Chapter 8: Metabolism

what is energy

the capacity to do work

what kind of processes does energy include

building complex molecules and moving substance in and out of the cells

what happens without a source of energy

all life on earth would stop

what is kinetic energy

energy of motion

what is thermal energy 

the kinetic energy associated with random movement of atoms or molecules 

what is heat

thermal energy in transfer between objects

what is potential energy

energy stored in the location or structure of matter

what is chemical energy

potential energy associated with the position of electrons specifically the orbital level of the electrons from the nucleus

what are types of cellular work 

chemical work, mechanical work, and transport work 

what is chemical work

synthesis of complex molecules

what is mechanical work

cell motility and movement of structures within cells

what is transport work

take up of nutrients, elimination of wastes, and maintenance of ion balances

what laws does life obey 

laws of thermodynamics 

what do cells obtain their energy from

their environment, often conserved as ATP

what kind of reactions play a critical role in metabolism

oxidation-reduction reactions (redox)

what are chemical reactions organized into

pathways, each reaction of a pathway is catalyzed by an enzyme and biochemical pathways are regulated

what is thermodynamics the study of 

energy transformations 

what is an isolated system unable to do

exchange energy or matter with its surroundings

what can an open system do

energy and matter can be transferred between the system and its surroundings

what kind of systems are organisms

open systems

first law of thermodynamics

the energy of the universe is constant, energy can be transferred and transformed, but it cannot be created or destroyed

second law of thermodynamics 

every energy transfer or transformation increases the entropy (disorder) of the universe 

what is Gibbs free energy

expresses the change in energy that can occur in chemical reactions and other processes, amount of energy available to do work

what is the equation for gibbs free energy

delta G = delta H - T delta S

what is delta G

change in free energy, amount of energy available to do work

what is delta H 

change in enthalpy, heat content 

what is T

temperature in kelvin

what is delta S 

change in entropy 

what does a negative delta G mean

the reaction is spontaneous, heat releasing, exergonic, exothermic, the reactants are higher than the products, and the activation energy is above

what does a positive delta G mean

the reaction is non spontaneous, heat requiring, endergonic, endothermic, the reactants are lower than the products, and the activation energy is throughout

how do catabolic pathways release energy

by breaking down complex molecules into simpler compounds

what are types of catabolic pathways 

fueling reactions, energy conserving reactions

what do catabolic pathways provide

ready source or reducing power (electrons)

what do catabolic pathways generate

precursors for biosynthesis

what do anabolic pathways consume energy for

to build complex molecules from simpler ones

what do anabolic pathways acquire their energy from

catabolic pathways

what is transferred during redox reactions

electrons

from where do redox reactions release their energy 

energy stored in organic molecules, ultimately used to synthesize ATP 

what do many metabolic processes involve

redox reactions

what do electron carriers transfer

electrons from an electron donor to an electron acceptor which can result in energy release which is stored as ATP, more electrons = more energy

what are redox reactions

chemical reactions that transfer electrons between reactants

oxidation 

substance loses electrons, is oxidized 

reduction

substance gains electrons, reduced (amount of positive charge is reduced)

what is the standard redox potential (E0)

equilibrium constant for an oxidation reduction reaction

what is the standard redox potential a measure of

the tendency of the reducing agent to lose electrons, a more negative E0 is a better electron donor and a more positive E0 is a better electron acceptor

how are electron carriers organized into ETC 

the first electron carrier has the most negative E0, the potential energy stored in the first redox couple is released and used to form ATP, the first carrier is reduced and electrons are moved to the next carrier and so on 

why is it essential to do the ETC in a stepwise fashion

to maximize ATP production

how do redox reaction transfer electrons

either alone or accompanied by protons

what is energy coupling

use of an exergonic process to drive an endergonic one, most energy coupling is mediated by ATP

what are the three types of ATP synthesis 

substrate level phosphorylation, oxidative phosphorylation, and photophosphorylation 

substrate level phosphorylation

transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP

oxidative phosphorylation

series of redox reactions occurring during respiratory pathway

photophosphorylation

in photosynthetic organisms, utilizing the energy of sunlight

what is activation energy 

the initial energy needed to start a chemical reaction and reach a transition state, can be in the form of thermal energy 

what helps to overcome activation energy

enzymes

what are enzymes

most are proteins, and are catalyst that decrease the activation energy of a reaction which increase the rate, they are often grouped to carry out sequential reactions, and they are specific meaning they only work with specific substrates

what do substrates bind to

active site

how can the active site lower the activation energy barrier 

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

enzymes generally have optima which means

optimal conditions favor the most active shape for the enzyme molecule

what are cofactors

non protein enzyme helpers that are inorganic such as metal in ionic form and minerals

what are coenzymes

enzyme helpers of enzymes that are organic cofactors such as vitamins

what are the three kinds of enzyme inhibitors 

competitive, uncompetitive, and noncompetitive 

competitive inhibitor

utilize the same active site but the product is never released

uncompetitive inhibitor

bind atop site and blocks active site

noncompetitive inhibitors

binds to secondary site, changes tertiary structure 

what are controls of enzyme synthesis 

regulation of enzymatic action at the genetic level by controlling the synthesis of degraded enzymes that need replacement 

what is enzyme repression

automatic suppression of enzyme synthesis when end product builds to excess, response time is longer than for feed inhibition but effects are more enduring

enzyme induction

enzymes are made only when suitable substrates are present, enables the organism to adapt to nutrients and prevents waste of energy

what are exoenzymes

transported extracellularly, where they break down large food molecules or harmful chemicals, examples are cellulase, amylase, and penicillinase

what are endoenzymes 

retained intracellularly and function there, most enzymes are endoenzymes 

what are constitutive enzymes

always present, always produced in equal amounts or equal rates, regardless of the amount of substrate

what are regulated enzymes

not constantly present; production is turned on (induced) or turned off (repressed) in response to changes in the substrate concentration

negative feedback inhibition in enzymes

also called end product inhibition, inhibition of one or more critical enzymes in a pathway regulates entire pathway

what are the important equations to know for this chapter 

6CO2 + 6H2O —> C6H12O6 + 6O2 (photosynthesis) 

