How should an ideal enzyme for regulatory intervention be able to dictate in relation to all other reactions in a pathway?

The ideal regulatory enzyme for intervention is one whose quantity (E_t) or catalytic efficiency (K_cat or K_m) dictates that the unique reaction it catalyzes is slow relative to all others in the pathway.

What are two ways to change the amount of an enzyme?

Induction or Repression

Cis elements, specific DNA sequences
located upstream of regulated genes, and transcription factors relate to which form of enzyme regulation?

Changing the total amount of an enzyme through either induction or repression

Which form of enzyme regulation involves conformational changes?

Changes in the intrinsic catalytic efficiency of an enzyme
through via conformational changes (without changing the amount of the enzyme)

Glycolytic enzymes present specifically in the cytosol as well as Urea cycle enzymes present specifically in mitochondria matrix and/or the cytosol are examples of what form of enzyme regulation?

Compartmentalization of enzymes

Which form of enzyme regulation ensures metabolic efficiency?

Compartmentalization of enzymes in specific organelles or cytosol

Name 5 ways to alter the intrinsic catalytic capacity of a regulatory enzyme:

What regulates the induction or repression of enzymes?

Hormones (water or lipid soluble) that act as first messengers

What turns on the transcription factor, CREB?

Protein Kinase A

Activated protein phospohtase-1 dephosphorylates what enzymes? Is this enzyme active or inactive?

Protein phosphatase-1 dephosphorylates and activates glycogen synthase;

Protein phosphatase-1

dephosphorylates and inactivates glycogen phosphorylase

What are the three domains of steroid hormone receptors?

1. Ligand binding doman

2. DNA binding domain

3. Transactivation domain

What two hormones induce PEPCK? When does this occur?

PEPCK, a gluconeogenesis enzyme, is induced by cortisol and glucagon during the fasting (stressed) state

What binds to GRE?

Cortisol binds to the Glucocorticod Response Element (GRE)

GRE and CRE elements (genes) are located _______ of the PEPCK gene

GRE and CRE elements (genes) are located upstream of the PEPCK gene

Would insulin repress or induce PEPCK?

Insulin would repress PEPCK because PEPCK is a gluconeogenesis-involved (catalytic) enzyme that is turned OFF during the fed state when biosynthesis of glycogen is occuring

Phosphorylation and dephosphorylation of regulatory enzymes as a response to hormones is an example of __________. What kinds of hormones facilitate this?

Covalent modification of regulatory enzymes (a change in the K_cat) facilitated by peptide hormones (glucagaon, insulin, epinephrine, etc.)

How is covalent modification between peptide hormones and regulatory enzymes mediated?

Second messengers

Phosporylation/Dephosphorylation of regulatory enzymes by second messengers occurs on what amino acid residue types?

Side-chains of amino acid residues modified
are Ser, Thr, and Tyr

The actions of __________ lead to activation of a protein
phosphatase which dephosphorylates enzymes during FED state

Insulin

The actions of ___ and ___ leads to activation of protein kinase A (PKA) which phosphorylates a bunch of regulatory enzymes in the fasting state.

Glucagaon/epinephrine

Why doesn't cortisol lead to activation of protein kinase A (PKA), which phosphorylates a bunch of regulatory enzymes in the fasting state?

Cortisol, a steriod hormone, binds directly to the GRE instead of activating PKA;

What hormone binds to β-3 receptor in adipose tissue? What regulatory enzyme is activated from this binding?

Epinephrine binding to β-3 receptor in adipose tissue leads to activation of hormone-sensitive lipase

A phosphorylated regulatory enzyme will be ____ if it catalyzes a reaction in a
metabolic pathway that is TURNED ON during FASTING

A phosphorylated regulatory enzyme will be ACTIVE if it catalyzes a reaction in a
metabolic pathway that is TURNED ON during FASTING

A dephosphorylated regulatory enzyme will be ____ if it catalyzes a reaction in a metabolic pathway that is TURNED ON during the FED state

A dephosphorylated regulatory enzyme will be ACTIVE if it catalyzes a reaction in a metabolic pathway that is TURNED ON during FED state

α-1 and β-2 adrenergic receptors, activated by ________, stimulate ___________  in the liver.

