Microbial Metabolism Survey

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Bubonic Plague

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Yersinia pestis

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Scrub Typhus

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Orientia tsutsugamushi

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Stomach Ulcers

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Helicobacter pylori

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Legionnaires' Disease

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Legionella pneumophila

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Metabolism

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all of the chemical reactions that take place in the cell

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Catabolism

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breaking down food for energy

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Anabolism

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using energy to build cell parts

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Ultimate function of metabolism

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reproduction

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Catabolism __________ energy

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releases - exergonic

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Anabolism __________ energy

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uses - endergonic

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Pathway

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steps of catabolism or anabolism occur as a series of reactions

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Catabolism + Anabolism =

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Metabolism

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Metabolic Pathway

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a series of reactions, the product of one reaction is the substrate for the next reaction

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What is required at each step of the pathway

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a specific enzyme

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What happens to the pathway if there is an enzyme missing or it doesn't work?

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Pathway stops at that step

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Enzyme

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catalyst; something that speeds up a reaction without being consumed; usually a protein; enzymes are specific for a substrate

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protein folding, structure=

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function

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Activation energy

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amount of energy required for a reaction to occur

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Enzymes speed up reactions by

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lowing the activation energy of a reaction

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Isomerases

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rearrange atoms within a molecule

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Transferases

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transfer a chemical group from one compound to another

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Dehydrogenase (reductase)

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remove and transfer electrons (usually as H) from one compound to another

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Holoenzyme

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active form of the enzyme; will bind to substrate

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Active (catalytic) site

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specific place on the enzyme that binds to the substrate

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Enzyme Structure can contain
1
2
3

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protien
cofactors
coenzyme

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Cofactor

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inorganic ion
iron, magnesium, zinc, copper ions

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Coenzyme

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Organic molecule
(NAD+, NADP+, FAD)

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To be functional enzymes can require
1
2
3
4

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1. nothing
2. cofactor
3. coenzyme
4. cofactor and coenzyme

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active site of the enzyme is specific to a

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substrate
Induced-fit model

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Factors that influences enzyme activity

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Temperature
pH
Enzymes and substrate concentration
presence of inhibitors

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What does temperature do to atoms and molecules

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increase temperature increases movement

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All proteins have an optimum temperature to maintain 3D structure and is the most active, too high and too low changes what in proteins

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changes the hydrigen bonding with in the 2 and 3 structure --> changes the shape and function

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All proteins have an optimum pH to maintain 3D structure, too high and too low changes what in protein

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changes hydrogen bonding within 2 and 3 structure, changing the shape and function

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as enzyme concentration increases, the rate of reaction

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increases

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Enzyme concentration is controlled by

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1. gene expression
2. physical separation

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Saturation Point

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the concentration of substrate in which all enzyme active sites have been filled

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Inhibitors

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Substances that block an enzyme's active site - directly or indirectly

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Three types of inhibitors

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Competitive
Noncompetitive
Feedback (negative) inhibition

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Competitive inhibitors

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bind to the active site on the enzyme

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Noncompetitive inhibitors

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bind to the allosteric site of the enzyme, changing the shape of the enzyme

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Feedback (negative) inhibition

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a metabolic product inhibits the first enzyme in the pathway

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REDOX
Oxidation-Reduction Reactions

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a set of chemical reaction in which electrons are transferred

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Redox reactions always occur as a pair of reaction, a what and a what

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a reduction reaction & a oxidation reaction

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Electron acceptors become

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reduced, (a reduction reaction)

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Electron donors become

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oxidized, (a oxidation reaction)

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Reduction reaction

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acceptor gains a free electron or an electron in hydrogen

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Oxidation reaction

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donor can lose a free electron, lose a electron in hydrogen, or can gain an oxygen

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electrons are rarely floating in the cytoplasm alone, they are

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carried by electron carrier molecules
nicotinamide adenine dinucleotide (NAD)
nicotinamide adenine dinucleotide phosphate (NADP)
flavine adenine dinucleotide (FAD+)
all are derived from vitamins

