Cell biology


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Cell biology

  1. 1. Cell BiologyCells and Organelles1. Define the terms (i) cell (ii) subcellular organelle with approximate dimensions12. What are the basic differences between prokaryotes, eukaryotes and viruses23. What range of scale can be seen by a light microscope vs an electron microscope34. What would you use a transmission electron microscope and a scanning electronmicroscope for?45. What rule of physics defines the maximum size of a cell?56. How do specialist cells overcome this problem67. What are the components in the cytosol that make up the cytoskeleton and whatis its main function?78. Under what circumstance do the chromosomes of the nucleus condense?89. Which organelle is responsible for fusion of vesicles within the cell which are usedto deliver hormones and neurotransmitters?91 A cell is a semi-independent (or independent) living unit containing mechanisms for metabolism, growthand replication (by division), size ranges from 2-100 micrometres. Organelles are subunits within a cell,some may be membrane bound, size ranges 100nanometres-10micrometres2 Prokaryote = a single celled organism with ribosomal DNA, e.g. bacteria, Eukaryote = has a membranebound ʻtrue nucleusʼ DNA expressed as chromosomes, all complex organisms are eukaryotes. Virus =assemblage of DNA/RNA which is parasitic and incapable of replication by division alone, lack their ownplasma membrane.3 LM = 100nm-1mm, EM = 1 angstrom - 1mm4 TEM = to look inside a cell, SEM = to see the cellʼs surface (scattering heavy metal particles)5 Fickʼs law, the rate of diffusion across a membrane. Diffusion is not efficient above 50 micrometres6 In neurons and oligodendrocytes (really long cells) a system of protein filaments such as actin filaments ormicrotubules, give the cell its shape and capacity for directed movement7 Actin (thinnest), microtubules (thickest, pull daughter cells apart in division) and intermediate filaments(mechanical strength). Cytoskeleton function = to contribute to mechanical strength and control cell shape.8 Become condensed/visible when cell divides9 The Golgi body - its function is the packaging of proteins
  2. 2. 10.What structure is responsible for the transmission of electrical signals betweencells?1011.Define & give biological functions for the following:(i) lysosome11(ii) peroxisome12(iii) nuclear envelope13(iv) chromatin14(v) nucleolus15Autonomic Nervous System1. Where are the ganglia of sensory fibres located?162. In what way is the location of motor neuron cell bodies different to sensory?173. What are the key differences between the anatomy of an autonomic never vs asomatic nerve?184. Whereabouts in the CNS are the roots of (i) sympathetic (ii) parasympatheticneurons found?195. What is the difference between white ramus and grey ramus?2010 Actin cables11 Electron dense spheres that contain acid hydrolase enzymes that break down waste materials in the cell12 Found in virtually all eukaryotic cells and responsible for the breakdown of long chain or branched fattyacids and amino acids. Involved in detoxification.13 2 layers of membrane form the nuclear envelope which contains the nucleolus and chromatin. Nuclearpores allow transport in and out.14 Complex of DNA, histones and non-histone proteins found in the nucleus of eukaryotic cells15 Where the rDNA is transcribed and ribosome subunits assembles within the nucleus16 In posterior root ganglia of the spinal nerves, sensory ganglia of the cranial nerves.17 Motor neurons lie in ganglia outside of the CNS, motor neurones innervate smooth muscle and glands, soonly need to be connected to the autonomic nervous system. 1 nerve leaves CNS, separate nerveinnervates the target structure.18 Autonomics are made up of 2 neurons, 1 myelinated and rooted in the CNS, one unmyelinated and rootedin the effector region. Somatic neurons only use Ach as neurotransmitter whereas autonomics use Ach or NE19 Sympathetics = T1-L2 (thoracolumbar), Parasympathetics = Cranio-spinal (either end of spinal column),S2-S4.20 White ramus = preganglionic outflow of the sympathetic nervous system. Grey ramus = post ganglionicand post synapse.
