Unit 4 notes from textbook + slides

Question 1

what are the two ways organisms can harvest energy from their environment?

Answer 1

from the sun (phototrophs ie.plants)
from chemical compounds (chemotrophs ie. animals)

Question 2

how else can organisms be classified?

Answer 2

can also be classified by where they get their carbon from
some convert CO2 into glucose (autotrophs ie.plants)
some obtain their carbon from organic molecules, eat other organisms (heterotrophs ie. animals)

Question 3

classification of plants

Answer 3

photoautotrophs

Question 3

what does metabolism mean?

Answer 3

the set of chemical reactions that convert molecules into other molecules and transfer energy in living organisms

Question 3

classification of animals

Answer 3

chemoheterotrophs

Question 4

chemical energy definition

Answer 4

form of potential energy held in the chemical bonds between pairs of atoms in a molecule
strong bonds do not contain much chemical energy (ie. do not require a lot of energy to remain intact)
weak covalent bonds require lots of chemical energy to stay intact which is why carbohydrates, lipids and proteins are rich sources of chemical energy

Question 4

two branches of metabolism

Answer 4

catabolism: the set of chemical reactions that break down molecules into smaller units and in the process produces ATP
anabolism: the set of chemical reactions that build or synthesize molecules from smaller units and require an input of energy (ATP)

Question 5

the more stable configuration is always the one with….

Answer 5

lower potential energy

Question 6

structure of ATP

Answer 6

molecules of adenosine(adenine + 5 carbon sugar ribose) covalently linked to three phosphate groups with high potential energy

Question 7

what is chemical equilibrium?

Answer 7

the rate of the forward reaction equals the rate of the reverse reaction and the concentrations of the reactants and products do not change

Question 8

what is delta G?

Answer 8

the amount of energy available to do work
free energy of the products-free energy of the reactants
positive delta G-requires an input of energy

Question 9

endergonic reaction definition

Answer 9

require an input of energy, positive delta G, not spontaneous

Question 10

exergonic reaction definition

Answer 10

releases energy, neagtive delta G, spontaneous
ex. ATP hydrolysis

Question 11

what is ATP broken down into?

Answer 11

ADP and Pi (inorganic phosphate)

Question 12

what is the free energy difference influenced by?

Answer 12

concentration of reactants and products
the pH of the solution in which the reaction occurs
temperature
pressure

Question 13

energetic coupling definition

Answer 13

process in which a spontaneous reaction (-deltaG) drives a nonspontaneous reaction (+deltaG)

Question 14

cellular respiration process definition

Answer 14

a series of catabolic reactions that convert energy from food (ie. glucose) to ATP

Question 15

how many molecules of ATP are produced from cellular respiration?

Answer 15

32

Question 16

what are the two ways ATP is produced in cellular respiration?

Answer 16

1) substrate level phosphorylation: an organic molecule transfers a phosphate group directly to ADP to make ATP. produces a small amount of ATP.
2) oxidative phosphorylation: the chemical energy of organic molecules is transferred first to electron carriers. electron carriers transport electrons released during the catabolism of organic moloecules to the respiratory electron transport chain. They transfer electrons along a series of membrane associated proteins to a final electron acceptor (Oxygen) and in the process harness the energy released to produce ATP.

Question 17

what are the four stages of cellular respiration?

Answer 17

stage 1: glucose is partially broken down to produce pyruvate and energy is transferred to ATP and reduced electron carriers, glycolysis
stage 2: pyruvate is oxidized to another molecule called acetyl-coenzyme A (acetyl-CoA), producing reduced electron carriers and releasing carbon dioxide
stage 3: citric acid cycle, in this series of chemical reactions the acetyl group is completely oxidized to carbon dioxide and energy is transferred to ATP and reduced electron carriers
stage 4: oxidative phosphorylation, reduced electron carriers generated in stages 1, 2, 3 donate electrons to the respiratory electron transport chain and a large amount of ATP is produced

Question 17

purpose and products of glycolysis

Answer 17

glycolysis results in the oxidation of glucose and the synthesis of a relatively small amount of both ATP and reduced electron carriers
“splitting of glucose”
glycolysis begins with a molecule of glucose and produces pyruvate, 2 ATP, and 2 NADH

Question 17

where do the steps of cellular respiration take place in eukaryotes and bacteria?

