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Fall 2022 Junior Year > Biochem Exam III > Flashcards

Biochem Exam III Flashcards

1
Q

signal transduction

A

the reception of an environmental stimulus by a cell, leading to metabolic change that adapts the cell to that stimulus
- outside stimulus –> something perceived by cell
- necessitates a response (change and adapt)
- how does it “know” what to do? (based on the signal they receive)

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2
Q

Cells receive signals from the environment beyond the plasma membrane. Types of signals include? where to they go? which signal goes to the nucleus?

A
  • antigens
  • hormones
  • neurotransmitters
  • light
  • touch
  • pheromones
  • they go to plasma membrane… most signals stay outside of the cell except HORMONES
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3
Q

how do signals affect cell’s composition and function

A
  • differentiation and antibody production
  • growth in size or strength
  • sexual versus asexual reproduction
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4
Q

When does signalling start?

A

when a stimulus (change) causes a hormone to be secreted (released)

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5
Q

hormone

A

chemical messenger; PRIMARY message; downstream effects

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6
Q

what are the 3 key features of signal-transduction? describe them.

A
  1. specificity = signaling ligand fits binding site on its complementary receptor; other ligands do not fit
  2. sensitivity = (sensitivity to ligand); receptor has high affinity (low Ka) for signaling ligand (L)
  3. amplification = tiny amount of hormone/signal present leads to big responses/changes cellularly
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7
Q

what are receptors?

A
  • membrane-bound proteins or soluble protein or protein complex, which exerts a physiological effect (intrinsic effect) after binding its natural ligand
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8
Q

3 types of receptors and an example of each

A
  1. G-protein coupled receptors (epinephrine receptor)
  2. enzyme-linked receptors (insulin receptor)
  3. ligand-gated ion channels (nicotinic acetylcholine receptor)
  4. nuclear receptors (steroid receptor)
  5. other membrane receptors (integrin receptors)
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9
Q

gated ion channel… what does the ion insinuate

A
  • cause something to happen
  • example: the acetylcholine stuff affecting muscles
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10
Q

GCPRs

A

receptors coupled to G proteins

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11
Q

dimerize

A
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12
Q

glucagon

A
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13
Q

kinetics

A

rate/speed of a reaction

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14
Q

how to study/measure kinetics

A

color of reactant or product –> speed it up and it changes (measure absorbance)

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15
Q

first order

A

rate = k[a]

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16
Q

second order

A

A+B —> C + D
rate = k[A][B]

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17
Q

zero order

A

rate = k

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18
Q

why study enzymes

A

can develop drugs
- enzyme inhibitors (stop something from happening)

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19
Q

what is the speed of reactions without enzyme

A

can be extremely slow… like 1 million years slow

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20
Q

how fast is reaction with smaller Ea? bigger Ea?

A

smaller Ea = faster reaction
bigger Ea = slower reaction

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21
Q

induced fit model

A

conformational change needed to bind to enzyme

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22
Q

structural evidence of conformational change

A

glucose binding to enzyme
- hexokinase catalyze phosphorylation of glucose
- fluorescence occurs when absorb light but emit energy at a lower wavelength
- aromatic rings fluoresce
- without vs. with changes = we can study conformational change

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23
Q

catalytic mechanisms

A
  1. electrostatic catalysis
  2. catalysis by approximation
  3. covalent catalysis
  4. general acid base catalysis
  5. metal ion catalysis
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24
Q

electrostatic catalysis

A
  • IMFs help achieve S binding
  • collision theory: molecules always moving; in order to react molecules ave to run into each other with the right amount of energy and in correct orientation
  • example
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25
Q

catalysis by approximation

A
  • enzyme brings reactive species close together in an approximate orientation
  • example
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26
Q

covalent catalysis

A
  • a transient covalent intermediate is formed between the enzyme and the substrate
  • example
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27
Q