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oxidized form
NAD+
FAD

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reduced form
NADH
FADH2

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ATP characteristic

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nucleotide
short-term energy storage molecule
must be constantly replenished

ATP --> ADP + PO4 2-

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ADP + PO4 2- --> ATP
this reaction is called

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phosphorylation

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Cell make ATP by phsophorylation in three ways

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substrate level phosphorylation
oxidative phosphorylation
photophosphorylation

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substrate level phosphorylation

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transfer phosphate from a phosphorylated organic compound to ADP

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oxidative phosphorylation

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energy from redox reactions of respiration is used to attach phosphate to ADP

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photophosphorylation

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light energy is used to add phosphate to ADP

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glucose catabolism goal

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breakdown glucose to CO2 to release energy (ATP)

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Ways to breakdown glucose

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glycolysis & respiration
1. aerobic respiration
2. anaerobic respiration

Glycolysis & fermentation

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Glycolysis facts

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multi-step pathway, involving many enzymes
does not require oxygen
occurs in the cytoplasm

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Glycolysis products

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2 pyruvic acid
2 ATP
2 NADH

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Glycolysis REDOX

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electrons taken from glucose (oxidized) and transferred to NAD+(reduced)

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Glycolysis
Whats happens to glucose

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glucose (6C) broken down into 2 pryruvic acid (3C)

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Glycolysis 4 ATP made by

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substrate level phosphorylation
2ATP used in glycolysis

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Fermentation facts

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Metabolism of pyruvic acid
Does not require O2; does not require respiration enzymes
Organism that ferment generate ATP by glycolysis only

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Fermentation
What

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Pyruvic acid is reduced to waste products

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Fermentation
Why

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recycle NADH to NAD+ to keep glycolysis going

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Fermentation
Why isn't it perfect

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good if in an anaerobic environment, but not perfect
still energy left in bonds of waste products
waste product can be toxic (acids, alcohols)

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Respiration
What

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Complete oxidation of pyruvic acid to CO2

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Respiration
Phases

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1. synthesis of acetyl-CoA
2. Kreb's cycle
3. electron transport chain

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Respiration
REDOX

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electrons removed from pyruvic acid are used to make ATP via oxidative phosphorylation

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Respiration
Synthesis of acetyl-CoA

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chemical form that can enter the Kreb's cycle
a redox reaction
one CO2 produced per pyruvic converted
allows the carbons to enter the mitochrondira

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Respiration
Kreb's cycle
Location

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Prokaryotes - cytoplasm
Eukaryotes- mitochrondria

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Respiration
Kreb's cycle
ATP made how

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made by substrate level phosphorylation

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Respiration
Kreb's cycle
Products

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Two turns per glucose
each turn
3 NADH
1 FADH2
2 CO2 released
1 ATP

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Respiration
ETC
where electrons come from

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glycolysis: 2 NADH/glucose
formation of acetyl CoA: 2 NADH/glucose
Kreb's cycle: 6 NADH & 2 FADH2/ glucose

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Respiration
Acetyl-CoA
products

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2 NADH/glucose
2 acetyl-CoA/glucose
2 CO2/glucose

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Respiration
ETC
what

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series of membrane bond carriers that pass electrons to one another and ultimately to a final electron acceptor (chemical)

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Respiration
ETC
what it makes

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the energy of passing electrons is used to create a H+ proton gradient

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Respiration
ETC
Proton gradient

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H= gradient used to make ATP (lots)

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Respiration
ETC
electron carriers

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electron carriers are recycled to keep glycolysis and Kreb's cycle going

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Respiration
ETC
where

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Prokaryotes: ETC is on the cell membrane
Eukaryotes: ETC is on the inner mitochrondrial membrane

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Respiration
ETC
Composition

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Derived from Vitamin B2
Metal contain proteins
Lipid-soluble quinone (from Vit. K)
Cytochromes

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Cytochrome

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pigmented proteins that contain heme

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Respiration
ETC
Different Organism

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Carriers are different
Arranged differently
Process is the same
Differences used to identify species

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Respiration
ETC
Final Electron acceptor

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Aerobic Respiration - O2
Anaerobic Respiration - not O2
NO3
CO3
SO4

