metabolism

all chemical reactions and physical workings of the cell

collects and spends energy in the form of ATP or heat

anabolism

biosynthesis of cell molecules and structures, requires energy input

catabolism

break the bonds of larger molecules, release energy

catalysts

speed up the rate of a chemical reaction without becoming part of the products or being consumed in the reaction

enzymes overcome activation energy allowing the reaction to proceed by

increasing thermal energy to increase the velocity of molecules

increasing the concentration of reactants to increase the rate of molecular collisions

adding a catalyst

enzyme characteristics checklist

most composed of protein and may require cofactors

act as organic catalysts to speed up the rate of cellular reactions

lower the activation energy required for a chemical reaction to proceed

have unique characteristics such as shape, specificity, and function

enable metabolic reactions to proceed at a speed compatible with life

substrates

reactant molecules upon which enzymes act

simple enzymes

consist of protein alone

conjugated enzymes

contain protein and some other nonprotein molecule

holoenzymes

whole conjugated enzymes

apoenzyme

protein portion of holoenzyme

cofactor

nonprotein protein of holoenzyme

can be organic or inorganic

active site or catalytic site

actual site where the substrate binds

three-dimensional crevice or groove formed by the way amino acid chains are folded

each enzyme has a different

primary structure, variation in folding, unique active site

metallic cofactors

iron, copper, magnesium, manganese, zinc, cobalt, selenium, etc.

assist with precise functions between enzyme and substrate

coenzymes

organic compounds that work with apoenzyme to alter substrate

remove chemical group from one substrate and add it to another substrate

vitamins are an important component of

coenzymes

oxidation

loss of electrons

a compound that loses electrons is oxidized

reduction

gain of electrons

a compound that gains electrons is reduced

two examples of coenzyme carriers

NAD and FAD

exoenzymes

transported extracellularly

break down large food molecules or harmful chemicals

endoenzymes

retained intracellularly and function there

most enzymes of metabolic pathways

constitutive enzymes

always present in relatively constant amounts, regardless of the cellular environment

regulated enzymes

production is turned on (induced) or turned off (repressed) in response to changes in concentration of substrate

denaturation

weak bonds that maintain the shape of an apoenzyme are broken by heat, low or high pH, or certain chemicals, distorts shape and prevent substrate attachment

competitive inhibition

a molecule that resembles the substrate occupies the active site, preventing the substrate from binding

enzymes cannot act on the inhibitor and is effectively shut down

noncompetitive inhibition

some enzymes have two binding sites - the active site and the regulatory site

regulated by the binding of molecules other than the substrate to the regulatory site

enzyme repression

stops further synthesis of an enzyme somewhere along its pathway

enzyme induction

enzymes appear (are induced) only when suitable substrates are present

exergonic reactions

release energy as they go forward

energy is available for doing cellular work

endergonic reactions

require the addition of energy to move forward

the removal of hydrogens from a compound during a redox reaction is called

dehydrogenation

NAD

most common electron carrier

carries hydrogens and a pair of electrons from dehydrogenation reactions

reduced NAD is presented as NADH + H+ or NADH

FAD

reduced FAD is presented as FADH

NADP

NAD phosphate

catabolic pathways

electrons are extracted and carried through a series of of redox reactions to a final electron acceptor

aerobic metabolism

oxygen is the final electron acceptor

anaerobic metabolism

some other inorganic or organic compound is the final electron acceptor (not oxygen)

adenosine triphosphate

three-part molecule

adenine, ribose, three phosphate groups bonded to the ribose

adenine

nitrogen base

ribose

5 carbon sugar

three phosphate groups bonded to ribose on ATP

bulky and negative, repelling electrostatic charges imposes a strain between the last two phosphate groups, removal of phosphates releases free energy

ATP

primary energy currency of the cell

it must be replaced, ongoing cycle

substrate-level phsophorylation

generation of ATP through a transfer of phosphate group from a phosphorylated compound directly to ADP

oxidative phosphorylation

a series of redox reactions occurring during the final phase of the respiratory pathway

photophosphorylation

ATP formed through a series of sunlight-driven reactions in phototrophs

three basic catabolic pathways

aerobic respiration, anaerobic respiration, fermentation

glycoysis

most common pathway used to break down glucose

fermentation pathway

facultative and aerotolerant anaerobes

uses only glycolysis

oxygen not required and use organic compounds as electron acceptors

aerobic respiration

a series of enzyme-catalyzed reaction

principal energy-yielding scheme for aerobic heterotrophs

provides ATP and metabolic intermediates for other pathways

glycolysis

glucose is enzymatically converted to pyruvic acid

may be the first phase of aerobic respiration or the primary metabolic pathway

synthesizes a small amount of ATP anaerobically

pyruvic acid is essential intermediary metabolite

pyruvic acid

a central metabolite

used in several pathways by many organisms

pyruvic acids in strict aerobes (and some anaerobes)

