Review for Lecture 1 Chapter 1 Introduction to Cells • All living creatures are made of Cells. The simplest forms of life are solitary Cells that propagate by dividing in two.
• Higher organisms, such as ourselves, are like Cellular cities derived by growth and division from a single founder cell. • Cells can be very diverse: superficially, they come in various sizes, ranging from bacterial cells such as Lactobacill us, which is a few micrometers in length, to larger cells such as a frog’s egg, which has a diameter of about one millimeter. • Despite the diversity, cells resemble each other to an astonishing degree in their chemistry. For example, the same 20 Amino acids are used to make proteins. Similarly, the genetic information of all cells is stored in their DNA. Although Viruses contain the same types of molecules as cells, their inability to reproduce themselves by their own efforts means that they are not considered living matter. • Viruses contain the same types of molecules as cells so they are considered living matter. False (True or false) • A cell reproduced by duplicating its DNA and then dividing in two, passing a copy of the genetic instructions encoded in its DNA to each of its daughter cells. That is why daughter cells resemble the parent cell. However, the copying is not always perfect, and the instructions are occasionally corrupted corrupted by mutations that change the DNA. That is why daughter cells do not always match the parent cell exactly. • Mutations are always bad for the offspring False (True or false) • Evolution - the process by which living species become gradually modified and adapted to their environment in more and more sophisticated ways. Evolution offers a startling but compelling explanation explanation of why present-day cells are so similar in their fundamentals. A process that can be understood based on the principles of mutation and selection. • A cell’s genome - that is, the principles of mutation and selection – provides a genetic program that instructs the cell how to function, and, for plant and animal cells, how to grow into an organism with hundreds of different cell types. • Match the type of microscopy on the left with the corresponding description provided provided below. There is one best Fluorescence , D. phase-contrast, E. scanning match for each. A. confocal, B. transmission electron, C. Fluorescence, electron, F. bright-field D uses a light microscope with an optical component to take advantage of the different refractive indices of light passing through different regions of the cell. F employs employs a light microscope and requires that samples be fixed and stained in order to reveal cellular details. requires the use of two sets of filters. The first filter narrows the wavelength range that reaches the C requires specimen and the second blocks out all wavelengths that pass back up to the eyepiece except for those emitted by the dye in the sample. A scans the specimen with a focused laser beam to obtain a series of two-dimensional optical sections, which can be used to reconstruct an image of the specimen in three dimensions. The laser excites a fluorescent dye molecule, and the emitted light from each illuminated point is captured through a pinhole and recorded by a detector. B has the ability to resolve cellular components as small as 2 nm. E requires requires coating the sample with a thin layer of a heavy metal to produce three-dimensional three-dimensional images of the surface of a sample. • Eukaryotic cells are bigger and more elaborate than prokaryotic prokaryotic cells. By definition, all eukaryotic cells have a Nucleus, usually the most prominent organelle. organelle. Another organelle found in essentially all eukaryotic cells is the
mitochondrion, which generates the chemical energy for the cell. In contrast, the Chloroplast is is a type of organelle found only in the cells of plants and algae, and performs photosynthesis. If we were to strip away the plasma membrane from a eukaryotic cell and remove all of its membrane-enclosed organelles, we would be left with the Cytosol. which contains many long, fine filaments of protein that are responsible for cell shape and structure and thereby form the cell’s cytoskeleton.
• Use the list of structures below to label the schematic drawing of an animal cell
A. plasma membrane B. nuclear envelope C. cytosol D. Golgi apparatus E. endoplasmic reticulum F. mitochondrion mitochondri on G. transport vesicles
=3 =5 =1 =2 =4 =7 =6
• Circle the appropriate cell type in which the listed structure or molecule can be found. Note that the structure or molecule can be found in more than one type of cell
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1. Select the answer that best completes the following statement: Chemical reactions in living systems occur in an D ______ environ ment, within a narrow range of tem peratures. ______
(a) optimal (b) organic (c) extracellular (d) aqueous
2. A covalent bond between two atoms is formed as a result of the _______A_______. (a) sharing of electrons.
(b) loss of electrons from both atoms. (c) loss of a proton from one atom. (d) transfer of electrons from one atom to the other.
3. An ionic bond between two atoms is formed as a result of the ________D______. (a) sharing of electrons. (b) loss of electrons from both atoms. (c) loss of a proton from one atom. (d) transfer of electrons from one atom to the other.