  3. 3. 6. What are the sympathetic chains/trunks?217. What are the main differences in the structure of a parasympathetic neuron vs. asympathetic neuron?228. What are the basic functions of the:(i) Pons23(ii)Medulla24(iii)Hypothalamus25(iv)Thalamus26Lipids and Membrane Structure1. How are (i) proteins (ii) carbohydrates (iii) lipids expressed in the fluid mosaicmodel of membrane structure?272. List the 4 main functions of lipids in the body283. What do serine, choline, ethanolamine and inositol have in common withreference to phospholipids?294. Describe the structure of a phospholipid305. What does it mean if something is amphiphatic?3121 Paired (either side of spinal cord) which run from the skull to the coccyx and allow sympathetic neurons tointerconnect. Interacts with the spinal nerves via rami communicantes.22 Sympathetics synapse far from the target and their postsynaptic (unmyelinated) neurons are longer.Parasympathetics synapse at the target organ so their longest neuron is myelinated. Sympathetics mayinduce their effects by stimulating an endocrine gland which then induces the target response by hormonesecretion into the circulation, the PNS does not use hormones.23 Higher levels of respiratory control24 Processing centres for complex visceral reflexes25 Sympathetic and parasympathetic HQ26 Emotions and sensory input27 Proteins are ʻislandsʼ in the membrane and may be membrane spanning channels or only sit on one sideof the membrane. Carbohydrates visible as ribose or chains attached to the end of phosphoglycoproteins.Phospholipids (hydrophilic head, hydrophobic tail) chains make up the majority of the membrane.28 1/ Energy stores - triglycerol, 2/ Precursors for vitamins/hormones, 3/ Cholic acid (bile salts) foremulsification of fat in the GI tract, 4/ Membrane structure (phospholipid bilayer)29 These are all amino acids which commonly form the polar heads of phospholipid molecules.30 A polar head (amino acid) attached to a glycerol backbone via a phosphate group. The glycerol is attachedto 2 fatty acid chains by ester bonds.31 Where the same molecule is both hydrophobic (lipophilic) and hydrophilic
  4. 4. 6. Describe the structure of sphingomyelin327. What is the difference between fully saturated, mono-unsaturated andpolyunsaturated fatty acids and give one example of each338. How does lipid content affect the fluidity of a membrane?349. List 5 classes of membrane proteins3510.What is the difference between (i) integral/intrinsic proteins, (ii) anchoredproteins (iii) peripheral proteins3611.What type of protein in (10) are (i) RAS, (ii) alkaline phosphatase (iii) spectrin3712.Name the 4 classes of phospholipase and where they break bonds onphospholipids3813.What classes of membrane protein can be removed by (i) high salt substances, (ii)detergent, (iii) phospholipase 39Functional Organisation of the Respiratory System1. What is minute ventilation (V)?4032 One of a class of lipids that contain a sphingosine backbone in the place of glycerol. It still contains thephosphate group and amino acid (in this case choline) and has one fatty acid chain attached to the NH groupon the sphingosine.33 Fully saturated = no double bonds (Stearic, Palmitic or Myristic acid), mono unsaturated = one doublebond (Oleic acid), polyunsaturated = several double bonds (arachidonic acid)34 Fluidity is the ease with which lipid molecules move about in the plane of the bilayer. Short chain fattyacids and unsaturated fats increase fluidity. High cholesterol and saturated fats decrease fluidity.35 Structural (e.g. cytoskeleton/cell-cell contact), receptors, ion channels, transporters (e.g. GLUT-4),enzymes (may be found on membrane)36 Integral = embedded in the bilayer and usually span across the bilayer (alpha helixes or beta pleatedsheets), Anchored = membrane covalently bound to glycolipids fatty acids (inside edge), although the proteinitself is not deeply embedded 3/ Peripheral - attach to the membrane surface by ionic interactions withintegral proteins or polar head (outside edge)37 RAS and alkaline phosphatase = anchored (attached to lipid), Spectrin = peripheral (attached to polargroup)38 PLA 1 and 2 = the ester bonds between fatty acids and glycerol backbone, PLC = phosphate to glycerol,PLD = polar group to phosphate39 High salt = peripheral (breaks bond with polar group), Detergent = all (degrades bilayer int detergentmicelles), phospholipase = anchored (breaks polar group bond with fatty acids)40 volume entering the lungs per minute
  5. 5. 2. What is alveolar ventilation (Va)?413. What is the approximate volume of dead space in a typical respiratory system?424. What is approximate alveolar ventilation at rest?435. What is ‘Helium dilution’446. What happens to the lower six ribs in forced breathing once the limit ofabdominal compliance is reached and central tendon of the diaphragm is fixed?457. What would alveolar pressure be at functional residual capacity?468. What is the function of alpha-1 antitrypsin?47Amino Acids and Proteins1. What defines something as an essential amino acid?482. What are the two stable forms of secondary protein structure?493. What is the basic structure of a basic amino acid?5041 volume taking part in gas exchange per minute42 150ml43 5L/min44 Used for measuring lung volume. Subject inhlaes helium (which is poorly aborbed by the blood), the gasvolume that was originally in the lungs can be deduced from the fall in helium concentration as the inhaledgas and original lung gas mix.45 Lower 6 ribs can be raised upwards and outwards to allow lungs to thorax to expand further46 Although pressure in the airways would be negative alveolar pressure is maintained at zero by the surfacetension created by surfactant. It is negative when breathing in and positive when breathing out.47 A protease inhibitor which protects lung tissue in particular from the enzymes of inflammatory cells. Forexample, it is responsible for protecting elastin from the damaging effects of neutrophil elastase. (COPD/emphysema can be a result of deficiency)48 An amino acid that cannot be synthesised by the body and therefore has to be supplied in the diet49 Alpha helix and B pleated sheet50 All amino acids have an amine group (NH2) at one end, a COOH group at the other and a carboxyl groupin-between with an R group attached (H = glycine, CH = alanine).
