Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Exam 3 (Final) > Flashcards

Exam 3 (Final) Flashcards

1
Q

What is the model for membrane structure?

A

Fluid mosaic model - integral membrane proteins are icebergs floating in a lipid sea

  • everything depends on temperature/fluidity
  • there is free lateral diffusion with membrane bilayer
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How was free lateral diffusion within bilayers proven?

A
  • Confirmed by the fusion of a mouse and a human cell
  • GFP and RFP labelled mouse and human cell
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What can be used to measure the rate of lateral diffusion?

A

a FRAP experiment = fluorescence recovery after photobleaching

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How are FRAP experiments performed?

A

1) Attach a fluorophore to an integral membrane protein (or lipid molecule)
2) Fluorescence on membrane - laser pulse to photobleach a small region, destroys fluorescence
3) Measure the rate at which fluorescence increases in the bleached area

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is transverse diffusion?

A

between inner and outer leaflet

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Describe transverse diffusion in membranes.

A
  • We know it is not a spontaneous process because we observe an asymmetric distribution
  • flippase (inner-outer), floppase (outer-inner), and flip-floppase (can do both)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Describe an experiment to measure transverse diffusion.

A
  • Feed cells w/ 1-min pulse of radio-labelled 32PO4^(3-)
  • newly synthesized phospholipids will contain the 32P label, and they will all go to the inner leaflet
  • treat cells with TNBS (not cell permeable, will only modify lipids on the outer membrane) modifies amine group phosphatidyolethylamine
  • observe the rate of phospholipids with both labels appearing over time
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is a molecule that is usually only expressed on one leaflet of the bilayer?

A
  • Phosphatidylserine - only shown on the inner leaflet
  • When shown on the outer leaflet is a signal of apoptosis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the secretory pathway?

A
  • proteins that reside in the ER, golgi, lysosomes, cell membrane, extracellular space
  • have an N-term signal peptide (13-36aas)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Describe the process of the secretory pathway.

A
  1. The signal peptide is the first thing translated, the signal recognition particle (SRP) binds to it immediately
  2. The SRP binds to GDP, when this turns to GTP it halts ribosomal synthesis (allowing time for the ribosome to dock to the ER membrane)
  3. The SRP binds the SRP receptor (bound to GTP) and the translocon
  4. GTP hydrolysis occurs, ribosome continues to synthesize
  5. N-term of polypeptide enters the ER through the translocon
  6. The signal peptide is cleaved
    1. Polypeptide is glycosylated (N-linked sugars are added cotranslationally), folded, disulfide bonds are formed and it is transported to the golgi
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the major players in the secretory pathway?

A

Ribosome - ER - Golgi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Describe the golgi.

A
  • made of cisternae (membranous sacs)
  • cis golgi (closest to the ER)
  • trans golgi (farthest from the ER)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the two types of vesicle transport?

A
  • anterograde - ER - cis - trans
  • retrograde - trans - cis - ER
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is cisternal progression?

A

cis cisternae become trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What happens in the Golgi?

A
  • O-linked glycosylation added
  • N-linked glycans are trimmed and elaborated
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How do all proteins in the secretory pathway proceed?

A

all proteins go from the ER to the CIS to TRANS golgi then back to wherever they belong

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Describe secretory vesicles.

A
  • inside is equal to the extracellular matrix
  • carbohydrates are on the inside and when they fuse with the membrane they point out
  • transport occurs in coated vesicles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What does “coated” vesicles mean?

A

there are proteins specific to different types of vesicles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are three types of vesicles?

A
  • clathrin (Golgi → plasma membrane)
  • COP I (Golgi → ER) - retrograde
  • COP II (ER → Golgi) - anterograde
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What do vesicles play a role in?

A

vesicles release neurotransmitters

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Describe how vesicles mediate neurotransmitter release.

A
  • neurotransmitters are contained in intracellular vesicles
  • when there is a nerve impulse at the synapse there is fusion of synaptic vesicle that contain neurotransmitters w/ the presynaptic membrane
  • neurotransmitters are released to the synaptic cleft
  • neurotransmitters bind to receptors on the post-synaptic neuron
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How does fusion of membranes occur?

