Important to know for final Flashcards

Question

Components of a checkpoint for DNA damage

Answer 1

1) sensor-is DNA damaged, ATM?ATR proteins 2) transducer-create a signal, Cdc25, p53, MPF protein 3) effector-change key enzyme action or protein, phosphorylated histones, lamins, ubiquintin, p21

Answer 2

- radiate from centrosome - form aster - help position mitotic apparatus - determine cleavage plane - shortening help pull centrosomes apart

Answer 3

- duplication of centrosomes during S-phase - two centrioles arranged perpendicularly - where microtubules are nucleated and start growth - microtubules grow outward from the MTOC (minus end in the MTOC) - two types: basal bodies associated with cilia and centrosomes - embedded in nuclear membrane

Answer 4

- attach to chromosomes at kinetochore | - pull chromosomes to different poles

Answer 5

- interdigitate with opposing pair - support framework - help push centrosomes apart

Answer 6

* biggest in size - minus end points toward centrosome and away from kinetochore, low rate of assembly=alpha tubulin subunit - plus end points away from centrosome, high rate of assembly=beta tubulin subunit - attachment occurs at kinetochore - rapid fluctuations in length by polymerization (gain) and depolarization (loss) of tubulin subunits at + end - hollow, rigid cylindrical tubes - greatest amount of strength and durability - made from tubulin dimer with alpha and beta tubulin subunits, which polymerizes to form protofilaments (form cylinder) that are asymmetric and all with same polarity - asymmetrical and polarized - initial polymerization is spontaneous but slow and requires the gamma tubulin subunit which will dissociate from the microtubule after polymerization - when gamma tubulin subunit is attached, there is no gain of subunits at the minus end, only at the PLUS end - depolymerization can be spontaneous but slow as well - constantly being polymerized and depolymerized - rates of assembly and disassembly (growth) depends on tubulin concentration in the environment - assembly and disassembly allows for cell movement - instability controlled by the hydrolysis of GTP bound by tubulin * **as long as the tubbulin has GTP, it can attach, but if GDP is only present, it won't be able to attach * **after a bit of time, suddenly all the GTP have been hydrolyzed to GDP, and now the filament can't grow anymore and will collapse - some drugs stabilize and some destabilize microtubules - microtubule orientations can be variable in different parts of the cell * two subunits are added at the same time, whereas only one subunit is added at a time on microfilaments

Answer 7

- motor protein - walk toward + end of microtubule - help move vesicles along a microtubule * smallest of motor proteins (dyneins are bigger) - pair of globular heads generate the force - stalk and fan-shaped tail binds the cargo and determines what will bind - movements are mediated by ATP hydrolysis (1 ATP per step, 1 dimer at a time (ex-stays on alpha subunits and skips beta subunits) - moves along single microtubule protofilament - go toward the plasma membrane from the golgi - cargo is bound by scaffolding proteins which is required in order for movement to occur - walking steps: 1) binding of cargo 2) only one head of kinesin with ADP bound will bind to microtubule 3) ATP replaces ADP on bound head and causes the neck to pivot 4) second head binds, replaces ADP with ATP, bends neck 5) ATP is hydrolyzed to allow trailing head to release microtubule

Answer 8

- motor protein - walk toward minus end toward centrosome - head is the moving end of protein - help move vesicles along a microtubule - ubiquitous eukaryotic motor protein * bigger motor protein than kinesin - head generates force - 2 identical heavy chains - cargo attached by dynactin - functions: 1) chromsome movement in mitosis 2) positioning of golgi 3) momevnt of vesicles and organelles through cytoplasm 4) axonal retrograde movement of organelles 5) in fibroblasts and endothelial cells, move endosomes, lysosomes, golgi-derived vesicles toward cell center

Answer 9

- actin and myosin II slide past one another, tighten the noose, shorten length - myosin head rotates and causes sliding of actin

Answer 10

- gene knockout, interfere with RNA, use of antibodies - cells replicate chromosomes but unable to divide, results in one large multinucleated cell able to have rapid gene expression and lots of RNA/protein

Answer 11

- tool to inhibit protein functions - binds with high specificity to antigen - may disrupt normal function of protein due to steric hindrance (like antibody binding to myosin prevents cells to divide) - block protein translation in prokaryotes, which kills bacteria

Answer 12

- storage and decoding of genetic information (DNA condensed and organized) - largest organelle - structure: nuclear matrix (network), nucleolus (rRNA synthesis, granular region, site of ribosome assembly), surrounded by nuclear envelope

Answer 13

euchromatin-active chromatin, appears lighter, open, dispersed heterochromatin-inactive chromatin, darker and located near periphery of nucleus, not transcribed or translated

Answer 14

- defects in lamin A (nuclear lamina) - premature aging - nuclear chromosomes aren't held in place correctly - disease that can arise due to alternative splicing - nuclear lamins form network lining inside nuclear envelope, mutation in intermediate filaments=progeria

Answer 15

- opening is lined with proteins=nuclear pore complex - nucleoporin - octagonal symmetry - cytoplasmic filaments extend to cytoplasm - regulate transport of RNA and proteins into and out of nucleus - very fast transport of small molecules, but large proteins must be assisted

Answer 16

- specific amino acid sequence marks proteins entering the nucleus through nuclear pores - positive charge - turnstile ticket

Answer 17

- recognize the NLS, binds to alpha subunit and bring proteins in - work in the opposite direction, but recognize other signals

Answer 18

- spontaneous movement of molecules from high concentration to low concentration - small molecules enter and exit by diffusion - energy is dissipated when molecules flow down the gradient - energy is stored until released which permits molecules to move down their concentration gradient

Answer 19

1) histones 2) fibres 3) looped domains 4) mitotic chromosomes

Answer 20

-group of 4 histones in DNA organization

Answer 21

- carriers of genetic information - form dyads during S phase (chromosome duplicate) - sister chromatids=attached duplicated chromsomes - translocations (movement to new chromosome), inversions (portion of chromosome flipped), deletions (section removed), insertions (section inserted) - share all chromsomes with chimps except 2

Answer 22

- constricted part of chromosome - DNA contains alpha-satellite - attach to kinetochores during M phase - made of non-transcribed repetitive sequences

Answer 23

- non-coding regions at ends of chromosomes - short repeated sequences - specialized proteins - capped end structure protects ends of chromosomes from nucleases - helps distinguish chromosome ends from broken DNA - prevent chromosomes from fusing together - attachment to nuclear scaffold - problem=when chromosomes replicate, telomeres get shorter - cause of aging process - cloned Dolly has shorter telomeres than normal sheep (premature aging)

Answer 24

- enzyme that replicates DNA strands | - builds in 5' to 3' direction

Answer 25

- elongates telomere - RNA containing enzyme that adds more nucleotides to 3' end of telomere - absent in normal tissue - present in tumour cells, one celled organisms, germ cells, stem cells

Answer 26

- telomeres shortening - accumulated errors and mutations - chronic risk exposures like oxidants and UV - glycation (sugar binding DNA, proteins and lipids)

