Biochem Exam 2 Ch 14-15

Digestion

begins with physical process of chewing, through the stomach, and finishes in the intestine

Usable molecules in food

lipids, carbs, and proteins

Stomach pH

1-2

pepsin

proteolytic enzyme that works at the low optimal pH of the stomach

Converting food to energy

biomolecules from food broken into smaller molecules, small molecules processed into Acetyl CoA, complete oxidation of Acetyl CoA to yield ATP

Post-stomach digestion

food and some stomach acid pass into intestines, low pH indicates movement and stimulates release of secretin

secretin

stimulates release of NaHCO3 from pancreas to neutralize pH

Protein Digestion

high recirculation of proteins in body as AA

Proteases

break peptide bonds via hydrolysis into oligopeptides, broad or highly specific

Zymogens

inactive precursors of proteases, prevents self-digestion

Activating zymogens

by protease digestion

Self-activating zymogens

pepsinogen and pi-chymotrypsin

CCK actions

increase release of pancreatic enzymes and bile salts from gall bladder

Stimulation for CCK release

peptides in food/food intake

Protease inhibitors

prevent self-digestion by limiting time and location of activity

Peptidases

cleave oligopeptides into individual AAs to go to blood stream

Peptidases locations

in cells or their membranes

Enteropeptidase

from intestine, activates trypsinogen to trypsin, trypsin activates a variety of others

Alpha-amylases

initial carb digestion starting in saliva, cleaves 1,4-bonds only

Final Carbohydrate digestion

requires specific enzymes for final clippings (Ex. lactase for lactose)

SGLT

Glucose & Galactose symport with Na+ into cell

GLUT5

channel, allows fructose to enter a cell

GLUT2

channel, allows glucose, galactose & fructose to exit a cell into the bloodstream

Emulsification of lipids

initial stage of lipid digestion, bile salts surround fat droplets to increase solubility in intestines

Glycocholate

cholesterol derived molecule in bile salts, mostly hydrophobic but has a polar, charged region for solubility

Lipases

removes 1 FA chain at a time from triacylglycerols

Micelles

formed from free FA, increased solubility with bile salts

FABP

transports FA & monoglycerols into cells

FATP

brings FA & monoglycerols to SER to be repackaged as triacylglycerols

Chylomicrons

triacylglycerol + protein + cholesterol + phospholipids, exported into lymph/muscle/adipose tissue

Gluten

a class of storage proteins high in Gln and Pro concentration, used by plants

Celiac Disease

Incomplete digestion of gluten by proteases, produces inflammatory response

Snake Venom

modified saliva containing 50-60 proteins for digestion prior to consumption, useful drug treatment

Caloric Homeostasis

maintaining adequate, but not excessive, energy stores

Short term hormone signaling for caloric homeostasis

register satiety/fullness, decrease hunger

Food intake (short term signaling)

causes release of CCK & GLP-1

Long term hormone signaling for caloric homeostasis

report energy states

Insulin

report & regulate glucose levels, from beta-pancreatic cells

Leptin

report TAG levels, from adipocytes

GLP-1

slows emptying of gastric system, and activates beta-pancreatic cells for insulin

CCK & GLP-1 Similarity

act via g-protein coupled receptors

Energy usages

mechanical work, synthesis of biomolecules, active transport

Phototrophs

obtain energy from sunlight (ex. plants)

Chemotrophs

obtain energy from oxidation of carbon fuels (ex. animals)

Intermediary Metabolism

all metabolic pathways defined in a cell

Metabolic pathways

how molecules are synthesized and degraded along a series of rxns

formation of ATP

oxidation of carbon fuels

Rxn types for metabolism

limited number of rxn types and intermediates

Pathway thermodynamics using ATP

Unfavored pathways must be linked w/other rxns to have a net favorable effect. Unfavored + ATP (highly favored) = overall favored

ATP energy

contains 2 high-energy phosphoanhydride bonds, release up to -50kJ/mol, increase Keq by 10^8, highly exergonic

Catabolism

breaking down, generate energy, Fuel = Co2 + H2O + ATP

Anabolism

building up, requires energy input, ATP + simple molecules = complex molecules

Shared Rxn Distinctions

Catabolism and anabolism share rxns, but regulated, non-reversible rxns are distinct to a path