  6. 6. 4. What are the special properties of a peptide bond?515. What happens when a protein becomes denatured?526. What is the difference between primary structure and secondary structure?537. How is solubility affected by globular or fibrillar structure?548. What is the difference between tertiary and quaternary structure?559. Hydrogen bonds are formed by electronegative elements in the protein structure,what are H-bond donors and what are acceptors?5610.Where will you find the R groups in a b-pleated sheet?5711.What kind of fibrillar proteins have B-pleated sheets and what characteristic doesthis give them?5812.Describe the nature of the peptide bond between amino acids5913.Describe the main structural features of an alpha helix6051 Contains some features of a double bond, shorter than a C-N bond, no rotation, partial -ve charge on Oatom, partial +ve charge on N atom52 Hydrogen bonds which gave the protein its original formation have been broken, although basic proteinstructure remains.53 Primary = arrangement of amino acids in chain, secondary = hydrogen bonding between water and/orother protein chains to give protein either an alpha helix or b-pleated sheet.54 Globular = soluble, fibrillar = insoluble55 tertiary = peptide chain (in alpha helix or beta pleated sheet) folds in on itself, Quaternary = folded peptidechains join together, held together by hydrogen and S-S bonds.56 Nitrogen and oxygen can be donors or acceptors57 either side of the plane of the sheet (alternating)58 Fibrillar proteins such as fibroin - gives them high tensile strength but little elasticity59 A covalent chemical bond formed between two molecules when the carboxyl group of one binds to theamino group of the other molecule60 Secondary structure brought about between hydrogen bonding between N-H groups and C=O group.
  7. 7. Properties of Enzymes and Enzyme Kinetics1. What are the 6 classes of enzyme and their main function?612. Give an example of a ligase enzyme623. Describe the basics of enzyme structure634. What is the ‘induced fit’ model645. What are the co-enzymes for:(i) alcohol + NAD+65(ii)succinate + FAD66(iii)Glucose + ATP676. What is the Michaelis menton reaction model?687. What is the Michaelis-Menton equation?698. Define the terms:(i) Initial velocity70(ii) Km71(iii)Vmax7261 Oxoreductases (redox reactions, catalyse transfer of hydrogens), transferases (transfer functional groups),hydrolases (cleave bonds using water), lysases (add groups to C=C bonds), Lysases (form C-C or C-Nbonds using ATP)62 DNA ligase - joins DNA molecules together with C-C or C-N bonds using ATP63 Enzymes are proteins composed of 1 or more folded peptide chains, stabilized by hydrogen bonds. Weakbonds between protein chains mean enzymes are highly sensitive to their environment.64 Where one molecule changes the structure of an enzyme so that the binding site can be filled.65 Alcohol dehydrogenase66 Succinate dehydrogenase67 Glucokinase68 Enzyme + Substrate <-k1/k-1-> Enzyme/Substrate complex <-k2-> Enzyme + Product69 Initial reaction velocity = Vmax x [S]# # # Km + [S]70 written as V0 initial velocity is measured as soon as enzyme and substrate are mixed so no substrate hasbeen used up yet71 Km is the substrate concentration at which the initial velocity is half the Vmax72 Vmax is the maximum velocity of an enzyme catalysed reaction when all active sites are fully saturatedwith substrate
  8. 8. 9. What is Kcat?7310.What is the difference between competitive inhibitors and non-competitiveinhibitors?7411.Give an example of clinical use of enzyme inhibitors7512.List 3 biological mechanisms for the regulation of enzyme activity76Cell Motility and the Cytoskeleton1. What functions/characteristics of the cell can be determined by the cytoskeleton?772. What are the 3 components of the cytoskeleton?783. What is required for the growth of an actin filament?794. What are the 3 main functions of actin within the cell?805. Where in the cell are the intermediate filaments most dense?816. What are dimers and tetramers?8273 The turnover number - equivalent to the number of substrate molecules converted to product in a givenunit of time on a single enzyme molecule when the enzyme is saturated with substrate. Two enzymes mayhave the same Kcat but different Km.74 Competitive Inhibitors block the enzyme active site (alter the apparent Km not the Vmax. Non-competitiveinterfere with mechanism in any other way (e.g. allosteric)75 1/ Control of angiotensin production by treatment of heart failure with ACE inhibitors to reduce bloodpressure and edema.76 Allosteric modification (e.g. ATP and citrate affecting phosphofructokinase), covalent modification by otherenzymes (e.g. kinase adding a phosphate), increase or repression of enzyme synthesis (e.g. adrenaline canregulate the amount of insulin and release glucagon).77 Cell shape and polarity, tissue structure, adhesion, cell movement, intracellular movement of vesicles orchromosomes78 Actin (microfilaments, actin binding proteins, double helix), Intermediate filaments (fibrillar), microtubules(literally small tubes)79 ATP can add actin monomers to either end, it is much easier to add to the +ve end, ADP remains bound.80 Mechanical support, cell shape changes and maintenance, cell motility81 Nearest the membrane, they then extend out into the periphery82 Helical dimers are formed by intermediate filament monomers, helical dimers then form the basis fortetramers which link in a staggered formation to form a multilayered fibrillar intermediate filament.
