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179 Cards in this Set
- Front
- Back
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Basic Properties of Cells (9) |
-Organized -Maintain and utilize a genetic program -Can reproduce -Can acquire and utilize energy -Support enzyme-catalyzed chemical reactions -Engage in mechanical activities -Respond to stimuli -Capable of self-regulation -They evolve |
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Two Classes of Cells |
1) Prokaryotic: Bacteria, no ER or golgi, and has nucleoid of DNA no nucleous.
2) Eukaryotic: Protists, fungi, animals, and plants. More structurally complex. |
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What is a Virus and what does it do? |
-Non cellular macromolecular packages that can function and reproduce only within living cells. -Outside of cell is called a virion -Binds to cell surface via specific proteins, than utilizes cellular machinery to synthesize nucleic acids and proteins |
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2 types of viral infections |
1) Lytic: production of virus particles rupture and kills cell
2) Non-lytic: call can survive but often with impaired function. |
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Functions of Biological Membranes (6) |
-Cell boundary -Define/enclose compartments -Control movement of material into and out of cell -Allows response to external stimuli - Enable interactions between cells -Provide scaffold for biochemical activities |
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Structure of Biological Membranes |
-Fluid mosaic model -Components are mobile -Components can interact -Contain a hydrated lipid bilayer of phospholipids with polar heads and non-polar tails -Asymmetrical: 2 leaflets have distinct lipid composition, often the outer leaflet contains glycolipids and glycoproteins |
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Common Properties of all Membranes |
-~6nm thick -Stable -Flexible -Capable of self assembly |
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3 Classes of Membrane Proteins |
1) Integral: span the lipid bilayer
2) Peripheral: associate with the surfaces of the lipid bilayer
3) Lipid-anchored: attached to lipid in bilayer |
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What determines fluidity (2 things) and what regulates it? |
1) Nature: unsaturated increases fluidity, saturated decreases fluidity.
2) Temperature: warm increases fluidity (liquid crystal), cold decreases fluidity (crystalline gel)
--> Regulated by cholesterol, added to crystalline gel makes it more fluid, added to liquid crystal makes it less fluid |
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What does it mean for a membrane to be dynamic? |
-Lipids move easily, laterally, within leaflet
-Lipid movement to other leaflet is slow
-Membrane proteins can diffuse within bilayer |
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What Happens During Signal Transduction? |
-A signaling molecule activates a specific receptor protein on the cell membrane
-A second messenger transmits the signal into the cell, eliciting a physiological response |
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What are Lipid Rafts? |
-Membrane microdomains -Small relatively rigid areas of the plasma membrane that are rich in certain types of lipids, that decrease fluidity -Some membrane proteins accumulate in rafts -Function is contraversial |
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4 ways molecules move across membrane |
1) Simple diffusion 2) Diffusion through a channel 3) Facilitated diffusion 4) Active transport |
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Simple Diffusion |
-Small, uncharged molecules flow down a concentration gradient -O2, H2O, CO2, etc |
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Diffusion Through a Channel |
-Small, charged molecules (ions) flow down a concentration gradient -Na+, K+, Cl- |
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Facilitated Diffusion |
-Compounds bind to a specific integral membrane protein called a facilitative transporter -Change in confirmation of transporter allows compound to be released on the other side of the membrane -Moves down a concentration gradient -Glucose |
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Active Transport |
-Compounds bind to a specific integral protein called an active transporter -Change in confirmation of transporter allows compound to be released on the other side of the membrane -Moves against concentration gradient -Requires input of energy
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3 types of gated channels |
1) Voltage-gate: responds to changes in charge across membrane
2) Ligand-gated: responds to binding of a specific molecule (ligand)
3) Mechano-gated: respond to physical force on membrane |
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Extracellular Matrix |
-ECM: organized network of material produced and secreted by cells -Many cells of multicellular organisms contact on ECM -Cells bind to ECM (via intergins) and this influences cells survival and activity -Call to ECM interactions define tissue and organ function |
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Components of ECM |
-Produced by cells -Assembled into a network -Proteins and glycoproteins (collagen, fibronectin, laminin) -Proteogylcans: proteins with long chains of polysaccharides |
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What is Glycocalyx |
-Assembly of carbohydrate groups attached to proteins an lipids outside of the plasma membrane -Mediates cell-cell and cell-ECM interactions -Provides mechanical protection -Serves as a barrier to some particles -Binds regulatory factors |
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What is the cell wall composed of? |
Cellulose, hemicellulose, pectin, and proteins |
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Cytosol |
-Protein synthesis -Many metabolic pathways |
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Lysosomes |
-Degradation of cellular material |
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Endosomes |
-Sorting and recycling |
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Peroxisomes |
-Oxidation of toxic molecules |
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Mitochondria |
-ATP synthesis -Under go fusion and fission |
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Explain fusion and fission |
-Fusion is the combining of mitochondria to create a more diverse mitochondrial network
-Fission is the splitting of mitochondria typically during DNA replication |
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2 mitochondrial membranes |
