Exam #3.

Cellular Respiration

The coupling of favorable glucose oxidation with unfavorable ATP synthesis

Cellular Respiration Chemical Equation

C₆H₁₂O₆ + 6O₂ = 6CO₂ + 6H₂O ₊ ATP

Glucose + Oxygen = Carbon dioxide + w+Water + Chemical Energy

Stages of Cellular Respiration & Their Locations

1. Glycolysis = Cytosol

2. TCA/Krebs Cycle = Mitochondrial Matrix

3. E^- Transport Chain (ETC) = Inner Mitochondrial Membrane (IMM)

4. Mitochondria ATP Synthesis = Inner Mitochondrial Membrane (IMM)

Glycolysis Yield

• 2 Pyruvate (C₃)

• 2 ATP

• 2 NADH (high energy electrons)

How many steps does Glycolysis have and which ones are irreversible?

10 steps: steps 1,3, and 10 are irreversible because they involve and input of energy

When and how does Glycolysis Regulation occur?

• Step #1: Hexokinase is competitively inhibited by its own product (too much and it shuts down)

• Step #3: PFK is allosterically regulated

  • ATP, Lactate (no O₂), and Citrate shut it off

  • AMP stimulates it

Glycolysis under anaerobic (No O₂) Conditions

1. Fermentation (in yeast): Pyruvate converts to acetyl aldehyde which converts to ethanol to cause NAD⁺ regeneration

2. Pyruvate concerts to lactate to cause NAD⁺ regeneration

Mitochondria Structure

• Outer Membrane = Very leaky

• Inner Membrane Space = Ion content mirrors cytosol

• Inner Membrane = Impermeable / high protein content

• Matrix

Why does the Inner Mitochondrial Membrane have so many folds?

The folds are there to increase the surface area and subsequently increase metabolic activity because that is where the majority of cellular respiration occurs

TCA Cycle Yeild

• 1 GTP

• 4 NADH (High energy electrons)

• 1 FADH₂ (High energy electrons)

• 3CO₂

(PER Pyruvate Molecule)

What forms does pyruvate (C₃) enter the TCA Cycle?

Acetyl-CoA (C₂)

(Formed from the reaction with the CoA enzyme)

How many steps are there in the TCA Cycle and what is the first one?

9 Steps (8 in the cycle, and 6 coupled to harvesting)

The first step in the cycle is the reaction of Oxolacetate(C₄) + Aceyl-CoA(C₂) to make Citrate(C₆)

How are high energy electrons transported within the cell?

They form hydride ions which are transported by carrier molecules NAD⁺ & FADH⁺

(These reduced carrier molecules will give up the hydride in an energetically favorably way)

Electron Transport Chain

Couples favorable oxidation of NADH & FADH₂ with the unfavorable pumping of protons into the inner mitochondrial space

How many photosystems does the electron transport chain have and in what order?

4 Photosystems: I, III, II, IV

How many protons does 1 NADH Pump?

10 H⁺

• Photosystem I = 4H⁺

• Photosystem III = 4H⁺

• Photosystem IV = 2H⁺

How many protons does 1 FADH₂ Pump?

6H⁺

• Photosystem I = 0

• Photosystem III = 4

• Photosystem IIV = 2

ATP Synthesis

The flow of protons from the inner mitochondrial space back into the matrix through ATP Synthetase drives the phosphorylation of ADP

(4H⁺ = 1 ATP)

How does the newly formed ATP exit the mitochondria?

Since the matrix is so negative, it is energetically favorable to it to transport 4ATP out and 3ATP in to make itself slightly less negative

How does phosphate and pyruvate enter the mitochondria?

Through a symporter

Photosynthesis Chemical Equation

6CO₂ + 6H₂O + Light Energy/Photons = C₆H₁₂O₆ + 6O₂

Carbon dioxide + water + sunlight = Glucose + Oxygen

(OPPOSITE of cellular respiration)

Chloroplast Structure

• Outer Envelope = Outer membrane + inner membrane

  • Properties mimic mitochondria membrane properties

• Stroma

• Thylakoid (A continuous compartment)

  • Chemistry occurs in the membrane

  • Stack = Grana

Stages of Photosynthesis & their locatoin

1. Light Dependent Reactions = Thylakoid membrane

2. Light Independent Reactions = Stroma

Chlorophyll

A pigment molecule that has its electrons excited by a photon & passes it from chlorophyll to chlorophyll

(The antenna complex/key pair of chlorophyll transfer the energy to the ETC

What is the Chloroplast ETC composed of?

Photosystem II & I

Steps of Light Reactions

1. H₂O splitting

2. e^- dumped into ETC

   1. Proton pumping is done with the energy from photosystem II

3. High energy electrons from photosystem I reduce NADP⁺ to NADPH

4. ATP is synthesized by ATP Synthetase from proton flow into stroma

(ATP & NADPH Enter the Calvin cycle)

Light Independent Reactions

Calvin-Bensen Cycle / The Reduction of carbon

1. Carbon Fixation

2. Reduction

3. Regeneration

Calvin Cycle

1. CO₂ + Ribulose (RuBP) through Rubisco enzyme = 3-PGA

2. Energy from ATP & NADPH convert 3-PGA into G3P

   1. 1 G3P molecule exits the cycle to synthesize larger sugars

3. G3P + ATP regenerates RuBP/Ribulose

Why is Rubisco a terrible enzyme?

Because it only reacts 3x/sec however it makes up for this inefficiency through its prevalence because it is the most abundant enzyme

When does protein folding begin?

As soon as it begins emerging from the ribosome

Where does all protein synthesis begin?

In the cytosol on a free ribosome

Protein Targeting

If a protein has a specific hydrophobic signal sequence (4-20aa)…

1. Translation stops

2. Signal recognition protein interacts with the ribosome

3. Ribosome docks on the ER

4. Translation resumes with Protein spooling into the ER

Jamison & Palade Experiment

Pathway of protein secretion: ER - Golgi - Secratory Vesicles

1. Secretory pancreas cell culture / radioactive leucine

2. Pulse

3. Wash off radioactive leucine

4. Fill w/ non-radioactive media

5. Image w/ radiography to track the radioactive proteins

(Some proteins stay in the ER & Golgi, not all end up in SV)

Rothman & Lodisn Experiment

1. Protein Insertion occurs during translation

2. Insertion happens early in translation (first 30aa)

3. N-terminus is in the cytosol in a protein

Used spike proteins encoded by viral mRNA

• Invitro translation

• Presence and absence of mircosomes (glycosolation) or protease(destruction/direction)

What is the direction of a protein in a cell vs. in a solution

In a cell, the N-terminus is outside in the cytosol

In a solution, the C-terminus is outside in the solution

Glycosolation

The adding of sugar trees by enzymes only in the ER lumen

(Changes the mass of the protein)

N-Terminal Signal Sequence

Drives insertion through the membrane

1. NTSS is exposed from ribosome

2. Signal Recognition Protein (SRP) binds

3. Translation stops

4. SRP complex docks

5. Translation resumes with protein inserted across the membrane

6. Signal Peptidase cuts off the NTSS to free protein

Rules of Signal Sequences

1. All signal sequences end up as transmembrane/ membrane spans

2. NTSS is always cleaved off by SP

3. With NTSS = New N-term lumen/outside & W/O NTSS = N-term in cytosol

Internal Signal Sequence

A part of the protein that will be transmembrane and does not get off

Protein Asymetry

Glycosolation trees are added to Asparagine in the ER and to Serine or Theorine in the golgi