Bio Exam Study Part 3

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cytoskeketon:

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a complex scaffold of proteins that give the cell structure and motility, facilitate cell migration, and anchor organelles

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endomembrane system:

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a network of membrane-bound chambers where protein targeting and processing takes place

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rough endoplasmic reticulum:

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a type of ER that is coated with ribosomes

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smooth endoplasmic reticulum:

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a type of ER plays a major role in synthesizing lipids and in degrading toxins

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glycosylation

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the process in which carbohydrates are added to proteins; occurs in the Golgi apparatus.

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Golgi apparatus:

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an endomembrane system involved in processing proteins; where carbohydrates are added to proteins

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hydrolytic enzyme:

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enzymes within lysosomes which degrade material within the vesicles

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intermediate filaments:

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made of fibrous proteins wrapped around one another to form a thick cable-like structure, they play an important role in supporting cell structures and anchoring organelles in the correct position within the cell. A cytoskeleton component.

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lysosome:

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vesicular compartment that is involved in breaking down material.

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microfilament:

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the smallest cytoskeletal fibers which play a critical role in cell motility, where they facilitate cellular migration or, as in the case of muscle cells, contraction

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microtubules

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hollow tubes consisting of rows of paired tubulin molecules which are very important to major cellular events (e.g., mitosis) and they also have a major structural role within the cell. A cytoskeleton component.

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nuclear pores:

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holes” in the nuclear membrane through which messenger RNA (and other molecules) exits the nucleus

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nuclear scaffold:

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structural proteins that help to anchor and organize the chromosomal DNA.

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nucleolus:

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contains a very active group of genes that encode and transcribe ribosomal RNA

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nucleus:

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one of the most visible organelles in the cell, and plays a central role in providing genetic information to the cell.

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secretory vesicle:

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the final transport vesicle that buds from the trans face of the Golgi apparatus which binds and fuses with the internal face of the plasma membrane by interacting with specific membrane proteins.

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signal sequence:

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sequences on proteins that facilitate their sorting within the cell

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signal recognition particle (SRP):

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helps to direct proteins to their correct “docking” site on the rough ER; they facilitate association with the rough ER and then this translational complex docks to the rough ER at a specific receptor site located within rough ER pore complexes

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turgor pressure:

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osmotic pressure of a cell.

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vacuole:

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rimarily storage organelles, and in plant cells are used to maintain turgor pressure.

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What is the major function of the nucleus and what are the key descriptive features? What structures are there within the nucleus?

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The nucleus plays a central role in providing genetic information to the cell. The most notable function of the nucleus is to store the major source of genetic material within every eukaryotic cell; namely, the nuclear chromosomes (additional genetic information is also found within mitochondria and chloroplasts). In addition to storage, the nucleus is also the site of all gene expression.

The nucleus is one of the most visible organelles in the cell. It is usually only about 5 microns in diameter (approximately 1/20th the thickness of a human hair), and it is surrounded by a double membrane called the nuclear envelope. The structure of the nucleus can be further broken down to include the nucleolus and the nucleoplasm.

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What is the purpose of the nucleolus?

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The nucleolus contains a very active group of genes that encode and transcribe ribosomal RNA.

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Where and how are chromosomes organized in the nucleus? What holds these chromosomes in place?

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The nucleoplasm contains the genetic material of the cell (i.e., chromosomal DNA). In order for chromosomal DNA to fit into the nucleus, it must be highly organized; a network of structural proteins, called the nuclear scaffold, helps to anchor and organize the chromosomal DNA. It also helps maintain the shape of the nucleus.

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How does mRNA leave the nucleus? Where does it go after leaving the nucleus?

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mRNA leaves the nucleus through nuclear pores in the nuclear membrane. These “holes” allow mRNA to pass through to be translated by ribosomes

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What is the endomembrane system? What part does it play in the life of a cell? What is it made up of?

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Protein targeting and processing takes place in a network of membrane-bound chambers called the endomembrane system. The process begins in a network called the endoplasmic reticulum (ER), which literally means "network within the cytoplasm." There are two types of ER: rough ER and smooth ER. The Golgi apparatus is also part of the endomembrane system.

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What is the endoplasmic reticulum (ER)? What are the different kinds and what processes occur at each type of ER?

