Last Exam 2 Flashcards
Why are enzyme reactions regulated? [3]
- To respond to energy-production needs as energy expenditure varies (e.g. during exercise vs at rest)
- To respond to physiological needs (e.g. after meal vs before a meal) to produce only what we need, when we need it
- To avoid futile cycles (i.e. regulating opposing cycles so both aren’t “running” at same time)
Metabolic pathways need to be regulated to keep organism in ___________. Give an example of how this could be done.
Homeostasis (negative feedback of one product acting to block an earlier enzyme in the pathway - like pyruvate dehydrogenase being inhibited by ATP)
What effect does glucagon have on glycogen and glucose in liver cells? What about insulin?
How is a balance achieved?
What general factors can affect enzyme reactions? In organisms, what is the primary mechanism for change?
Increased glycogenolysis and gluconeogenesis (+ decreased glycogen synth + glycolysis). Opposite in the case of insulin.
Often, there are different enzymes involved in at least part of catabolic/anabolic pathways (eg: gluconeogenesis bypass reactions)
Substrate/reactant concentrations, pH, temperature. In organisms: altering the enzymes themselves
Three overarching methods of metabolic enzyme regulation?
Compartmentation, altering enzyme concentration, altering enzyme activity
Give an example of compartmentation (enzyme regulation)
What is microcompartmentation?
B-oxidation in mitochondria, fatty acid synthesis in cytosol
Regulation (eg: by concentration) within the same area (eg: cytosol) of cell (eg: enzymes attached to inner plasma membrane = activity only in those areas)
How do you change the concentration of an enzyme?
Give an example of this…
Why might this example not work with metabolic regulation?
Make more or less of it (altered gene expression)
Lac operon: operator represses transcription when allolactose is not bound (releases when bound), activator will only bind when cAMP levels are high (and bound to it) [= low glucose]
Less ability to fine tune, and can take a while to respond
Changing enzyme concentration: how could you make less of it?
Why might this also be problematic for metabolic regulation?
Degrade it (ubiquitin tagging -> proteosome)
Once it is gone, it will take time to restore (so difficult to fine tune)
How could you alter active enzyme concentration (as opposed to making more or less)?
Give an example of this process
Is this quicker or slower than altering gene expression? What might still be a drawback?
Zymogen (inactive precursors) activation
Pepsinogen -> pepsin
Quicker (drawback: binary - active or not, and irreversible)
Pepsinogen activation is __________ and _____________ (initially), and then _____________
What needs to be cut off to make it active? Where is it found?
When is it activated? Why is it done this way?
autocatalytic (cleaves itself), intramolecular, intermolecular
Pro domain (sits in active site of pepsin)
Low pH (of stomach) and presence of proteins causes the cleavage of pro domain - it is a non-specific protease (which would eat up the wrong proteins)
Which pancreatic enzymes are secreted as zymogens?
How are they cleaved to their active forms?
Trypsinogen, chymotrypsinogen, proelastase
Enteropeptidase (specific intestinal protease) cleaves trypsinogen to trypsin (which can cleave chymotrypsinogen to chymotrypsin and proelastase to elastase)
Changing metabolic flow by changing enzyme activity: ________ modification via _____________ by kinases. What does this do? What are the benefits?
Where does this process occur? Thus, which aminos can it happen to?
What difference does this make to the molecule?
covalent, phosphorylation - makes the enzymes active/inactive/better/worse (fast, reversible, allows fine-tuning, not binary)
OH groups of amino acid R groups (serine, threonine, tyrosine - only ones with such groups)
Adds bulky and negatively charged group (alters structure and therefore activity - form is function!)
Changing metabolic flow by altering enzyme activity: what peptide loops are important in enzymes?
In an unphosphorylated enzyme that is inactive, what would phosphorylating do to these loops?
What type of enzyme adds/removes phosphates?
Activation loop and catalytic loop
It would move the activation loop away from the catalytic loop, thus allowing the substrate access to the active site
Kinase adds, phosphatase removes
Three advantages of using phosphorylation as a form of metabolic regulation
Fast (enzyme-catalysed changes in protein structure), reversible (kinases/phosphatases), and allows for fine-tuning (varying extent of phosphorylation)
Changing metabolic flow by changing enzyme activity: Covalent modification (eg: phosphorylation) is one method. What is the other? What is this?