  9. 9. 7. What is the monomer unit for microtubules?838. Which organelles polymerize microtubules?849. What are the functions of intermediate filaments?8510.Give an example of an actin-based cell movements?8611.Describe the mechanism by which actin moves cells?8712.What is a lamellipodium?8813.What is the microtubule associated protein which initiates movement?8914.What are the functions of microtubules?9015.Which two proteins are associated with the movement of vesicles alongmicrotubules?9116.What is a processive motor?9217.Give examples of drugs/therapeutic agents given to stabilise or destabilisemicrotubules and inhibit cell division9318.Give examples of diseases caused by actin abnormalities9483 Tubulin monomers (alpha tubulin and beta tubulin)84 centromeres (+ve end of microtubule faces outwards towards the periphery, -ve85 For support of cells which need to be a particular shape for their function: microvilli, actin sheets inerythrocytes, stereocilia in inner ear, axons.86 Migration of neutrophils to sites of infection87 Cell pushes out protrusions at the front edge of cell, protrusions adhere to the surface on which the cell ismoving. Actin filaments drag the cell towards anchorage points, actin depolymerizes at the rear of the cell88 Name for the actin projection from the motile side of a cell used to move the cell and sample theenvironment. Actin joins to myosin and forms cross bridge.89 dyenin (a -ve end directed motor protein)90 Support, anchoring cells together, transport of organelles between cells or along axons to synapses.91 Kinesin and dyenin92 A motor protein which stays attached throughout the ATP hydrolysis cycle (unlike myosin which completelydetaches at end of cross bridge cycle), and is therefore capable of moving long distances.93 Colchicine (destabilize), vinblastine (stabilize) and taxol (stabilises)94 Muscular dystrophy, Usherʼs syndrome (deafness and blindness)
  10. 10. 19.Give examples of diseases caused by intermediate filament abnormalities9520.Give examples of diseases caused by microtubule abnormalities96Regulation of the Cell Cycle and Cancer1. What is the criteria for a cell to be considered capable of ‘the cell cycle’?972. What are the stages of mitosis?983. What is interphase?994. What are the 3 stages of interphase?1005. What is the restriction point?1016. What is G0/quiescence?1027. How does the length of the cell cycle vary for embryonic tissues?1038. What proteins must be activated in order to move from one stage to another?1049. What causes the proteins in (8) to activate at the correct time?10595 Epidermolysis bullosa symplex (skin is sensitive to mechanical injury, blistering, sloughing), Amyotophiclateral scletosis96 Alzheimerʼs, Herediary Spastic Paraplegia (mutations in spastin, a microtubule severing protein)97 Division into 2 daughter cells98 1/ Prophase (condensation of chromosomes), 2/ Prometaphase (breakdown of nuclear envelope), 3/Metaphase (chromosomes assemble on the spindle of the centre of the cell 4/ Anaphase (separation ofchromosomes to opposite ends of the cell, 5/ Telophase (reformation of nuclear envelopes) 6/ Cytokinesis(separation of the 2 daughter cells)99 The time between cell division of a particular cell (20 hours), DNA synthesis & chromosome replication100 G1 (12 hours) cell determines whether the environment is favourable or has had growth signals i.e.correct DNA, is cell big enough to divide, S (6-8 hours) the stage of chromosome replication (chromosomesx2), G2 (4 hours) more checkpoints, is the cell big enough to divide & have all the chromosomes beenreplicated101 The ʻcheckpointʼ of G1102 If the cell decides that it cannot divide in G1 and remains static without dividing.103 As little as 8 hours (22-24 when born), as the G1 phase is reduced104 Cyclin dependent protein kinases. Present in cell all the time but active when moving between G1/S andG2/M105 Dependent on a family of proteins called cyclins. Cyclin E controls G1-S phase, cyclin A S-G2 phase andcyclin B controls G2/M phase