Epinepherine; glycogenolysis

 Via α-1-receptor in hepatocytes, increased _____ leads to activation of PKC, which phosphorylates and inactivates ________.

Ca⁺²; glycogen synthase

Epi binds to ___ receptors in hepatocytes to increase cAMP and thus increased ____, leading to activation of glycogen phosphorylase.

β-2 receptors; PKA

True or false: unphosphyorylated glycogen synthase is active in the fed state.

True; insulin activates protein phosphatase to dephosphorylate glycogen synthase and make it active

Increased cAMP/PKA in adipose tissue from epinephrine binding to what adrenergic receptor leads to active hormone sensitive lipase?

β-3 receptor

What type of regulatory enzymes are usually oligomeric or multisubunit?

Allosteric enzymes

Allosteric enzymes usually display _______ kinetics.

sigmoidal

Will it be allosteric activators or inhibitors that have this type of effect on regulatory enzymes?

↓ K_m (S_0.5) and/or ↑­ V_max

Allosteric Activators

Will it be allosteric activators or inhibitors that have this type of effect on regulatory enzymes?

↑­ K_m (S_0.5) and/or ↓ V_max

Allosteric Inhibitors

Allosteric effectors are usually ___________ of biosynthetic pathways and/or ___________.

end products (heme, cholesterol); energy metabolites (ATP, ADP, citrate, NADH, Acetyl CoA)

What is often true about the regulated reaction in a metabolic pathway?

The regulated reaction is often the first committed step in a metabolic pathway

The regulated step is _______ for the pathway

rate-limiting

The end product of a simple unbranched metabolic pathway usually is an essential metabolite such as a nucleotide or an amino acid. What are two ways that this essential metabolite can block further synthesis of itself when it's produced in sufficent amounts?

The essential metabolite blocks further synthesis of itself through feedback inhibition or regulation of the allosteric enzyme catalyzing the first committed step.

What do you call a molecule that binds to the allosteric site of a regulatory enzyme?

An effector or modulator

Binding of substrate or effector alters the conformation of the occupied subunit and thereby alters the conformation of other interacting subunits in allosteric enzymes. What kinds of interactions are these?

Cooperative interactions (positive or negative) usually refer to interactions between the subunits of an oligomeric allosteric enzyme.

What type of proteins bind to enzymes and influence enzymatic activity?

Modulator proteins (PKA, Ca²⁺-calmodulin proteins, small monomeric G-proteins)

"Dissociation of the regulatory subunit (modulator protein) activates the catalytic subunits; reassociation suppresses the activity of the catalytic subunits". This mechanism could be used to describe the regulation of what enzyme?

PKA

(Ca+2-calmodulin proteins, and small
monomeric G-proteins could be other examples of modulator proteins)

Metabolic pathways are regulated by _________ and __________.

Hormones & metabolites

Conversion of F6-P to F-2,6-BP is stimulated by high levels of F6-P. This is an example of ____________ in glycolysis.

Feedforward regulation; this ensures that intermediates in metabolic pathways do not accumulate uselessly in glycolysis.

Nucleotide binding (NB) Feedback regulation can be positive or negative; NB Feedback regulation is not synonymous with _________.

feedback inhibition

GTP will have cause an increase in ______, which is converted from IMP, in ATP nucleotide biosynthesis.

Adenylosuccinate (AS); this eventually leads to the increased production of ATP so that there are equal levels of the two nucelotides.

ATP will have cause an increase in ______, which is converted from XMP, in GTP nucleotide biosynthesis.

ATP will have cause an increase in GMP, which is converted from XMP, in GTP nucleotide biosynthesis.

AMP and GMP similarly affect ______ production in feedback regulation of nucleotide biosynthesis.

IMP

What are two things that may be different in isozymes?

1. Kinetic parameters (e.g., K_m and/or V_max)

2. Regulation

Appearance of the hybrid isozyme, CK2 in plasma is virtually diagnostic of myocardial infarction.

1. Glucokinase and Hexokinase
2. Aldolase A and Aldolase B
3. CPS I and CPS II
4. Creatine kinase

5. Carbonic Anhydrase I and II

This is a list of different types of _______ .

Isozymes

Troponin T and I are the newest markers for what disorder?

