UNIT 3

Question 1

endergonic reaction

Answer 1

results in increase in free energy (nonspontaneous)

Question 2

exergonic reaction

Answer 2

results in a decrease in free energy. (spontaneous)

Question 3

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

Answer 3

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

Question 4

enzyme

Answer 4

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

Question 5

why does each enzyme only catalyze one reaction?

Answer 5

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

Question 6

can enzymes change the free energy of reactants/products?

Answer 6

No, don’t make spontaneous reactions non or viceversa

Just make it more likely spontaneous reactions will actually occur

Question 7

saturated enzyme

Answer 7

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

Question 8

rate of reaction

Answer 8

(amount of product produced per unit time)

Question 9

Vmax

Answer 9

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.

Question 10

km

Answer 10

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

Question 11

Kcat/turnover number

Answer 11

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

Question 12

Michaelis-Menten equation

Answer 12

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

Question 13

Lineweaver-Burk plot

Answer 13

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

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

Question 14

Molecules that inc./dec activity of an enzyme

Answer 14

activators/inhibitors

Question 15

Reversible inhibitors are classified into:

Answer 15

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

Question 16

Cellular respiration key things (2)

Answer 16

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

Question 17

Major steps of cellular respiration

Answer 17

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

Question 18

Glycolysis

Answer 18

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

Question 19

pyruvate processing

Answer 19

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

Question 20

citric acid cycle

Answer 20

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

Question 21

ETC

Answer 21

• 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)

Question 22

ATP synthase (complex V)

Answer 22

• 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

Question 23

oxidative phosphorylation

Answer 23

• 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

Question 24

Fermentation

Answer 24

• 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

Question 25

anaerobic

Answer 25

oxygen free

Question 26

aerobic

Answer 26

oxygen

Question 27

activator

Answer 27

increase the activity of an enzyme

Question 28

increase the activity of an enzyme

Answer 28

molecules that decrease the activity of an enzyme

Question 29

Allosteric regulation

Answer 29

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.

Question 30

allosteric inhibition

Answer 30

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

Question 31

allosteric activation

Answer 31

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

Question 32

allosteric enzymes

Answer 32

- 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.

Question 33

cooperativity

Answer 33

- 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)

Question 34

cofactors

Answer 34

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

Question 35

coenzymes

Answer 35

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

Question 36

compartmentalization

Answer 36

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

Question 37

feedback inhibition

Answer 37

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

Question 38

first committed step

Answer 38

first step that’s irreversible

Question 39

Photosynthesis

Answer 39

- 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

Question 40

photosynthesis 3 major stages

Answer 40

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.

Question 41

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

Answer 41

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

Question 42

chloroplasts

Answer 42

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.

Question 43

NADPH

Answer 43

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

Question 44

Calvin cycle

Answer 44

- 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

Question 45

Rubisco

Answer 45

- 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

Question 46

stoma/stomata

Answer 46

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

Question 47

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

Answer 47

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.