  11. 11. 10. What are the functions of activated CDK?10611.What makes transformed or neoplastic cells different to normal cells?10712.What is the role of p53 in preventing damage?10813.What is the intrinsic error rate of the DNA replication machinery (mutations/gene/division)?10914.How many times does a single gene mutate in a lifetime?11015.What gene which regulates actin and microtubule skeletons could causetransformation of cell type (e.g. epithelial to mesothelial)?111Structure and Properties of Nucleoacids1. What are the components of a DNA molecule?1122. What are the names of the 4 nitrogenous bases?1133. What is the common unit shared by AMP, ADP and ATP?1144. What type of bond strings together DNA nucleotides in a chain?1155. How many OH groups can a single nucleotide (in a chain) be attached to?116106 Activates DNA polymerase, Phosphorylated histones and lamins and stimulates kinetochore formation107 They cannot be regulated because they divide in the absence of growth factors and exhibit densityindependent growth when cultured (loss of contact inhibition).108 p53 is a tumour supressor gene, it is phosphorylated (activated) following DNA damage and inducestranscription of p21 which inhibits the activation of cyclin dependent kinase preventing entry into the S phaseor M phase.109 1x 10^-6 mutations/gene/division110 10^10 per lifetime111 Ras112 Deoxyribose H (no OH). Ribose OH. Phosphate. Nitrogenous base (A, C, T or G)113 Adenine, Guanine, Thymine and Cytosine114 Adenosine, 5115 Phosphodiester bonds between nucleotide. O (from OH on ribose) to P (on phosphate group)116 3, bound to the ribose
  12. 12. 6. What is the 5 end and the 3 end?1177. What is X-ray diffraction?1188. What is the diameter of the DNA helix and the length of one full twist?1199. What is the nature of the bonds between C-G and A-T?12010.What is done to DNA to make it into chromosomes?12111.Approximately what length of DNA is stored in a single nucleus?12212.What is chromatin?12313.What are histones?12414.What is a nucleosome?12515.How many chromosomes and genes are there in the human genome?12616.What are introns?12717.What proportion of human DNA actually codes for proteins?128DNA Transcription117 5 end = phosphate, 3 end = hydroxyl group118 Firing a DNA sample with X rays to project an image of it onto a photographic plate, the X ray imagingshows diffraction in an X pattern consistent with the DNA being a helix, also showed the spacing of thenitrogenous bases.119 2nm diameter, 3.4nm one full twist120 2 hydrogen bonds for A-T, 3 hydrogen bonds for G-C121 DNA packaged by proteins into chromosomes so that it can fit into the nucleus (chromosomes consist ofDNA plus protein)122 1.8 metres of DNA in a single nucleus123 The combination of DNA proteins that make up a cell nucleus124 Proteins which package DNA into nucleosomes for storage in nucleus125 Densely packed DNA on a chromatin fibre for storage in a nucleus. Tightly wound but can be unwound fortranscription.126 23 pairs of chromosomes, 23,000 genes127 Non-coding areas of DNA, present in eukaryotic genes but not prokaryotic ones128 Only about 2%
  13. 13. 1. Which enzyme synthesizes RNA strands?1292. Describe the direction of addition of RNA nucleotides1303. What are the three main steps of transcription?1314. What happens at stage 1?1325. What is sigma factor?1336. What happens at stage 2?1347. What happens at stage 3?1358. What is a stop sequence?1369. How is RNA transcription different in prokaryotes?13710.What is an exon?13811.What is an intron?13912.What is gene splicing?140129 RNA polymerase - forms strand from nucleotides by phosphodiester bonds130 Synthesis can only occur from the 5 end (phosphate group) towards the 3 end (hydroxyl group)131 Initiation, elongation, termination132 Initiation - RNA polymerase is directed to the start site of transcription on the double stranded DNA,enzyme finds the transcription start site133 A bacterial factor that enables RNA polymerase to bind to coding strand134 Elongation - Reading of DNA sequence on a synthesis of a messenger RNA135 Termination - Reaching of transcriptional termination site, mRNA synthesis finishes, controlled by STOPsequences136 GC rich region of the DNA which forms a hairpin loop, preventing further trasncription by RNA polymerase137 More complex, more proteins involved - includes polymerases, initiation factors, elongation factors andadditional mRNA processing,138 A region of DNA within a gene unit that is found in mature mRNA “expressed” regions139 Regions of DNA within a gene unit that are not found in mature mRNA i.e. are not coding regions140 Removal of intronic segments and collation of exon coding regions