4. Equal sharing of electrons yields a(n) nonpolar covalent bond. If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These polar covalent bonds should not be confused with the weaker hydrogen bonds that are critical for the threedimensional structure of biological molecules and for interactions between these molecules.
5. Although covalent bonds are 10–100 times stronger than noncovalent interactions, many biological processes depend upon the number and type of noncovalent interactions between molecules. Which of the noncovalent interactions below will contribute most to the strong and specific binding of two molecules, such as a pair of proteins? (a) electrostatic attractions
(b) hydrogen bonds (c) hydrophobic interactions (d) Van der Waals attractions
6. The amino acids glutamine and glutamic acid are shown below. They differ only in the structure of their side chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine. What types of interactions are these? (a) ionic bonds
(b) hydrogen bonds
(c) van der Waals interactions (d) covalent bonds
7. Proteins are polymers built from amino acids, which each have an amino group and a carboxyl group group attached to the central central carbon . There are twenty possible 20 that differ in structure and are generally referred to as “R.” In solutions of neutral pH, amino acids are zwitterionic , carrying both a positive and negative charge. When a protein is made, amino acids are linked together through peptide bonds, which are formed by condensation reactions between the carboxyl end of the last amino acid and the amino group end of the next amino acid to be added to the growing chain.
8. As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains. Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation. Form inside to out, trying to protect the hydrophobic side from water
9. A protein chain folds into its stable and unique three-dimensional structure, or conformation, by making many noncovalent bonds between different parts of the chain. Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules. From the list provided, choose the class(es) of amino acids that are most important for the interactions detailed below. A. forming ionic bonds with negatively charged DNA (basic) B. forming hydrogen bonds to aid solubility in water (uncharged polar) C. localizing an “integral membrane” protein that spans a lipid bilayer (nonpolar) D. tightly packing the hydrophobic interior core of a globular protein (nonpolar) Acidic, nonpolar, basic, uncharged polar
10. Fill in the blank spaces in the table below. The first row has been completed for you. Amino Acid Alanine Arginine Asparagine Aspartic Acid Cysteine Glutamic acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tyrosine Tryptophan Valine
3 letter Ala Arg Asn Asp Cys Glu Gln Gly His Ile Leu Lys Met Phe Pro Ser Thr Tyr Trp Val
1 Letter A R N D C E Q G H I L K M F P S T Y W V
Side-chain char. Nonpolar Basic Uncharged Polar Acidic Nonpolar Acidic Uncharged Polar Nonpolar Basic (+) charge Nonpolar Nonpolar Basic Nonpolar Nonpolar Nonpolar Uncharged Polar Uncharged Polar Uncharged Polar Nonpolar Nonpolar
11. Indicate whether the following statements are true or false or false.. If it’s false, explain why it is false. A. A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation. TRUE (need 4) B. A single polypeptide tends to adopt 3–4 different conformations, which all have equivalent free-energy values ( G). False (polypeptides has one form and one function usually, would need more kinds)
12. A newly synthesized protein generally folds up into a stable conformation. All the information required to determine a protein’s conform ation is contained contai ned in its amino ami no acid sequence. On being heated, a protein molecule will become denatured as a result of breakage of non-covalent bonds.
13. Explain 4 different protein structural levels and name the most important force(s) are involved in maintaining each structure. Primary, The amino acid sequence of a protein. secondary- local folding pattern of a polymeric molecule. In proteins, it refers to ! helices and " sheets. hydrogen, tertiary- Complete three-dimensional structure of a fully folded protein. van der waals, quaternary- formed by multiple, interacting polypeptide chains within a protein molecule. hydrophobic
14. What are the noncovalent bonds held proteins fold?
hydrogen bonding electrostatic attraction Van Der Waals interactions Hydrophobic Interactions
**. the sequences for three different tripeptides are written out below. indicate whether you expect to find them in the inner core or ion the surface of a cytosolic protein, and explain your answer. A. Serine-Threonine-Tyrosine: Surface because they are hydrophilic; water loving. B. Alanine-Glycine-Leucine: Inner core because they are hydrophobic water fearing. C. Proline-Serine-Alanine: Inner core because they are also hydrophobic
**the variations in the physical characteristics between different proteins are influence by the overall amino acid compositions, but even more important is the unique amino acid ________. A) number b) sequence
c) bond D) orientation
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Review 3 1. Match the general type of biochemical reaction catalyzed in the left column with the class of enzyme listed in the