ATP Stability

less stable that ADP + Pi, more energetically favored than hydrolysis of other phosphate esters

Electrostatic Repulsion of ATP

4 negative charges in a small molecule, high repulsion, less stable

Resonance of ATP

fewer resonance possibilities than ADP + Pi, Pi has 4, ATP has 3, less stable

Entropics of ATP

Disorder increases as ATP is split to ADP + Pi, less stable as ATP

Hydration of ATP

ATP cannot bind with H2O, Pi binds to H2O after split from ATP

Phosphate Transfer Potential

ability to transfer P to another molecule

Molecules w/higher transfer potential that ATP

phosphoenolpyruvate, 1,3-bisphosphoglycerate, creatine phosphate

What if ATP had the highest P transfer potential

we would never have the chance to form it, always wants to dissociate, ATP could never be a P carrier for signaling

ATP Regeneration

continuously regenerated since no large reserves, enough stored to support 1 sec of contraction

Creatine phosphate

reservoir of high-energy phosphate, good for a few seconds to a minute

oxidation of carbons

e- lost and indirectly transferred to O2

Oxidation Energy

oxidized molecule is low energy, gave up its energy to generate ATP

Capturing delta G°’

stored in compounds with high phosphate transfer potential or ion gradients

Oxidation of multiple carbons

does not occur simultaneously within a molecule, carried out 1C at a time

FA oxidation

more fully reduced Cs, more energy provided to make ATP

Oxidation of Carbon steps

1. e- captured & high transfer potential molecule is made

2. high potential acylphosphate is stabilized by loss of phosphate group, donated to ADP

Commonalities in metabolism

metabolites, regulatory schemes, intermediates connecting different paths, laws of physics and chemistry

Coenzymes

small, organic molecules from vitamins, needed for some enzymatic functioning

Activated Carriers

carry activated functional groups of metabolic rxns

Phosphate carriers

ATP

Electron carriers in oxidation

NAD+, FAD, FMN. pickup & shuttle e-

Electron carriers in biosynthesis

NADPH. bring & donated e- to a reduced molecule

2C-unit carrier

Coenzyme-A

NAD+

oxidized form, accepts 2e- and 1H+ (AKA H:-) to become reduced NADH, typically for rxns with release of H+ like carbonyl formation

FAD

oxidized form, accepts 2e- and 2H+ to become reduced FADH2, 2 active sites on N

NADPH

reduced form, donates 2e- and 2H+ to become oxidized NADP+

Coenzyme A

2C carrier, links with acetyl group to become activated Acetyl CoA

Coenzyme A structure

Adenosine Diphosphate + Pantothenate + beta-mercaptoethylamine (with reactive thiol site)

Thiol group of CoA

forms thioester to become acetyl CoA

Acetyl transfer from Acetyl CoA

Thioester lacks resonance compared to typical ester due to orbital overlap, low stability means acetyl is activated.

Acetyl CoA breakdown

Acetyl CoA = CoA + acetate, highly exergonic and favorable

Pantothenate Activation

done by pantothenate kinase, needed to form CoA.
pantothenate + ATP = pantothenate-P + ADP

Hallervorden-Spatz

lacking pantothenate kinase, leads to neurodegenerative disease since NS needs CoA for respiration

Activated Carrier Features

Kinetically stable, energy is high but not too high (can be donor or acceptor), versatile, derived from B vitamins

Kinetic stability

-delta G, but high Ea, not reactive with O2, resistant to hydrolysis

Isoenzymes

different forms of an enzyme that catalyze different reactions and are under different regulations, typically in different tissues

Mechanisms for Metabolic Regulation

control [E], control catalytic activity of E, control accessibility of S

Enzyme concentration & environment

Cell will increase [E] in response to presence of substrate in environment

Controlling catalytic activity of E

allosteric, post-translational modification, covalent modifications (phosphorylation), energy charge

Energy charge equation

(ATP + 1/2(ADP))/(ATP+ADP+AMP)

Energy Charge

what percent of A nucleotides are in high energy form

ATP-generating paths & energy charge

will slow down as cell has more high energy A nucleotides

ATP-utilizing paths & energy charge

accelerates w/ increase in high energy nucleotides

Controlling accessibility of substrate

Compartmentalization to keep S from E when rxn not needed

FA synthesis location

cytoplasm

FA oxidation location

mitochondria