Cell & Molecular Biology Test 1 Prade

4.3 What are the four weak non-covalent interactions that determine the conformation of a protein?

Ionic bonds

Hydrophobic interactions

Hydrogen bonds

Van Der Waals forces (dispersion attractions, dipole moments).

4.4 What are the major properties that distinguish different amino acids from one another? What roles do these differences play in the structure and function of protein?

Their R groups.

Some are basic, acidic, hydrophobic, hydrophilic, and polar.

These groups interact in many different ways with each other chemically and twist and fold the polypeptide structure into a mature protein. Form dictates function in proteins.

4.5 When proteins denature and renatured, some fully recover its original conformation and function, and others partially renature and remain functionally inactive. Why is this happening?

When a protein is denatured (by pH, temp) it loses its side chain conformation. When it is renatured, the protein will fold back to its original shape. If it renatures and is functionally inactive, it is because that protein uses a special group (heme, iron, copper, manganese) in its binding site which will not return when the protein is renatured.

4.6 What is a molecular chaperone? Why are they important in the crowded cytoplasm?

Proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.

Crowding can accelerate the folding process. Also can reduce the yield of correctly-folded protein by increasing protein aggregation. Crowding could increase the effectiveness of the chaperone protein.

4.7 Protein structure is dictated by the amino acid sequence. Should a protein, in which the order of all amino acids is reversed, (ABC->CBA) have the same structure as the original protein? Explain with supporting information.

Will not have the same structure.

Polarity of the molecule changes because the N and C terminus changes. So the protein will be read differently.

4.8 Explain how it is possible that living cells contain such an enormously diverse, but structurally stable, set of proteins? How is function and specificity determined in proteins?

There are an enormous amount of amino acids and combinations of them.

Function and specificity: structure. amino acid sequence.

4.9 Use a rough diagram to compare the structure of a protein a-helix and an anti-parallel B-sheet. For simplicity, show only the backbone atoms of the protein.

4.10 What common feature of alpha helices and beta sheets makes them universal building blocks for proteins?

The makeup of backbone structure makes it possible for the protein to fold and form hydrogen bonds with other parts of the backbone structure, causing it to form a-helixes and B-sheets. Since the backbone atoms are universal throughout proteins, this makes them always form these structures.

4.11 Why do you suppose that only L-amino acids and not a random mixture of L- and D- amino acids are used to make proteins?

L-amino acids are more stable.

D-amino acids are toxic because they have the H is in the wrong positions.

L and D have opposite stereochemistry.

4.12 Explain the coiled coil protein structure.

Repeated pattern of hydrophobic and charged amino acid residues.

4.13 What do we mean by primary, secondary, tertiary, and quaternary structure of proteins?

Primary: amino acid sequence of the polypeptide chain. Held together by covalent and peptide bonds.

•Secondary: highly regular local sub-structures. (alpha helix and beta strand). Patterns of hydrogen bonds between the main-chain peptide groups.

•Tertiary: 3-dimensional structure of a single protein molecule. the folding of the protein driven by the hydrophobic interactions.

•Quaternary: larger assembly of several protein molecules. Polypeptide chains.

4.14 The protein structure in the Figure below contains four a-helices arranged in a bundle. Label each helix by number (1 to 4) starting going from the N terminus to the C terminus.

4.1 Draw the general structure of an amino acid.

R

+NH3-C-COOH-

H

4.2 Draw the structure of a peptide bond

4.15 Why are the membrane-spanning regions of transmembrane proteins frequently alpha-helical?

Because the side chains have to interphase with the membrane so they have to be non-polar (hydrophobic).

4.16 Given that proteins act as molecular machines explain why conformation changes are so important in protein function.

If you change the conformation of a protein, the binding site geometry is changed and alters the specificity of the protein completely changing its function and binding ability.

4.17 Describe the structural and functional properties of a cellular enzyme.

Structural: globular proteins. activities are determined by 3D structures (tertiary structure).

Functional: catalyze chemical reactions. allow for faster reaction rates by lowering the required activation energy.

4.18 How does the structure of a protein determine how it will function?

The structure determines function.

Structure is determined by the shape of the protein, shape determined by primary structure, primary structure determined by amino acid sequence.

Depending on its structure, the protein can have many different bonds which control how the protein folds, which determines function of protein.

4.19 Provide a detailed and complete description of a typical protein-binding site interacting with its ligand (also substrate, antigen). Make sure you provide an explantion that accounts the physical and chemical elements involved in the interaction.

The binding site is caused by the folding of the side chains which react with the ligand. Hydrogen bonds and covalent bonds attach the protein to the ligand and substrate.