acid-base catalysis

A
  • acids and bases neutralize
  • reactions involve “charge build-up” on the substrate or enzyme as the reaction proceeds
  • the enzyme uses any acid/basic residue in proton transfer reactions to participate in the reaction and stabilize the charge
  • example:
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28
Q

metal ion catalysis

A
  • enzymes use metal ions to help form nucleophiles or they can act as electrophiles direactly
  • they may interact with a substrate to neutralize a charge
  • metaloprotein, redox, nucleophile, electrophile
  • involves metal ion bound to the enzyme
  • interacts with substrate to facilitate binding (stabilize negative charges)
  • metal may participate in any REDOX reactions
  • EXAMPLE: CARBONIC ANHYDRASE
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29
Q

carbonic anhydrase

A

CO2 + H2O —-> H2CO3 —-> HCO3- + H+
- metals like Os
- affects pKa
- nucleophile attack carbonyl and interact with zinc

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30
Q

What can enzymes use in catalysis?

A
  • amino acid residues
  • metal ions
  • coenzymes/cofactors
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31
Q

catalysis

A

speed up rate of rxn by a catalyst that is unchanged by the reaction

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32
Q

Enzyme kinetics equation

A

E + S —->< ES —-> E + P

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33
Q

steady state assumption

A
  • time period where [ES] is constant, we assume the rate is constant for the reaction
  • [ES] is formed and broken at the same time
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34
Q

how do enzyme and substrate change in rxn

A
  • enzyme is constant (we know how much is there bc we put it there)
  • [substrate] decreases as [product] increases until there’s no more substrate left
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35
Q

pre-steady state

A

[ES] is forming… slowly building up to a constant concentration

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36
Q

Michaelis-Menton Curve
- Km
- Vmax
- Kcat

A
  • allows us to plot observed rate vs [substrate]
  • Km = substrate at 50% Vmax
  • Vmax is top of curve where it’s leveling out
  • kcat = Vmax/E
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37
Q

What are the units for Kcat?

A

inverse of time

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38
Q

Kcat/Km

A
  • BIGGER VALUE = BEST SUBSTRATE FOR THE ENZYME
  • bigger = catalytic efficiency
  • we want a lower Km bc it means better binding
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39
Q

Lineweaver-Burk Plot
- slope
- Km
- Vmax
- Kcat

A
  • inverse of Michaelis-Menten curve plotted 1/v vs 1/s
  • linear graph
  • slope: Km/Vmax
  • y-intercept: 1/Vmax
  • Km = slope x Vmax
  • Vmax = 1/y-int
  • Kcat is still Vmax/E
40
Q

Lineweaver-Burk use in inhibition and kinetic mechanisms

A

different graphs depending on type of inhibition
- competitive: intersecting lines

41
Q

what are the 3 types of inhibition

A
  1. competitive
  2. uncompetitive
  3. irreversible
42
Q

competitive inhibition
- what about Ki

A
  • one of the most widely applied results of studies
  • structurally and functionally understand enzyme and substrate = make something that looks like substrate but alters the function once it binds to the enzyme so that the substrate cannot bind
  • good for drug research designs
  • smaller Ki = more effective inhibitor
43
Q

we use kinetics to show that we have a competitive inhibitor

A
44
Q

competitive inhibition and lineweaver burk

A
  • competitive inhibition affects Km
  • DECREASE substrate binding
  • we need MORE substrate concentration to get 1/2 Vmax (bc it’s competing)
  • competitive inhibitor graph and normal graph INTERSECT
45
Q

what about Ki and competitive inhibition

A
  • we need Ki inhibitor to be LOWER than Km substrate so that it binds better
46
Q

uncompetitive inhibition
- what is it
- how does it affect Vmax and [S]?

