Biology Exam 2

Front 1

All Cells Have to Be:

Back 1

1. Shaped Properly
2. Physically Robust (to resist mechanical pressure that would push or pull on a cell)
3. Properly Structured (internally)

Front 2

Once a cell is formed, does it stay the same for it's entire life?

Back 2

the cell has to be able to reorganize its internal structures on command when it needs to divide, or move or adapt to a changing environment. Proteins of cytoskeleton are both strong and easy to assemble and disassemble.

Front 3

Three major classes of cytoskeletal proteins are:

Back 3

1. Microfilament
2. Intermediate filaments
3. Microtubules

Front 4

What protein are Microfilaments made of and what does it do?

Back 4

(made of the protein actin) – determines cell shape, responsible for pinching the cell in two during cytokinesis, responsible for much of the cell movement

Front 5

What class of protein are Intermediate filameents made of and what does it do?

Back 5

(bread class of proteins) – with many functions like adhering cells together, forming continuous channels between two cells that span both membranes.

Front 6

What protein are Microtubules made of and what does it do?

Back 6

(made of the protein tubulin) serve transport roles because they are like railroad tracks along which motor proteins move vesicles & organelles. Microtubules form the mitotic spindle involved in precise chromosome segregation during cell division.

Front 7

How can a cell increase their ability of absorption, enzymatic activity, etc?

Back 7

by an increase in surface area.

Front 8

Why are Proteins are recycled and made fresh in the cell

Back 8

To ensure quality control

Front 9

This type of cytoskeletal protein makes up tight junctions which ensure that no molecules or fluids seep between cells.

Back 9

Intermediate filaments

Front 10

(spot welds) allow 2 cells from being pulled apart

Back 10

Desmesones

Front 11

allows for continuity between adjacent cells. Small and larger molecules move rapidly through these protein pores (animal cells)

Back 11

Gap Junctions

Front 12

What are Gap Junctions called in plant cells and what do they assist with

Back 12

Plasma Desmata. Cell walls don’t exist here and proteins make pores so molecules move rapidly from one cell to the other.

Front 13

How do microtubles organize movement?

Back 13

by connecting organelles with tracks, motor proteins then change conformation by binding, hydrolyzing and releasing ATP and ADP & Pi, move organelles or vesicles along these tracks from one site to a destination.

Front 14

Nucleus is surrounded by a double phospholipid bilayer that is known as what?

Back 14

The nuclear envelope

Front 15

How do molecules travel through the nuclear membrane, what is it's permiability.

Back 15

the typical nucleus has 3000-4000 pores in it and these pores allow movement of molecules less than 50,000 daltons. Molecules larger than that must be selected by the proteins that line the pore. There must be good communication between the nucleus and the cytoplasm because the nucleus houses the DNA and all RNA is made there and RNA holds the instructions for the proteins.

Front 16

How is it that 6 feet of DNA fits into an organelle that is 6 microns in diameter?

Back 16

We condense the DNA by wrapping it around proteins known as histones. This is both an organized and compact way to package the genetic information contained in our case, humans 46 linear chromosomes.

Front 17

What happens to the nucleus during mitosis (nuclear division)? What happens to the chromosomes?

Back 17

It fragments, at mitosis, the chromosomes condense even further and line up on the mitotic spindle for separation into separate daughter cells

Front 18

Underlying the inner bilayer of the nuclear envelope is the ______ ________ which is the protein scaffold that helps the nucleus maintain its shape and helps organize some activities within the nucleus.

Back 18

nuclear lamina

Front 19

What does the nuclear lamina do?

Back 19

It is the protein scaffold that helps the nucleus maintain its shape and helps organize some activities within the nucleus.

Front 20

Is the Nuclear Lumin and the Lumin of the ER connected, can something that is in one travel to the other.

Back 20

No

Front 21

What is the ER continuous with?

Back 21

with the space between the inner and outer layers of the nuclear envelope.

Front 22

Is the nucleus cut off from the cytoplasm?

Back 22

No, because because proteins and nucleic acids (RNA) and small molecules can pass from the cytoplasm through the pores into the nucleus and vice versa.

Front 23

How do proteins of the cell reach their target destination?

Back 23

The localization sequences are built into the primary structure of the polypeptide. They are like zip codes.

Front 24

Is the lumen of the Rough and Smooth ER connected?

Back 24

Yes

Front 25

What are the two types of ER? How are they different

Back 25

Two types of Endoplasmic Reticulum, rough endoplasmic reticular and smooth endoplasmic reticulum. Their internal spaces (lumen) are connected. Even though they are connected there are different enzymes and structures embedded in the two different types of ER. Ribosomes are not in the smooth ER. Most cells have far more rough ER than smooth ER. Rough ER is rough because it is covered in Ribosomes (sites of protein synthesis). Smooth ER lacks ribosomes and SER is the place of lipid metabolism. Liver, which processes lipid soluble molecules has much SER. It is a place where cholesterol is synthesized and a place where lipid soluble molecules are made more polar to allow for excretion out of the body.

