Cell Biology and Physiology CH 1-4

Which method is most suitable for determining the three-dimensional structure of an extremely large integral membrane protein complex?

cryoelectron microscopy Large proteins produce confounding signals on NMR spectra, and large integral membrane complexes are hard to crystallize for x-ray crystallography. Structural studies of large integral membrane protein complex could be performed with cryoelectron microscopy. In this method, the purified protein complex is embedded in ice and a beam of electrons is used to collect projected images in multiple orientations.

What is the pH of pure water? Complete the following rxn: CH3COOH + H20 <-> _________________ Will the rxn above occur more readily (driven to right) if the pH of the solution is high?

7. H3O+ + CH3COO- yes, it will go more to the right because you are trying to make it more acidic to counteract.

Given the periodic table below, how many electrons does an oxygen atom have?

8 The atomic number is the number of protons in the nucleus of an atom. For an atom to remain electrically neutral, the number of electrons is equal to the number of protons. Thus oxygen, with an atomic number of 8, has 8 electrons.

What purpose does NADPH serve in biosynthetic reactions like the one pictured below?

donating electrons for a reduction reaction NADPH is a carrier of electrons that are used in reduction reactions often used in biosynthesis of molecules. In the process, NADPH donates electrons, and itself becomes oxidized to NADP+.

Living systems can generate and maintain order without violating the second law of thermodynamics because they generate

heat Even though living systems produce ordered structures from smaller building blocks, this does not violate the second law of thermodynamics because they still create disorder by releasing energy in the form of heat. Heat is energy in its most disordered form.

Biochemical subcompartments that form inside the nucleus are distinct from their immediate surroundings because of the

high concentrations of interacting proteins and RNA. Biochemical subcompartments can form inside of organelles by the aggregation of interacting proteins, RNA, and protein complexes that perform a concerted function. These "intracellular condensates" are simply concentrations of molecules; they are not bound by a membrane, nor are they hydrophobic droplets.

A readily available source of energy that cells use to drive reactions is stored in the ___________ bond.

hydrogen Nucleotide triphosphates, notably ATP, have three phosphoanhydride which can be hydrolyzed easily to release energy.

Which of the following occurs by bringing nonpolar surfaces together to exclude water?

hydrophobic forces Surfaces with nonpolar bonds cannot favorably interact with water. These hydrophobic surfaces prefer to come together to exclude water. This is referred to as hydrophobic force.

f a reaction is energetically favorable (exergonic), then it must produce a(n)

increase in entropy. Reactions that are energetically favorable increase the entropy (or disorder) of the universe. This can be through either the release of free energy in different forms, or the release of energy as heat (energy in its most disordered form).

When a ligand binds to an allosteric enzyme's regulatory site, it changes the activity of that enzyme by

inducing a conformational change. Once a regulatory molecule or ligand binds to a regulatory site, an allosteric protein undergoes a conformational change that is transmitted to the active site. Inducing the conformational change can change the activity of the enzyme, but it does NOT directly block the active site.

Covalent bonds in macromolecules are primarily important for..

interactions with other macromolecules. Covalent bonds are strong and are used within molecules to form the linkages between monomers that form the polymer. Noncovalent bonds are more important for the three-dimensional conformation and for interactions with other molecules.

Enzymes increase the speed of a chemical reaction because they

lower the activation energy needed to start the reaction. Enzymes work by lowering the threshold energy input, called the activation energy, needed to start a reaction.

Strong and specific associations between macromolecules or between an enzyme and its substrate are due to...

many weak noncovalent bonds. Two macromolecules in a cell come together in a very specific way through many weak noncovalent associations between them. This allows more specificity, but also easier reversibility, as molecular interactions often must be relatively short lived in cells.

A binding site on the surface of a protein interacts specifically with another protein through

many weak noncovalent interactions. Covalent interactions are rarely used between protein molecules because they are difficult to break, often requiring an enzyme. Interactions between proteins and their partners need to be reversible but very specific. A specific interaction, but one that is able to be altered, can be achieved through formation of many weak noncovalent interactions between proteins and their binding partners.

