Microbiology- metabolism

catabolic reaction

breaking down nutrients for energy; provide simple organic building blocks for synthesizing new cell components

anabolic reaction

uses simple organic building blocks to produce complex components

what is another term for anabolism?

biosynthesis

activation energy

helps converts substrate to product

which type of metabolism requires a higher amount of activation energy?

anabolic reactions

shape of energy levels on catabolism graph

middle, high, low

shape of energy levels on anabolism graph

low, high, middle

enzymes: effects on reaction

• increase rate of biological reactions

• are not consumed in reaction

• do not determine direction

• increase frequency of substrate reaching transition

how do enzymes affect activation energy?

lower the amount of AE needed to complete a reaction

enzyme characteristics

• suffix -ase

• have an active site (usually a divot where substrate attaches)

  • may undergo a conformational change during catalysis

enzyme reactive groups: types

• prosthetic groups

• coenzymes

prosthetic groups

• covalently bound to enzyme

  • ex: heme, Fe-S cluster

coenzymes

• move between enzymes

• recycled

• ex: NAD+, FAD, coenzymeA

oxidation-reduction reaction (redox): reactants to products

glucose → CO2

O2 → H2O

oxidation-reduction reaction: electron movement

• electron donor = oxidized

• electron acceptor = reduced

  • acceptors receive both e- and H+

redox tower

all electron donors have reduction potentials; a donor can only give up e- to an acceptor lower on the redox tower

*an acceptor in one reaction can donate in another

what are electron transfers facilitated by?

electron carriers - aka, coenzymes

• accept e- from catalytic enzymes → move to another site → donate those e- to an acceptor lower on the redox tower

• cells recycle carriers, cycling between reduced & oxidized states

examples of electron carrier coenzymes

NAD(P)+, FAD+

what is the energy currency of the cell?

high energy bonds (ATP Phosphate bonds)

2 ways to make ATP

• substrate level phosphorylation

• oxidative phosphorylation

glycolysis

glucose catabolism

• occurs in all living cells

• does not require oxygen

• produces energy and essential precursor molecules for biosynthesis

glycolysis: when is ATP being spent?

stage 1 - steps 1 and 3 - use 1 ATP each

glycolysis: when is ATP being generated?

stage 2 - steps 7 and 10 - produce 2 ATP each

glycolysis: net ATP

2 ATP

glycolysis: important products (intermediates)

• G3P and DHAP

• produced in step 4 (split from fructose-1,6-biphosphate)

• DHAP is converted into another G3P in step 5

glycolysis: where/how is NADH produced?

stage 2 - step 6 only - 2 NADH total

• NAD+ gains electrons

  • G3P is oxidized —→ NAD+ is reduced —→ NADH

• produces 1 NADH per G3P, so 2 total

glycolysis: end products

• 2 pyruvate (3C)

• 2 ADP

• 4 ATP

• 2 NADH

substrate-level phosphorylation

the transfer of high energy phosphate bonds from intermediate → ADP → ATP

2 methods of recycling reduced coenzymes (producing ATP)

• fermentation

• respiration

fermentation

• anaerobic conditions

• no ETC

• organisms must do this if they have no good terminal e- acceptor

fermentation: products

• 2 ATP

• Lactate or Ethanol depending on the organism

  • commercially useful products

respiration: pathways that occur

• ETC - generates PMF

• TCA cycle

• oxygen-aerobic

• chemiosmotic coupling by ATP synthase

• yields 36-38 ATP

aerobic respiration: products

26-38 ATP

TCA cycle: what happens right before the cycle begins?

pyruvate is converted to acetyl-CoA

• produces NADH

• releases CO2

happens twice per glucose

TCA cycle: electron transfers

NAD+ → NADH (3 times per cycle)

FAD → FADH (1 time per cycle)

TCA cycle: ATP generation

1 ATP produced per cycle

TCA cycle: CoA recycling

• Acetyl-CoA brings CoA into cycle

• CoA is released

• CoA recycled (used elsewhere), to convert pyruvate or carry molecules

TCA cycle: carbon leaving

carbon leaves as CO2

2 CO2 released per cycle

TCA cycle: reactants

Acetyl-CoA, NAD+, FAD, ADP, Pi

TCA cycle: products

CO2, NADH, FADH, ATP; (CoA recycled)

electron transport chain: purpose and products

oxidize and recycle NADH & FADH → form NAD+ and FAD+

ETC: which way does it move on the redox tower?

moves down the redox tower

ETC: e- carriers

• coenzymes: quinones

prosthetic groups:

• flavin: e- carrying group

• cytochrome: heme

• Fe-S protein: transfer e-

Proton Motive Force (PMF): how is it created?

during ETC, protons are moved across the membrane

• stores energy for ATP synthesis

ETC: chemiosmotic coupling

forms proton gradient that drives ATP synthesis

• ATPase uses PMF energy to make ATP

what is the terminal electron acceptor?

oxygen; before that, e- are bouncing around

fermentation vs respiration products

fermentation: 2 ATP

respiration: 38 ATP

chemoheterotrophs use ___ as their source of energy

organic compounds

chemoheterotrophy: generate ATP through…

• fermentation

• anaerobic respiration

• aerobic respiration

phototrophy: generate ATP through…

• redox reactions powered by light

• produces ATP and NADH → used in biosynthesis

anaerobic respiration requires?

• TCA cycle

• ETC

• Terminal acceptor that is not oxygen

• Chemiosmotic coupling by ATPase

what pathways are possible in aerobic conditions?

• glycolysis

• fermentation

• aerobic respiration

what pathways are possible in anaerobic conditions?

• glycolysis

• fermentation

• anaerobic respiration

Biosynthesis of sugars: how is it done?

• done by gluconeogenesis: reversing TCA cycle and glycolysis

biosynthesis of sugars: pathway specifics

citric acid cycle → oxaloacetate → phosphoenolpyruvate → reversal of glycolysis → glucose-6-P → PPP

biosynthesis of sugars: nucleic acids sugar pathway

• come from pentose phosphate pathway

• glucose-6-P → ribonucleotides → RNA / or / NADPH forms deoxyribonucleotides → DNA

biosynthesis of amino acids: citric acid cycle

• Ketoglutarate: Glutamate family

• Oxaloacetate: Aspartate family

biosynthesis of amino acids: glycolysis

• Pyruvate: Alanine family

• 3-phosphoglucerate: Serine family

biosynthesis of amino acids: pentose phosphate pathway

intermediate produces aromatic amino acids

biosynthesis of amino acids: transaminases

move amino groups between molecules

biosynthesis of nucleotides

• Carbon and nitrogen atoms come from amino acids

• Single carbons from CO₂ and folic acid

biosynthesis of nucleotides: folic acid

helps cycle single carbons

biosynthesis of fatty acids: pathway

• Acetyl-ACP and Maloney-ACP react to start the chain.

• Reaction is repeated with malonyl-ACP adding by 2 carbons until 16C chain is formed

• The 16C chain is transferred to glycerol to form lipids.

biosynthesis of fatty acids: acyl carrier protein (ACP)

carrier on which the fatty acid is built