A
  • membranes negatively charged when close together will repel
  • SNARES - integral membrane proteins that mediate fusion
  • R and Q snares zip together a pull membranes close together
  • they determine the selectivity of membrane fusion because they will only bind to their partner snares
  • they also physically drive the fusion process
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the two types of SNAREs?

A
  • R-SNARE (Arg) - vesicle membrane
  • Q-SNARE (Gln) - target membrane
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What type of molecules must be transported across membranes?

A
  • water, metal ions, metabolites (eg glucose), drugs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the difference between thermodynamics and kinetics?

A

Thermodynamics describes the overall properties, behavior, and equilibrium composition of a system; kinetics describes the rate at which a particular process will occur and the pathway by which it will occur.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What does the thermodynamics of transport involve?

A
  • Aout ←→ Ain
  • GA = RT ln[A]
  • ∆GA = GA(out) - GA(in)
  • ∆GA =RT ln( [Ain] / [Aout] )
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What do [A] indicate about ∆GA?

A
  • If the concentration of A is greater on the outside of the membrane than the inside: movement of A from out to in is spontaneous/favorable (∆GA < 0)
  • If the concentration of A is greater on the inside of the membrane than the outside: movement of A from out to in is non-spontaneous/unfavorable (∆GA > 0)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is ∆GA

A

free energy of A / chemical potential of A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What happens with charged molecules/ions?

A
  • movement of charged species results in charge difference across membrane (membrane potential)
  • Membrane potential - difference in charge across a membrane
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Describe the membrane potential of living cells.

A

∆Ψ = -100mv

  • inside of cells more negative than outside
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are the three types of thermodynamics involving membrane potential?

A
  • movement of uncharged species
  • both diffusion and charge favor movement in the same direction
  • concentration and charge are opposing
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What are the two types of transport?

A
  • non-mediated and mediated
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Describe non-mediated transport.

A
  • diffusion across cell membrane (passive)
  • high to low concentration
  • rate of diffusion depends on ∆conc and solubility in membrane
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Describe mediated transport.

A
  • carrier protein is involved
  • 2 types
  1. Passive/facilitated diffusion: high → low concentration, molecule forms channel
  2. Active mediated transport: low → high concentration, coupled to exergonic process (ATP or coupled w high → low)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What are 5 Passive Mediated Transport systems?

A
  • ionophores
  • porins
  • ion channels
  • aquaporins
  • transport proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are ionophores? What are two types?

A
  • peptides that increase permeability of membrane to ions
  1. Carrier Ionophores - e.g. Valinomycin: K+ is bound by carbonyl groups in valinomycin, then on outside have hydrophobic valine side chains that allow it to pass through
  2. Channel forming ionophores - e.g. Gramicidin: K+ ions travel up this channel
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What are porins?

A
  • beta- barrel structures with aqueous channels
  • size of the channel and the residues that line the channel determine what is transported
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What is an example of a porin?

A
  • Maltoporin: transports maltodextrin (an alpha (1-4) linked glucose
  • has aromatic groups that bind to the hydrophobic face of maltodextrin on one side
  • has a greasy slide face on one side of the membrane that allows it to slide through
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are three things transported by ion channels?

A

Na+, K+, Cl-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Describe the potassium ion channel.

A
  • KcsA
  • K+ channel, made of an integral membrane protein
  • alpha helical structure
  • right at the entrance to the channel are negatively charged residues that attract K+
  • there are neutral residues inside once it enters the channel
  • has a selectivity filter that lines the inside of the channel
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Describe how the selectivity filter functions in KcsA.

A
  • Selectivity filter is TVGYG sequence that lines the inside of the ion channel
  • initially K+ is hydrated and when it gets to the S.F. K+ gets dehydrated
  • carbonyl O from residues lining the channel replaces the hydration shell
  • selectivity comes from the fact that Na+ is too small for interaction with carbonyl O - can’t use this channel
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Ion channels are _______

A

gated - selectively opened and closed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What are four types of ion gated channels?

A
  • mechanosensitive - responds to deformities in the lipid bilayer
  • ligand-gated - respond to extracellular signal e.g. neurotransmitters
  • signal-gated - intracellular binding to signal
  • voltage-gated -responds to change in membrane potential
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What ion channels play a role in nerve impulses?

A
  • ligand gated and voltage gated
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Describe concentrations of Na+ and K+ normally in cells.