A
  • an inhibitor binds to an allosteric site where substrate does not bind
  • most cases inhibitor can only bind after S (bc it needs conformational change to bind)
  • cant be rationally created because we don’t know if they exist
  • [S] is unaffected
  • Vmax either full or no activity
  • adding more [S] doesn’t cancel this issue out… might enhance the problem because more substrate bind = more allosteric sites ready for inhibitor
47
Q

how many substrates are there in a real system

A

more than one. maybe 2

48
Q

uncompetitive inhibition and lineweaver burke

A

lines are PARALLEL
- can remove something by adding more inhibitor

49
Q

irreversible inhibition
- ‘suicide inhibitors’

A
  • the inhibitor forms a COVALENT BOND (so not actually irreversible but it would require energy to break a bond)
  • mechanism-based inhibition
  • kills the enzyme without a chance of recovery

EX: serine and diisopropylfluorophosphate
- Ser attacks the DFP and F leaves and Ser covalently bonds on
- the active site is now fully unreactive
- the enzyme is stuck and can’t do anything

50
Q

Mechanisms of Substrate binding

A
  1. random sequential
  2. ordered sequential
  3. ping pong
51
Q

Mechanisms of Substrate binding: random sequential

A
  • random: have multiple S and either of them can bind
  • sequential: once 1 substrate binds, the other immediately follows
  • there is a ternary complex (enzyme with both substrates)
52
Q

Mechanisms of Substrate binding: ordered sequential

A
  • S2 specifically cannot bind until S1 does
  • this is bc S2 can’t bind until conformational change from S1 binding happens
  • also has a ternary complex (enzyme with both substrates)
53
Q

Mechanisms of Substrate binding: Ping Pong
- which catalytic mechanism goes hand in hand with ping pong?

A
  • NO TERNARY COMPLEX
  • S1 binds
  • product 1 leaves
  • S2 binds
  • product 2 leaves

ex: chymotrypsin

54
Q

lineweaver burke and kinetic mechanisms of S binding

A
55
Q

show you understand extent of regulation
- transcription factors
- mRNA 1/2 life
- enzyme level

A
  • can happen at EVERY level in a cell
  • sooo many transcription factors (turning genes on and off)

mRNA level: mRNA has a set lifetime dependent on the gene which impacts the cell
- longer mRNA = more proteins made = might need lots of enzymes

enzyme level: sequestration, association with regulatory protein, allosteric regulation, covalent modification, zymogen control

56
Q

the central problem: flux v. homeostasis

A
  • we’re always in a state of flux BUT we need to maintain homeostasis
  • ability to activate, deactivate, and slow down/affect speed
57
Q

Regulation: sequestration

A
  • regulated by insulin for example
  • increase insulin = increase blood sugar
  • Glucose: needs enzymes and transporters so we phosphorylate it and it can’t leave because it needs a transporter
  • Hexokinase IV is what phosphorylates glucose and it is only activated in the cytosol
  • With a regulatory protein bound to it, hexokinase is stuck in the nucleus and is sequestered in the nucleus - cant phosphorylate
58
Q
  • product inhibition graph
  • how does a product inhibit activity?
A
  • looks like M-M curve but starts going down
  • inhibition is when the enzyme activity starts to decrease
  • it tries to make more product but more product leads to less activity (quick/immediate regulation)

how does a product inhibit activity?
- allosteric inhibition

59
Q

allosteric control/regulation
- product inhibition vs. feedback inhibition
- where does Kd come into play
- what is it all based off of

A

All based off of cellular concentrations (quick changes)

Product Inhibition:
- if the First product in a chain of reactions/enzymes inhibits the chain, we have product inhibition

Feedback Inhibition:
- when a later product inhibits a previous enzyme
- it’s common because if you have enough of the downstream products, you can turn off the production
- works well because it all ties back to Kd
- Kd: in the beginning, we don’t have enough enzyme so the reaction keeps happening, but when the conc. enzyme increases, the Kd value increases (more ligand bound) so we decrease activity
- this cycle repeats: then once E goes down again after the process has been halted, we will eventually need more and make more