Which of the following chemical groups could confer nonpolar/hydrophobic characteristics on the region of a molecule in which it is found?

methyl group (-CH3) Bonds between carbon and hydrogen are nonpolar and molecules with mostly nonpolar bonds are hydrophobic. Bonds between H and electronegative atoms like O and N are polar and tend to impart hydrophilic characteristics.

A base is a molecule that will ___________ a proton in water.

neutralize. Bases accept protons in water, removing a proton from a water molecule, forming OH?2_ ions. If the hydrogen atoms in water are more attracted to the electronegative atom of a base, they can be stripped off as a proton.

If the products of a reaction have more free energy than the reactants, then that reaction is

not energetically favorable. Reactions that have products with LESS free energy than the reactants will release free energy and create more disorder in the system. These will proceed spontaneously and are energetically favorable. However, when products of a reaction have MORE free energy than the reactants, there is no release of energy, and the reaction is not energetically favorable.

The _______ _______ is made up of two concentric membranes and is continuous with the membrane of the endoplasmic reticulum.

nuclear envelope

A nucleotide is different from a nucleoside because a nucleotide has a

phosphate group(s) A nucleotide is a sugar (either ribose or deoxyribose), attached to a nitrogen-containing base, and one or more phosphate groups. A nucleoside simply lacks any phosphate groups.

What is the name used for a molecule in which two carbons of glycerol are attached to fatty acid chains, and the third carbon is attached to a phosphate group?

phospholipid Glycerol molecules have three carbons attached to −OH groups that can be linked to fatty acids or other molecules. When two fatty acids and a phosphate are attached to glycerol, it is called a phospholipid. If three fatty acids are attached, it is called a triacylglycerol.

The function of feedback inhibition of an enzymatic pathway is to

turn off synthesis of a product when it is in abundance. Feedback inhibition keeps the cell from accumulating unnecessarily large amounts of biological compounds by reversibly inhibiting an enzyme in the biosynthetic pathway for that compound. These mechanisms shut down the enzymes early in the pathway so that wasteful intermediates do not accumulate.

Condensation reactions are energetically ___________ and hydrolysis reactions are energetically ___________.

unfavorable; favorable Condensation reactions reduce the disorder in the universe and are energetically unfavorable. Hydrolysis reactions increase the disorder in the universe and are energetically favorable.

The following image shows two triacylglycerol molecules with different fatty acid chains. If these fatty acids were in a phospholipid molecule, which of the two would form the most fluid membrane?

unsaturated Unsaturated fatty acids have double bonds in their hydrocarbon chains, and so have kinks in them; these keep them further apart. Thus, membranes made from unsaturated fatty acids are more fluid because they cannot pack as closely together as saturated fatty acids, which have no double bonds and are straighter.

What is the value of ΔG at equilibrium?

zero When equilibrium is reached, the forward and reverse reactions are equal, so there is no net change in the number of reactants and products. The reaction does not proceed forward or backward at this point and ΔG is equal to zero.

What is the relationship between ΔG and ΔG0?

ΔG0 is the free-energy change at standard temperature and concentrations. The value of the free-energy change of a reaction, ΔG, is dependent upon the concentration of reactants and products, as well as the temperature of the system. ΔG0 is the standard free-energy change at standard temperature and concentrations to allow comparison of different reactions.

Which of the following organelles has both and outer and an inner membrane? A. ER B. mitochondria C. lysosome D. Peroxisome

B

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material "burned" and the form of energy produced during cellular respiration? (a) fat, ADP (b) sugar, fat (c) sugar, ATP (d) fat, protein

C

A molecule with a lot of polar covalent bonds is likely to...

be highly soluble in water. Polar covalent bonds are formed when two atoms unequally share an electron, forming partial positive and partial negative charges at either end of the bond. Water also has partial positive and negative charges, and thus will easily interact with other molecules' partial charges, thus making it soluble.

Why is CO2 an end product of cellular respiration?

because it is the most stable form of carbon in our atmosphere Cellular respiration is the breakdown of carbon-containing molecules through oxidation to release energy. Because the most energetically stable form of carbon in the presence of oxygen is carbon dioxide, this is the final end product of respiration.

