biochem exam 4

catabolism

breaks things down

releases energy

cell captures released energy by phosphorylating adp→atp and reducing nad+→nadh

anabolism

builds things up

uses energy

amphibolic

both catabolic and anabolic

ex tca cyle

3 pathway topologies of metabolism

linear, cyclic, and branched

why take steps

1 step can be too much of a jump and releasae energy as heat, so small steps capture atp and nadh

compartmentalization

pathways in specific compartments to control flow

channeling

enzyme complexes directly handoff enzymes and substrates

atp structure

adenine + ribose = adenosine

+ phosphates = amp, adp, atp

ribose to alpha phosphate bond

phosphodiester bond

bond between phosphates

phosphoanhydride bonds

atp conc. in cells

~5mM

atp hydrolysis favorable but has actibvation barrier

coupling

combining delta gs to make negative to make favorable

atp is universal

every cell uses atp as energy currency

energy is cycled

cells dont store atp its spent and reearned continuously

fuel = what

reduced carbon = c w lots of c-h bonds

3 stages of catabolism

1. digestion/hydrolysis

2. conversion to acetyl-coA

3. tca + etc + atp synthase

activated carriers

atp → carries phosphoryl groups

nadh/fadh2 → carries electrons

acetyl-coA → carries 2 carbon acyl units

phosphoryl transfer

phosphate moves from 1 molecule to another

oxidation-reduction

electrons move between substrate and NAD+/FAD

decarboxylation

carbon leaves as CO2

group transfer/isomerization

rearranging a substrate or moving a group from one molecule to another

allosteric regulation

fastest, small effector molecule binds away from actie site

ex. pfk-1 inhibited by atp, activated by amp

covalent regulation

minutes, kinase adds phosphate, phosphatase removes it

ex. glycogen synthase

transcriptional regulation

hours, change how much enzyme exists

ex. insulin + glycogen

irresverisble steps

1-way reactions, these steps set it

sit far from equilibrium

committed step

1st irreversible step thats unique to reaction

feedback inhibition

end product slows pathway

ex. ctp inhibits atcase in pyrimidine synthesis

feed-forward activaiton

upstream surge priems downstream enzyme fro substrate

ex. F1,6BP activates pk in glycolysis

energy charge

sense atp/adp/amp ratios; ato inhibits + amp activates

ex pfk-1

PFK-1

enzyme that catalyzies committed step of glycolysis

3 layers of control

fast allosteric pfk 1

atp and citrate inhibit pfk-1

amp activates it

medium, hormonal, pfk1

insulin and glycogen act on pfk2 which sets fructose-2,6-bisphosphate, pfk-1 main actiavtor

slow, transcriptional

sustatined diets and hormonal state alter how much pfk1 the cell synthesizes

glycolysis

glucose broken in 2

runs in cytoplasm

works w or w/o oxygen

glycolysis starting materials

1 glucose, 2 nad+, 2adp, 2Pi

glycolysis products

2 pyruvate, 2 nadh, 2atp(net_, 2 H2O

glucose phase 1 steps

glucose → G6P → F6P → F1,6BP → GAP and DHAP→GAP

phase 2 glycolysis

2x GAP → 1,3BPG→3PG→2PG → PEP → pyruvate