reduction

substance gainsd electrons, or is reduced (electrons negative, so charge is reduced)

Oxidizing & Reducing Agents

reducing agent gives electrons, oxidizing agent gains electrons

Covalent Bonding in Redox Rxns

soem redox rxns do not transfer electrons but change the ecltron sharing in covalent bonds (ex: rxn betweren methane and carbon dioxide)

How E is released from redox rxns

elctron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one, releasing chemical energy that can be put to work

Cellular Respiration Redox Rxns

Glucose is oxidized and oxygen is reduced; organic molec w/ H are sources of high E electrons, E released as electrons associated w/ H ions transferred to ions, a lower E state

NAD⁺

electron acceptor, functions as an oxidizing agent during respiration; NADH is reduced form of NAD⁺ & represents stored E used to synthesize ATP; NADH passes electrons to electron transport chain

Glucose Breakdown in Steps

broken down in a series of reactions instead of one because hydrogen and oxygen are very reactive together, which release a large amount of energy (exergonic) that the cell cannot properly harvest

Stages of Cellular Respiration

Glycolysis (breaks glucose down into 2 pyruvate molecules); Citric Acid Cycle (completes breakdown of glucose, AKA Krebs Cycle); Oxidative phosphorylation (accounts for most of ATP synthesis)

Substrate level phosphorylation v. Oxidative Phosphorylation

small amnt of ATP made in substrate level phosphorylation (glycolysis & citric acid cycle) by enzyme transfering a phosphate group from a substrate molecule to ADP; Oxidative Phosphorylation most ATP made, inorganic phosphate to ADP produces ATP

Glycolysis: purpose, input, output, location

glucose → 2 pyruvate (6-C to 2 3-C) + 2 H₂O

2 ATP used, 4 ATP made, net gain 2 ATP

2 NADH and 2 H⁺ made

occurs in cytoplasm; 2 phases: E investment & E payoff; no oxygen needed, present in all organisms

pyruvate enters mitochondria

Pyruvate Oxidation

before the citric acid cycle begins, pyruvate must be converted to acetly coenzyme A (acetyl CoA), links glycolysis to citric acid cycle

carried out by multienzyme compelx that catalyzes 3 rxns: oxidartion of pyruvate & release of CO_2, reduction of NAD⁺ to NADH, and combination of 2-C fragment & coenzyme A to form acetyl CoA

Citric Acid Cycle

AKA Krebs Cycle, completes breakdown of pyruvate to CO_2, no more C bonds

2 turns for 2 pyruvates, generates 2 CO₂, 1 ATP, 3 NADH, 1 FADH₂ per turn; occurs in mitrochondria

all E is harvested, electron carriers go to ETC

Electron Transport Chain

in inner membrane (cristae) of mitochondria (increased surface area); electrons continually drop in free energy as they go down the chain (each protein more electronegative than next) until passed to O₂, forming H₂O; electron carriers alternate between reduced and oxidized states as they accept and donate electrons

Cytochromes

electrons apssed through a number of proteins to O₂

Chemiosis

E released as electrons passed down ETC used to pump H⁺ ions from mitochondrial matrix into intermemrbane space, H⁺ then moves downs its concentration gradient thought protein complex ATP synthase, casues it to spin that catalyzes phosphprylation of ADP to ATP (use of E in H⁺ gradient to drive cellular work)

Proton-motive force

certain electron carriers in ETC accept & release H⁺ along w/ electrons, energy stored in H⁺ gradient across a membrane couples the redox rxn of ETC to ATP synthesis, movement of H⁺ forms ATP

Path & Products of Cellular Respiration

glucose → NADH → ETC → proton-motive force → ATP

34% of energy in glucose is transferred to ATP, about 30-32 ATP made; rest of E is lost as heat

Variation in ATP production

phosphorylation & redoc rxn not directly coupled, ratio of NADh to ATP not a whole number

ATp yield varies on whther electrons are passed to NAD+ or FAD⁺ in mitochondrial matrix, FADH₂ brings in electrons at a lower carrier, produces less E

proton-motive force used to dsrive other cellular work

Fermentation

harvesting chemical energy without using either oxygen or ETC (without cellular respiration); consists of glycolysis (2 ATP made) & rxns to regenerate NAD⁺, which can be reused by glycolysis

