BIOL215 Exam 2 Flashcards

CWRU Burden-Gulley Exam 2 Complete Flashcards

Where does protein translation begin?

The cytoplasm

What are the 3 mechanisms of protein transport?

The three mechanisms of protein transport are co-translational translocation, post-translational translocation, and vesicular transport.

What are signal sequences?

Short sequences of amino acids that direct proteins to their location; required for proteins to get to target site

Where does post-translational translocation bring proteins?

From the cytosol to the mitochondria, peroxisome, chloroplast, or nucleus.

Where does co-translational translocation bring proteins?

From the cytosol to the lumen of the endoplasmic reticulum.

Where does vesicle transport bring proteins?

From the ER to the Golgi, and from the Golgi to the cell exterior (secreted proteins), plasma membrane, or lysosome.

What occurs at the ER?

Protein processing such as folding.

What occurs at the Golgi?

Further modifications and the proteins are sorted into compartments that correspond to certain destinations in a cell.

How does the secretory vesicle move?

By ATP dependent motor proteins (kinesin) traveling on microtubules extending from the ER.

What is the lysosome?

A membrane-bound organelle that contains newly synthesized digestive enzymes; the site of degradation, with an interior of low pH.

Describe the steps of co-translational translocation.

The N-terminal signal sequence is translated in the cytoplasm; a signal recognition particle (SRP) binds and pauses translation; the SRP binds to a receptor and translation resumes inside of the ER lumen; ribosome binds to translocator, SRP releases and receptor moves away. The N-terminal signal sequence binds to the channel, and movement of the polypeptide strand moves the plug to enter the lumen. Once translation is complete, the signal sequence is cleaved by signal peptidase; the signal sequence then degrades and the plug closes the channel

What is constitutive secretion?

The default mechanism of continuous secretion to extracellular space.

What is regulated secretion?

Specialized cells that have concentrated proteins in vesicles that are only released in response to a specific signal.

How are lysosomal enzymes unique?

They move from the ER to the Golgi and become phosphorylated, then are directly inserted into the lysosome.

How do start and stop signals in a polypeptide strand affect the movement of the protein?

Start signals move the protein into the ER lumen while stop signals stop the movement of the protein into the ER lumen.

If the first start signal sequence is on the N-terminal, where will the N-terminus be found?

In the ER lumen.

If the first start signal sequence is on the internal, where will the N-terminus be found?

In the cytosol.

What does the location of the C-terminus depend on?

The amount of start-stop sequences.

Fill in the Blank: In general, a stop-transfer signal directs its following segment in the protein to the _ side of the membrane

cytosolic

What does it mean to be topologically equivalent?

The side of the protein will not change the side it faces; the cytosolic side of the protein will always be on the cytosolic region of the cell; the lumen side of the protein will always be in the lumen region of the cell.

What does a hydropathy plot do?

Use the chemical characteristics of amino acids in a polypeptide strand to predict transmembrane domains. Positive regions of the plot indicates amino acids with nonpolar characteristics.

How is post-translational translocation unique in mitochondria?

The N-terminus becomes the “presequence”, which is the mitochondrial targeting sequence. The protein is fully translated in cytosol and chaperone proteins prevent folding.

How is post-translational translocation unique in chloroplast?

The N-terminus becomes the “transit peptide”, which is the chloroplast targeting sequence. The protein is fully translated in cytosol and chaperon proteins prevent folding.

What is the ∆G of an exergonic reaction?

Negative (less than 0)

What is the ∆G of an endergonic reaction?

Positive (greater than 0)

What is reaction coupling?

The coupling to phosphorylation by ATP to make reactions exergonic overall.

What are phosphorylation reactions?

When a phosphate ion is transferred to the molecule, leaving ADP; this may change the shape of the protein due to the new negative charge repulsions

What determined reaction speed?

The orientation of reactants and activation energy.

What solves the problems of the determinants of reaction speed?

Enzymes, which are catalysts that localize in an organelle to increase the probability that they will encounter their substrates.

What does the Michaelis-Menten Kinetics Model compare?

Rate of reaction (y-axis) vs the substrate concentration (x-axis).

What is Vmax in the M-M Model?

The maximum velocity of the given reaction, indicating that the enzymes are saturated.

What is Km in the M-M Model?

The Michaelis-Menten Constant, which is ½ of Vmax.W

What does a low Km mean for the reaction and affinity between enzyme and substrate?

Fast reaction and high affinity.

What is Kcat in the M-M Model?

The turnover number, found by diving Vmax by the concentration of the enzyme.

How do you find the efficiency in the M-M Model?

You divide Kcat by Km.

What are the M-M Assumptions?

Reversibility, steady-state, initial velocity, substrate concentration, and single substrate.

What is the reversibility assumption in the M-M Model?

The reverse reaction is negligible.

What is the steady-state assumption in the M-M Model?

The rate of formation of the intermediate is equal to the dissociation of the intermediate, so the enzyme-substrate concentration remains constant.

What is the initial velocity assumption in the M-M Model?

The concentration of product is negligible since the initial rate of reaction is an accurate measurement of reaction rate.

What is the single substrate assumption in the M-M Model?

Only one substrate is involved with interacting with the enzyme.

What is the M-M Equation?

What does competitive inhibition do and how does it affect Km and Vmax?

Blocks the substrate from binding; Km is reduced while Vmax is unaffected.