Answer 27

``` RNA polymerase I: -transcribes rRNAs RNA polymerase II: -complex of proteins -transcribes genes -makes hnRNA in nucleus (before mRNA) the primary transcript, has a half-life RNA polymerase III: -transcribes tRNA -5S rRNA ```

Answer 28

- DNA binding proteins that regulate transcription | - have DNA binding domain, activation domain, and site to bind a second subunit to form a dimer

Answer 29

1) core promoter-on/off regulation of the gene, binds general transcription factors 2) proximal promoter: regulate frequency of transcription, binds general transcription factors 3) distal promoter: response elements, binds specific transcription factors 4) enhancers: activate gene expression, binds specific transcriptional activators, one enhancer can activate multiple genes

Answer 30

a) still some transcription activity, even though the on/off switch has been taken out b) removing the suppressor makes transcription activity go over and above, gene expression happens whether you want it or not

Answer 31

by altering histone-binding and making the gene accessible to RNA polymerase

Answer 32

- link transcription factors to general transcription factors and chromatin re-modeling enzymes - enhances RNA polymerase activity - pre-initiation complex work

Answer 33

- 5'UTR cap = start - 5' untranslated region near cap - 3'UTR untranslated to coding region = end - poly-A-tail

Answer 34

- removes introns from the hnRNA - complex of snRNA, hnRNA and proteins=snurps (snRNPs) - formed in nucleus during transcription - does the mRNA splicing - matching, cutting, ligation of hnRNA

Answer 35

snurps - when small nuclear RNAs (snRNAs) bind to U proteins - move introns snorps - in nucleus only - removal of spacers and base modifications - cut, methylate nucleotides, convert some to pseudouridines

Answer 36

- catalytic RNA - splicing reaction in protozoa, mitochondria, chloroplasts - part of the intron - catalytic function of snRNPs is in this RNA portion (snRNA) - synthesizes proteins

Answer 37

- stabilizes 5' end to protect from exonucleases - aids in transport out of nucleus - starts translation process

Answer 38

- gradually removed by poly A ribonuclease - when only a small fragment left, mRNA is degraded by exonuclease at both ends - determines half-life - if shortened on mRNA, it can no longer be translated

Answer 39

- different combinations of exons gives proteins with different activities and function - provides control of gene expression - increases the number of proteins made at least 2-fold - sound pitches, sex-determination genes - skips over weak splice sites (weak exons)

Answer 40

- disease that can arise from a defective tau protein - defective MAPs result in Alzheimer's disease (abnormally high phosphorylation of MAPs or tau proteins that are implicated in this fatal neurodegenerative disease where hyperphosphorylated tau proteins stick together into neurofibrillary tangles in neurons so microtubules disintegrate) * fruit flies with mutations in tau proteins exhibit neural, motor and cognitive defects like climbing a wall and courtship training where females reject the dance of the male, releases a pheromone and males don't learn to stop courting

Answer 41

- gets cut out by spliceosome - allows for variety of proteins to be derived from one gene - some have regulatory sequences - permit exon shuffling

Answer 42

- small - translate the information encoded in nucleotide of mRNA into amino acid of polypeptide (with help of ribosome) - adaptor functions: amino acid to tRNA and codon to anticodon - carriers of amino acids and becomes activated - bind to mRNA at the codon - anticodon: three sequential nucleotides in middle of loop that recognizes complementary RNA codon - anticodon has a wobble position which can bind to non-complementary nucleotides=degenerative code - transcribed by RNA polymerase III

Answer 43

- assembled in nucleolus - proteins imported from cytoplasm - structural and catalytic function - lots of internal base-pairing - makes ribosomes - 5S rRNA is NOT made in nucleolus, transcribed by RNA polymerase III, requires no processing, shipped to nucleolus after synthesis, required to make large subunit of ribosome

Answer 44

- made of one large (60S) and small (40S) subunit = 80S eukaryotic ribosome - made up of rRNA and proteins - structural, ribozyme and catalytic functions - subunit assembly takes place in nucleolus - once assembly done, ribosome sent to cytoplasm for translation - where mRNA strand assembles - make proteins in cytoplasm - some free in cytoplasm and some attached to endoplasmic reticulum

Answer 45

transcription=nucleus | translation=cytoplasm

Answer 46

- synthesis of proteins - nucleotide code (codons) translated into amino acid sequence - takes place in cytoplasm - occurs on circularized mRNA template, many ribosomes attached - mRNA can no longer be translated if poly A tail is shortened

Answer 47

- create loss-of-function mutant - use antisense RNA (double stranded RNA) to block translation - RNA interference - use antibodies - gene knockout

Answer 48

1) double-stranded RNA (dsRNA) enters cell 2) Dicer cuts dsRNA into short interfering RNA (siRNAs) 3) RNA-induced silencing complex (RISC) binds siRNA and unwinds, one strand kept 4) RISC and single strand looks for mRNA with exact complementary match 5) slicer (protein of RISC) cuts mRNA and is attacked by exonucleases and destroyed - add double stranded RNA specific for gene and gene is silenced by destroying all mRNAs with exact match to dsRNA - Dicer and RISC not found in prokaryotes

Answer 49

``` short term: -make dsRNA in vitro -liposomes -inject -shoot -feed long term: -genetic transformation ```

Answer 50

- anticancer therapy: siRNAs injected to reduce liver tumour size - antiviral therapy: cells treated with siRNA specific for gene to prevent HIV

Answer 51

- combine gene with gene promoter (glue DNA fragments) - insert recombinant DNA into gene shuttle like a transposon - introduce into new host by injection, gene gun, electric shock, lipid capsules, viruses

Answer 52

- add gene to see change in phenotype - must be dominant gene - turning on different transcription factors that turn on tissue specific proteins - alternative splicing

Answer 53

- remove or turn off gene to see change in phenotype - RNA interference technology (add double stranded RNA specific for gene and gene is silenced by destroying all mRNAs with exact match to dsRNA) - differences in miRNAs (RNA blocked)

Answer 54

- mobile DNA fragments that move around genome and cause mutations - our genome loaded with them - can be used for loss of function mutants (RNA interference)

Answer 55

- naturally occurring dsRNAs 1) pre-miRNAs processed by Dicer into miRNAs 2) RISC complex unwinds miRNA and guides target mRNA - miRNA do not bind to target with 100% complementary - bind to 3'UTR - translation blocked and turn off gene expression - single miRNA can bind to more than one gene - expressed as tissue-specific manner

Answer 56

- budding and fusing carriers that transport molecules between compartments - transport proteins in endomembrane system - travel along microtubules - anchored on microtubules by proteins like dynactin - propelled by motor proteins like dynein and kinesin - covered by protein coat - have receptors like integral membrane proteins that bind ligands with high specificity and high affinity

Answer 57

- network of membranous tubules in cytoplasm - involved in production of phospholipids, proteins - rough and smooth ER

Answer 58

- studded with ribosomes - continuous with nuclear envelope - synthesis of proteins to be compartmentalized and destined in lysosomes, integral membrane proteins, proteins in lumen of endomembrane system, endoplasmic reticulum, golgi, plant vacuoles and secretory vesicles - synthesis of integralproteins - membrane biosynthesis, some lipid biosynthesis - glycosylation of proteins

Answer 59

- no ribosomes - site of synthesis of specialized enzymes - in specialized cells: skeletal muscle, kidney tubules, endocrine glands, secretory cells - synthesis of steroids - synthesis of detoxification enzymes - enzymes involved in glucose release - release of Ca2+ ions used in muscle contraction - lipid biosynthesis

Answer 60

- ensures tertiary structure of proteins is properly folded - proteins that bind to alter folding of new proteins - associate with proteins in cytoplasm or ER - facilitate folding by unfolding incorrect structures - if unable to refold, proteins are exported out of ER and destroyed by proteasome

Answer 61

-enzyme that cuts protein to make it functional or nonfunctional

Answer 62

- most proteins destined for secretion, extracellular matrix, endomembrane system and plasma membrane=glycoproteins - in golgi=step-wise glycosylation of proteins - adding sugars to a protein - N-linked glycoproteins: occurs in rough ER - O-linked glycoproteins: only occurs in Golgi - makes proteins more hydrophilic - allows to bind to extracellular matrix - reduces susceptibility to proteases - provides structural complexity - provides more specificity in interactions with other proteins - abundance of glycosylated proteins found on cell's surface for cell-cell interaction

Answer 63

- cytosolic proteins - peripheral proteins of inner cell membrane - sent to nucleus - destined for chloroplasts, mitochondria, peroxisomes

Answer 64

- hydrophobic - required on proteins destined for rough ER - recognized by signal recognition particle (SRP) - signal peptide binds to interior of translocon to allow translated protein into rough ER - removed by signal peptidase enzyme

Answer 65

- protein channel or translocator - allows ribosome to bind, then signal peptide to bind to interior, and allow translated protein to enter rough ER - allows lateral movement of hydrophobic segment of an integral protein into the lipid bilayer

Answer 66

- proteins embedded in the membrane that spans the entire membrane - has hydrophobic section with stop transfer or nonpolar amino acids in alpha-helical conformation - do not end up in ER lumen - hydrophobic segment stops in translocon - orientation is guided by how the transmembrane sequences are oriented within translocon - roles: communication between cells, organelles and cytoplasm, ion transport, nutrient transport (aqueous channel through lipid bilayer), connections for cytoskeleton - receptors on vesicles that bind ligands at high specificity and high affinity

Answer 67

- destroy proteins that were unable to be properly refolded by chaperones - protein-degrading machine - not a membrane bound compartment - in cytoplasm and nucleoplasm - in both prokaryotes and eukaryotes - functions: 1) housekeeping (clearing out protein from cytoplasm and nucleoplasm at end of their lifespan) 2) remove improperly folded proteins 3) remove ubiquin-tagged proteins with MULTIPLE ubiquintin chains on cytosol proteins - barrel-like structure of globular proteins

Answer 68

- too many unfolded proteins are produced at once, which is monitored by ER sensors - Bip (keeps sensors inactive) releases sensors to help fold proteins and to tells cell to make more chaperones, and to prevent protein synthesis

Answer 69

- keeps sensors of unfolded protein response inactive - once too many unfolded proteins are found in ER, BiP releases sensors, helps fold proteins and tells cell to make more chaperones, and prevent protein synthesis - misfolded proteins are bound to BiP which transports them into cytoplasm by reverse translocation through a translocon to be destroyed by proteasomes

Answer 70

- chaperones - recognize unfolded proteins due to heat shock, cold, anoxia - use ATP hydrolysis to unfold misfolded polypeptides and gives chance to refold properly - recognize misfolded proteins by looking for hydrophobic regions on surface that are exposed that shouldn't be - exposure to a gradual increase in heat gives the cell a chance to make more HSPs and not be killed by extreme heat and cardiac failure

Answer 71

- abnormal forms of proteins - causes kuru, scrapie, mad cow disease - anti-chaperones that change shape of proteins into the wrong configuration (normal prion protein in brain = alpha helices, into mutant prion = beta sheets) - don't get removed due to their shape that protects them from being processed by the cell's machinery that removes misfolded proteins

Answer 72

- protein half-life | - N-terminal amino acid

Answer 73

- ubiquintin=small, conserved protein - ubiquintin ligase=recognize proteins destined for destruction and adds ubiquintin units * single ubiquintin destined for endosomes * multiple ubiquintin chains destined for proteasomes