A
  • Na+ has a higher concentration on the outside of the cell
  • K+ has a higher concentration inside the cell
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

Describe how nerve impulses work.

A
  1. Resting potential of membrane is normally at -60mv
  2. Neurotransmitter release
  3. Opens ligand-gated Na+ channels, Na+ travels from out → in
  4. Membrane potential becomes positive
  5. Voltage-gated Na+ channels open
  6. Membrane potential spikes (+20mv): called the action potential
  7. Voltage gated K+ channels open after a lag, K+ travels from inside to outside
  8. Membrane potential decreases, if it dips below resting potential it is called hyperpolarization
47
Q

Describe the structure of Kv channels.

A
  • Kv channel - a type of voltage-gated K+ ion channel
  • N-term cytoplasmic domain
  • Transmembrane domain has 6 helices S1-S6
  • C-term cytoplasmic domain
48
Q

Describe how voltage gating works in Kv channels.

A
  • S4 Helix contains 5 positively charged side chains which function as a voltage sensor
  • When membrane potential increases → S4 Helix moves → S4-S5 linker moves → S5 and S6 move to form pore
  • Kv channels also have a second gate: which ensures that channels close a few minutes after opening
    • the second gate happens at the N-term inactivation ball → when the channel opens the ball unravels itself and snakes its way into the pore of the channel
49
Q

What are aquaporins?

A
  • type of passive mediated transporter
  • transports H2O across membrane
  • exists in tetramers where there are four channels in one aquaporin
  • at its narrowest point width = 2.8Å = vanderwaal’s radius of water (size selection)
  • pore is lined with hydrophobic residues inside (charge selectivity)
  • His+Arg residues disrupt H-bonding between H2O molecules, prevent H+/H3O+ transport
50
Q

What are transport proteins?

A
  • e.g. GLUT1 glucose transporter
  • glucose binds, bottom opens and top closes, glucose dissociates and is delivered inside
  • may be uniporters, symporters or antiporters
51
Q

What are uniporters? What is an example?

A

transport a single type of molecule at a time e.g. GLUT1

52
Q

What are symporters?

A

Transport two different molecules in the same direction

53
Q

What are antiporters?

A

transport two different molecules in opposite directions

54
Q

Describe active transport.

A
  • endergonic
  • against concentration gradient
  • coupled to ATP hydrolysis
55
Q

What are 5 types of active transporters?

A
  1. P-Type ATPase - undergo phosphorylation during transport Na+, K+, Ca2+
  2. F-Type - H+ in mitochondria/bacteria
  3. V-Type - H+ in vacuoles/lysosomes
  4. A-Type - anions
  5. ABC transporter - ions, metabolites, drugs
56
Q

Give an example and describe a P-Type ATPase.

A
  • Na+-K+ ATPase → move Na+ out and K+ in to cells (opposite of ion channels during nerve impulses)
57
Q

How does Na+-K+ ATPase work?

A
  • Exists in an E1 and E2 state
  • In the E1 state a glutamate is attached to the protein (facing inside of the cell)
  • ATP binds, and 3 Na+ bind from inside the cell
  • ATP is converted to ADP and the E1 is converted to E2 which prefers to face outside of the cell
  • The Na+ are released outside of the cell, 2 K+ bind the E2 state and phosphate is released
  • When phosphate is released the enzyme returns to the E1 state which prefers to face inside the cell
  • The K+ are transferred to inside the cell and the cycle repeats
58
Q

What is an example of an ABC transporter?

A
  • a p-glycoprotein - a protein that pumps drugs out of the cell
  • this is also known as a multi-drug resistance transporter
    • there are 2 ATP binding pockets
    • drug binds to transporters and gets kicked back out
    • CFTR is an example
59
Q

Where are p-glycoproteins overexpressed?

A
  • resistant cancer cells often over-express p-glycoproteins
60
Q

What is an enzyme?

A
  • protein-based catalyst
  • increases the rate of a reaction (impacts kinetics)
  • catalyst not consumed, always regenerated at the end of reaction cycles
61
Q

What are some characteristics of enzymes?

A
  • high reaction rate accelerations: 106-1014 times the rate of uncatalyzed rxn
  • high specificity - geometry and charge of active site
  • can be stereospecific
  • some enzymes use cofactors
62
Q

Describe how enzymes use cofactors.