Answer 17

in euk: glycolysis takes place in the cytoplasm, while pyruvate oxidation, the citric acid cycle and oxidative phosphorylation take place in the mitochondria
in bacteria: glycolysis+pyruvate processing+citric acid cycle take place in cytoplasm, oxidative phosphorylation takes place in the cell membrane

Question 18

three phases of glycolysis

Answer 18

1st phase: prepares glucose for the next two phases by the addition of two phosphate groups to glucose. destabilizes the molecule so it can be broken down in phase 2
Requires 2 molecules of ATP
2nd phase: cleavage phase, for each molecule of glucose entering glycolysis, two 3-carbon molecules enter phase 3
3rd phase: payoff phase, 4 ATP and two electron carrier NADH are produced. Net ATP production= 2
two molecules of pyruvate are produced

Question 19

difference between what happens to pyruvate when oxygen is present and when it isn’t

Answer 19

when oxygen is present, pyruvate is converted to Acetyl-CoA, which then enters the citric acid cycle
when oxygen is not present, pyruvate is metabolized along a number of pathways (ex. fermentation)

Question 20

fermentation definition

Answer 20

when oxygen is not present fermentation is a process for extracting energy from fuel molecules that does not reply on oxygen or the electron transport chain but instead uses an organic molecule as en electron acceptor NADH is converted to NAD+ when pyruvate is reduced when there is no terminal electron acceptor ie oxygen

Question 21

two major fermentation pathways

Answer 21

lactic acid fermentation: electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+ ethanol fermentation: occurs in plants and fungi, pyruvate releases CO2 to form acetaldehyde and electrons from NADH are transferred to acetaldehyde to produce ethanol and NAD+ fermentation only produces 2 molecules of ATP

Question 22

pyruvate oxidation purpose and products

Answer 22

in the presence of oxygen, pyruvate can be further oxidized to release more energy, first to Acetyl-CoA and then even further in the series of reactions in the citric cycle the synthesis of acetyl-CoA from pyruvate results in 1 molecule of CO2, 1 molecule of NADH. However, a single molecule of glucose in glycolysis produces 2 pyruvate so... 2 CO2, 2 NADH and 2 acteyl-CoA are produced

Question 23

mitochondria distinction of different spaces/membranes

Answer 23

rod shaped organelle surrounded by a double membrane intermembrane space: the space between the inner and outer membrane mitochondrial matrix: space enclosed by the inner membrane

Question 24

details of pyruvate oxidation

Answer 24

pyruvate is transported into the mitochondrial matrix, where it is converted into acteyl-CoA First, part of the pyruvate molecule is oxidized and splits off to form CO2 the electrons lost in the process are donated to NAD+, which is reduced to NADH the remaining part of the pyruvate molecule, COCH3, still contains potential energy that is then transferred to coenzyme A (CoA) this process forms the first substrate in the citric acid cycle, acteyl-CoA

Question 25

where does the citric acid cycle take place?

Answer 25

in the mitochondrial matrix

Question 26

result of the citric acid cycle

Answer 26

results in the complete oxidation of the acetyl group of acetyl Co-A, releases CO2 (source of CO2 that we exhale when we breathe) produces 2 Acetyl-CoA molecules produced from a single molecule of glucose yield---2 ATP, 6 NADH, 2 FADH2

Question 27

permeability of the inner mitochondrial membrane

Answer 27

selectively permeable protons cannot passively diffuse across this membrane, use transporter/channel proteins

Question 28

what results from the pumping of H+?

Answer 28

the result of pumping H+ into the intermembrane space is a proton gradient two components of the proton gradient: a chemical gradient that results from the difference in concentration of protons and an electrical gradient that results from the difference in charge between the two sides of the membrane

Question 29

oxidative phsophorylation result

Answer 29

the electron carriers NADH and FADH2 lead to the generation of a proton electrochemical gradient. this gradient is a source of potential energy used to synthesize ATP

Question 30

chloroplasts structure

Answer 30

chloroplasts are bounded by two membranes in the center of the chloroplast is a third, highly folded membrane that encloses a fluid filled space called the lumen. the photosynthetic electron transport chain is located in this membrane the entire structure is called the thylakoid. the thylakoid is folded into grana, which resemble stacks of pancakes the region between the inner membrane and the thylakoid membrane is called the stroma

