Exam 2

Question 1

Describe the differences in enzyme kinetics of Michaelis-Menten and allosteric enzymes

Answer 1

1. Michaelis-Menten Kinetics: describes the rate of enzymatic reactions by relating reaction rate to the concentration of a substrate. These enzymes follow a hyperbolic relationship between substrate concentration and reaction rate
2. Allosteric enzymes: these enzymes have multiple binding sites and can be regulated by molecules that bind at sites other than the active site
   - exhibit an S-shaped curve, cooperative binding

Question 2

concerted and sequential models of allosteric enzyme kinetics

Answer 2

1. Concerted (MWC) Model: Allosteric enzymes exist in two conformations (Tense [T] and Relaxed [R]). Substrates bind more easily to the R state, and the binding of a substrate shifts the equilibrium towards the R state
   - All subunits transition between the T and R states simultaneously (concertedly)
2. Sequential Model: Binding of the substrate induces conformational changes in individual subunits. Unlike the concerted model, subunits transition between the T and R states independently

Question 3

Define the committed step in a metabolic pathway

Answer 3

committed step = irreversible reaction that commits the substrate to continue down the pathway, leading to the final product

Characteristics:
1. Irreversibility: usually reversible under normal cellular conditions
2. Regulation: often highly regulated to control the flux through the pathway. Enzymes catalyzing this step are frequently subject to feedback inhibition by the end products of the pathway
3. Commitment: substrate is committed to being converted into the final products of the pathway

Question 4

Identify the enzyme that catalyzes the committed step for a given pathway

Answer 4

Glycolysis: enzyme = PFK-1
Committed Step: conversion of fructose-6-phosphate to fructose-1,6-bisphosphate

Fatty Acid Synthesis: enzyme = ACC
Committed Step: conversion of acetyl-CoA to malonyl-CoA

Question 5

Describe how allosteric enzymes are used to activate/inhibit metabolic pathways

Answer 5

Activation:
Binding - Allosteric activators bind to a specific regulatory site on the enzyme (not the active site)
Conformational Changes: induces a conformational change in the enzyme, increasing its affinity for the substrate or enhancing its catalytic activity
Result: Enzyme becomes more effective at converting substrates to products, thus activating the metabolic pathway

Inhibition:
Binding - Allosteric inhibitors bind to the regulatory site of the enzyme
Cooperativity - often exhibit cooperative binding, where the binding of one molecule of substrate or regulator affects the binding of additional molecules. This can result in an S-shaped enzyme activity curve

Question 6

What are the key features of allosteric enzymes that are used to activate/inhibit metabolic pathways

Answer 6

Feedback regulation: Many metabolic pathways are regulated through feedback inhibition, where the end product of the pathway acts as an allosteric inhibitor of an enzyme earlier in the pathway. This prevents the overproduction of the end product

Cooperativity: Allosteric enzymes often exhibit cooperative binding, where the binding of one molecule of substrate or regulator affects the binding of additional molecules. This can result in a sigmoidal (S-shaped) enzyme activity curve

Fine-tuned Regulation: Allosteric regulation allows for fine-tuned control of enzyme activity, enabling cells to adjust metabolic flux in response to changing conditions

Question 7

Differentiate between hemoglobin and myoglobin

Answer 7

Hemoglobin: transports oxygen from lungs to tissues and carries carbon dioxide back to lungs for exhalation. Tetramer composed of four subunits (2 alpha, 2 beta) and each subunit has a heme group that binds one oxygen molecule. Found in red blood cells
- exhibits cooperative binding (sigmoidal curve)
- binding of one oxygen molecule increases the affinity for additional oxygen molecules
- regulated by pH (Bohr effect), carbon dioxide, and BPG

Myoglobin: stores oxygen in muscle tissues, provides a reserve supply of oxygen during intense muscular activity
- monomer with a single polypeptide chain, contains one heme group that binds one oxygen molecule
- found primarily in muscle tissues (cardiac and skeletal)
- exhibits non-cooperative binding (hyperbolic curve)
- high affinity for oxygen, facilitating oxygen storage
- NOT regulated allosterically

Question 8

How do hemoglobin and myoglobin differ structurally

Answer 8

Hemoglobin:
Tetramer - composed of four subunits (2 alpha, 2 beta)
- each subunit contains one heme, allowing hemoglobin to bind four oxygen molecules in total
- quaternary structure, subunits interact with each other, contributing to its cooperative binding behavior
- exists in T and R states, corresponding to low and high oxygen affinity

Myoglobin:
Monomer: consists of a single polypeptide chain
- contains one heme group, allowing myoglobin to bind one oxygen molecule
- Tertiary structure: single subunit, which does not exhibit cooperative binding
- higher affinity for oxygen, facilitating oxygen storage in muscle tissues

Question 9

How do hemoglobin and myoglobin differ functionally

Answer 9

Hemoglobin:
- Oxygen transport: transports oxygen from the lungs to tissues and organs throughout the body
- helps carry carbon dioxide from the tissues back to the lungs for exhalation
- Cooperative binding: the binding of one oxygen molecule increases the affinity for subsequent oxygen molecules

Myoglobin:
- Oxygen Storage: stores oxygen in muscle tissues, providing a reserve supply that can be used during periods of intense muscular activity
- high affinity for oxygen, which facilitates the storage and release of oxygen in muscle cells
- Non-cooperative binding: binds oxygen more tightly and releases it slowly, ensuring a steady supply during muscle contraction

Question 10

What are the differences between hemoglobin and myoglobin in oxygen affinity as pO2 changes?