1) Outer mitochondrial membrane (OMM) - contains many enzymes with diverse metabolic functions, eg. porins: large channels, when open, membrane is freely permeable 2) Inner mitochondrial membrane (IMM) - high protein:lipid ratio (3:1) - forms double layer folds (cisternae) - cristae: increase membrane surface area, contain machinery for aerobic respiration and ATP formation -Rich in phospholipid called cardiolipin |
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Aqueous Compartments of Mitochondria |
1) intermembrane space 2) matrix -high protein (gel like) -contains mitochondrial ribosomes -contains mitochondrial DNA (mtDNA): encodes polypeptides that are intergrated into IMM and ribosomes |
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What is oxidative phosphorylation |
-ATP synthesis in the mitochondria |
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Steps of oxidative phosphorylation |
1) high-energy electrons pass from coenzymes NADH and FADH2 in the matrix to electron carriers in the IMM 2) they are passed through a series of 4 electron carriers called the electron transport chain 3) Potential energy in electrochemical gradient across IMM converted to ATP in the matrix |
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Apoptosis |
-Programmed cell death -A normal occurrence in which a coordinated sequence of events leads to the death of a cell -Initiated by intracellular stimuli -Proapoptotic proteins stimulate mitochondria to leak proteins -This activates caspasses and commits the cell to apoptosis
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Apoptosis is characterized by (5 things) |
-shrinking of cell -blebbing of plasma membrane -fragmentation of DNA and nucleus -loss of attachment to other cells -engulfment by phagocytosis |
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What is GFP and how is it used |
-Green fluorescent protein (from jelly fish) -You take the coding sequence from the GFP and the coding sequence from the desired protein and combine them into a plasmid -The fluorescence from the fusion protein can be seen under a microscope and be monitored to provide important information |
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Structure of Secretory Cell |
-Secreted protein (eg. mucin, a glycoprotein component of mucus) -Synthesized in rough ER -Processed in ER -Further processed in Golgi -Concentrated in vesicles -Delivered to plasma membrane |
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Endoplasmic Reticulum |
-Interconnected network of membrane enclosed tubules and flattened sacs (reticular) -Interior (lumen) is separate from cytosol -ER membrane is continuous with outer membrane of nucleus |
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Functions of smooth ER |
-Production of steroid hormones -Detoxification -Storage |
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Functions of rough ER |
-Protein synthesis, modification, and transport -Synthesis of membrane phospholipids -Glycosylation of proteins (addition of carbohydrate chains) -Proteins folding (quality control) |
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Protein synthesis |
-Ribosomes synthesize polypeptides from mRNA (translation), happens in the cytoplasm |
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How is the site of translation determined |
-Ribosomes are targeted to the ER membrane by a signal sequence in the protein being translated -Protein has a signal sequence (contains several consecutive hydrophobic amino acids located at it's amino-terminus) -Signal sequence directs synthesis to ER -Protein moves through channel into ER = cotranslational import |
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Cotranslational Protein Import |
- after translation of signal sequence 1) signal recognition particle (SRP) binds to signal sequence, translation stops 2) targeting of translation complex to ER, SRP binds to SRP receptor 3) SRP is released and ribosomes bind to translocon, protein synthesis resumes 4) the polypeptide enter the ER (through translocon) as it it translated |
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2 Pathways for Fully Synthesized and Properly Folded Proteins |
1) it is retained in the ER 2) it is transported from the ER to the golgi complex for further modification and delivery to the distal parts of the biosynthetic/secretory pathway -Once in the ER, a protein is part of the secretory endomembrane system and may become part of a compartment therein or be secreted |
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Transport from ER to Golgi Complex |
-Exit sites: membrane and ER lumen bud off to form vesicles -ER - Golgi intermediate compartment (ERGIC) region between ER and golgi, transport vesicles fuse to form larger vesicles and interconnected tubules = vesicular-tubular clusters (VTCs), these then form the cis-golgi network -Material moves from ER to golgi and then towards plasma membrane and other compartments |
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Golgi complex |
-Protein modification -Transport and sorting of proteins -Packaging of proteins and lipids -Glycosylation -Fully processed proteins and exported from the trans cisternae, enter the TGN and are delivered to final destiations (endosomes, secretory granules, lysosomes, plasma membrane) |
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Structure of Golgi Complex |
-Smooth, flattened cisternae -0.5 to 1nm - <8 cisternae per stack -Polar: cis golgi network (CGN), cis and medial and trans cisternae, then trans golgi network (TGN) |
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Vesicular Trafficking |
-Transport of material between compartments -Targeted movement (directed, uses cytoskeleton, sorting signals recognized by receptors) -Bud off donor compartment and fuse with acceptor compartment -COP l and COP ll are clatherin coated vesicles (protein helps select cargo), COP l moves in retrograde dirctions, COP ll moves in an anterograde dircetion |
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Steps in vesicular transport |
1) Movement of vesicle: uses cytoskeleton and motor proteins 2) Tethering of vesicle to target compartment: uses protein called RABs 3) Docking of vesicles to target compartment: uses proteins called SNARES 4) Fusion of vesicle and target membrane: vesicle membrane contains proteins required for its delivery, attachment to and fusion with plasma membrane |
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Examples of vesicular transport |
- ER --> golgi - organelle --> PM = exocytosis - PM --> organelle = endocytosis - organelle --> organelle |
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Biosynthesis of a Secreted Protein |