column on the right. I removes a phosphate group from a molecule
A. ATPase
A hydrolyzes ATP
B. polymerase
F hydrolyzes bonds between nucleotides
C. ligase
D adds phosphate groups to molecules
D. kinase
G catalyzes reactions in which one molecule is
E. isomerase
oxidized and another is reduced
F. nuclease
H hydrolyzes peptide bonds
G. oxido-reductase
C joins two ends of DNA together
H. protease
B catalyzes the synthesis of polymers such as
I. phosphatase
RNA and DNA E rearranges bonds within a single molecule
2. Any substance that will bind to a protein is known as its ligand . Enzymes bind their substrate at the active site.
Enzymes catalyze a chemical reaction by lowering the activation energy. because they provide conditions favorable for the formation of a high-energy intermediate called the transition state. Once the reaction is completed, the enzyme releases the enzyme of the reaction. activation energy, inhibitors, products, active site, isomers, substrates, free energy, ligand, transition state, highenergy, low-energy
3. The active site of an enzyme usually occupies only a small fraction of the enzyme surface ( True or False) 4. Catalysis by some enzymes involves the formation of a covalent bond between an amino acid side chain and a substrate
molecule. (True or False) 5. Allosteric enzymes have two or more binding sites. ( True or False) 6. The specificity of an antibody molecule is contained exclusively in loops on the surface of the folded light-chain
domain. (True or False) Variable portions of heavy and light chain 7. Affinity chromatography separates molecules according to their intrinsic charge. (True or False)
8. Feedback inhibition
1). The final product, R, will most likely inhibit which reaction? a. 1 b. 2 c. 3 d. 4 e. 5
2). Which two enzymes would be the most likely ones to regulate if this pathway is freely reversible and can go both ways? a. 1 and 2 b. 1 and 3 c. 1 and 5 d. 2 and 4 e. 4 and 5
9. Fill in the blanks with the labels in the list below to identify various parts of the antibody structure in Figure.
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10. The human immune system produces billions of different immunoglobulins, also called antibodies, which enable the immune system to recognize and fight germs by specifically binding one or a few related antigens. The hypervariable structural element that forms the ligand-binding site is comprised of several loops. Purified antibodies are useful for a variety of experimental purposes, including protein purification using Affinity chromatography. Affinity, billions, ligands, Antibodies, coiled-coils, loops, Antigens, hundreds, size-exclusion, ! strands, ionexchange,
11. Regulation of protein function •
Amount of protein
•
Location of protein
•
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o
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o
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o
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o
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o
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Review 5 1. The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of 4 different nucleotides, which gets transcribed into RNA, which is then translated into proteins, made up of 20 different amino acids. In eukaryotic cells, DNA gets made into RNA in the nucleus, while proteins are produced from RNA in the cytoplasm. The segment of DNA called a Gene is the portion that is copied into RNA; this process is catalyzed by RNA polymerase. Gene, 4, proteasome, exported, nucleus, 20, Golgi, replisome, polymerase , transferase, 109, kinase, sugar-phosphate, translated, 128, nuclear pore, transcribed, cytoplasm
2. use the numbers in the choices below to indicate where in the schematic diagram of a eukaryotic cell those processes take place.
1. transcription nucleus cytoplasm 2. translation 3. RNA splicing nucleus 4. polyadenylation nucleus nucleus 5. RNA capping
3. Which of the following are required for the DNA-dependent RNA polymerase reaction to produce a unique RNA transcript? a) ATP b) CTP c) GTP d)dTTP e) UTP f) DNA g)RNA h) Promoter sequence I)operator sequence J) terminator sequence 4. Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of 3-D shapes. This is largely because (a) RNA contains uracil and uses ribose as the sugar. (b) RNA bases cannot form hydrogen bonds with each other. (c)RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. (d) RNA is single-stranded.
5. For a cell’s genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called transcription. Various kinds of RNA are produced, each with different functions. mRNA molecules code for proteins, tRNA molecules act as adaptors for protein synthesis, rRNA molecules are integral components of the ribosome, miRNA molecules regulate gene expression, and other noncoding RNAs molecules are important in the splicing of RNA transcripts, gene regulation, telomere maintenance, and many other processes. (pg. 228) 6. Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5 -AGTCTAGGCACTGA-3 3 -TCAGATCCGTGACT-5 A. If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template? bottom B. What will be the sequence of that RNA (be sure to label the 5 and 3 ends of your RNA molecule)? AGUCUAGGCACUGA ! !
!
!
!
!