Answer 74

- single ubiquintin destined for endosomes - network of cytoplasmic tubules and vesicles that receives material taken up by receptor-mediated endocytosis - early endosomes located near peripheral of cell - late endosomes located in interior and receive material from early endosomes and golgi, can develop into lysosomes

Answer 75

- asymmetrical composition in the lipid bilayer - hydrophobic tails (fat soluble) and hydophilic polar heads (water soluble)=amphipathic - lipid composition made in smooth ER by integral membrane proteins - made by inserting new lipids into existing membrane - made primarily of phosphoglycerides - new lipids added on CYTOSOLIC side, NOT LUMEN - asymmetry due to flippases, enzymatic modifications of polar head groups, preferential incorporation and phospholipid-transfer proteins=increases membrane durability and withstand physical stresses - functions: compartmentalization, site for biochemical activities, selectively permeable membrane, transporting solutes, responding to external signals, intracellular interaction, energy transduction - permeable to: lipids, steroids, O2, CO2 - less permeable to: H20 - impermeable to: water soluble compounds like K+, Na+, Ca2+, Cl-, glucose, RNA - structure: lipids, proteins, carbohydrates - fluid mosaic model: lipids in fluid state, rotating and moving laterally, proteins are discontinuous and dynamic

Answer 76

- 1) move laterally on one surface of lipid bilayer 2) flip from one surface to another by flippases 3) transfer to new locations by vesicles 4) single lipids can be carried from one organelle to another

Answer 77

- stacks of cisternae - cell's shipping department - cis region: sugars and proteins are phosphorylated - medial region: enzymes remove carbohydrates added in ER and then add new ones - trans region: where lysosomes are sorted, rich in acid phosphatase - glycosylation of proteins (adding sugars) - anterograde movement (forward): rough ER, cis golgi network, cis cisternae, medial cisternae, trans cisternae, trans golgi network, secretory vesicles and lysosomes - retrograde movement (backward): secretory vesicles and lysosomes, trans golgi network, trans cisternae, medial cisternae, cis cisternae, cis golgi network, rough ER

Answer 78

- are sorted in trans region of golgi - rich in acid phosphatases (hydrolytic enzyme) - cell's digestive organelle - surrounded by membrane - hydrolytic enzymes (lysozyme) break down organic substances like cell wall, nucleic acids, proteins... - proteins destined for lysosomes are tagged with phosphorylated mannose residue, MPRs collect enzymes into budding vesicles - clathrin protein coat on this vesicle - internal acidic pH - membrane contains proton pump (H+ATPase) to maintain acidity - acidic and glycosylated integral proteins line interior to protect membrane from enzymes - functions: 1) heterophagy (degradation of foreign material brought into cell by phagocytosis) 2) autophagy (digestion of intracellular components that are damaged 3) autolysis (cellular self-destruction by rupturing itself and killing cell with its contents) 4) extracellular digestion (discharge enzymes in environment)

Answer 79

- helps bind dynein to a vesicle to anchor and move it along a microtubule - cargo attached by dynactin

Answer 80

COP II-anterograde (forward) movement COP I-retrograde (backward) movement Clathrin-trans golgi network to other destinations like lysosomes and endocytosis

Answer 81

- allows for docking of vesicles on target cell - proteins that each have different locations or targets - direct vesicle traffic from a membrane to specific target - t-SNAREs: target snares located on receiving membrane - v-SNAREs: located on vesicle, type determined by type of COP

Answer 82

- tether the vesicles to the target membrane to then be fused - GTP-binding proteins - extended fibrous proteins - scaffolding protein that binds cargo to microtubules potofilament

Answer 83

- cellular uptake of particles and macromolecules - mechanisms: pinocytosis (bulk phase endocytosis that brings up extracellular fluid), receptor mediated endocytosis (specific uptake of ligands)

Answer 84

- uptake of material and delivery to lysosome - enclosed in phagosome which is acidic, contains lysozyme to degrade cell wall, oxidases that produce hydrogen peroxide to kill bacteria

Answer 85

1) phosphoglycerides: double bond or kink (unsaturated) increases fluidity 2) sphingolipids: decreases fluidity by packing closer together due to one fatty acid chain, more rigid than phosphoglycerides 3) cholesterol: at high temp=decreases fluidity, low temp=increases fluidity 4) longer chains: decreases fluidity

Answer 86

- outside lipid bilayer of membrane - non-covalent bonds - on either extracellular or cytoplasmic surface - attached to hydrophilic head groups of phospholipids or hydrophilic portion of integral proteins - on cytoplasmic surface, function in transmembrane signal transduction

Answer 87

- inside or outside of membrane | - covalently linked to lipid

Answer 88

- diffusion of water across selectively permeable membrane driven by difference in concentrations - membrane must be permeable to water but not to dissolved ions and small organic solutes - water goes from low SOLUTE concentration to high SOLUTE concentration - causes changes in volume and pressure

Answer 89

hypertonic environment: high salt concentration outside cell causes water to flow out of cell = cell shrinks hypotonic environment: low salt concentration outside the cell causes water to flow into cell = cell swells and mus burst -cells return to normal after some time due to channels regulating the concentrations inside the cell

Answer 90

- water flows in due to plants being hypertonic to their environment = turgor pressure - cell wall is rigid and prevents pressure from exploding the cell - plasmolysis occurs if in hypertonic environment

Answer 91

- free living protozoa like amoeba - use contractile vacuole due to hypotonic environment where water flows into cell - uses vacuole to expel water by exocytosis - uses lots of energy to pump ions into vacuole and even more energy to recover the ions

Answer 92

-voltage potential created when membrane selectively permeable for charged ions -only if channel is present that ions can move down concentration gradient -high concentrations inside cell: K+ (flows out of cell) high concentrations outside cell: Ca++, Na+ (flows into cell)

Answer 93

- transmembrane (integral) proteins create pore where ions and small hydrophilic molecules can pass by diffusion - protein channels opened or closed = gated - ligand-gated ion channels: ligand binds to receptor but is not transported through channel, it opens and closes gate - mechanically-gated ion channels: sound waves bend cilia in ear and open up ion channels=nerve impulses - voltage-gated ion channels: channels open and close in response to impulses across plasma membrane of neuron and muscle cells

Answer 94

Active transport: transmembrane (integral) proteins or transporters use ATP to force ions or small molecules through membrane against their concentration gradients Passive transport: do not use ATP, and move down their concentration gradient, carriers and channels, can be gated

Answer 95

- diffusion through pores for movement of water - transmembrane protein - passive, so don't need energy - water moves down concentration gradient - more aquaporins at the cell surface means more water uptake for kidney cells

Answer 96

- carrier mediated passive transport | - insulin regulates translocation of glucose transporter

Answer 97

direct active transport: transporter binds ATP directly and uses energy of hydrolysis indirect active transport: transporter uses energy of gradients created from direct active transport, cotransport

Answer 98

- pump out 3 Na+ and pump in 2K+ against concentration gradients - creates resting potential of the cell to prepare for nerve and muscle impulses and contractions - more sodium outside cell allows for osmotic balance - provides energy to indirect pumps - one third of all energy generated by animal cells used to run this pump

Answer 99

- in resting striated muscles, high concentration of Ca2+ in sarcoplasmic reticulum (ER) - contraction= Ca2+ pumped back into smooth ER or sarcoplasmic reticulum - located in plasma membrane of all eukaryotic cells

Answer 100

1) P-type trasnporter: gets phosphorylated, (Ca2+ pump of smooth ER) 2) V-type transporter: pump on vacuoles of plants for H+, and for animals on lysosomes, vesicles in kidney 3) ABC type: ion transporters, transmembrane proteins, have ATP-binding domain, helps move noxious chemicals across membranes to detoxify cells * cancer cells deal with chemotherapy and escape death by mutations in this transporter

Answer 101

symport: driving ion and pumped molecule go in same direction (Na+/glucose cotransporter used to absorb water into intestinal or gut cells during diarrhea or cholera=water loss) antiport: driving ion diffuses through pump and other ion goes in opposite direction (Na+/Ca2+ exchanger in skeletal muscles)

Answer 102

- causes cystic fibrosis disease when lungs become thick with mucous and cause impaired breathing - mucous needs to be wet, not gel like for cilia to beat in lungs - Cl- flow in the disease is not enough so mucous becomes gel-like

Answer 103

1) signal bind to receptors on cells that secreted them 2) bind to receptors of nearby cells 3) hormones are secreted into the blood (steroid hormones) 4) signal passed through synapse between transmitting cell and receiving cell 5) cells have adjacent plasma membranes

Answer 104

lipophilic: signal can cross the plasma membrane lipophobic: signal can't cross the plasma membrane, water soluble

Answer 105

- propagation of signal through the cell across the membrane or transferred to other molecules - occurs by direct phosphorylation or by G proteins

Answer 106

- process where signal is multiplied and increased - intracellular signal is amplified by second messengers - permits initial signaling molecule like a hormone to be in limited concentrations but still effective - one hormone activates numerous enzymes - *coordination of several different pathways simultaneously - one receptor turns on several G-proteins which can then activate several effectors

Answer 107

- endocrine signals - small and fat soluble - lipophilic - made from cholesterol - travel through bloodstream bound to carrier proteins - cortisol - easily enter cell by high affinity receptors present in cytoplasm or nucleus - increases gene expression - slow and long term response