Cells that produce lots of proteins destined for secretion out of the cell have lots of Rough ER compared to cells that do not specialize in protein export.

Hint 25

In addition to high concentrations of enzymes and molecules involved in the particular functions carried out by the particular organelles. The organelles may maintain ionic concentration gradients . The ER stores Calcium so there is low Ca concentration in the cytoplasm, much higher in the ER and outside the cell.

What happens in the golgi apparatus? The glycosylated protein is modified. Sugars are added, others removed, then if destined to be secreted from the cell or function in another organelle (lysosomes, etc.) it gets packaged in a vesicle that buds off from the trans face.

Front 26

What is found floating free in the cytoplasm or transiently attached to the ER membrane or the outer nuclear membrane.

Back 26

Ribosomes

Front 27

Is there a difference between the Ribosomes found floating in the cytoplasm and the ones attached to the ER

Back 27

No

Front 28

Ribosomes free in the cytoplasm sinthesize proteins destined to function in:

Back 28

1. Cytoplasm 2. Nucleus 3. Peroxisomes 4. Mitochondria/chloroplasts

Front 29

If synthesis of a protein finishes on a ribosome attached to the RER or outer nuclear envelope, this protein may function in:

Back 29

1. The ER 2. Gogli apparatus 3. Lysosomes 4. “any” membrane including plasma membrane 5. Secreted from the cell

Front 30

Where does all synthesis of proteins begin? (exceptions exist in the mitochondria and chloroplasts that have some DNA themselves.)

Back 30

on a free ribosome in the cytoplasm. Whether this protein gets finished on a free ribosome or is translocated to a membrane, depends on the primary structure of the polypeptide.

Front 31

What do cells that produce lots of proteins destined for secretion out of the cell have lots of?

Back 31

Rough ER

Front 32

How can a cell maintain ionic concentration gradients?

Back 32

The ER stores Calcium so there is low Ca concentration in the cytoplasm, much higher in the ER and outside the cell.

Front 33

Nucleocide>Nucleotide>Amino Acids
DNA>RNA>Proteins

Copy pages of the textbook into RNA is called

Back 33

transcription. Which amino acids are strung together is based on the actual sequence of RNA nucleotides. This is called translation

Front 34

What are the s/e of Atropine?

Back 34

-May worsen ischemia
-may induce VT/VF

Front 35

What is the process whereby the cell digests some of it’s own contents.

Back 35

Autophagy

Front 36

List the endomembrane systems (within)?

Back 36

ER, Golgi, Lysosomes

Not included: Nucleus, Mitochondria, peroxisomes, chloroplasts (Plants)

Front 37

In which direction does vesicle budding in the ER happen?

Back 37

Vesicles budding from the ER will move on to the golgi stacks where further modification of the cargo in these vesicles takes place. Vesicles can bud off from each golgi stack and fuse with a later stack in the cis>medial>trans direction and some sort of maturation of an entire stack may be involved. Some whole compartment may move on and the enzyme to work in earlier compartments and travel in vesicles backwards. Absolutely retrograde movement, from trans stacks to cis or medial or ER, etc.

Once a protein’s modification s completed and the protein is located in the trans stack, where can the protein travel to? It depends on the proteins function. If it works in the ER, vesicle buds off to the ER, if it’ to be secreted, the vesicle fuses with the plasma membrane and you have exocytosis. If the protein functions in the lysosome, it travels to the lysosome.

Front 38

Our recycling macromolecules, delivering the monomers back to the cytoplasm for reuse.

Back 38

What are Lysosomes

Front 39

What do lysosomes contain?

Back 39

Digestive enzymes that break down basically any biological macromolecule.

Front 40

Why is the entire cell not digested by the digestive enzymes inside the lysosome

Back 40

we sequester them inside the membrane bound vesicle and acidify the lysosome to a pH 100 times more acidic than the cytoplasm. Then the hydrolysis are optionally active and acidic pH. (side note: there are lysosome storage disorders, and avatosis – cell kills itself.)

Front 41

What does the Lysosome do for the cell?

Back 41

Lysosomes are involved in breaking down materials that the cell took in by endocytosis once it fuses with the endosome, lysosomes are also involved in helping the cell rid itself of organelles and other cytoplasmic macromolecules it is no longer in need of. It does this by fusing to an autofagosome.

Front 42

What occurs during Autophagy?