Myocardial Infarction

A number of proteins, most notably digestive proteases are synthesized as inactive precursors. What are these called and what advantage does this type of synthesis give? 

Zymogens, which are precursors that can be transported to their site of action in the inactive form (so that they don't become activated in the wrong place).

Zymogens differ from their corresponding active enzyme by an extra sequence of amino acids. What does this prevent?

This sequence of amino acids prevents the protein from assuming an active conformation or blocks its active site.

Trypsinogen, chymotrypsinogen, proelastase, and procarboxypeptidase A and B are synthesized in the _______ as inactive enzymes zymogens.

Pancreas

What can Diisopropylflurophosphate (DIFP) inactivate?

Serine Proteases Can be inactivated by
Diisopropylflurophosphate (DIFP)

DIFP inactivates acetylcholinesterase by forming a covalent complex with the active site serine that cannot be hydrolyzed by water; the result is buildup of acetylcholine in preganglionic synaptic clefts, which can lead to death.

What is the autoimmune disease caused by antibodies directed against nicotinic acetylcholine receptors in
skeletal muscle?

Myasthenia Gravis

In patients with M.G., antibodies & receptors crosslink to form complexes, which get endocytosed and
degraded in lysosomes. This results in...

Result is there are fewer functional receptors for acetylcholine to activate

Recall organophosphorus compounds in insecticides do irreversibly inhibit __________ at synaptic clefts of both sympathetic and parasympathetic preganglionic
neurons.

acetylcholine esterase

Atropine, an antagonist of muscarinic Ach receptors is an antidote of sarin and organophosphorus poisoning. Pralidoxime (2-PAM) can reverse organo-phosphate poisoning. How does 2-PAM do this?

2-PAM works by inhibiting the binding of organophosphates to Acetylcholine esterase

From high to low, the carbohydrate/lipid/protein makeup of myelin is...

Lipid (79%) > Protein (18%) > Carbohydrate (3%)

From high to low, the carbohydrate/lipid/protein makeup of mitochondrial inner membrane is...

Protein (76%) > Lipid (24%) > Carbohydrate (0%)

From high to low, the carbohydrate/lipid/protein makeup of human erythrocyte membrane is...

Protein (49%) > Lipid (43%) > Carbohydrate (8%)

What are the three types of lipids in membranes?

Phospholipids, sphingolipids, and cholesterol are the primary lipids of membranes

Phospholipids are arranged with _______ to the aqueous side and ________ facing the core side.

Phospholipids arranged with head
groups facing the aqueous side and
hydrophobic tails facing the core

"This" is Extremely stable, but fluid... Non‐covalently bonded... Hydrophobic in interior...Self‐ sealing

Lipid Bilayer

What's a liposome?

An artificial organelle used for delivery of drugs or DNA to cells for therapeutic purposes

Phosphatidyl-Choline, Phosphatidyl-Ethanolamine, Phosphatidyl-serine, & sphingomyelin contain __________

portions of the lipid bilayer.

Polar

Sphingolipids are polar molecules in the lipid bilayer that are generally longer and with a straight tail. What can embed in the thicker regions created by sphingolipids?

Proteins

What polar molecules are known to create lipid rafts in the lipid bilayer?

Sphingolipids

Where do the polar sugars of glycoproteins attach and extend?

They attach only on the outer plasma membrane of to the serine backbone of glycoproteins, extending into the aqueous region

 What sits, interspersed in the plasma membrane, in pockets where unsaturated cis fatty acids are bent?

Cholesterol, which affects membrane fluidity

Which can easilly pass through the lipid bilayer, small charged molecules or small non-polar molecules?

small non-polar molecules

Which of the following does NOT account for the driving forces that allow for formation of lipid bilayers?

A. electrostatic attractions between phospholipid head groups;
B. hydrophobic forces on the phospholipid fatty acid chains;
C. Repulsion between (+) charges of phospholipid fatty acids;
D. Van der Waals contacts between phospholipid charged groups;
E. Electrostatic attractions, H+ bonds and van der Waals contacts;

C. Repulsion between (-) charges of phospholipid fatty acids is a driving force

Peripheral proteins are ________ whereas integral proteins are __________.