Answer 10

Hemoglobin:
- cooperative binding leads to a sigmoidal curve
- low affinity at low pO2, high affinity at high pO2
- efficient oxygen transport and release

Myoglobin
- non-cooperative binding leads to a hyperbolic curve
- high affinity at all pO2 levels
- effective oxygen storage in muscles

Question 11

Be familiar with the structure of heme and how it binds to hemoglobin and oxygen

Answer 11

Structure of Heme: group composed of an iron ion at the center of a large organic ring structure
- Fe^2+ can form six coordination bonds: four with nitrogen atoms of the pyrrole rings, one with the nitrogen of a histidine residue from the globin protein, and one with an oxygen molecule

Hemoglobin binding: each subunit (alpha or beta) contains one heme group. This heme is held in place within a hydrophobic pocket of the globin protein

Oxygen binding: iron ion in the heme group binds reversibly to an oxygen molecule, binding is facilitated by the sixth coordination site of the iron ion

Conformational change: When oxygen binds to the heme group, it causes a conformational change in the hemoglobin molecule. This change increases the affinity of the remaining subunits for oxygen (cooperative binding), leading to efficient oxygen uptake and release

Question 12

Understand how 2,3-BPG acts as an allosteric regulator of hemoglobin…..What form of hemoglobin (T state vs. R state) does 2,3-BPG stabilize upon binding?

Answer 12

2,3-BPG as an Allosteric Regulator:
- Binding site: 2,3-BPG binds to the central cavity of the deoxygenated (deoxy) form of hemoglobin, specifically between the beta subunits
- Effect on oxygen affinity: binding of 2,3-BPG decreases its affinity for oxygen. This helps facilitate the release of oxygen from hemoglobin to the tissues (especially during high-altitude adaptation or intense exercise)

Stabilization of hemoglobin forms:
T State (Tense State): 2,3-BPG stabilizes the T state of hemoglobin. The T state is the low-affinity form of hemoglobin, which is more likely to release oxygen
R State (Relaxed State): In contrast, the R state is the high-affinity form of hemoglobin, which binds oxygen more tightly. 2,3-BPG binding reduces the transition of hemoglobin from the T state to the R state

Question 13

Understand how 2,3-BPG acts as an allosteric regulator of hemoglobin…..Which amino acids are involved in the binding of 2,3-BPG?

Answer 13

Lysine (Lys82)
Histidine (His2)
Histidine (His143)
Valine (Val1)
Alanine (Ala1)

these are located in the central cavity of the deoxygenated form of hemoglobin (T state) and the binding decreases the affinity of hemoglobin for oxygen, promoting oxygen release to tissues

Question 14

Understand how 2,3-BPG acts as an allosteric regulator of hemoglobin…..What is the molecular basis for fetal hemoglobin binding more tightly to oxygen than
adult hemoglobin?

Answer 14

Fetal Hemoglobin (HbF):
- made of 2 alpha and 2 gamma subunits (𝛼2𝛾2)
- gamma subunits in HbF have a reduced affinity for 2,3-BPG compared to the beta subunits in adult hemoglobin
- gamma chains in HbF lack some of the + charged amino acids (such as histidine) present in the beta chains, which are crucial for binding 2,3-BPG

Effect on Oxygen Affinity:
- Since HbF binds 2,3-BPG less effectively, its oxygen-binding affinity is higher. 2,3-BPG normally decreases the oxygen affinity of hemoglobin by stabilizing the T state. With less 2,3-BPG binding, HbF remains more often in the R state, which has a higher affinity for oxygen
- This higher affinity for oxygen allows HbF to effectively extract oxygen from the maternal blood supply across the placenta, ensuring the fetus receives adequate oxygen

Question 15

Explain how the Bohr Effect (changes in [CO2] & pH) affects hemoglobin’s affinity for oxygen

Answer 15

Bohr Effect: describes how changes in carbon dioxide (CO₂) concentration and pH affect hemoglobin’s affinity for oxygen

Effect of CO₂: Increased levels of CO₂ lower the pH (increase acidity) in the blood.

Effect of pH: A decrease in pH (more acidic conditions) leads to a decrease in hemoglobin’s affinity for oxygen.