Why is sunlight the ultimate source of energy for nearly all living things on Earth?

because photosynthetic organisms produce food molecules using light energy Organic molecules for energy are obtained by animals through their diet, by consuming either plants or animals that eat plants. Plants produce organic molecules using energy from the sun, thus the source of energy from food molecules in plants is ultimately from the sun.

Hydrogen bonding between N-H and C=O groups of every fourth amino acid within a polypeptide chain results in which type of folding pattern?

α helix The hydrogen bonds that form a β-pleated sheet structure occur between the N-H and C=O groups of amino acids in different segments of a single polypeptide chain lying side by side. Amyloid structures are β sheets that interlock with each other through their side chains. The α helices are formed by hydrogen bonds between every fourth amino acid in the primary structure.

A folded protein structure with which free-energy (G) value would likely have the most stable conformation?

1 (or whatever the lowest value is) Free energy is designated by the letter G. If the free-energy value decreases during protein folding, the reaction is energetically favorable. Proteins generally fold along the most energetically favorable pathway, so the conformation with the lowest free-energy (G) value, 1, is the correct answer.

Glucose has a molecular weight of 180 grams per mole. To prepare 1 liter of a 100 mM solution, how many grams of glucose would you dissolve in water for a total volume of 1 liter?

18. Glucose has a molecular weight of 180 g/mole, which means that dissolving this mass of glucose in a liter would give a 1 M solution. Because 100 mM is 0.1 M, it is 1/10 of the concentration. Using 1/10 of the molecular weight (18 g) in the same volume would give a 1/10 concentration, thus a 0.1 M or 100 mM solution.

If 0.5 mole of glucose weighs 90 g, what is the molecular mass of glucose?

180 Daltons. 0.5 x 2 = 1 mole 90g x 2 = 180 Daltons

How many bonds are made by a carbon atom?

4. Carbon has four electrons in its outer shell and it needs eight to fill it. To fill its outer shell, carbon can share electrons with four different atoms, forming four bonds.

What is the concentration, in grams per liter (g/L) of a 0.25 M solution of glucose?

45 g/L 0.25mol/L x 180g/1 mol = 45 g/L

How many molecules are there in 1 mole of glucose?

6 x 10^23 Molecules

The figure below shows a depiction of an antibody. Which label correctly identifies the region(s) of the antibody that contains variable amino acids for binding of a specific antigen?

A Unique antigen-binding sites in antibodies are formed by varying the terminal amino acid sequences in the heavy chain and the light chain, which come together into a unique three-dimensional conformation for specific side-chain interactions with the antigen. Since each antibody is made up of two heavy chains and two light chains, there are two antigen-binding sites per antibody.

In the following condensation reaction, how does ATP power the formation of product A-B?

A phosphate is first transferred to reactant A−OH to form a high energy intermediate. ATP powers the formation of energetically unfavorable bonds between two molecules by first breaking its own high-energy phosphoanhydride bond and transferring the phosphate to another molecule. This new phosphate linkage can then be broken to power the bond formation between molecules.

Notes which cell type fits in the structure or molecule. DNA Nucleus Plasma Membrane Chloroplasts Cell Wall Lysosome Mitochondrion Golgi apparatus

Animal, plant, bacterial Animal, plant Animal, plant, bacterial Plant Plant, bacterial Animal, plant Animal, plant Animal, plant

If protein folding is determined by the sequence of amino acids in the polypeptide chain, why are chaperone proteins needed to assist folding in the cell?

Certain proteins easily aggregate with other proteins. All proteins can fold on their own without assistance due to the energetically favorable interactions between amino acid side chains and/or the polypeptide backbone. However, the cytoplasm is crowded and some proteins can form favorable interactions with other proteins before they have a chance to fold. These aggregates could impede proper folding.

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies? A. amenability to genetic manipulation B. ability to grow under controlled conditions C. rapid rate of reproduction D. all of the above

D

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar covalent bonds? A. Molecular oxygen B. Methane C. Propane D. Water

D

Which of the following is a role that sugars can play outside of their role in energy production and storage?