Peripheral proteins are extrinsic whereas integral proteins are intrinsic.

Peripheral (extrinsic) proteins are loosely associated by ionic interactions to polar head groups of lipids and to integral proteins. How can they be removed without disruption of the lipid bilayer?

Peripheral (extrinsic) proteins can easily be removed at low salt concentrations without disruption of the lipid bilayer

The transmembrane domains, rich in hydrophobic amino acid sequences

_______ proteins of the lipid bilayer are tightly associated.

Integral (intrinsic) proteins

How are integral (intrinsic) proteins primarily associated?

Integral (intrinsic) proteins are associated primarily by hydrophobic interactions

The external GPI anchor protein attaches to the lipid bilayer via its __ terminus

C-terminus

What modifications allow for many integral membrane proteins to be more stable?

many integral membrane proteins are lipid modified
for stability

Fatty acyl or isoprenyl groups are seen on what type of anchor proteins?

Internal anchored proteins

Carbohydrates in the lipid bilayer are conjugated to what?

1. Lipids (glycolipids)

2. Proteins (glycoproteins)

Most glycocalyx proteins are bound to what?

Proteins embedded in the lipid bilayer

What molecule of the glycocalyx specifically imparts a negative charge to the surface of most cells?

Sialic acids in the glycoproteins and glycolipids

Fibronectin is a major fibrous protein in the glycocalyx that has binding sites for other extracellular matrix proteins. What major extracellular matrix protein that helps to maintain tissue architecture
binds tightly to fibronectin?

Collagen

In freeze fracture, the cleavage plane runs through the middle of the bilayer membrane. What proteins remain imbedded in fractured leaflets?

Integral (intrinsic)

Except for glycolipids, assymetry of lipids in the lipid bilayer is usually not _______.

Absolute

In Red blood cells, phosphatidylethanolamine and phosphatidylserine are mainly in the
inner leaflet of the lipid bilayer. What's located in the outer leaflet?

sphingomyelin and phosphatidylcholine
are preferentially located in the outer leaflet

Whereas glycophorin may pass through the lipid bilayer once in red blood cells, what protein could possibly pass through several times?

Adenylate Cyclase

Proteins

Longer chain length, more saturation, and increased cholesterol content are viewed in the membrane analysis of a histological section of a patient's tissue cells. These cells would be expected to show what type of fluidity in comparison to normal cell membranes?

Decreased fluidity

What can cause increased fluidity for fatty acid side chains in lipid bilayers?

More unsaturation and shorter side chain length

An increase in temperature would have what type of effect on membrane fluidity?

Increased temperature would increase membrane fluidity

What effect does cholesterol have on the transition temperature between the gel-liquid crystalline state?

Cholesterol broadens the transition temperature between the gel-liquid crystalline state

Why is turnover of membrane lipids and proteins continuous and sometimes very rapid?

To maintain organelle size in context of budding and merging

Lipid and protein turnover is equivalent to...

Metabolic replacement

Occluding junctions seal cells together in an epithelial  sheath. Communicating junctions allow for direct passage of chemical or electrical signals from cell to cell. What do adhesive junctions do?

Adhesive junctions mechanically attach cells to one another or to the ECM

The apical and basal sides of an epithelial cell are defined by...

Occluding (tight) junctions that form a cell between adjacent cells

Claudins & Occludins

Adherens junctions and Desmosomes hold cells in fixed positions and are prominent in epithelial tissues associated with cytoskeleton. They rely on associations between what type of proteins, that may differ in unique cell types?

Cadherins

Cadherins cross the plasma membrane and are linked to the cytoskeleton by linker proteins. Different cell types produce different types of cadherin proteins. What type of protein will a cadherin interact with?

A cadherin protein will interact only with an identical type of cadherin (homophilic binding).

Adherens junctions join actin bundles in one cell to actin bundles in an adjoining cell. Which of the folling about adherens junctions is NOT true?

A. Cadherins linked to actin microfilaments extend into the cell and bind to intracellular cadherins

B. Adherens junctions are often in a continuous belt
around the cell=adhesion belt
C. Adherens junctions can also be in a bundle, found in heart and thin cell layers covering organs or lining cavities

D. Actin microfilaments can contract
E. Adherens junctions can be involved in coordinating invaginations during development

A. Cadherins linked to actin microfilaments extend out of the cell and bind to cadherins of an adjoining cell

Desmosomes link the intermediate filaments of adjoining cells. Which of the following is true about desmosomes?