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The ER is part of the endomembrane system that helps to process newly-made proteins. There are two types of endoplasmic reticulum in the cell: a smooth endoplasmic reticulum and a rough endoplasmic reticulum. The smooth endoplasmic reticulum plays a major role in synthesizing lipids and in degrading toxins. Rough ER is coated with ribosomes, unlike smooth ER, and facilitate sorting and processing of proteins.

Front 27

How are proteins directed to the rough ER? Describe the process of directing a protein to the rough ER and discuss the different compounds involved.

Back 27

Newly synthesized proteins destined for export have a unique signal sequence that directs them to the rough endoplasmic reticulum. If a translational complex (1) has a growing protein with this sequence at its N-terminus (the end that is synthesized first), then a signal recognition particle (SRP) binds to the growing polypeptide (2). The SRP facilitates association with the rough ER and the translational complex docks to the rough ER at a specific receptor site located within rough ER pore complexes (3). The growing polypeptide is then inserted through the pore and translation continues (note: the polypeptide is now being inserted into the lumen of the rough ER as it is synthesized (4). Specific peptidases inside the lumen recognize the signal sequence and this short stretch is removed (5). Once translation is completed, the translational complex dissociates, leaving the newly synthesized protein inside the rough ER.

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What is a translational complex? Where is this complex located throughout the process of directing a protein to the rough ER?

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A translational complex is the combination of a ribosome, attached mRNA, a signal recognition particle (SRP) and the signal sequence on the new protein. At first the translational complex is in the cytosol, but after a translational complex has “docked” at the rough ER’s translocation complex, it will remain there temporarily so that the growing protein is directly inserted into the rough ER’s lumen.

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Where do proteins go after they leave the rough ER? How do they get there?

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Proteins go directly to the cis (“receiving”) face of the Golgi apparatus via membrane bound transport vesicles from the ER.

Front 30

What chemical change do proteins undergo in the Golgi apparatus? Draw this organelle and label the two faces and internal structure. Also, show how proteins travel through the Golgi body.

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The Golgi apparatus is where carbohydrates are added to proteins in a process called glycosylation. The side of the Golgi apparatus where proteins enter is referred to as the cis face; it can be thought of as the receiving end of the Golgi apparatus. Transport vesicles, containing partially processed proteins, bud from the folds of the Golgi apparatus (cisternae) on the cis face and fuse with cisternae on the more distal side (trans face). In this manner, proteins traverse the Golgi apparatus as they are prepared for transport to their final destinations either within the cell or for export outside of the cell.

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Front 31

How do proteins leave the Golgi apparatus, and where do they go? What is the difference between a transport vesicle and a secretory vesicle?

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When a protein is fully processed, glycosylated, and ready for export, it next makes the trip from the endomembrane system to the cell's plasma membrane or other internal compartments (e.g., a lysosome) via transport vesicles. If a transport vesicle that buds from the trans face of the Golgi apparatus fuses with the cell’s plasma membrane and is secreted from the cell, that transport vesicle is termed a secretory vesicle.

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What is the cell cytoskeleton, and what purposes does it have?

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The cytoskeleton is a complex scaffold of proteins that give the cell structure and motility, facilitate cell migration, and anchor organelles

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What are the three major components of the cytoskeleton? Describe each. What are they made of and how are they structured? What do they do in the cell and how are they unique?

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The cytoskeleton is made up of three major components: microfilaments, intermediate filaments, and microtubules. Microfilaments are made of many subunits of the globular protein actin, which are strung together like beads on a string. Microfilaments play a critical role in cell motility, where they facilitate cellular migration or, as in the case of muscle cells, contraction. Intermediate filaments are somewhat larger than microfilaments, yet smaller than microtubules. They are made of fibrous proteins wrapped around one another to form a thick cable-like structure. Intermediate filaments play an important role in supporting cell structures and anchoring organelles in the correct position within the cell. Unlike microfilaments and microtubules, intermediate filaments are relatively static within the cell. Microtubules are the largest cytoskeletal element that we will discuss. They are hollow tubes consisting of rows of paired tubulin molecules. Microtubules are very important to major cellular events (e.g., mitosis) and they also have a major structural role within the cell.

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What are molecular motors and how are they associated with the cytoskeleton? How do they control movement in the cell? Give examples.

