Topic 3 BIO 205

anabolism/ biosynthesis

-it’s a cellular process that synthesizes and assembles the subunits of macromolecules (animo acids, nucleotides, monosaccharides, and fatty acids) using the energy of ATP

-uses precursor metabolites produced in catabolism

catabolism

-metabolic processes that harvest energy released during the breakdown of components, like glucose, using it to synthesize ATP

-produces precursor metabolites used in biosynthesis

exergonic

-chemical reaction that releases energy

-starting compounds have more free energy than the products

endergonic

-chemical reaction that requires an input of energy because the products have more free energy than the starting compounds

energy coupling

cells use the energy released in an exergonic reaction to power an endergonic one

metabolic pathway

series of chemical reactions in a cell that converts one or more starting substrates into end products

substrate

a reactant in an enzyme catalyzed reaction

metabolic intermediate

when the product of one reaction serves as the substrate for the next

linear metabolic pathway

-series of chemical reactions with a distinct beginning and end.

-The result of one reaction (like an intermediate) becomes the starting material, or substrate, for the next reaction

ex. glycolysis

branched metabolic pathway

a series of reactions that splits into different routes. An intermediate can be used in more than one reaction, leading to different end products

ex. glucose metabolism

cyclical metabolic pathway

a series of reactions that regenerates a starting molecule, allowing the pathway to repeat. Instead of ending as a chain, it forms a loop.

ex. krebs cycle

ATP

-composed of ribose, adenine, and 3 phosphate groups

-energy currency of cells

-hydrolysis of the bonds between its phosphate groups can be used to power endergonic reactions

ADP

a molecule that accepts and inorganic phosphate (Pi), generating ATP

the 2 processes chemoorganotrophs use to make ATP

substrate level phosphorylation and oxidative phosphorylation

substrate level phosphorylation

ATP is synthesized using the energy of an exergonic reaction to transfer a phosphate group from a donor compound to ADP

oxidative phosphorylation

ATP is synthesized using the energy of a proton motive force to add an inorganic phosphate group (Pi) to ADP

-catalyzed by enzyme called ATP synthase

proton motive force

form of energy that results from an electrochemical gradient across a membrane being established by the electron transport chain (ETC)

phosphorylation

how photosynthetic organisms can generate ATP using the energy of a proton motive force created by harvesting energy of light

how do cells get energy to make ATP?

electrons move from a molecule with a low electron affinity to one with a higher affinity which releases energy

energy source

a compound that a cell oxidizes to get energy- an electron donor

terminal electron acceptor

a chemical that’s reduced because of fermentation or respiration- an electron acceptor

dehydrogenation

the removal of an H atom- oxidation

hydrogenation

the addition of an H atom- reduction

electron carriers

-molecules that cells use to shuttle electrons

-the same electron carrier can assist many different enzymes

-3 main types in their oxidized/ reduced forms:

1.NAD+/NADH

2.NADP+/NADPH

3.FAD/FADH2

NAD+/NADH

-nicotinamide adenine dinucleotide

-2 electrons and 1 proton

-generates proton motive force to drive ATP synthesis

NADP+/NADPH

-nicotinamide adenine dinucleotide phosphate

-2 electrons and 2 protons

-generates proton motive force to drive ATP synthesis

FAD/FADH2

-flavin adenine dinucleotide

-2 electrons and 1 proton

-used to power anabolic reactions (biosynthesis)

reducing power

represented by reduced electron carriers whose bonds contain a form of energy that can be used by a cell

precursor metabolites

-metabolic intermediates that can be used to make the subunits of macromolecules or can be oxidized to generate ATP

-once made in catabolism, it can be further oxidized to released energy or can be used in biosynthesis

2 key processes of the catabolism of glucose

1.oxidizing glucose molecules to produce ATP, reducing power, and precursor metabolites done in a series of reactions called the central metabolic pathways

2.transfering the electrons carried by NADH and FADH2 to the terminal electron acceptor which happens as part of cellular respiration or fermentation

central metabolic pathways

glycolysis, the TCA cycle, and the pentose phosphate pathway

glycolysis

-this splits glucose and gradually oxidizes it to form 2 molecules of pyruvate

-provides cell with small amount of energy in form of ATP, some reducing power, and 6 precursor metabolites

-ATP: 2 molecules, net gain; 2 are spent early in pathway, but 4 are made by substrate level phosphorylation after the 6-carbon molecule is split in half

-Reducing power: 2 molecules NADH

-Precursor metabolites: 6 total (glucose-6-phosphate, fructose-6-phosphate, dihydroxyacetone phosphate, 3-phosphoglycerate, phosphoenolpyruvate, and pyruvate)

pentose phosphate pathway

-breaks down glucose but its primary role is to produce compounds used in biosynthesis, including 2 precursor metabolites and reducing power in the form of NADPH

