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Balliet SyPh CH 1-3
NYCC Sys Phys Ch 1-3 Quiz 1, Exam 1 FA10
| Question | Answer |
|---|---|
| extracellular ions (3) | sodium, chloride, bicarbonate |
| extracellular molecules for nutrition (4) | oxygen, glucose, fatty acids, amino acids |
| intracellular ions (3) | Potassium (always!), Magnesium, Phosphate |
| Which ion is ALWAYS intracellular? | Potassium K+ |
| constancy is a good adjective for | homeostasis |
| how is extracellular fluid moved? | vessels to capillaries and intercellular spaces between tissue cells |
| how do large amts of fluid and dissoved constituents move between blood and tissue spaces? | DIFFUSE due to kinetic motion of molecules |
| what system uses the lungs to exchange oxygen for CO2? | Respiratory |
| organ of respiratory | lungs |
| tool of respiratory | alveolar membrane (where gas is exchanged) |
| mechanism of respiratory | diffusion |
| what system uses the heart to obtain nutrients? | GI tract |
| substrates of GI tract | carbohydrates, fatty acids, amino acids |
| tool of GI tract | GI tract wall |
| mechanism of GI tract | absorption |
| what system uses the lungs to exchange oxygen for CO2? | Respiratory |
| organ of respiratory | lungs |
| tool of respiratory | alveolar membrane (where gas is exchanged) |
| mechanism of respiratory | diffusion |
| what system uses the heart to obtain nutrients? | GI tract |
| substrates of GI tract | carbohydrates, fatty acids, amino acids |
| tool of GI tract | GI tract wall |
| mechanism of GI tract | absorption |
| what system uses movement to obtain nutrients? | musculoskeletal system |
| substrates of musculoskeletal system? | glucose and food |
| tool of musculoskeletal system | movement towards food and away from harm |
| mechanism of musculoskeletal system | mastication and contraction/peristalsis |
| which system uses chemical change, modification and storage to obtain usable substrates? | liver and famous 4: fat cells, GI mucosa, kidneys, endocrine glands |
| substrates of liver and famous 4: fat cells, GI mucosa, kidneys, endocrine glands? | unabsorbed GI tract substances |
| the liver and famous 4: fat cells, GI mucosa, kidneys and endocrine glands are called _________ organs. | metabolic |
| most abundant of all end products of metabolism | carbon dioxide from lungs |
| waste removal from lungs is | CO2 out |
| waste removal from kidneys involves what substances? | urea, uric acid, excess ions and water from extracellular fluid |
| from what does the kidneys filter urea, uric acid, excess ions and water from extracellular fluid? | plasma |
| where does the kidney send plasma for filtration? | glomeruli and nephron tubules |
| what do the kidney tubules do? | reabsorb precious things like glucose, amino acids, H2O and ions |
| waste from plasma is reabsorbed poorly at the nephron and so passes to __________ as urine. | renal tubules |
| 3 components of Nervous system | sensory input - CNS/integration - motor output |
| how does the Nervous system detect the state of the body and its surroundings? | Sensory receptors! |
| which segment of the nervous system operates at the subconsious level, controlling fcns of internal organs (heart pumping), GI motility, and secretion of glands? | autonomic system |
| biochemical component of cell that is a medium for reactions | water 70-85% of cell |
| name the ion components of a cell | potassium, magnesium, phosphate, bicarbonate, sodium, chloride, calcium |
| 2 types of proteins | structural vs. functional |
| example of a structural protein | microtubule |
| example of a functional protein | enzyme |
| almost all functional proteins are | enzymes |
| percentage of protein in the cell | 10-20% |
| can make up anywhere between 2-95% of the cell | lipids |
| types of lipids in cell (3) | phospholipids, cholesterol, triacylglycerides |
| the cell membrane is composed primarily of what two lipids? | phospholipids and cholesterol |
| what are triglycerides used for? | fat/energy |
| carbohydrate percentage in cell | 1-6% |
| type of carbohydrate used by muscles in a storage form | glycogen |
| the cell membrane is composed almost entirely of ____________ & ___________ | proteins and lipids (phospholipids) |
| determines degree of membrane permeability/impermeability of bilayer to water-soluble constituents of body fluids | cholesterol |
| controls much of membrane fluidity | cholesterol |
| ions, glucose and urea are | water-soluble molecules that cannot pass through the cell membrane/bilayer |
| what kind of molecules CAN get into the lipid bilayer and thereby enter the cell? | lipid-soluble |
| what are the lipid soluble molecules that can pass through the lipid bilayer? | Oxygen, Carbon dioxide, Alcohol |
| most membrane proteins are | glycoproteins |
| Regarding structural and functional proteins, what are the two types of functional proteins? | Integral membrane proteins and Peripheral Membrane proteins |
| type of IMP (Integral Membrane Protein) that forms channels for water soluble molecules and water soluble substances (ions) to pass through. Selective. | IMP pores |
| type of IMP that transports otherwise disallowed substances through the lipid bilayer | IMP carriers |
| example of an IMP carrier job | active transport against the concentration gradient |
| Most ________ are functional proteins. | enzymes |
| Functional proteins that are IMP's and are almost always functional proteins. | IMP enzymes |
| IMP's for water soluble molecules like peptide hormones. Used during G-protein linked 7-pass transmembrane second messenger cascades (whew. I mean really.) | IMP receptors! |
| what do IMP receptors couple with? | ligands |