Answer 108

- GTP-binding protein - in nematodes, mutations of G-protein can cause abnormal changes in movement - integral proteins - alpha helix structure - turn on effector molecule to make second messenger - when ligand binds, there is a conformational change in GPCR shape and allows G protein to interact - to stop signaling, it hydrolyzes GTP to inactivate itself - activate adenylyl cyclase when bound by glucagon and epinephrine - our sense of smell is based on GPCRs on olfactory sensory neurons (affinity for more than one odorant) - dogs can sniff out cancers which produce unusual metabolites due to lots of GPCRs and odorant receptors - insects use GPCRs to detect pheromones (males seeking females or ants following chemical trail to food sources) - receptor of epinephrine and glucagon

Answer 109

- Na+/glucose cotransporter used to absorb water into intestinal or gut cells during diarrhea or cholera=water loss - cAMP induces chloride channel remains open and water loss occurs due to cholera toxin binding to G-protein and can no longer hydrolyze GTP, so adenylyl cyclase remains active all the time

Answer 110

- from adrenal gland - increases blood glucose during stress = adrenaline hormone - when bound to GPCR, activates adenylyl cycase, which then forms cAMP, binds to PKA, cascade of phosphorylation, glycogen production stops and gluconeogenesis increases by activation of PEPCK gene - induce lipid second messengers (DAG and IP3) through G-proteins

Answer 111

- primary energy source | - stored as insoluble polymer, glycogen

Answer 112

- released from pancreas - increases blood glucose - when bound to GPCR, activates adenylyl cycase which then forms cAMP, binds to PKA, cascade of phosphorylation, glycogen production stops and gluconeogenesis increases by activation of PEPCK gene

Answer 113

- storage of glucose as an insoluble polymer - glycogen to glucose accomplished by hormones - broken down into glucose-1-phosphate - produced when glucose levels in the blood is too high

Answer 114

-increases gluconeogenesis (increase glucose production) when blood glucose levels are low

Answer 115

cytoplasmic conversion of glycogen | gluconeogenesis takes longer due to having to go through transcription and translation

Answer 116

-phospholipase C which produces two signal molecules: DAG (stays embedded in membrane, activates PKC and opens Ca2+ channels in smooth ER) and IP3 (highly soluble, enters cytoplasm, Ca2+ released) that activate gluconeogenesis

Answer 117

- antiduretic hormone - increase ion and water uptake from nephrons of kidney cells and retuns it to bloods, reduces urine volume - the more aquaporins at the surface of the cell = more water uptake - binds to GPCR, activates adenylyl cyclase, cAMP, PKA and vesicles with aquaporins move to plasma membrane

Answer 118

- effector in the cell used to increase glucose production - activated by GPCRs - activates cAMP and PKA to begin phosphorylation cascade

Answer 119

- receptor is an enzyme/protein - phosphorylates target proteins at tyrosines - single transmembrane segment (monomer) - regulate growth, cell division, survival and death, cell attachments and migrations - function as dimers when one ligand binds to both monomers or one on each - can autophosphorylate each other once dimerized and become activated - insulin receptor - epidermal growth factor receptor to stimulate cellular growth, proliferation and cellular differentiation (causes changes in gene expression, activate transcription factors, overexpression or overactivity from mutation in EGFR can cause cancers)

Answer 120

- produced when blood glucose increases after eating - causes glucose uptake by liver, mucle, fat cells - acts to decrease blood sugar by producing glycogen or fat - gluconeogenesis is inhibited

Answer 121

- defect in insulin signaling - high levels of glucose in bloods, loss of glucose in urine, excessive water loss from frequent urination, high blood pressure - Type 1: no insulin produced by pancreas, autoimmune disorder, heritable - Type 2: insulin resistance in cells that should take in glucose (loss of sensitivity) due to faulty insulin receptor or intracellular signaling - to increase sensitivity to insulin: remove off switch or negative regulator for insuling receptor, or protein tyrosine phosphatase (PTP=gene knockout in mice to produce insulin-sensitive mice)removes P from insulin receptor

Answer 122

- both first and second messenger - released form internal vesicles in response to calcium channels on cell surface=calcium induced release - rapid amplification and rapid coordination - voltage dependent channels: nerves and muscles with receptor-mediated calcium channels - fertilization: calcium channels open (calcium influx) in oocyte after a sperm has entered to prevent another sperm from entering=activation of cyclins to start cell division

Answer 123

- inorganic gas - extracellular messenger and secondary messenger - autocrine and paracrine hormone - induces production of cGMP and causes muscles to relax for better blood flow

Answer 124

convergence: two receptors cause the same secondary signal to be activated crosstalk: where pathways interconnect to receive different combinations of signals, but cell decides which one is priority to respond to (inhibit cell division to first make glucose when under stress) *override priorities

Answer 125

Anabolism: synthesis of complex compounds from simpler ones Catabolism: break down of complex compounds into simpler ones

Answer 126

1) electromagnetic: light energy | 2) chemical: stored energy in molecules with electron orbitals and bonds

Answer 127

- all organisms use it * occurs in cytoplasm - breaks down glucose * end products: 2 pyruvate, 2 ATP, 2 NADH - no oxygen required

Answer 128

* occurs in mitochondria for eukaryotes and cytoplasm for prokaryotes - oxidative phosphorylation - breakdown of pyruvate into acetyl CoA and NADH * end products: 3NADH, FADH2, 2CO2, GTP - net gain of ATP from TCA amd ETC is 36 ATP

Answer 129

- uses NADH and FADH2 * end products: ATP (NADH=3ATP and FADH2=2ATP), H20 (when 02 accepts electrons - net gain of ATP from TCA and ETC is 36 ATP

Answer 130

- function: produce lots of ATP - 1500 per liver cell or 15-20% of cell volume - vary in shape and size, as well as number of cristae * 300,000 mitochondria in oocytes due to lots of cell division without getting any larger - in sperm: concentrated around base of flagellum (lots of energy needed to swim) - in renal tubular cells: between baso-lateral membrane invaginations and around periphery with ATPase pumps to create concentration gradients * structure: outer membrane (nonselective porins), intermembrane space (heavily folded/convoluted), inner membrane (electron transport chain, ATP synthase, greater surface area), matrix (TCA cycle, circular DNA strands coding for 13 polypeptides, ribosomes) - divide by fission - highly metabolic organelle that does lots of oxidation and free radical by-products - has porins which controls what comes in

Answer 131

- integral proteins - form large, nonselective membrane channels - in outer membrane of the mitochondrion

Answer 132

- double membrane with cardiolipin (membrane composition) * divide by binary fission from preexisting mitochondria/bacteria * circular DNA encoding rRNA and tRNA * endosymbiosis theory: mitochondria in eukaryotes evolved from aerobic bacteria living within their cells, engulfed but not digested

Answer 133

1) electrons transferred to NAD+ to make NADH and FADH2 2) NADH and FADH2 create a proton gradient 3) energy from gradient used by reversible proton pump, ATP synthase, to make ATP 4) oxidation (loss of electron) and reduction (gain of electron) 5) energy from electron transport chain used to pump H+ out and from H+ gradient 6) (separate reaction) H+moves down concentration gradient through ATP synthase

Answer 134

by generating an ionic (electrochemical) gradient

Answer 135

* protons: translocated across membrane from matrix and accumulate in intermembrane space * electrons: transported along the membrane by protein carriers - oxygen: terminal electron acceptor of electrons and H+ to produce water - NADH delivers H+ and electrons to electron transport chain =proton gradient increases and H+ builds up outside inner mitochondrial membrane

Answer 136

- used to make ATP - protons can escape through porins - electrochemical gradient - 20% of stored energy due to concentration difference of H+ (low in matrix and high in intermembrane space, enough to cause a 1 pH change so from 7 to 6) - membrane impermeable to hydrogen ions - 80% of stored energy is electrogenic (voltage generated gradient) not permeable to counter-ions that protects cytoplasm from pH difference of one pH unit

Answer 137

1) energy stored in proton gradient drives phosphorylation of ADP 2) catalyzed by ATP synthase 3) ATP synthase has a F1 headpiece projecting into matrix and F0 basepiece embedded in lipid bilayer (contains H+ channel) 4) controlled movement of H+ through channel induces a conformational shape change and chemical change, driving ATP formation

Answer 138

- ATPase molecule engineered to be a motorized propeller - create flow of liquid across a plate - used to deliver drugs or manufacture miniaturized components of larger instruments

Answer 139

1) pre-sequence signal (positively charged alpha helix) recognized by receptor on mitochondria 2) cytosolic chaperone protein unfold protein to enter single file into pore 3) chaperone refolds protein once inside and pre-sequence cut off

Answer 140

-when protons re-enter mitochondrial matrix without contributing to ATP synthesis (proton leak or mitochondrial uncoupling) by this proton channel and results as heat

Answer 141

- where thermogenin is found in tissue | - brown in colour due to high levels of mitochondria

Answer 142

-primary means of heat generation in newborn and hibernating animals

Answer 143

- accumulated mtDNA mutation due to being an oxidative organelle, which can cause damage and result in mutations - old people have more mtDNA mutations than young people - mutator strain in mice of mtDNA mutations age prematurely and die at half the normal age