Mechanism: CO₂ binds to hemoglobin and forms carbaminohemoglobin, which stabilizes the T (tense) state of hemoglobin, reducing its affinity for oxygen.

Result: In tissues where CO₂ is high and pH is low, hemoglobin releases oxygen more readily. In the lungs, where CO₂ is low and pH is higher, hemoglobin’s affinity for oxygen increases, allowing for oxygen uptake

      - High CO₂ / Low pH: Hemoglobin releases oxygen (lower affinity).
      - Low CO₂ / High pH: Hemoglobin binds oxygen more tightly (higher affinity)

Question 16

Describe how the sickle cell mutation in hemoglobin contributes to disease….What is the amino acid substitution

Answer 16

Normal Hemoglobin (HbA): Glutamic acid (hydrophilic) at position 6 in the beta-globin chain

Sickle Cell Hemoglobin (HbS): Valine (hydrophobic) replaces glutamic acid at position 6

Altered Structure: The substitution of valine for glutamic acid causes hemoglobin molecules to stick together under low oxygen conditions

Sickle-shaped Cells: This aggregation leads to the formation of long, rigid fibers, causing red blood cells to become rigid and take on a sickle shape

Blockages and Oxygen Delivery: Sickle cells can block blood flow in small vessels, reducing oxygen delivery to tissues and causing pain, organ damage, and complications

Hemolysis: Sickle cells have a shortened lifespan, leading to hemolysis and chronic anemia

Question 17

Describe the basic structure of monosaccharides and their stereochemistry

Answer 17

• Contains a carbonyl group (aldehyde or ketone) and multiple hydroxyl groups (-OH)
• (𝐶𝐻2𝑂)𝑛, where 𝑛 is typically 3-7
• classification depends on the number of carbon atoms and the position of the carbonyl group

Stereochemistry:
- Chirality: chiral centers, leading to stereoisomers
- Enantiomers: mirror-image isomers, such as D- and L- forms, based on the configuration of the chiral center farthest from the carbonyl atom
- Epimers: Differ in configuration at only one chiral center (e.g., glucose)
- Anomers: isomers that differ at the anomeric carbon formed during ring closure (e.g., α and β forms of glucose)

Question 18

How to identify epimers when shown open chain forms of monosaccharides and how to Identify α/β anomers when shown cyclical forms of monosaccharides

Answer 18

Identifying Epimers in Open Chain Forms:
- Epimers: Monosaccharides that differ in configuration at only one specific chiral carbon atom.
- Identification: Compare the structures of two monosaccharides and look for a difference at a single chiral carbon while the rest of the molecule remains identical.
- Example: Glucose and galactose are epimers. They differ only at carbon 4 (C4):
- Glucose: -OH on C4 is on the right.
- Galactose: -OH on C4 is on the left

Identifying α/β Anomers in Cyclical Forms:
- Anomers: Isomers that differ at the anomeric carbon (carbon that was the carbonyl carbon in the open-chain form) formed during ring closure.
- Identification:
- α-Anomer: The -OH group attached to the anomeric carbon is on the opposite side (trans) of the ring relative to the CH₂OH group attached to the last chiral carbon.
- β-Anomer: The -OH group attached to the anomeric carbon is on the same side (cis) of the ring as the CH₂OH group attached to the last chiral carbon.

Question 19

How to differentiate between ketose and aldose molecules

Answer 19

Aldoses: Contain an aldehyde group (−𝐶𝐻𝑂) at the end of the carbon chain
- Ex. Glucose, where the carbonyl group is at position 1

Ketoses: contain a ketone group ( > C = O ) within the carbon chain, usually at position 2
- Ex. Fructose, where the carbonyl group is at position 2

Question 20

How to identify which carbons react to generate the cyclic forms of monosaccharides

Answer 20

Aldoses: Carbon 1 (carbonyl, aldehyde group) + Carbon 4 or 5 (hydroxyl) → ring formation

Ketoses: Carbon 2 (carbonyl, ketone group) + Carbon 5 or 6 (hydroxyl) → ring formation

Question 21

Differentiate between the various polysaccharides of glucose, both in terms of structure and function (glycogen, amylose, amylopectin, and cellulose)

Answer 21

Glycogen:
- highly branched polymer of glucose, α(1→4) glycosidic bonds form the linear chains, α(1→6) glycosidic bonds form the branch points - approx. every 8-12 glucose units
- Main storage form of glucose in animals, provides a quick source of energy during physical activity or fasting

Amylose:
- linear polymer of glucose
- α(1→4) glycosidic bonds form the straight chains
- typically forms a helical structure
- Serves as an energy reserve, providing glucose during periods of low photosythetic activity

Amylopectin:
- branched polymer of glucose
- α(1→4) glycosidic bonds form the linear chains
- α(1→6) glycosidic bonds form the branch points every 24-30 glucose units
- provides a readily accessible source of glucose for plant metabolism