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Molecular motors are responsible for cellular movement such as moving large vesicles, or even entire organelles. Recent experimental evidence suggests that many of these molecular motors actually "walk" along cytoskeletal fibers. During mitosis, a molecular motor located at the kinetochore participated in chromosomal movement. Molecular motors in muscle cells allow muscle cells to contract.

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What do lysosomes do in the cell? What compounds do they utilize?

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Lysosomes are involved in breaking down material using hydrolytic enzymes.

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What are vacuoles and how are they different in plant and animal cells?

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Vacuoles are primarily storage organelles, but in plant cells are also used to maintain turgor pressure.

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Draw out a eukaryotic cell and include all the major organelles and structures. Draw it large enough to show some of the features and characteristics of each organelle. Label and describe each organelle and structure.

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Draw out a eukaryotic cell and include all the major organelles and structures. Draw it large enough to show some of the features and characteristics of each organelle. Label and describe each organelle and structure.

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activation energy:

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the input of energy required to “start” exergonic reactions.

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active site:

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the spot where a substrate fits into an enzyme, much like a key into a lock

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allosteric enzyme:

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complex molecules which are controlled by allosteric regulation. They are composed of at least two protein subunits, and conformational changes occur when allosteric sites are filled, thereby changing the shape of the active site itself

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allosteric regulation:

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a process by which enzymatic regulation is achieved, in which an inhibitor binds to a site distant from the active site and causes a conformational change in the enzyme, thereby decreasing its ability to bind with the substrate and hence, catalyze the reaction.

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antioxidant:

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organisms or substances which have the ability to detoxify oxygen by reducing it with electrons from other molecules.

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catalyst:

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a substance, usually used in small amounts relative to the reactants, that modifies and increases the rate of a reaction without being consumed in the process

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circular DNA

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the form of DNA which mitochondria posses. It provides clues to the origins of mitochondria.

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coenzyme:

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are not themselves catalysts, but are required for normal catalytic functioning of the enzyme

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cyanobacteria:

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the first organisms to have the ability to use H2O and CO2 to make organic molecules with the help of solar energy (i.e. photosynthesis)

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endosymbiosis

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a type of symbiosis in which one organism began living within the body of another

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enzyme:

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protein catalysts which facilitate reactions not by adding energy, but by hastening reactions by lowering the activation energy necessary so that the reactions can occur at normal metabolic temperatures.

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enzyme substrate complex

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the unit that forms when an enzyme and its substrate(s) join

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feedback inhibition (negative feedback):

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a reaction's end-products inhibit the reaction itself by halting it when a certain amount of product has accumulated.

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feedback stimulation (positive feedback):

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a reaction's end-products stimulates the reaction by halting it when a certain amount of product has accumulated.

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inhibitor:

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slow down or halt the activity of enzymes by attaching themselves to active sites and interfering with the binding of substrates

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phosphofructokinase:

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an important enzyme that is involved in the early stages of glycolysis; is a critical enzyme because it represents the first point of metabolic regulation in cellular respiration.

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protoeukaryote:

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the prokaryotic ancestors of modern eukaryotes

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protomitochondrion:

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the prokaryotic ancestors of modern mitochondria

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serial endosymbiosis:

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sequential endosymbiotic events

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substrate:

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that upon which an enzyme works

Front 58

Review the different stages of cellular respiration. Draw out each stage and discuss the major events that occur as they progress. What role do enzymes play in these processes?

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Cellular respiration involves glycolysis, the Krebs cycle, and the electron transport chain. Glycolysis, which takes place in the cytosol of cells, breaks down single molecules of glucose into twin molecules of the compound pyruvate. In addition, a small amount of ATP (the energetic currency of cellular metabolism) is released in this process. A catabolite of pyruvate, acetyl CoA, is fed into the Krebs cycle. The Krebs cycle is a collection of enzymes located in the mitochondrion (plural, mitochondria). These enzymes convert acetyl CoA further (again, producing a small amount of ATP directly) and generate the highly reduced compounds NADH and FADH2, that in turn, send their electrons through the electron transport chain in the mitochondrial membrane where they are typically donated eventually to oxygen. The energy generated by the flow of electrons causes the buildup of a hydrogen gradient across this membrane, representing an enormous store of potential energy in the form of a charge differential (voltage). The charge differential is dissipated when hydrogen ions flow through the membrane via molecules of ATP synthase, which use their energy to form a relatively large amount of ATP by oxidative phosphorylation.