7. List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription. 1) Multiple types of RNA polymerases in eukaryotes, 2) eukaryotes deal with nucleosomes, 3) bacteria can initiate transcription on its own. 8.Name three covalent modifications that can be made to an RNA molecule in eukaryotic cells before the RNA molecule becomes a mature mRNA. 1) 5' cap added: G-P-P-P 2) Polly A tail added A-A-A-A-A-A-A 3) exon junction complex 9.Match the following types of RNA with the main polymerase that transcribes them. Types of RNAs Polymerases A most rRNA genes 1 RNA polymerase I B tRNA genes 2 RNA polymerase II C 5s rRNA genes 3 RNA polymerase III D protein-coding genes E miRNA genes
8. In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor TFIID to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the TATA box, which is typically located 25 nucleotides upstream from the transcription start site. Once RNA polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor TFIIH. 9. The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides, whereas the length of the mRNA produced from this gene is 4000 nucleotides. What is the most likely reason for this difference? The introns got sliced out
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Review 9 for Chapter 11 Membrane Structure 1. Lipids are compounds that are insoluble in water and but soluble in nonpolar organic solvents. 2. Classified according to their chemical nature, lipids fall into two main groups. One group, which consists of open-chain compounds with polar head groups and long nonpolar tails, includes fatty acids, phospholids. The second major group consists of fused ring compounds, the steroids; an important representative of this group is cholesterol. 3. Lipid molecules in biological membranes are arranged as a continuous double layer called the Lipid Bilayer , which is about 5 nm thick. 4. All the lipids found in membranes are said to be amphipathic because they have one hydrophilic end and one hydrophobic end. 5. When amphipathic molecules are placed in an aqueous environment, they tend to aggregate so as to bury their hydrophobic ends and expose their hydrophilic ends to water, giving rise to two different kinds of structures, either spherical micelles or planar bilayers with the hydrophobic tails sandwiched between the hydrophilic head groups. 6. Cell membranes consist mainly of Lipids and Proteins, also contain carbohydrates that are linked to lipids and proteins. 7. Unsaturated fatty acids usually have several double bonds. 8. Eukaryotic plasma membranes contain especially large amounts of Cholesterol, which enhances the mechanical stability of the lipid bilayer. 9. The most useful agents for disrupting hydrophobic associations and destroying the bilayer are Detergents, which are small amphipathic molecules that tend to form micelles in water. 10. Sugar containing lipids called glycolipid are found only in the outer half of the bilayer and their sugar groups are exposed at the cell surface.
11. The association of membrane proteins with lipids in the membrane bilayer always involves (a) electrostatic interactions (b) hydrophobic interactions (c) covalent linkages (d) all of the above 12. Biosynthetic enzymes bound to the cytosolic monolayer of the ER membrane produce new phospholipids from free fatty acids and insert them into the cytosolic monlayer. Enzymes called scramblases then randomly transfer phospholipid molecules from one monolayer to the other, allowing the membrane to grow as a bilayer. When membranes leave the ER and are incorporated in the Golgi, they encounter enzymes called flippases , which selectively remove phosphatidylserine and phosphatidylethanolamine from the noncytosolic monolayer and flip them to the cytosolic side. This transfer leaves phosphatidylcholine and sphingomyelin concentrated in the noncytosolic monolayer. 13. We can estimate the relative mobility of a population of molecules along the surface of a living cell by fluorescently labeling the molecules of interest, bleaching the label in one small area, and then measuring the speed of signal recovery as molecules migrate back into the bleached area. What is this method called? What does the abbreviation stand for? (a)SDS (b) SPT (c)GFP (d)FRAP 14. Cell membranes are fluid, and thus proteins can diffuse laterally within the lipid bilayer. However, sometimes the cell needs to localize proteins to a particular membrane domain. Name three mechanisms that a cell can use to restrict a protein to a particular place in the cell membrane. Proteins can be tethered to the cell cortex inside the cell, to extracellular matrix molecules outside the cell, or to proteins on the surface of another cell. Diffusion barriers can restrict proteins to a particular membrane domain. 15. There are several ways that membrane proteins can associate with the cell membrane. Membrane proteins that extend through the lipid bilayer are called Integral/ transmembrane proteins and have hydrophobic, regions that are exposed to the interior of the bilayer. On the other hand, membrane-associated proteins do not span the bilayer and instead associate with the membrane through an ! helix that is amphipathic. Other proteins are covalently attached to lipid molecules that are inserted in the membrane. peripheral Membrane proteins are linked to the membrane through non-covalent interactions with other membrane-bound proteins.