Formation of support structures Sugars play many roles outside of being an energy source that is stored and/or harvested for powering cellular processes. Sugars also form support structures like cell walls, exoskeletons, or adherent structures on the cell surface.

For the following uncatalyzed reaction at equilibrium, how would the reaction change if it was now an enzyme-catalyzed reaction at equilibrium?

Forward reaction A would increase. Enzymes lower the activation energy for reactions and thus increase the probability that the energy barrier can be surpassed for the reaction to proceed. They do not change the equilibrium point (the relative levels of reactants and product at equilibrium).

Which type of noncovalent interaction can involve either the polypeptide backbone or amino acid side chains?

Hydrogen Bonds The backbone of the polypeptide consists of uncharged polar covalent bonds. Because the bonds in the backbone are neither charger nor hydrophobic (i.e. nonpolar), hydrophobic forces and electrostatic interactions do not involve the backbone. Hydrogen bonds, however, are formed between atoms in the polar covalent bonds found in both amino acid side chains and in the carboxyl group and amino groups of the polypeptide backbone.

The pH of an aqueous solution is an indication of the concentration of available protons. However, you should not expect to find lone protons in solution; rather, the proton is added to a water molecule to form a _______ ion.

Hydronium

Which of the following has a higher concentration in the cell to allow it to be available to accept electrons from oxidation of food molecules?

NAD+ Cells maintain high concentrations of NAD+ so that it is readily available to accept electrons from the oxidation of food molecules in catabolic reactions.

Shown below is the ATP hydrolysis cycle of a motor protein. What sentence BEST describes the state of the motor protein in "C"?

The hydrolysis of ATP to ADP caused a conformational change in the protein. (A) is the state where no ATP or ADP is bound. The protein is bound to the filament with one of its two filament-binding domains, while the other binding domain is unbound. (B) shows that upon ATP binding, a conformational change moves the unbound domain forward one step to interact with the filament. In (C), ATP is hydrolyzed to ADP, creating a conformational change to release the rear filament-binding domain and bring it forward.

Why is the oxidation of NADPH energetically favorable?

The oxidized form of NAD NADPH carries two high-energy electrons. Losing these electrons in an oxidation reaction is energetically favorable because the oxidized form, NADP+, is more stable than the reduced form (NADPH).

Which of the following is a reason why ATP hydrolysis has a negative ΔG0?

The removal of the phosphate is energetically favorable. The products of the ATP hydrolysis reaction—ADP and free phosphate—are more stable and have a lower free energy. Release of free phosphate is energetically favorable because it relieves the repulsion of the negative charges of the neighboring phosphate groups and the aqueous environment to make hydrogen bonds with the phosphate.

What is the role of activated carriers in cells?

They capture energy from energy releasing reactions and transfer it to other reactions. Activated carriers collect electrons from oxidation of molecules in catabolic reactions and transfer them to anabolic reactions that require electrons for the reduction of molecules.

Which of the following is true about amyloid protein structures?

They consist of stacked β sheets. Amyloid protein structures are β sheets that interlock with each other through their side chains and form stacks. Since they are made from many β sheets, they form strong structures that have many roles in the cell, including formation of important cellular compartments. However, some amyloid structures, but not all, are abnormal and cause disease.

The technique that scientists used to determine that hemoglobin was a single large macromolecule rather than a loose conglomeration of small organic molecules was...

Ultracentrifugation Scientists at first did not believe that molecules could be as large as hemoglobin, and thought they were a lot of smaller molecules held together in close association. Separating molecules by size in ultracentrifugation allowed scientists to see if macromolecules were just one molecule of a large size, or many small molecules.

Which of the following is UNLIKELY to be hydrophilic?

a molecule with primarily nonpolar covalent bonds. Hydrophilic molecules carry positive or negative charges, allowing them to interact with the partial charges on water molecules. Polar covalent bonds form partial charges, whereas nonpolar covalent bonds do not.

By definition, prokaryotic cells do not possess...

a nucleus

What is a protein family?

a structurally related group of proteins A protein family is a set of proteins that have similar primary structures (amino acid sequences) and thus have related three-dimensional structures. If the structure of one member of a protein family is determined, it can be used to make predictions about the structure of other members of the protein family.