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What are exergonic and endergonic reactions? What is activation energy? Describe how activation energy is associated with some exergonic reactions.

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Chemical reactions that release free energy are called exergonic reactions. Exergonic reactions release energy, whereas endergonic reactions require (absorb) energy. Even exergonic reactions require some input of energy, which is referred to as activation energy.This energy is needed to break bonds in the reactant molecules; then, even more energy is released (in an exergonic reaction) when the bonds in the product molecules form.

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What does it mean for a reaction to occur “spontaneously”? How can you force a spontaneous reaction to occur? How can you stop a spontaneous reaction from occurring at the wrong time?

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Spontaneous reactions are, by definition, exergonic reactions. Spontaneous does not mean instantaneous. Although spontaneous reactions release free energy which a cell needs to function, they do not occur without some input of initial energy, called activation energy. You can force a spontaneous reaction to occur by applying extra energy, or by using enzymes to lower the amount of activation energy needed. You can stop a spontaneous reaction by removing enzymes or by reducing the amount of extra energy available in the system (so that there is not enough activation energy for the spontaneous reaction to occur).

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What is needed to initiate a spontaneous reaction? How is it possible that reactions that give off energy still require energy to begin? How does this energy initiate a reaction?

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Activation energy is needed to initiate a spontaneous reaction. Energy is needed because it is necessary to break bonds in the reactant molecules so that even more energy is released (in an exergonic reaction) when the bonds in the product molecules form. Therefore, an exergonic reaction (one that gives off energy) requires energy to break its initial bonds, but it will result in an even greater release of energy. The net product of an exergonic reaction is the production of energy. that gives off energy) requires energy to break its initial bonds, but it will result in an even greater release of energy. The net product of an exergonic reaction is the production of energy.

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What are enzymes? How do enzymes assist in the activation of reactions?

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Enzymes are protein catalysts which facilitate reactions not by adding energy, but by hastening reactions by lowering the activation energy necessary so that the reactions can occur at normal metabolic temperatures. By using enzymes, no extra energy is needed to start a spontaneous reaction.

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Draw and label an example of an enzyme-substrate complex. How is the 3-D shape of enzymes important to this complex?

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The 3-D shape of an enzyme renders it highly specific and allows it to act only on a certain type of molecule (i.e., its substrate; substrates fit into the active site of an enzyme, much like a key fits into a lock).

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What is the substrate and what happens to it when it enters the complex? How does the enzyme change it?

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A substrate is that upon which an enzyme acts. A substrate binds to an enzyme's active site, it is held in a position that initially promotes the breaking of chemical bonds and later, the formation of new bonds associated with the product.

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What happens to the enzyme after the reaction occurs? How does the enzyme change?

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The enzyme emerges unchanged from the reaction, and it proceeds to catalyze more reactions after one reaction is finished.

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How many types of reactions can one type of enzyme catalyze? Can sucrase break down lactose into its monomers?

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The fit between an enzyme and its substrate is very specific, and each enzyme can catalyze only one kind of reaction involving a specific substrate or set of substrates. Therefore, sucrase has only one role in the cell, and it is not capable of switching functions and breaking down the sugar lactose.

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Name some different conditions that affect enzymes and change their ability to catalyze reactions? How do these conditions affect enzymes?

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Changes in temperature and pH. If temperature is too high, the enzymes may begin to degrade. Changes in pH can affect the stability of chemical bonds and the integrity of active sites.

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What happens to an enzyme’s structure when it is denatured?

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When an enzyme denatures, the bonds stabilizing the three-dimensional structure of the protein start to degrade, which disrupts the conformation of its active site.

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hat purpose do coenzymes serve? Are they catalysts? How do they assist enzymes?

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Coenzymes are not themselves catalysts, but are required for normal catalytic functioning of the enzyme. If cells are deficient in certain coenzymes, their associated enzymes will not work properly. The vitamins and minerals that are essential in our diets are often coenzymes or they are the raw materials required to manufacture these important compounds.

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What are inhibitors? How can they regulate reactions?