- translation begins on free ribosomes - signal sequence emerges on new protein - signal recognition particle binds signal sequence --> causes co-translational import of protein into ER - protein is processed in ER then exported to golgi complex - protein is modified as it is transported through golgi complex (cis --> medial --> trans) - at TGN, protein is packaged into vesicles and delivered to plasma membrane |
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Lysosomes: Digestive Organelles |
- 25nm - 1um - internal pH of 4.6: H+ ATPase - hydrolytic enzymes: acid hydrolases - lysosomal membrane: glycosylated proteins (protective lining next to lumen) |
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Lysosome Function |
1) Autophagy = organelle turnover -destruction of organelles and their deplacement -lysosome fuses with ER derived autophagic vacole --> auto-phagolysosome -contents enzymatically digested (residual body can be released (exocytosis) or retained (in lipofusion granules) 2) Degradation of internalized material: -eg. plasma membrane components -bacteria (in phagocyctic cells) |
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Plant Vacuoles |
- <90% of cell volume - fluid filled, membrane bound organelle - vacuolat membrane is the tonoplast (product of secretory pathway, contains active transport systems) |
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Functions of Plant Vacuoles |
-intracellular digestion (low pH and acid hydrolases) - storage - mechanical support |
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Cytoskeleton |
-dynamic network of interconnected filaments and tubules that extend throughout the cytosol of eukaryotes -functions: structural support, intracellular transport, movement, spacial organization |
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Microtubules |
-largest cytoskeletal element (25nm) polymer of proteins a-tubulin and B-tubulin -2 major types: i) axonemal MT, highly organized, stable, part of structure involved in cell movement. ii) cytoplasmic MT, loosely organized, dynamic, located in cytosol |
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Structure of Microtubules |
-a/B heterodimers form long protofilaments - 13 protofiliments form longitudinal array (hollow cylinder) - heterodimers aligned in the same direction (head-->tail, structural polarity) - MTs have fast growing plus end and slow growing minus end |
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Microtubule Assembly and Dis-assembly |
- in viro, this leads to rapid turnover of most MTs within the cell, half life in minutes, dynamic instability -shrinkage can occur very rapidly at plus end (catastrophe) -formation of MTs is regulated/controlled -MT organizing centre (MTOC) = central site MT assembly -centrosome is major site of microtubule organization in animal cells |
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Microtubule Associated Proteins (MAPs) |
-several different proteins bind MTs (modulate assembly/function, mediate interaction with other cellular structures) -stabilize MTs or stimulate assembly |
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2 classes of MAPs |
1) non-motor MAPs: -control MT organization in cytosol 2) motor MAPs: -2 main types: kinesin and dyein (can power intracellular transport) -use ATP -can move material along MT track -can generate sliding force between MTs -dyein: minus end directed -kinesin: plus end directed |
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Intermediate Filaments |
-intermediate size (10-12nm) -exclusive to multicellular animals -provide structural support, mechanical strength -stable -fibrous proteins, contain central a-helical domain -5 classes (1-V) eg: -keratin: epithelial cells -neurofilaments: neurons -lamins: nucleus of all cells |
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Structure of Intermediate Filaments |
-a-helical domains wrap around eachother forming rope-like dimer (coiled coil) -monomers aligned in parallel, IF dimers are polar molecules with different N- and C- termini -dimers associate anti-parallel, assembled filaments not polar |
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Microfilaments |
-smallest (~8nm) -polymer of protein actin -polypeptide = 42 kDa, bind ATP (individual molecules = G-actin, polymerized microfilament = F-actin) -G-actin monomers have polar structure -monomers are incorperated into the filament in the same orientation -F-actin is polar --> plus and minus ends |
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Microfilament Functions |
- maintain cell shape - cell movement - cytokinesis - muscle contraction |
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F-Actin Microfilament Assembly |
- polymerization/depolymerization and structure/organization of F-actin Filaments are regulated by actin-binding proteins (filaments can be loose arrays/networks or tight bundles/cables) - G-actin polymerized reversibly: -nucleation (slow): G-actin --> dimers --> trimers --> short filaments - elongation (fast): monomers add to both ends, faster at plus end |
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Actin Binding Proteins |
- eg, nucleating proteins, polymerizing proteins -F-actin networks can be highly branched -the coordinated activity of actin-binding proteins controls microfilament formation in a lamellipodium to allow directed movement of cells -microtuble based and microfilament based motor are involved in vesicular transport |
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Myosin |
-F-actin associated motor protein -large family of proteins -divided into 2 groups: 1) conventional mysoins, type ll, primary motors for muscle contraction 2) unconventional myosins, type l, lll-XVlll, generate force and contribute to motility in the non-muscle cells -myosin-based contraction pulls trailing edge forward |
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Nucleus |
- contains genome, DNA, RNA synthesis, ribosome assmebly |
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Structure of Nucleus |
-nuclear envalope: nuclear membrane, nuclear pores, nuclear lamina -nuclear contents: chromatin, nucleoplasm, nuclear matrix, mucleolus |
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Function of Nucleus |
- storage, replication and repair of genetic material -expression of genetic material (transportation: mRNA, tRNA, rRNA, splicing) -ribosome biosynthesis |
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Nuclear Envalope |
- 2 parallel phospholipid bilayers - separated by 10-50nm -outer membrane binds ribosomes and is continuous with rough ER -inner membrane bears integral proteins which connect to nuclear lamina |