  14. 14. 13.What is 5’ capping?14114.What is polyadenylation?14215.What additional processes are involved in eukaryotic transcription as opposed toprokaryotic transcription?143Translation and the Genetic Code/Protein Synthesis1. What are the three STOP codons?1442. What is the start codon with which all proteins begin?1453. What are the functions of mRNA, tRNA and Ribosomes?1464. What are the 4 ends/loops of a ‘clover leaf’ tRNA molecule?1475. What is wobble pairing?1486. What is the reaction equation for activation of an amino acid from tRNA?1497. What is the basic difference between 70S and 30S subunits?150141 Process for getting mRNA out of the nucleus to be translated (after having been transcribed). Stabilisesimmature mRNA making it mature so methyl group is added to guanine position.142 Addition of AAAAA chain to the 3 (hydroxyl) end of an RNA chain. Happens at the end of a genetranscription.143 Despite less proteins involved, eukaryotic transcription involves the additional processes of capping,splicing and 3 polyadendation.144 UAG, UGA and UAA145 AUG (Met)146 mRNA = carries sequence of information to make protein, tRNA = bring individual amino acids to sites ofprotein synthesis, Ribosomes = contain ribosomal RNA, machinery of protein synthesis and bind mRNA andtRNA147 3 end (where amino acid attached), D loop, T loop, anticodon loop148 Last base on anticodon part of anticodon loop can form non Watson-crick base pair. Allows a single tRNAspecies to recognize more than one codon without changing the amino acid sequence, because itsanticodon can vary.149 Amino acid + tRNA + ATP --> aminoacyl-tRNA + PPi + AMP (energy for addition of amino acid to tRNAcomes from hydrolysis of ATP)150 These are two parts (subunits) of the ribosomal DNA, the 50S is the larger subunit and the 30S is thesmaller one
  15. 15. 8. What are the 3 binding sites on the prokaryotic ribosome?1519. Describe the initiation stage of translation in prokaryotic cells15210. What is the Shine-Dalgarno sequence?15311. Describe the elongation stage of translation in prokaryotic cells15412.What are the main differences between prokaryotic and eukaryotic transcription?155Protein Targeting1. How is an mRNA molecule in the cytosol coupled to its corresponding place inon the endoplasmic reticulum membrane?1562. What is responsible for cleaving the signal sequence protein?157151 E site, P site and A site152 Initiation = formation of initiation complex comprising of the ribosome, mRNA and initiator tRNA. Initiationproteins IF1, IF2 and IF3 are required. GTP dependent. 30S subunit binds factors, binds mRNA and 1sttRNA. Once bound to IF2 the 50S subunit arrives and binds to the whole complex, releasing energy (Pi) fromGTP to GDP153 Sequence in a gene upstream of the ʻstartʼ (AUG) sequence. It is basically the initiation sequence. Soevery time you want to start translation you need 1/ Ribosome binding site, 2/ Shine Dalgarno sequence, 3/AUG start codon154 The activated tRNA binds to EF (elongation factor) and GTP, ʻproof readingʼ (GTP to GDP). Peptidyltransferase then makes a bond between the first and second amino acids and the ribosome moves one overand one RNA strand is released.155 Prokaryotic has and Eukaryotes ribosome. mRNA translated as soon as synthesised.Prokaryotes EukarotesRibosome: 30S + 50S (70S) Ribosome: 40S + 60S (80S)mRNA translated as soon as synthesised hnRNA has to be modified by capping, splicing andpolyadendation before leaving nucleusInitiator: fmet-tRNA Initiator: met-tRNAStart: Shine-Dalgano sequence (start) Start: Cap 5 and mRNAmRNA codes for multiple proteins mRNA codes for one protein156 ER signal sequence grows out of side of mRNA, joined to a signal recognition particle. SRP picked up bya receptor on the ER membrane which pulls the mRNA into a translocation channel.157 Signal peptidase
  16. 16. 3. What are the products of the transport vesicles given off by the endoplasmicreticulum once they have passed through the Golgi body?1584. Name the receptor regions on the protein vesicle and plasma membrane thatintertwine to cause the vesicle and membrane to fuse together1595. What are the processes of protein folding and glycosylation that occur in theendoplasmic reticulum and Golgi body?1606. Which organelle receives unfolded proteins (not vesicles) from the cytoplasm andfolds them up for its own use?1617. What are the locations within the cell of transcription and translation?1628. Name the protein responsible for carrying other proteins into the nuclearenvelope1639. What is the function of a lysosome?16410.Which receptor/tag molecule is added to lysosomal proteins when they arepackaged into vesicles in the Golgi body16511.What could cause waste proteins to be secreted instead of going into lysosomes?16612.How are proteins transported:(i) across the organelle membrane to ER