Cellulose:
- Linear polymer of glucose
- β(1→4) glycosidic bonds form straight chains. These chains form H bonds with each other, creating strong, fibrous structures
- Provides rigidity and strength to plant tissues

Question 22

Differentiate between types of glycosidic linkages

Answer 22

• α vs. β Linkages: α-linkages result in helical and branched structures (e.g., starch and glycogen), while β-linkages result in linear and fibrous structures (e.g., cellulose).
  - Branching: α(1→6) linkages create branching points in polysaccharides, important for energy storage

1. α(1→4) glycosidic bonds:
   - forms between the anomeric carbon (C1) of one glucose molecule and the C4 carbon of another glucose molecule
   ex. found in amylose and the linear chains of glycogen and amylopectin
2. α(1→6) glycosidic bonds:
   - Forms between the anomeic carbon (C1) of one glucose molecule and the C6 carbon of another glucose molecule
   ex. found at branch points in glycogen and amylopectin
3. β(1→4) Glycosidic Bond:
   - Structure: Forms between the anomeric carbon (C1) of one glucose molecule and the C4 carbon of another glucose molecule.
   Ex: Found in cellulose, leading to the formation of straight, fibrous structures.
4. β(1→6) Glycosidic Bond:
   - Structure: Forms between the anomeric carbon (C1) of one sugar molecule and the C6 carbon of another sugar molecule.
   Ex: Less common but can be found in some polysaccharides and oligosaccharides

Question 23

N-glycosidic vs. O-glycosidic

Answer 23

N-Glycosidic: Anomeric carbon of a sugar bonds with a nitrogen atom of another molecule. Important in nucleic acids.
- Essential in forming the structure of nucleic acids (DNA and RNA)

 O-Glycosidic: Anomeric carbon of a sugar bonds with an oxygen atom of another molecule. Important in carbohydrates
        - Essential in carbohydrate structure and metabolism, enabling the formation of complex sugars and polysaccharides

Question 24

Which amino acids form glycosidic bonds between proteins and carbs?

Answer 24

N-Glycosidic Bonds: Asparagine (Asn)

O-Glycosidic Bonds: Serine (Ser), Threonine (Thr)

Question 25

Is there a common motif shared between all N-linked oligosaccharides or all O-linked oligosaccharides?

Answer 25

N-Linked Oligosaccharides: - Common Core Structure: (Man)₃(GlcNAc)₂ - Attachment: Linked to asparagine (Asn) residue. O-Linked Oligosaccharides: - Common Linkage: Linked to serine (Ser) or threonine (Thr) residues. - Diverse Structures: No common core structure; highly variable.

Question 26

Outline the three classes of glycoproteins and their respective functions (glycoproteins, proteoglycans, mucins)

Answer 26

1. Glycoproteins: proteins with short, branched oligosaccharide chains - involved in cell surface recognition and signaling - assist in proper folding and increase stability of proteins - Transport molecules: act as receptors, enzymes, and transport proteins 2. Proteoglycans: Proteins with long, unbranched glycosaminoglycan (GAG) chains - Provide structural support in the extracellular matrix - facilitates cell adhesion and migration - regulates water retention and tissue hydration 3. Mucins: High-molecular-weight glycoproteins with extensive O-glycosylation - provide lubrication and protect epithelial surfaces - form protectice barriers against pathogens and environmental damage - play a role in cell signaling and immune responses

Question 27

Differentiate between the five classes of lipids in terms of their structure and function

Answer 27

1. Fatty Acids: long hydrocarbon chains with a carboxyl group at one end. Serves as building blocks for more complex lipids, provide energy storage, and are involved in signaling 2. Triacylglycerols (Triglycerides): Composed of 3 fatty acids esterified to a glycerol backbone. Main form of energy storage in animals, provide insulation for organs 3. Phospholipids: consists of 2 fatty acids, a phosphate group, and a glycerol backbone. Phosphate group is often linked to additional polar groups. Major components of cell membranes, forming bilayers that provide structural integrity and regulate permeability 4. Steroids: Composed of a fused ring structure with three six-membered rings and one five-membered ring (e.g., cholesterol). Serves as components of cell membranes (cholesterol), precursors for steroid hormones (testosterone, estrogen), and Vitamin D 5. Sphingolipids: Contain a sphingoid base (long-chain amino alcohol), one fatty acid, and a polar head group. Involved in cell signaling, cell recognition, and forming specialized domains in cell membranes

Question 28

Be familiar with the basic structure and nomenclature of free fatty acids

Answer 28

Basic Structure: Long hydrocarbon chain with a carboxyl group (-COOH) at one end. Saturated Fatty Acids: Named with "-anoic acid" suffix (e.g., hexadecanoic acid). Unsaturated Fatty Acids: Named with "-enoic acid" suffix, indicating double bond position (e.g., 9-octadecenoic acid). Omega Nomenclature: Indicates the position of the first double bond from the methyl end (e.g., omega-3)