Question 31

Photosystem 1 and 2

Answer 31

Electrons flow from 2 to 1 along the photosynthetic electron transport chain. The energy captured by 2 allows electrons to be pulled from water; the energy captured by 1 allows electrons to be transferred to NADP+ to form NADPH

Question 32

Z scheme

Answer 32

there is a large increase in energy as the electrons pass through each of the two photosystems. Overall decrease in energy occurs as electrons move between the two photosystems. This decrease in energy explains why electrons move in one "direction" through the photosynthetic electron transport chain. Running these reactions in the opposite direction would require an input of energy

Question 33

photosynthetic electron transport chain products and purpose

Answer 33

produces NADPH and ATP, electrons flow from H2O to NADPH, electron flow is coupled to the pumping of protons, creating an electrochemical gradient used to synthesize ATP by ATP synthase water donates electrons to one end of the photosynthetic electron transport chain, whereas NADP+ accepts electrons at the other end

Question 34

what is responsible for the buildup of protons in the thylakoid lumen?

Answer 34

the oxidation of water releases protons and O2 in the lumen

Question 35

bio element definition

Answer 35

elements found in cells and that are required for cellular function

Question 36

what is the carbon source for humans typically?

Answer 36

glucose

Question 37

electron sources: organic or inorganic compounds

Answer 37

organic= "Organo" ex. glucose or glycerol Inorganic= "Litho" ex. water, nitrite, ammonia

Question 38

if a molecule has the most oxygens bonded to a single carbon atom it is said to be the most...

Answer 38

oxidized

Question 39

if a molecule has the most hydrogens bonded to a single carbon atom it is said to be the most...

Answer 39

reduced

Question 40

in the cell, reduced carbon such as glucose is oxidized to CO2 to form products that are....

Answer 40

more strongly bonded have less potential energy more oxidized forms to carbon

Question 41

purpose of cellular respiration

Answer 41

capture energy released, harnessed in the form of ATP

Question 42

which steps of cellular respiration produce CO2?

Answer 42

pyruvate processing and oxidative phosphorylation

Question 43

how is ATP synthesized in glycolysis?

Answer 43

via substrate level phosphorylation

Question 44

cellular respiration overview

Answer 44

oxidation of glucose to CO2 the energy in the carbon bonds in glucose are broken down in steps the energy is captured (harnessed) in the form of ATP and other high energy intermediates (NADH, FADH2)

Question 45

what does CO2 production indicate in cellular respiration?

Answer 45

carbon atoms from glucose have been completely oxidized

Question 46

substrate level phosphorylation vs oxidative phosphorylation

Answer 46

substrate level: substrate with phosphate then an enzyme removes phosphate from substrate to phosphorylate ADP then ATP is synthesized Oxidative: involves membrane-bound enzymes and H+ gradient that drives ATP phosphorylation

Question 47

what comes in and out in stage 1 og glycolysis?

Answer 47

IN: 2ATP glucose 2NAD+ OUT: 2ADP 2 pyruvate 2NADH

Question 48

in the absence of a terminal electron acceptor/cellular respiration a cell can still make ATP by substrate level phosphorylation in glycolysis if it...

Answer 48

oxidizes NADH to NAD+ to regenerate NAD+ for glycolysis

Question 49

how is pyruvate converted to acteyl-CoA?

Answer 49

giving up 2electrons to NAD+ becomes NADH oxidizing one carbon as CO2 (released as waste) the acetly group left has lots of potential energy it is transferred to coenzyme A to become Acetyl CoA

Question 50

citric acid inputs and outputs

Answer 50

IN: Acetyl CoA NAD+ FAD ADP OUT: CO2 NADH FADH2 ATP CoA

Question 51

why is the citric acid cycle called that?

