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Bio 234 > Basic Biochemistry > Flashcards

Basic Biochemistry Flashcards

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1
Q

A cell is tasked with creating order (structure) from disorder (raw materials). What does this require?

A

Energy, raw materials that you can break and can build up, instructions, enzymes to drive chemical processes

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2
Q

The chemical processes by which the cell drives its function.

A

Metabolism

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3
Q

Breaking down to make raw materials and energy (oxidizing)

A

Catabolism

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4
Q

Building up macromolecules with energy

A

Anabolism

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5
Q

Despite the creation of order, we’re not violating the 2nd Law of Thermodynamics

A

Order is paid for by the discharge of heat into the enviornment
-fun fact: we burn off 1000-1500 kcal by just being human

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6
Q

All reactions have a change in free energy (delta G)

A
  • delta G takes entropy, enthalpy, and temp into account

- Can only tell us what can be done– not if and how fast!

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7
Q

(-) delta G

A

spontaneous reaction

-rxn favors product and has some small degree of substrate (at equilibrium implies more product than substrate)

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8
Q

(+) delta G

A

nonspontaneous reaction

-can undergo a reaction if coupled to a spontaneous rxn.

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9
Q

Some cellular problems of reactions (even if rxn is spontaneous)

A
  • Rxn can occur, but won’t w/out some sort of kick start
  • Rxn can and does occur, but not fast enough
  • Rxn can occur, but substrate(s) are not in the correct place or time
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10
Q

What is needed for a rxn to take place in a cell?

A

Enzymes! To overcome cellular problems of rxns. we need an enzyme– a biological catalyst– and the proper compartmentation.

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11
Q

Activation energy: Minimum of energy needed in a “collision” between 2 molecules that will result in a rxn.

A
  • Enzymes lower the amount of bombardment needed to get a rxn.
  • Random collisions can get you near the peak of Ea
  • Free energy (delta G) isn’t changed!
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12
Q

In cells, not many molecules can reach the Ea alone. Why is this useful?

A

Control!

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13
Q

Reactants that are below Ea, will not react unless something pushes them to the Ea

A

Metastable state

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14
Q

How do we control enzymes in the cell?

A
  • feedback inhibition from downstream products
  • physical separation of enzymes and substrates (compartmentalization)
  • can use other chemicals
  • gene promoters can control txn
  • control mRNA and protein degredation
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15
Q

Speeds up rxn rate but isn’t changed in the end.

A

Catalyst

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16
Q

Basic properties of BIOLOGICAL CATALYSTS (enzymes)

A
  1. increases the rate (probability) of rxn by lowering Ea: rxn occurs w/out thermal activation
  2. Forms a transient interaction w/ the substrate(s), facilitating interaction
  3. Changes only the rate: cannot make a (+) delta G move forward w/out added energy. Rate can increase greatly
  4. No changed during the rxn
  5. Can be proteins (most are and end in -ase) or RNA
  6. Most are highly specific
  7. Readily coupled to other enzymatic rxns.
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17
Q

How do you couple?

A

Harness energy by linking molecules together. Couple favorable with unfavorable.

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18
Q

Substrate binding

A

“lock and key”

  • “induced fit” is what we really call it
  • maximizing chemical rxns between substrate and enzyme
  • shape will bend and twist to get the induced fit
  • when enzyme and substrate are in complex with each other, that’s the Ea hump.
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19
Q

Features of Enzymes

A

Some have a tightly bound prosthetic group: metal ion, heme, etc…, for function (often electron acceptor)
-Folding dictates active site

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20
Q

A pocket or groove formed by amino acids (tertiary structure) where the substrate(s) bind.

A

Active Site

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21
Q

Enzymes can be hyper-specific: succinate dehydrogenase

A
  • Name refers to the reversible process
  • Catalyzes the reduction of fumarate into succinate
  • Enzymes are named for only one direction of the rxn, so it can be misleading
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22
Q

Types of enzymes to memorize!

A

pg 144, table 4-1

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23
Q

Redox rxns “LEO GER”

  • To tell if redox rxn, look for:
    1. charge differences
    2. oxygen
    3. protons
    4. formation/loss of double bonds
A

Oxidoreductases

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24
Q

Transfer of functional groups from one molecule to another (kinases: cause phosphorylation)

A

Transferases

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25
Q

Hydrolytic cleavage of a molecule (nucleases, proteases, phosphatases, etc…)

  • Using H2O to break stuff
  • condensation is the reverse process
A

Hydrolases

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26
Q

Movement of a functional group within a molecule

A

Isomerases

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27
Q

Joining 2 molecules together (polymerases, ligases–often are condensation rxns)

A

Synthases

28
Q

Joining of 2 molecules or breaking 1 into 2 with an electron rearrangement (break or form double bonds)

  • When breaking apart, one molecule will get a double bond
  • When join together, a molecule will lose a double bond
A

Lyases

29
Q

Conditions affecting enzymes

A

Temp

pH

30
Q

T or F: enzymes do not remain static.

A

True

31
Q

How do we get the enzyme and substrate together?

A

All has to do with rate:

  • diffusion
  • scaffolding: put them in some assembly together
  • limiting space of diffusion (ex vesicles)- still diffuse, but space is limited
  • activation of proximal proteins- can put them next to each other, but can’t react with some chemical change in the environment happens.
32
Q

Enzyme kinetics

A

when rate of rxn and substrate concentration graph starts to level off, all enzymes are occupied by substrate.
-called Vmax, and can be increased if enzyme amount is increased
LOOK AT NOTES FOR EXTRA INFO

33
Q

Concentration needed to reach 1/2 max V.