60
Q

regulation: covalent modification
- post translational?
- reversibility?
- most common example?
- how does this work

A
  • NOT post translational
  • is typically reversible bc controlled by regulatory enzymes (add group and take it off whenever bc it’s about regulation not function)
  • most common example: phosphorylation
  • HOW? IMFs and conformational change of course
61
Q

examples of covalent modification

A
  1. phosphorylation
  2. adenylylation
  3. acetylation
  4. myristoylation (fatty acid)
  5. ubiquitination
  6. methylation
62
Q

kinase vs phosphatase

A

kinase = adds phosphate
phosphatase = removes (hydrolyzes) a phosphate group

63
Q

zymogen control
- what is a protease
- what is specifically targetted?
- list 2 examples of inactive forms

A
  • inactive precursor protein
  • original protein is MADE in an inactive form
  • protease: catalyze the hydrolysis of peptide bonds; cleaves inactive parts (very specific - adjacent to negative charge or something)
  • specific proteins are NOT targeted - specific PEPTIDE BONDS are
  • proteases NEED to be regulated because they will break down everythinggg (pancreatitis is so dangerous and deadly)

Examples:
1. trypsinogen
2. chymotrypsinogen

64
Q

example of zymogen control (bigger picture example/systems example)

A

DIGESTIVE PROTEASES
- they come from the pancreas
- if something happens to the pancreas like a blocked duct you get deadly pancreatitis
- even ONE active molecule can start a chain reaction of active proteases and they will just chop chop chop all of the proteins and it will kill you without intervention

65
Q

example of zymogen control (specific enzyme example)

A

Chymotrypsinogen to Chymotripsin
- this is not usually through conformational change
- this is from a physical piece of the protein literally physically being blocked (something over the active site)

66
Q

which delta G values are good for driving metabolism

A

NEGATIVE

67
Q

what is spontaneous vs not spontaneous reaction

A
  • spontaneous is when the reaction actually runs forward

DG = - RTlnKeq
- when the rxn is at equilibrium
- bio reactions don’t really sit at equilibrium though

68
Q

what is the standard state?

A

[H+] = 1 x 10^-7 M
[Mg] = 1 mM
37 degrees C (BODY TEMPERATURE)

69
Q

what do ppl usually do to get delta G negative?
why can’t we?
what do we do instead?

A
  • usually you would change the temp
  • in biochem, changing the temp kills your proteins
  • Instead, we PAIR REACTIONS and use Hess’s Law (path independent, add up the energies)
70
Q

The source of energy is ATP buttttt we need to couple reactions sometimes

A
71
Q

There are tons of REDOX reactions but what drives everything?

A

OXYGEN REDUCTION

72
Q

where is all energy derived from?
- which redox example contributes

A

electrons!!!
- we get ATP from the electron transport chain
- NAD+ reduced to NADH and NADH goes to electron transport chain

73
Q

What is an inorganic and an organic electron carrier examples?

A
  • metal ions: Fe+2/+3 and sometimes Cu+1/+2
  • NAD, FAD
74
Q

What are the 4 types of REDOX reactions

A
  1. direct electron transfer
  2. Transfer of H atoms (as 2 electrons and 2 H+)
    - not stressed
  3. as hydride ion
  4. direction reaction with oxygen
75
Q

what does direct electron transfer use?

A

metal ions

76
Q

know every wittle step of glycolysis

A
77
Q

know the big funnel to ATP

A
78
Q

how is NADH present in the cell

A

A POOL LIKE AT HOME WOO
- there is a set number but you can make more but you typically have a set amount

79
Q

what is NAD in reduced and oxidized form

A

reduced: NADH
oxidized: NAD+

80
Q

what is the cori cycle

A

anaerobic metablism
- pyruvate to lactate
- when we are out of ATP we replenish NAD+ so that we can do glycolysis again
- the cori cycle is what we do with all of the excess lactate produced (bc in reality the purpose is to get more NAD+ it has nothing to do with lactate)
- lactate goes back to glucose through gluconeogenesis

81
Q

when does anaerobic metabolism usually happen? where?

