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UTMSBS_Block1_U1_Wk1
Cell Biology Review, Chemistry Review
| Question | Answer |
|---|---|
| The cell is the basic functional unit of the human body. Each cell: (list 4) | 1. is surrounded by the plasma membrane 2. consists of fluid suspension, cytosol 3. contains nucleus, organelles and inclusions 4. contains cytoskeleton |
| What do you call all of the material within the plasma membrane that is NOT part of the nucleus? | cytoplasm |
| What do you call the membrane bound unit that contains the vast bulk of genetic material (DNA) | nucleus |
| Cytoplasm consists of cytosol AND... (list 3) | organelles, inclusions and cytoskeleton |
| What part of the cell is unique to eukaryotes? | plasma membrane |
| What is the critical factor in obtaining clear images for light microscopy? | resolving power |
| What is the resolving power in light microscopy? | the smallest distance between 2 particles at which they can be observed as separate particles. |
| What is the maximum resolving power of a light microscope? (of a human eye?) | 0.22 um (100um) |
| What can you see smaller stuff with, an electron microscope or a light microscope? | electron microscope |
| What is used to visualized cells and follow their movement? | light microscope |
| How do you increase the resolution of a light microscope? | decrease the wavelength of the illuminative radiation |
| What type of microscope requires thinn sections for penetration of the sample by illuminating radiation? electron microscope | |
| Which type of microscopy is kinetic, dynamic? light microscope | |
| What kind of microscopy do you use to capture cellular processes over time? light microscope | |
| What kind of microscope can only capture static images? electron microscope | |
| A longitudinal crossection is cut: along the long axis | |
| a transverse crossection is cut: perpendicular to the long axis | |
| an oblique crossection is: diagonal and neither longitudinal nor transverse | |
| a tangential crossection is: a longitudinal crossection that is perpendicular to the radius | |
| How can we isolate cell constituents? differential centrifugation | |
| What are the steps in differential centrifugation? 1. dissociate tissue 2. separate by gravity 3. separate by repeated centrifugation, at progressively higher speeds | |
| how can we study cell growth? cell culture | |
| how can we study cell differentiation and function? cell culture | |
| ____ are the fundamental units of life which evolved ______ years ago. Cells; 3.8 billion | |
| What is the approximate diameter of a human cell? 10 micrometers | |
| What is the approximate length of a mitochondria? 1 micrometer | |
| ______ microscopy is much easier to use than _______ microscopy & allows for observation of live cells. light; electron | |
| In light microscopy objects of about _____ can be seen. 1 micrometer | |
| In light microscopy objects of about the size of a _______ can be seen. mitochondria | |
| ______ microscopy has a much higher resolution than light microscopy (10 nm). electron | |
| Biochemical composition can be studied by isolation and characterization of different cellular components by: differential centrifugation | |
| what do we use to study mechanics of cell growth, differentiation, cellular function, stem cell research and many other cell properties? cell culture | |
| What are 6 structures that make up the intracellular membrane system? 1. RER 2. SER 3. Golgi 4. glycogen granules 5. Mitochondria 6. Lysosome | |
| Where might diseases of improper protein folding/export originate? ER | |
| What are 3 dx with dysfunctional ER origins? 1. hypothyroidism (protein folding prob) 2. CF (transmembrane regulator not exported due to mut.) 3. osteogenesis imperfecta (pro-collagen) | |
| Why is the smoothe ER not rough? | no ribosomes |
| Where does lipid metabolism take place? | SER |
| Where does the detoxification of drugs take place? | SER |
| What cellular structure might be referred to as a "mini liver"? | SER |
| Which cellular structure uses enzymes in the cytochrome P450 family and why? | SER for drug detoxification |
| what structure radiates off the nucleus? | SER |
| What structure is covered by ribosomes on its outer surface? | RER |
| What is the site for protein synthesis? | RER |
| Protein secretory cells have what? | more RER |
| What is continuous with the nuclear envelope? | RER |
| proteins synthesized and packaged in the RER are transported where for modification and final packing? | Golgi |