-does not make ATP by substrate level phosphorylation

-a product of the pathway feeds into glycolysis

-Reducing power: variable amount of reducing power in form of NADPH

-Precursor metabolites: ribose-5-phosphate and erythrose-4-phosphate

tricarboxylic acid cycle (TCA cycle)

-aka Krebs cycle

-the transition step just before the cycle converts the pyruvate from glycolysis into acetyl-CoA and one molecule of carbon dioxide is released as a result

-TCA cycle then accepts the 2-carbon acetyl group, oxidizing it to release 2 molecules of carbon dioxide

-the cycle turns twice for each glucose that enters glycolysis to complete that sugar’s oxidation

-the transition step and the TCA cycle together generate the most reducing power of all the metabolic pathways. they also provide 3 precursor metabolites and ATP

-ATP: 2 molecules made by substrate-level phosphorylation. In eukaryotic cells, this step reduces GTP that can be used to make ATP

-Reducing power: 6 molecules of NADH and 2 molecules of FADH2

-Precursor metabolites: alpha-ketoglutarate and oxaloacetate

cellular respiration

metabolic process that transfers electrons stripped from a chemical energy source to an electron transport chain (ETC), generating a proton motive force which is then used to synthesize ATP

aerobic respiration

metabolic process in which electrons are transferred from the electron transport chain (ETC) to molecular oxygen

anaerobic respiration

metabolic process in which electrons are transferred from the electron transport chain (ETC) to a terminal electron acceptor OTHER THAN oxygen

fermentation

metabolic process that stops before oxidizing glucose or other organic compounds completely, using an organic intermediate as a terminal electron acceptor

-makes very little ATP

are enzymes consumed during a reaction?

no, enzymes aren’t consumed or permanently changed during a reaction which means that a single enzyme can function repeatedly

cofactor

non-protein component required for the activity of some enzymes

co-enzymes

non-protein organic compound that assists some enzymes, acting as a loosely bounds carrier of small molecules or electrons

-some remain bound during transfer process while others separate

-the same coenzyme can assist many different enzymes

-can be reused and are only needed in small quantities

why does vitamin deficiency have serious health consequences?

most coenzymes are derived from certain vitamins. without these vitamins, any enzyme that requires the corresponding coenzyme for its activity cannot function

environmental factors that influence enzyme activity

-temp, pH, and salt concentration all effect how well enzymes function

-most enzymes function best as low salt concentrations, pH slightly above 7, and warm conditions

allosteric

refers to enzymes that can be controlled through use of allosteric sites

-by regulating key activity of enzymes, cells can adjust flow of metabolic pathways

-when a regulatory molecule binds to an allosteric site, the shape of the enzyme changes, altering the affinity the enzyme has for its substrate (reversible with temporary effects)

-allosteric enzymes usually catalyze the 1st step of a pathway

-if pathway is biosynthetic, the end product usually acts as an allosteric inhibitor

allosteric inhibitor

decreases affinity of enzyme for its substrate

allosteric activator

increases affinity of enzyme for its substrate

competitive inhibition

inhibitor competes with normal substrate to bind to the active site

-inhibitor has similar chemical structure as substrate

non-competitive inhibition (by regulatory molecules)

inhibitor binds to site other than active site and changes the shape of the enzyme

-reversible and used by cells to control the activity of allosteric enzymes

non-competitive inhibition (by enzyme poisons)

inhibitor binds to site other than active site and permanently changes the shape of the enzyme, making it not functional

The 3 metabolic pathways degrade organic molecules, generating:

-ATP by substrate level phosphorylation

-reducing power in forms of NADH, FADH2, and NADPH

-precursor metabolites

pyruvic acid/ pyruvate

weak organic acids that are sometimes intermediates and end products of metabolic pathways

ED pathway

form of glycolysis that generates half as much ATP. some organisms have this in addition to the EM pathway

-useful for microbes in large intestine because it degrades gluconate

-useful for bacterial identification because it involves unique enzymes and distinct intermediates

Transition step

oxidizes the end product of glycolysis (pyruvate) and converts it into the compound used to begin TCA cycle (acetyl-CoA).

-occurs twice per glucose molecule

-Carbon dioxide is produced as metabolic waste

-Reducing power: 2 molecules of NADH

-Precursor metabolites: acetyl-CoA

oxidative phosphorylation

the synthesis of ATP using the energy of a proton motive force

ATP synthase

enzyme complex that harvests the energy of a proton motive force to synthesize ATP

chemiosmotic theory

the theory that a protein gradient is formed by electron transport chain (ETC) and then used to power ATP synthesis

the electron transport chain (ETC)

group of membrane embedded electron carriers that pass electrons accepted from NADH and FADH2 from one carrier to another, with each successive carrier having a higher electron affinity

-the eneergy released as the electrons are passed allows the EtC to pump protons across the membrane generating an electrochemical gradient called a protein motive force

-in eukaryotic cells,