A

Km

34
Q

Michaelis-Menten equation

A

V= Vmax [S] / Km + [S]

35
Q

When [S]<Km,

A

then v=Vmax [S]/Km , and initial reaction velocity is roughly proportional to [S]: 1st order region f the M-M plot

36
Q

When [S] > Km,

A

Then V=Vmax[S]/[S] or V-Vmax, or 0 order rxn where substrate concentration no longer matters

37
Q

What dictates Vmax?

A

Enzyme concentration

38
Q

When [S]=Km, then

A

V=Vmax/2. Thus, Km is the point at half Vmax: this is the Michaelis constant (Km)

39
Q

Enzyme regulation: how else can we control enzyme reactions? Why would this be important?

A

Feedback inhibition implies that product comes back to inform of a change.

  • Enzyme can be informed b/c of its multiple binding sites
  • downstream or immediate products can bind to regulate by changing enzyme shape.
40
Q

Inhibition of Enzymes

A

Competitive inhibition

Noncompetitve inhibition

41
Q

Inhibitor and substrate both bind to the active site of the enzyme. Binding of an inhibitor prevents substrate binding, thereby inhibiting enzyme activity
-inhibitor looks like substrate

A

Competitive inhibition

42
Q

Inhibitor and substrate bind to different sites. Binding of the inhibitor distorts the enzyme, thereby decreasing likelihood of substrate binding.

  • Inhibitor binds to somewhere other than active site
  • Also called Allosteric
A

Noncompetitive inhibition

43
Q

Regulation of an enzyme with a molecule that is not the substrate or product- binds to another site.
-Often at the level of a “committed step” which will possibly have activated and inhibitory sites

A

Allosteric regulation

44
Q

Allosteric regulation

A

Allosteric inhibition

Allosteric activation

45
Q

An enzyme subject to allosteric _________ is active in the uncomplexed form, which has a high affinity for its substrate. When the allosteric _______ binds, the enzyme is stabilized in its low affinity form, resulting in little or no activity.

A

Allosteric Inhibition

46
Q

When the allosteric ________ binds to the enzyme, the enzyme turns into its high affinity form, resulting in enzyme activity

A

Allosteric activation

47
Q

Types of inhibitors (Chemical modifications)

A
  1. Irreversible

2. Reversible

48
Q

Covalently bound inhibitors (nerve gases, penicillin, asprin) that can be done in cells as well—phosphorylation
-refers to not being able to spontaneously be removed

A

Irreversible inhibitors

49
Q

Inhibitors that can bind and dissociate (can be competitive or noncompetitive); noncovalent bonds

A

Reversible inhibitors

50
Q

Basic protein functions

*note: none of these work without proper structure–protein folding!

A
  • enzymes
  • motor proteins
  • receptors
  • structural proteins
  • storage
  • gene regulation
  • transport
  • signaling
  • can have overlap of functions too
51
Q

Proteins form by:

A

polymerization of amino acids

52
Q

Protein folding happens by

A

Chemical interactions between side chains or backbone. Also covalent and hydrophobic interactions can dictate folding.
-folding creates binding sites and specificity

53
Q

Levels of protein organization

A

1, 2, 3, 4

54
Q

Composition of amino acids in a polypeptide chain

A

primary protein structure

55
Q

structures formed by the backbone: alpha-helicies and beta-sheets; localized backbone interactions; atoms H bond with themselves

A

Secondary protein structure

56
Q

3D; formed by interactions of R groups of a single polypeptide chain

A

Tertiary protein structure

57
Q

Multiple polypeptide chain interactions; also 3D

A

Quaternary protein structure

58
Q

Active site is made possible by

A

folding of R groups

59
Q

What happens with a substrate is bound?

A
  • substrate binds weakly to R group components
  • distortion of bonds-opening up to catalytic attack (hight energy state; activation energy)
  • enzyme accepts or donates proton, changing the reactivity of a substrate (pH sensitive)
  • accepts or donates electrons, formation of temporary (high energy) covalent bonds
  • stablilzes “unstable” bonds by all favorable rxns it makes with substrate
60
Q

Analysis of proteins: electrophoresis after breaking cells open

A
  • unfolded tertiary structure
  • need to uniformly charge proteins by adding a detergent to ensure negatively charged proteins that will not escape gel.
61
Q

What do you need for gel electrophoresis?

A
  • Gel matrix: polyacrylamide
  • Buffer
  • Denaturing agents: to make consistent band lengths (heat)
  • Anionic detergent (SDS): to give uniform charge, thus uniform separation
62
Q

SDS-PAGE

A

Sodium dodecyl sulfate polyacrylamide gel electrophoresis

63
Q

Things to do after SDS-PAGE

A
  • stain and visulaize the sizes and amounts of proteins present
  • bring out of 3D into 2D
  • transfer proteins to a membrane and probe for specific proteins
    - use antibodies (Western blot) or molecules that bind to other proteins (secondary Ab)
  • elute proteins off gel and ID via mass spec.
  • enzymatic rxns in the gel
64
Q

Problems with transferring proteins to a membrane and probing for specific proteins after SDS-PAGE

A

-protein is denatured, so epitopes may be no more

65
Q

Immunoprecipitation

A
  • break open cells
  • add and Ab to bind to a specific protein in the cell extract
  • add an agarose bead that contains a protein that will bind the Ab you added
  • Spin down the beads and wash away the rest of the non-Ab bound extract
  • remove the Ab/protein complex from the beads
  • add the soln that was precipitated by the Ab to an SDS-PAGE
  • Western blot for proteins that have been precipitated

Bio 234 (8 decks)

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