Answer 144

1) divide by fission to have multiple chromosomes for daughter 2) highly metabolic organelle that needs lots of protein turn-over 3) extra copies of genes allows for removal of damaged DNA by superoxide molecules (free radicals)

Answer 145

- membrane bound vesicles - don't have their own genome - good at metabolizing molecules like fatty acids * have oxidative enzymes (urate oxidase and amino acid oxidases) that produce hydrogen peroxide as a toxic by-product that destroys membranes and proteins * converts hydrogen peroxide to something less toxic - similarities to mitochondria: oxidative metabolism, import proteins into organelle, form by dividing from pre-existing organelles - have high concentrations of catalase to remove highly reactive peroxide and free radicals (charged molecules of oxygen) for a prolonged cell function - ex) fruitflies with extra copies of catalase gene live longer - ex) nematodes induced to increase catalase activity livelonger - move along microtubules - capable of hydrolyzing - mops up the free radicles of mitochondria

Answer 146

- remove highly reactive peroxide and free radicals for prolonged cell function - ex) fruitflies with extra copies of catalase gene live longer - ex) nematodes induced to increase catalase activity live longer

Answer 147

- heterotroph: gets organic compounds from another organism, earliest forms of life used carbon sources abiotically - autotroph: use CO2 to make organic molecules - chemoautotroph: use energy stored in inorganic molecules to convert CO2 into organic compounds, bacteria that live in high temperatures use this - photoautotroph: use radiant energy to convert CO2 into organic compounds, used by plants, eukaryotic algae, protists, prokaryotes like blue-green bacteria

Answer 148

1) light reactions: photochemical reactions * products: ATP (primary source of chemical energy) and NADPH (primary source of reducing power) - occurs in thylakoid membranes of chloroplasts 2) dark reactions: thermochemical reactions - opposite of mitochondrion that breaks down carbohydrates, whereas the chloroplast build up carbohydrates - ATP and NADPH used to synthesize carbohydrates - occurs in stroma of chloroplasts * NADH (in mitochondria) used for catabolism and NADPH (in chloroplasts) used for anabolism

Answer 149

- organelle where photosynthesis takes place - opposite of mitochondrion that breaks down carbohydrates, whereas the chloroplast build up carbohydrates / NADH (in mitochondria) used for catabolism and NADPH (in chloroplasts) used for anabolism - 3 types of membranes 1) smooth outer membrane: freely permeable to molecules 2) smooth inner membrane: contains transporters (integral membrane proteins that regulate the passage in and out of chloroplast of sugar and proteins synthesized in cytoplasm but used in chloroplast) 3) thylakoid membranes - divide separate from the cell cycle by fission where two contractile rings pinch themselves (one inside and one outside) which occurs at the same time as DNA replication - ATP synthase embedded in thylakoid membrane - endosymbiotic theory: chloroplast startedas a photosynthetic bacterium that got assimilated by a larger cell - resemblance to bacteria: circular genome, double membranes, photosynthetic enzymes

Answer 150

Mitochondria: has porins that controls what comes in, break down of carbohydrates (catabolism), uses NADH, different electron acceptors Chloroplasts: freely permeable to molecules, build up carbohydrates (anabolism), uses NADPH, different electron acceptors Similarities: - both have ATP synthase to produce ATP - both divide separate from the cell cycle, by fission where they pinch themselves with contractile rings which occurs at the same time as DNA replication * binary fission (like bacteria as well) - both produce reactive oxygen due to being a highly metabolic organelle - both can produce heat - proton gradient drives ATP formation - endosymbiotic theory: grew in symbiosis with a bacteria providing it with its capabilities and receiving safety within as well as nutrients - circular genome - double membrane - generation of chemical energy (electron transport coupled to proton gradient)

Answer 151

- enclose lumen (system of vesicles interconnected) - grana stacked in arrays - in light reactions, these three proteins are embedded here 1) photosystem I: chlorophyll and carotenoid molecules, integral proteins 2) photosystem II: chlorophyll and carotenoid molecules, electron transport chain 3) ATP synthase: make ATP like in mitochondria

Answer 152

- fluid with enzymes needed to carry out dark reactions: CO2 into organic molecules like glucose and ATP into NADPH energy to build sugars - has DNA carrying complete chloroplast genome which is transcribed in the nucleus, translated in the cytoplasm and transported in the chloroplast

Answer 153

- chloroplast-specific protein - world's most abundant protein - does carbon dioxide fixation during Calvin Cycle or Dark Reactions

Answer 154

- energy from sun travels in photons (energy packets) 1) photon absorbed 2) compound converted to higher energy state=excited state 3) returns to ground state in three different ways: energy dissipated as heat, re-emitted as longer wave length or transferred to another molecule (photosynthetic pigment)

Answer 155

- pigments: molecules that contain a chromophore - chromophore: packet of chlorophyll capable of absorbing light at a particular wavelength * red and blue absorbed, green is emitted (this is why plants are green) * overlap of absorbance and action spectra is where photosynthesis is working at optimal efficiency

Answer 156

- involved in photosystem I and II in the light reactions - orange in colour * secondary light collectors (absorbs colours that chlorophyll cannot, so increases efficiency of absorbing light - absorb blue and green, reflect yellow, orange and red - protects photosynthetic machinery from reactive oxygen species damage and dissipate excess energy as heat * animals can't make carotenoids but obtain it from their diet - uses: ornamental colouring of flamingos, salmon lobsters; is an antioxidant (reduces risk of developing cancer with eating carotenoid rich diets); lycopenes in tomatoes decrease lipid peroxidation and heart attacks and increase fertility in males

Answer 157

1) P680 (reaction center chlorophyll) absorbs photons/light most strongly at 680nm 2) P680 gives up electrons to primary electron acceptor of higher reducing potential (stronger affinity) 3) P680 replenishes its electrons from H20 by splitting it (removes electrons from H20 which generates a proton gradient) 4) H20 is oxidized and O2 released as a by-product 5) excited electron is passed to primary electron acceptor (02) 6) photosynthesis in thylakoid takes electrons from H20 and passes to P680 to replace electrons passed to primary electron acceptor

Answer 158

7) passed to photosystem I by electron transport chain 8) ATP produced to be used in Calvin Cycle 9) P700 chlorophyll uses light to excite the electron to primary acceptor 10) electron sent down another chain to create NADPH or for the Calvin Cycle 11) back to P700 to form ATP

Answer 159

- noncyclic pathway: electrons taken from chlorophyll not recycled back down to ground state but end up on NADPH * electrons move in linear path from H20 to NADP+, uses PSI and PSII, formation of ATP, NADPH and O2 - cyclic pathway: only photosystem I used, electrons are excited, passed down the chain, create ATP and then go back to P700 to be used again (oxygen and NADPH are not produced) * electrons move from P700 to ferredoxin and back to P700, involves PSI only, formation of ATP

Answer 160

- two photosystems I and II act in series - electron flow: 1) between H20 and PSII 2) between PSII and PSI, electron transport chain 3) between PSI and NADP+ - electrons flow in Z, H+ ions move from stroma to inner compartment of thylakoids - proton gradient is the end result (high in lumen of thylakoid and low in stroma)

Answer 161

- formation of ATP due to electrons moving through PSI and PSII - proton gradient drives ATP formation - ATP synthase embedded in thylakoid membrane

Answer 162

- replace fossil fuels as energy sources - convert sunlight, water and CO2 into hydrogen, water and carbohydrates - hydrogen as a new energy source=clean fuel - genetically alter cyanobacteria to release H+ - engineered enzymes as solar cells - use artificial dark reaction in hopes to mop up excess CO2 in atmosphere

Answer 163

light reaction: - occurs in grana of chloroplasts - depends on light to use PSI and PSII - photolysis of water and oxygen is liberated - ATP and NADPH is produced and used to drive dark reaction dark reaction: - occurs in stroma of the chloroplast - does not require light or photosystems - carbon dioxide absorbed - glucose produced - NADP is oxidized

Answer 164

- splitting of water in thylakoid lumen - translocation of protons from stroma to thylakoid lumen by cytochromes - reduction of NADP+ in stroma

Answer 165

- functions 1) structure and support (scaffolding to give cells their shape, shape associated to function, cytoskeleton can resist mechanical stresses with strength of focal adhesions, cytoskeleton can rearrange itself to change the shape of the cells) 2) intracellular transport (not static, movement of objects from interior to exterior but not all the way to perimeter, microtubules are the tracks where vesicles and mRNA macromolecules run on, movement of membranous carriers from ER to golgi, movement of neurotransmitter-containing vesicles from synthesis site to axon terminal, transport of peroxisomes on microtubules) 3) contractility and motility (cilia, flagella and pseudopodia are force generating elements that help single -celled organisms to move, multicellular organisms have independent locomotion like sperm, white blood cells, fibroblasts, growing axon tip) 4) spatial organization (framework to position organelles and molecules, anchored in place of organelles by interactions of proteins adhering to cytoskeleton like polarized epithelial cells or neurons, arranged in pattern along axis from apical to basal end of the cell) 5) separating chromosomes and cytokinesis during cell division - cytoskeleton fibers: microtubules, intermediate filaments, microfilaments - cytoskeleton defects caused by drugs or mutations which result in the misplacement of organelles and causes reduced organization

