chp. 12: anabolism

anabolism

uses the energy from catabolism for biosynthetic pathways (building)

• lots of energy needed

• carbon source and inorganic molecules → new organelles and cells

• macromolecules made from monomers

what is the cofactor for anabolism?

NADPH (for catabolism it was NADH)

can the same enzymes be in catabolism and anabolism?

yes, alot do double duty (forward + reverse) but the pathways themselves r not identical

are rxns separated in anabolism?

YES in eukaryotes for instance B-oxidation is the catabolism breaking down fatty acids, and in anabolism they r making lipids but it happens somewhere else. in prokaryotes anabolism can happen in the periplasmic space to separate

what builds new cells?

carbon source + inorganic molecules

what does catabolism make thats necessary in anabolism?

precursor metabolites like the 12 carbon skeletons (most r used for a.a)

• ex: peptidoglycan is made of sugars and a.a, RNA is made of nucleotides, ATP is a ribonucleotide

nucleoside vs nucleotide

a nucleoside contains only a nitrogenous base and a five-carbon sugar, whereas a nucleotide is a nucleoside with one or more phosphate groups attached

what elements do the carbon skeletons have associated w them?

CHOPS but do not have N!!! acetyl-CoA and Succinyl-CoA has S

what r most of the carbon skeletons used to make?

amino acids

• oxaloacetate makes a lot of a.a

• ribose-5-P used for RNA + DNA

• Erythrose-4-P used to make aromatic a.a

• acetyl-coA can make fatty acids

• alpha-ketoglutarate important in nitrogen assimilation to make glutamate

what is the carbon source of autotrophs?

CO2 so they need a CO2 fixaiton pathway like Calvin Benson cycle or reductive TCA cycle

what r the CO2 fixation pathways?

• Calvin-Benson cycle

• Reductive TCA cycle

Archaea has some that we wont study. Both of these input CO2 as starting rxn

what is another name for calvin-benson cycle?

reductive pentose phospate cycle (starts w 5C, ends w 6C)

Calvin-Benson cycle

a CO2 fixation pathway whose main goal is to make glyceraldehyde-3-P from 3 CO2.

• it starts w 5C and ends w 6C

has 3 phases:

1) carboxylation phase

2) reduction phase

3) regeneration phase

3 ATPs and 2 NADPHs used per 1 CO2

where does the calvin cycle happen in eukaryotes?

in the stroma of chloroplasts

where does calvin cycle happen in prokaryotes?

occurs in carboxysomes (not an organelle, but a specialized location w/in cytoplasm like a storage inclusion)

• in cyanobacteria and some nitrifying bacteria, and thiobacilli

in the calvin cycle, how many ATPs and NADPH r used per one CO2?

3 ATPs and 2 NADPHs

carboxylation phase of Calvin cycle

the 1st step! Takes 5C sugar (ribulose 1,5-bisphosphate (RuBP)) and 1 CO2 and puts it together, then splits it in half

• catalyzed by the enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCo)

CO2 + ribulose-1,5-bisphosphate (RuBP) → 2 3-phosphoglycerate

• intermediate of EMP

what is the starting 5C sugar of Calvin cycle?

ribulose-1,5-bisphosphate (RuBP)

ribulose-1,5-bisphosphate (RuBP)

the starting 5C sugar in the Calvin cycle. It combines with 1 CO2 to become 2 3-phosphoglycerate

• catalyzed by RuBisCo

ribulose bisphosphate carboxylase/oxygenase (RuBisCo)

the enzyme that catalyzes the carboxylation phase in Calvin cycle

• 1 CO2 + RuBP → 2 3-phosphoglycerate

what is the product of the carboxylation phase in Calvin cycle thats also an EMP intermediate?

2 3-phosphoglycerate (3 carbons)

reduction phase of Calvin cycle

3-phosphoglycerate → Glyceraldehyde 3-P

• can do biosynthesis w/ it or can regenerate 5C sugar at top (RuBP)

regeneration phase of Calvin cycle

RuBP (rubulose-1,5-bisphosphate) is regenerated from G3P

• frucose and glucose are produced (reverse of PPP)

what is used up in Calvin cycle?