Amino acids with side chains that contain −COOH groups, like those shown below, would be ___________ in the aqueous environment of a cell.

acidic Amino acids like glutamic acid and aspartic acid have side chains that terminate in carboxylic acid groups (−COOH). This group loses a proton in water and is acidic in nature.

Which method is used for separating proteins based on specific interactions with other molecules?

affinity chromatography Affinity chromatography separates proteins from one another by using a known molecular interaction with the protein of interest. Gel electrophoresis and mass spectrometry separate protein fragments by size and charge. X-ray crystallography is a method for determining the three-dimensional structure of a protein; it is not used for separation.

How does binding of GTP to a GTP-binding protein affect its activity?

always activates the protein Proteins in the GTP-binding protein family are always in their active conformation when GTP is bound, in contrast to phosphorylation of a protein, which can activate or inactivate a protein. The hydrolysis of GTP to GDP returns the protein to the inactive state.

Reactions that build larger molecules in the cell are called ___________; reactions that break down molecules into smaller ones are called ___________.

anabolic; catabolic Metabolism is the sum total reactions in a cell, which are of two types. Catabolic reactions are the reactions where cells break down the large molecules in foodstuffs into their constituent building blocks. Anabolic reactions are biosynthetic—they build larger molecules from smaller building blocks.

All amino acids have which of the following chemical groups in common?

carboxyl group All amino acids have an amino group (NH2) and a carboxyl group (−COOH) attached to a central carbon. They differ in which side groups are attached to the central carbon, such as a methyl group or aromatic rings, for example.

Long polymers are made from single subunits in cells using a ___________ reaction, which ___________ water.

condensation; releases A condensation reaction joins two monomers together, releasing water. A hydrolysis reaction uses water to split the bond that joins two subunits of a polymer.

How does phosphorylation of a protein affect its activity?

could increase or decrease activity Phosphorylation of amino acid side chains in a protein changes their charge to a negative charge. It could lead to changes in conformation of the protein, differences in binding to partners, and either increased or decreased activity of an enzyme. Thus, the effects of protein phosphorylation are particular to the protein itself.

Disulfide bonds stabilize protein shape outside the cell by

covalent bonds between cysteines. Using mechanisms such as noncovalent bonds between charged side chains, proteins fold into their final conformation based on their amino acid sequence inside the cell. However, in the harsh environment outside the cell, this structure needs to be stabilized to keep its final form and function. Disulfide bonds are covalent cross-linkages between cysteine groups juxtaposed in the three-dimensional structure, and they act to hold the shape of the protein.

You wish to explore how mutations in specific genes affecting sugar metabolism might alter tooth development. Which organism is likely to provide the best model system for your studies, and why? (a) horses (b) mice (c) E. coli (d) Arabidopsis

B. able to grow under controls, rapid reproduction rate, has teeth, genome similar to humans

A stretch of amino acids in a polypeptide chain that is capable of independently folding into a defined structure is called a...

Domain A domain is a sequence of amino acids in a polypeptide chain that adopts a defined folding pattern based on the interactions of the side chains, as well as contributions from the polypeptide backbone molecules. This is distinct from a subunit, which is a term used for a single, complete polypeptide chain that can interact with other subunits to form a larger complex.

Which of the following is INCORRECT regarding how enzymes lower the activation energy of a reaction?

Enzymes reduce the free energy of the products of the reaction.

T or F With respect to cellular respiration, the only organelles used by animal cells are mitochondria, while plant cells use both mitochondria and chloroplasts.

F. Chloroplasts are only used for photosynthesis, not respiration

T or F Lysosomes are small organelles where fatty acid synthesis occurs.

F. Lysosomes breakdown 'waste' products as well as old organelles/cells

What is one of the main differences between DNA and RNA?

RNA has two hydroxyl groups on the sugar, DNA has one. RNA uses the sugar ribose, which has a 2′ and a 3′ −OH, whereas DNA uses the sugar deoxyribose, which only has a 2′ −OH. This leads to fundamental differences in the self-replication and stability of these molecules.