A

exercise bc youre rapidly burning ATP
- muscle cells
- lactate produced goes to blood and then to liver to make more glucose

82
Q

Example of how sugars enter energy metabolism

A

EAT LACTOSE (DAIRY)
- we break lactose down into glucose and galactose which
- glucose goes to glycolysis
- galactose becomes glucose-6-phosphate

83
Q

FEEDER PATHWAYS FOR GLYCOLYSIS

A
  1. sucrose (fructose and glucose) –> turn to glucose
  2. lactose –> use glucose for glycolysis
  3. fructose –> turned into fructose-1-phosphate
84
Q

starch vs. glycogen

A

starch: eat (potatoes)
glycogen: no eat

  • both are storage molecules made out of glucose
  • sugar = initial source of energy (so we neeeeed to maintain glucose levels)
85
Q

WHAT do we do if we’re not eating

A
  • glycogen stores in the liver are burned through in one do
  • enzymes break down the glycogen so we can get some glucose
86
Q

1 —> 4 carbon
vs.
1 —> 6 carbon

A
  • with 1 to 4 we have a linear chain with anomeric carbon connected to 4th

with 1 to 6 we can get some BRANCHING
- we get branches for
a) storing/being compact
b) gives more ENDS to work with instead of 1 end from the linear option - can release lots of energy when not eating

87
Q

enzyme bound glucose-1,6-biphosphate
- what do we do if we need to raise blood sugar
- where does this reaction happen

A
  • where? LIVER
  • need to get glucose out of the cell? well there is no glucose transporter that allows those phosphate groups so we have to dephosphorylate it in order to raise that blood sugar back up
88
Q

We have 2 potential needs
1. make ATP
2. raise blood sugar

A
  1. turn glucose to G6P
  2. get G6P to Glc
89
Q

what happens if we aren’t eating and our glucose stores are out?

A

GLUCONEOGENESIS
- we need to make glucose

90
Q

where does gluconeogenesis happen?

A

mostly liver but sommmmee reuptake in the kidneys because there is a lot of blood flow to the kidneys
- liver has the right enzymes for the process

91
Q

Why can’t we just easily reverse glycolysis and be happy

A

it has a large - delta G and can’t be reversed… so you have some key reactions to reverse instead

92
Q

anaplerotic enzyme
- pyruvate carboxylase

A

enzyme can function for 2 reasons
1. convert bicarbonate + pyruvate to oxaloacetate for gluconeogenesis
2. need more oxaloacetat for CAC

93
Q

biotin

A

a coenzyme that functions as a 1-C shuttle where C is in the form of CO2

94
Q

where do the processes occur?
1. glycolysis
2. gluconeogenesis
3. CAC

A
  1. in cytosol
  2. step 1 in mitochondrion
  3. mitochondrion
95
Q

Why might we want the first step of gluconeogenesis to happen in the mitochondrion?

A

Oxaloacetate is stuck in the mitochondrion and doesn’t have a transporter to exit it… so it stays in there for the CAC and helps with regulation/control
- we do this also so there is no net change of NADH

96
Q

G6Pase is:

A
  • membrane bound in the ER lumen
  • expressed in the liver, kidney, and epithelial cells
  • good to be membrane bound bc the substrate has to get there
  • more regulated this way
  • we make Glc and send it out (liver)
  • if this happened in every cell we’d be stressed bc you lose a lot of ATP to go backwards so we control for this by only expressing the appropriate enzymes in few places… mostly the liver
97
Q

What is the energy difference in gluconeogenesis and glycolysis but why is this not stressful

A
  • gluconeogenesis burns FOUR ATP!! and glycolysis only generates 2 net…
  • this is alrighty because the liver cells do not rely on glucose for energy

Fall 2022 Junior Year (9 decks)

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