4.20 What defines binding and catalytic site?

The binding site is specific because of its unique shape that matches with the substrate to form hydrogen bonds, activating the enzyme. The catalytic site is where the work of the enzyme is done (i.e. cutting, combining, etc) and is non-specific.

4.21 How can enzyme activity be regulated?

Allosteric inhibition : when something (an ion, an organic chemical, etc.) bonds to a site on the enzyme (not on the active site), and changes the shape of the enzyme, thus changing the function.

Competitive Inhibition: when something (an ion, an organic chemical, etc.) enters the active site so that the true substrate cannot enter into the enzyme to have a reaction.

4.22 How does lysosome catalyze the hydrolysis of the glycosydic bond?

The enzyme functions by attacking peptidoglycans and hydrolyzing the glycosidic bond that connects N-acetylmuramic acid with the fourth carbon atom on N-acetylglucosamine. The lysozyme then distorts the fourth sugar in hexasaccharide (the D ring) into a half-chair conformation. In this stressed state, the glycosidic bond is easily broken.

4.23 Based on the energy requirement shown above, describe the course of an enzymatic reaction.

Enzymes lower the activation energy without changing the course, reactants, products, or itself in the reaction.

11.1 What are the differences of micelles and lipid bilayers?

Micelles: single layer of phospholipids. solid sphere.

Lipid Bilayer: 2 layers. membrane

11.2 Describe the types of lipid movements that occur at lipid bilayers. Explain the type of movement that happens less often too.

The lipids in one layer very rarely flip to the other layer. They can flex or rotate their tails, or they can move laterally through the layer they are in.

11.3 What is the role of cholesterol in membrane bilayers?

Provides structure. Makes it rigid. Helps with strength.

11.5 How are proteins anchored or attached to membranes? Discuss at least three different modes.

1.Transmembrane:a protein that goes from one side of a membrane through to the other side of the membrane. function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as in the case of waste byproducts.

2.Membrane-Associated:

3.Lipid-linked: a covalently attached fatty acid serves to anchor them to either face of the cell membrane.

4.Protein-attached:

11.6 How different are membrane bilayer lipids? How are these components arranged?

Some are positioned differently. Some are outside the cell, some are facing inside cell.

11.7 What defines a transmembrane domain in proteins? How many amino acids and what type of amino acids are needed to form a transmembrane domain?

Transmembrane proteins go from one side of membrane to the other. At least 20 amino acids are needed.

Nonpolar side chains on AA.

11.8 How do detergents work? Why are they useful to study membrane-inserted proteins?

11.9 Describe the protein spectrin - focus on the domains and how they function in human blood cells.

12.1 Describe the types of molecules that diffuse through membranes without any specific aid. Thinking on the molecules Na+, O2, H2O, K+, and CO2 order them based on their ability to permeate the membrane - from very fast to very slow.

Fastest: O2 > CO2 > H2O > Na+ > K+ :Slowest

12.2 What are the differences between channel and carrier proteins?

Carrier proteins transport molecules by changing shape. First, a molecule on one side fits the binding site, and by changing their configuration, the carrier can push the molecule to the other side of the membrane.

Channel proteins usually transport ions or very small molecules down a concentration gradient, and are more like a hollow tube that can open or shut.

12.3 How does an electrochemical gradient interfere with the rate of passive transport?

Accumulation of a charge on either side of a cell will invert the field. This could increase or decrease the transport.

12.4 Provide functionally complete descriptions for three distinct modes of active transport.

Coupled Transport: linked transport of two substances across membrane. Sym and Anti.

•ATP-Driven Transport: Sodium-potassium pump. pumps sodium out, potassium in.

•Light-Driven Transport: light is used to excite protons making a gradient and providing energy for transport across membrane.

15.1 Why does the nucleus consist of an envelope instead of a membrane?

Because DNA is stored in the nucleus. It needs to be able to get out of the nucleus in the form of RNA to be used to make proteins in ribosomes.

15.2 Explain active transport of proteins entering through nuclear pores.

Nuclear pores are large protein complexes that cross the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus.

Allow the transport of water-soluble molecules across the nuclear envelope.

Small particles: can pass by passive diffusion.

Larger particles: efficient passage requires several protein factors.

3.1 In the stepwise conversion of methane to carbon dioxide via the formation of methanol, formaldehyde, and formic acid as intermediates, describe how oxidation and reduction involves a shift in the balance of electrons?

Addition of hydroxyls rearrange the electrons.

