BIOLOGY NOTES MM1 PDF

Extracellular components - outside of cell membrane: - cell wall → shape, protection, support, structure of cell - bacteria = peptidoglycan, archaea = pseudopeptidoglycan, plant cell = cellulose, fungi = chitin, yeast = glucan and mannan - thicker than cell...

Extracellular components - outside of cell membrane: - cell wall → shape, protection, support, structure of cell - bacteria = peptidoglycan, archaea = pseudopeptidoglycan, plant cell = cellulose, fungi = chitin, yeast = glucan and mannan - thicker than cell membrane and strongly attached to it + thicker, stronger, more rigid than extracellular matrix of animal cells - plant cells: 1. primary cell wall → thin, flexible, not as rigid = allows cell to grow - many cellulose microfibrils = tensile strength - middle lamella between primary walls of adjacent cells → sticky polysaccharide pectin → plant cells glued together (= resistance to compression) → polysaccharide glycan → binds tightly to cellulose microfibrils = helps to cross-link microfibrils into complex network - when cell matures, stops growing → strengthens its wall by secreting hardening substances into primary cell wall or adding secondary cell wall 2. secondary cell wall (between cell membrane and primary cell wall) → strong, durable = protection, support; lignin - wood mainly composed of secondary cell walls - plasmodesmata → perforations/holes in cell walls that connect cytoplasms (chemical environments) of adjacent cells - communication between cells = most of plant unified into one living continuum - facilitated transfer of molecules - cellulose → β-glucose molecules connected by glycosidic bonds (very strong); parallel chain polymers connected by hydrogen bonds (not as strong) between hydroxyl groups (= holds chains firmly together) → microfibrils with high tensile strength → very rigid cellular strands - resistment from osmotic pressure → allows plant cell to develop high internal pressure (turgor) due to water uptake, without danger of cell bursting (main difference between cell water relation of plants and animals) - strength + support to tissues (leaves, trees) - transport role → helping to form channels/tubes for movement of substances (water + minerals/water + sugars) + signal molecules in plants - modifications - trichome (hair-like projections from leaves) → capture air, prevent water evaporation, protection against pathogens - strong outer covering for leaf → epidermal cells tightly connected to one another - xylem (tubes) = remaining cell walls of died cells → transport of water + minerals throughout plant - extracellular matrix (animal cells) → secreted/synthesized locally by cells in matrix (secreted by cells called fibroblasts) - (mainly) water + proteoglycan molecule = network of sugars - proteoglycan network (covalently attached oligosaccharides), large fibrous proteins (collagen + glycoproteins) and integrins (cell receptors) - roles:  - adhesion between cells (binds them together) → cells form compact tissues and organs - strengthens cell membrane and protects cell - communication between cells - important in interactions between cells that cause them to differentiate and move; stem cells encouraged to become new cell types as result of interaction with extracellular matrix - support and structure in some animal tissues (bone, cartilage) - concentrates calcium phosphate minerals (main inorganic components of human bones and teeth) - abundance of collagen proteins → structural support - movement of cells (tissue used to make tendons and ligaments composed mainly of extracellular matrix - collagen) - integrins/transmembrane proteins → cell receptors that span membrane - bind to extracellular matrix on outside and proteins attached to microfilaments on inside (cytoplasm) - hold tissue together, structural support to tissue - cell communication → allows transmission of signals between cell’s external environment and interior = change in cell behavior to respond to local environment - during movement/contraction of ECM integrins rearrange internal microfilaments → send signal to nucleus to turn on/off certain genes and adapt to behaviour of changing environment - fibrous proteins embedded in proteoglycan network → structure + attach ECM to other nearby cells 1. collagen → very large and strong fibrillar protein embedded in a web of proteoglycan complexes - bound side by side and end to end → forming of strands = collagen fibrils - most abundant glycoprotein in extracellular matrix - forms triple helix (3 strands of polypeptides) = extra strength - abundant in