A
  • Examples of cofactors include metal ions and prosthetic groups (heme, PLP, biotin)
  • apo-enzyme (inactive) + cofactor → holoenzyme (active)
63
Q

What is the transition state theory?

A

When A-B + C → A + B-C the reaction must travel through a high energy, unstable transition state

64
Q

What does a transition state diagram show?

A
  • free energy (G) vs reaction coordinate
  • reaction coordinate: path of minimum free energy which reactants use to form products
65
Q

What is the rate of a reaction determined by?

A
  • if it is a multistep reaction, the overall rate of the reaction is determined by the largest ∆G+= (delta G double dagger)
66
Q

How does a catalyst impact a transition state diagram?

A
  • catalyst lowers (∆G+= ) activation energy
  • lowers activation energy for a reaction in both directions - forward and reverse reactions are accelerated
67
Q

What equation indicates the efficiency of a catalyst?

A
  • ∆G+=uncat - ∆G+=cat = ∆∆G+=uncat
  • this is the change in activation energy between catalyzed and uncatalyzed reactions
68
Q

What are the 6 functional classes of enzymes?

A
  1. Oxidoreductases - oxidation/reduction
  2. Transferases - transfer of a functional group
  3. Hydrolases - breaks a bond using water
  4. Lyases - group elimination - C=C
  5. Isomerases - isomerize - don’t add or remove an atom
  6. Ligases - bond formation reaction, typically requires energy input
69
Q

What are the catalytic mechanisms?

A
  1. acid-base
  2. covalent
  3. metal ions
  4. proximity and orientation
  5. preferential binding to transition state
70
Q

Describe acid-base catalysis.

A
  • position acidic/basic groups in perfect orientation for proton transfer
  • RNAase A → cleaves phosphodiester bonds in RNA
  • can cleave 1000s of RNA molecules b/c of perfectly placed basic and acidic groups
71
Q

Describe covalent catalysis.

A
  • transient formation of a covalent bond between enzyme and substrate (covalent enzyme substrate complex)
  • Activates nucleophile/electrophile
  • Nucleophile - e- ser/thr, tyr, histidine, cysteine, lysine
  • Electrophile - e- acceptors
  • Example: cysteine protease → Mpro in SARS-Cov2
72
Q

Describe metal-ion catalysis.

A
  • Catalysts: Fe3+/Fe2+ Cu2+ Mn2+ Co2+
  • Structural: Na+ K+ Ca2+
  • Both: Zn2+ Mg2+
  • Catalysts:
    • orient substrates and shield from build up of negative charges
  • Example: carbonic anhydrase
73
Q

Describe proximity and orientation effects.

A
  • bring substrates into close contact (pseudo intramolecular interaction)
  • bring substrates together in the proper orientation for reaction to occur
  • reduces translational and rotational motion
74
Q

Describe preferential binding to the transition state.

A
  • enzyme binds tightly to the transition state to stabilize it, pushes the reaction towards forming the transition state
  • stabilizing the transition state serves to lower activation barrier
  • Proline Racemase is an example
75
Q

What must be considered when designing an enzyme inhibitor?

A
  • when designing an inhibitor design a molecule that resembles the transition state more than the reactants
  • enzyme binds to the inhibitor rather than the transition state
  • Example: Proline racemase - there are inhibitors that the enzyme prefers to bind to
76
Q

How do enzymes usually catalyze reactions?

A

They use multiple different strategies

77
Q

What does lysozyme do?

A
  • destroys bacterial cell wall (MurNac-GlcNac)
  • 108 enhancement rate
  • stabilizes half chair and lysozyme cuts
  • acid-base, then covalent catalysis
  • inhibited by f-lactone analog (mimics transition state)
  • residues are Glu and Asp
78
Q

What do serine proteases do? What are examples? What pathway are they active in?

A
  • they use serine nucleophiles
  • cleave amide bonds on proteins
  • examples are digestive enzymes:
    • trypsin cleaves next to positively charged residues- Lys/Arg
    • chymotrypsin cleaves bulky aromatic/hydrophobic (Trp, Phe, Tyr)
    • elastase cleaves small neutral (Ala, Gly, Val)
  • also active in the blood clotting pathway: “factor” enzymes inactivate zymogen, have to be cleaved by another protease to form active protease → people with Hemophilia lack one of these
79
Q

Describe how serine proteases function. What is a critical structural component?