Answer 166

- tough, ropelike fibers - made of a variety of related proteins * medium in size

Answer 167

- solid - made of actin * smallest in size

Answer 168

- plants lack centrosomes - duplication of centrosomes during S-phase in the microtubule organizing centers (MTOC) - in animals, 2 centrioles that are perpendicular to one another surrounded by a cloud of molecules (pericentriolar material) - cylindrical structures * composed of 9 fibrils fused with 3 microtubules - centrioles involved in recruiting molecules like gamma tubulin subunits for microtubule nucleation * microtubule plus end grows away from the centrosomes

Answer 169

1) MAPs 2) drugs 3) GTP bound to tubulin

Answer 170

- attached to microtubules * help support and stabilize microtubules even in the absence of GTP and it will not fall apart - alter assembly and disassembly rates=regulators - crosslink adjacent microtubules to ensure they are parallel to one another - activity controlled by addition and removal of phosphate on amino acid residues by protein kinases and phosphatases - defective MAPs result in Alzheimer's disease (abnormally high phosphorylation of MAPs or tau proteins that are implicated in this fatal neurodegenerative disease where hyperphosphorylated tau proteins stick together into neurofibrillary tangles in neurons so microtubules disintegrate) * fruit flies with mutations in tau proteins exhibit neural, motor and cognitive defects like climbing a wall and courtship training where females reject the dance of the male, releases a pheromone and males don't learn to stop courting

Answer 171

- move cargo by attaching to microtubules - control movement by where microtubules are placed or by regulating motors - movements are a power stroke and a recovery stroke - kinesins, dyneins, myosins

Answer 172

- motor protein * incoming electrical signals of a neuron is at the dendrites * outgoing electrical signals of a neuron is at the axon - motility arises from conformational changes in motor domain as ATP is bound and hydrolized, and products are released - transport in nerve cell axons (neurotransmitter vesicles all must be brought by motor proteins to the axon endings): 1) vesicles are handed over to the actin network due to microtubules unable to reach the periphery of the cell 2) axon endings have an extensive actin cytoskeleton 3) myosin V takes over to transport vesicles along actin filaments to plasma membrane at the synapse - large family - move along actin microfilaments while hydrolyzing ATP - myosin II found in skeletal muscle = conventional myosin, two heavy chans with globular motor domain, a binding site for ATP and domain that interacts with actin - myosin V has two heavy chains like myosin II but has a longer neck region - can take longer strides and carry larger cargo - attached to the trailing ends of actin and pulls the rest of the cell along when using lamellipodia

Answer 173

- cell must decide if kinesin or dynein gets priority of ATP (nature of stimulus determines which one will get more ATP to move cargo) - rapid dispersal of pigment when octopus is under stress (neural transmission caused chromatophores (kinesins) and melanosomes to disperse)

Answer 174

- where pigments (chromatophores) are stored in organelles | - darken entire cell or aggregated to lighten cell

Answer 175

Cilia: -shorter and numerous -like oars or swimming strokes=cell movement is perpendicular to direction of cilia -in multicellular organisms, used to move fluids -ciliary escalator= in upper respiratory tract move thin sheets of mucous upward to remove dust and bacteria trapped Flagella: -in sperm, mitochondria are concentrated around base of flagellum (lots of energy needed to swim) -longer and rarely more than two -tend to be aligned in the direction of movement Similarities: - made of microtubules surrounded by plasma membrane - core is 9+2 arrangement=axoneme (9 peripheral doublet microtubules and 2 central single micotubules, 1 complete and 1 incomplete) - at base is the basal body or MTOC - ciliary dynein arms and radial spokes attached to A tubules - A tubule linked to B tubule by nexin bridge - microtubule doublets slide past each other - heads attached to the right and tails attached to the left side - dynein arms walk along wall of adjacent doublet - nexin bridges ensures they don't detach, which allows for stretching or bending so the microtubules don't just slide past one another - HYPOTHESIS: dynein arms are regulated by central microtubule and radial spokes, central pair rotates while beating, rotation promotes sequential contacts with each radial spoke, spoke signal to dynein arm on adjacent microtubule

Answer 176

- lacks central pair of microtubules - no locomotory function - only one per cell - antenna that picks up chemical signals and carry other signalling molecules up and down microtubules - mechanoreceptors (if bent, it sends a signal to the cell to undergo different events) - in kidney (kidney epithelium), pulse of fluid flow pressure triggers primary cilia to bend and opens calcium channels (calcium current goes to sarcoplasmic reticulum and causes contraction to slow things down)

Answer 177

- motor proteins fixed to microchips - heads can still move to shuttle microtubules across chip's surface - coated surface with kinesin - used to sort materials, assembly of different components, concentrating components for enhanced detection (blood sorting)

Answer 178

- stretchy and compressible - strongest tensile strength (stretched 3X normal strength) - made of fibrous proteins that intertwine to make dense, rope-like fibers - in cells that endure huge physical stresses like muscles, neurons and epithelial cells - holds different components of cytoskeleton together by cross-linking proteins like plectin * more types of intermediate filaments than microfilaments and microtubules - alpha helix with globular domains at terminals - structure: 1) two monomers wrap around each other to form a dimer parallel to each other 2) dimers bind to form tetramers aligned in opposite orientations and staggered (tetramers are not polar) 3) tetramers aggregate to form intermediate filaments which continuously assemble and disassemble (subunits can insert in the middle or ends) - functions: 1) mechanical support 2) hair, fingernails, skin made of keratin intermediate filaments 3) nuclear lamins form network lining inside nuclear envelope, mutation=progeria 4) neurons filled with neurofilaments 5) useful in cancer diagnosis to find where tumour originated (keratin have subtypes unique to different epithelial cells, antibodies bind a keratin subtype in colon cancer cells) 6) hold cells together (keratin intermediate filaments) by forming junctions (desmosomes), attach cells to matrix (hemidesmosomes), or form loops into plaques spreading out into the cytoplasm

Answer 179

- smallest of the fibers * no diversity - composed of actin - monomers of protein actin polymerize to form long, thin fibers - polar due to actin monomer * nucleotide charged (ATP) needed to add subunit - adds a single subunit unlike microtubule where two subunits are added at the same time - functions: 1) form band under plasma membrane providing mechanical strength for the cell 2) links transmembrane proteins to cytoplasmic proteins 3) anchors centrosomes at opposite poles during mitosis 4) pinches dividing animal cells (cytokinesis) with the help of actin and myosin 5) generate cytoplasmic streaming 6) generate locomotion in white blood cells and amoeba (actin network granules move quickly which is the goop in the amoeba) 7) interact with myosin filaments in skeletal muscle fibers to provide force of muscular contraction 8) form growing extensions of cells undergoing ingestion (phagocytosis) 9) form extracellular extensions during cell movement

Answer 180

microfilaments: only one subunit is added at a time, ATP needed to add subunit, anchors centrosomes to opposite poles during mitosis microtubules: two subunits are added at the same time, GTP used to add subunits, pull out centrosomes to poles

Answer 181

- myosin V takes over to transport vesicles along actin microfilaments to plasma membrane at the synapse - myosin V has two heavy chains like myosin II but has a longer neck region - carries cargo over twisting track of actin - has large walking strides due to neck region much longer than mysoin II - walks along one side of the filament

Answer 182

- myosin II found in skeletal muscle = conventional myosin, two heavy chans with globular motor domain, a binding site for ATP and domain that interacts with actin - heads interact with actin microfilaments in a reaction cycle: 1) ATP binding causes conformational change that causes myosin to release actin 2) ATP is hydrolyzed and a conformational change (flexing of the neck) results in myosin weakly binding actin at different place on the filament 3) Pi release results in conformational change that leads to stronger binding and a power stroke 4) ADP dissociation leaves the myosin tightly bound to actin (absence of ATP is in state of rigor = muscle rigidity)

Answer 183

- cells capable of movement without cilia or flagella use and extend these - rich in actin - growing actin filaments cause lamellipodium growth - myosin attached at trailing ends of actin pull the rest of the cell along - formed by actin meshwork through initiation of actin polimerization and addition of actin monomers at cell membrane with the help of proteins (in response to signaling stimuli and serve to cros link actin network) - enzymes can cause depolarization of actin filaments towards the base of the lamellipodium by destablizing and severing factors, and those being lost can be recycled for another filament

Answer 184

- solitary life when food abundant - aggregated into a multicellular assembly called pseudoplasmodium/slime moulds when food is limited - forms fruiting body to produce spores to be carried in the wind and find more food - amoebae look for each other with chemoreceptors (cAMP receptor) and move toward concentrated sources of cAMP - cell movement: 1) cAMP reception at cell membrane activates G-protein 2) G protein stimulates adenylyl cyclase 3) cAMP diffuses out of cell into medium 4) internal cAMP inactivates external cAMP receptor so it doesn't follow its own trail=oscillatory behaviour (cell fluctuates between being able to detect or not detect cAMP) 5) different G-protein stimulates phospholipase C 6) IP3 induces calcium ion release 7) calcium ions act on cytoskeleton to induce extension of pseudopodia * forward movement=activation of signals is high at the front and low at the back in the beginning, then becomes high inhibiting signals at the back and low inhibiting signals at the front (cAMP concentrations are high at the front of the amoeba) - forward movement requires assembly of growing cytoskeleton at the front and disassembly at the back