| Into what does the golgi package proteins for transport? | secretory vescicles |
| what cell structure is a series of flattened, slightly curved membrane-bound cisternae | Golgi |
| Which structure is almost continuous with the ER? | golgi |
| Which structure has a secondary role of carbohydrate synthesis? | RER |
| What type of microscope would you use to visualize vescicles going back and forth from the golgi? | light microscope |
| What structure is the "sorting machine" that enable proteins to get to their place? | golgi |
| Where are the three levels of cisternae | in the golgi |
| which level of the cisternae is closest to the RER, entry phase and convex in shape? | Cis-face |
| what is the middle of the cisternae called? | medial face |
| Which part of the cisternae is convex? | trans-face |
| what part of the cisternae is leading outside of the golgi to the exit phase? | trans-face |
| What structure produces the storage form of energy? | Mitochondria (ATP) |
| What structure has a smooth outer membrane and a folded inner membrane? | mitochondria |
| What is the name for the inner folded membrane of the mitochondria? | cristae |
| What is the variability in length of the mitochondria? | 0.5 to 1 micrometers (and up to 7 micrometers) |
| What structure fuels cellular processes? | mitochondria |
| What is the matrix of the mitochondria called and what's in there? | called inter-cristae; mtDNA |
| Carioencephalomyopathy, deafness and Type II diabetes are all disorders of what cellular structure? | mitochondria |
| what structure can divide by fission but also fuse? | mitochondria |
| how big are peroxisomes? | 0.2 to 1 micrometer |
| what structure utilizes oxygen, but does not produce ATP? | peroxisomes |
| are peroxisomes membrane-bound? | yes |
| what is the "work horse" of the peroxisomes? | catalases |
| what structure is responsible for the catabolism of fatty acid chains? | peroxisomes |
| what highly toxic material does a peroxisome contain? | hydrogen peroxide |
| what happens inside a peroxisome? | oxidation specific organic substrates remove hydrogen atoms transferred to molecular oxygen to form hydrogen peroxide |
| what changes the hydrogen peroxide into 2H20 and O2 in a peroxisome? | catalase |
| what structure contains 40-50 oxidative enzymes, such as urate, oxidase, and catalase? | peroxisomes |
| Zellewegers syndrome is an example of a _______(organelle) disorder. Disorders of this organelle are generally lethal. | peroxisome |
| what is the approximate size of a lysosome? | 0.3 to 0.8 micrometers |
| what organelle contains 40 different types of acid hydrolases (e.g. sulfatases, proteases, nucleases, etc.)? | lysosome |
| what is the function of the acid hydrolases inside lysosomes? | tear up proteins & microorganisms |
| what is the "trash can" of the cell? | lysosomes |
| what organelle digests particulate matter that enters the cell? | lysosomes |
| what organelle is a membrane-bound compartmentalization of degradative enzymes away from the rest of the cell? | lysosome |
| what is the lumen pH of the lysosome? | 5 (acidic) |
| why is the pH of the lumen lysome so low? | degradative enzymes operate at optimal pH in these conditions |
| what cell structures have little or no metabolic activity, are not really considered organelles and consist mainly of accumulated metabolites? | cytoplasmic inclusions |
| what is the storage form of glucose? | glycogen |
| where is the storage form of glucose found? | glycogen found mostly in liver and muscle cells |
| How large is glycogen? | 10-40 nm |
| what is a storage form of fatty acids? | triacyglycerols |
| what are lipids associated with in the cell? | mitochondria?? |
| what are cells enclosed by? | a plasma membrane |
| what are the two regions that cells can be divided into? | nucleus and cytoplasm |
| what is the part of the cell that excludes the nucleus and membrane-bound organelles? | cytosol |
| _______ contains a concentrated mixture of small and large molecules which carry out many essential biochemical processes. | cytosol |
| _____ are the site of protein synthesis | ribosomes |
| _____ is a network of flattened sacs and tubules in the cytoplasm | ER |
| this structure is the site of lipid synthesis and calcium accumulation and release | SER |
| this structure is is the site of protein synthesis and packaging | RER |
| ______ modifies and stores proteins and pacakages them into secretory vescicles | golgi |
| "powerhousees" of the cell | mitochondria |