3.2 How does ATP couple reactions? What are the essential underlining chemical and physical principles that make coupled reactions work (favorable)?

The energy given off by ATP breaking down into ADP and inorganic P provides enough energy to be the activation energy for a reaction that doesn't have sufficient energy to go by itself. Such hydrolysis reactions often involve the transfer of the terminal phosphate in ATP to another molecule. This phosphorylation reaction powers the molecular motors that enable muscle cells to contract and nerve cells to transport materials from one end of their long axons to another.

3.3 Distinguish between catabolic and anabolic pathways of metabolism, and indicate in a general way, how such pathways are linked to one another in cells?

Catabolism: break down of large molecules to smaller ones, like glucose breaking down to pyruvate, which breaks down to CO2 and acetyl Co-A. Ultimately leading to energy in the form of ATP, which powers many of the cell's functions.

Anabolism: build up of larger molecules from smaller ones, like amino acids adding to another through peptide bonds to form a protein, which the cells use for structure and function.

3.4 Animals and plants use oxidation to extract energy from food molecules. Explain how.

The NADH and FADH2 made directly or indirectly from glucose (food) molecules are then oxidized to NAD+ and FAD++ as they pass their protons into the inner mitochondrial space of the mitochondria, where the protons are then used to power ATP pumps.

3.5 In the reaction 2 Na + Cl2 >2 Na+ 2Cl-, what is being oxidized and what is being reduced? How can you tell?

Oxidized: Na, because it ends with a loss of electrons, making it a positive ion.

Reduced: Cl because it ends with a gaining of electrons, making it a negative ion.

3.6 Discuss the statement. The criterion for whether a reaction proceeds spontaneously is Delta G and not Delta G prime, because Delta G takes into account the concentration of substrates and products.

ΔG measures the amount of disorder created int he universe when a reaction takes place that involves specific molecules. ΔGº is independent of concentration; it depends only on the intrinsic characters of the reacting molecules, based on their behavior under ideal conditions where the concentrations of all the reactants are set to the same fixed value of 1 mole/liter.

3.7 Many of the products in cells are produced by condensation reactions. Explain how these reactions work and how they are activated. As an example use the production of glycogen.

Condensation reactions occur when two molecules combine, releasing water. glycogen is formed by multiple glucose molecules combing as the OH of one glucose combines with the H of an OH on another glucose, realizing water and forming a bond between the two glucose molecules where the O is in the middle. Such reactions are activated by one glucose molecule receiving a phosphate group from an ATP and then releasing that phosphate group when combining with the other glucose.

13.8 Oxidation of glucose to CO2 and H2O in cells happens in a stepwise mode as compared with direct burning of sugar. Why do you think cells employ this stepwise oxidation approach?

Burning releases heat rather than a usable energy source like ATP, as it does in a stepwise mode.

13.9 Describe briefly the three stages of cellular metabolism that lead form food to waste products in animal cells.

Glycolysis: breaking down glucose to pyruvate, producing some ATP and NADH.

(then pyruvate to acetyl Co-A and CO2 (waste)).

Krebs Cycle: further break down of the acetyl Co-A into CO2 (waste) and producing NADH and FADH2 and ATP.

ETC: produces much ATP from NADH and FADH2, ADP and P, and much water from O2 and NADH and FADH2.

14.1 Describe the membrane structure and compartments of chloroplasts and mitochondria.

Chloroplasts: have thylakoids stacked on top of each other. These membranes transport electrons. The thylakoids have an inner thylakoid space where protons are put into by the oxidation of NADPH, which will drive the ATPase. Electrons on water molecules are excited by photons which split the water into O2 as a byproduct and more protons from the thylakoid space.

Mitochondria: also have intermembrane compartments that receive and pass electrons.

14.2 How does ATP couple reactions? What are the essential underlining chemical and physical principles that make coupled reactions work (favorable)?

By pulling electrons off of the phosphate group through favorable reactions, unfavorable reactions are coupled to it, lowering the DeltaG allowing the reaction to occur.

14.3 Why is ATP useful to cells?

It is used to drive unfavorable reactions in the cell, which the cell needs to produce the molecules essential for life.

14.4 Describe how the proton gradient drives ATP synthesis.

14.5 How can protons be pumped across membranes?

14.6 Describe the NADH dehydrogenase complex and its role in the respiratory chain.

14.7 Describe the differences between cytochrome b-c1 and cytochrome oxidase complex.

Both help pass protons through the membrane by passing electrons down the ETC. Cytochrome b-c1 passes the electrons to a cytochrome c molecule. Cytochrome oxidase complex passes electrons to Oxygen, which helps convert 1/2O2 and 2H's to water.