connective tissue - mutation - no 3 strands → muscle weakness, degeneration and abnormally fixed joints; brittle bone disease - intertwined by fibronectins 2. fibronectin → insoluble fibers between cells that connect collagen fibers to cellular membrane - transmembrane proteins (integrins) - cytoskeleton → network of proteins (protein filaments) - not an organelle (everywhere within cell); not a fixed structure (can disassemble and reassemble again when needed) - attached to cell membrane via proteins - provides physical and mechanical support (especially important for animal cells, which lack walls), maintains shape/structure of cell, anchors/holds position of organelles, cytosolic enzyme molecules and cells, maintains internal organization - enables cells to carry out essential functions → cell division - allows cell motility in interaction with motor proteins (changes in cell location + movements of parts of cell) → bending of cilia and flagella, contraction of  muscles, movement of vesicles/other organelles inside cell (endomembrane system), cell locomotion - regulation of biochemical activities in cell in response to extracellular mechanical stimulation → forces exerted by extracellular molecules via cell-surface proteins transmitted into cell by cytoskeletal elements (may even reach nucleus) 1. microfilaments/actin filaments (protein actin) - thinnest/smallest - globular actin monomers polymerize into filaments, strands - plus end → polymerization (growth); minus end → depolymerization - hydrolyze ATP → assembling of microfilament filament guided by ATP (when bound, depolymerization) - movement of organelles and cell (gliding) - muscle contraction - skeletal muscle cells composed of muscle fibers - made of sarcomeres (each contains overlapping myosin and actin) - myosin motor proteins glide - actin filaments approach each other → shortening of sarcomere = shortening of muscle - reinforcing of cell against pulling forces, maintaining shape of cell - structural role = microvilli → increase surface of cell membrane - internal epithelial cells → absorption of food - ameboid movement in single celled organisms → crawling-like type of movement achieved by protrusion of cytoplasm = formation of pseudopodia - actin filaments with myosin squeeze the interior, push cytoplasm into one direction and extend - plant cell → cytoplasmic streaming driven by myosin motors attached to organelles that interact with actin - layer of cytoplasm cycles around cell, moving over actin filaments arranged in parallel pattern → transport of vesicles 2. intermediate filaments → intermediate diameter - primary filament - no plus or minus end = not used for movement - fibrous proteins (diane → tetramer → octamer → filament) - made of multiple different filaments - differ based on type of cell (epithelial cells - keratin, nerve cells - neurofilaments, muscle cells - desmin,...) - help maintain shape, structure of cell + attach neighboring cells to one another and to surfaces - hold position of organelles inside cell; attach to nuclear envelope → position and anchor nucleus - movement/transport of vesicles → they slide along side actin filaments and microtubules by attaching with heads 3. microtubules (protein tubulin) - largest/thickest filaments - molecules polymerise into tubules (hollow in center)  - α and β tubulin monomers form protofilaments → 13 of them form microtubule (constantly changes, breaks apart, reassembles) - plus and minus end = dynamic structure → grows on one end and gets shorter on the other - maintenance of cell shape → resisting external compression - guiding of secretory vesicles from ER to GA - during division of cells form mitotic and meiotic spindle → can be elongated and shrinked = pull chromosomes to either side of cell - centrosome (near nucleus) → high concentration of tubulin - microtubules grow out of centrosome - organizes microtubules during cell division - made of 2 pairs of centrioles (9 triplets of microtubules); replicate before cell replication - only animal cells (plant and fungi cells only have microtubules) - serve as ropes, along which motor proteins transport organelles - motor proteins: dynein and kinesin → dynein travels along microtubules towards minus end → generates force that makes flagella and cilia move → kinesin walks along microtubules towards plus end → facilitates material transport, mitosis - movement: - cilia and eukaryotic flagella → membrane + cytoplasm + 9 pairs of microtubules and one central (9 * 2 + 2) - basal body → triplets of microtubules, no central (9 * 3) - cell locomotion - movement of fluid over the surface of tissue (trachea, oviduct) - signal-receiving antennae (transmit molecular signals from environment into the cell) - hydrolyze ATP - prokaryotes → no actin, intermediate filaments or microtubules - intercellular junctions → connect adjacent cells allowing intercellular transport (passage of ions, sugars, other small molecules) and communication - play important roles in cell multiplication, cell migration and prevent unregulated movement of materials between cells 1. plasmodesmata (plants) → big holes in cell’s wall, continuous cell membrane from one cell to another (lines plasmodesma - narrow thread of cytoplasm) - continuum of cytoplasm → easier transport of water molecules, ions 2. gap junctions (animal cells) → cytoplasmic channels from one cell to adjacent cell (similar in function to plasmodesmata - easier transport of molecules) - consist of alined membrane proteins, forming continuous pore - cell-to cell transfer of small molecules: easy passage of ions, sugars, amino acids, other small molecules → easy and fast communication between cells - e.g.: heart muscle cells (quick depolarization - simultaneous = fast flow of sodium), animal embryos, brain tissue, smooth muscle → gap junctions allow quick flow of ions that let these cells contract  3. tight junctions (epithelial cells) → form tight seal between adjacent cells = plasma membranes of neighboring cells very tightly pressed against each other, bound together by specific proteins - division of compartment + prevent leakage of extracellular fluid across layer of epithelial cells - no substances can pass through uncontrolled - impermeable/semi permeable barrier between adjacent cells → act as barriers to transportation of material, control movement of membrane transport proteins between apical and basal layers of epithelia - prevent passage of unregulated molecules through intercellular space of adjacent cells - materials must actually enter cells (diffusion/active transport) in order to pass through tissue - in blood cells, lining urinary bladder (urine doesn’t leak into extracellular spaces), epidermis and kidney tubules 4. adhesive/anchoring junctions: adherens junctions, desmosomes (one of stronger adhesion types) → transmembrane proteins of adjacent cells connect forming plaques (tension reducing network of fibres) - facilitate cell–cell adhesion in tissues to ensure structural stability and allow the cells to withstand mechanical stress (strong but flexible) - also connect to intermediate filament cytoskeleton network (keratin) → structural continuity - found in tissue that experience intense mechanical stress: cardiac muscle tissue, bladder tissue, gastrointestinal mucosa, epithelial cells - hemidesmosomes → specialized junctions connecting plasma membrane to extracellular matrix (epidermis) - atypical cell structures in eukaryotes - stratiated (skeletal) muscle cells → role = movement, need to contract - each cell very long (longer than typical cells), spindle shaped - multiple nuclei located towards periphery of cell → formed from multiple cells which have fused together and work as a single unit (→one nuclei cannot control such large intercellular space, needs more proteins???,...) - significance: - presence of multiple nuclei allows for simultaneous transcription of genes → enhanced synthesis of proteins essential for muscle contraction and repair - cells densely packed with myofibrils (contractile structures) → large amounts of cytoskeleton ensuring effective muscle contraction - hyphae → long, feathery filaments that make up multicellular fungi - mycelium → root-like structure of fungus consisting of mass of branching, thread-like hyphae - secretes enzymes into environment which break down food sources (biological polymers into smaller units - monomers) → absorbed into mycelium by facilitated diffusion, active transport - in nature very extensive and irregular; small differences in substrate affects growth  - in agar culture dishes → symmetrical, circular growth (each circle = colony grown from single spore) - mushroom = reproductive organ → production of spores (reproductive structures) - only grows when two nucleus of complementary sexes merge - lower fungi → aseptate fungal hyphae/coenocytic hyphae = no divisions, each hypha = uninterrupted tube-like structure with continuous cytoplasm and many nuclei (multinucleate) - origin: nuclear divisions without subsequent cell division - higher fungi (septate hyphae) → multiple cells (cell-like sections) divided by septa with pores (still continuous cytoplasm) - role