A
  • catalytic triad: Asp - His - Ser
  • Asp and His activate the serine nucleophile
  • Covalent catalysis and transition state stabilization
  • have specificity pockets
80
Q

Describe the specificity pockets of serine proteases.

A
  • Trypsin - negatively charged Asp interacts with positively charged lysine on the substrate (negative residues, positive substrates)
  • Chymotrypsin - big pocket
  • Elastase - small pocket (large residues, small substrate)
81
Q

What is BPTI?

A
  • a natural protein inhibitor for trypsin
  • prevents H2O from attacking the transition state
  • BPTI remains covalently bound to trypsin
82
Q

What are zymogens?

A
  • inactive precursors, have distorted active sites
  • are activated when cleaved by another protease
  • Examples:
    • zymogen of trypsin is trypsinogen
    • zymogen of Factor Xa is Factor X
83
Q

How does enzyme regulation work? (General)

A
  • If one enzyme in a pathway is tightly regulated it regulates the flux through the whole pathway
  • if x is highly active the entire pathway is affected (Le Chatlier’s principle)
84
Q

What are two general ways that enzyme activity is controlled?

A
  1. control of enzyme amount
  2. control of enzyme activity
85
Q

How is enzyme activity controlled through changing the enzyme amount?

A
  • as the concentration of an enzyme increases, the rate of the reaction increases
  • rate of synthesis and degradation of an enzyme directly impacts reaction rate
86
Q

How can enzyme behavior be regulated by influencing enzyme activity?

A
  1. Changing the concentrations of substrates and products influences enzyme activity through le chatliers principle
  2. Product inhibition - a product of a reaction has some affinity to an enzyme, when there are high concentrations it remains associated w the enzyme and prevents its functioning
    1. Endogenous inhibitors: BPTI
  3. Allosteric effectors
  4. Covalent modification: zymogens and phosphorylation
87
Q

What is allosteric control?

A

inhibition or activation of an enzyme by a small regulatory molecule that interacts at a site (allosteric site) other than the active site

88
Q

What is an example of an enzyme that undergoes allosteric control? What reaction does it catalyze? Why is this reaction important?

A
  • Aspartate Transcarbamoylase (ATCase)
  • catalyzes reaction of:
    • carbamoyl phosphate + aspartate → carbamoyl aspartate + phosphate
  • this is the first step of pyrimidine synthesis in the body
89
Q

Describe the structure of Aspartate transcarbamoylase (ATCase)

A
  • C6R6 one unit is made up of 6 catalytic and 6 regulatory units
  • the catalytic subunit alone is active, and has typical enzyme properties
    • hyperbolic binding curve
  • when the C6R6 unit is formed, the enzyme has unusual properties
    • sigmoidal binding curve
    • cooperative enzyme - binding of the substrate to one catalytic unit increases the substrate affinity to other catalytic units within the C6R6 complex
90
Q

Describe the states that ATCase exists in. How is this balance regulated?

A
  • Enzyme exists in T - R
    • T - inactive
    • R - active
  • CTP
  • When carbamoyl phosphate is produced it goes through a pathway eventually releasing CTP
  • High CTP levels lead to feedback inhibition of the first reaction
  • CTP decreases enzyme activity
  • ATP
  • ATP is a purine, want your rates of purine and pyrimidine synthesis to be coordinated
  • When ATP levels are high, and CTP levels are low you want to activate ACTase to make more pyrimidines - ATP increases enzyme activity
91
Q

Explain how CTP and ATP regulate T - R of ATCase.

A
  • ATP and CTP bind regulatory units on C6R6
  • CTP binds to T state
  • ATP binds to R state
  • When ATP binds it changes the contacts between subunits and changes it to the R-state
92
Q

What is an example of covalent modification (strategy of enzyme regulation)?

A
  • phosphorylation
  • Ser/Thr/Tyr residues are phosphorylated by protein kinases (ATP → ADP)
  • These residues are de-phosphorylated by protein phosphatases (H2O → Pi, hydrolyzes off phosphate)
93
Q

What is an example of an enzyme that is regulated by covalent modification?

A
  • Glycogen phosphorylase
  • Breaks off one monomer of glucose (from glycogen) to glucose-1-phosphate
  • Very tightly regulated by allosteric inhibition and phosphorylation
94
Q

Describe the regulation of glucose phosphorylase.