| convey information from the outside/extracellular environment to the inside/intracellular environment | Integral Membrane Proteins (IMP's) |
| Most membrane proteins are | glycoproteins |
| almost always enzymes or controllers of transport of substances through pores | peripheral membrane proteins |
| PMP's (pimps) | peripheral membrane proteins - the enzymes or controllers |
| almost always occur with proteins and lipids as glycoproteins or glyclolipids | Membrane CARBOHYDRATES |
| most integral membrane proteins are | glycolipids |
| most membrane proteins are ____________ and most integral membrane proteins are _____________. | glycoproteins, glycolipids |
| mainly carbohydrates around a small protein core | proteoglycans |
| bound outer cell membrane and form the glycocalyx | proteoglycans (carbs + protein cores) |
| the _________is basically the sugar coating on the outside of the cell that is negatively charged (due to proteoglycans) to repel other negative charged molecules and is sticky to other cells. | Glycocalyx |
| the glycocalyx is composed of | proteoglycans |
| 4 functions of glycocalyx/proteoglycan cell covering | is neg chg'd so repels other negatively charged molecules, and is sticky to allow for cell-cell attachments. Many glycocalyx carbs are receptors for peptide hormones and function in Immune response |
| 4 carb/Proteoglycan/glycocalyx functions: | Neg. chg to repel other neg., sticky for cell-cell attachments, has receptors for peptide hormones, Immune rx via ABO blood typing |
| Rough Endoplasmic reticulum | has ribosomes attached (RNA and proteins) that synthesize new protein materials in the cell |
| The E.R. in general is responsible for (2) | post-translational modification of protein (RER) and lipid synthesis (SER) |
| what organelle is prominent is secretory cells? why? | Golgi apparatus, prominent in secretory cells so it's located on the side of the cell from which secretory substances are extruded |
| series of flattened sacs or cisternae | Golgi apparatus |
| along with the RER, the Golgi apparatus is also responsible for | post-translational modification and sorting of proteins and lipids, along with exocytosis of its products |
| how do lysosomes and secretory vesicles get into the cell | via the ER then the Golgi apparatus |
| provide an intracellular digestive system | lysosomes |
| has a single membrane and contains acid hydrolases | lysosome |
| what is an acid hydrolase? | a digestive enzyme acid within a lysosome |
| combines the H+ part from a water molecule with one part of a split compound and combines the hydroxyl portion of the water molecule with the other part of the compound, in effect HYDROLYZING (digesting) with water | lysosome |
| protein is hydrolyzed to form | amino acids |
| glycogen is hydrolyzed to form | glucose |
| lipids are hydrolyzed to form | fatty acids and glycerol |
| A lysosome contains hydrolases (digestive) enzymes and uses water. A ___________ contains oxidases and combines oxygen with H+ to make hydrogen peroxide. | peroxisome |
| H2O2 | hydrogen peroxide from a peroxisome |
| Not only do peroxisomes contain oxidases to combine oxygen and hydrogen, making hydrogen peroxide, they contain __________, another oxidase enzyme present to oxidize poisonous substances such as alcohol. | catalase |
| Since peroxisomes contain large amounts of catalase in conjunction with oxidase to capture and kill otherwise poisonous substances such as alcohol, where might they be found in great number? | LIVER!, and phagocytic cells like neutrophils and macrophages |
| About half the alcohol a person drinks is detoxified by the __________ of the liver cells via catalase and oxidase. | peroxisomes |
| almost all secretory substances are formed by the tag team of | ER-Golgi apparatus |
| enzymes that are not yet activated | proenzymes |
| present in numbers that depend on the amount of energy required by the cell | mitochondria |
| describe structure of mitochondria | outer and inner complete lipid bilayers. Inner membrane folds (christae)holding oxidative enzymes and matrix full of dissolved enzymes that extract nutrients, the oxidation of which releases CO2 + H2O and is used to make ATP. |
| mitochondria are self-__________ | replicative |
| 2 tissue types with the most mitochondria | nerve and muscle |
| name of process used by mitochondria to produce ATP | OXIDATIVE PHOSPHORYLATION |
| organelle that divides in two during each cell cycle | mitochondria |
| Fibrillar proteins of the cell are usually organized into __________ or __________. | filaments or tubules |
| how do filaments and tubules come about (who makes them?) | ribosomes make the precursors, which then assemble (polymerize) to form filaments |
| Large numbers of ________ filaments are found in the ectoplasm (outer zone of the cytoplasm)to form an elastic support for the cell membrane. | actin |
| What kind of filaments are organized in muscle tissue into a special contractile machine that is the basis for muscle contraction? | actin and myosin |
| what composes the strong microtubules? | polymerized tubulin |
| where are microtubules often found?, | flagellum of sperm, cilium of cell, centrioles, mitotic spindle |
| the primary function, apart from being present in flagellum, cilium, centrioles and mitotic spindles, is to provide rigid physical structures for the cell called the ____________. | cytoSKELETON |
| large quantities of DNA contained in the nucleus are called | genes |
| determine the characteristics of the cell's proteins, including structural proteins, and the intracellular enzymes that control cytoplasmic and nuclear activities | genes (DNA) in the nucleus |
| control reproduction of the cell itself | genes |
| formation of two daughter cells | mitosis |
| what material organizes into chromosomes? | chromatin in the nucleus |