| this structure uses oxygen to remove hydrogen and form hydrogen peroxide | peroxisomes |
| this structure digests particulate matter that enters into the cell | lysosome |
| this structure contains it's own genetic information (chromosomes) | mitochondria |
| what are 3 types of material transport in the cell? | 1. gated transport 2. transmembrane transport 3. vesicular transport |
| this type of transport involves signal sequences for which protieins can recognize and bind to | gated transport |
| in this type of transport, nuclear pores function as selective gates | gated transport |
| this type of transport is used to move specific macromolecules & macromolecule assemblies | gated transport |
| this type of transport allows for diffusion of smaller molecules | gated transport |
| this type of transport is a receptor-driven event | transmembrane transport |
| in this type of transport selected proteins from cytosol are moved to ER lumen, mitochondria or peroxisome | transmembrane transport |
| in this type of transport, protein molecules usually must unfold to pass through the translocator | transmembrane transport |
| this type of transport is usually by specific receptors that recognize signal peptides | transmembrane transport |
| this type of transport allows for transfer of soluble proteins for ER to Golgi | vesicular transport |
| this type of transport allows for their cargo to be discharged into target components | vesicular transport |
| what is an example of vesicular transport? | endocytosis |
| in this type of transport, vescicles are pinched off from the donor compartment and transported to the target component | vesicular transport |
| this is a process by which a cell ingests substances from the extracellular space | endocytosis |
| endocytosis of a LARGE vesicle is: | phagocytosis |
| endocytosis of a small vesicle is: | pinocyosis |
| what is it called when a cell catabalizes itself? | autophagy |
| in this process a membrane forms around non-functional organelle or excess cytoplamsic structures, followed by fusion with lysosomes | autophagy |
| what is the last step of endocytosis? | vesicle fuses with lysosomes for digestion |
| what are different pathways to the lysosome? | phagocytosis, endocytosis, autophagy |
| What is the process occuring following cell death resulting from injury ("Free for all") | necrosis |
| what processes is necessary for separating digits? | apoptosis |
| what process is messed up when there is a fusion between digits? | apoptosis |
| What is programmed cell death called? | apoptosis |
| of the two "cell death processes" necrosis and apoptosis, which involves inflammation? | necrosis |
| in this process, cellular components are released as cells perish. Phagocytes do not consume the cells or their contents | necrosis |
| in this process, an uncontrolled release of cell contents can trigger an immone response | necrosis |
| what is notably lacking in apoptosis compared to necrosis? | inflammation |
| in this porcess, there are characteristic patterns of changes in cell morphology resolting from degradation of organelles by activated caspases: | apoptosis |
| what are some processes that occur during apoptosis (list 5) | 1. blebbing of cell membrane 2. cell rounding/shrinkage 3. pyknosis (chromatin condensing) 4. fragmentation of nucleus/chromosomal DNA 5. break into vescicles called apoptotic bodies |
| Unlike ________, membranes around _________ bodies signal macrophages and surrounding cells to engulf. | necrosis; apoptotic |
| in this process, nuclei are pyknotic | apoptosis |
| in this process, large cytoplasmic blebs form and detach from cell, but remain within the plasma membrane (no cytoplasm is released) | late apoptosis |
| cell death is characterized by: | typical nuclear chages |
| what type of cell death is required for normal development of multicellular organisms? | apoptosis |
| _________ is marked by chromatin condensation along the nuclear membrane | apoptosis |
| What is the amino acid side chain whose pKa is closest to neutral? | histidine |
| which of the following determines a protein's native structure? | the protein's linear amino acid sequence |
| which of the following secondary structures is most likely to be found in a membrane-embedded portion of a protein? | an alpha helix composed entirely of hydrophobic residues |
| which of the following best describes the arrangement of amino acid side chainsin an alpha helix? | side chains point outward away from helical axis |
| which of the following best describes an alpha helical region of a polypeptide? | Right-handed, 4.6 aa/turn |
| structural and biochemical aspects of polypeptide chain formation to create amino acid sequence is determined by | primary structures |
| can two proteins have the same amino acid sequence? | no; each protein has a unique amino acid sequence |
| peptide bond "backbone" is essentially ______ because of the rigid ________-like characteristics | planar; double bond |
| what kind of bond involves the transfer of electrons where they're not truly shared | ionic |
| two atoms with unpaired electrons in their outer shells can form _______ bons with eachother by sharing electron pairs | covalent |
| what type of bond is a peptide bond? | covalent |
| chemical reactions that require the most energy entail the breaking and forming of | covalent bonds |
| ionic bonds can be described by __________ interactions and ______ law. | electrostatic; coulomb |
| these bonds are weak electrostatic interactions: approx. 4-13kJ | Hydrogen bonds |
| these bonds depend upon the distance between two atoms and the non-symmetrical charge distribution around each. | van der waals interactions |
| what is the van der Waals contact distance? | the point at which the two atoms exhibit the greatest attraction for each other |
| closer than van der Waalss contact distance results in: | repulsive forces |
| what is considered the "universal solvent"? | water |
| with the exception of van der waals forces, the non-covalent interaction is greatly affected by: | water |
| Is non-covalent ionic bond strength greater in water or a vacuum? | a vacuum. non-covalent interactions are very weak in water. |
| Water is a ________ molecule with an asymmetric distribution of charge. No net charge, but the ______________ ___________ creates a polar solvent that can interact with charged particles. | polar; electric dipole |
| Water is highly __________ through hydrogen bond interactions. | cohesive |
| water is an excellent solvent for ___________ molecules as it: | polar; competes for electrostatic interactions between other polar molecules. |
| The ____________ of water diminishes the strength of electrostatic attractions between other polar molecules. | high dielectric constant |
| what is the hydrophilic effect? | water interacting with other polar molecules |
| what is the hydrophobic effect? | describes water interacting with nonpolar molecules |
| Nonpolar molecules aggregate together in water which leads to: | the release of free energy (higher entropy) |
| increase in entropy leads to a release of | free energy |
| the hydrophobic effect and the release of free energy play a role in which biochemical rxn? | correct protein folding |
| when water acts as an acid, it _______ a H+ | donates |
| when water acts as a base it _______ a H+ | accepts |
| when an acid is dissolved in H2O, it donates its H+ to a H2O molecule; in this case, H2O acts like a (acid/base)? | base |
| when a base is dissolved, it accepts a H+ from an H2O molecule; in this case H2O acts like a (acid/base)? | acid |
| a weak acid [HA] produces a _________ conjugate base= | strong; =good pH buffering |
| a weak base [A-] produces a ________ conjugate acid= | strong; =good pH buffering |
| a __________ produces a strong conjugate base | weak acid [HA] |
| a ___________ produces a strong conjugate acid | weak base [A-] |
| Strong acids (HCl) and bases (KOH) produce _________ which are _________ and thus unimportant to us | weak conjugate bases/acids; poor pH buffers |
| What remains relatively constant when pH buffer is strong/good. | [H+] |
| Henderson Hasselbach (H-H) equation predicts the pH of a buffer by: | -log [weak acid]/[weak base] |
| when does the pH = pKa? | when [A-]=[HA] or weak acid concentration equals weak base concentration |
| how do you make a strong pH buffer | weak acid + strong conjugate base |
| what is the best pH for buffering the human body's acid-base balance? | 7.4 |
| when someone's breathing is shallow, there can be an increased H+ in blood due to hypoventilation and a build up of CO2. What is this called? | respiratory acidosis |
| respiratory acidosis can be caused by pulmonary problems, head injury, drugs (sedatives, anesthetics) or brain tumor. How can these affect the blood's pH? | Build up of CO2 leads to pH falling below 7.4 or becoming more acidic |
| when someone is hyperventilating, there is a decrease of H+ in the blood, expelling CO2 rapidly from circulation. What is this called? | respiratory alkalosis |