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Nuclear Envelope Functions |
- separates nuclear content from cytoplasm, separates transcription and translation -selective barrier, allows limited movement of molecules between nucleus and cytoplasm -Supported by nuclear lamina |
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Nuclear Lamina |
-thin mesh work of filamentous proteins (next to nucleoplasmic leaflet), lamins -bound to inner surface of NE -provides structural support for NE -attachment sites for chromatin |
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Nuclear Pores |
-gateway between cytoplasm and nucleoplasm -3000-4000 pores a nucleus -inner and outer membranes fuse --> pores (~120nm) -pores contain a complex protein structure, nuclear pore complex NPC |
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Nuclear Pore Complex |
-composed of nucleoporins (NUPs) -octagonal symmetry -fits into the pore -projects into cytoplasm and nucleoplasm -functional 9nm diameter -large supramolecular complex -molecular mass: 1.25x10(5) kDa |
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Functions of NCP |
-passive diffusion of molecules smaller than 50 kDa or 9nm (rapid, 100/min/pore) -regulated movement of larger molecules (slow, 6/min/pore) -regulated movement of proteins into the nucleus requires a nuclear localization signal (NLS) = short stretch of plus charged amino acids within protein |
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Nucleoplasmic Trafficking |
-cellular function acutely dependent upon nuclear import and export -nucleotides -structural proteins (lamins and nuclear matrix proteins) -DNA packaging proteins (histones) -proteins for RNA processing and export -proteins for ribosome synthesis and export |
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Nucleolus Functions |
-tRNA synthesis -ribosome biogenesis: -synthesis of rRNA -rRNA processing -assembly of subunits (rRNA + proteins) -40s and 60s subunits are exposed to cytoplasm |
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Nuclear Matrix |
-network of insoluble protein fibers -maintains shape and organization of the nucleus -scaffolding for organizing chromosomes into discrete and specific regions within the nucleus -anchors machinery required for nuclear processes |
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DNA |
-Deoxyribonucleic acid is a polymer -Each subunit is a nucleotide comprised of: -a phosphate group -a five carbon sugar (2-deoxyribose) -one of four cyclic nitrogenous bases |
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The four nucleotides of DNA |
Pyrimidines -Thymine -Cytosine -Urical (RNA) Purines -Adenine -Guanine -nucleotides in polynucleotide chains are connected by phosphodiester bonds |
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DNA strands are... |
-DNA strands are polar -Each strand of DNA has chemical polarity: -5ʼ end (five prime end) has a free phosphate group -3ʼ end (three prime end) has a free hydroxyl group |
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DNA is... |
-DNA is double-stranded and the strands are antiparallel -The double helix is right-handed -The strands are held together by hydrogen bonds between bases on opposing strands and by hydrophobic interactions between adjacent stacked bases -Opposing strands are said to be complementary |
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Base Pairing |
-Base pairing is specific and is mediated by hydrogen bonds - A with T (or U) - G with C |
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Most common form of DNA |
B-DNA -There are two grooves of different width: -the major groove -the minor groove |
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-DNA that gets folded over many times becomes... |
-The functional prokaryotic chromosome is highly compact -The DNA in living cells is supercoiled -The DNA found in mitochondria and chloroplasts exists in circular chromosomes that resemble those of prokaryotes. -Like prokaryotic genomes, plastid genomes are circular -Eukaryotic chromosomes are composed of proteins, histones, DNA, & RNA |
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The first level of condensation |
-Packaging DNA as a negative supercoil into nucleosomes -produces an 11 nm fibre -146 nucleotide pairs of DNA wrapped 1 3/4 turns around an octamer of histones -DNA is wrapped around a nucleosome core of 8histone proteins and anchored by a 9th |
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the second level of condensation |
-an additional folding or supercoiling of the 11 nm fibre to produce a 30 nm fibre -driven by nucleosomal interactions -Histone H1 involved -two models that describe the substructure: the solenoid and the zig-zag models |
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the third level of condensation |
-attachment of the 30 nm fibre at many positions to a (nonhistone) protein scaffold -becomes a metaphase chromosome (DNA in its most condensed form) |
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Telomeres |
-protects chromosome ends -resist degradation by DNases -prevent fusion of chromosomal ends -facilitate replication of the ends of the linear DNA |
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Centromeres |
-Centromeres provide the point of attachment of chromosomes to microtubules in the mitotic spindle -prokaryote centromeres are smaller -Centromeres in multicellular eukaryotes are much larger and more complex Three essential regions: -regions I and III are conserved sequences that bind proteins involved in spindle attachment -region II ~90 bp, >90% A, T -binding site for a protein called CENP (related to Histone H3) |
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Functions of the genetic material |
-The genotypic function – replication -The phenotypic function – gene expression -The evolutionary function - mutation
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An overview of gene expression |
-A gene is a transcribed region of DNA 1)DNA transcription (nucleus) 2)RNA processing 3)mRNA 4)translation (cytoplasm) 5)protein now can function |
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five known types of RNA |
-snRNA -rRNA -tRNA -mRNA -Pre-miRNA |
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RNA |
-RNA uses the pyrimidine uracil instead of thymine -The RNA pentose sugar is ribose, not a deoxyribose
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-The transfer of information from DNA to protein is a two step process in all organisms -The central dogma of molecular biology
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Transcription |
-The DNA double helix is locally unwound during transcription -DNA sequences position RNA polymerase to begin transcription at the beginning of a gene and cause it to dissociate at the end of the gene -3 steps: initiation, elongation, termination -introns spliced out
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TATA box |
-Sequences in eukaryotic promoters also position the RNA polymerase for accurate initiation of transcription -The “TATA box” is a highly conserved feature of many protein-coding genes -Area with high concentration of A and T |
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Eukaryotic termination |
-Cleavage by endonuclease -Addition of poly-A tail |
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Introns |
-are noncoding sequences located between coding sequences. Introns are removed from the pre-mRNA and are not present in the mature mRNA. Introns are variable in size and may be very large. |
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Exons |
- (both coding and noncoding sequences) are composed of the sequences that remain in the mature mRNA after splicing. -The mature messenger RNA contains both coding and non-coding sequences -messenger RNA molecules are an intermediate between DNA and protein |
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Translation |
-In prokaryotes, an RNA sequence positions the ribosome to begin translation at the beginning of a coding sequence or open reading frame -In eukaryotes, the RNA sequence around the AUG influences where translation begins and the ribosome scans from the 5’ end until a suitable start codon is found -Proteins are assembled on the ribosome according to the mRNA sequence (the genetic code) |
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The genetic code is... |
-There are no spaces between codons codons are adjacent -non-overlapping each nucleotide is part of one codon -degenerate most amino acids are specified by more than one codon -ordered amino acids with similar properties are specified by related codons -(nearly) universal with minor exceptions, each triplet/codon has the same meaning in all organisms |
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Translation termination |
1) Release factor 1 binds to termination codon at A site and tRNA leaves E site 2) Release of polypeptide and RF-1 and transfer of tRNA from P site to E site 3) Dissociation of the mRNA-tRNA-ribosome complex |
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What gets split up during mitosis |
-Cellular organelles and cytoplasmic contents are divided more or less equally between daughter cells -Endoplasmic reticulum and Golgi complex are fragmented at the time of division and reformed in the daughter cells -Mitochondria and chloroplasts are randomly divided between daughter cells -Nuclear chromosomes must be duplicated exactly and distributed equally and exactly to daughter cells |
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Cell Cycle |
-Cell division goes through a series of stages that, collectively, are called the cell cycle -G1 phase (Gap 1) growth, cellular metabolism -S phase (Synthesis) DNA replication (chromosome duplication) -G2 phase (Gap 2) preparation for mitosis -M phase (mitosis) chromosomal “pas de deux” and cytokinesis -Interphase – the time between successive mitoses (G1 + S + G2) -Cells that are not actively cycling may exit the cell cycle From G1 they enter a state called G0 These cells are said to be quiescent |
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Centrosome Cycle |
-The centrosome cycle, in which centrioles are duplicated, progresses along with the cell cycle -In animal cells, the centrosomes are microtubule organizing centres (MTOCs) |
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Interphase |
-duplicate chromosomes called sister chromatids joined at the centromere by cohesin -the centrosome is duplicated |
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Prophase |
-initiation of spindle formation -condensation of duplicated chromosomes -fragmentation of ER and Golgi -nucleolus disappears -Nuclear membrane breaks down -spindle microtubules invade the nuclear space |
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Prometaphase |
-chromosomal microtubules attach to the kinetochores, which are on the outer surface of centromeres -chromosomes move towards the equator of the spindle |
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Kinetochores |
Outer kinetochore: -microtubule binding -microtubule motor activity -signal transduction Inner kinetochore: -centromere replication -chromatin interface -kinetochore formation |
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Metaphase |
-duplicated chromosomes are aligned midway between the spindle poles -this equatorial plane is called the metaphase plate |
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Anaphase |
-centromeres split and chromatids separate -chromosomes move towards opposite spindle poles -spindle poles move further apart |
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Telophase |
-chromosomes cluster at opposite spindle poles -chromosomes become dispersed and decondense -nuclear envelope assembles around chromosomes -Golgi and ER reform -daughter cells form by cytokinesis |
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n number of chromosomes
2n number of chromosomes |
-the haploid state
-the diploid state |
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Synapsis |
-Pairing of homologous chromosomes -is often facilitated by formation of a synaptonemal complex |
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Crossing over |
-Crossing over involves breakage of chromatids and the exchange of the broken pieces between homologous chromosomes (non-sister chromatids). -Following crossing over, homologous chromosomes start to pull apart, but remain joined at the cross over junctions (called chiasmata) |
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Meiosis I (also called reduction division) |
-Meiosis I produces two haploid daughter cells that are genetically distinct -Meiosis involves DNA replication and two cell divisions
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Prophase I |
-chromosomes, each consisting of two sister chromatids, begin to condense -homologous chromosomes begin to pair -homologous chromosomes are fully paired -homologous chromosomes separate -paired chromosomes condense further and become attached to spindle fibers |
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Metaphase I, Anaphase I, Telophase I |
-paired chromosomes align on the equatorial plane in the cell -homologous chromosomes disjoin and move to opposite poles of the cell (chromosome disjunction) -chromosome movement is complete and new nuclei begin to form |
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Meiosis II |
-Meiosis II resembles a mitotic division, but the products are haploid -Kinetochore position changes between prophase I and II |
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Prophase II, Metaphase II, Anaphase II, Telophase II |
-chromosomes, each consisting of two sister chromatids, condense and become attached to spindle fibers -chromosomes align on the equatorial plane in each cell -sister chromatids disjoin and move to opposite poles in each cell -chromosomes decondense and new nuclei begin to form |
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Cytokinesis |
-the haploid daughter cells are separated by cytoplasmic membranes |
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Gregor Mendel (1822-1884) |
-Mendelʼ s peas were highly in-bred Because flower structure promoted selffertilization - they therefore “bred true” e.g. when two tall plants were crossed, they only produced tall progeny -Mendelʼs experiments were designed so that he could study one trait at a time |
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A monohybrid cross |
-In a genetic cross, the parents are referred to as the parental (P) generation -their offspring represent the first filial (F1) generation -their grand-offspring, the F2 generation etc. |
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What did the experiment show |
-Each trait appeared to be controlled by a heritable factor that came in one of two forms: dominant and recessive -Mendelʼs heritable factor = gene -dominant & recessive forms called alleles -Homozygous – both alleles are identical -Heterozygous – the two alleles are different |
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Locus |
-is a fixed position on a chromosome (plural loci) |
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Mendelʼs Principle of Dominance |
- In a heterozygote, one allele may conceal the presence of another In a heterozygote, one allele may conceal the presence of another |
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Mendelʼs Principle of Segregation |
-Neither allele is typically changed by coexisting with the other in a heterozygote -Two different alleles segregate from each other during the formation of gametes (Anaphase I) |
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Dihybrid cross |
- are two traits inherited independently 1) Each parental homozygote produces one kind of gamete 2) The F1 heterozygotes produce four kinds of gametes in equal proportions 3) Self fertilization of the F1 heterozygotes yeilds four phenotypes in a 9:3:3:1 ratio |
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Mendelʼs Principle of Independent Assortment |
-The alleles of different genes assort/segregate independently of each other -The further apart two genes are on a chromosome, the more likely that they will assort independently |
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Punnett square for dihybrid cross |
-For 2 different genes there are: 2x2 = 22 = 4 possible haploid genotypes (gametes) -Combining 4 different gametes from each of two parents: 4 x 4 = 16 possible diploid genotypes |
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Punnett square for monohybrid cross |
-For 1 gene with 2 alleles there are: 1x2 = 21 = 2 possible haploid genotypes (gametes) -Combining 2 different gametes from each of two parents: 2x2 = 4 possible diploid genotypes |
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Forked line method |
-The forked line method for predicting the outcome of a cross involving three independently assorting genes |
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The rules of probability – the multiplicative rule |
-If the events A and B are independent, the probability that they occur together is the product of their individual probabilities of occurrence - P(A) x P(B) |
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The rules of probability – the additive rule |
-If the events A and B are independent, the probability that at least one of them occurs is the sum of their individual probabilities of occurrence minus the probability of their joint occurrence - P(A) + P(B) - (P(A) x P(B)) -If the events A and B are independent and don’t occur together, the probability that at least one of them occurs is the sum of their individual probabilities of occurrence - P(A) + P(B) |
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Using porbability to predict the outcome |
Since the genes assort independently, we can treat them one at a time: -Probability of being tall = probability of being homozygous dominant or heterozygous = ¼ + ½ = ¾ -Probability of being green = probability of being homozygous recessive = ½ x ½ = ¼ -Probability of being wrinkled = probability of being homozygous recessive = ½ x ½ = ¼ -Probability of being all three = ¾ x ¼ x ¼ = 3/64 (by the multiplicative rule of probability) |
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Consider a cross between two plants that are each heterozygous for four different genes (Aa Bb Cc Dd) What fraction of the progeny will be homozygous recessive for all four alleles? |
-Given Mendelʼs Principle of independent assortment, we can consider each gene one at a time P(aa) = P(a) x P(a) = ½ x ½ = ¼ Similarly, P(bb) = P(b) x P(b) = ½ x ½ = ¼ Therefore P(aa bb cc dd) = ¼ x ¼ x ¼ x ¼ = 1/256 |
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Test cross |
-Since a heterozygote may have the same phenotype as the homozygous dominant, a test cross may be performed to determine the individualʼs genotype. -In a test cross, the individual of unknown genotype must be crossed with a homozygous recessive individual -e.g. a test cross involving an individual of the genotype DD Gg Ww would involve crossing this individual to one with the genotype dd gg ww |
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A trait is likely showing a dominant mode of inheritance if: |
-every affected individual has at least one affected parent -the trait is manifested in at least one individual in every generation once the trait appears -(the spontaneous appearance of a dominant allele is extremely rare) |
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A trait is likely showing a recessive mode of inheritance if: |
-the trait suddenly appears in a pedigree -the trait “skips” a generation -In the absence of evidence to the contrary, assume that unrelated individuals marrying into the family do not carry the recessive allele
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onsider a couple, each heterozygous for a recessive allele that causes a serious disease in homozygous individuals.
If they have four children, what is the probability that exactly one is affected? |
We must first recognize that there are five possible outcomes and multiple ways of arriving at some of them: 1. 4U, 0A {UUUU} 2. 3U, 1A {AUUU, UAUU, UUAU, UUUA} 3. 2U, 2A {UUAA, UAAU, AAUU, UAUA, AUAU, AUUA} 4. 1U, 3A {UAAA, AUAA, AAUA, AAAU} 5. 0U, 4A {AAAA}
We can calculate the probability of all possible outcomes: Treat each birth as independent P(A) = P(cc) = ½ x ½ = ¼ P(U) = P(CC) + P(Cc) = ¼ + ½ = ¾ |
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Binomial probability |
-Mathematically, for a total number of n progeny, we can calculate the binomial probability that exactly x progeny will fall into one class, and y into the other class as: (n! / x!y!) pxqy -where the two classes are P and Q, with probabilities of occurrence of p and q -since there are only two classes p = 1-q -The solution to the previous problem is: (4! / 3!1!) (¾)3(¼)1 = 4 x (27/64) x (1/4) = 108/256 |
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Mutations |
Mutations can arise spontaneously, as a result of an error during DNA synthesis - incorporation of rare isoforms of the four bases that have altered base pairing properties - the inherent fallibility of replication proteins |
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Tautomers |
-The nitrogenous bases of DNA exist in two isoforms (tautomers) -Rare and common -The rare isoforms have altered base pairing properties (A:C, G:T) -Incorporation of a rare isoform during DNA replication can lead to a change in DNA sequence -Mutations of DNA in the germ line (e.g. during the mitotic divisions of spermatogonia) will be inherited |
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Hot spots for spontaneous mutations during DNA replication |
-Simple repeats (eg. A A A A A, GC GC GC GC, TAC TAC TAC) -Symmetrical repeats (inverted repeat) -Palindromes (GAATTC, CTTAAG) |
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Mutations induced by exposure to chemical mutagens |
Chemical mutagens can be divided into two groups: -Those that are mutagenic only to replicating DNA (e.g. base analogues, acridine dyes) -Those that are mutagenic to both replicating and non-replicating DNA (e.g. alkylating agents) – ethyl methane sulphonate (EMS) |
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Mutations induced by exposure to radiation |
-Adsorption of UV energy by pyrimidines results in their dimerization (eg. two thymine makes a thymine dimer) |
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Effects of single base mutations |
-Gene mutations can affect the encoded proteins -Original AGA (Arginine) -Silent AGG (Arginine) -Non-sense TGA ("stop") -Missense AAA (Lysine) |
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Simple mutations |
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Expanding genes |
-At least 15 human inherited disorders result from expanding triplet/trinucleotide repeats -Usually <40 copies of the triplet repeat are stably inherited -Larger numbers of copies are unstable and prone to expansion -The expanding triplet/trinucleotide repeat diseases can show increased severity and/or earlier onset from one generation to the next |
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Mutations induced by DNA itself |
-Gene segments separated by transposale elements |
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Mutations that affect the coding region |
1. Change the protein to a non-functional form • changes to protein folding - prevent proper localization of the protein - targeted for degradation - compromised activity • post-translational modification - prevent proper localization of the protein - “unactivatable” |
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Mutations that affect non-coding regions |
1. Prevent or reduce transcription
2. Prevent or reduce translation • mRNA is unstable • ribosomes can’t bind • mutation of the start codon • nuclear export of MRNA |
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Nucleotide expansion in non-coding regions |
Myotonic dystrophy type I CTG expansion in the untranslated region (UTR) of an mRNA transcribed from chromosome 19 encoding an enzyme (kinase) Myotonic dystrophy type II CCTG expansion in an intron of a gene on chromosome 3 encoding a zinc finger transcription factor In both cases, the mRNA may become too large for efficient export to the cytoplasm |
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Outside Mendelʼs garden, things are not so simple |
-Genes may (and usually) have more than 2 alleles -Different alleles may affect the phenotype in different ways -A single gene may control several traits -Multiple genes may control a single trait |
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Most common allele |
-the wild type – designated with a superscript + (e.g. A+ or c+) -Any allele found at appreciable frequencies (at least 1%) in the population is considered to be a polymorphism -all other alleles are considered as mutants |
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What makes an allele dominant or recessive |
-Recessive mutations almost always involve a loss of gene function -complete loss of function (null allele) -partial loss of function (hypomorphic allele) -Loss of function mutations are usually recessive because, for most genes, one functional copy is enough for a normal (wild type) phenotype |
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Dominant mutations |
- can involve a loss of function or a gain of gene function |
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Loss of function mutation |
– for those genes for which one functional copy is not enough (haploinsufficiency) |
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Dominant negative mutation |
-a loss of function mutation that interferes with the normal function of the wt allele |
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Gain of function mutation |
-enhances the normal function of the gene |
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Incomplete dominance |