Alcohol Fermentation

pyruvate is converted to ethanol by: release of CO₂ from pyruvate, then producing NAD⁺ and ethanol; done by yeast, used in brewing, winemaking, and baking

Lactic Acid Fermentation

pyruvate is reduced by NADH, forming NAD⁺ and lactate as end products (NO release of CO₂); used by fungi, bacteria, makes cheese & yogurt; human muscle cells use it to geenrate ATP during strenuous activity when O₂ is scarce

Obligate anaerobes

carry out only fermentation or anaerobic respiration and cannot survive in the presence of oxygen

Facultative anaerobe

an organism that makes ATP by aerobic respiration if oxygen is present but that switches to anaerobic respiration or fermentation if oxygen is not presen

Obligate aerobe

requires oxygen to survive and can’t live without it

Catabolism of Fats

fats are digested to glycerol and fatty acids; fatty acids broken down by beta oxidation and yield acetyl CoA, NADH, adn FADH₂; produces 2x mroe ATP than carbs

Phosphofructokinase

pacemaker for cellular respiration; enzyme that catalyzes step 3 of glycolysis (1st step that commits substrate irreversibly to glycolytic pathway), controls rate of step, cell can speed up or slow down the entire catabolic process

allosteric enzyme inhibited by ATP and stimulated by AMP

Regulators

uses internal mechanisms to control internal change in the face of external fluctuation

Conformer

allows its internal condition to change in accordance with external changes in the particular variable

Homeostasis

maintain a “steady state” or internal balanceregardless of external environment

Mechaniams of Homeostasis

for a given variable above or below a set point serve as a stimulus, these are detected by a sensor; control center then generates output that triggers a response; reponse returns variable to set point

Negative Feedback

form of regulation in which accumulation of an end product of a process slows the process; mainly used to maintain homeostasis (ex: sweating)

Positive Feedback

amplifies a stimulus and does not usually contribure to homeostasis in animals (ex: contractions during childbirth)

Circadian Rhythm

governs physiological changes htat occur roughly every 24 hours

Acclimatization

animal’s physiological adjustment to changes in its external environment; temporary change

Thermoregulation

process by which animals maintain their body temperature within a normal range

Endotherms

maintain a stable body temperature even in the face of large fluctuations in the environmental temperature; generate heat by metabolism, E used (birds & mammals); advantage of generating more movement, no need to warm up, but E used & more food needed

Ectotherms

animals gain heat from external sources (invertebrates, fishes, amphibians, nonavian reptiles); advantage in no E used & less food, tolerate larger fluctuations in internal temp

Poikilotherm

body temp varies w/ environment *NOT ALL ECTOTHERMS

Homeotherms

body temp is relatively constant *ALL ENDODERMS

Balancing Heat Loss & Gain

Radiation (E trasnfer w/ contact), Evaporation (heat loss by liquid into gas), Convection (heat transfer through the movement of a fluid like air or water), Conduction (heat transfer through direct contact between objects)

Integumentary System

heat regulartion by skin, hair, and nails of animls; adaptations include insulaion, circulatory adaptations, cooling by evaporative heat loss, behavioral responses, adjusting metaboliuc heat production

Insulation

major thermoregulatory adaptation in mammals and birds; skin, feathes, and blubber reduce heat flow between an animal and its environment

Ciculatory Adaptations

regulation of blood flow near body surface affects thermoregulation, alter amnt of blood flowing between body core and skin

Vasodilation

blood vessels dilate, blood flow in the skin increases, facilitating heat loss

Vasoconstriction

blood vessels constrict, blood flow in skin decreases, lowering heat loss

Countercurrent Exchange System

transfer of heat (or solutes) between fluids that are flowing in opposite directions; arteries & veins are adjacent to each other, blood flows in opp directions, warm blood moves outward in the arteries from the body core, it transfers heat to the colder blood in the veins returning from the extremities

Cooling by Evaporative Heat Loss

lose heat through evaporation of water from skin; sweating or bathing moistens skin, cools animal down; water absorbs body heat to evaporate to cool down; panting increases cooling effect in birds & mammals

Behavioral Responses

seek warmer places when cold and orient themselves toward heat sources; when hot they bathe, move to cooler areas, or change orientation to minimize heat absorption

Thermogenesis

adjustment of metabolic heat production to maintain body temp; increased by muscle activity like moving or shivering; nonshivering thermogenesis takes place when hormones cause mitochondria to increase metabolic activity