6CO2, 18 ATP, 12 NADPH

in the calvin cycle, what enzyme turns 3-phosphoglycerate → 1,3-bisphosphoglycerate?

phosphoglycerate kinase it uses 1 ATP

phosphoglycerate kinase

this is a reversible enzyme that functions in Calvin cycle and EMP

• In Calvin cycle, it turns 3-phosphoglycerate → 1,3-bisphosphoglycerate using 1 ATP

• in EMP, it turns 1,3-bisphosphoglycerate → 3-phosphoglycerate making 1 ATP

can use SLP

in EMP, what molecule turns 1,3-bisphosphoglycerate → 3-phosphoglycerate?

phosphoglycerate kinase, it generates 1 ATP

in Calvin cycle, what turns 1,3-bisphosphoglycerate → glyceraldehyde-3-phosphate?

glyceraldehyde-3-phosphate dehydrogenase, it uses 1 NADPH

in EMP, what enzyme turns G3P → 1,3-bisphosphoglycerate?

glyceraldehyde-3-phosphate dehydrogenase, it makes 1 NADH

glyceraldehyde-3-phosphate dehydrogenase

a reversible enzyme that catalyzes rxns btwn G3P and 1,3-bisphosphoglycerate using NAD(P)H

• in Calvin cycle: turns 1,3-bisphosphoglycerate → G3P using 1 NADHP

• in EMP: turns G3P → 1,3-bisphosphoglycerate making 1 NADH

when the Calvin cycle goes in reverse what is the flow of products and enzymes?

G3P ← 1,3-bisphosphoglycerate ← 3-phosphoglycerate

1) G3P dehydrogenase catalyzes 1st step and uses NADPH

2) phosphoglycerate kinase catalyzes 2nd step and uses ATP

Reductive TCA cycle

a CO2 fixation pathway that is the reverse of oxidative TCA cycle. It uses energy!

• used by some chemolithoautotrophs

  • depends on ferredoxin, limited to anaerobes

Needs:

• fumarate reductase

• alpha-ketoglutarate synthase

• ATP-dependent citrate lyase

Overall: 4 CO2 → oxaloacetate

• to PEP w the help of pyruvate and PEP synthases

who is the reductive TCA cycle used by?

some chemolithoautotrophs and more common in anaerobes

what nonreversible things does the reductive TCA cycle need?

• fumarate reductase

• alpha-ketoglutarate synthase

• ATP-dependent citrate lyase

what is the net rxn of reductive TCA cycle?

4 CO2 → oxaloacetate

• to PEP w the help of pyruvate and PEP synthases

• uses ATP and NADH

gluconeogenesis

makes glucose from pyruvate (reversal of glycolysis) but the 2 pathways r not identical! Uses ATP and NADH

• pacemaker is fructose 1,6-bisphosphatase

what is the pacemaker for glycolysis?

phosphofructokinase

what is the pacemaker for gluconeogenesis?

fructose 1,6-bisphosphatase

what are some of the enzymes unique to gluconeogenesis?

• glucose 6-phosphatase

• PEP carboxykinase

• pyruvate carboxylase

• fructose 1,6-bisphosphatase

pyruvate carboxylase

one of the enzymes unique to gluconeogenesis. It uses CO2 and ATP to convert pyruvate → oxaloacetate

PEP carboxykinase

one of the enzymes unique to gluconeogenesis. It uses GTP and CO2 to convert oxaloacetate → PEP

glucose 6-phosphatase

one of the enzymes unique to gluconeogenesis. It converts glucose 6-phosphate → glucose

fructose 1,6-bisphosphatase

the PACEMAKER enzyme for gluconeogenesis. It turns fructose 1,6-bisphosphate → fructose 6-phosphate using H2O to cleave the P

what r some enzymes unique to glycolysis?

• hexokinase

• phosphofructokinase

• pyruvate kinase

hexokinase

an enzyme unique to glycolysis. It turns glucose → glucose 6-phosphate

phosphofructokinase

the PACEMAKER for glycolysis!! It turns fructose 6-phosphate → fructose 1,6-bisphosphate by using ATP

pyruvate kinase

an enzyme unique to glycolysis. it turns PEP → pyruvate and generates an ATP

when is phosphofructokinase activated (glycolysis)?

• when high lvls of AMP and ADP (low energy signals)

• lots of fructose 6-P

  • if theres accummulation, means enzmye isnt going fast enough so we need to do glycolysis

• fructose-2,6-bisphosphate (euk)

when is phosphofructokinase inactivated?

with high energy signals

• high ATP

• high citrate

when is fructose 1,6-bisphosphatase activated (gluconeogenesis)?

high energy signals → too much energy, store it

• high ATP

• high citrate

when is fructose 1,6-bisphosphatase inactivated? (gluconeogenesis)

w/ low energy signals

• increased AMP and ADP

• increased fructose 1,6-bisphosphate

• increased fructose 2,6-bisphosphate (euk)

what energy is used to synthesize sugars?