16. Please understand Common Features of Biological Membranes. http://www.ks.uiuc.edu/Services/Class/BIOPHYS490M/02-biological-membranes.pdf 17. Plant membranes have a higher percentage of unsaturated fatty acids than animal membranes. Animal membranes are (less or more) fluid than plant membranes. 18. Membrane Fluidity is controlled by fatty acid composition and cholesterol content. The membranes of prokaryotes, which contain no appreciable amounts of steroids are the most fluid. (True or false) 19. Glycolipids on the surface of cells are especially important as cell markers. (True or false) 20. Membranes are transported by the process of vesicle budding and fusing. Here, a vesicle is shown budding from the Golgi apparatus and fusing with the plasma membrane. Note that the orientations of both the membrane lipids and proteins are preserved during the process: the original cytosolic surface of the lipid bilayer (green) remains facing the cytosol, and the non-cytosolic surface (red) continues to face away from the cytosol, toward the lumen of the Golgi or transport vesicle—or toward the extracellular compartment. Similarly, the glycoprotein shown here remains in the same orientation, with its attached sugar facing the non-cytosolic side.
Review for Membrane Transport I & II 1. Cells use membranes to help maintain set ranges of ion concentrations inside & outside the cell. Which of the following ions is the most abundant inside a typical mammalian cell? (a) Na+
(b) K+
(c) Ca2+
(d) Cl–
2. Specific proteins called Membrane Transport proteins must be present in order for cell membranes to be permeable to small polar molecules such as ions, sugars, & amino acids. 3. There are two classes of membrane transport proteins: Transporter proteins, which bind specific solutes & change conformation to transfer the solute across the membrane; & Channel proteins which form water-filled pores that allow specific solutes to cross the membrane down their electro-chemical gradients. 4. Two general transport processes control the entry of solutes into cells: passive transport requires no energy input by the cell, whereas Active transport pumps specific solutes across a membrane against an electrochemical gradient. 5. A molecule moves down its concentration gradient by passive transport, but requires active transport to move up its concentration gradient. Transporter proteins & ion cha nnels function in membrane transport by providing a hydrophilic pathway through the membrane for specific polar solutes or inorganic ions. Transporters are highly selective in the solutes they transport, binding the solute at a specific site & changing conformation so as to transport the solute across the membrane. On the other hand, Ion channels discriminate between solutes mainly on the basis of size & electrical charge. 6. designate whether the transporter works by uniport, symport, or antiport mechanisms. Transporter Type of Transport Energy Source Function + Na K Antiport ATP Keeps high concentration of Na+ outside the (ATP-driven) cell. Maintain gradient across membrane + + Na Glucose Symport Na Import of glucose across plasma membrane (coupled pump) + + Ca pump uniport ATP Keep cytosolic Ca low inside the cell (ATP-driven) bacteriorhodopsin (Light driven pump) Light energy Generate cellular energy independently of chlorophyll 7. For an uncharged molecule, the direction of passive transport across a membrane is determined solely by its concentration gradient. On the other hand, for a charged molecule, the membrane potential must also be
considered. The net driving force for a charged molecule across a membrane therefore has two components & is referred to as the Electrochemical gradient. Active transport allows the movement of solutes against this gradient. The transporter proteins called coupled transporters use the movement of one solute down its gradient to provide the energy to drive the uphill transport of a second solute. When this transporter moves both ions in the same direction across the membrane, it is c onsidered a(n) Symport ; if the ions move in opposite directions, the transporter is considered a(n) Antiport.
8. channel proteins form hydrophilic pores across membranes; almost all such proteins in eukaryotic plasma membranes are concerned with inorganic ion transport & are therefore referred to as Ionic channels. 9. Three kinds of perturbation that can cause gated ion channels to open or close are voltage-gated channel , ligand-gated channel , & mechanically-gated channel .
10. The uneven distribution of ions on either side of the plasma membrane gives rise to a voltage across the membrane known as the Resting membrane potential . This voltage depends crucially on the existence of k+ selective leak channels, which make most animal cells much more permeable to K+ than to Na+.
11. The action potential is a wave of Depolarization that spreads rapidly along the neuronal plasma membrane. This wave is triggered by a local change in the membrane potential to a value that is Less negative than the resting membrane potential. The action potential is propagated by the opening of Voltage -gated channels. During an action potential, the membrane potential changes from Negative to positive. The action potential travels along the neuron’s axon to the nerve terminals. Neurons chiefly receive signals at their highly branched Dendrites.