or mitochondria167158 Secretory vesicles, lysosomes, peroxisomes.159 v-SNARE on the vesicle and t-SNARE (target) on the membrane, vesicle fuses into membrane to releaseproteins160 Protein folding = formation of tertiary protein structure (disulphide bridges), Glycosylation = processing ofsugars to give diversity, adding sugar residues to protein161 Mitochondria162 Transcription (RNA synthesis) = nucleus, Translation = cytoplasm/ER ribosomes163 Importin164 To degrade unwanted proteins, RNA etc. (enzymes require acidic pH)165 Mannose-6-phosphate166 Defective mannose-6-phosphate tagging mechanism. Inclusion-cell disease caused by mutant enzymefor phosphorylating mannose. Named because waste accumulates in ʻinclusion bodiesʼ.167 Protein translocators/ signal recognition particles
  17. 17. (ii)from the ER to lysosomes or plasma membrane168(iii)Into the nucleus from the cytosol169Antibiotics and Protein Synthesis Control1. List the stages at which protein synthesis can be controlled1702. How many genes are there in the human genome?1713. How does transcriptional control work?1724. What is the Leucine zipper?1735. What is negative regulation?1746. What is positive regulation?1757. What mechanism of negative feedback could occur in protein synthesis control?1768. List examples of translational/post translational control1779. What are the actions of transcription factors?178168 In vesicles which may fuse with the target membrane169 Free diffusion of small molecules through nuclear pores, larger ones transported by protein ʼimportinʼ170 Transcription, RNA processing in nucleus, RNA transport, mRNA degradation, translation, protein activity(i.e. protein may be synthesised but not activated (by phosphorylation, acidic conditions etc.), folding ofprotein etc.171 22,000172 transcription factors act on a promoter and distort the DNA allowing RNA polymerase to work better. Canbe based on hnRNA synthesis rate, processing/export rate or mRNA degradation173 Is a 3D structural motif in proteins which is part of the DNA binding domain, they regulate geneexpression.174 Where an inhibitor binds to the DNA, inhibiting its transcription175 transcription only occurs when the transcription factor binds to the DNA176 Where the protein being synthesised or a molecule associated with it contains the ligand for switching theDNA polymerase off and stops too much of itself being synthesised177 Regulating the efficiency of translation, the folding/maturing of proteins, the protein degradation ofproteins, the targeting of proteins to sites of activity178 Distort double helix, allow RNA polymerase to recognize the start site for transcription, repress ability ofRNA polymerase to transcribe the gene (e.g. Leucine Zipper)
  18. 18. 10.Name the glucocorticoid hormone released in the starving state which stimulatesthe liver to increase production of glucose?17911.Explain what is meant by chromatin remodeling18012.What is micro-RNA18113.What is the mechanism behind protein degradation?18214.What is the cytoplasmic site of proteolysis?18315.What is the mechanism of the following antibiotics:(i) Actinomycin184(ii)Rifamycin185(iii)Streptomycin186(iv)Erythromycin187(v)Chloramphenicol188(vi)Tetracyclines18916. Describe the mechanisms of these other translational inhibitors:(i) Puromycin190(ii) alpha-aminitin191179 cortisol180 The dynamic modification of chromatin architecture (packaged chromosomes) to allow access ofcondensed genomic DNA to the regulatory transcription machinery proteins, controlling gene expression.181 A small, non-coding molecule, form base pairs within mRNA molecules which silences the target gene(about 1/3 of human genes are targeted).182 Turnover/lifespan of protein may be affected by transcription factors. Proteolysis is the breakdown ofproteins into inactive fragments by enzymes, occurs in lysosomes (where unwanted proteins are disposedof) also in cytoplasm.183 Proteosome - a cap within this recognises and binds proteins destined for digestion and they are digestedback down into peptides within the proteosomeʼs cylindrical structure.184 binding DNA at transcription initiation complex185 Inhibition of DNA dependent RNA synthesis through binding to prokaryotic RNA polymerase186 Affects initiation of prokaryotic 30S subunit and causes misreading of codons187 Binds to 50S subunit188 Inhibits peptidyl transferase by binding on 50S subunit189 Inhibit binding of aminoacyl tRNAs to ribosome190 causes premature chain termination during translocation191 Inhibits RNA polymerase
