CR & PH

Question 1

Catabolism vs anabolism

Answer 1

in catabolic reactions, E gets released and the reaction is spontaneous (breakdown reaction)
in anabolic, E has to be invested and the reaction is non-spontaneous (forming bonds)

Question 2

What is ATP
glucose oxidation efficiency

Answer 2

the universal energy-transfer molecule containing E that gets released from chemical bonds when glucose gets oxidized in CR (only 40% converted to ATP, the rest lost as heat) – it can’t pass through the membrane so it must be synthesized inside each cell

Question 3

Reduction and oxidation
compare in terms of O2, e-, H+, bonds, E of the yield

Answer 3

coupled processes (one causes the other), e- get relocated from the less to the more electronegative atom and this transfer releases E, the atom that loses e- is oxidized and the one that gains it is reduced
loss/gain, gain/loss, gain/loss, C-H/C-O, higher/lower

Question 4

How does breaking of covalent bonds release E

Answer 4

they store potential energy because they are made out of electrons which, when transported, release E – in the presence of a strong oxidizing agent (which’ll get reduced), destabilized bonds will easily break

Question 5

What is the main oxidizing agent in CR and what is the other name for an oxidizing agent?

Answer 5

NAD+, electron/hydrogen carrier (O2 only used during the final step), it’s reduced form is NADH+H+

Question 6

Why does CR have many steps?

Answer 6

because glucose has to be oxidized gradually in order to get the most energy from it by maximizing the number of NADH+H+ molecules generated (they will release E to form ATP in the final CR step)

Question 7

Mitochondrion, list components

Answer 7

the location of aerobic respiration, where pyruvate undergoes full oxidation to yield CO2, H2O, and ATP – mitochondrial matrix, inner membrane, outer membrane, cristae, narrow intermembrane space, mDNA

Question 8

How is mitochondrion structure adapted to its function?

Answer 8

cristae create large SA that is needed for the electron transport chain, narrow intermembrane space allows fast accumulation of protons, the fluid matrix contains enzymes that are involved in the Krebs cycle

Question 9

Respirometer

Answer 9

device used to measure the rate of cell respiration of a living organism

Question 10

What happens in anaerobic CR after glycolysis?

Answer 10

happens in the cytoplasm, in humans: lactate (lactic acid) is produced from pyruvate, in yeast: ethanol and CO2 are produced (so no ATP production!!)

Question 11

Four stages of aerobic cell respiration

Answer 11

glycolysis, link reaction, Krebs cycle, and electron transport chain and oxidative phosphorylation

Question 12

Glycolysis
substeps
draw the process

Answer 12

anaerobic, in the cell cytoplasm, it’s a partial breakdown of glucose into pyruvate
phosphorylation (hexose into hexose biphosphate), lysis (hexose biphosphate into two triose phosphates (TP)), and main oxidative stage (each TP into pyruvate, 2 ATP and 2 NADH+H+ formed)
…

Question 13

Phosphorylation
substrate level phosphorylation

Answer 13

the phosphate groups added make the molecule less stable and more likely to react and they allow for a stronger interaction between the hexose and the enzyme that catalyzes lysis
when ATP is made by direct transfer of phosphate groups from the substrate to ADP (in the main oxidative state)

Question 14

Link reaction
what is decarboxylation

Answer 14

in the mitochondrial matrix, 2 pyruvates get decarboxylated into 2 acetyl groups (2 CO2 and 2 NADH+H+ produced) and the CoA (coenzyme A) temporarily joins with the acetyl groups to form acetyl-CoA
when the carboxyl group (COO-) gets removed in the form of CO2

Question 15

Krebs cycle

Answer 15

aerobic (O2 not directly used), in the mitochondrial matrix – acetyl groups get further decarboxylated to yield 2 CO2 and oxidated to yield 6 NADH+H+ and 2 FADH2 (acetyl-CoA joins with C4 acceptor group and forms citric acid (C6), CoA gets released, C6 undergoes oxidative decarboxylation to form C5 (NADH+H+ and CO2), C5 undergoes oxidative decarboxylation to form C4 (NADH+H+ and CO2), C4 gets regenerated into C4 acceptor group and produces 4 NADH+H+, 2 FADH2 and 2 ATP)

Question 16

Draw the ATP, NADH+H+ and FADH2 yield for each step of the CR (table)

Answer 16

glycolysis: 2, 2, 0
link reaction: 0, 2, 0
Krebs cycle: 2, 6, 2
total ATP: 4, 103=30, 22=4