| 2 organelles that have 2 lipid bilayers (albeit positioned differently in relationship to one another) | mitochondria and Nucleus (nuclear membrane) |
| how is the nuclear membrane designed | one lipid bilayer inside the other |
| the nuclear membrane is also called the nuclear _____________ | envelope, because it's one bilayer inside the other like a letter in an envelope |
| the nuclear membrane is continuous with the | ER |
| the nuclear membrane is penetrated by several thousand of these | nuclear pores |
| nuclear pores allow molecules to pass through with reasonable ease. What does the nuclear pore contain to do this? | transporter subunits |
| the nuclear pores make the nuclear membrane freely permeable to water and small ions but how do nuclear RESIDENT PROTEINS enter? | receptor complexes around the pore guard it like sentries |
| perinuclear space | space between the inner and outer lipid bilayers of the nuclear envelope |
| where is RNA stored in the nucleus until it is needed in the cytoplasm to form mature ribosomes? | nucleoli |
| what distinguishes a cell from lower forms of life? | a nucleus |
| Most substances pass through the cell membrane by _________ and ___________ __________. | diffusion and active transport |
| __________ involves simple movement through the membrane caused by random molecular motion | diffusion (either molecules move through the pores or the lipid bilayer, depending on their type of solubility) |
| involves the cell actually carrying a substance through the membrane via physical protein structure that penetrates all the way through the membrane | active transport |
| Very large particles enter the cell by a specialized function of the cell membrane called | endocytosis |
| principal forms of endocytosis | pinocytosis and phagocytosis |
| ingestion of minute particles that form vesicles of extracellular fluid and particulates inside the cytoplasm | pinocytosis |
| ingestion of large particles, such as bacteria, whole cells, or portions of degenerating tissue | phagocytosis |
| "true endocytosis" has two forms: | fluid-phase endocytosis (pinocytosis) and receptor-mediated endocytosis (via clathrin coated pits) |
| Describe "true endocytosis" (pinocytosis in text book) | ie, 3 proteins attach to appropriate receptor aggregates in clathrin-coated pits. Clathrin is akin to a latticework under the coated pit. Once proteins attach, entire pit invaginates inward, closes off, & pinches into a pinocytotic vesicle inside the cell |
| 2 types of mammal cells in which phagocytosis occurs | macrophages and neutrophils |
| phagocytosis occurs similarly to pinocytosis, but it involves | large particles instead of small molecules |
| engulfing the particle with a plasma membrane | phagocytosis (remember: phago is for particles -large while pino is for el nino molecules -tiny) |
| how do nutrients escape into the cell from phagocytized or pinocytized vesicles? | lysosomes attach to the vesicle and release their digestive hydrolases directly into it. Digestive vesicle forms. Proteins, carbs, lipids hydrolyzed/broken so amino acids, glucose, phosphates can diffuse through the vesicle's membrane into the cytoplasm. |
| how does the digestive vesicle, now empty of nutrients but full of indigestible substances, leave the cell? | as a residual body, excreted through the cell membrane by EXOcytosis (essentially the opposite of endocytosis) |
| what organelle causes tissues of the body to regress to a smaller size when not used or no longer needed (mammary glands after lactation, atrophied muscles, uterus after pregnancy)? | lysosomes are responsible for much of this regression |
| job includes removal of damaged cells or portions of cells from tissues | lysosomes |
| damage to the cell - heat, cold, trauma, chemicals, or any other factor - induces __________ to rupture | lysosomes |
| explain how a cell autolysis | lysosomes rupture from damage to tissue, releasing hydrolases that digest the cell from the inside out. The cell is completely removed and a new cell is reproduced by an adjacent cell via mitosis. Replaces the old. |
| what neutralizes phagocytized bacteria within a lysosome? | lysoZYME, which dissolves the bacterial membrane, and lysoFERRIN which binds iron before it can promote bacterial growth. Bacteria loves some iron! ACID at a pH of 5.0 that activates the hydrolases and inactivates bacteria. |
| how is the acid in lysosomes formed and why doesn't it eat through the lysosome membrane? | Acid hydrolase is the precursor or proenzyme inside the lysosome. It is cut/cleaved at a pH 5.5 and becomes active at pH 5.0. This 5.0 shuts down bacterial metabolic machinery. An ATP-proton pump maintains lysosome pH. |
| each gene is a _______ acid called DNA and automatically controls the formation of another ________ acid, called RNA | nucleic, nucelic |
| The _______ spreads throughout the cell to control the formation of a specific protein. | RNA |
| two types of protein classes | structural & enzyme |
| structural proteins couple with _______ and ________ to form intracellular organelles. | carbs and lipids |
| enzyme proteins do what? | catalyze rx |
| end goal of DNA transcription and RNA translation | cell function. |
| composition of DNA | phosphoric acid, deoxyribose, one of 4 nitrogenous bases |
| what forms the backbone in a DNA helix | phosphoric acid and deoxyribose sugars |
| 1 P + 1 deoxyribose + 1 Nitrogenous base = | acidic nucleotide, ergo 4 separate nucleotides can be formed based on each of the nitrogenous bases available |
| nitrogenous bases of DNA | purines: adenine and guanine, pyrimidines: cytosine and thymine |
| genes are made of DNA ________ code. | triplet |
| the process of going from DNA code/template to an mRNA codon/complement | transcription |