A. Cadherins are linked to myosin intermediate filaments inside the cell, then extend across the PM to
associate with identical myosin intermediate filaments of an adjacent cell
B. The cadherins and keratin filaments are anchored to lipid rafts, called a plaque, making them button‐like
C. Desmosomes are abundant in skin, heart, and the neck of the uterus where they are needed to withstand mechanical stress
D. Desmosomes are also important in maintaining cell differentiation during development

C. Desmosomes are abundant in skin, heart, and the neck of the uterus where they are needed to withstand mechanical stress

What are cadherins linked to inside of a cell?

Cadherins are linked to keratin intermediate filaments
inside the cell, then extend across the PM to
associate with identical cadherins of an adjacent
cell

What do cadherins and keratins anchor to?

The cadherins and keratin filaments are anchored to a
dense mixture of attachment proteins called a
plaque, making them button‐like

Hemidesmosomes link keratin intermediate filaments to the basal lamina. What are linked to keratin filaments inside the cell and extend across the PM to bind to laminin in the basal lamina?

Integrins

Gap junctions facilitate transfer or exchange of materials and cell‐cell communication exchange of metabolites. Which of the following about Gap junctions is NOT true?

A. Gap junctions consist of 12 transmembrane proteins called connexins
B. Six connexins make up a connexon or hemichannel
C. Aqueous channel closing is induced by Ca++ and H+
and is also controlled by membrane potential & hormone-induced phosphorylations
D. Gap junctions are common in smooth & skeletal muscle
E. Blocking gap junctions can disrupt development

D. Gap junctions are common in smooth & cardiac muscle

What statement about membrane transport is false?

A. Diffusion is passive

B. Facilitated transport may be passive or active

C. Simple diffusion is always against a concentration gradient

D. At equilibrium, there is no gradient for solutes to travel down because of continuous exchange

C. Simple diffusion is always down a concentration gradient

What is Fick's law?

Diffusion Rate= surface area x concentration difference
     distance

Which of the following is true about Fick's law?

A. Volume depends on the surface area

B. The ability to meet cellular requirements depends on the surface area:volume ratio

C. There's a limit on the maximum size for a single cell of about 100 nm

D. Bigger cells have a bigger surface area/volume ratio

B. The ability to meet cellular requirements depends on the surface area:volume ratio

Which of the following does NOT diffuse through a lipid bilayer freely?

A. O₂

B. CO₂

C. Lipophilic molecules

D. Peptide hormones

D. Peptide hormones

Which of the following is not a way by which water goes through the lipid bilayer?

A. Through ion channels
B. Pores
C. Around lipids in the bilayer
D. Special pores‐ aquaporins

C. Around proteins in the bilayer

Water will move (diffuse) from areas
of ___ solute to areas of ___ solute

Water will move (diffuse) from areas
of low solute to areas of high solute

Hypotonic Solution is:

lower solute concentration than a cell

A higher solute concentration than a cell is a ______ solution

Hypertonic

Which of the following is NOT true about Passivle Mediated Transport?

A. Transport proteins specific for one molecule
(usually)
B. Substances can only cross a membrane if it
contains the appropriate receptor protein
C. No energy is involved
D. Substances can only move down their
concentration gradient

B. Substances can only cross a membrane if it
contains the appropriate transport protein

Which of the following are true about Channel Proteins?

A. Channel proteins form a water‐filled pore or channel in the membrane
B. Channel proteins allow charged substances (usually ions) to diffuse across membranes
C. Channel proteins can be gated (opened or closed), allowing the cell to control entry and exit of ions

D. All of the above

D. All are true

Which of the following about Carrier Proteins is true?
A. Carrier proteins have a non-specific binding site for most solutes
B. Carrier protein structure flips between two states so that the site is alternately open to opposite sides of the membrane.
C. Substance will bind on the side of low concentration
and be released on the side of high concentration

D. All of the above

B. Carrier protein structure flips between two states so that the site is alternately open to opposite sides of the membrane.