A
  • Inactive dimer, AMP is allosteric activator, ATP and G6P are allosteric inhibitors
  • Phosphorylase kinase activates, phosphoprotein phosphatase deactivates
95
Q

Describe the pathway through which adrenaline provides a burst of energy.

A
  1. Adrenaline binds to receptors on the cell surface - GPCRs
  2. GPCRs produce CAMP
  3. CAMP activates protein kinase A (PKA)
  4. PKA phosphorylates phosphorylase kinase (activating it)
  5. Phosphorylase kinase phosphorylates glycogen phosphorylase (activating it)
  6. Glycogen is broken down
  7. Glucose and ATP concentrations rise, inhibiting glycogen phosphorylase
96
Q

Describe drug discovery.

A
  1. Identify protein target
  2. Establish activity assay - fluorescent/UV-vis readout
  3. High throughput inhibitor screen
  4. Identify lead compound
  5. Optimize compound
  6. Arrive at a potent, selective inhibitor
  7. Animal studies (pharmacokinetics)
  8. Human studies
97
Q

What is a high throughput inhibitor screen?

A
  • 96-well plate with different compounds
  • Want an enzyme inhibitor that decreases the amount of product formed
98
Q

How do you optimize a compound in drug discovery?

A
  • Structure base drug design - get crystal structure of protein bound to the compound, what groups can you add to the compound to make it bind better to its target
98
Q

How do you optimize a compound in drug discovery?

A
  • Structure base drug design - get crystal structure of protein bound to the compound, what groups can you add to the compound to make it bind better to its target
99
Q

What is a potent/selective inhibitor?

A
  • potent - how well does it bind to its target
  • selective - does it bind to other cellular targets
100
Q

What does pharmacokinetics assess?

A
  • stability in vivo
  • oral bioavailability
  • metabolism
  • excreted by kidneys
101
Q

What are the phases of human clinical trials?

A
  • Phase I: safety (20-100) healthy individuals
  • Phase II: efficacy (100-500) diseased vs placebo
  • Phase III: long term safety/efficacy in larger population
  • FDA approval: phase IV - still collecting data
102
Q

What molecule is involved in drug safety/adverse drug reactions?

A
  • cytochrome p450s - humans have 50-60
  • they metabolize drugs
  • they are mono-oxygenases - have heme center
  • cytochrome p450s hydroxylate your drug
  • drug-drug interactions - one drug takes away a p450 that binds to another, making the level of the second higher
  • Pfizer Mpro inhibitor - combination therapy
    • add HIV drug to prevent drug metabolism
103
Q

What are steady state conditions?

A
  • Aka Michaelis-Menten kinetics
  • concentration of substrate is much greater than concentration of enzyme, concentration of enzyme substrate complex stays constant with time
  • therefore, rate of the reaction is proportional to the concentration of [ES]
104
Q

How do you produce a Michaelis-Menten plot?

A
  • Michaelis-Menten Equation describes the relationship between rate and [S]
105
Q

What is the Michaelis-Menten Equation?

A
106
Q

What are Km and Vmax on a Michaelis-Menten plot?

A
  • Vmax= k2[ET] (when enzyme is saturated w substrate)
  • Km is the concentration of substrate at which V = (Vmax/2)
107
Q

What is Km?

A
  • Michaelis Constant
  • Represents the affinity of an enzyme for a substrate
  • Lower Km = higher rate at lower [S] → more efficient catalysis
  • Km is unique for each enzyme substrate pair
108
Q

What is Kcat? What does it allow you to calculate?

A
109
Q

What is catalytic efficiency of an enzyme? Describe this for the most efficient enzymes.

A
  • (Kcat) / (Km) = catalytic efficiency → allows you to compare two different enzymes
  • the most efficient enzymes have a catalytic efficiency = 108 - 109 M-1s-1
    • this is known as the diffusion controlled limit
    • Eg. acetylcholinesterase, and catalase (breaks down hydrogen peroxide)
110
Q

What is the linearized Michaelis-Menten equation?

A
111
Q

Describe the plot of a Lineweaver-Burke Eq.

A
112
Q

Describe the kinetics of first and second order reactions.

A

Biochemistry (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions