Lecture 15: Cell Energetics I

Question 1

Organisms use _____to build _______molecules, maintain ___ and ___

Answer 1

Organisms use energy to build complex biological molecules, maintain their structure and move

Question 2

What are the 2 sources of energy available to organisms?

Answer 2

electromagnetic and chemical.

Question 3

autotrophs

Answer 3

Electromagnetic energy = light energy. Used in photosynthetic organisms

Question 4

heterotrophs

Answer 4

Chemical energy = energy stored in molecules as covalent bonds. Used by non-photosynthetic organisms

Question 5

aerobic respiration

Answer 5

In animals, breaks down food molecules into CO2. Oxygen accepts the electrons in the food molecule bonds at the end of the electron transport chain to produce H2O.

Question 6

Is energy released or used to break covalent bonds

Answer 6

It takes energy to break covalent bonds, and energy is released when they form…

Question 7

exergonic

Answer 7

(releases energy)

Question 8

Describe why ATP is a good energy currency

Answer 8

The close negative charges on the phosphates destabilize the P-O “phosphoanhydride” bonds.
So these bonds are really easy to break! (less energy input needed)
But, there aren’t phosphoanhydride bonds in the products that are formed using ATP as a reactant (hydrolysis being an example here). So these bonds release the ‘normal’ amount of energy when they’re formed. So cleaving off the terminal phosphates don’t take much energy to break, but normal amounts of energy are formed on bond formation when the products are formed = energy released

ATP can also be used to transfer it’s terminal phosphate to a different molecule (small molecule or protein).
This releases some energy (same idea as above).
The phosphoester bond in the new molecule is also pretty easy to break, and thus energy is also released when it is hydrolyzed. This is exactly what occurs when proteins such as the Na+/K+ gets phosphorylated, and then the phosphate is hydrolyzed off to drive protein movement.

Question 9

Describe how NADH and NADPH carry ‘high-energy’ electrons, and what makes the electrons ‘high-energy’

Answer 9

In many reactions, two electrons from an equally shared bond (e.g. a C-H bond in glucose) are moved to an electron carrier such as NAD+ or NADP+.
One proton is picked up from the surrounding solution, and this forms a new covalent C-H bond in NADH or NADPH.
These are still equally shared, so still have high potential energy, which is why we call them ‘high-energy’ electrons. These electrons can later be transferred to other molecules in redox reactions.

Question 10

Metabolism

Answer 10

• sum total of all chemical changes that occur in cells.

- each reaction is catalyzed by a specific enzyme.

Question 11

metabolite

Answer 11

• compounds formed in each step along the pathway

Question 12

Catabolic pathways

Answer 12

• breaking of chemical bonds in large, complex molecules to form small simple molecules; exergonic (energy-releasing)

Question 13

Anabolic pathways

Answer 13

• synthesis of large molecules by chemically bonding together small molecules; endergonic (energy- consuming)

Question 14

Describe the endosymbiotic theory on how mitochondria and chloroplasts arose

Answer 14

The early Earth was populated by anarobes, which captured and utilized energy by oxygen-independent glycolysis & fermentation reactions.

• Oxygen accumulated in the primitive atmosphere after cyanobacteria appeared.
• Aerobes evolved to use oxygen to extract more energy from organic molecules.
• Then eukaroytes evolved from archaea

• endosymbiotic theory: at some point a heterotrophic anarobe engulfed a
bacterial aerobe. That initial aerobe gave rise to all of the mitochondria in all eukaryotic cells today

Question 15

Note that most eukaryotic cells can do :

Answer 15

Note that most eukaryotic cells can do both aerobic respiration and anaerobic fermentation.

Question 16

Describe evidence that suggests mitochondria were once prokaryotes

Answer 16

• Double membrane may be a remnant of being engulfed
• Membrane composition of mitochondria more closely resembles that of bacteria (high in cardiolipin, no cholesterol)
• Membrane channels made of beta-sheets
• Both bacteria and mitochondria divide by fission (independent of host cell’s divisions)
• Both have a circular DNA – encoding some unique rRNAs and tRNAs, and MtCh have 13 proteins encoded by their genome which are involved in electron transport chain are more similar to those in bacteria

Question 17

outer membrane

Answer 17

porins: beta-sheet integral proteins that form large, nonselective membrane channels

Question 18

intermembrane space

Answer 18

• where high H+ conc. is stored

- includes the space enclosed by the cristae too!!

Question 19

What is the function of the cristae?

Answer 19

Increase the SA of the inner membrane

Question 20

inner membrane

Answer 20

• Selective for what they let in - electron transport chain

- ATP synthase

Question 21

Matrix

Answer 21

i. Pyruvate dehydrogenase complex
ii. TCA cycle
iii. DNA (genes for 13 polypeptides, next slide) iv. ribosomes
v. Other metabolic enzymes (fatty acid catabolism, some amino acid synthesis)

Question 22

Do you think mtDNA contains introns?

Answer 22

No bc they are prokaryotes

Question 23

What can mutations to mitochondrial genes lead to?

Answer 23

Mutations in the MtCh genes that encode for the electron transport chain can cause myoclonic epilepsy and ragged red fiver disease (cells that use a lot of ATP such as neurons and muscle cells don’t work properly)

Question 24

Describe how nuclear-encoded proteins that function in the mitochondria are imported into the mitochondria

Answer 24

• most mitochondrial proteins (except the 13 encoded by MtDNA) are encoded in the nuclear genome
• the exceptions are made by mitochondrial ribosomes in the matrix
• Nuclear-encoded proteins are recognized as targeted to the mitochondria using a signal system that is recognized by different carrier proteins and a mitochondrial receptor
• the signal includes a series of positively charged amino acids in an a helix on the N-end of a new protein; termed the presequence
• Cytosolic chaperone proteins unfold the protein to let it enter the mitochondrial pore
• The are then passed through the TOM complex (outer membrane) and, if matrix proteins, the TIM complexes Mitochondrial proteins refold the protein once inside; presequence is cut off

Question 25

How do mitochondria fuse?

Answer 25

Mitochondria can fuse with one another, or split in two.
– The balance between fusion and fission is likely a major determinant of mitochondrial number, length, and degree of interconnection.

• There is cell signaling between the nucleus and the mitochondria to control mitochondrial fusion/fission

• Certain proteins are required before mito. can divide.
– Removal of an outer membrane protein from mitochondria called MDM10 results in altered mitochondria division.

Question 26

What happens when MDM10 is knocked out?

Answer 26

Fission doesn’t occur resulting in giant mitochondrion

Question 27

List the steps of aerobic respiration, and where these steps occur

Answer 27

Glycolysis: in cytosol, breaks down glucose to 2 pyruvate. Makes 2 ATP and 2 NADH.

Pyruvate dehydrogenase: takes the 2 private and makes 2 actyl CoA and 2 NADH

TCA cycle: in MtCh matrix, takes 2 acetylCoA and for each makes 6 NADH, 2 FADH2, and 2 ATP.

OxPhos: Takes the energy from the NADH and FADH. Makes H+ gradient to make 30(sih) ATP

Question 28

Describe the function of glycolysis, and what the inputs and outputs of this pathway are

Answer 28

• a universal catabolic pathway in all cells (same in prokaryotes and eukayotes)
• breakdown of one glucose to two pyruvate.
• occurs in presence or absence of O2.
• occurs in cytosol.

Inputs: 1 glucose + 2 ATP

Outputs: 4 ATP, 2 NADH (which in the presence of O2 enter MtCh to give electrons to the ETC, 2 pyruvate (which are fed into TCA cycle if aerobic respiration is active)

Net ATP: 2 (through substrate-level phosphorylation)

Question 29

Describe what occurs in the TCA cycle, and what molecules the TCA cycle uses and produces

Answer 29

1. Pyruvate from glycolysis gets transported to mitochondrial matrix and converted to acetyl- CoA by pyruvate dehydrogenase (makes a NADH)
2. Broken down stepwise by enzymes in the matrix (except for succinate dehydrogenase, which is bound to the inner membrane)
3. Four of those steps makes NADH
4. One step makes FADH2
5. These each carry a pair ‘high-energy
   electrons’ to the electron transport chain (next slide)
   NAD+ and FAD are reduced to NADH and FADH2

Question 30

Describe the ETC and what it does

Answer 30

The basic idea is that the energy from the electrons carried by NADH and FADH2 is used to create an electrochemical gradient of H+ ions across the inner membrane. The high concentration of protons is in the inter membrane space.
These stored energy from this electrochemical gradient is used to drive the synthesis of ATP through the action of ATP synthase by oxidative phsophorylation. This is different than ‘substrate level phosphorylation’ done in glycolysis.
This system was proposed in 1961 by Peter Mitchell, who called in the chemiosmotic hypothesis

Question 31

List the order of the complexes, and at which steps H+ pumping occurs

Answer 31

NADH transfers H+ ions and electrons into the electron transport system.
•
• •
•
Protons are translocated across the membrane, from the matrix to the intermembrane space
Electrons are transported along the membrane, through a series of protein carriers
Oxygen is the terminal electron acceptor, combining with electrons and H+ ions to produce water. This is catalyzed by the cytochrome c oxidase complex.
As NADH delivers more H+ and electrons into the ETS, the proton gradient increases, with H+ building up outside the inner mitochondrial membrane

Question 32

Describe how O2 is consumed by the ETC

Answer 32

Oxygen is the terminal electron acceptor, combining with electrons and H+ ions to produce water. This is catalyzed by the cytochrome c oxidase complex.

Question 33

List the sources of protons that accumulate across the inner membrane, and where the proton concentration is the
highest

Question 34

List the components of ATP synthase, and describe how it makes ATP