Back 42

The autophagosomes fuse with lysosomes and membranes which can also non specifically form around soluble molecules in the cytoplasm returning monomers back to the cell for re-use. (Note: why would you no longer need something in the cell, no longer drinking as much so you no longer need as much SER)

Front 43

What will extensive autophagy lead to?

Back 43

cell death as cell digests itself.

Front 44

Do plants have lysosomes?

Back 44

No, but digestion occurs in vacuoles, even the central vacuole contains digestive enzymes.

Front 45

What is the Mitochondria (in animals) and Chloroplasts (in plants)

Back 45

1. Contain some of their own DNA and ribosomes. 2. Imports some of the proteins from cytoplasm 3. Double membrane 4. Extensive membranes because proteins that carry out the function of organelles are embedded there.

Front 46

This organelle carries out a reaction that makes hydrogen peroxide as intermediate and this is broken down to water and O2. Organelles capable of digesting particular molecules.

Back 46

What is peroxisome?

Front 47

is defined as the capacity to do work which is to move matter against an opposing force like gravity or friction.

Back 47

What is Energy?

Front 48

What is energy in Motion?
What is energy Stored?

Back 48

Kinetic Energy
Potential Energy

Front 49

What type of energy is an Ion concentration gradient

Back 49

Potential Energy

Front 50

the study of energy transformations that occur in a collection of matter.

Back 50

What is Thermodynamics?

Front 51

What are the two laws of Thermodynamics

Back 51

1. Energy in the universe is constant. It can neither be created or destroyed but it can be transferred or transformed.
2. One usable form of energy cannot be completely converted into another usable form of energy. Some energy is lost to the surroundings, usually as heat. Entropy = term used to measure disorder.

Front 52

In the universe, what is a constant

Back 52

Energy is a constant, but the quality is not.

Front 53

Term used to measure disorder

Back 53

Entropy

Front 54

Equation:

Total Energy=Usable Energy+unusable energy (cannot do work) which is:

Back 54

Enthalpy=Free Energy+Entropy which is

Hint 54

H = G + TS

or

G = H + TS keeping them constant

∆G = ∆H -T∆S with change

Front 55

∆G = Free Energy (Final state/Products) – Free Energy (Initial State/Reactants)

What if: ∆G<0 =

Back 55

Spontaneous , which could take place very slow however,

Exergonic = energy releasing

What if: ∆G>0 =

Hint 55

non spontaneous, will take place w/o an input of energy.

Front 56

Can an enzyme alone make a non-spontaneous reaction occur?

Back 56

An enzyme alone cannot make a non-spontaneous reaction occur. Enzymes do “couple” reactions together. An exergonic reaction is coupled to an endergonic reaction.

Front 57

Is ∆G is negative, what kind of reaction do you have?

Back 57

an exergonic reaction

Front 58

Is ∆G is positive, what kind of reaction do you have?

Back 58

an Endergonic reaction.

Front 59

What does every chemical reaction involve?

Back 59

Every chemical reaction involves breaking bonds and making bonds (bond forming). Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state. (transition molecule) before the reaction can proceed.

Front 60

What is the energy required to contort the starting molecule ?

Back 60

Energy of Activation

Front 61

What is the magnitude of energy of activation proportional to?

Back 61

to the difficulty of breaking the bonds in the starting molecule.

Front 62

What would happen if we used heat to surmount the Ea (Energy of Activation) in our bodies?

Back 62

we would nonspecifically accelerate all reactions in our body including denaturing proteins, so we need another tack. (Our molecules do not possess enough kinetic energy on their own to overcome Ea.

Front 63

In our bodies, what do we use to lower the E.a.?

Back 63

Enzymes speed up the rates of reactions by lowering the E.a. The ∆G does not change. The products and reactions are at the same free energy amounts if the enzyme is present or absent.

Front 64

600 polypeptides w/ arginine at their C-terminal position are in a solution. It takes 7 years for half (300) of the arginine’s to be clipped off the carboxyl terminals, what enzyme can speed the process and by what time.

Back 64

carboxypeptidase, a catalyzing reaction, in how much time will 300 arginines release? Half a second!

Front 65

`. Reactions with enzymes can be up to how many times faster?

2. What is the typical amount of molecules that an enzyme can reactive with?

3. How many reactions do fast enzymes catalyze with?

Back 65

1.up to 10 billion times faster
2.between 1 and 10,000 molecules per second.
3. up to 500,000 reactions per second.

Front 66

Enzymes lower the energy input necessary because they:

Back 66

1. Hold the reactants in the proper orientation for them to react
2. The enzyme clasps around the reactant in the “Induced fit” to put stress on the bonds that need to break and like the orientation above, promote bonds that need to form
3. The side chain of the amino acids that line the “pockets or “groves” of the catalytic site (active) can participate in the reaction.

Front 67

What happens to an enzyme at the end of a reaction?

Back 67

Enzymes are unchanged at the end of each reaction. If they donated a proton to help catalyze the reaction, they receive that proton back before the products are released, same goes if they make a covalent bond with the substrate (reactants), they break that covalent bond and remain unchanged.

Front 68

contains precisely positioned atoms that alter the electron distribution in atoms that directly participate in making and breaking of covalent bonds.

Back 68

What is the active site?

Front 69

What are often helpers to enzymes, sitting in the active sites and participating in the reactions.

Back 69

Vitamins

Front 70

The enzymes will change their shape upon binding the substrates, to bring chemical groups of the active site into positions that enhance their ability to catalyze the reaction. What is this called?

Back 70

Induced fit

Front 71

What must a substrate have in order to be compatible with an enzyme?

Back 71

Substrate must have complementary size, shape and charge since enzymes are very specific to their substrate(s). Enzymes discriminate based on the size, charges throughout the atoms that line the active site and the shape of their active site so two very closely related molecules may be discriminated against.

Front 72

What affects an enzyme’s activity?

Back 72

pH and Temp. Changing the pH can drastically alter the conformation of the active site and the protein in general. Ionic bonds can be broken and changes in the charges of the active site will have great consequences on the ability to bind the native substrates.

Front 73

Can altering the temperature of an enzyme affect it? How?

Back 73

Increasing the temperature above a certain value, and your enzyme denatures. (no longer functional)

Front 74

Enzymes have an optimal?

Back 74

pH and Temp.

Front 75

What is an enzyme that works in the stomach, what is it's optimal pH

Back 75

Pepsin. pH of 2

Front 76

What is an enzyme that works in the intestine, what is it's optimal pH

Back 76

Trysin, pH of 8

Front 77

Increasing the substrate concentration will increase the rate of the reaction until what point?

Back 77

until all enzymes are saturated with substrate.

Front 78

Adding more substrate at this maximum value will not increase the rate of the reaction, what can?

Back 78

adding more enzyme.

Front 79

Energy is required (usually, it is the hydrolysis of ATP) that supplied the energy.

Back 79

in Endergonic reactions. Enzymes facilitate the coupling of an exergonic reaction (ATP hydrolysis) to the endergonic reaction. Basically making the entire reaction exergonic. You couple a more energy releasing reaction to a less energy requiring reaction so you can pay for it. The coupling makes overall reaction exergonic.

Front 80

The three main types of energies requiring work the cell perform:

Back 80

1. Building polymers from monomers
2. The action of pumps and motor protons
3. Muscle contractions

Front 81

ATP hydrolysis yields energy:

Back 81

ATP – ADP + Pi is like a $50.00 bill, usually enough to pay for a reaction.
ATP – AMP + P-P is like a $100.00 bill (pyrophosphate, Pi + Pi)

Front 82

Why does the Release of the phosphate group(s) come with a release in energy

Back 82

because the negatively charged phosphate groups do not like to be together. There is a repulsion between similarly charged oxygens.

Hint 82

Hydrolysis of ATP to AMP + P-P Pyrophosphate and the subsequent hydrolysis of the pyrophosphate to two phosphate groups releases about 2 times the amount of free energy as hydrolysis of the terminal phosphate group ATP – ADP + Pi.

Front 83

What do regulatory sites do?

Back 83

They inhibit reactions

Front 84

What type of reaction is The conversion of glutamate into another amino acid glutamine

Back 84

endergonic. (∆G=3.4 Kal/mol) An enzyme couples the hydrolysis of ATP to this conversion. Hydrolysis of ATP (under standard conditions releases 7.3 kcal/mol (∆G = -7.5kmol). Overall, the coupled reaction is exergonic: ∆G = -3.9kcal/mol. In this reaction the enzyme phosphorylates the glutamate (temporarily) making it unstable. This allows the glutamate to throw off the phosphate and pick up the amino group it needs to become glutamine.

Front 85

What are the two types of inhibitors?

Back 85

1. One is competitive, it competes with the natural substrate for a place in the active site
2. The second is non-competitive inhibitor: binds away from the active site but changes its shape which will obviously change its function

Front 86

What dictates what binds to the active sites.

Back 86

The concentration of the substrate versus the competitive inhibitor

Front 87

What is a non-competitive inhibitor?

Back 87

A non-competitive inhibitor both under the category of an allosteric regulator, something that binds the enzyme and changes its shape (therefore its activity). We have both negative regulators (non-competitive inhibitors) and positive regulators that enhance the activity of the enzyme.

Hint 87

Allosteric regulators that are found in our bodies naturally bind reversibly with the enzymes. (they can unbind)

Front 88

What is the (regulation) enzymatic pathway where the product of one enymatic action is the substrate for the next enzyme in the pathway. These pathways are often regulated by the end product.