Question 29

How to identify the location and conformation (cis vs. trans) of the double bond

Answer 29

Location of Double Bond: Number carbon atoms from carboxyl end (COOH) for IUPAC naming. In systematic naming, use the number of the first carbon involved in the double bond. Conformation: 1. Cis: Hydrogen atoms attached to the carbons of the double bond are on the same side. Creates a "kink" or bend in the fatty acid chain 2. Trans: Hydrogen atoms attached to the carbons of the double bond are on opposite sides. Results in straighter fatty acid chain, similar to saturated fats

Question 30

What characteristics differentiate Omega-3 fatty acids from other polyunsaturated fatty acids?

Answer 30

Omega-3: First double bond at the third carbon, anti-inflammatory, supports heart and brain health. Omega-6: First double bond at the sixth carbon, pro-inflammatory, found in vegetable oils. Omega-9: First double bond at the ninth carbon, monounsaturated

Question 31

Explain how changes in fatty acid composition would affect the melting point

Answer 31

Chain Length: Longer chains = higher melting point. This is from an increase in van der Waals interactions Saturation: Saturated = higher melting point; Unsaturated (especially polyunsaturated) = lower melting point. There are more van der Waals interactions with saturated b/e the straight chains are packed closely together Double Bond Configuration: Cis = lower melting point; Trans = higher melting point. Kinks in the chain reduce the ability of the molecules to pack closely together

Question 32

How to identify structural differences between the three common types of membrane lipids (phospholipids, glycolipids, steroids)

Answer 32

Phospholipids: Glycerol backbone, two fatty acids, phosphate group, polar head group. Glycolipids: Sphingosine backbone, one fatty acid, carbohydrate group. Steroids: Fused ring structure, may have hydroxyl group

Question 33

Define membrane permeability and explain why lipid bilayers are more/less permeable to different molecules (charged/polar molecules vs nonpolar molecules)

Answer 33

Nonpolar (hydrophobic) Molecules: High permeability; can dissolve in the lipid bilayer and pass through without resistance (e.g., O2 and CO2) Polar (hydrophilic) Molecules: Low permeability; require transport proteins (e.g., channels or carriers) b/e the hydrophobic core of the bilayer acts as a barrier to polar molecules Charged Molecules (Na+, K+, Cl-): Very low permeability; require specific transport mechanisms b/e the hydrophobic core of the lipid bilayer strongly repels charged particles. Use of ion channels or active transport pumps

Question 34

Explain how cells alter membrane fluidity in response to temperature (prokaryotes vs eukaryotes)

Answer 34

-Prokaryotes: - Low Temperature: Increase unsaturated fatty acids. - High Temperature: Increase saturated fatty acids. - Eukaryotes: - Cholesterol: - Low Temperature: Increases fluidity. - High Temperature: Decreases fluidity. - Fatty Acid Composition: Similar adjustments as prokaryotes

Question 35

Which types of protein structures will span membranes and which types will not

Answer 35

Span Membranes: 1. α-Helices: - common structures that span the lipid bilayer; consists of a single continuous helical segment of amino acids. - Ex. GPCRs 2. β-Barrels: - cylindrical structures formed by beta-sheets that curve and close back on themselves. They create a pore-like structure that spans the membrane. DO NOT span membrane: 1. Peripheral Membrane Proteins: - Do not span the lipid bilayer. Instead, they are associated with the membrane through interactions with integral membrane proteins or lipid head groups. - Ex. cytoskeletal proteins and signaling proteins that interact with the membrane surface 2. Globular proteins: - soluble proteins with a spherical shape. They are not typically associated with membranes. - Ex. Enzymes, hemoglobin, and many other proteins found in the cytoplasm or extracellular spaces

Question 36

Passive vs active transport

Answer 36

Passive Transport: Movement of molecules across the cell membrane without the use of energy (ATP) Types: - Simple diffusion: Movement of small, nonpolar molecules (e.g., O₂, CO₂) directly through the lipid bilayer. - Facilitated Diffusion: Movement of larger or polar molecules (e.g., glucose, ions) through specific transport proteins (channels or carriers) - Concentration gradient: Moves molecules down their concentration gradient (from high to low concentration) Active Transport: Movement of molecules across the cell membrane using energy (ATP) Types: - Primary Active Transport: Direct use of ATP to transport molecules against their concentration gradient (e.g., Na⁺/K⁺ pump) - Secondary Active Transport: Uses energy stored in the form of an ion gradient, created by primary active transport, to drive the transport of other molecules (e.g., glucose-sodium co-transport) - Concentration Gradient: Moves molecules against their concentration gradient (from low to high concentration). ex. Na⁺/K⁺ pump actively transports sodium out of the cell and potassium into the cell. Glucose-sodium co-transport in intestinal cells.