| respiratory alkalosis can be caused by psychiatry anxiety, drugs such as asprin and caffeine, lung disease such as pneumonia, fever or stroke. How can these affect the blood's pH? | decreased H+ in the blood leads to pH increasing above 7.4 or becoming more basic |
| what happens to pH and pCO2 during uncompensated respiratory acidosis? | pH decreases, pCO2 increases |
| what happens to pH and pCO2 during uncompensated respiratory alkalosis? | pH increases, pCO2 decreases |
| what are three ways the acid-base physiological equilibrium is achieved in the body? | 1. renal elimination 2. chemical buffering within the body 3. pulmonary elimination (pCO2) |
| what type of ionic form do amino acids take on at physiological pH? | zwitterion/hybrid ion/dipolar ion |
| in solution, the amino acid molecule appears to have a charge which changes with: | pH |
| at low pH, what part of the amino acid is charged? | amino terminus; positively charged |
| at high pH what part of the amino acid is charged? | the carboxyl terminus; negatively charged |
| how do we define pI in terms of pH? | the isoelectric point is the pH at which the total net charge=- and therefore will not move in an electric field |
| What type of amino acid isomers are most common in the human body? | L isomers; D isomers are more rare (D found in bacterial cell walls and peptide antibodies) |
| which is the only achiral amino acid? | Gylcine; it has a Hydrogen as an R-group |
| What are the non-polar, neutral R-groups? (name 6) | Glycine (G), alanine (A), valine (V), leucine (L), Isoleucine (I) and Methionine (M). |
| What are the aromatic R groups? (name 3) | Phenylalanine (F), Tyrosine (Y), Tryptophan (W) |
| Trp & Try or Y & W are equal to what percentage of amino acids in an average protein mixture? | about 4.6% |
| what are the aliphatic hydroxyl R groups (polar)? (name 2) | Serine (S) and Threonine (T) |
| the -OH groups on serine and threonine result in what? | hydrophilic characteristics and stronger chemical reactivity |
| what are the aliphatic sulfhydryl (thiol) R groups (polar)? | cysteine (C) |
| what are the basic R groups that are very polar and positively charged @ pH 7? (name 3) | Lysine (K), Arginine (R) and Histidine (H) |
| what are the acidic R groups that are very polar and negatively charged @ pH 7? (name 4) | Aspartate (D), Glutamate (E), Asparagine (N) and Glutamine (Q) |
| which is the aa "A"? | alanine |
| which is the aa "K"? | lysine |
| which is the aa "F"? | phenylalanine |
| which is the aa "Q"? | glutamine |
| which is the aa "E"? | glutamic acid |
| which is the aa "R"? | Arginine |
| which is the aa "W"? | tryptophan |
| which is the aa "Y"? | Tyrosine |
| what does it mean for something to be an essential aa? | it means that it must be supplied in the diet as humans cannot synthesize these specific amino acids (total of 9 out of 20) |
| the alpha-carboxyl group of one amino acid is _____ linked to the alpha-amino group of another amino acid by a ________ bond. | covalently; peptide (amide or covalent) |
| more than two amino acids linked together form a ___________. | polypeptide chain |
| each _________ bond formed requires an input of free energy (+21 kJ/mol) and results in the loss of a water molecule | covalent peptide |
| the peptide bond "backbone" is essentially a _______ structure because of rigid _______-like characteristics | planar; double bond |
| for each pair of linked aa's there are X atoms within the same plane = amide plane | X=6 |
| amide bond has stability because of | resonance characteristics |
| the aa backbone contains a carbonyl group (>C=O), a hydrogen bond _________ and an amine group (>N-H; except for _________) a hydrogen bond _______. | acceptor; proline; donor |
| planar peptide bonds (amide plane) can have one of two configurations; one on each side of the peptide bond. What are they and which is more common? | cis, trans; trans is more common |
| the angle of rotation between the nitrogen of the amino group and the alpha carbon is called: | phi |
| the angle of rotation between the alpha carbon and carbon atom of the carbonyl is called: | psi |
| what was YGGFL (Leu-enkephalin) used to demonstrate? | the amino terminal is always at the beginning of the polypeptide chain and the amino acid sequence only goes in one direction |
| Disulfide bonds are formed by the ______ of the -SH side groups of a pair of cysteine residues to S-S, linking the two cysteines _________ to form one cysteine | oxidation; covalently |
