biochem exam 3 #1: Enzyme Catalysis and Metabolism

why use histidine within acid-base catalysis

histidine has a pka of 6, close to physiological ph, so it can readily lose and donate a proton

what is the henderson-haselbach equation

pH = pKa + log([A]/[HA])

why does enzyme activity depend on pH

if a protein is overly protonated or deprotonated, it will have lower activity because it may not be able donate or receive protons

what is the result of an enzyme’s activity being heavily based on pH

very narrow pH range

active site of chymotrypsin

catalytic triad that serves as a proton relay system

how does the catalytic triad within chymotrypsin work

aspartate stabilizes already protonated histidine → can take proton from serine → can attack peptide bond of a protein

when pH < PI

positive

when pH > PI

negative

oxidation-reduction as a chemical strategy in metabolism

transfer of electrons (oxidation) to release energy

key component of oxidation-reduction strategy

when oxidation occurs, something must also always get reduced (carrier molecules like NAD+ capture electrons)

two primary electron carriers and purpose

NAD+ and FAD, once reduced, they store energy for later use

phosphoryl transfer as a chemical metabolic strategy

transfer of phosphoryl groups (REMEMBER A PHOSPHORYL GROUP IS PO3) to release energy

why even have high-energy reactants if you’re going to end up with ATP as an intermediate most of the time anyway

ATP cannot be created from a lower energy molecule → need high energy molecule like PEP for creation of ATP from ADP

key points of energy coupling

nonspontaneous reactions (+G), are driven by reactions with stronger spontaneity (-G)

why use ATP?

kinetically stable (won’t break down in water), but thermodynamically unstable (breaking bonds releases lots of energy)

what happens before glycolysis even begins

glucose enters cell through passive transport of GLUT transporters

why do some tissues have a low km and some a high km with regards to GLUT transporters

tissues like the brain and heart need constant energy, but some tissues like the liver and pancreas are just for storage of glucose at times

describe energy investment phase of glycolysis

two phosphorylation reactions → destabilizes the molecule and increases metabolic reactivity

step 1 of glycolysis (MUST BE MEMORIZED)

glucose → glucose-6-phosphate (first phosphorylation)

enzyme: hexokinase

step 3 of glycolysis (MUST BE MEMORIZED)

fructose-6-phosphate → fructose-1,6-biphosphate (second phosphorylation)
phosphofructokinase

step 6 of glycolysis (MUST BE MEMORIZED)

glyceraldehyde-3-phosphate (GAP) → 1,3-biphosphoglycerate
NADH produced

step 7 of glycolysis (MUST BE MEMORIZED)

1,3-biphosphoglycerate → 3-phosphoglycerate
ATP produced

step 10 of glycolysis (MUST BE MEMORIZED)

PEP → pyruvate
ATP produced

before entering energy payoff phase, what is key that occurs

cleavage → now we have two three carbon molecules

net glycolysis yield

2 ATP
2 NADH
2 Pyruvate

how are hexokinase and phosphofructokinase regulatory

hexokinase → inhibited by its product, glucose-6-phosphate

Phosphofructokinase → commits the glucose for glycolysis purposes, inhibited by ATP accumulation (allosteric enzyme)

how does glycolysis act as a metabolic hub

can produce energy, but also supports biosynthesis of other macromolecules

purpose of fermentation

allows glycolysis to continue when oxygen is limited AND regeneration of electron carrier NAD+

two primary fermentative pathways + examples

lactic acid fermentation
- pyruvate → lactate + NAD+
- muscle cells during intense exercise

alcoholic fermentation
- pyruvate → ethanol + CO2 + NAD+
- yeast

warburg effect

cancer cells undergo aerobic glycolysis (fermentation even in presence of oxygen)

increase lactate production

how do cancer cells keep up with normal cells if net outcome is less ATP for their respective pathways

cancer cells eat a LOT more sugar (can be shown in PET scans)

significance of step 6 in glycolysis

GAP → 1,3-bisphosphoglycerate
NAD+ is reduced to NADH

is glycolysis linear or cyclical

linear

where does glycolysis occur

cytosol

significance of first glucose phosphorylation

traps glucose inside cells (cannot leave through GLUT now)

difference between step 6 of glycolysis as opposed to steps 7 and 10

glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate is a redox reaction producing NADH

1,3-bisphosphoglyceride → 3-phosphoglycerate and PEP → pyruvate are substrate level phosphorylation producing 2 ATP each