Question 37

Simple vs facilitated diffusion

Answer 37

Simple Diffusion: - Definition: Movement of small, nonpolar molecules directly through the lipid bilayer without the need for transport proteins. - Mechanism: Driven by the concentration gradient, moving molecules from an area of high concentration to an area of low concentration. - Molecules: Typically involves small, nonpolar molecules such as oxygen (O₂), carbon dioxide (CO₂), and lipid-soluble molecules. - Does **not** require energy (passive process). Facilitated Diffusion: - Definition: Movement of larger or polar molecules across the cell membrane through specific transport proteins (channels or carriers). - Mechanism: Driven by the concentration gradient, moving molecules from an area of high concentration to an area of low concentration, but facilitated by proteins. - Molecules: Typically involves larger, polar molecules such as glucose, ions, and amino acids. - **Does** not require energy (passive process).

Question 38

Primary vs secondary active transport

Answer 38

Primary Active Transport: - Direct use of ATP. - Transport proteins/pumps. - Example: Na⁺/K⁺ pump. Secondary Active Transport: - Uses electrochemical gradient. - Symporters and antiporters. - Example: Sodium-glucose co-transport. Primary Active Transport: - Direct use of energy (ATP) to transport molecules across a membrane against their concentration gradient. - Mechanism: Transport proteins, often known as pumps, hydrolyze ATP to provide the necessary energy. - Ex: The Na⁺/K⁺ pump (sodium-potassium pump) uses ATP to transport sodium (Na⁺) out of the cell and potassium (K⁺) into the cell, maintaining concentration gradients across the cell membrane. Secondary Active Transport: - Uses the energy stored in the form of an electrochemical gradient, created by primary active transport, to drive the transport of other molecules. - Mechanism: Transport proteins, such as symporters and antiporters, use the energy from the movement of one molecule down its gradient to transport another molecule against its gradient. - Ex: The sodium-glucose co-transport in intestinal cells uses the gradient created by the Na⁺/K⁺ pump to transport glucose into the cell along with sodium ions.

Question 39

Methods of ion transport (ionophore vs ion channel (voltage- ligand-gated))

Answer 39

Ionophores: Small, lipid-soluble molecules that transport ions across membranes by forming complexes or creating pores. Voltage-Gated Ion Channels: Open/close in response to changes in membrane potential (e.g., Na⁺, K⁺ channels). Change in voltage across the membrane alters the conformation of the channel protein, allowing specific ions to pass through. Ligand-Gated Ion Channels: Open/close in response to ligand binding (e.g., nicotinic acetylcholine receptors). Binding of the ligand causes a conformational change in the channel protein, allowing specific ions to pass through

Question 40

What are the basic mechanisms of ion channel gating and describe how potassium channels are selective for K+ ions

Answer 40

Ion Channel Gating: - Voltage-Gated: Respond to membrane potential changes. - Ligand-Gated: Respond to ligand binding. - Mechanosensitive: Respond to mechanical forces. - Light-Gated: Respond to light. K⁺ Channel Selectivity: - Selectivity Filter: Specific amino acid sequence. - Mechanism: K⁺ ions interact with carbonyl oxygens, excluding other ions. 1. Voltage-Gated Channels: - Mechanism: Open or close in response to changes in membrane potential. - Ex: Voltage-gated sodium (Na⁺) and potassium (K⁺) channels in neurons. 2. Ligand-Gated Channels: - Mechanism: Open or close when a specific ligand (e.g., neurotransmitter) binds to the channel protein 3. Mechanosensitive Channels: - Mechanism: Open or close in response to mechanical forces or changes in membrane tension. - Ex: Stretch-activated channels in sensory cells. 4. Light-Gated Channels: - Mechanism: Open or close in response to light (photons). - Ex: Channelrhodopsins in certain microorganisms. Selectivity Filter: - Structure: The narrowest part of the channel, composed of a sequence of amino acids that specifically interact with K⁺ ions. - Mechanism: K⁺ ions shed their hydration shell and interact with carbonyl oxygen atoms lining the selectivity filter. - Selective Permeation: The size and spacing of these interactions are optimal for K⁺ ions, allowing them to pass through while excluding smaller ions like Na⁺.