Two atoms held together solely by ionic bonds are referred to as a(n) element.

Salt. Atoms are the simplest form of an element that still retain the properties of that element. When multiple atoms come together, it is called a molecule, but when those bonds are solely ionic bonds, it is often called a salt.

Ionic bonds are ___________ than covalent bonds and are ___________ common in cells.

Stronger; less Ionic bonds are weak bonds commonly found in salts that form ions in aqueous solution. Because the cell environment is primarily aqueous, ionic bonds are dissociated by interaction with water.

T or F Membrane components in the cell are made in the ER

T

T or F The Golgi apparatus is made up of a series of membrane-enclosed compartments through which materials destine for secretion must pass.

T

For a reaction Y à X with a very high equilibrium constant, K, which of the following is true? You can refer to the following two equations in formulating your answer.ΔG = ΔG° + RT ln

The amount of product will be higher than the amount of substrate at equilibrium. If the equilibrium constant, K, is very high, it means that there is far more of the product X than substrate Y at equilibrium (i.e., when forward and reverse reaction rates are balanced). This corresponds to a free-energy change that is large and negative.

The chemical reactions that take place in a cell, as compared to the chemistry in nonliving matter, primarily occur Correct!

between carbon-based moleces. The chemistry of living things follows all the same chemical and physical laws of the chemistry that occurs in the nonliving world. The difference is that the chemical compounds of life are mostly carbon-based polymers that undergo complex reactions in an aqueous environment.

Which way do the fatty acid tails of a phospholipid face in a cell membrane?

both directions To form cell membranes, phospholipids form a bilayer, with the fatty acid tails facing each other. Thus, one layer has the fatty acid tails facing inward and the other layer has the fatty acid tails facing outward.

Which of the following shows protein organizational units in the correct order from smallest to largest?

domain < subunit < complex A domain is a portion of an amino acid sequence that folds into a three-dimensional structure and is the smallest of the organizational units. A subunit is a single, complete polypeptide chain and may be made up of one or more domains. Two or more subunits can assemble into a complex.

Cellular respiration ___________ energy and produces ___________, whereas photosynthesis ___________ energy and produces ___________.

produces; water + carbon dioxide; consumes; oxygen + sugars Cellular respiration is the process by which cells break down food molecules for energy, producing water and carbon dioxide as waste products. Photosynthesis uses energy from the sun to make food molecules (sugars) and oxygen.

Which of the following levels of protein structure involves the interaction of more than one polypeptide chain into a three-dimensional structure?

quaternary Primary structure is the linear order of amino acids in a polypeptide chain. The secondary structure is the formation of organized arrangements to form segments like α helices and β sheets. The tertiary structure is the overall three-dimensional shape of a protein. The quaternary structure is the assembly of multiple folded polypeptide chains into a larger complex.

In an enzymatic reaction, a molecule gains an electron. This is known as a(n) ___________ reaction.

reduction Gain of electrons by a molecule is called reduction; loss of electrons is called oxidation.

Chemical modifications like phosphorylation and acetylation of proteins occur on ___________ of amino acids and can affect interaction of proteins with other cell components or structures.

side chains The chemical modification of phosphorylation and acetylation occurs on the side chain of the amino acid and can affect how proteins interact with other proteins or components of the cell. This effect can occur through the direct alteration of binding sites if the phosphorylation and acetylation occur on an amino acid in a binding site, or through a conformational change that indirectly alters the binding site.

Which of the following is an inorganic compound?

table salt (NaCl) Organic compounds are made up of carbon atoms linked together, frequently along with other atoms and chemical groups. Inorganic compounds do not contain multiple linked carbon atoms.

The Michaelis constant (KM) of an enzyme is a measure of

the binding strength of enzyme to substrate. Enzyme activity is measured using two values. The first is the rate at which the enzyme converts the substrate to product, which is called Vmax. This value is determined by measuring the rate of product formation in conditions where all enzyme binding sites are occupied by substrate. The Michaelis constant measures the relative binding strength of the enzyme to substrate, determined by the concentration of substrate at which the enzyme operates at half of its Vmax.