of septa → damage control - hypha gets damaged, cytoplasm flows out and septa pores become plugged - significance of aseptate fungal hyphae: - rapid nutrient distribution → lack of septa facilitates rapid cytoplasmic streaming (nutrients, organelles, other cellular materials can be quickly distributed throughout hyphae) - metabolic boost → multinucleated nature supports increased metabolic activity (beneficial to the fungus as it seeks to extract and absorb nutrients from its environment or host) 1 - bone tissue - osteocyte → primary cell of mature bone (maintain bone tissue, located in matrix); lacks mitotic activity → maintain mineral concentration of matrix via secretion of enzymes - red blood cells (erythrocytes) → biconcave, disc-shaped cells primarily tasked with transporting oxygen from lungs to various tissues of body - mature blood cells in mammals do not contain nucleus or organelles (ER, GA, mitochondria) - significance: - maximised O2 transport → absence of nucleus and organelles enables cell to carry large volume of O2 binding pigment hemoglobin maximizing oxygen-carrying capacity - biconcave shape of red blood cells = large surface area to volume ratio + flexibility (movement through tiny capillaries) - erythropoiesis → process of erythrocyte development - phloem sieve tubes → specialized plant cells found in phloem tissue - primary role is transport of nutrients (especially products of photosynthesis - e.g. sucrose) throughout plant - during their functional phase lack nucleus + no end cell wall and lack many cell organelles (nuclei, mitochondria, ribosomes, vacuole) - significance: - facilitates flow of nutrients → absence of nucleus and other organelles creates more open interior - adjacent to each sieve tube element is companion cell → assists in maintaining metabolic functions that sieve tube 1 https://open.oregonstate.education/aandp/chapter/6-3-bone-structure/  element cannot perform due to lack of organelles (maintain cytoplasm of sieve tubes) A2.3 VIRUSES Common features of all viruses → result of convergent evolution (shared characteristics because of functional reasons rather than because of common ancestor) - viruses = small infectious/pathogenic particles, not classifies as organisms or cells - very simple structures → no cytoplasm, ribosomes, metabolism, protein synthesis or other structural features (only have genetic material and few to no enzymes) - cannot replicate and reproduce outside of host cell - obligate intracellular parasites = dependent on host cell - energy → don’t have their own source of energy like living cells do, must rely on host cell to provide energy needed for viral replication - nutrients → don’t have ability to obtain their own nutrients and must rely on host cell for necessary building blocks for viral replication - replication machinery→ no machinery needed to replicate their own genetic material, must rely on host cell’s machinery (ribosomes, enzymes) to transcribe and translate their genetic material into viral proteins - transport → some viruses use host cell’s transport machinery to move to different parts of body or spread to other host cells - small structures (must be smaller that host cell they infect) - 20-500 nm - largest: almost 1 μm (Ebola), smallest: 20 nm - contain fixed number of components, each with fixed size which determine overall size → viruses don’t grow - virion → complete virus particle consisting of RNA or DNA core with protein coat, sometimes with external envelopes; extracellular infectious form of virus - viroids (not viruses) → extremely small particles that consist only of naked RNA without a protective layer (protein coat - capsid); infect plants - capsid → protein coat that surrounds and protects genetic material - nucleocapsid = nucleic acid + capsid - cells. genetic material always DNA; viruses: either RNA or DNA - double (herpes viruses, variola virus, bacteriophage lambda) or single (parvovirus) stranded DNA - double (rotaviruses) or single (HIV, influenza, coronaviruses) stranded RNA - plus sense RNA/DNA → can act as mRNA immediately or minus sense RNA/DNA → used as a template (sequence complementary to mRNA), must first be transcribed to plus sense - circular or linear - contain few to no enzymes (not essential for most; those that have them, require them for successful infection and replication) - some bacteriophages contain enzymes resembling lysozymes = attacks cell wall → used to make small hole in bacterium’s peptidoglycan layer which allows nucleic acid from virion to get into host’s cytoplasm - similar protein