Question 17

Electron transport chain and oxidative phosphorylation

Answer 17

aerobic, along the inner mitochondrial membrane, the main ATP producing pathway of CR – turns each NADH+H+ molecule into 3 ATPs and each FADH2 into 2 ATPs

Question 18

Describe the etc and op process

Answer 18

an electron transporter oxidates NADH+H+/FADH2, and the 2 e- taken from it get passed on from weaker to stronger e- carrier along the electron transport chain in a series of redox processes until the final and the strongest oxidizing agent, O2 which combines with the 2 e- and H+ released in oxidation of NADH+H+/FADH2 and forms water as a CR byproduct
other H+ released in NADH+H+/FADH2 oxidation are released in the matrix and eventually diffuse into the intermembrane space, once the C are equalized, E released from the e- transport chain is used to further pump H+ and build a C gradient (potential E) and when ATP synthase on the inner membrane opens, protons diffuse through it and release E which is used for reduction of ADP into ATP

Question 19

Chemiosmosis
oxidative phosphorylation

Answer 19

E released by the passage of H+ down the concentration gradient is used to drive ATP synthesis (mechanism that couples release of E by oxidation to ATP production)
ADP gets phosphorylated using E released in oxidation

Question 20

Which organisms perform photosynthesis?

Answer 20

photoautotrophic organisms, e.g. cyanobacteria, algae, plants

Question 21

Chloroplast structure

Answer 21

double membrane, stroma (thick fluid containing starch grains, lipid droplets, 70S ribosomes, cDNA), and thylakoids (made out of thylakoid membranes and arranged in grana) which contain chlorophyll and other pigments

Question 22

Wavelengths of visible (white) light

Answer 22

from 400 to 700 nm

Question 23

Pigments
the most important example

Answer 23

substances that absorb visible light
chlorophyll (a and b), its structure allows it to absorb other colors better than green so it reflects (appears) green, there are also red, brown, and yellow pigments

Question 24

Absorption spectrum and action spectrum

Answer 24

a diagram that shows the absorption of different wavelengths by a certain pigment
a diagram that shows the rate of photosynthesis at different wavelengths (effectiveness of each wavelength)

Question 25

NADPH
photosystems

Answer 25

a molecule that temporarily stores energized electrons and protons (H+), produced during the LDS and is a substrate for LIDS
a light-harvesting unit located in the thylakoid membrane (PS I and PS II absorb light best at slightly different wavelengths) consisting of antenna pigment molecules, reaction center, and primary e- acceptor

Question 26

Light-dependent stage function and process

Answer 26

using solar power to generate ATP and NADPH to provide chemical E and reduce power in the light-independent stage (Calvin cycle)
photon energizes one pigment molecule in PSII, its lost e- goes from one antenna pigment molecule to another until it reaches the reaction center and the primary e- acceptor from where it is transferred along the e- transport chain until it reaches PSI where it goes through the same process, at the end of the second electron transport chain it reduces NADP+ into NADPH (H+ from water – photon used for photolysis, O2 byproduct)
H+ from water diffuse from stroma into thylakoid space, E released in e- transport chains is used to further pump protons into the thylakoid space after C have been equalized to create a C gradient, ATPase in the thylakoid membrane opens, protons diffuse through it, and E is released which is used to reduce ADP into ATP, the e- gets back to PSII to stabilize the energized pigment molecule

Question 27

Photophosphorylation

Answer 27

the production of ATP using E from an excited e- from a photosystem

Question 28

Light-independent stage function and process

Answer 28

forms carbohydrates by taking H from NADPH, E from ATP, and C from CO2, in the stroma – CO2 combines with ribulose bisphosphate (RuBP – 5C sugar) to create glycerate-3-P (G3P) through carbon fixation, G3P then gets reduced to triose phosphate (TP) and NADPH+H+ and ATP are oxidized to provide E, H+, and high energy e- (TP is a substrate for a variety of organic molecules), only one out of 6 produced TP is turned into glucose-phosphate (GP), the other five are used to regenerate RuBP to allow more CO2 to be fixed – RuBP is both produced and consumed in LIDS

Question 29

Factors affecting the rate of photosynthesis

Answer 29

light intensity (proportional, saturation point), CO2 levels (proportional, saturation point), temperature (optimal temperature for enzymes involved in photosynthesis)

Question 30

Limiting factor

Answer 30

the factor that determines the rate as the one that is the furthest from its optimum (growth is controlled by the scarcest resource)