14.8 What are the roles of ubiquinone and cytochrome c.

Pass electrons from one complex (protein) to the next.

14.9 Why is the respiratory chain organized in the sequence NADH-dehydrogenase, cytochrome b-c1, and cytochrome oxidase?

Redox potential of active sites between each enzyme. Potential needs to go down stepwise.

14.10 Unlike mitochondria, chloroplasts do not have a transporter that allows them to export ATP to the cytosol. How then does the rest of the cell get the ATP it needs to survive?

14.11 Describe the Calvin cycle.

Light independent. Inside chloroplasts. Forms glucose from CO2, recycling ATP and NADPH.

Draw the picture: 3 CO2 going in, boxes forming a circle with one of them being rubisco, and then NADPH, ATP, and glucose being the product.

14.12 Why do plants have two photo systems (I & II)?

Electrons need to be going down the ETC constantly, and thus the membrane of the thylakoids need photons to continue the excitation of the electrons, even when there is no light available.

14.13 Why are plants green?

Green is reflected from the plant because of the chlorophyll pigment which absorb a majority of the photons for the excitation of the electrons in the ETC. Other colors are primarily absorbed by the plant cells. Green is detected by the cone cells in the eye.

2.1 If the isotope 32S has 16 protons and 16 neutrons, how many protons and how many neurons will the isotope 35S have?

2.2 A carbon atom contains six protons and six neutrons. What are its atomic number, atomic weight, and how many electrons does it have? How many additional electrons must it add to fill its outermost shell?

Atomic Number: 6

Atomic Weight: 12

Electrons: 6

Additional Electrons: 4

2.3 How is an ionic bond formed?

By the gain and loss of electrons between atoms.

2.4 What are the differences between a covalent and ionic bond?

Covalent Bonds- sharing of electrons between atoms (molecule)

Ionic Bonds- transfer of electrons between atoms (a positive ion and a negative ion)

2.5 Why are polar covalent bonds and the resulting permanent dipoles so important in biology?

Electrons shared by the atoms spend a greater amount of time closer to the electronegative atom than anything else in the molecule. The result of this pattern of unequal electron association is a charge separation in the molecule, where the electronegative atom will have a partial negative charge.

•Important: These dipoles and polar molecules will allow only certain bonding. Examples: water and hydrophobic molecules will not bond. This helps form the phospholipid bilayer membrane.

2.6 Describe a hydrogen bond.

Formed when a charged part of a molecule having polar covalent bonds forms an electrostatic interaction with a substance of opposite charge. Weak bonds because they are easily and rapidly formed and broken. Any compound that has polar covalent bonds can form hydrogen bonds.

-Importance: Water. Used to stabilize and determine the structure of large macromolecules like proteins and nucleic acids. Involved in enzyme catalysis.

2.7 Why are substances such as sugars soluble in water and others such as lipids not?

Hydrophilic: substances that dissolve readily in water (Sugars). Composed of ions or polar molecules that attract water molecules. Ionic substances dissolve because water is attracted to the positive or negative charge on the ion. Polar substances dissolve because they form hydrogen bonds with the water.

•Hydrophobic: contain a preponderance of non-polar bonds are insoluble in water (Lipids). Water is not attracted to such molecules.

2.8 What does the "p" in pH stand for?

p: potential

H: hydrogen.

Def: the acidity of a solution is defined by the concentration of H+ ions it possesses. pH scale: 7=pure water. <7 Acidic. >7 Alkaline.

2.9 Why does an acid donate protons when in water?

Def of Acid: substances that release hydrogen ions into solution. "Electron donating".

Water contains an electronegative atom (Oxygen). This atom is polar covalently bonded to two hydrogens, making it a partial negative charge. The Acid will donate a proton to the Oxygen on the water molecule.

2.10 What does a pH=7 of pure water mean?

It means that there is 10^-7 moles of protons in the water. The number of H+ ions are equal to the number of OH- ions. Therefore making pure water neutral at pH of 7.

2.11 If non-covalent interactions are so weak in a water environment, how can they possibly be important for holding molecules together in cells?

They enable one large molecule to bind specifically to another.

Critical in maintaining the structures of protein and nucleic acids.

Multiple non-covalent bonds determine how large molecules will fold or which regions of different molecules will bind together. Several different weak bonds can bind two protein chains together. Other arrangements on the two surfaces would not allow the molecules to bind so tightly.

2.12 Why are hydrogen bonds formed (describe physical forces and chemical properties) and why are they so important in cell function and structure? Give a detailed and complete description.

