12 - Metabolism and Bioenergetics

catabolism

cells break down large molecules to release free energy and small molecules

anabolism

free energy and small molecules used to rebuild larger molecules

chemoautotrophs

organisms where almost all metabolic building materials and free energy from simple organic compounds CO2, N2, H2, S2

photoautotrophs

organisms whose metabolism mainly needs CO2, H2O, nitrogen source, and sunlight (mainly freen plants)

heterotrophs

organisms that directly or indirectly obtain all their building materials and free energy from organic compounds produced by chemo or autotrophs

includes animals, why mammals rely on food produced by other organisms (after digested and absorbed, becomes source of metabolic energy and materials to support animal’s growth and other activities)

4 main aspects of human diet

proteins, nucleic acids, polysaccharides, triacylglycerol

what catalyzes digestion in mouth, stomach, and small intestines

catalyzed by hydrolytic enzymes

• amylase (saliva) breaks down starch

• gastic and pancreatic proteases degrade proteins

• lipases secreted by pancreas

how do monosaccharide digestion products enter cell

enter via active transporters, such as Na+-glucose system (similar active transporters bring amino acids, dipeptides, tripeptides into cell)

how do very hydrophobic lipids enter cell

diffuse through membrane, some require transporters

once back in cell, triacylglycerol digestion products reform triacylglycerols ; some fatty acids link to cholesterol to form cholesterol esters (like cholesterol stearate)

lipoproteins form when…

triacylglycerols and cholesterol esters and certain proteins are packaged together → particles specifically known as chylomicrons

chylomicrons made of, what they do

packages of triacylglycerols, cholesterol esters, some proteins

relay into lymphatic circuit, then bloodstream for delivery to tissues

where do most of a meal’s nutrients go following digestion?

mostly to liver, where they’re catabolized, stored, or released back into bloodstream

lots of circulating monomers (some taken up to fulfill immediate needs, but some tissues specialized for long-term storage of nutrients)

what do liver and muscles use monosaccharides for?

synthesize glycogen (storage polymer of glucose)

what happens to glucose that doesn’t become part of glycogen

can be catabolized to 2-carbon acetyl units and converted into fatty acids for storage as triacylglycerols

are proteins dedicated storage molecules for amino acids? what happens when the body has excess aas?

not dedicated storage molecules; excess amino acids can be broken down and converted to carbohydrates (stored as glycogen) or converted to acetyl units (can be converted to fat)

what are metabolic fuels?

amino acids, monosaccharides, fatty acids; can be broken down by processes that make free energy available for cells’ activities

how and when is glycogen degraded

usually via phosphorylysis; only when glucose runs low does adipose tissue mobilize its fat stores

what happens when lipid hydrolyzes triacylglycerol

releases fatty acids into bloodstream (bind to proteins), heart is really only part of body that uses fatty acids as primary fuels

2 major mechanisms for degrading unneeded proteins

lysosomes, proteasomes

what are lysosomes/what do they do

organelles with proteases and other hydrolytic enzymes → breaks down proteins in membraneous vesicles (membrane proteins, extracellular proteins for endocytosis, and intracellular proteins)

what are proteasomes/how do they work

barrel-shaped structures that allows proteins to enter when they’re tagged with ubiquitin; breaks them down

what is ubiquitin

proteasomes must be tagged with it before proteins can enter; ubiquitous 76-residue protein that’s highly conserved in eukaryotes

how is ubiquitin attached to proteins

via enzymes linking ubiquitin c-terminal to protein lysine side chain, need ≥ 4 ubiquitin subunit chain of ubiquitin to mark protein for proteosome destruction

what are metabolic pathways

series of reactions/steps required to break down monomeric compounds or build them up from smaller precursors

metabolites present in almost all metabolic pathways, in order

6 carbon sugar (glucose), is split → 2 molecules of glyceraldehyde 3-phosphate → pyruvate, gets decarboxylated → acetyl CoA (CoA linked with 2C acetyl group)

glyceraldehyde 3-phosphate

pyruvate structure

acetyl CoA structure

OILRIG

oxidation is loss of electrons, reduction is gain of electrons

what are oxidation-reduction reactions

as one compound becomes more oxidized (gives up/loses hold of electrons), another compound becomes reduced (receives/tightens grip on electrons)

how does oxidation of carbon atoms frequently appear/occur

replacement of C-H bonds (where C-H shares electrons equally) with C-O bonds (electronegative O pulls electron away from carbon) therefore carbon ‘gives up’ some electrons

cofactors/coenzymes

when metabolic fuel is oxidized, electrons are transferred to them

NAD+, NADP+

reduction of ubiquinone to ubiquinol, how it compares to NAD+

stepwise; ubiquinone can take one electron and be QH. (radical) or two electrons and be QH2

NAD+ is strictly a 2 electron carrier

how are many reduced cofactors (created from catabolic pathways such as citric acid cycle) reoxidized

via anabolic reactions of via ADP + Pi → ATP

oxidative phosphorylation in mammals

reoxidation of NADH + QH2 and concurrent ATP production; requires reduction of O2 → H2O

what kind of process is reverse of either CO2 → fatty acid carbon or carbohydrates, what does it look like?

reduction process; C atoms regain e- as C-O bonds are replaced by C-H bonds

requires free energy (such as sunlight) for CO2 → CH2O therefore reduced carbon of carbs is a form of stored free energy

5 main important features of metabolism

metabolic pathways all connected (products of one = substrates of another)

pathway activity regulated

not every cell carries out every pathway

each cel has unique metabolic repertoire

organisms may be metabolically interdependent

how are metabolic pathways regulated

via flux (flow of intermediates); won’t synthesize polymers if lacking monomers; won’t catalyze fuels if low need for ATP

why are some amino acids and unsaturated fatty acids considered essential

the human body can’t synthesize them

do humans synthesize vitamins

no

how was first b-vitamin discovered

studying beriberi, caused by deficiency of thiamine and vitamin B

what is pellagra, treating symptoms

vitamin deficiency disease missing niacin (a component of NAD+ NADP+)

symptoms alleviated by taking more tryptophan, which humans can convert to niacin

Keq for reaction A+B — C+D at equilibrium

[C]eq[D]eq / [A]eq[B]eq

standard free energy change equation

delta G knot prime = -RT ln Keq

what does larger value of free energy change indicate

reaction is farther from equilibrium; stronger tendency for reaction to proceed

equation to calculate free energy changes

delta G = delta G knot prime + RT ln [C][D]/[A][B]

mass action ratio

concentration term of actual, noneq concentrations → [C]^c[D]^d / [A]^a[B]^b

delta g at eq

0

what impacts delta g

temperature, mass action ratio

how do unfavorable reactions occur

they’re coupled to favorable ones

common favorable reaction couples to unfavorable ones

ATP + H2O → glucose-6-phosphate + ADP

delta G knot prime = -16.7 kJ/mol

ATP to/from ADP + Pi cycle more stable compound, why

ATP hydrolysis products are more stable than reactants

a compound with phosphoanhydride bond experiences less resonance than hydrolysis products; ADP + Pi has more resonance stability (which reflects degree of electron delocalization in a molecule)

why does ATP function as an energy currency

its hydrolysis reaction is highly exergonic (delta G much less than 0)

therefore favorable ATP → ADP rxn can pull another, unfavorable reaction with it as long as sum of delta G is less than 0 for both

common unfavorable reaction