Back 88

Feedback inhibition

A Enzyme 1 > B Enzyme 2 > C Enzyme 3 > D Enzyme 4 > Product (which then returns to Enzyme 1 (Feedback Inhibition)

Hint 88

If the concentration of the end product builds up, the endpoint negatively regulates (usually) an enzyme at the very beginning of the pathway. This allosteric regulation is reversable, binding such that if the concentration drops , the product unbinds from the enzyme and the enzyme functions again.

Front 89

How can enzymes work more efficiently?

Back 89

Arrangement of enzymes into long multi-enzyme complexes allows the intermediate to be passed in an efficient fashion from one enzyme to the next.

Hint 89

We can also embed enzymes into metabolic pathways in the same membrane to facilitate transfer or attach them to the same protein. (cytoskeleton).

Front 90

Why do cells undergo cellular respiration?

Back 90

To make the currency molecule ATP that will be use to power work in the cell.

Front 91

In cellular respiration, what is the endergonic reaction?

Back 91

The energy is extracted in the form of electrons stripped from molecules we ingest.

Front 92

How is the cell making ATP?

Back 92

Two ways,
1 substrate level phosphorylation.

Substrate & P + ADP = ATP (through glycolysis & citric acid cycle)

2. Oxidative phosphorylation – Electron transport chain
Pi + ADP = ATP

Front 93

How fast does the typical mammalian cell hydrolyze and restore (by phosphorylation of ADP) their entire pool of ATP molecules? how many is that?

Back 93

Every 1 to 2 minutes, thats approx 10,000,000 molecules turned over in that time.

Front 94

What happens to the electrons stripped off of glucose during cellular respiration?

Back 94

Glucose is going to be stripped of its electrons. These electrons will be captured by electron carriers (NADH/FADH2) which shuttles the electrons over to the electron transport chain & drops them off. The passage of electrons along this chain allows a concentration gradient to be set up. This concentration gradient (of H+) will be used to phosphorylate ADP.

Front 95

What does OIL RIG stand for

Back 95

Oxidation is loss of electrons, Reduction is gain of electrons.

Reduction/oxidation reactions go hand in hand. One molecule gives up electrons to the second one that accepts the electrons.

Front 96

Is NAD+ oxidized or reduced?

Is FAD oxidized or reduced?

Back 96

NAD+ is always the oxidized form ready to accept.

NAD+ = 2 electrons/1proton = NADH Reduced form ready to vie off electrons

FAD (oxidized form) = FADH2 (reduced form)

Electrons often travel with proton, so ultimately the reduced molecule may have picked up a hydrogen atom and an electron.

Front 97

During Cellular respiration what is the electron flow?

Back 97

Glucose = NAD, then NADH = electron transport chain = oxygen (final electron accepted, also picked up protons to become H2O)

Front 98

Why do we bother going through all the steps of glycolysis and so on?

Back 98

So we can trap the energy released from the exergonic reactions in activated carrier molecules (like NADH, FADH2, ATP). We break it down in steps that have smaller activation energies that are overcome by enzymes in our cells.

The stepwise nature of the process allows the energy of oxidations to be released in small packets, so that much of it can be stored in activated carrier molecules (NADH, FADH2, ATP), rather than being released as heat.

C6H12O6(C is oxidized) + O2(O is Reduced since in H2O, the electrons are close to the O) = CO2 + H2O

Front 99

In cellular respiration, where do the following reactions take place?

Glycolysis =
Krebs Cycle =
Electron transport chain =

Back 99

Glycolysis = Cytosol
Krebs Cycle = Mitochondrial Matrix
Electron transport chain = embedded in inner convoluted membrane

Front 100

Is the ATP made in glycolysis, Krebs cycle and ETC the same?

Back 100

Same ATP is made in each of the steps (glycolysis, Krebs cycle, and electron transport chain) but very little ATP is made in glycolysis and Krebs cycle. The main point of glycolysis & Krebs cycle is the generation of NADH & FADH2. Most ATP is made during E.T.C. & oxidative phosphorylation.

Front 101

What is the point of the glycolysis and Krebs cycle if most of the ATP is not made there.

Back 101

The main point of glycolysis & Krebs cycle is the generation of NADH & FADH2.

Front 102

In glycolysis, in what steps are ATP made?

Back 102

If you look at the first 5 enzymatic reactions of glycolysis, you’ll notice that 2 ATP have been used (to phosphorylate substrates (intermediate) and no activated carriers have been made yet.

In steps 6-10, 4 ATP overall and 2 NADH are made. ATP are made by substrate level phosphorylation and the NADH can shuttle electrons to the E.T.C. in the mitochondria.

Front 103

If ATP is made in glycolysis and Krebs Cycle, why go on?

