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bio 215 > UNIT 3 > Flashcards

UNIT 3 Flashcards

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Biology 101 flashcards
1
Q

endergonic reaction

A

results in increase in free energy (nonspontaneous)

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2
Q

exergonic reaction

A

results in a decrease in free energy. (spontaneous)

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3
Q

energetic coupling can make chem reactions spontaneous, BUT doesnt mean it’ll make them fast. why? (why aren’t exergonic reactions always fast?)

A
  1. spatial orientation: reactants move inside cytosine/inside organelles at random. unlikely they’ll bump into each other in the orientation for old bonds to break and new ones to form
  2. activation energy: in the transition state, the reactants are much less stable than before reaction, causing spike in free energy
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4
Q

enzyme

A

proteins that act as catalysts, meaning that they make reactions go faster but aren’t changed by them–the structure of an enzyme is the same before and after the reaction. More specifically, proteins have areas called active sites where a particular chemical reaction takes place

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5
Q

why does each enzyme only catalyze one reaction?

A

size, shape, and chem comp of active site is such that reactants bind to R groups in a way that places them: 1) in correct orientation to e/o, and in close proximity to charges/other components that stabilize the transition state and lower activation energy

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6
Q

can enzymes change the free energy of reactants/products?

A

No, don’t make spontaneous reactions non or viceversa

Just make it more likely spontaneous reactions will actually occur

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7
Q

saturated enzyme

A

all available enzyme molecules are already tied up processing substrates. the rate of reaction is limited by the concentration of enzyme.

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8
Q

rate of reaction

A

(amount of product produced per unit time)

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9
Q

Vmax

A

maximum velocity; y value at which graph plateaus

depends on the amount of enzyme used in a reaction. Double the amount of enzyme, double the Vmax.

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10
Q

km

A

The substrate concentration that gives you a rate that is halfway to Vmax. also known as the Michaelis constant.

also inv proportional of an enzyme’s affinity for (tendency to bind to) its substrate.

Km is always the same for a particular enzyme characterizing a given reaction

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11
Q

Kcat/turnover number

A
  • measure of velocity ind of enzyme concentration
  • Vmax/[enzyme]
  • constant for an enzyme under certain conditions
  • units: time^-1
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12
Q

Michaelis-Menten equation

A

V = Vmax [S]/Km + [S]
- used to experimentally det. Vmax and Km of enzyme-catalyzed reaction
- rate of reaction = V

assumptions:
1. steady state: conc of ES complex remains constant (rate of ES formation = rate of ES breakdown)
2. initial velocity is measured (conc of substrate is much higher than conc of product)
3. single substrate
4. reversibility: reverse reaction negligible under typical conditions
5. substrate concentration: [S]»[E] such that [S] is effectively constant when measuring the instantaneous velecoity

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13
Q

Lineweaver-Burk plot

A
  • double reciprocal of Michaelis-Menten eq.
    1/V = (Km/Vmax)(1/[s])+(1/Vmax)

slope: Km/Vmax
y-int: 1/Vmax

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14
Q

Molecules that inc./dec activity of an enzyme

A

activators/inhibitors

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15
Q

Reversible inhibitors are classified into:

A

Competitive inhibitors: “competes” with substrate. binds to an enzyme and blocks binding of substrate (ex. binding to active site)
- decreases reaction rate only when not much substrate,

No competitive inhibitors: blocks enzyme from doing its job
- enzyme molecules with inhibitor is “poisoned” and will never reach normal maximum rate even with a lot of substrate

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16
Q

Cellular respiration key things (2)

A
  1. Redox reactions (OIL RIG)
  2. no energy is created or destroyed (transferred or transformed)
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17
Q

Major steps of cellular respiration

A
  1. glycolysis
  2. pyruvate processing
  3. citric acid cycle
  4. electron transport chain (ETC)
  5. ATP synthase
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18
Q

Glycolysis

A
  • sequence of 10 enzyme catalyzed reactions
  • glucose -> two 3-carbon molecules (pyruvate)
  • produces 2 ATP
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19
Q

pyruvate processing

A
  • occurs in a multiunit enzyme complex (1 enzyme)
  • pyruvate-> acetyl coenzyme A (acetyl-CoA)
  • oxidizes two carbons in glucose to CO2
20
Q

citric acid cycle

A
  • nine enzyme catalyzed reactions
  • acetyl-CoA-> complete oxidation of glucose to CO2
  • produces 2 ATP
21
Q

ETC

A
  • collection of multiple proteins arranged into 4 complexes in the mitochondria (embedded in the inner membrane) (2134 L2R)
  • uses oxygen and yields water as a product
  • releases energy that is used to pump protons into mitochondria tubules and flattened sacs
  • electrons trigger redox reactions
  • complexes connected by e carrier Q
  • complex 4 has subunit that allows O2 to be e acceptor and turn into water (final movement)
22
Q

ATP synthase (complex V)

A
  • converts ADP and inorganic phosphate (Pi) into ATP using energy stored in proton gradient
  • embedded in mitochondrial inner membrane
  • machine consisting of over 25 ind proteins
    1. proteins enter through F0 subunit making base spin like rotor
    2. axle attached to rotor spins in response to
    3. twisting force generated by axle makes F1 subunit change shape to catalyze the addition of a phosphate group to ADP to form ATP
23
Q

oxidative phosphorylation

A
  • combined action of ETC and ATP synthase
  • e-s with high potential energy transferred to electron carriers NADH (complex I) and FADH2 (complex II) which shuttle e-s to the ETC
  • The term is appropriate because 1) oxygen is used as the final electron acceptor in the ETC that generates the proton gradient, and 2) ADP is phosphorylated to yield ATP.
  • how 90% of ATP that results from cellular respiration is produced
24
Q