• The phenotype of the heterozygote is midway between the phenotypes of the two homozygotes. • One allele is partially, or incompletely, dominant over the other. -Incomplete Dominance: heterozygotes (with one copy of the dominant allele) have half the functional gene dosage -eg Red x White = Pink |
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Codominance |
• The heterozygote expresses the phenotypes of both homozygotes. • Neither allele is dominant. -Multiple alleles of a single gene with a dominance hierarchy -eg Albino x Grey w Black tips = chinchilla colour |
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Allelic Series |
-An allelic series describes the dominance hierarchy of multiple alleles. -eg c+ > cch ≥ ch > c |
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Allelic Series for blood type |
-IA and IB codominant both are dominant over i -Blood types: -A (IAIA, IAi) -B (IBIB, IBi) -AB (IAIB) -O (ii) |
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Complementation test |
-Testing whether two alleles that confer a particular phenotype are in the same gene |
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What influences the phenotype |
-Phenotypes are influenced by both genetic and environmental factors • The “environment” can be both physical (external) and biological (internal) • Conditional alleles / conditional mutations • Examples – Drosophila shibire mutation (temperature) – Phenylketonuria (diet) – Pattern baldness (gender) |
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Conditional mutations |
-Expressivity is environmentally-dependent -est. 400,000,000 people worldwide have G6PD deficiency (enzyme involved in the pentose phosphate pathway) -Life-threatening haemolytic anemia (affected red blood cells particularly sensitive to oxidants) - but only under rather unusual conditions eg. eating fava beans, taking a particular anti-malarial drug -Diet influences a missense mutation in the human phenylalanine hydroxylase (PAH) protein -Temperature influences a missense mutation in the Drosophila Dynamin protein |
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Incomplete Penetrance -Polydactyly |
-Individuals do not express a trait even though they have the appropriate genotype: -Variable expressivity: the Lobe eye mutation -This dominant trait is not manifested uniformly among individuals that show it. -Gene interactions: Chicken comb shape -Different combinations of alleles from two genes result in different phenotypes. |
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Epistasis |
• In epistasis, an allele of one gene overrides the effect of other genes on the phenotype. • In Drosophila, – The cinnabar mutation produces bright red eyes. – The white mutation produces white eyes. – When both mutations are present in the same fly, the eyes are white. – The white mutation is epistatic to the cinnabar mutation -When homozygous, the recessive w allele is epistatic over the dominant alleles of the upstream genes |
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Pleiotropic gene |
-A gene that affects multiple phenotypes is pleiotropic Some examples of pleiotropic genes: • The phenylalanine hydoxylase gene affects brain development and hair color • The Drosophila singed gene affects bristle shape on the cuticle and egg production |
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Gene overview |
-Gene action is affected by biological and physical factors in the environment. - Two or more genes may influence a trait. - An allele of one gene is epistatic to an allele of another gene if it has an overriding effect on the phenotype. - A gene is pleiotropic if it influences multiple aspects of an individual’s phenotype. |
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Genomes and gene regulation |
-In general, genome size increases with organismal complexity (viruses, bacteria, fish, mammals), but the number of genes does not increase in proportion
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Are genes lost in the course of cell differentiation? |
-Cloning by nuclear transfer argues against gene loss -A lot of the “extra stuff” in the genomes of more complex organisms has to do with the regulation of genes -A lot also has no known function (but may turn out to be involved in regulating gene expression in ways that we do not yet understand) |
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Transcription in eukaryotes |
-Transcription is a major point of regulation of gene expression in eukaryotes -The transcription of eukaryotic genes is regulated by interactions between proteins and DNA sequences within or near the genes, or far from them. |
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Enhancers |
-Genes consist of enhancers, as well as promoters and coding regions: the Drosophila yellow gene -Enhancers regulate where and when genes are expressed -Like promoters, enhancers contain binding sites for transcription factors -Each enhancer contains binding sites for regulatory transcription factors -Tissue-specific enhancers constitute additional regulatory regions of a gene -that can make defining the physical boundaries of a gene difficult |
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Proteins that regulate transcription |
-Basal transcription factors are proteins that bind to specific sequences within the promoter to facilitate RNA polymerase binding • Expressed themselves in most, if not all cells -Regulatory transcription factors are proteins that bind to sequence elements in promoters or enhancers, thereby facilitating the function of the basal transcription factors and RNA polymerase • Expressed themselves in more restricted, tissue-specific patterns |
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DNA compaction |
-Chromosomes are not uniformly condensed: heterochromatin and euchromatin -DNA compaction is regulated and is an additional level of control over gene expression -Many regulatory proteins modify histone tails, thereby making the chromatin more or less accessible to the transcription machinery |