12. Neurons communicate with each other through specialized sites called Synapses. Many neurotransmitter receptors are ligand-gated ion channels that open transiently in the postsynaptic cell membrane in response to neurotransmitters released by the presynaptic cell. Ligand-gated ion channels in nerve cell membranes convert chemical signals into electrical ones. Neurotransmitter release is stimulated by the opening of voltage-gated Ca2+ channels in the nerve-terminal membrane.
13. In nerve & skeletal muscle cells a depolarizing stimulus causes voltage-gated Na + channels to open, allowing a small amount of Na+ to enter the cell down its electrochemical gradient. 14. In many nerve cells Voltage-gated K+ channels help bring the activated plasma membrane back to its original negative potential by allowing an efflux of K+. 15. Which statements does not accurately describe the events involved in the propagation of an action potential? (a) An initial influx of Na+ through a small cluster of channels causes local depolarization of the membrane. +
(b) Local depolarization causes nearby Na channels to open. (c) Channels in depolarized regions of the membrane are inactivated until the resting membrane potential is reestablished. +
(d) The opening of transmitter-gated K channels helps to repolarize the membrane.
16. Figure illustrates changes in membrane potential during the formation of an action potential. What membrane characteristic or measurement used to study action potentials is indicated by the arrow?
Action Potential Membrane potential
Threshold potential Depolarizing stimulus
Resting membrane potential
17. Indicate whether the statements below are true or false. If a statement is false, explain why it is false. (A.) Neurotransmitters are small molecules released into the synaptic cleft after the fusion of synaptic vesicles with the presynaptic membrane.(True) (B.) Action potentials are usually mediated by voltage-gated Ca2+ channels.(False action potentials are usually mediated by voltage-gated Na+ channels)
(C.) Voltage-gated Na+ channels become automatically inactivated shortly after opening, which ensures that the action potential cannot move backward along the axon.(True) (D.) Voltage-gated K+ channels also open immediately in response to local depolarization, reducing the magnitude of the action potential. (False) they do not open immediately
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Review for Energy 1. Living organism are able to exist because of a continual input of energy. Part of this energy is used to carry out essential reactions that support cell metabolism, growth movement, and reproduction; the remainder is lost in the form of heat. 2. The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of chemical bonds. 3. During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration? (a)CO2, H2O (b)CH3, H2O (c) CH2OH, O2 (d) CO2, O2 Free Energy of a System !G < 0 spontaneous exergonic-energy released !G= 0 Equilibrium !G > 0 Nonspontaneous endergonic-energy required 4. According to thermodynamics, favored processes are a. ones that require energy. b. ones that release energy. 5. A spontaneous reaction is a. exergonic. b. endergonic. c. at equilibrium. d. none of the above. 6. The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO 2 and H2O in a single step is that ________________. (a) more free energy is released for a given amount of glucose oxidized. (b) no energy is lost as heat. (c) energy can be extracted in usable amounts. (d) more CO2 is produced for a given amount of glucose oxidized.
Coupling of Production and Use of Energy The coupling of energy-producing and energy-requiring reactions is a central theme in the metabolism of all organisms Energy cannot be used directly, must by shuttled into easily accessible forms of chemical energy “High Energy” bonds: bonds that require or release convenient amounts of energy, depending on the direction of the reaction ATP is essential high energy bond-containing compound Phosphorylation of ADP to ATP requires energy Hydrolysis of ATP to ADP releases energy •
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7. Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells use potential kinetic energy to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in ______ reactions. (a) oxidation (b) hydrolysis (c) condensation (d) reduction 8. The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of _______________ in a process called _____________. (b) water, hydrolysis. (a) ATP, phosphorylation. (c) hydroxide, hydration. (d) acetate, acetylation. 9. The energy released during metabolism of nutrients can be used to synthesize ATP from ADP and phosphate. a. True / False
Metabolism: the chemical reactions of biomolecules. It is the biochemical basis of life processes • catabolism: the breakdown of larger molecules into smaller ones; an oxidative process that releases energy • anabolism: the synthesis of larger molecules from smaller ones; a reductive process that requires energy •
10. In general, catabolism is? a. is an oxidative process that releases energy b. is a reductive process that releases energy c. is an oxidative process that requires energy d. is a reductive process that requires energy e. none of these 11. During reduction a. electrons are lost. b. electrons are gained. c. electrons may either be lost or gained. d. hydrogen is formed. 12. Figure represents a cell lining the gut. Draw numbered, labeled lines to indicate exactly where inside a cell the following processes take place.