produced in later stages of infection to lyse host cell and release new virions 1. bacteriophage attaches to surface receptors of host cell by tail fibers  2. tail pins connect to cell outer membrane (lipopolysaccharide layer), tail tube penetrates outer membrane and digests small opening through peptidoglycan layer with lysozyme 3. tail contraction and ejection of genetic material into host cell??? - some animal viruses also contain enzymes that aid release from host - e.g.: influenza virus = flu → envelope proteins (neuraminidases) destroy glycoproteins and glycolipids of animal cell connective tissue, liberating virions - retroviruses (e.g.: HIV) → contain enzyme reverse transcriptase: RNA-dependent DNA polymerase (transcribe RNA into DNA in host cell, then mRNA is synthesized) 1. retrovirus attaches to surface membrane receptors 2. membrane of virus fuses with host (with help of proteins) - endocytosis 3. protein coat disassembles → RNA is released 4. reverse transcription → double stranded DNA → integration in host’s DNA 4.1. either immediate transcription to mRNA and protein synthesis → new viral proteins + new viral RNA 4.2. or enters cell genome and dormant (slowly destroying immune cells) until triggered to start transcribing 5. assembling of protein coat 6. budding = enables viruses to exit host cell (mostly used by enveloped viruses) - must acquire host-derived membrane enriched in viral proteins to form their external envelope → new virion Diversity of structure of viruses 1. shape → nucleocapsid specific for type of virus - proteins assemble into different geometric shapes - helical → capsid twisted around enclosing genetic material (hollow cylinder) - polyhedral → genetic material surrounded by many-sided capsid - spherical (coronavirus) → enclosed in envelope, spike with sugary proteins = attachment and entering host cell - complex (bacteriophage) → head + helical body + tail fibers = attachment to cell membrane and transfer of genetic material 2. envelope - naked virus (smaller - most bacterial viruses) → no envelope - viruses without envelope may be more stable and resistant to environmental factors than enveloped viruses - lipid envelopes may become damaged by heat, light and chemicals - e.g.: norovirus, adenovirus, bacteriophage lambda - enveloped virus (many animal viruses) → envelope of phospholipid bilayer (taken from host cell membrane when released) + coral proteins - helps protect capsid, provides additional layer of protection to viral genome, helps disguise virus from immune system of host cell and helps virus attach and enter new host cells - e.g.: HIV, influenza  3. genetic material - Baltimore classification of viral genomes 7 classes divide viruses based on genome (+ virion shape, capsid shape, envelope, nucleic acid sequence…) - genomes of viruses either DNA or RNA (some viruses use both at different stages in replication cycle) - only one type of genomic nucleic acid is found in virion of any particular type of virus - viral genomes can be single-stranded (ss) or double-stranded (ds) and circular or linear - virus containing a single-stranded genome may be: - plus/positive sense: exact same base sequence as of viral mRNA that will be translated to viral proteins - minus/negative sense (antisense): viral genomes (used as template) complementary in base sequence to viral mRNA and positive sense - great diversity in size of genome: - complex viruses - 350 genes, ‘giant’ virus - estimated to contain 2500 genes, smallest bacterial genome - 110 genes, smallest viral genomes (infect animals) only 2 genes - bacteriophage lambda (bacteriophage) → DNA virus - non-enveloped - one double stranded DNA molecule with positive and negative sense strands, 32 genes coding for 29 proteins including 4 enzymes (e.g.: holin - helps bacteriophage make holes in cell wall of bacterium it is infecting) - can follow either lytic cycle (reproduces and kills cell host as it bursts out) or lysogenic cycle (integrates its DNA, does not kill host) - has short collar, tail and tail fibers to attach to cell it is infecting - host: archean or (gram negative) bacterium - e.g.: E. coli - COVID-19 (coronavirus) → RNA virus with crown like shape - enveloped with membrane and envelope proteins on surface + large spike proteins - one single stranded RNA genome, 16 genes coding for 29 proteins including 6 enzymes - capsid made up of multiple copies of nucleocapsid protein, which binds to RNA genome and forms a helical structure - zoonosis → infectious disease transmitted between species from animals to humans - host: human