What does noncompetitive inhibition do and how does it affect Km and Vmax?

Blocks the reaction from occurring; Vmax is dramatically reduced while Km is unchanged since the substrate is still able to find.

How are concentrations found on the Lineweaver-Burk Plot (where is it higher/lower)?

Higher concentrations are closer to (0, 0) while lower concentrations are further away.

What is one downside of the Lineweaver-Burke Plot?

It is very sensitive to the results from experiments with low concentrations.

What is more energetically favorable, stepwise oxidation or breaking down energy in a single step?

Stepwise oxidation.

Fill in the Blank: NADH is the _ form of NAD⁺.

reduced

Fill in the Blank: FADH₂ is the _ form of FAD.

reduced

What is the order of cellular respiration?

Glycolysis → Pyruvate Processing / Link Reaction → Krebs Cycle / Citric Acid Cycle / TCA Cycle → Oxidative Phosphorylation (ETC → ATP Synthase).

Where does glycolysis occur?

In the cytosol.

What are the net products of glycolysis per glucose molecule?

2 ATP, 2 NADH, and 2 pyruvate molecules.

Where does pyruvate processing occur?

In the mitochondrial matrix.

What are the products of pyruvate processing PER CYCLE?

1 CO₂, 1 NADH, and 1 Acetyl-CoA.

What are the products of pyruvate processing PER GLUCOSE MOLECULE?

2 spins of the cycle: 2 CO₂, 2 NADH, and 2 Acetyl-CoA.

Where does the Krebs Cycle occur?

In the mitochondrial matrix.

What are the products of the Krebs Cycle PER CYCLE?

3 NADH, 1 ATP, 2 CO₂, and 1 FADH₂.

What are the products of the Krebs Cycle PER GLUCOSE MOLECULE?

2 spins of the cycle: 6 NADH, 2 ATP, 4 CO₂, 2 FADH₂.

What happens after the Krebs Cycle?

The electron carriers NADH and FADH₂ travel to the ETC to transfer the electrons.

Where does the ETC occur?

In the inner membrane of the mitochondria (the one between the matrix and the intermembrane space).

What are the products of the ETC PER CYCLE?

1 NAD⁺, 1 FAD, and 1 H₂O (water).

What are the products of the ETC PER GLUCOSE MOLECULE?

10 NAD⁺, 2 FAD, 6 H₂O (water), and 34 ATP.

What is the final electron acceptor in both photosynthesis and cellular respiration?

O₂

Under ideal conditions, how many ATP do NADH produce?

3 ATP molecules.

Under ideal conditions, how many ATP do FADH₂ produce?

2 ATP molecules.

What is the anaerobic form of cellular respiration?

Fermentation.

What are the products of lactic acid fermentation PER CYCLE?

2 ATP, 2 NAD⁺, and 2 lactate molecules.

Fill in the Blank: Fermentation only produces ~_% of the amount of ATP that cellular respiration creates per glucose molecule.

5

What is metabolic flux?

The movement of a metabolite through a pathway over time, containing reversible (ΔG close to 0) and irreversible steps (negative ΔG).

Fill in the Blanks: Increasing the _ of reactants/products causes the reaction to move forward/backward until _ is reached.

concentration, equilibrium

What type of regulation do pathways have?

End product inhibition, allosteric inhibition, allosteric activation, enzyme deactivating by a phosphatase.

Fill in the Blanks: Photosynthesis turns _ energy into _ energy.

kinetic, chemical

CO₂ in photosynthesis is reduced to what?

Glucose

Water in photosynthesis is oxidized to what?

O₂

What are stomata?

Openings in the epidermis of plants that allow CO₂ to enter and O₂ to exit.

What are chloroplasts?

Specialized, double-membrane organelles that allow a cell to photosynthesize.

What is the thylakoid?

Found in the stroma (space in the chloroplast), it contains pigments involved in capturing the kinetic energy of the sun to initiate photosynthesis.

What are pigments?

Molecules that contain a hydrophobic tail that allows for the embedding in the thylakoid membrane and ring structures that provide the capability to absorb light.

What is the primary pigment?

Chlorophyll A

What are the products of the light-dependent reactions and what are they used for?

1 ATP and 1 NADPH, which are used for the Calvin Cycle.

What is the process of the light-dependent reactions?

Light energy strikes pigment molecule, exciting electrons; energy is then transferred to the Special Pair which then donate the electrons to an acceptor who carries it to the ETC and follows the rest of that path.

Where does the Calvin Cycle occur?

In the stroma.

What is the process of the Calvin Cycle?

Beginning with rubisco incorporating 3 CO₂ and driving carbon fixation. Then it becomes 3 6-carbon intermediate, then into 6 3-PGA, which releases 6 NADP⁺ and 6 ADP and becomes 6 G3P. One of these G3P leaves to become glucose while the other 5 are recycled to become 3 RuBP, which uses 3 ATP and releases 3 ADP.

What are the products of the Calvin Cycle?

9 ADP, 6 NADP⁺, and 1 G3P molecule.

What are the products of ONE CYCLE of the Calvin Cycle?

3 ADP, 2 NADP⁺, and 1 G3P molecule.

Why is Rubisco inefficient and the rate limiting step for the Calvin Cycle?

It is very slow and binds to both CO₂ and O₂.

What is done so that Rubisco is not so inefficient?

An abundance is found within the cell to make up for being slow.