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Inhibitors slow down or halt the activity of enzymes by attaching themselves to active sites and interfering with the binding of substrates.

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What is feedback inhibition and how does it regulate the rate and frequency of reactions?

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Feedback inhibition is a forms of metabolic regulation, in which a reaction's end-products inhibit the reaction itself by halting it when a certain amount of product has accumulated.

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What is allosteric regulation? What is an allosteric site and how is it different from the active site?

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Allosteric regulation is a form of enzymatic regulation in which an inhibitor binds to a site distant from the active site and causes a conformational change in the enzyme, thereby decreasing its ability to bind with the substrate and hence, catalyze the reaction. Allosteric enzymes are generally complex molecules, composed of at least two protein subunits; conformational changes occur when allosteric sites are filled, thereby changing the shape of the active site itself.

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How can allosteric regulation be either activating or inhibiting? What does it do in each case and how does it change the enzyme?

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Allosteric regulation can involve stimulation of enzyme activity and feedback inhibition. Certain allosteric sites bind activators, which leads to changes that stabilize an enzyme's active site, and thus, increase its affinity for substrate. On the other hand, an inhibitor can bind to an allosteric site and change the conformation of an enzyme so that its affinity for a substrate is reduced.

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What is the difference between competitive and noncompetitive inhibition?

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Noncompetitive inhibition is inhibition in which allosteric sites are used to change the conformation of the substrate to decrease the affinity of an enzyme for its substrate. Competitive inhibition simply inserts molecules into the active site of an enzyme, so that the substrate cannot attach.

Front 75

Name and describe the enzyme that is responsible for the first metabolic regulation in the process of glycolysis. Use the terms related to enzymes to describe how it catalyzes, controls, and regulates this reaction.

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Phosphofructokinase is a critical enzyme in the glycolytic pathway because it represents the first point of metabolic regulation. Phosphofructokinase removes a phosphate from ATP and transfers it to an intermediate product, fructose 6-phosphate, thereby transforming this compound into fructose 1, 6-bisphosphate. It has allosteric sites that bind inhibitors and activators, influencing the affinity of the active site for the substrate fructose 6-phosphate. Subsequent reactions, catalyzed by different enzymes, create a sequence of intermediates which eventually culminate in the production of pyruvate as the glycolytic end-product.

Front 76

Why is regulation of glycolysis important? How does the way it is activated and inactivated make it efficient but also quickly available for the organism?

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Glycolysis is the first component of cellular respiration; it produces raw materials for the Krebs cycle and ultimately, the electron transport chain, which operates to provide cells with the ATP they need for metabolic processes. ATP and the compounds required for its synthesis are of great importance, but cells would not be operating at peak efficiency if they produced pyruvate constantly. During times of low activity, energy requirements are less and therefore, there is no need to divert valuable organic molecules into either ATP or the intermediates of cellular respiration. In other words, when ATP levels are high, there is little need for pyruvate.

High levels of AMP indicate that ATP is in short supply and that it needs to be regenerated. By "turning on" glycolysis, the cell can increase the production of compounds that feed into the Krebs cycle and the electron transport chain; thus, elevating the rate of ATP synthesis.

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Why is the compartmentalization and concentration of enzymes in different part of the cell important for cell processes?

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The compartmentalization of enzymes increases the efficiency of reactions and prevents enzymes from getting lost in the shuffle of cellular metabolism. Similarly, many of the enzymes involved in cellular respiration are concentrated at specific sites within cells. For example, while glycolytic enzymes are found in the cytosol, the enzymes involved in the Krebs cycle are located within the mitochondrial matrix. Enzymes of the electron transport chain are actually imbedded within the inner membrane of mitochondria where they are clustered in functional groups, allowing reactions to take place in sequence. Compartmentalization and concentration of enzymes is important because they are “at hand” when specific reactions in the cell need to occur, and time is not lost in transport.

Front 78

Review the structure of mitochondria. What is unusual about mitochondria? How does mitochondrial structure allow the production of ATP?

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Mitochondria are enclosed in a double membrane; a smooth outer membrane and an inner membrane that is contorted into a complex of infoldings called cristae. Cristae provide extensive surface area for processes such as the electron transport chain, which takes place within the inner membrane. This membrane typically contains thousands of copies of electron transport chain proteins. The space within the cristae is the mitochondrial matrix. Recall, this is where the Krebs cycle occurs. Mitochondria contain their own DNA, separate from that in the cell’s nucleus.