cells, possibly cells in other mammals - HIV (retrovirus) → converts RNA genome to DNA after infecting host - AIDS in humans - envelope with many glycoproteins - used by virus to gain access into host cell - unusual, cone shaped capsid with two copies of single-stranded positive-sense RNA, 9 genes coding for 15 viral proteins including 4 enzymes - contains enzyme reverse transcriptase → makes double-stranded DNA copy of viral RNA genome which is integrated into host cell chromosome - host: T-helper cells in human immune system Replication cycle of viruses - gaining access to host cell machinery:  1. endocytosis → viruses can taken up by host cell endosome (an invagination of host cell membrane) 2. receptor-mediated fusion → process by which virus binds to receptor on host cell membrane to fuse with host cell membrane and enter cell - direct injection of genetic material (e.g.: bacteriophage lambda) - once virus (or only injected viral genome) has entered host cell, viral genome will circularize and undergo replication - two main methods of viral genome reproduction inside host cell: 1. lytic cycle → bacteriophage genome takes over host cell machinery - immediate transcription and synthesis of new phage DNA + proteins - rapid production of new viral particles, which lyse/burst host cell, destroying it and causing new viral particles to be released into environment → infection of another cell 2. lysogenic cycle (provirus?) → viral genome becomes integrated into host chromosome = prophage; as host cell reproduces, each new daughter cell is infected, containing bacteriophage genome - virus is „temperate“ → does not kill host, minimal harm - benefit for host cell → viral DNA may contain genes from previous host → increased genetic diversity of bacterial host = facilitated evolution - inherited by daughter cell, but cannot spread by infecting uninfected cells - occasionally prophage genome is excised from host cell genome, forming bacteriophages → lytic cycle and lysis - genes in prophage must be activated in response to stimuli from outside or inside cell (environmental stress) - some of prophage genome can be left behind in host cell’s, or some of host cell genome can be taken with prophage - some viruses use only lytic or lysogenic cycle, some viruses switch between them when exposed to certain environmental conditions - UV light, chemical stressors (e.g.: bacteriophage lambda) - streptococcus pyogenes - when affected with phage becomes even more virulent (expression of exotoxin) → causes scarlet fever - herpes viruses → enveloped DNA viruses (herpes zoster, shingles, herpes simplex - genital + cold sores)) - replicate in host cell’s nucleus (acquire their envelopes from cell’s nuclear membranes) - alternates between 2 phases: - dormant lysogenic phase → while inside nuclei of certain nerve cells, herpesvirus DNA may remain permanently dormant, without destroying these cells - lytic active phase → from time to time, physical (cold, sunburn) or emotional stress may stimulate herpesvirus DNA to begin production of virus, which then infects cells at body’s surface and causes symptoms - varicella zoster  - first encounter = chicken pox → systemic disease (rash, bubbles,...) - immune system afterward suppress virus, but it stays in nuclei of nerve cells → herpesvirus DNA may remain permanently in dormant lysogenic phase, without destroying these cells - erupts again when low immune system, physical (cold, sunburn) or emotional stressor, old age → stimulate herpesvirus DNA to begin production of virus - infects cells at body’s surface and causes symptoms = herpes zoster (shingles) Origin of viruses (only hypotheses no theory) - viruses exhibit huge diversity in structure and genetic material → several possible origins: - may have originated from ancient RNA or DNA molecules that became encapsulated in a protective protein coat → encapsulated gen. material = ‘proto-virus’ may have been able to replicate, evolve, eventually forming viruses we know today - may have evolved from viroids (small infectious agents consisting only of short strand of RNA and infect angiosperms - flowering plants) - may have originated from transposons - genetic elements that can move around within an organism’s genome - may have evolved from ancient cells that lost ability to live independently and became dependent on other cells for reproduction 1. Progressive hypothesis (simple → more complex) - all known viruses require host cell for replication → viruses evolved at some time after cells first appeared on Earth (about 4 billion years ago) - viruses → remnant cell components that evolved an ability to replicate with assistance from cell - retrotransposons → type (sequence) of DNA that can move around within genome by first transcribing/copying themselves into RNA, then converting RNA back into DNA - new DNA copy is inserted into another location in genome - effect gene expression - pos. and neg. effects on genome → help create new genes and regulatory elements; can disrupt existing genes = mutations 1. transcription and translation 2. formation of ribonucleoprotein complexes = enzymes, that make more DNA copies of transposons by reverse transcription 3. reverse transcription of RNA → process of copying info. found in RNA into DNA, catalyzed by enzyme reverse transcriptase 4. integration of those copies into cells chromosomes at random positions - viruses may have evolved from retrotransposons, which gained capsid proteins from host cell → both use coded RNA to replicate themselves whenever they enter new cell + similar method for entering and exiting cells  - ???retrotransposons became independent, containing genes for reverse transcriptase → forming of proteins → forming of capsid around RNA → retrovirus??? 2. Regressive hypothesis (complex → simple) - viruses evolved from cells, by gradual loss of some cell components - small single-celled organism enters bigger single-celled organism → forms mutualistic relationship → smaller organism loses its protein-building structures → smaller organism is able to replicate itself and infect new organisms = virus - proteomics = method for comparison of proteomes (entire set of proteins that is/can be expressed by genome, cell, tissue, organism at certain time) of viruses and cells - viruses are not cells (=no ribosomes) it has been impossible to place viruses on universal tree of life comparative rRNA sequences - virus origin from ancient cells containing segmented RNA genomes and existing before LUCA of modern cells appeared; in “RNA World” - Arguments for hypothesis: - RNA viruses older than DNA viruses - dsRNA viruses most ancient of all viruses (many different types of dsRNA viruses contain segmented genomes, possible remnant from their virocell ancestors) - retroviruses appear to be ancient and may have played a role in transition from an RNA to a DNA world - variability of viruses → small + simple or big + complex; some have their own enzymes and perform functions that most viruses have lost → simplification could have happened multiple times - mimivirus → very large dsDNA virus, with enzymes - performs some functions, that most viruses leave to host - genome larger than some prokaryote genome (overlap with very small bacteria) - variability of bacteria - most bacteria are self-reliant; some parasitic species replicate inside host cell - some bacteria lost ability to perform certain metabolic functions - some bacteria have very small genomes with few genes - smallest cellular genomes belong to parasitic or endosymbiotic (cells living in other cells) bacteria - Chlamydia (600 genes) - likely to have evolved from independent organism, that became parasitic - Nasuia deltocephalicola → absolute smallest genome discovered so far; sap-feeding insect symbiont, genome only 112 kbp - totally dependent on insect host cells for survival and nutrients; in turn provide insect with essential amino acids and other nutrients that insect cannot synthesize  - genomes of most human pathogens (Mycoplasma, Chlamydia, Rickettsia) are smaller than largest known viral genome (Pandoravirus) - smallest genomes among parasitic prokaryotic cells: M. genitalium, N. equitans → hyperthermophile, parasite of another hyperthermophile, lacks virtually all genes that encode metabolic proteins and depends on host for most catabolic and anabolic functions → viruses might have evolved from intra parasitic bacteria that lost their ability to live independently (food from host) and became dependent on other cells for reproduction - loss of more and more life functions (respiration, protein synthesis… - genome became smaller) - some bacteriophage uses universal genetic code, but doesn’t have the same bases in DNA - diaminopurine (labeled Z) instead of adenine - this modification makes DNA more heat-stable and protects from attack by host - How does this affect our understanding of the origin of viruses and genetic code?... - convergent evolution → structural features shared by viruses could be regarded as similar independently evolved traits, resulting from adaptation to similar environments or selective pressures - some viruses that infect different cell