| 3 mRNA bases equals one | codon |
| one codon = | one amino acid (3 nucleotide bases together forms a codon when referring to RNA so 3 bases is a codon is an amino acid) |
| an amino acid is made of | a sequence of RNA codons (nucleotide complements of the DNA code/template) strung together to form a protein |
| If transcription is DNA to mRNA, what is translation? | mRNA to protein (via t-RNA anticodons) |
| the importance of DNA | It's ability to control protein formation in the cell, via the genetic code |
| How does DNA control protein formation in the cell? | the genetic code |
| The genetic code consists of successive triplets of bases. 3 successive bases is a code ______. | word. |
| Successive ________ (code words) eventually control the sequence of amino acids in a protein molecule that is to be synthesized in the cell. | triplets |
| The first step of Translation is listed in the notes as "RNA polymerase binds to the promoter sequence." What is the actual first step, which we will call the "pre-step": | RNA-Poly activates the RNA nucleotides with two phosphates apiece, forming a triphosphate, then combines it with a high energy Phos. bond from ATP |
| DNA is sequestered in the cell and cannot leave. How does it control the happenings in the cytoplasm? | It transfers its code to a trusty emissary - RNA! |
| The transfer process between DNA and mRNA is called | transcription |
| How does the RNA get out of the nucleus with its codon message? | nuclear pores |
| Differences in the RNA codon from the DNA one? | RNA uses ribose instead of deoxyribose, and RNA uses Uracil neucleotide instead of thymine. |
| Read DNA from ___' to ___' and RNA from ___' to ___'. | DNA is 3-5, RNA is 5-3 |
| DNA is ___' to ____' | 3-5 |
| How do the 4 RNA nucleotides get activated? | RNA Polymerase adds 2 phosphates to each nucleotide, forming a triphosphate, then combines it with high-energy phosphate bonds from ATP. All this newly available ATP encourages the addition of ea new RNA nucleotide to the end of the developing RNA chain. |
| The DNA template (code) forms the RNA ________ (______). | complement (codon) |
| enzyme which directs mRNA molecule/codon formation | RNA polymerase |
| RNA poly can recognize what marker on the DNA code/template which tells it where to dock and begin transcription. | promoter |
| After RNA polymerase recognizes the promoter on the DNA helix, it docks and then... | unwinds the DNA 2 turns (20 base pairs) and separates the strands. |
| RNA polymerase continues to unwind and separate DNA after it begins at the promoter. As it moves along the DNA strand, it adds a newly activated (triphosphate) RNA ___________. | nucleotide that is the RNA equivalent of the DNA nucleotide (all the same except for uracil) |
| Why does RNA polymerase initially add two phosphates to the RNA nucleotides before beginning transcription? | When RNA Polymerase is actually transcribing the DNA, as it adds each of its RNA nucleotides to its chain, it breaks the 2 phosphate bonds and so much energy is freed up that a covalent bond can be made with the remaining phosphate on the nucleotide. |
| what happens to the final phosphate bond on the RNA nucleotide when RNA polymerase breaks off the other two it added earlier? | Much energy released-enough to form a covalent bond between the nucleotide and the ribose sugar at the end of the chain RNA Poly is assembling. |
| After an RNA nucleotide goes from monophosphate to triphosphate then back to monophosphate, it has now formed _______ | mRNA! |
| Eventually during transcription, RNA Polymerase will reach a ______ code on the DNA. | stop (chain-terminating sequence) |
| Once RNA Polymerase is freed of a DNA strand, what happens to it? | It's a big enzyme and it goes to work on another RNA chain |
| Why does DNA so easily let go of RNA Polymerase and the mRNA chain it made, once the stop code is reached? | DNA has self-affinity (prefers to bond with its own nucleotides) so zips back up, breaking the weak H+ bonds that held it to RNA Polymerase and the mRNA chain. |
| name the 5 steps of transcription as the basic 3: | Initiation (steps 1,2,3) - Elongation (step 4) - Termination (step 5) |
| Where does Balliet use the word "activated" in the steps, is she talking about nucleotides or amino acids? | Amino ACIDS: in step 4 Elongation when she says the "Activated" RNA molecules react with the growing end of the RNA strand and are added to the 3' end. |
| To which end does RNA Poly add nucleotides when making mRNA? | 3' |
| In step 4 Elongation of transcription, mRNA is formed as the complement of bases to DNA. This base pairing has transcribed a DNA code into an | mRNA codon. |
| Termination (step 5) continues until? | the stop code is reached on the DNA |
| Do protein coding segments lie next to each other or are they separated? | separated by intervening non-protein coding segments called INTRONS |
| First chemical step of protein synthesis, regarding actual amino acids, not nucleotide assembly of mRNA: | 1. protein assembly: Each a.a. is ACTIVATED by ATP combining with it to form adenosine monophosphate + aa complex, giving up two high-energy Phosphate bonds when this happens. This makes AMP |
| second step of protein assembly in the cytosol: | 2. protein assembly: ACTIVATED aa, having an excess of E, comines with its specific t-RNA (transfer RNA) to form an amino acid+tRNA complex, and @ once releases the AMP. |
| third step of protein assembly | 3. protein assembly: t-RNA carrying the aa complex contacts the mRNA in the ribosome. The anticodon of tRNA attaches to mirror mRNA codon, lining up the aa with the right place in the chain. Peptide bonds form b/w aa and chain, due to peptidyl transferase |