Answer 51

it produces citrate

Question 52

photosynthesis definition

Answer 52

conversion of light energy to chemical energy (stored in the bonds of carbohydrates)

Question 53

photosythesis light dependant and independant reactions

Answer 53

phosphorylation- an electron transport chain light dependant reaction: water is oxidized to produce O2 NADP is reduced to form NADPH ATP is synthesized vis proton gradient driven by chemiosmosis input photons and water output ATP, NADPH, O2 light independant reaction: then the calvin cycle uses these ATP and NADPH CO2 is reduced to form carbohydrates (Carbon fixation)

Question 54

light dependant reactions- "Photophos" in more depth

Answer 54

1) electrons are supplied by H2O 2) light energy is required for photosystem 2 to "strip" the electrons from the water 3) electrons move along the electron transport chain to provide energy to pump protons into the lumen 4) an electrochemical gradient is created in the thylakoid lumen 5) more light energy input at photosystem 1. This energizes the electrons to drive the reduction of NADP+ 6) NADPH is synthesized in the stroma and will be used in the calvin cycle 7) ATP is synthesized in the stroma via chemiosmosis. H+ moves through the ATP synthase

Question 55

what is oxygens role in cellular respiration?

Answer 55

oxygen accepts the electrons at the end of the chain-called terminal electron acceptor and is reduced to water

Question 56

which direction are protons pumped?

Answer 56

matrix to intermembrane space

Question 57

where does the energy to transport protons come from?

Answer 57

electron transport chain the energy from the transfer of electrons is released in a series of redox reactions. the energy is used to pump protons.

Question 58

the stroma in the chloroplast is analagous to_______in the mitochondria

Answer 58

Matrix similar to cytoplasm

Question 59

the thylakoid lumen in the chloroplast is analogous to______in the mitochondria

Answer 59

intermembrane space

Question 60

ATP synthesis occurs in the chloroplast in the stroma and in the mitochondria it occurs in______

Answer 60

Matrix

Question 61

In the light-dependant reactions of photosynthesis, light energy is used to oxidize _______to__________

Answer 61

H2O to O2

Question 62

The electrons derived from H2O are used to reduce _______ to ________ in the light-dependant reactions

Answer 62

NADP+ to NADPH

Question 63

oxygenic photophosphorylation

Answer 63

electrons from water reduce the photosystem 2 and realease O2 oxygenic meaning oxygen is a product of the reactions and released

Question 64

why does phosphorylation not have a terminal electron acceptor?

Answer 64

the electrons end up on a molecule that is already present in the chloroplast i.e. NADP+ since it is already present in the cell it is NOT by definition a TERMINAL electron acceptor but a FINAL electron acceptor

Question 64

endosymbiont theory

Answer 64

evidence that mitochondria and chloroplast evolved from ancient prokaryote like bacterial cells they have: -double membranes -both have circular DNA -both grow and multiply by binary fission -both have their own ribosomes, synthesize proteins

Question 65

location of calvin cycle in chloroplasts

Answer 65

stroma

Question 66

carbon being fixed definition

Answer 66

converted from inorganic (ie. CO2) to organic form (has C-H bonds)(carboxylation reaction)

Question 67

where does the ATP and NADPH for the calvin cycle in chloroplasts come from?

Answer 67

phosphorylation in the chloroplast thylakoids

Question 68

the calvin cycle oxidizes the light-dependant reaction product_______to _________; and the electrons derived from this redox reaction are used to reduce ________to ________ in a light independant manner

Answer 68

NADPH to NADP+; CO2 to G3P

Question 69

3 main phases of the clavin cycle

Answer 69

1. carbon fixation: each CO2 (3CO2's) reacts with RuBP producing two 3-phosphoglycerate molecules. The enzyme that catalyzes this reaction is called Rubisco. the attachment of CO2 to an organic compound is called carbon fixation 2. reduction: the two 3-phosphoglycerate molecules are phosphorylated by ATP and reduced by NADPH to produce G3P 3. regeneration: the remaing G3P is used in ATP dependant reactions that regenerate RuBP

Question 70

how is the G3P related to cellular respiration?

Answer 70

after glucose splitting in glyoclysis the substrate produced is G3P, the G3P from the calvin cycle can enter glycolysis

Question 71

fate of G3P in the chloroplast

Answer 71

these reduced forms of carbon can now be used in cellular respiration or be used to build other macromolecules

Question 72

inputs and outputs of the calvin cycle

Answer 72

3CO2 in one G3P out 6ATP and 6NADPH in 6ADP and 6NADP out rubisco is regenerated so it is not counted as an input/output