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Bio 234 > Basic Biochemistry > Flashcards

Basic Biochemistry Flashcards

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
Hydrolytic cleavage of a molecule (nucleases, proteases, phosphatases, etc...) - Using H2O to break stuff - condensation is the reverse process
Hydrolases
26
Movement of a functional group within a molecule
Isomerases
27
Joining 2 molecules together (polymerases, ligases--often are condensation rxns)
Synthases
28
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
Lyases
29
Conditions affecting enzymes
Temp | pH
30
T or F: enzymes do not remain static.
True
31
How do we get the enzyme and substrate together?
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
Enzyme kinetics
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
Concentration needed to reach 1/2 max V.
Km
34
Michaelis-Menten equation
V= Vmax [S] / Km + [S]
35
When [S]
then v=Vmax [S]/Km , and initial reaction velocity is roughly proportional to [S]: 1st order region f the M-M plot
36
When [S] > Km,
Then V=Vmax[S]/[S] or V-Vmax, or 0 order rxn where substrate concentration no longer matters
37
What dictates Vmax?
Enzyme concentration
38
When [S]=Km, then
V=Vmax/2. Thus, Km is the point at half Vmax: this is the Michaelis constant (Km)
39
Enzyme regulation: how else can we control enzyme reactions? Why would this be important?
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
Inhibition of Enzymes
Competitive inhibition | Noncompetitve inhibition
41
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
Competitive inhibition
42
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
Noncompetitive inhibition
43
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
Allosteric regulation
44
Allosteric regulation
Allosteric inhibition | Allosteric activation
45
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.
Allosteric Inhibition
46
When the allosteric ________ binds to the enzyme, the enzyme turns into its high affinity form, resulting in enzyme activity
Allosteric activation
47
Types of inhibitors (Chemical modifications)
1. Irreversible | 2. Reversible
48
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
Irreversible inhibitors
49
Inhibitors that can bind and dissociate (can be competitive or noncompetitive); noncovalent bonds
Reversible inhibitors
50
Basic protein functions | *note: none of these work without proper structure--protein folding!
- enzymes - motor proteins - receptors - structural proteins - storage - gene regulation - transport - signaling - can have overlap of functions too
51
Proteins form by:
polymerization of amino acids
52
Protein folding happens by
Chemical interactions between side chains or backbone. Also covalent and hydrophobic interactions can dictate folding. -folding creates binding sites and specificity
53
Levels of protein organization
1, 2, 3, 4
54
Composition of amino acids in a polypeptide chain
primary protein structure
55
structures formed by the backbone: alpha-helicies and beta-sheets; localized backbone interactions; atoms H bond with themselves
Secondary protein structure
56
3D; formed by interactions of R groups of a single polypeptide chain
Tertiary protein structure
57
Multiple polypeptide chain interactions; also 3D
Quaternary protein structure
58
Active site is made possible by
folding of R groups
59
What happens with a substrate is bound?
- 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
Analysis of proteins: electrophoresis after breaking cells open
- unfolded tertiary structure - need to uniformly charge proteins by adding a detergent to ensure negatively charged proteins that will not escape gel.
61
What do you need for gel electrophoresis?
- Gel matrix: polyacrylamide - Buffer - Denaturing agents: to make consistent band lengths (heat) - Anionic detergent (SDS): to give uniform charge, thus uniform separation
62
SDS-PAGE
Sodium dodecyl sulfate polyacrylamide gel electrophoresis
63
Things to do after SDS-PAGE
- 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
Problems with transferring proteins to a membrane and probing for specific proteins after SDS-PAGE
-protein is denatured, so epitopes may be no more
65
Immunoprecipitation
- 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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