  19. 19. (iii) Cycloheximide192(iv) Diptheria toxin193DNA Replication/Mutation/Analysis1. What are the respective time periods for the following parts of the cell cycle ineukaryotic cells: G1, S phase, G2 and Mitosis1942. What is semi conservative replication1953. What is the function of DNA helicase?1964. What is the difference between the leading and lagging strands?1975. What are Okazaki fragments?1986. What is positive supercoiling?1997. What are the functions of DNA primase and DNA polymerase III?2008. What is the function of DNA ligase?2019. What is the function of nuclease enzyme?202192 Inhibits protein biosynthesis by interfering with translocation step (in eukaryotes)193 Inhibits RNA translation by inactivating elongation factor 2194 G1 = 6-9 hours, S phase = 8-9 hours, G2 = 5-6 hours, Mitosis = 1-2 hours, TOTAL = 20-26 hours195 Each DNA molecule contains one parent and one daughter strand196 Separation of 2 strands of DNA, breaking hydrogen bonds to form 2 replication forks (one ʻ3 and one ʻ5)197 The replication fork strand moving in the 3 to 5 direction (from the hydroxyl 3 towards the phosphate 5),so the original strand it is being synthesised from is in the opposite 5 to 3 direction. It is called leadingbecause it is being synthesised in the same direction as the fork opening, i.e. the newest synthesised DNA isthat nearest the junction of the fork. Lagging is the opposite (synthesised 3-5), its synthesis is furthest awayfrom the activity of the DNA helicase.198 DNA primase forms these short fragments on the lagging strand, since its movement is not continuouswith DNA helicase199 Where the separation of the two strands by DNA helicase makes the coils tighter further down the helix200 Primase makes the RNA primer so that DNA synthesis can begin. DNA polymerase III synthesizes newDNA strand201 Joins discontinuous fragments together making a phosphodiester bond202 Removes wrong/miscopied nucleotides so correct gene is copied without mutation, can work as astandalone enzyme or as a function of DNA polymerase III
  20. 20. 10.What are the functions of the following types of DNA polymerase in prokaryoticreplication: alpha, delta, beta, epsilon?20311.How is mitochondrial DNA replication different to that of other eukaryoticorganelles?20412.What is a telomere?20513.What enzyme catalyses the formation of telomeres?20614.What kind of cells have the ability to lengthen their telomeres (and so preventcell aging)?20715.Define (i) point mutation (ii) silent mutation (iii) missense mutation (iv) Nonsensemutation20816.What are the 4 types of gross mutation?20917.How does mutation happen from replication slippage?21018.What is deamination?21119.How does UV radiation cause DNA damage?21220.List some causes of induced mutations (physical and chemical)213203 A = assembles primers and synthesizes lagging strand, D = synthesizes lagging strand and hasproofreading ability. B & E = Involved in DNA repair204 Mitochondrial DNA have their own circular chromosome. Synthesised by DNA polymerase gamma.205 A region of repetitive nucleotide sequences at the end of each chromatid, protects the end of thechromosome from deterioration from fusion with neighboring chromosomes because the end of eachchromosome shortens with every round of replication.206 Telomerase, acts by extending the 3ʼ end of the chromosomal DNA207 Gametes and most tumor cells (85%)208 Point = single base changed, Silent = mutation that still codes for the same amino acid, Missene =mutation that codes for a different amino acid, Nonsense = change in code from amino acid to a stop codon209 Inversion, translocation, deletion, duplication210 Where a part of one of the coding strand slips backwards or sideways so that the strand beingsynthesised misses that part of the code211 Deletion of one amine group from a sequence212 Forms a dimer between adjacent thymidine residues213 Ionising radiation, UV light, various agents that react with bases (nitrous acid, alkylating agents, freeradicals)
  21. 21. 21.How does 06 methylguanine act to repair DNA?21422.What is Xeroderma pigmentosum?21523.What virus has the highest mutation rate of anything observed to date?216214 directly repair the damage by removing damaged region and re-synthesize it215 Genetic disorder causing defective repair of UV damage and over 1000x risk of skin cancer from sunlight216 HIV, this is why it is so difficult to treat. HIV reverse transcriptase does not possess a 3-5 exonuclease sois unable to proofread/correct mutations