sent to the Krebs cycle

pyruvic acid in facultative anaerobes

re-reduced into acids or other products

the Krebs cycle

pyruvic acid into acetyl coenzyme A

oxidation releases first CO2

enzymes and coenzyme A dehydrogenate pyruvic acid to a 2-carbon acetyl group

NAD reduced to NADH

NADH is shuttled to ETC to produce ATP

how many times does the Krebs cycle happen

twice

Krebs cycle purpose

transfer energy stored in acetyl CoA to NAD+ and FAD by reducing them

main products of the Krebs cycle

reduced NADH and FADH2

two ATP produced through substrate-level phosphorylation

electron transport system

chain of special redox carriers that receives electrons from NADH and FADH2

electrons are passed sequentially from one redox molecule to the next

flow of electrons allows the active transport of hydrogens outside the cell membrane

oxygen receives hydrogesn and electrons and produces water

energy cascade sequence

NADH dehydrogenase

FMN

coenzyme Q

cytochrome b

cytochrome c1

cytochrome c

cytochromes a and a3

ATP synthase

stationed along the membrane in close association with the ETS carriers

captures released energy from the ETS carriers

oxidative phosphorylation

the coupling of ATP synthesis to electron transport

each NADH that enters the ETS gives rise to three ATP molecules

NAD and FMN enter the ETS at a different point, so there is less energy released, and only give rise to two ATP molecules

chemiosmosis

as the electron transport carriers shuttle electrons, hydrogen ions are actively pumped into the periplasmic space or the space between the cell wall and the cytoplasmic membrane

this sets up a concentration gradient of hydrogen ions called the proton motive force

proton motive force

consists of a difference in charge between the outside of the membrane (+) and the inside (-)

separation of charges temporarily stores potential energy

H+ can only diffuse into the membrane through ATP synthase, which sets the stage for ATP synthesis

aerobic respiration ATP production

total possible ATP is 40, but only keep at most 38 because must expended 2

4 from glycolysis

2 from krebs

34 from ETC

non ATP products of respiration

6 CO2 (Krebs)

6 O2 (consumed during ETC)

6 H2O (produced during ETC)

2 H2O (glycolysis) but 2 used in Krebs

anaerobic respiration: nitrate and nitrite reduction systems

found in E. coli

nitrate reductase catalyzes the removal of oxygen from nitrate reducing it to nitrite and water

alcoholic fermentation

occurs in yeast or bacteria species that have metabolic pathways for converting pyruvic acid to ethanol

decarboxylation of pyruvic acid to acetaldehyde

reduction of acetaldehyde to ethanol

homolactic fermentation

lactic acid bacteria reduce pyruvate to lactic acid mainly

heterolactic fermenation

glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide

mixed acid fermentation

members of the family enterobacteriaceae possess enzyme systems for converting pyruvic acid to several acids simultaneously

acetic, lactic, succinic, formic acids, as well as CO2

accounts for accumulation of some types of gas in the intestine

lipases

break apart fatty acids joined to glycerol which is converted to dihydroxyacetone phosphate which can enter step 4 of glycolysis

beta oxidation

oxidation of fatty acids

2-carbon units transferred to coenzyme A, creating acetyl CoA (Krebs)

oxidation of 6-carbon fatty acid yields 50 ATP, compared to 38 for a 6-carbon sugar

proteases

break down proteins to their amino acid components

amino groups removed through deamination

remaining carbon compound can easily converted to Krebs cycle intermediate

amphilbolism

most catabolic pathways contain strategic molecular intermediates that can be diverted into anabolic pathways

a given molecule can serve multiple purposes to derive maximum benefit from all nutrient and metabolites

catabolic and anabolic pathway are integrated to improve cell efficiency

precursor molecule

a compound that is the source of another compound

pyruvate as a precursor

provides intermediates for amino acids

gluconeogenesis

pyruvate is a starting point for glucose synthesis in the event of inadequate glucose supply

acetyl CoA as a precursor

can be converted into one of several amino acids

can be condensed into hydrocarbon chains for fatty acid and lipid synthesis

precursors to DNA and RNA

pathways that synthesize purines and pyrimidines originate in amino acids

can be dependent on intermediates from the Krebs cycle

carbohydrate biosynthesis

crucial role of glucose in metabolism and energy utilization

major component of cellulose cell walls and storage granules

glucose-6-P used to form glycogen

proteins

large proportion of cell's contents

essential components of enzymes, cytoplasmic membrane, cell wall, and cell appendages

twenty amino acids are needed to make these proteins

light-dependent reactions

proceed only in the presence of sunlight

catabolic, energy-producing reactions

light-independent reactions

proceed regardless of the lighting conditions

anabolic, synthetic reactions

carbon atoms from CO2 are added to the carbon backbones of organic molecules

the calvin cycle

occurs in the chloroplast stroma or the cytoplasm of cyanobacteria

use energy produced in the light phase to synthesize glucose

oxygenic photosynthesis

dominant type on earth

occurs in plants, algae, and cyanobacteria

anoxygenic photosynthesis

occurs in green and purple bacteria that utilize bacteriochlorophyll

have only cycling photosystem I

generate a small amount of ATP

use H2, H2S

many are strict anaerobes