BIS 2A midterm 2

microfilaments (actin)

thin, double-stranded, used for cell shape, muscle contraction, and punching the cell in two during division

• soluble: G-actin

• insoluble: F-actin

G-actin and F-actin are reversable

microtubules (tubulin)

hollow tubes; act as highways for organelles and make up the structure of cilia and flagella

Kinesins

motor proteins that move cargo towards the plus end of microtubules (outward towards cell periphery, anterograde, exocytosis)

dyneins

motor proteins that move cargo towards the minus ends (inward toward nucleus/centrosome, retrograde), endocytosis

how do the cytoskeleton and motor proteins function together to address various problems associated with transport

the cytoskeleton functions like tracks on a railway system and motor proteins are the engines that pull the vesicles, solves the problem of diffusion being too slow for large eukaryotic cells

How do kinesins work

• hand-over hand model

  • globular parts of kinesin depend on ATP for movement where they deposphorylate the ATP into ADP when stepping forward.

centrioles

pair of cylindrical arrangements of short microtubules, important for organizing the mitotic spindle during cell division. They also play a role in the formation of cilia and flagella.

functions of the cytoskeleton

maintains and controls cell shape, controls internal organization of the cell, generates force for transport of cellular cargo, cell movement, and chromosome movement and cell division

larger values in the tower of energy want..

more electrons

deltaEº

measure of the tendency of a chemical species to acquire electrons and be reduced, difference in standard reduction potential for the redox couple, positive E is spontaneous and negative E is nonspontaneous, measured in volts

change in energy

deltaGº= -nFdeltaEº

NAD redox reaction

NADH carries 2 e- and 1 proton plus one associated proton

oxidation

loss of electrons from a substance, resulting in an increase in oxidation state.

reduction

gain of electrons by a substance, resulting in a decrease in oxidation state.

redox reaction

A chemical reaction involving the transfer of electrons from one substance to another, resulting in oxidation and reduction.

reducing agent

A substance that donates electrons to another substance and is oxidized, causing reduction in that substance.

oxidizing agent

A substance that accepts electrons in a redox reaction and is reduced, causing another substance to be oxidized.

NAD+

a coenzyme that functions as an electron carrier in cellular respiration

FAD+

electron carrier involved in metabolic reactions like the Krebs cycle.

table of reduction potentials (redox tower)

a ranking of electron donors and acceptors based on their reduction potentials

top of tower: strongest reducing agents (most negative, best electron donors)

bottom of tower: strongest oxidizing agents (most positive, best electron acceptors)

Conservation of mass in metabolism (input)

mass enters the cell as reduced organic molecules (glucose, fatty acids, amino acids), and these molecules contains high amounts of carbon and hydrogen

conservation of mass in metabolism (output)

through metabolic oxidation, the carbon and hydrogen that enters the cell are combined with oxygen to leave the cell as oxidized molecules, specifically H2O and CO2. The total mass of atoms entering equals the mass exiting.

How is the conservation of energy applied to central metabolism?

energy is conserved as it moves from sources (molecules with low reduction potential like glucose) to sinks (molecules with high reduction potentials like O2). Energy is transferred via high-energy electrons (carried by NADH or FADH2) and stored temporarily as a proton motive force (electrochemical gradient) or directly in bonds of ATP.

ATP components

nitrogenous base (adenine), ribose sugar, and three phosphate groups (alpha, beta, gamma)

What are the high-energy bonds in ATP?

phosphoanhydride bonds, located between phosphate groups (specifically beta-gamma and alpha-beta bonds)

What makes a bond high energy?

When the products of breaking the bond are more stable than the reactants

Why is water important in determining the negative ΔG0’ of the hydrolysis of a phosphoanhydride bond in ATP?

ATP hydrolysis has a very negative ΔG0’ because water acts as a nucleophile (electron donor). In the products (ADP+Pi), there is a reduced electrostatic repulsion and increased hydration of the resulting ions, making the final state much more stable

How can ATP hydrolysis be coupled to drive endergonic reactions?