Answer 185

- make contact with each other - in tissues, between tightly packed cells used to hold cells together, cushion or protect cells - fills out space between cells - reservoir for growth factors and hormone - creates environment for molecules and cells to migrate - every organism uses it - cell wall in plants, fungi and bacteria=cellulose - chitin in arthropods (exoskeleton) - cellulose and chitin most abundant biopolymers on earth - composed of water, proteins and carbohydrates (GAGs, collagen, elastin, fibronectin, laminin, proteoglycans - fibroblast cells secrete connective tissue ECM - osteoblast cells secrete cartilage-forming ECM - chondroblast cells secrete cartilage-forming ECM - fibroblasts and epithelial cells make basement membrane ECM (basal lamina) - functions: 1) mechanical support 2) biochemical barrier 3) medium for extracellular communication, stable positioning of cells in tissues, repositioning of cells by cell migration during cell development and repair 4) tensile strength for tendons 5) compressive strength for cartilage 6) hydraulic protection for cells 7) elasticity to walls of blood vessels 8) calcified to form bones, teeth, cell wall of bacteria, shells of molluscs 9) chitinized to form exoskeleton of insects and arthropods - all components interact with each other and interact or bind to cells

Answer 186

- extracellular space of ECM - carbohydrates attached to cell membrane proteins and lipids forms this cell coat - cytosolic glycoprotein scaffold - involved in: 1) mediating cell-cell interactions 2) mediating cell-substrate interactions 3) mechanical protection of the cell 4) binding regulatory factors on cell surface

Answer 187

- extracellular matrix located around muscle cells, fat cells, under epithelial tissues, under endothelial lining of blood vessels - functions: 1) provide mechanical support for attached cells 2) generating signals to maintain cell survival 3) separating adjacent tissues 4) acting as a barrier to some macromolecules 5) establishes cell polarity 6) orient organelles where the nucleus will be down towards the lamina to then secrete things into the lumen

Answer 188

- major component of ECM - unbranched polymers of repeated modified disaccharides * negatively charged due to sulfates, so attracts Na+, which attracts water and causes cell to puff up into a gel - only 10% of ECM mass but 90% volume - provide compressive strength - metabolically cheap bulking agent - proteoglycans bind to GAGs to increase volume and water drawing capacity - good for cushioning

Answer 189

- major component of ECM * GAGs and proteoglycans swell up and draw in water, serve same purpose, get fluffy, negatively charged due to sulphate - more carbohydrates than porteins (protein backbone) - good for cushioning due to spongy texture - most abundant in cartilage - bone extracellular matric rich in collagen and proteoglycans but hardened by impregnation of calcium phosphate

Answer 190

* **most abundant protein of the extracellular matrix * **represents 25% of all protein in humans (most abundant protein in human body) - produced by fibroblasts (cells of connective tissue), smooth muscle, epithelial cells - 20 different types - fibrous protein constituent of skin, cartilage, bone and connective tissue - functions: 1) scaffolding for body 2) controls cell shape and differentiation 3) remodeled (broken down and rebuilt) to help broken bones regenerate, heal and direct blood vessels to grow to feed healing areas - can be shortened and lengthened to allow cells to migrate on collagen tracts to move around - trimer protein (3 alpha chains that intertwine to for triple helix) - assemble into fibrils to increase strength - are cross-linked at hydroxylated residues (need vitamin C to assist in hydroxylation) - problems with collagen: 1) scurvy: lacking vitamin C could result in bruising of skin due to lack of collagen 2) increased cross-linking occurs with age causing decreased elasticity of skin 3) mutations of type 1 collagen results in osteogenesis imperfecta (thin skin, fragile bones) 4) mutation in gene results in hyperflexible joints and extensible skin(not hydroxylated enough) - in tendons, collagen fibers are parallel in line with direction of the tensions exerted - in eye's cornea, layers of collagen are perfectly arranged perpendicularly to other layers to give strength but light can still pass

Answer 191

- multifunctional protein in ECM - dimer with domains that can bind to different components of ECM and cell receptors - helps guide cells as they move through body - during embryogenesis, guides movements of cells like neural crest cells to move out and form nervous system or primordial germ cells to migrate to gonads - looks like a tong

Answer 192

- cell receptor that binds many components of ECM - integral membrane protein - interact with actin network with adaptor proteins - has two polypeptides, alpha and beta chains - cytosolic domains bind to adaptor proteins to link cytoskeleton (actin filaments) - extracellular domains bind ligands in ECM - promotes anchoring of the cell to the ECM by starting a signal cascade (cells can't survive if not anchored to extracellular matrix=anchorage dependence, but lost when a cell is cancerous)

Answer 193

- anchors cells to ECM - pinpoints or suction cups - rich in integrin proteins which are anchored to cell's intracellular skeleton of actin microfilaments by using adapter proteins (vinculin and talin) - this binding to adapter proteins to integrin results in activation of focal adhesion kinase (FAK) (lets cell know when they made contact to ECM and tells the cell to start changing shape) * **know this actin network does not adhere directly to integrin but to Adaptor proteins

Answer 194

Hemidesmosome: * uses integrins * an integrin protein - link cell to ECM more tightly than focal adhesion - specialized structure composed of dense plaque of protein (often plectin) to which keratin fibers are embedded in cell (keratin linked to outside of cell by integrin which binds to ECM proteins) - defect in integrin can result in loss of hemidesmosomes=lower layer of epidermis fails to attach to basement membrane and chronic blistering disease called epidermolysis bullosa * anchors intermediate filaments in a cell to the extracellular matrix Desmosome: * uses cadherins * connects intermediate filaments in one cell to those in the next cell - strong anchoring attachment - forms thick plaques of proteins which are anchored to intermediate filaments of cytoskeleton - disc-shaped adhesions present on cells subjected to mechanical stresses like muscles and epithelia - uses cadherins on extracellular side - provides more protein contact between cells - autoimmune disorder = pemphigus vulgaris attacks cadherin proteins in desmosomes resulting in blistering

Answer 195

- helps cells recognize each other - cadherins, immunoglobulin superfamily, selectins, integrins, connexins - plants don't have cell adhesion molecules due to being covered by thick cell wall made of cellulose, polysaccharides and glycoporteins; they have plasmodesmata

Answer 196

- cell adhesion molecules - integral protein * heterophilic interaction (bind with specific carbohydrates on other cells) - found on epithelial cells - used to mediate interactions with leukocytes (white blood cells) - involved in first adhesions then integrins assist

Answer 197

- cell adhesion molecules - non-attached = antibodies and secreted proteins - cell bound = Ig-cell adhesion molecules * homophilic (bind to each other) and heterophilic (bind to others) especially in immunity related cells and activities - mediate cell adhesion of lymphocytes, vascular and neural cells - some viruses have protein on surface that looks like IgCAM, it tricks its host cell to bind and deliver RNA into it - however, can recoat virus by delivering a molecule that blocks it from injecting the RNA

Answer 198

- cell adhesion molecule - an integral glycoprotein - 5 tandem domains that Ca2+ separates - real strength is from number of cadherins attached to each other, not from getting closely packed together * homophilic interaction (attach to each other) - anchored to actin network through adapter proteins (catenin) - during embryogenesis, production of cadherins promotes cells of similar type to adhere - when cells migrate to new tissue, they lose adhesive properties (cadherins endocytosed) * new cadherins are used as new cell contacts develop

Answer 199

* seals gap between epithelial cells * homophilic interactions - brings cell membranes super close together almost to the point of fusion - much more waterproof than other adhesions (not entirely waterproof), and prevent easy flow of solutes - found at apical end of cells - produce occludins and claudin proteins which form a line of spot welds on both cells' membranes - claudins permeable to certain ions allowing for controlled leakage - found in epithelia - mutations in claudins result in tissue failure where skin leaks water and animals die of dehydration - epithlia of the lung: have a growth stimulant (heregulin) on apical surface and its receptors are on the basolateral surface, tight junctions provide tight seal so there is no stimulation of its receptors as long as the sheet of cells remains intact, but if broken heregulin reaches receptors causing an autocrine stimulation of mitosis leading to healing of the wound; disorder of lung like chronic bronchitis of smokers, asthma and cystic fibrosis increases permeability of the airway epithlium resulting in autocrine stimulation causing proliferation of epithelial cell (small legions=buildup of cells), and too much stimulation can result in cancer

Answer 200

* connects actin filament bundle in one cell with that in the next cell * homophilic interactions - ring-like structure like a belt attaching all neighbouring cells on all sides - junctions between cells using cadherin molecules - on intracellular side, cadherins attach to network of cytoskeleton fibers (actin) - attach to actin via catenin - maintains tissue integrity at tissue surface - form discrete patches holding cells together - loss of functioning adheren junctions could lead to tumour metastasis