| what does peptidyl transferase require in order to form a peptide bond between the growing protein and the newly positioned amino acid (by tRNA) so tRNA will let go of it? | 2 additional high-energy bonds, making a total of 4 high-energy bonds used for each aa added to the protein chain. Thus, making a protein is damned expensive energy-wise for the cell. |
| fourth step of protein assembly | 4. protein assembly: stop codon (either UAA,UAG,UGA) encountered by ribosome, ending transcription. |
| Exon | Ex-pressed, meaning an exon is the coding part of the mRNA, the part the nucleus ordered. |
| Intron | In-tervening, meaning the "junk" in between sequences/exons on the mRNA that the spliceosome removes by looping out, then gluing the exons back together to stay true to what protein the nucleus ordered. Lariat is used by spliceosome. |
| To which end of mRNA is the Phosphate cap added, while it is still in the nuclear pore? | 5' end, thus a 5P-cap |
| To which end is the poly-A tail added to mRNA while it is still in the nuclear pore? | 3' end, thus a 3-A'd monster! |
| Each gene (some 30,000 in all) has at least one mechanism of __________ control. | feedback |
| genes responsible for forming the enzymes needed to make something | structural genes |
| the place on the DNA strand, or the sequence of genes on the chromosome, that tells what enzymes will be needed to control the process of making anything (the management pool from which the cell chooses) | operon |
| a group of nucleotides on the DNA strand that has a specific affinity for RNA-Polymerase | the promoter |
| the desired concentration of a cell product or reaction is controlled automatically through either ________ or _________ feedback. | negative or positive (negative means there is enough of the product so stop making it, therefore the product itself is what controls its production.) |
| Once the 5'P-cap is added to the head and the Poly-A tail is added to the 3' end of the mRNA, what happens to it? | it leaves the nuclear pore and goes into the cytoplasm |
| what do the 200 Adenosine residues of the Poly-A tail on the 3' end of mRNA do? | keep it from being degraded |
| what does the 5'P-cap added to the 5' end of the new mRNA head do? | prevents unraveling |
| the complementary sequence to the DNA strand | mRNA |
| organized in codons/triplet bases | mRNA |
| each codon/triplet codes for one | amino acid |
| how many codons/triplets make an amino acid? | one |
| start codon | AUG |
| the name for swapping or losing the last letter of a codon/triplet | single nucleotide polymorphism |
| where does translation take place? | cytoplasm |
| translation requires 3 things: | mRNA, ribosomes, t-RNA with attached amino acid |
| activation and attachment to the tRNA stem requires what enzyme? | aminoacyl-tRNA-synthetase |
| why is the attachment of the proper aa to the tRNA an ATP dependent step? | the the bond releases two high-energy phosphates, forming AMP |
| how many ATP's required to make a protein? | 4 ATP |
| acts as a carrier molecule during translation | tRNA |
| ___ (energy) is with the amino acid while ____ (energy) is with the chain. | ATP, GTP |
| 3 steps of translation | initiation, elongation, termination (same steps as transcription) |
| initiator codon of translation | AUG |
| what happens to AUG during translation initiation? | AUG attracts the small ribosomal subunit to the mRNA |
| promotes association between AUG and small ribosomal subunit | Initiation factor |
| what does tRNA do when it detects the initiation factor? | AUG is met with tRNA carrying UAC/methionine and attaches to the mRNA |
| Once the tRNA has brought over and attached the AUG anticodon to the UAC/methionine amino acid, what happens? | the initiation factors drop away and the large ribosomal subunit binds |
| what must happen before the large ribosomal subunit will bind to the smaller one? | tRNA shows up with its UAC/Methionine amino acid, attracted to the mRNA by the initiation factor, and then binds to the mRNA. The initiation factor, having done its match-making, drops away and the large ribosome subunit binds. |
| Regarding the P and A sites of the ribosome, P stands for? A stands for? | Primary, Added (there is also an E site, for EPA, and for Enter, but it is not discussed in this class) |
| ___ site: tRNA molecule with the amino terminal portion of the newly synthesized protein still attached to the acceptor stem | P-site (primary means still attached) |
| __site: tRNA molecule sits with appropriate amino acid before incorporation | A-site (attachment) |
| what part of translation is AUG to UAC/methionine? | Initiation |
| Initiation uses an initiation factor to attract the tRNA with the methionine. What does the elongation step use? | why, an Elongation factor, of course! |
| the Elongation factor requires ____(energy). We know this because we remember the amino acid requires ATP but the protein, where we are now, requires _____. | GTP |
| what kind of bonds link the amino acids to one another during the Elongation process? | peptide! |
| _______ bonds connect amino acids, forming a polypeptide chain. | Peptide |
| First tRNA breaks bond to first amino acid, tRNA moves away, then ribosome slides one codon down mRNA strand. What is this called and what is being made? | Elongation, polypeptide |
| Initiation uses an initiation factor, Elongation uses an elongation factor, and Termination uses a __________ factor to make sure there is a happy ending. | release |
| During __________, a site reaches a stop codon (UGA, UAA, UAG) but will continue until the _________ factor binds. | termination, release |
| Once the release factor binds during termination, the protein is now free and requires? | GTP! |
| when multiple ribosomes translate a single mRNA simultaneously | POLYribosome |
| responsible for transcription processing | DNA |
| responsible for transporting to complement to cytosol, translation, and for mRNA stability | RNA |
| 2 types of proteins | structural, enzymes (functional) |
| type of protein responsible for protein activity/control | enzymes |
| What is responsible for protein trafficking? | free ribosomes and RER |
| synthesizes secretory proteins | RER |
| synthesizes peripheral membrane proteins | free ribosomes |
| synthesizes cytosolic proteins | free ribosomes |
| synthesizes integral membrane proteins | RER (ER and cell alike) |
| synthesizes proteins destined for nucleus, mitochondria and peroxisomes | free ribosomes |
| synthesizes proteins headed for lysosomes, golgi apparatus and nuclear membrane | RER |
| why does it make sense for RER to synth proteins headed for golgi apparatus, lysosomes and nuclear membrane? | Golgi is secretory, nuclear membrane is studded like RER and lysosomes are studded like RER with protein receptors. The RER makes these integral membrane proteins. |
| proteins made for cellular organelles, and export or insertion into membranes are modified with a particular __________ __________ so they will be recognized as special. | signal sequence |
| the signal sequence attached to the beginning of proteins bound for cellular organelles, or for export or for insertion into a membrane is the first __-__ amino acids on the amino terminal end. | 20-30 |
| each cell has powerful internal __________ mechanisms that keep various functional operations of the cell in time with each other | feedback |
| two methods by which biochemical activities of the cell are controlled: | enzyme regulation & genetic regulation |
| feedback mechanism where the degree of activation of the genes themselves is controlled | genetic regulation feedback control |
| controlling activity levels of enzymes already present in the cell is called | enzyme regulation feedback control |
| to make a biochemical product, a cell requires the formation of certain _________ to catalyze steps on the way to making a non-protein endproduct. | enzymes |
| all of the genes needed to form the specific enzymes required to catalyze a biochemical product are usually contained on the same DNA strand/chromosome. This complex that controls the enzymes and therefore the biochemical product output is called an? | Operon! |
| components of an operon | Activator(ion) regulator, Promoter sequence, Repressor(ion) regulator, structural gene for enzyme 1, structural gene for enzyme 2, structural gene for enzyme 3, etc. |
| what are the enzyme genes in an operon called? | structural genes - because the formation of these genes will result in a biochemical product |
| an operon is the complex which codes for a specific ________ product | intracellular |
| a group of nucleotides on the operon which has a specific affinity for RNA polymerase | Promoter |
| essential element for activating the operon | the promoter |
| why is the promoter THE essential element for activating an operon? | because it attracts RNA polymerase which must then bind before it can begin moving along the DNA strand to synthesize RNA |
| what band of nucleotides lies within the promoter region? | the repressor operator of the operon |
| what does the repressor operator of an operon do? | if there is already too much product, negative feedback (presence of that product) will cause a REGULATORY PROTEIN - a repressor protein to be exact - to bind to the repressor operator, shutting down the operon enzyme/rx/product machine |
| what does an activator operator do? | in the case of not enough product, an activator protein will bind to the activator operator upstream of the promoter, turning on the promoter which attracts RNA-Poly and then begins RNA synthesis |
| a Negative regulatory protein would block what? | RNA polymerase from binding to the promoter. |
| Why is smack in the middle of the promoter a good place for the repressor operator? | because it attracts a negative regulatory protein- the repressor protein -which cockblocks RNA-Polymerase from binding to the promoter, ergo it can inhibit the operon at the promoter if it is right in the middle of the damn thing! |
| A regulatory protein that helps attract RNA Poly to the promoter is called what and goes where? | Activator protein, goes to Activator operator |
| what two ways can negative feedback regulation shut down an operon? | a repressor protein binds to the repressor operator OR the activator protein separates from the activator operator upstream - either way, the operon becomes inhibited. |
| Besides the binding of a repressor protein to the repressor operator or the disjoining of activator protein to activator operator, what other ways can the cell control transcription of the operon? | regulatory GENE(not protein)elsewhere forms regu. protein that turns the operon off or on. The same regulatory proteins can fx to activate one operator but repress another = REGULON. Operon control may be elsewhere. Transcription factors. Hormones. |
| Mechanism for gene control associated with activator and repressor proteins, as well as negative feedback. | operon = genetic regulation as negative feedback |
| intracellular activators or inhibitors that act directly on specific intracellular enzymes is a form of | enzyme regulation as direct feedback |
| in enzyme regulation as direct feedback, which enzyme in the sequence does the product interact with? | the very first one (which is why it's called DIRECT)- this stops intermediate products from forming. Cuts it off at the start. Nips it in the bud. Puts the kaibosh on the ol enzyme. You get? |