ATP hydrolysis is highly exergonic, by coupling it to an endergonic reaction the overall net energy change for the combined process becomes negative and allows the non-spontaneous reaction to proceed

explain substrate-level phosphorylation (SLP) and how to identify the SLP reactions when given a collection of reactions, such as in a pathway

Substrate-level phosphorylation (SLP) is the direct transfer of a phosphoryl group from a high-energy metabolic intermediate (the substrate) to ADP to form ATP. To find SLP rxns, look for rxns where a phosphate is removed from a carbon compound and results in the production of ATP (or GTP) without the use of an electron transport chain.

what is the importance of the reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the harvesting of energy in glycolysis?

The reaction catalyzed by GAPDH is the bridge between the investment and payoff phases, it’s the only step in glycolysis that captures energy through a redox reaction to drive the addition of an inorganic phosphate without consuming ATP. The exergonic oxidation of the G3P is coupled to the endergonic formation of a high-energy thioester intermediate and subsequently a high energy acyl-phosphate bond (1,3-BPG)

Key steps of GAPDH reaction

• a cysteine residue in the active site forms a covalent thioester linkage with G3P

• substrate is oxidized as a hydride ion is transferred to NAD+, forming NADH, the catalytic histidine acts as a base to facilitate this

• inorganic phosphate (Pi) attacks the thioester bond, releasing the product (1,3-BPG). The energy of the thioester bond is conserved in the acyl-phosphate bond, which has a high enough group transfer potential to later synthesize ATP.

glucose

C6H12)6, primary energy source for cells

ATP

adenosine triphosphate, energy currency of the cell, nucleotide that stores and transfers energy within cells

phosphorylation

addition of a phosphate group to a molecule

dephosphorylation

removal of a phosphate group from a molecule, often leading to a decrease in energy.

aerobic

process that requires oxygen

anaerobic

processes that occur in the absence of oxygen

glycolysis

initial metabolic pathway that breaks down one molecule of glucose into two molecules of pyruvate, producing a small net gain of ATP and NADH

allosteric

relating to the regulation of an enzyme by binding an effector molecule at a site other than the active site, causing a change in shape

Thioester

a high-energy chemical bond formed between a carboxylic acid and a thiol (sulfur-containing group), such as the bond in Acetyl-CoA

decarboxylation

a chemical reaction that removes a carboxyl group and releases carbon dioxide

coenzyme A (CoA)

coenzyme that plays a critical role in the oxidation of pyruvate and the synthesis/oxidation of fatty acids, often carrying acetyl groups (as Acetyl-CoA)

fermentation

an anaerobic process used by calls to regenerate NAD+ from NADH, allowing glycolysis to continue in the absence of oxygen

conservation of mass in metabolism

mass is neither created nor destroyed, inputs are high-energy, reduced organic molecules and outputs and lower-energy, oxidized inorganic molecules and nitrogenous waste. atoms entering as food as the same atoms leaving as waste or being incorporated into cell biomass

conservation of energy in metabolism

energy is transferred from electron sources to sinks. sources are molecules with lower reduction potentials (glucose) that hold high energy electrons and sinks are molecules with high reduction potentials acting as the final electron acceptors (O2). Energy is stored temporarily as chemical potential energy (ATP bonds) or electrochemical gradient energy

central role of acetyl CoA

universal metabolic intermediate, formed from pyruvate (carbohydrates), beta-oxidation (fatty acids), and amino acid catabolism. functions as it feeds carbon into the TCA cycle for energy or serves as the building block for lipid synthesis when energy levels are high

how are cyclic processes involved in energy harvesting and the inter-conversion of molecular types?

cyclic processes like the TCA cycle allow the cell to harvest energy through repeatedly stripping electrons from intermediates and using the intermediates as precursors for amino acids or lipids, maintaining a steady state of “shuttle” molecules

Coenzyme A (CoA) function

contains a thiol group (-SH) at the end of its structure, forms high energy thioester bonds with acyl groups, activating the group and making the transfer of the acyl unit thermodynamically favorable for subsequent reactions

role of glucose in creation of medium and long-term energy storage compounds

medium term is when glucose is polymerized into glycogen or starch for rapid mobilization and long term is when glucose is converted via acetyl CoA into fats which offer higher density for long-term storage in adipose tissue.