Back 103

To continue extracting more energy.

75% of initial energy held in glucose molecule has yet to be extracted. It is now held in the 2 pyruvate molecules and there is also more energy that can be “cashed in” energy available in NADH.

Front 104

What happens if ATP is in high concentrations in the cell?

Back 104

Cells are thrifty, expedient and responsive to their needs. Why bother going through all the steps of glycolysis if ATP is in high concentrations in the cell? We don’t, we inhibit the 3rd reaction of glycolysis. ATP is an allosteric regulator of the enzyme that catalyzes the reaction and inhibits it when bound. That same enzyme can positively regulate by the binding of AMP & ADP.

Front 105

What is an allosteric regulator of the enzyme that catalyzes the reaction of ATP production and in what reaction of glycolysis does this happen

Back 105

ATP, we inhibit the 3rd reaction of glycolysis. ATP is an allosteric regulator of the enzyme that catalyzes the reaction and inhibits it when bound. That same enzyme can positively regulate by the binding of AMP & ADP.

Front 106

What does Glycolysis yield?

Back 106

Glycolysis yields ATP, pyruvate (has the most potential since it has many chemical bonds and electrons yet to be stripped off) and NADH (electrons to be cashed in).

Front 107

In cellular respiration, what happens if Os is present? If it's not?

Back 107

If Oxygen is present, oxidation of pyruvate, followed by the Krebs cycle and then the ETC will follow, If Oxygen is not present in sufficient quantities, the cell cranks out fermentation. We have an enzyme that takes the electrons from NADH and reduces pyruvate producing lactic acid (lactate) and NAD+. Glycolysis requires sufficient NAD+, glycolysis stops.

Front 108

What is the oldest form of energy production, does it require oxygen?

Back 108

Glycolysis is the oldest form of energy production, came about before there was O2 in the atmosphere

Front 109

What do humans make during fermentation? What do yeasts and bacteria make?

Back 109

We make lactic acid while yeast and some bacteria have enzymes that produce ethanol when they reduce pyruvate during fermentation. (to regulate their NAD+)

Front 110

After glycolysis, if sufficient O2 is present, what happens to the pyruvates produced? What are they converted to?

Back 110

If sufficient oxygen is present, pyruvate enters the matrix of the mitochondria and is converted into acetyl CoA., and Acetyl CoA will enter the Krebs cycle

Front 111

What happens to the pyruvates before they enter the Krebs Cycle?

Back 111

The conversion from pyruvate, a (3C) to acetyl (CoA), a 2 carbon molecule results in the loss of a carbon from pyruvate as CO2 (this is a waste product). Some NADH is also formed during this reaction. (see page 170)

Front 112

What is the point of the Krebs Cycle?

Back 112

Slow oxidation of the energy storing molecule (acetyl CoA that became citrate). The energy stripped from the citrate is stored in NADH, FADH2 and some ATP.

The Krebs cycle is called a cycle since citrate (citric acid) is regenerated at the end of the reactions when a 4 carbon molecule is combined with acetyl CoA (that what produces citrate). But the reason to go through all the reactions of the Krebs cycle is to produce heaps of NADH and FADH2.

Front 113

What happens if O2 is not available to serve as the final acceptor of the ETC?

Back 113

If O2 is not available to serve as the final electron acceptor of the electron transport chain, the Krebs cycle stops too. This is because the NADH & FADH2 made by the Krebs cycle have no place to drop off their electrons. So, NAD+ and FAD will no longer be available to let the cycle continue.

Front 114

Is there any allosteric regulation in the Krebs Cycle? What is it?

Back 114

Certain enzymes of the Krebs cycle including the one that combines certain acetyl CoA & oxaloacetate 46 to become citrate are negatively regulated by ATP. Allosteric regulation (negative regulation in this case)

Front 115

What does the ETC need in order for it to make ATP?

Back 115

The ETC will be accepting the electrons from NADH and FADH2. (Whether these carriers picked up their electrons from glycolysis or the Krebs cycle). The ETC proteins are imbedded in the inner convoluted membrane of the mitochondria, so NADH and FADH2 made in the matrix can drop it off pretty easily.

Front 116

How does the ETC work? What happens to the electrons?

Back 116

The electrons will be passed from one carrier to the next one adjacent to it in a specific sequence. There is a specificity of functional interactions. As the electrons are passed from one carrier to the next, protons are pumped through specific carriers. They are pumped from the matrix into the intermembrane space. There is a concentration gradient of protons across the ion convoluted memebrane. The pH of the matrix is higher than the pH of the intermembrane space. NADH passes its electrons off to the first complex so three pumps can pump protons in response to the passage of electrons from NADH. FADH2 passes its electrons off later in the ETC. It bypasses the first pumping of protons. Less protons are pumped across the inner membrane when FADH2 donates its electrons.