1. glycolysis 2. citric acid cycle 3. conversion of pyruvate to activated acetyl groups 4. oxidation of fatty acids to acetyl CoA 5. glycogen breakdown- not mitochondria 6. release of fatty acids from triacylglycerols 7. oxidative phosphorylation
13. Select the best option to fill in the blanks of the following statement: Fermentation is a/an _____________ process that converts__________ into carbon dioxide and _____________________. (a) anaerobic, pyruvate, ethanol (b) anaerobic, lactate, ethanol (c) eukaryotic, glyceraldehyde 3-phosphate, ethanol (d) prokaryotic, lactate, propanol 14. It can be useful to analyze the steps of glycolysis with respect to the four basic types of enzymes required by this central catabolic pathway and to consider whether each enzyme produces or harvests the energy of an activated carrier. For each step of glycolysis (see Figure 13–5 or Panel 13-1), indicate which type of enzyme. Also, indicate whether an activated energy carrier is involved, and, if so, how. Step 1 ___________ Step 2 ___________ Step 3 ___________ Step 4 ___________ Step 5 ___________ Step 6 ___________ Step 7 ___________ Step 8 ___________ Step 9 ___________ Step 10 ___________ 15. The citric acid cycle is outlined in Figure. Some of these reactions produce small molecules that are used in the electron-transport chain or as energy for other reactions. Select from the list below to fill in the empty boxes. Keep in mind that some choices may be used more than once and others not used at all.
GTP! D NADH!B, C, G FADH2! E ONE TURN OF THE CYCLE PRODUCES THREE NADH, ONE GTP, AND ONE FADH2, AND RELEASES TWO MOLECULES OF CO2
Review for Intracellular transport II (April 07) Entry into the ER lumen or membrane is usually only the first step on a pathway to another destination. That destination, initially at least, is generally the Golgi apparatus; there, proteins and lipids are modified and sorted for shipment to other sites. Transport from the ER to the Golgi apparatus - and from the Golgi apparatus to other compartments of the endomembrane system - is carried out by the continual budding and fusion of transport vesicles. This process is called vesicular transport. A major outward secretory pathway starts with the synthesis of proteins on the ER membrane and their entry into into the ER, and it leads through the Golgi apparatus to the cell surface. •
A major inward endocytic pathway, which is responsible for the ingestion and degradation of extracellular molecules, moves materials from the plasma membrane, through endosomes, to lysosomes. •
Vesicles that bud from membranes usually have a distinctive protein coat on their cytosolic surface and are therefore called coated vesicles. The coat serves two functions 1. helps shape the membrane into a bud 2. captures molecules for onward transport. •
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The clathrin – coated vesicles bud from both the Golgi apparatus on the outward secretory pathway and from the plasma membrane on the inward endocytic pathway. At the plasma membrane, the cargo receptors, with their bound cargo molecules, are captured by adaptins, which also bind clathrin molecules to the cytosolic surface of the budding vesicles. •
A small GTP-binding protein called dynamin assembles as a ring around the neck of each deeply invaginated coated pit, pinch off the vesicle. After the budding is complete, the coat proteins are removed, and the naked vesicle can fuse with its target membrane. •
How does a transport vesicle select its particular cargo? This is the function of a second class of coat proteins called adaptins: Secure the clathrin coat to the vesicle membrane and elp select cargo molecules for transport •
After a transport vesicle buds from a membrane, coated vesicle rapidly lose its protein coat and then it must find its way to its correct destination to deliver its contents. HOW? Docking and fusion are mediated by proteins on the surface of the vesicle and target membrane, •
Name two types of protein modification that can occur in the ER but not in the cytosol. Glycolysation & disulfide bond formation •
For each of the following sentences, choose one of the two options to make a correct statement. New plasma membrane reaches the plasma membrane by the [regulated/ constitutive] exocytosis pathway. Insulin is secreted from pancreatic cells by the [regulated/constitutive] exocytosis pathway. The interior of the trans Golgi network is [acidic/alkaline]. Proteins that are constitutively secreted [aggregate/ do not aggregate] in the trans Golgi network. •
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Eukaryotic cells are continually taking up materials from the extracellular space by the process of endocytosis. One type of endocytosis is pinocytosis, which uses clathrin proteins to form small vesicles containing fluids and molecules. After these vesicles have pinched off from the plasma membrane, they will fuse with the endosomes, where materials that are taken into the vesicle are sorted. A second type of endocytosis is phagocytosis, which is used to take up large vesicles that can contain microorganisms and cellular debris. •