| important for controlling intracellular concentrations of amino acids, amino acid derivatives, and intermediate substrates and products of carbohydrate, lipid, and protein metabolism. | gene regulation negative feedback |
| responsible for controlling intracellular concentrations of multiple amino acids, purines, pyrimidines, vitamins, and other substances | Enzyme inhibition (direct form of negative feedback) |
| Activating an enzyme that is mostly dormant but suddenly needed is called | enzyme activation |
| example of enzyme activation of a usually dormant enzyme | When ATP breaks down, cAMP forms so buildup of latter activates phosphorylase enzyme to split glycogen and replenish ATP stores. This is ENZYME ACTIVATION of Phosphorylase |
| in the case of ATP and phosphorylase enzyme activation example, what is enzyme activator for phosphorylase? | large amts of cAMP resulting from breakdown of ATP (signals activation of phosphorylase so glycogen can be broken down to replenish ATP stores) |
| what is an example of enzyme activation and inhibition happening at the same time? | purines and pyrimidines: presence of purines inhibits more enzymes for purine synthesis but activates enzymes for pyrimidine synthesis and vice versa. |
| what is the purpose of having activation and inhibition of enzymes at once? | cross-feed which keeps levels of each equal |
| two principal methods by which cells control proper portions and proper quantities of different cellular constiutents: | gene regulation and enzyme regulation. The genes and enzymes alike can be activated, inhibited or both. Functions as a Neg Feedback mechanism. Sometimes hormones control. |
| Sometimes, _______ control the intracellular biochemical reactions by activating or inhibiting one or more of the intracellular control systems. | hormones |
| DNA controls cell reproduction, as well as growth (via genes regulation) and products (via enzyme regulation). If there is any central theme to life, it is the DNA-______ system. | genetic |
| the period from one cell reproduction to the next | life cycle of the cell |
| When mammalian cells are not inhibited, what are they doing? | reproducing! |
| How long is the cell life cycle between reproduction/mitosis? | 10-30 hours |
| termination of the cell life cycle by the series of events from which is borne two new daughter cells | mitosis |
| Since the actual stage of mitosis lasts about 30 min, in what stage does the cell spend 95% of its life? | interphase |
| what almost always slow or stop cell reproduction tendencies? | inhibitory factors (some for only 10 hours at a time- like marrow cells; some for an entire human lifetime in which the cell never divides - as in the case of nerve cells) |
| where does reproduction begin | nucleus |
| first step of reproduction in the nucleus | replication (duplication) of all DNA in the chromosomes |
| Mitosis cannot take place until all the ____ in the chromosomes has been replicated. | DNA |
| difference between number of strands replicated in RNA vs DNA? | DNA is both strands of the chromosome, not just one, are replicated |
| The entire strand of the DNA helix is replicated in DNA replication, whereas in RNA transcription, what happens? | only a small portion is replicated |
| principle enzymes for replicating DNA | DNA polymerase, a complex of multiple enzymes |
| causes bonding of successive Oazaki fragments | DNA Ligase |
| DNA strand is made as hundreds of sites are replicated simultaneously and glued together by | DNA ligase |
| each new DNA strand remains coiled to | one half of the original chromosome, so that 2 new complete chromosomes exist, each having one old and one new |
| what uncoils DNA helix | DNA helicase |
| when does the intensive DNA proofreading and repair start? | in the hour between DNA replication and mitosis starting |
| wherever inappropriate DNA nucleotides have been matched up with the nucleotides of the original template, special enzymes cut out the defective areas and replace them with the right complementary bases. What is this called? | DNA proofreading |
| the unusual circumstance of repair and proofreading not correcting a mistake in the transcription process | mutation |
| How many mutations are expected in the 30,000 possible genes that are passed from parent to child? Why is this usually not a problem? | 10, because each human genome is represented by two separate sets of chromosomes with almost identical genes. The kid has one functional gene pair almost always available, despite mutations |
| DNA helices of nucleus are packaged in | chromosomes |
| The human cell contains ___ chromosomes arranged in ___ pairs. | 46,23 |
| why is it usually stated that different genes exist in pairs? | because most of the genes in the two chromosomes of each pair are identical |
| proteins in the chromosome around which DNA is coiled | histone core |
| how does a protein histone determine gene regulation? | as long as the DNA is coiled around the histone, it cannot be replicated either for DNA or RNA |
| a small addition to a protein histone that allows small segments at a time to form RNA | decondense |
| point at which the newly formed chromosomes remain attached to one another | centromere |
| duplicated but still attached chromosomes | chromatids |
| process by which cell splits into two new cells | mitosis |
| what forms the mitotic apparatus of spindle fibers? | centrioles |
| a pair of centrioles and their attached pericntriolar material | centrosome |
| how do the centrioles move away from one another | polymerization of microtubules growing at odds and pushing centrioles away from one another |
| forms from centrioles, microtubule SPINES that penetrate nuclear envelope and help separate chromosomes | asters |
| complex between centriole pairs | spindle |