The ETC carriers give off their electrons to O2 which also picks up protons to become H2O. (waste product) but the energy of the electrons served its purpose, to set up the proton concentration gradient. The protons are allowed to come down their gradient through a molecule known as an ATP synthase. As the protons bind, they change the shape of the catalytic region of the synthase and ADP phosphorylated (by (Pi)) to become ATP. The protons are released to the matrix once again.
1. With every passage, the electrons lose energy till they are at their lowest energy state where they are picked up by oxygen. (final electron acceptor).
2. Protons are pumped by particular carriers because they change their confirmation by picking and passing of electrons.

Front 117

Where does Photosynthesis occur?

Back 117

in the plants organelles known as chloroplasts

Front 118

Where is the surface area of the chloroplasts abundant?

Back 118

in the thylakoid stacks

Front 119

Is the chloroplast a single or double membrane organelle?

Back 119

double

Front 120

What does the membrane of the thylakoid stacks contain?

Back 120

The membrane of the thylakoid stacks (also known as stacks of grama) contain the proteins and other complexes involved in passing electrons and pumping protons. There are also ATP synthases embedded in the membrane because the proton concentration gradient will drive the phosphorylation of ADP = ATP by Pi.

Front 121

Another name for thylakoid stacks

Back 121

stacks of grama

Front 122

How are electrons passed along the ETC in the thylakoid membrane?

Back 122

Electrons that are passed along the ETC in the Thylakoid membrane come from high energy electrons passed off from specialized Chlorophyll molecules.

The electrons passed off by these specialized chlorophyll molecules will be replaced by electrons that are stripped from water. Ultimately, H2O donates the electrons that are passed along the ETC in chloroplasts. The electron carrier in chloroplasts is NADPH instead of NADH. It differs from NADH by one phosphate group which does not affect its ability to pick up and release electrons. (Chloroplast is much more complicated than mitochondria)

H+
NADP+ = NADPH
(oxidized form) 2e- (reduced form)

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What is photosynthesis? and how does it work?

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Photosynthesis – to make carbohydrates using the energy from the sun, this is split into 2 reactions: The light dependent reaction and the light – independent reaction/dark reaction/Calvin cycle. The Calvin cycle does not use light directly but it requires the product (ATP & NADPH) that the light reactions produce. Light reactions make ATP because of electrons passed along the ETC setting up a proton [ ] gradient and an ATP synthesis. NADPH is made because NADP+ is the final electron acceptor.

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Where does the Carbon of the carbohydrates produced from photosynthesis come from? Where does the O2 come from?

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The carbons of the carbohydrates that are made in the carbon cycle come from atmospheric carbon dioxide. The oxygen is a waste product of the light reaction and comes from splitting of two water molecules to get electrons for the ETC.

Front 125

What are the accessory pigments called?

Back 125

carotenoids

Front 126

How do carotenoids assist with photosynthesis or the production of energy in plants?

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The different chlorophyll molecules absorb different wavelengths of light. There are also “accessory pigments” called carotenoids. Carotenoids absorb wavelengths different from the chlorophyll, and therefore increase the total wavelength that can be used by the plant to boost
Electrons to higher energy levels so they can be passed along the ETC. Overall, the green wavelength are not absorbed, the energy from this wavelength is not utilized. It is reflected or transmitted, not absorbed.

Front 127

What happens to the green wavelengh in plants?

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It is not absorbed, it is reflected or transmitted.

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How are electrons boosted through the ETC?

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These chlorophyll molecules are absorbing radiant energy from the sun in order to boost electrons to a higher energy level / an orbital farther from the nucleus to allow their passage. (boost)

Once the chlorophyll molecule passes off this boosted electron it must receive an electron from another source so another molecule provides this electron to the specialized chlorophyll molecule that passed it off but his electron is at a lower energy state, water (once its split) provides the electron (low energy) to the molecule that gives it to the chlorophyll molecule.

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How is the passage of electrons similar in the mitochondria and the chlorplast?

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In both mitochondrial and chloroplasts ETC, the electrons lose energy w/ every passage.

Front 130

What needs to happen to electrons in chlorplasts?

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In chloroplasts electrons need to be boosted to higher energy levels twice before being passed on to the final electron acceptor which is NADP+.

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Why does the stroma and mitochondrial matrix have the same pH?

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Stroma & Matrix of mitochondria have the same pH which makes sense if you think about the catalytic region of the ATP synthase which (the protein that puts ADP + Pi together) is found in both of these regions.

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Why is the pH of the thylakoid 1000 times more acidic than the stroma?