Name three possible fates for an endocytosed molecule that has reached the endosome. Recycling, Degradation, Transcytosis •
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Review for Mitochondria and Chloroplasts 1. In which of the compartments of a mitochondrion are each of the following located? A. porin: outer membrane matrix B. the mitochondrial genome: matrix C. citric acid cycle enzymes: D. proteins of the electron-transport chain: inner membrane inner membrane E. ATP synthase: F. membrane transport protein for pyruvate: inner membrane 2. fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Mitochondria can use both pyruvate and glucose directly as fuel. NADH produced in the citric acid cycle donates electrons to the electron-transport chain. The citric acid cycle oxidizes acetyl groups and produces carbon dioxide as a waste product. Oxygen acts as the final electron acceptor in the electron-transport chain. The synthesis of ATP in mitochondria is also known as chemiosmosis. (acetyl groups, NADH, NAD+, NADP+, carbon dioxide, pyruvate, chemiosmosis, NADPH, Glucose, oxygen) 3. Which of the following terms describes ATP synthesis in mitochondria? a. substrate-level phosphorylation b. oxidative phosphorylation c. photophosphorylation 4. The pH in the mitochondrial matrix is higher than the pH in the intermembrane space. True or False 5. Which of the components of the electron-transport chain is required to combine the pair of electrons with molecular oxygen? Cytochrome C oxidase 6. In chloroplasts, a. the light reactions take place in the thylakoid disks, whereas the dark reactions occur in the stroma b. the dark reactions take place in the thylakoid disks, whereas the light reactions occur in the stroma c. the light reactions take place in the thylakoid space, whereas the dark reactions occur in the stroma d. the dark reactions take place in the thylakoid space, whereas the light reactions occur in the stroma
7. Stage 1 of oxidative phosphorylation requires the movement of electrons along the electron-transport chain coupled to the pumping of protons into the intermembrane space. What’s the final result of these electron transfers? (a)OH is oxidized to O2 (b)pyruvate is oxidized to CO2 (c) O2 is reduced to H2O (d)H is converted to H2 8. Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electrontransport chain. Where are the proteins of the electron-transport chain located in chloroplasts? (a) thylakoid space (b) stroma (c) inner membrane (d) thylakoid membrane 9.The process of ATP synthesis in chloroplasts is referred to as a. oxidative phosphorylation. b. photophosphorylation c. reductive phosphorylation d. substrate-level phosphorylation. 10. During cyclic electron transport a. only Photosystem II is involved. b. only Photosystem I is involved. c. both photosystems are involved. d. neither photosystem is involved. In the carbon fixation process in chloroplasts, carbon dioxide is initially added to the sugar ribulose 1,5-bisphosphate. The final product of carbon fixation in chloroplasts is the three-carbon compound glyceraldehyde 3-phosphate. This is converted into pyruvate (which can be used directly by the mitochondria), into sucrose (which is exported to other cells), and into starch (which is stored in the stroma). The carbonfixation cycle requires energy in the form of ATP and reducing power in the form of NADPH. •
1. Plant, algae, and photosynthetic bacteria such as cyanobacteria use electrons from water and the energy of sunlight to convert atmospheric CO2 into organic compounds. In the course of these reactions, water molecules are split, releasing vast quantities of O2 gas into the atmosphere. 2. Where does the light reaction take place? Thylakoid 3.Where does the dark reactions take place? stroma 4. Circle the right reactions (light reactions /dark reactions) produces molecular oxygen (O2) (light reactions / dark reactions)requires ATP (light reactions /dark reactions)produces NADPH (light reactions / dark reactions) produces three-carbon sugars (light reactions / dark reactions)requires CO2 • • • • •
5. Reduction of oxygen which forms water occurs during A) photosynthesis. B) respiration. C) both photosynthesis and respiration. D) neither photosynthesis nor respiration. E) photorespiration. 6. Reduction of NADP+ occurs during A) photosynthesis. B) respiration. C) both photosynthesis and respiration. D) neither photosynthesis nor respiration. E) photorespiration. 7. In the electron-transport chain in chloroplasts, ________-energy electrons are taken from __________. (a) high; H2O. (b) low; H2O. (c) high; NADPH. (d) low; NADPH.