| the entire set of microtubules plus the two pairs of centrioles | mitotic apparatus |
| prophase | chromatin condenses into chromatids |
| interphase | 95% of cell life cycle; chromatin of loosely coiled DNA |
| asters pierce the nuclear envelope and microtubules attach to the chromatids at the centromeres during this stage and chromatids are yanked apart | pro-metaphase |
| chromatids are yanked apart | pro-metaphase |
| actin slides the spines of the asters away from each other and chromatids are pulled to the CENTER to LINE UP along the equatorial plate | metaphase |
| the two chromatids of each chromosome are pulled apart at the centromere, forming two separate sets of 46 daughter chromosomes. The cell is fat, at this point. | anaphase |
| final phase of mitosis where mitotic apparatus falls apart, new nuclear membrane forms from ER, cell pinches in 2 via microfilaments | telophase |
| blood forming cells of bone marrow, germinal layers of skin, epithelium of gut | cells which reproduce constantly |
| smooth muscle cells produce | produce occasionally |
| neurons and Striated muscle cells produce | produce only once at fetal life |
| what kind of cells typically cannot regenerate | highly differentiated cells like nerve and muscle cells |
| often come from other parts of the body and control growth of a certain cell type | growth factors |
| some growth factors travel in the blood but some must be present in? | adjacent tissues and cause entrainment |
| most normal cells stop growing when they run out of | room (contact inhibition) |
| cell product accruing causes cell growth to stop. This is a method of | negative feedback growth inhibition |
| name the 3 ways cell growth is controlled: | growth factors, contact inhibition, negative feedback when cell products accumulate |
| determined almost entirely by the amount of functioning DNA in the nucleus | cell SIZE! |
| if replication of DNA doesn't occur, then a cell grows to a certain size and | stays at that size |
| chemical that can stop mitosis but allow DNA replication and therefore growth but not division to continue | colchicine |
| changes in physical and functional properties of cells as they proliferate in the embryo to form the different bodily structures and organs | cell differentiation |
| Since every cell carries an entire cache of necessary genetic info for development of all structures in the body, what causes cell differentiation? | selective repression of different genetic operons |
| Because a repressor regulatory protein can potentially wind a gene so tightly in histone that it is cut forever off from replication, the repressed ____ never functions again. | gene |
| Mature human cells produce a maximum of 8,000-10,000 proteins rather than the potential 30,000 or more proteins if all genes were active because of | repressor regulator proteins that coil some genes so tightly in histone that they are dormant forever |
| the 100 trillion cells of the body are controlled by regulating cell division and cell _____ | death (programmed cell death: apoptosis) |
| apoptosis | programmed cell death |
| necrosis | injury which causes a cell death |
| orderly cell death with no swelling vs. inflammation and cell death from acute injury | apoptosis vs necrosis |
| family of proteases that activates programmed cell death/apoptosis | caspases (stored as inactive procaspase, like a bottle of cyanide with a safety seal) |
| when most apoptosis occurs | during developmental tissue remodeling (ie, the formation of separate digits) |
| apoptosis may play a role in _______ disease (ie, neurodegenerative), cancer and autoimmune diseases | Alzheimer's |
| caused in almost all instances by mutation or some abnormal activation of genes that control cell growth and cell mitosis | cancer |
| abnormal cancerous genes | oncogenes |
| suppress the activation of many oncogenes | anti-oncogenes |
| why don't mutated cells in the body usually become cancerous? | less survival capacity, normal feedback controls even though mutants, often destroyed by immune system |
| abnormal protein formation activates the body's immune system and causes it to form ________ or lymphocytes that react against cancer cells | antibodies |
| why do people on immuno-suppressant drugs or with suppressed immune sys run the risk of cancer? | because the immune sys can't recognize the abnormal proteins made by any mutant cells |
| apart from cancer cell mutants being nonviable, destroyed, self regulated by feedback, what is the final reason mutations usually don't turn cancerous? | several different activated oncogenes are required simultaneously. The Perfect Storm is necessary. |
| why don't we all just get cancer? | precision of DNA chromosome replication, proofreading, repair before mitosis is allowed to happen at all! |
| factors that increase risk of mutant genes/cancer/oncogenes | ionizing radiation, chemical substances, physical irritants, heredity, viruses (not so much) |
| cancer substances that cause mutations | carcinogens |
| why is heredity a cancer factor? | one less mutation must take place (one is already present) |
| does the cancer cell have contact inhibition? | no, they don't mind crowded disgusting conditions |
| are cancer cells sticky like normal cells? | no, they wander all over the body and don't know where their home is |
| what can cancer cells produce that means they draw blood sources to them? | angiogenic factors cause new blood vessels to grow into the cancer |
| why do cancer cells kill? | cancer tissue competes with normal tissues for nutrients. They breed like fire and suck up the possibilities, starving normal tissue that has boundaries and limits. Don't date cancer. |
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