Question 41

Outline the general steps in a signal transduction pathway

Answer 41

1. Signal Reception: Ligand binding and receptor activation. 2. Signal Transduction: Intracellular signaling and amplification. 3. Signal Integration: Pathway crosstalk and regulation. 4. Cellular Response: Changes in gene expression or cellular behavior. 5. Signal Termination: Deactivation and homeostasis. 1. Signal Reception: - Ligand binding: A signaling molecule (ligand) binds to a specific receptor on the cell surface or within the cell - receptor undergoes a conformational change upon ligand binding, becoming activated 2. Signal Transduction: - Intracellular Signaling Proteins: Activated receptors initiate a cascade of intracellular signaling proteins and secondary messengers - signal is often amplified through a series of biochemical reactions, ensuring a robust cellular response 3. Signal Integration: - Different signaling pathways interact and integrate signals to coordinate a unified cellular response - Feedback mechanisms regulate the intensity and duration of the signal 4. Cellular Response: - Gene Expression: The signal ultimately leads to changes in gene expression, protein activity, or cellular behavior - Cellular responses may include cell growth, division, differentiation, apoptosis, or metabolic changes 5. Signal Transduction: - Deactivation: The signal is terminated by deactivating receptors, removing signaling molecules, or degrading secondary messengers - cell returns to its baseline state, ready to respond to new signals

Question 42

Classify common secondary messengers by the signaling pathways that use them

Answer 42

cAMP: GPCR pathways (adenylyl cyclase), activates PKA. - G protein-coupled receptor (GPCR) pathways, especially those involving adenylyl cyclase - Activates PKA -> phosphorylation of target proteins cGMP: Nitric oxide and natriuretic peptide pathways, activates PKG - Signaling pathways involving nitric oxide (NO) and natriuretic peptides - Activates PKG and regulates ion channels IP₃: PLC pathway (GPCRs), releases Ca²⁺ - often coupled with GPCRs - Releases calcium ions (Ca²⁺) from intracellular stores, leading to activation of various calcium-dependent processes DAG: PLC pathway (GPCRs), activates PKC - Often coupled with GPCRs - activates PKC, leading to phosphorylation of target proteins Calcium Ions (Ca²⁺): Various pathways, regulates multiple cellular processes - involves IP₃, voltage-gated calcium channels, and ryanodine receptors - Regulates numerous cellular processes, including muscle contraction, neurotransmitter release, and enzyme activity

Question 43

Differentiate between the three major classes of membrane receptors

Answer 43

- GPCRs: Seven transmembrane α-helices, activates G proteins (e.g., adrenergic receptors) - RTKs: Single transmembrane helix - ligand binding induces dimerization and autophosphorylation of tyrosine residues, leads to the activation of downstream signaling cascades (e.g., insulin receptor) - Ligand-Gated Ion Channels: multiple subunits forming a channel pore - Ligand binding directly opens or closes the ion channel, allowing specific ions to pass through and alter the membrane potential

Question 44

Which receptors correspond to each class of membrane receptors

Answer 44

1. G Protein-Coupled Receptors (GPCRs): - Adrenergic Receptors: Bind adrenaline and noradrenaline - Opioid Receptors: Bind endogenous opioids (e.g., endorphins) and exogenous opioids (e.g., morphine) - Rhodopsin: Involved in vision by responding to light 2. Tyrosine Kinase Receptors (RTKs): - Insulin Receptor: Binds insulin, regulating glucose uptake - Epidermal Growth Factor Receptor (EGFR): Binds epidermal growth factor, involved in cell growth and differentiation - Vascular Endothelial Growth Factor Receptor (VEGFR): Binds VEGF, involved in angiogenesis 3. Ligand-Gated Ion Channels: - Nicotinic Acetylcholine Receptor: Binds acetylcholine, involved in muscle contraction - GABA Receptor: Binds gamma-aminobutyric acid (GABA), involved in inhibitory neurotransmission - Glutamate Receptor (NMDA Receptor): Binds glutamate, involved in excitatory neurotransmission

Question 45

Construct the molecular events occurring in the G Protein-Coupled Receptor (GPCR) Pathway

Answer 45

1. Ligand Binding: - A signaling molecule (ligand) binds to a GPCR on the cell surface. 2. Receptor Activation: - The GPCR undergoes a conformational change and activates an associated G protein by exchanging GDP for GTP on the G protein's α-subunit. 3. Signal Propagation: - The activated G protein dissociates into α and βγ subunits, which then interact with and activate or inhibit target proteins such as adenylyl cyclase or phospholipase C. 4. Second Messenger Generation: - Activated adenylyl cyclase converts ATP to cyclic AMP (cAMP), while phospholipase C generates inositol triphosphate (IP₃) and diacylglycerol (DAG). 5. Cellular Response: - cAMP activates protein kinase A (PKA), leading to the phosphorylation of target proteins. IP₃ releases Ca²⁺ from intracellular stores, and DAG activates protein kinase C (PKC). 6. Signal Termination: - GTP is hydrolyzed to GDP on the G protein α-subunit, deactivating the G protein. cAMP and IP₃ are degraded by phosphodiesterases, and Ca²⁺ levels are restored

Question 46

Construct the molecular events occurring in the Receptor Tyrosine Kinase (RTK) Pathway

Answer 46

1. Ligand Binding: - A signaling molecule (ligand) binds to an RTK on the cell surface. 2. Receptor Dimerization: - Ligand binding induces dimerization (pairing) of the RTKs. 3. Autophosphorylation: - The dimerized RTKs phosphorylate each other on tyrosine residues in their intracellular domains. 4. Signal Propagation: - Phosphorylated tyrosine residues serve as docking sites for intracellular signaling proteins, such as Grb2 and SOS, which activate the Ras-MAPK signaling cascade. 5. Cellular Response: - Activated Ras initiates a kinase cascade involving Raf, MEK, and ERK, leading to changes in gene expression and cellular functions. 6. Signal Termination: - Phosphatases dephosphorylate the RTKs and downstream signaling proteins, terminating the signal.