Formed: when a hydrogen atom interacts with an electronegative atom (N, O, F). It covalently bonds with the atom. Weaker than covalent and ionic bonds. Intermolecular hydrogen bonding is responsible for the high boiling point of water.

-Important: partly responsible for structures of proteins and nucleic acids. responsible for the specific folding and shape of proteins and nucleic bases, which determines molecule's physiological role.

2.13 How do glucose, mannose, and galactose differ from each other?

Differ only in spatial arrangement: ISOMERS. Differ in the arrangement of groups around one or two carbon atoms. These only have minor changes in the chemical properties but proteins and enzymes recognize these changes.

Similarities: All have 6 carbons. Same formula (C6H12O6)All monosaccharides (simple sugars).

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

(0.5 mol/90g) : (1 mol/x)

X=45

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

(0.25 moles/ liter) : (180 g/ 1 mole of glucose)

45 grams per liter.

2.16 How many molecules are there in 1 mole of glucose?

Total atoms in 1 molecule of glucose= 24.

Atoms in one mole= 6.02 x 1023

24 X 6.02x1023 = 1.5x1025

2.17 Describe the formation (condensation) and distruption (hydrolysis) of a glycosidic bond.

Def of Glycosidic Bond: type of covalent bond that bonds the sugar to a hydroxyl group another compound (such as an alcohol).

Formation (condensation): Removal of a molecule of water in the linkage between sugars. Usually formed between carbon-1 on one sugar and carbon-4 on another. α: below the plane. β: above the plane.

Disruption (hydrolysis): bond is broken down by splitting of water into hydrogen cations (H+) and hydroxide anions(OH-).

2.18 Describe different glycosidic bonds? Try to figure out all the different types of bonding patterns.

Alpha: position on sugar

Beta: position on sugar.

Which carbon is it on? 1, 2, 3, 4...?

2.19 Describe the differences between a linear molecule such as cellulose and a non-linear molecule such as starch.

Linear molecule (cellulose): No branching, fibers.

Non-linear (starch): Branching, globular shape.

They have different structures, which provide different functions.

2.20 What is the role of glycerol in triglycerides?

Fatty acids are stored as an energy reserve (fats and oils) through an ester linkage to glycerol.

2.21 What are saturated and unsaturated fatty acids?

Saturated: fatty acid with No double bonds.

Unsaturated: fatty acid with double bonds.

2.22 Describe the basic structure of fatty acids and a phospholipid.

Fatty Acid: Carboxyl group with long hydrocarbon tail. (double bonds: unsaturated).

•Phospholipid: two of the -OH groups in glycerol are linked to fatty acids, while the third -OH group is linked to phosphoric acid. the phosphate is further linked to one of a variety of small polar groups (alcohols).

2.23 Why do phospholipids spontaneously form lipid bilayers when dissolved in water?

A phospholipid molecule contains a hydrophilic head and two hydrophobic fatty acid tails. When dissolved in water, the hydrophobic tails arrange themselves in a self-sealing membrane (bilayer).

2.24 Describe a micelle.

An aggregate of molecules in a colloidal solution, such as those in detergents.

Forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single tail regions in the center.

2.25 Place each of the 20 amino acids into one of the following groups: acidic, basic, uncharged polar, and uncharged non-polar.

Acidic: Aspartic Acid, Glutamic Acid.

•Basic: Lysine, Arginine, Histidine.

•Uncharged Polar: Asparagine, Glutamine, Serine, Threonine, Tyrosine.

•Non-Polar: Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Glycine, Cysteine.

2.26 Describe a peptide bond.

An amide linkage that allows amino acids to join together.

2.27 Describe the basic building blocks of nucleotides. Which components remain constant and which are the ones that are variable?

A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups.

•Nitrogen-containing bases: variable.

•Five-carbon sugar: variable depending on RNA or DNA.

•RNA: Ribose sugar.

•DNA: Deoxyribose sugar.

•Phosphate group: constant.

2.28 The nucleotide ATP is a building block for the synthesis of DNA. What other function does ATP perform in cells? Why?

Chemical work: supplying the needed energy to synthesize types of macromolecules that the cells needs.

Transport work: moving substances across cell membrane.

Mechanical work: supplying energy needed for muscle contractions.

2.29 What are the chemical differences between DNA and RNA?

DNA: deoxyribose sugar. Thymine present. Contains a chemical code which must be transcribed.

RNA: ribose sugar. Uracil present.

2.30 Both DNA and RNA are synthesized by covalently linking a nucleotide triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together?