Uridine diphosphate glucose (UDP-G)

• glycogen

• UDP-NAM-pentapeptide and UDP-NAG

what is the precursor to NAG?

fructose 6-phosphate

what is Uridine diphosphate glucose used for? (UDP-G)

for synthesis of sugars! It activates glucose. We put glucose together as glycogen so u have to activate it w/ this

• found in peptidoglycan

in order to make amino acids from the 12 carbon skeletons, what do u need to add?

amino group and sometimes sulfur

• nitrogen assimilation

• sulfur assimilation

what r the methods of synthesizing amino acids from carbon skeletons?

• nitrogen assimilation (add amino group)

• sulfur assimilation (some have S)

• amino acid biosynthetic pathways

anaplerotic rxns

balanced rxns. have to be balanced. if we make a.a we also need energy, we cant spend all of our 12 carbon skeletons

assimilatory pathways

inorganic nitrogen and sulfur are INCORPORATED into organic materials

• protein, nucleic acids, coenzymes

dissimilatory pathways

inorganic compounds are USED instead of oxygen as electron acceptors

• such as in anaerobic respiration

• product (NO3, NO2) is excreted into environment → cant keep iside of cell cuz pH drops → denaturation

nitrogen assimilation

we don’t have N in our 12 carbon skeletons but need it to survive (CHONPS). So we take inorganic N and incorporate it into organic molecules like a.a and nucleic acids

what r some potential sources of nitrogen for nitrogen assimilation?

• ammonia (NH3, more reduced) what we want!

• nitrogen (N2) lots in atmosphere but we cant use it

• nitrate (NO3, more oxidized) cant assimilate

assimilatory nitrate reduction

take somethig other than ammonia and turn it into ammonia. Used by bacteria to reduce nitrate → ammonia

• done by bacteria, fungi, and ohotosynthetic protists (euk)

• how microbes take NO3 from non usable form to usable NH3

NO3 → NO2 = nitrate reductase

NO2 → NH3 = nitrite reductase

where does assimilatory nitrate reduction happen in bacteria?

in cytoplasm

nitrate reductase

the enzyme that reduces nitrate → nitrite

NO3 → NO2

nitrite reductase

the enzyme that reduces nitrite → ammonia

NO2 → NH3

• produces water

nitrogen fixation

takes N2 gas and reduces it to NH3. (N2 → NH3)

• catalyzed by the enzyme nitrogenase

  • it is highly sensitive to O2 so if its present it wont function. Cells w nitrogenase will bind to O2 and get rid of it, not necessarily strict anaerobes

• only carried out by a few prokaryotes → diazotrophs

• exergonic process! needs 8 electrons and 16 ATP

nitrogen fixing bacteria can use 20% (1/5) of ATP made by host plant

what enzyme catalyzes nitrogen fixation?

nitrogenase

nitrogenase

the enzyme that catalyzes nitrogen fixation.

• it is super sensitive to O2 so it wont function if its present. the cells w nitrogenase will bind to O2 and get rid of it. not necessarily strict anaerobes tho

diazotrophs

the few prokaryotes that carry out nitrogen fixation

• chemotrophic bacteria and archaea (Klebsiella)

• plant symbionts (Rhizobium)

• cyanobacteria

what type of prokaryotes do nitrogen fixation?

diazotrophs!

• chemotrophic bacteria and archaea (Klebsiella)

• plant symbionts (Rhizobium)

• cyanobacteria

is nitrogen fixation endergonic or exergonic?

exergonic! requirs 8 electrons and 16 ATP

what r the 2 ways to incorporate ammonia?

• reductive amination

  • used when NH3 is high, no ATP needed

  • done by bacteria and fungi

  • alpha-ketoglutarate → glutamate by glutamate dehydrogenase (GDH)

• glutamine synthetase-glutamate synthase (GS-GOGAT)

  • done w bacteria ONLY

  • used when NH3 low, uses ATP

  • 2 steps

    • glutamate → glutamine by glutamine synthetase

    • alpha-ketoglutarate + glutamine → glutamate by glutamate synthase

reductive amination

a method to incorporate ammonia.