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While there is electron passage from one carrier to the next (with loss of electron energy with each passage) there is only one complex that pumps protons into the thylakoid interior as a result of the electron passage, yet the thylakoid interior is 1000 times more (pH dif. of 3) acidic than the stroma. How can this be?
1. Breakdown of water releases protons to the thylakoid interior as it results in O2 production & donates electrons to the reaction center chlorophyll molecule.
2. Pumping of protons through one cytochroma molecule from the stroma into the thylakoid interior.
3. The NADP+ picks up protons from the stroma, depleting protons from the stroma

Front 133

What comes out of Non-cyclic photophosphorylation?

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Electrons come from water and are ultimately passed off to the final electron acceptor NADP+, so NADPH is produced. O2 is produced because H2O is split and because electrons being passed results in proton pumping into the thylakoid interior, ATP is made. Uses both P.S.II and P.S.I Note: Possible essay question. FYI, in photophosphorylation, the electron comes from itself, it’s passed around.

Front 134

In Cyclic phosphorylation what happens?

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electrons are passed in a circle. This involves only photosystem I. Electrons are boosted to a higher energy level due to radiant energy of the sun, passed off to the normal electron acceptor of P.S. I (Fd), but this carrier passes the electron off to the cytochrome complex that can pump protons into the thylakoid interior. Electrons are then passed to one other carrier (PC) which passes it back (at low energy to P.S. where energy will be collected once again. So water is not split (O2 is not liberated) NADPH is not made. Cyclic photophosphorylation only produces ATP. All plants do it. Since scientists believe that the Calvin Cycle requires more ATP than the non-cyclic photophosphorylation alone can produce. (FYI: We make CO2 in Krebs Cycle and Plants use CO2 to make Sugar)

Front 135

What energy fuels the calvin cycle in plants, what is the purpose of it? What does it produce.

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ATP & NADPH from the light reactions will be used up in the Calvin Cycle which is a series of anabolic reactions that allow the plant to make sugar. These reactions are occurring in the stroma of the chloroplast and CO2 is taken up by the plant from the atmosphere through the Stomata and diffuses into the chloroplasts. The enzyme Rubisco (sluggish, turns out only 3, since it’s so slow, it is the most abundant protein on earth, a lot of it is needed) fixes carbon from CO2 attaching it to a 5 carbon sugar known as Ribulose 1-5 biphosphate (RuBP) an unstable carbon molecule immediately breaks down into two 3 carbon molecules known as phosphoglycerate. The energy from the hydrolysis of ATP to ADP & Pi plus the energy from the oxidation of NADPH to NAP+ allows the phosphoglycerate to be converted – through several steps to the all important G3P. From G3P, the plant can basically make any sugar, starch, etc. Plus, H has to use some of the G3P to resynthesize Ribulose 1,5 biphosphate (the starting molecule).

Front 136

What are Plants that produce two 3Carbon molecules upon initial fixation of Carbon are referred to as?

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C3 plants

Front 137

What can the G3P made in the Calvin Cycle be used for?

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G3P is also the exact same molecule made at steps 4-5 in glycolysis so the plant can shunt G3P into the glycolytic pathway after the initial energy investment. The product of the Calvin cycle can also be exported into the cytoplasm of the plant cell where they are converted by additional chemical reactions into any organic molecule that the plant needs to make.

Front 138

What happens in the plants stomata?

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Plants lose water through their stomata but the stomata have to be open for CO2 to be taken up from the atmosphere so the plant has to balance CO2 uptake against danger of dehydration.

Front 139

What reactions happen with Rubisco and CO2 and Rubisco and O2?

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Rubisco = CO2 + Ribulose 1.5 biphosphate = 2 molecules of PG=ATP (6 molecules of ADP) = NADPH (NAPH) = G3P

Rubisco = O2 + Ribose 1,5 biphosphate = Water (waste) ATP is used NADPH is used and no G3P is made.

Front 140

How much energy is made from the combination of O2 and Ribulose 1,5 biphosphate?

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None, the energy from ATP and NADPH is used so this is a waste of energy by the plant.

If stomata are closed (to prevent dehydration), but the light reaction continues, O2 concentrations builds up and photorespiration wants ATP & NADPH made in light reaction.

Front 141

How can a plant live in a hot arid environment? (environments where corn and sugar grow).

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A different enzyme with a much higher affinity for CO2 is used to “fix” CO2. This enzyme, (Pep Carboxylase) attaches carbon from CO2 to a 3-Carbon molecule making an initial 4-Carbon molecule known as Aloacetate. These plants are known as C4 Plants. This happens in a cell that does not contain Rubisco. The CO2 that has been fixed is now shunted into another cell type where Rubisco and all other enzymes of the Calvin Cycle are located. This is an increase in concentration of CO2 so to allow Rubisco to fix CO2 rather than O2.