| the molecular mass of a protein is dependent on the number of _________ in the protein | amino acids |
| what is the average molecular mass of one amino acid (in daltons)? | 110 daltons |
| If most proteins contain between 50 - 2K amino acid residues (aa), what is the range of molecular masses for these proteins? | (50 aa X 110 daltons= average molecular mass of one aa)= 5500 daltons; (2000 aa X 110 daltons) = 220,000; between 5.5kD and 220 kD |
| the alpha helix consists of a tightly coiled backbone with side chains extending _______ in a helical array | outward |
| All alpha-helices in proteins are ___________ because there is ___________ | right handed because there is less steric clash between R groups and the backbone |
| The alpha helix how many angstroms and residues per 360 degrees? | 1.5 angstroms wide and 3.6 residues per 360 degree turn |
| stabilization of secondary structures occurs by _________ between N-H and C=O groups of the backbone that are ____ residues apart in a staggered array. ________ backbone N-H and C=O groups are ___________. | hydrogen bonded; 4; ALL; hydrogen bonded |
| which type of alpha helix is predicted to be energetically favorable? | right-handed helix |
| adjacent amino acids in the beta strand are ______ angstroms apart. | 3.5 angstroms apart (greater than the alpha helix which is 1.5) |
| strands in a beta sheet can link as a mixture of both _______ and ___________. | parallel and antiparallel |
| a beta sheet is formed by linking two or more beta strands by ____________. | hydrogen bonds |
| this type of beta sheet has each amino acid on one strand H-bonded to two different amino acids on the opposite strand. | parallel beta-sheet |
| this type of beta sheet has the N-H group and C=O group of each amino acid H-bonded to the C=O group and N-H group of one amino acid directly opposite | anti-parallel beta-sheet |
| (T/F) proteins can have both alpha and beta structures | True |
| what secondary structure is described as "Flat and twisted" | beta sheets |
| Most proteins have compact globular shapes because of sharp bending of polypeptide chains, regardless of primary structure. The most common structural element to accomplish this is the: | reverse turn (Beta-turn, hairpin loop) |
| what's an omega loop? | another more elaborate structure responsible for chain reversals |
| are proteins ever symmetrical? | no |
| how do we describe the spatial arrangement of proteins containing more than one protein chain (subunits) and the nature of their interactions? | quaternary structure |
| Protein domains are compact globular protein regions of a __________ connected by flexible segment of polypeptide chain. Give example? | single protein; CD4 (four similar protein domains extending from helper T-cell surface) |
| what is the "general rule" for amphipathic proteins? | they're water soluble and amphipathic, folding into structures with nonpolar cores (hydrophobic cores) and hydrophilic R groups on the outside. |
| what is the example of exception to the general rule of water-soluble proteins? | Porin: outer membrane of bacteria is hydrophobic and inner structures are hydrophilic. |
| What type of protein allows polar molecules through its channel? | Porin: hydrophilic channel allows water and other polar molecules through |
| how do we describe the spatial arrangement of amino acid residues within the polypeptide chain that are far apart in sequence, including the patter of disulfide bonds? | protein tertiary structure |
| What are the rules that govern folding of protein into tertiary structures? (name 2) | 1. Thermodynamic stability: less energy to achieve 3-D is more desirable 2. contribution of each portion to overall polypeptide chain-folding mechanisms |
| one complete protein chain (eg. beta-chain of hemoglobin) represents what structure? | tertiary |
| the four separate chains of hemoglobin assembled into an oligomeric protein represents what structure? | quaternary |
| what is the name for the self-propagating form of chromosomally-encoded protein that is a proteinaceous infectious particle lacking nuclei | prion |
| what diseases do prions cause? | TSEs (transmissible spongiform encephalopathies); fatal neurodegenerative diseases affecting humans/mamals. Eg. CJD (1/million); scrapie, Bovine spongiform encephalopaty, chronic wasting disease; Kuru |
| normal prion proteins are ___________ and soluble. Prion dx are due to aggregates of insoluble __________. | alpha helical; prion beta-sheets |
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