Answer 201

* allows the passage of small water-soluble molecules from cell to cell * homophilic transduction - protein pipelines allowing direct contact between adjacent cells' cytoplasm - integral protein that lines the channel=connexin * **ring of 6 connexins (proteins) comprise a connexon - permits flow of small molecules like ions and simple sugars - flow is passive but channel can be gated - flow regulated by connexons (to increase flow of ions, increase number of connexons) - cilia need to be coordinated - functions: 1) for adjacent cells to respond in the same way 2) permit fast signalling for synchrony (heart sinoatrial node) 3) cAMP and IP3 can be delivered to adjacent cells when hormones trigger a single cell (tissue in harmony) 4) allows adjacent cells to connect to only those with the right connexon

Answer 202

*anchors actin filaments in cell to extracellular matrix

Answer 203

- plants don't have cell adhesion molecules due to being covered by thick cell wall made of cellulose, polysaccharides and glycoporteins - connect cells with adjacent plant cells - lined with cell membrane with desmotubule derived from SER (causes cell to swell or shrink, actin and myosin twist and tighten to open and close the gap) - pore allows molecules to pass through and controlled by dilation - some viruses can modify these proteins to open wider to allow passage of the virus through the plasmodesmata

Answer 204

1) mutations of genes in control of cell cycle - oncogenes: products stimulate mitosis even though normal growth signals are absent - tumour suppressor genes: inhibit mitosis (p53 gene product normally senses DNA damage and halts cell cycle to be repaires or trigger cell death) 2) genes that regulate apoptosis (programmed cell death) - allows cell to ignore signals telling it to commit suicide 3) genes that maintain telomeres - normal cells lose portion of telomeres after each division until too short and dies - cancer cells regain ability to express telomerase and become immortal 4) genes that stimulate angiogenesis - developing cancer stimulates growth of new blood vessels into itself by the release of angiogenesis stimulants (VEGF, vascular endothelial growth factor) - these blood vessels or capillaries can also be a means of escape into the bloodstream and into a new location of the body 5) metastasis genes - enable cells of tumour to separate from primary tumour and migrate to other parts of the body - mutations in genes whose products normally keep cells of tissue adhered (cadherin that hold epithelial cells together=carcinomas cancer) - mutations in genes whose products normally keep cells adhering to their substrate (integrin genes)

Answer 205

1) a single cell in a tissue (adult stem cell) suffers mutation of gene involved in cell cycle 2) cell now has slight growth advantage over other cells in tissue (hyperplasia: fastest growth compared to neighbours) 3) cell develops into a clone, some descendants suffer another mutation in another cell cycle gene = further deregulates cell cycle (dysplasia: irregular forms of cells) 4) rate of mitosis of clone increases, chances of further DNA damage increases (insitucancer: build up of irregular cells) 5) so many mutations have occurred that growth of clone is completely unregulated 6) full blown cancer * increasing chance of cancer as we age, have been exposed to chemicals for a longer period of time

Answer 206

Treatments: 1) surgery 2) radiation therapy *does not always kill all cancer cells (damage cells irreparably by radiation, normal cells can repair themselves) 3) chemotherapy *does not always kill all cancer cells (drugs that inhibit division, cancer cells still attempt division and die) New therapies: 1) antibodies - breast cancer has excess growth factor receptor Her2, so the antibody specific for Her2 disrupts receptor and allows tumour to regress - toxins or radioactive compounds attached to anitbodies that then carry the toxin to cancer cells 2) gene therapy - tumours lack p53, so adding it back could cause tumour regression - gene silencing technology used to turn off a targeted gene using double stranded RNA (dsRNA) 3) nanoparticles - sugar coated nano-sized particles taken in by cancer cells that deliver ferrous metal to make a magnetic field to cook the tumour cells 4) immunotherapy - inducing patient's own immune system to target cancer cells - harvest tumour cells, separate into smaller subsets of cells, treat with cytokine to stimulate growth of healthy immuno-responsive cells, select those cultures that kill tumour cells and reintroduce them back into the patient

Answer 207

- cells damaged by mechanical damage or exposure to toxic chemicals - cell and organelles swell and lose the ability to control the passage of ions/ water OR cell contents leak out, leading to inflammation of surrounding tissues

Answer 208

- death by suicide - cells are induced to commit suicide by going through this process: 1) cells shrinks 2) develops bubble-like blebs on their surface 3) DNA is degraded 4) mitochondria breaks down 5) break into small, membrane wrapped fragments - if phospholipid phosphatidylserine=signal is exposed on surface (normally hidden within plasma membrane), then it is bound to phagocytic cells' receptors to then be engulfed and secrete cytokines that inhibit inflammation - defects in apoptosis can lead to diseases like atrophy (tissue wasting=excessive apoptosis), cancer (insufficient apoptosis) or aging (loss in muscle and neural tissue where no new cells are coming to replace the old ones) - rate of apoptosis is pretty steady in both adults and children - why commit suicide? 1) for proper development (resorption of tadpole tail, formation of fingers and toes by removal of tissue between them, menstruation so the sloughing off of inner lining of uterus, and neural innervations in tissues requiring removal of surplus neurons) 2) for protection against the threat to integrity of the organism (cells infected with viruses killed by cytotoxic T lymphocytes, cells of immune system, cells with DNA damage so increase p53 protein as a potent inducer of apoptosis, and cancer cells)

Answer 209

1) withdrawal of positive signals - continued survival of many cells requires continuous stimulation from other cells and continued adhesion - growth factors and various cytokines stimulate mitosis - with damaged, it doesn't get the positive signal to keep dividing when in an open space 2) receipt of negative signals - increased levels of oxidants within the cell - damage to DNA by oxidants, UV light, X-rays and cytotoxic compounds - accumulation of misfolded proteins - death activators (molecules that bind to specific receptors on cell surface and signal cell to begin apoptosis

Answer 210

Intrinsic factors: * caspase 9 - signals come from within the cell due to damage to key organelles (mitochondria) - internal factors that can induce it: p53 (stops cells from dividing if DNA is damaged, also directly activates Bax proteins to punch holes in mitochondria and inducing caspases to begin apoptosis) and viral double stranded RNA or dsRNA (detected by PKR, a protein that first stops cell's translation machinery by inhibiting eIF and induces caspases) - process: 1) detects reactive oxygen, outer membranes of mitochondria display protein Bcl-2 on surface 2) internal damage to cell from reactive oxygen causes Bcl-2 to activate Bax which punches holes in outer AND inner mitochondrial membrane = cytochrome c leaks out 3) released cytochrome c binds to apoptosis-promoting proteins (Apaf-1 and procaspase-9) 4) proteins aggregate to form apoptosomes 5) ***apoptosomes activates executioner capsases (proteases) 6) expanding cascade of caspases which digest structural proteins in cytoplasm and degrade DNA 7) phagocytes recruited to destroy dying cell Extrinsic factors: * caspase 8 - death activators binding receptors at cell surface (tumour necrosis factor or TNF) - death activators come from immune system cells as a natural defense mechanism of virally-infected cells: 1) transport viral proteins to the cell surface 2) viral proteins coupled to MHC (major histocompatibility complex) proteins on surface to infected cell 3) MHC proteins allow binding with immune system cells like natural killer and cytotoxic T cells 4) cytotoxic T cells signal to infected cell through interaction of FasL protein (a TNF) with infected cell's Fas protein (cell surface receptor) 5) Fas induces infected cell to undergo apoptosis, however many viruses encode proteins that can inhibit apoptosis - process: 1) TNF receptors (TNFR1) are integral proteins that detect signals like tumour necrosis factor (a death activator) 2) TNFR1 cytoplasmic domains then bind to other proteins which recruit procaspase 8 3) activation of caspase 8 4) caspase 8 initiates a cascade of caspase activation 5) leads to phagocytosis of the cell

Answer 211

-another pathway of apoptosis -used by neurons and other cells does not use caspases in initial stages -a protein located in intermembrane space of mitochondria -process: 1) cell receives a signal telling it it is time to die either from an extrinsic signal or high levels of reactive oxygen species 2) AIF released from mitochondria (like release of cytochrome c in intrinsic pathway) 3) migrates into nucleus 4) binds to DNA 5) triggers destruction of the DNA and cell death

Answer 212

- cell shrinkage and rounding due to breakdown of cytoskeleton by caspases - chromatin undergoes condensation - nuclear membrane becomes broken and DNA inside is fragmented, nucleus also breaks into several pieces - cell membrane has irregular buds=blebs - cell breaks apart into several vesicles=apoptotic bodies then phagocytosed - progresses quickly and products quickly removed, making it difficult to detect or visualize

Answer 213

- loss of cells by apoptosis is balanced by production of more cells - some daughter cells differentiate into certain cell types - self-renewing (go through numerous cell divisions while maintaining undifferentiated state) - immortal due to active telomerase - as embryo develops, tissues form, cells acquire unique characteristics and become irreversibly differentiated - have potency (capacity to differentiate into specialized cell types) - as cells move up, they lose potency and can't produce any more cells and become undividing (intestinal cells) - totipotent: give rise to any mature cell type - pluripotent: can't become whole organism but can still produce a small variety of tissue (started to differentiate), different tissues have different stem cells - unipotent: can only produce one type of tissue - once a cell differentiated into a certain cell type it cannot be reversed=in vivo - medical applications: take stem cells and put them back in the damaged tissue, mature cells can be reprogrammed to become pluripotent, stem cell therapies (replace damaged or lost cells), generate new eggs from stem cells (reverse menopause/sterility), re-grow new structures or organs (use 3D printers to form tissues)

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