Fermentation

A
  • reaction pathways that provide carbon based molecule (pyruvate) that accepts electrons from NADH to regenerate NAD+
  • lactic acid fermentation
  • produces 5% the ATP of cellular respiration but is faster
25
Q

anaerobic

A

oxygen free

26
Q

aerobic

A

oxygen

27
Q

activator

A

increase the activity of an enzyme

28
Q

increase the activity of an enzyme

A

molecules that decrease the activity of an enzyme

29
Q

Allosteric regulation

A

any form of regulation where the regulatory molecule (an activator or inhibitor) binds to an enzyme someplace other than the active site. The place where the regulator binds is called the allosteric site.

30
Q

allosteric inhibition

A

Allosteric inhibitor binds to other site and changes shape of active site so enzyme can no longer bind to its substrate
- nearly all cases of noncompetitive inhibition (+ some cases of competitive inhibition) are forms of this

31
Q

allosteric activation

A

shape of active site is changed so that the substrate to bind at a higher affinity

32
Q

allosteric enzymes

A
  • typically have multiple active sites located on different protein subunits
  • When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed slightly so that they work less well.
33
Q

cooperativity

A
  • substrate itself can serve as allosteric activator
  • when it binds to one active site, the activity of all other active sites go up (considered allosteric bc substrate affects active sites far from its binding site)
34
Q

cofactors

A

non protein helper molecules for enzymes
may be attached through ionic/hydrogen/covalent bonds
- iron Fe2+ magnesium Mg2+

35
Q

coenzymes

A

subset of cofactors that are carbon based molecules (organic)
- dietary vitamins

36
Q

compartmentalization

A

enzymes needed for specific processes can be kept in places where they act (makes sure they can find substrates, don’t damage cell, and have right microenvironment to work well

37
Q

feedback inhibition

A

end product of a metabolic pathway acts on enzyme regulating entry to that pathway (helps cell not overmake product)

38
Q

first committed step

A

first step that’s irreversible

39
Q

Photosynthesis

A
  • processes that transform light energy into chemical energy.
  • source of the sugars that most organisms use to fuel cellular respiration and make ATP

CO2 + H2O + light energy → carbohydrate + O2
- H20 is oxidized
- CO2 is reduced

40
Q

photosynthesis 3 major stages

A

stage 1: energy in wavelengths of light is absorbed by pigments. e-s get excited. PQ is reduced and carries high E e- out of PSII and passes it to a ETC. ETC pumps protons across a membrane and drives production of ATP by ATP synthase

stage 2: in pigment molecules associated with PSI: excited e-s passed through carriers until reach enzyme that uses E to catalyze reduction of NADP+ -> NADPH (e- carrier)

stage 3: ATP and NADPH are used in Calvin cycle (results in reduction of CO2 to produce sugars.

41
Q

photon of appropriate wavelength strikes chlorophyll molecule (one of 3 things happen)

A
  1. e- drops back down to lower E state and releases excess E as heat/light
  2. E passes to a nearby pigment, exciting one of its e-s
  3. the e- is transferred to a different, non pigment molecule, reducing it
42
Q

chloroplasts

A

two outer membranes as well as inner membranes that form many flattened sacs arranged in stacks
- PSI, PSII, the ETC, and ATP synthase are all located in the membranes of these flattened sacs, and are oriented in a way that results in high proton concentrations inside the sacs.

43
Q

NADPH

A

molecule that is essential for reducing the carbon atoms in CO2 and producing sugars.

44
Q

Calvin cycle

A
  • reactions that use ATP and NADPH to reduce CO2 and produce sugars and do not require additional light energy
  • 13 reactions
  • CO2 added to 5 C sugar-> 6 C sugar -> 3 C sugars -> phosphorylation by ATP, reduced by e-s from NADPH-> some G3P leaves and is used to generate glucose -> ATP regenerates 5 carbon sugar
45
Q

Rubisco

A
  • enzyme that attaches a CO2 molecule to the 5-carbon sugar
  • produces two identical molecules of the 3-carbon sugar
  • bonds in co2 change after being added
  • most abundant enzyme on earth + most important
    characteristics:
    1. slow: has a quaternary structure made up of 16 protein subunits and has a total of eight active sites. Despite this, it only catalyzes a total of about three reactions per second
    2. When CO2 levels in the chloroplast are low, O2, instead of CO2 can bind to the active sites and be added to the 5-carbon sugar that acts as a substrate. However, when this occurs, co2 is released and chem energy is lost
    just has a lot of numbers to make up for this
46
Q

stoma/stomata

A

openings in stem and leave epidermis that aren’t covered in wax where co2 can diffuse in and o2 + h2o can diffuse out
- size regulated by guard cells

47
Q

The carbohydrates produced from photosynthesis have two roles in plants, algae, and photosynthetic bacteria.

A
  1. provide carbon-containing compounds that can be modified to build cellulose, nucleic acids, proteins, lipids, and many other molecules (produce mass of individual)
  2. To provide the glucose required to fuel cellular respiration and produce the ATP needed to keep plant cells alive and thriving.

bio 215 (3 decks)

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