C6H12O2 + 6O2 —> 6CO2 + 6H2O + ATP (cellular respiration) 

what is cellular respiration

an exergonic process that include both aerobic and anaerobic processes and transfers energy from glucose to form up to 32 ATP per glucose with 34% of energy lost as heat over 4 stages

what happens to high energy electrons during cellular respiration

they are removed from fuel molecules (oxidation) and are transferred to NAD+ (reduction) and the reduced NADH passes electrons to an electron transport chain and the energy is released as electrons fall from carrier to carrier and finally to O2

harvesting of cellular respiration

glucose and other organic compounds are broken down, the electrons from these compounds are transferred to NAD+ which is a coenzyme where each electron travels with a proton, the NAD+ then functions as an oxidizing agent which is reduced to NADH, and each NADH represents stored energy that is tapped to synthesize ATP

NAD+ as an electron shuttle

NADH passes the electrons to the electron transport chain in a series of steps in which the energy that is yielded is used to regenerate ATP

ATP produced during aerobic respiration 

32 ATP produced by substrate level phosphorylation 

explain chemiosmosis

chemiosmosis involves the electron transport aerobic chain which accounts for almost 90% of the ATP generated by cellular respiration, NADH and FADH2 shuttle high energy electrons to ETC chains in the membrane after which redox rxns release energy pumping H+ from the cytosol to the periplasmic space which is a proton motive force.

how is ATP produced in chemiosmosis

the electrochemical H+ gradient across the plasma membrane drives H+ back through the enzyme complies ATP synthase which synthesizes ATP making about 14 ATP per acetyl CoA or 28 ATP per glucose through oxidative phosphorylation (final electron acceptor is O2 which reduced to H2O)

how are bacterial and archaeal ETCs different 

located in plasma membrane, some resemble mitochondrial ETC, but many are different as they have different electron carriers, different oxidases, may be branched, may be shorter with fewer protons and therefore less energy 

how does chemisosmosis work in prokaryotes

H+ ions enter from the periplasmic space into the alpha subunit in which the binding of H+ induces a clockwise rotation of the C ring and the gamma subunit, the rotation of the gamma subunit also induced a conformational change in the alpha 3 beta 3 hexamer which causes ADP to convert to ATP and another H+ enter the alpha subunit, continuing the cycle

what kind of molecules do catabolic pathways funnel electrons from in cellular respiration

carbohydrates, proteins, fats, monomers of these molecules enter the system at various points

what does the amount of ATP produced during aerobic respiration depend on

growth conditions and nature of ETC 

under anaerobic conditions how many ATP does glycolysis yield 

2 

what are factors affecting ATP yield

bacterial ETCs are shorter and have lower P/O ratios, ATP production may vary with environmental conditions, PMF in bacteria and archaea is used for other purposes than ATP production (flagella rotation), precursor metabolite may be used for biosynthesis

what do chemoheterotrophs do

catabolize organic chemicals

what are chemoorganotrophic fueling processes

aerobic respiration rxn catabolizes to CO2, anaerobic respiration (non O2 electron carriers), fermentation

aerobic respiration rxn catabolizes to CO2 

glycolytic pathways (glycolysis), TCA cycles - O2 final electron acceptor, produces ATP (mostly through an ETC) 

aerobic respiration (non O2 electron carriers)

yields less energy - E0 of electron acceptor less positive than E0 of O2, examples include dissimilatory nitrate reduction which the use of nitrate as terminal electron acceptor makes it unavailable for cellular use, and denitrification in which reduction of nitrate to nitrogen gas causes loss of soil fertility

fermentation

oxidation of NADH produced by glycolysis, pyruvate or derivative used as endogenous electron acceptor, substrate only partially oxidized, oxygen not needed, ATP formed by substrate level phosphorylation, and oxidative phosphorylation does not occur, does not generate a PMF

what does amiphibolic mean

many pathways of metabolisms are bidirectional

in what ways do catabolic pathways that contain metabolites divert into anabolic pathways 

pyruvic acid can be converted into amino acids through amination, amino acids can be converted into energy sources through deamination, and Glyceraldehyde 3 phosphate can be converted into precursors for amino acids, carbohydrates, and fats. 

what is photosynthesis

an anabolic pathways that converts solar energy into chemical energy, a process that feeds the biosphere and can occur in plants, algae, certain protists, and some prokaryotes

how is photosynthesis the earth’s lifeline

the ultimate source of all the chemical energy in cells comes from the sun, on land green plants are primary photosynthesizers, and in aquatic ecosystems (80-90% of all photosynthesis) is filled by algae, cyanobacteria, and green sulfur, purple sulfur, and purple non sulfur bacteria

what is light 

a form of electromagnetic energy also called electromagnetic radiation that travels in rhythmic waves 

what is a wavelength

the distance between crests of waves, determine the type of electromagnetic energy

what is the electromagnetic spectrum

the entire range of electromagnetic energy or radiation

how does light behave

as though it consists of discrete particles called photons