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Respiration
ETC
Electrons

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electrons enter the chain as part of a hydrogen atom
some carriers only accept electron --> proton pumps

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Chemiosmosis

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the force of the proton gradient

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Using the proton gradient to make ATP
type of phosphorylation

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oxidative phosphorylation

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ATP Synthase

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uses the proton gradient to make ATP
(waterwheel analogy)

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Respiration
Aerobic respiration review

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glucose is completely oxidized to CO2 in Kreb's cycle
electrons from glucose are carried to the membrane ETC by NADH and FADH2
electrons passed from carrier to carrier in the ETC making a proton gradient
ATP synthase uses the proton gradient to make ATP
C6H12O6 + 6O2 --> 6CO2 + 6H2O + 38 ATP + heat
organism will grow fastest with aerobic respiration

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Lipid Catabolism
triglyceride

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3 fatty acids chain on a glycerol backbone

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Lipase

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an enzyme used to break fatty acid off of a triglyceride

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Lipid Catabolism
Glycerol

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energy is used to convert glycerol to dihydroxyacetonephosphate (DHAP)

DHAP is one intermediate in glycolysis

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beta oxidation

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complex set of reactions that breaks down the fatty acids 2 carbons at a time

2 carbon chunks are converted to acetyl-CoA

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beta oxidation
REDOX

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electron carriers are reduced

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beta-oxidation
location

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Eukaryotes: happens in the mitochrondria

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Protein Catabolism

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most are too big to enter the cell so they are broken up to individual amino acids

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Protease

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breaks proteins down to AA

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Deamination

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removing the amino group on the AA

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Protein catabolism
how

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AA deamination then remaining compound enters the Kreb cycle

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Pentose Phospahte Pathway

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alternative to glycolysis
break down glusoces to produce 2 NADPH and 1 ATP

many precursors are made along the way --> nucleic acid synthesis

many bacteria use this in addition to glycolysis

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Entner-Douderoff Pathway

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alternative to glycolysis breaks down glucose to produce NADPH and 1 ATP

only a few bacteria do this

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Catabolism& Anabolism are coupled

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cycle of breaking compounds down and building it back up

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Photosynthesis

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photophosphorylation + making sugar from CO2

Reverse of repiration

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Photosynthesis
location

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P: occurs in cytoplasm and on the cell membrane (thylakoids)
E: occurs at the thylakoid of the chloroplast
photoautotroph only

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Photosynthesis
General

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capture light --> ETC -->proton gradient to make ATP

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Photophosphorylation
pigments

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capture light and start ETC

chlorophyll a: green plants, algae, cyanobacteria
bacteriochlorophyll: "green and purple bacteria"

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Photosystem

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group of pigment and reaction center and electron acceptor

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Photophosphorylation
ETC start

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light captured by pigments
energy is sent to excite the reaction center
reaction center transfer electron to the electron acceptor

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Cyclic Photophosphorylation

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electrons of ETC are recycled back to the reaction center of the photosystem

Does not require a chemical source of electron

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Photophosphorylation
result of ETC

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ETC leads to a proton gradient and chemiosmosis

Uses ATP synthase --> Photophosphorylation

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Cyclic Photophosphorylation
used by who

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all phototrophs do this
some bacteria exclusively use this (photohetereotroph)

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Noncyclic Photophosphorylation

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electrons of ETC are not recycled and is only used by photoautotroph

so requires a source of electrons

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Oxygenic photosynthesis

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water is oxidized to O2

water is source of electrons

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Noncyclic Photophosphorylation
produces

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ATP and reduced electron carriers NADPH

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Photophosphorylation summary

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pigment absorb light energy
light energy is used via ETC to create proton gradient
cyclic: electron are recycle
noncyclic: final electron acceptor is NADP+
a chemical is used as electron source
ATP Synthase uses the proton gradient to make ATP

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Calvin-Benson Cycle

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reduced electron carriers (NADPH) and ATP from light reaction come here

used to reduced CO2 to glucose

photoautotroph

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ATP + NADPH + CO2

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reduction of CO2 to glucose

3CO2 --> 1 glucose