Question 47

Construct the molecular events occurring in the Ligand-Gated Ion Channel Pathway

Answer 47

1. Ligand Binding: - A signaling molecule (ligand) binds to a ligand-gated ion channel on the cell surface. 2. Channel Activation: - Ligand binding induces a conformational change in the ion channel, opening the channel pore. 3. Ion Flow: - Specific ions (e.g., Na⁺, Ca²⁺, Cl⁻) flow through the open channel down their electrochemical gradients. 4. Cellular Response: - The change in ion concentration alters the membrane potential, leading to cellular responses such as neurotransmitter release or muscle contraction. 5. Signal Termination: - The ligand dissociates from the ion channel, causing the channel to close and ion flow to cease. Ion concentrations are restored by active transport mechanisms

Question 48

Describe the adenyl cyclase cascade

Answer 48

1. Ligand Binding: Ligand binds to GPCR. 2. Receptor Activation: GPCR activates G protein. 3. Adenylyl Cyclase Activation: Gαs activates adenylyl cyclase. 4. cAMP Production: Adenylyl cyclase converts ATP to cAMP. 5. PKA Activation: cAMP activates protein kinase A (PKA). 6. Phosphorylation: PKA phosphorylates target proteins. 7. Signal Termination: cAMP degraded, G protein deactivates 1. Ligand Binding: - A signaling molecule (ligand) binds to a G protein-coupled receptor (GPCR) on the cell surface 2. Receptor Activation: - The activated GPCR undergoes a conformational change and activates an associated G protein by exchanging GDP for GTP on the G protein's α-subunit 3. Adenylyl Cyclase Activation: - The activated G protein α-subunit (Gαs) interacts with and activates the enzyme adenylyl cyclase, which is located on the inner side of the plasma membrane 4. cAMP Production: - Adenylyl cyclase catalyzes the conversion of ATP to cyclic AMP (cAMP), a secondary messenger 5. cAMP-Dependent Protein Kinase Activation: - cAMP binds to and activates protein kinase A (PKA) by releasing the catalytic subunits from the regulatory subunits 6. Phosphorylation of Target Proteins: - The activated catalytic subunits of PKA phosphorylate specific target proteins, leading to changes in their activity and resulting in a cellular response 7. Signal Termination: - cAMP is degraded by phosphodiesterases (PDEs) to AMP, terminating the signal. The G protein α-subunit hydrolyzes GTP to GDP, deactivating itself and reassociating with the βγ subunits

Question 49

Describe the phosphoinositide cascade

Answer 49

1. Ligand Binding: Ligand binds to GPCR on cell surface 2. Receptor Activation: GPCR undergoes conformational change and activates G protein by exchanging GDP for GTP on G protein's α-subunit 3. PLC Activation: Gαq activates phospholipase C (PLC), which is located on the inner side of the plasma membrane 4. PIP₂ Hydrolysis: PLC hydrolyzes PIP₂ into two **secondary messengers** (IP₃ and DAG) 5. IP₃-Mediated Calcium Release: IP₃ diffuses through cytoplasm, binds to receptors on ER, triggers Ca²⁺ release from ER into the cytoplasm 6. DAG-Mediated PKC Activation: DAG remains in plasma membrane, and increased Ca²⁺ levels activate PKC 7. Cellular Response: activated PKC phosphorylates target proteins (leads to changes in gene expression, metabolism, and cell growth) 8. Signal Termination: IP₃ dephosphorylation, Ca²⁺ restored by calcium pumps, DAG metabolized, PKC activity is regulated by phosphorylation and dephosphorylation

Question 50

Describe the insulin signaling cascade

Answer 50

1. Insulin Binding: Insulin binds to insulin receptor (IR) on the cell surface 2. Receptor Activation: Autophosphorylation of the insulin receptor (undergoes conformational change) 3. IRS Activation: Phosphorylation of insulin receptor substrates (IRS), primarily IRS-1 and IRS-2 4. PI3K Activation: IRS proteins activate PI3K, leading to production of PIP3 from PIP2 5. Akt Activation: PIP3 activates Akt/PKB through action of PDK1 6. GLUT4 Translocation: Activated Akt triggers translocation of GLUT4 to cell membrane, increasing glucose uptake 7. Glycogen Synthesis: Akt activates GSK3, leading to activation of glycogen synthase 8. Signal Termination: Dephosphorylation and return to baseline state