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How is mitochondrial DNA inherited?

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Mitochondria and their genetic material are maternally inherited in sexually reproducing organisms (the sperm mitochondria rarely enter the egg during fertilization). Therefore, mitochondria are passed to offspring in the cytoplasm of ova. Hence, your mitochondria are virtually identical to your mother's.

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Review symbiosis. What different kinds of relationships are there? What is endosymbiosis?

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Symbiosis is a close association of two organisms, including mutualism, commensalism, and parasitism. Endosymbiosis is a type of symbiosis in which one organism lives within the body of another (this type of association is very common).

Front 81

Explain the endosymbiont theory. How is it believed mitochondria originated?

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It is thought that mitochondria evolved from prokaryotes that inhabited the cells of other larger prokaryotes. Put simply, it is thought that a relatively large prokaryote (i.e., a protoeukaryote) engulfed a smaller prokaryote (i.e., a protomitochondrion), and instead of the larger consuming the smaller, they formed a lasting relationship that survives today.

Front 82

How does the endosymbiont theory explain the structure of mitochondria? What exhanges between protoeukaryotes and protomitochondria were made to create a mutualistic relationship?

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This engulfment would account for the existence of the inner membrane of mitochondria (i.e., the ancestral prokaryotic membrane) and the outer membrane (i, the symbiosis was mutualistic because it benefited both the protoeukaryote and the protomitochondrion; the protomitochondrion was provided with a safe environment and plenty of raw materials for respiration, and the protoeukaryote was provided with a rich, free supply of fuel in the form of ATP and some safety from the oxidizing power of O2 (to be discussed in the next section).

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What evidence is there to support the endosymbiont theory? What characteristics of mitochondria are similar to those of prokaryotes?

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Evidence from similarities to extant prokaryotes: mitochondria closely resemble currently existing bacteria. Mitochondria are similar in size, and they replicate in a fashion that is very similar to binary fission. Also, the inner membrane of mitochondria bears a strong resemblance to the membranes of prokaryotes, sharing several key proteins and transport systems. Additionally, mitochondria have their own DNA (which is circular, like that of prokaryotes), and they possess all of the cellular machinery required to transcribe and translate their genomes, thereby enabling them to produce their own proteins.

Evidence from mitochondrial DNA: The character of mitochondrial DNA is much like that seen in modern-day prokaryotes. For example, it is not typically bound to proteins (e.g., histones are associated with eukaryotic nuclear DNA, but not with prokaryotic DNA). Additionally, mitochondrial ribosomes are more similar in behavior, structure, and nucleic acid base sequence to the ribosomes of prokaryotes than they are to eukaryotic ribosomes. For example, there is high sequence similarity between the ribosomal RNA of mitochondria and that of modern endosymbiotic bacteria.

Front 84

How did protomitochondria detoxify oxygen? Why is this important to modern eukaryotic cells?

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Electron transport chains, such as the ones that exist in modern-day mitochondria, might have evolved as mechanisms for counteracting the destructive effects of O2, secondarily becoming a means of energy production over evolutionary time. The additional benefit that eukaryotes enjoy today, ATP synthesis, might be a derived function.

Front 85

What effect did the production of oxygen by ancient cyanobacteria have on the earth’s atmosphere? Why might this have selected for bacteria in endosymbiosis with protomitochondrion?

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For millions of years, cyanobacterial photosynthesis (which produced oxygen as waste) did not change the Earth's atmosphere; oxygen released by photosynthesizing mats of marine cyanobacteria combined with iron ions in the ocean, forming iron oxide that precipitated to the sea floor. When these iron ions were depleted, oxygen began to accumulate in sea water and eventually it diffused into the atmosphere.

Oxygen is a powerful oxidizer, and its tendency to strip electrons and attack the bonds of organic molecules can be very dangerous to living organisms. The atmospheric changes effected by cyanobacteria probably resulted in numerous extinctions, but conversely, they also led to novel adaptations, such as endosymbiosis. Ancestors of eukaryotes might have gained an advantage in an oxygen-rich atmosphere by adopting endosymbionts to detoxify O2.