What enzymes are likely to be affected by this? What does this do to Michaelis-Menten curves if it present?
What acts as an allosteric regulator?
Allosteric modification (molecule binds non-covalently to the enzyme away from the active site, alters overall shape of the enzyme, and +/- binding at active site)
Enzymes with quaternary structure (makes M-M curve sigmoidal [s shaped] as opposed to hyperbolic [normal])
Any cellular metabolite (ATP, AMP, G-6-P, etc)
Covalent modifications, allosteric effects, enzyme synthesis - put these in order of speed, in terms of effect, and say how long each one takes
Allosteric effects (milliseconds), covalent (seconds), ezyme synthesis changes (hours/days)
Reminder: steps of regulation of glycolysis? Name of enzymes? What do these steps have in common?
Steps 1 (Hexokinase), 3 (phosphofructokinase-1), and 10 (pyruvate kinase) - largest loss of free energy
Pyruvate kinase (glycolysis reaction 10): in its active state, is it phosphorylated or not? How could you figure this out if you didn’t know?
Unphosphorylated. Use your brain: this pathway is for the breakdown of glucose. Low serum glucose leads to production of glucagon; this activates kinases (which phosphorylate proteins). As you wouldn’t be breaking down glucose in this situation, you would expect a control mechanism to stop this process - so things like pyruvate kinase would be inactivated. As glucagon leads of phosphorylation, it seems likely that pyruvate kinase would be active when unphosphorylated.
Modifying pyruvate kinase is not the best way to regulate glycolysis? Why? What would be better?
No - it’s at the end of the pathway. Targeting an earlier enzyme (like hexokinase)
How is hexokinase regulated?
What does hexokinase do?
Is glucokinase (liver) regulated in the same way? Why?
Allosterically inhibited (by glucose-6-phosphate)
Converts glucose -> G6P (traps glucose in cell)
No. Needs to undertake much more glycogen production (which requires G6P - don’t want it being inhibited!)
After glucose has been converted to G6P, where can it go?
Should the cell regulate only hexokinase (and not other steps in glycolysis pathway)? Why?
Onwards to pyruvate or to the pentose phosphate pathway
No: G6P is used in other pathways, and hexokinase is bypassed in tissues that break down glycogen
Which is the most tightly regulated step of glycolysis? Why?
What allosterically regulates this step/enzyme?
What other enzyme regulates this step? How?
Step 3 (Phosphofructokinase-1: F6P to F1,6P) - rate limiting step (first committed step of glycolysis - irreversible)
ATP and PEP (Phosphoenolpyruvate - precursor to pyruvate) inhibits, AMP and ADP activates
PFK-2 (F6P to F2,6P) - catalyses forwards and reverse reaction. With high glucose (and insulin), increases forwards reaction (and F2,6P acts as an allosteric activator of PFK-1) [and then, as F6P is used up, reverse reaction will occur - Le Chatelier’s Principle]
What is reciprocal regulation? Examples?
Pathways involving opposite processes (glycolysis/gluconeogenesis or glycogen synthesis/breakdown) that need to be regulated independently, and should not both be active at the same time (eg: glycolysis yields 2ATP, gluconeogenesis bypass reactions cost 6ATP, so futile cycle of these two would be losing 4ATP each time)
Reciprocal regulation: Thinking of PFK-1 (step 3 of glycolysis) and F-1,6-biphosphatase (bypass step of gluconeogenesis), what would the presence of AMP do?
What about F-2,6-phosphate?
Allosterically activates PFK-1 and inactivates the biphosphatase (= ATP created through glycolysis, gluconeogenesis [high ATP cost] shut down).
Means there is lots of glucose = allosteric activation of PFK-1 and inhibition of biphosphatase
Reciprocal regulation: what are enzymes involved in glycogen synthesis and breakdown called?
How does G6P affect these?
Glycogen synthase and glycogen phosphorylase 1
Acts as allosteric activator of GS and allosteric inhibitor of GP-1