• used when NH3 is high, no ATP needed! but needs reducing power (NADPH)

• done by bacteria and fungi, acellular microbes

• alpha-ketoglutarate → glutamate by glutamate dehydrogenase (GDH)

who is reductive amination to incorporate ammonia used by?

bacteria, fungi, acellular microbes (viruses)

when NH3 is high what ammonia incorporation tactic is used?

reductive amination (requires no ATP)

glutamate dehydrogenase (GDH)

in reductive amination, it is the enzyme that turns alpha-ketoglutarate → glutamate by adding amino group

glutamate

the amino acid that is made when alpha-ketoglutarate gains an amino group either through reductive amination or GS-GOGAT

• when it donates its amino group again, it becomes alpha-ketoglutarate again

transaminases

donate amino group to make a.a or nitrogenous bases

• it takes the amino group from glutamate to turn it back into alpha-ketoglutarate

alpha-ketoglutarate → glutamate when NH3 is high and no ATP used is?

reductive amination, catalyzed by GDH

glutamine synthetase-glutamate synthase (GS-GOGAT)

a 2 step method for ammonia incorporation

• done in bacteria only!!

• happens when NH3 is low, uses ATP

1) glutamate → glutamine by glutamine synthetase

• gives another amino group, requires ATP

2) alpha-ketoglutarate + glutamine → glutamate by glutamate synthase

• donates amino group

GS-GOGAT ammonia incorporation is done by who?

bacteria only!

which ammonia incorporation method is used when NH3 is low?

GS-GOGAT

glutamate → glutamine

this is the 1st step in GS-GOGAT. it is catalyzed by glutamine synthetase which adds another amino group to glutamate

• uses ATP

glutamine synthetase

the enzyme that catalyzes the 1st step in GS-GOGAT. This enzyme adds another amino group to glutamate which turns it into glutamine.

• uses ATP!

alpha-ketoglutarate + glutamine → glutamate

the 2nd step in GS-GOGAT. It is catalyzed by glutamate synthase which donates amino group from glutamine to alpha-ketoglutarate so that we have 2 glutamates.

glutamate synthase

the enzyme catalyzing the 2nd step in GS-GOGAT which donates the 2nd amino group from glutamine to alpha-ketoglutarate so that we make a 2nd glutamate

what do we need sulfur for?

• synthesis of amino acids

  • cysteine → creates covalent disulfide bridges in tertiary and quaternary protein structure

  • methionine → start codon AUG

• synthesis of coenzymes (Co-A)

  • sulfur in thioester bond

what does cysteine do?

it donates reduced sulfur cuz u need sulfur assimilation to make cysteine (H2S)

sulfur assimilation

we can obtain sulfur from external sources and intracellular amino acid reserves

• sulfate (SO4, inorganic) more oxidized form

• phosphoadenosine 5’-phosphosulfate (PAPS)

• sulfate reduced to H2S → cysteine (will take S and donate it where needed)

sulfate (SO4)

the more oxidized inorganic form of sulfur, we want to reduce it to sulfide

phosphoadenosine 5’-phosphosulfate (PAPS)

While cysteine donates reduced sulfur (like thiol groups or persulfides) for things like iron-sulfur clusters, PAPS donates oxidized sulfur (sulfate, SO₄²⁻, or sulfonate, -SO₃⁻)

u need sulfur asimmilation to make what?

cysteine

• sulfate reduced to H2S → cysteine

amino acid biosynthesis

regulated by feedback mechanisms

• single precursor → several a.a

  • branching pathways

  • oxaloacetate → lysine, threonine, isoleucine, and methionine

in making a.a, what is the 1st thing oxaloacetate does?

accept amino group from glutamate which turns it into alpha-ketoglutamate

what element do we tag proteins with?

sulfur (we tag DNA w P)

the a.a acid L-Lysine is special in peptidoglycan cuz?

in gram (+) bacteria, it is the 3rd a.a and has 2 amino groups so can make 3 peptide bonds

there is feedback inhibition btwn which 2 amino acids?

threonine and isoleucine. (-) feedback to threonine to stop making isoleucine so we can have all 20 a.a

what amino acids does oxaloacetate make?

lysine, threonine, isoleucine, methionine

what r the aromatic amino acids?

phenylalanine, tryptophan, tyrosine

how r aromatic a.a made?

using the Shikimate pathway with starting products PEP + Erythrose-4-P

• not present in animals, only used by bacteria, fungi, and some protozoa (euk)

• need to make Chorismate intermediate