types have evolved similar mechanisms for entering and replicating within those cells - some that infect different types of host organisms have evolved similar mechanisms for evading host’s immune system and spreading to new hosts - some that infect different types of host organisms have evolved similar shapes and sizes - likely that convergent evolution occurred because there are only limited number of ways that viruses can effectively infect and replicate within host cells, and limited number of shapes/sizes optimal for infecting and replicating within host → different viruses arrived at similar solutions through different evolutionary pathways Rapid evolution of viruses - evolution in viruses described as process by which they change and adapt over time; evolve at much faster rate than most organisms, because : - many RNA viruses are retroviruses → high mutation rates because they copy their genetic material using error-prone mechanisms (reverse transcriptase enzymes and RNA polymerases - less accurate than DNA polymerases) - HIV, influenza, hepatitis C = RNA-based viruses - can have mutation rate up to 10 000 times higher than those of DNA viruses (mutations can be passed onto next generation of viruses) - exchange genetic material with each other through recombination and horizontal gene transfer → allows them to rapidly acquire new traits or adapt to new environments  - short generation times and high reproductive rates → can produce many offspring in short period of time = more opportunities for evolution to occur - viruses with higher mutation rate are harder to treat and vaccinate against + much harder for host’s immune system to recognise and control these viruses - SARS-Cov-2 (→ covid-19) → enveloped, ss(+)RNA - spike proteins on surface play a key role in recognition of host cell and fusion with host cell membrane - RNA virus = high rate of mutations (new strains every season) → some have deleterious effects (harmful/damaging to virus) or no effect; some in sequence of spike proteins increase transmissibility, reduce vaccine efficacy and aid virus in evading host cell immune system - high replication rate = makes many copies of itself inside host cell in set period of time, increasing likelihood that mutations will occur and accumulate - genetic recombination and mutations accumulate that make virus sufficiently different to original virus → new viruses = ‘variants’ (SARS-CoV-2 Delta, Omicron variants) - changes in RNA sequence of SARS-CoV-2 very frequent → can be used to track transmission of virus - can be helpful in developing public health measures to limit spread of disease - influenza virus → enveloped, ss(-)RNA; class V - causes respiratory disease/infection - enzymes: RNA-replicase - RNA dependent polymerase (used to make more RNA strands); RNA-endonuclease (cleaves RNA) - RNA polymerase does not have proofreading ability (like DNA polymerase) → many changes in RNA molecule = high frequency of mutations (influenza virus mutates frequently) - replication of genetic material by RNA replicase - enzyme that can produce RNA from an RNA template (converts minus-strand genome into plus strand) - RNA replicase → high mutation rate (unlike DNA polymerase doesn’t proofread/correct errors; less stable, changes chemically faster) = faster evolution - segmented genome → influenza A virus’ (common strain) genome is segmented into eight linear single-stranded molecules (890 - 2341 nucleotides, totaling 13.5 kb) - consequence of segmented genome: antigenic shift (major change in genome) = appearance of new strains → segments of RNA genome from two different strains infecting same cell are reassorted/assembled (e.g.: pig - host to human and animal strains) → forming highly virulent reassortant influenza virus - generates hybrid influenza virions that express unique surface glycoproteins/antigens unrecognized by immune system - thought to be responsible fo major outbreaks of influenza (e.g.: spanish flu) → immunity to new forms of virus absent from population - transmission between species (especially between birds and humans) → frequent appearance of new strains  - antigenic drift (subtle, progressive change) → slight variation in structure of influenza viral surface antigens - each strain of influenza virus can be identified by a unique set of surface glycoproteins (viral proteins) in envelope - hemagglutinin (HA or “H antigen”) → important in attaching influenza virus to host cells - neuraminidase (NA or “N antigen”) → important in releasing virus from host cells - each virus has one type of HA and NA on its viral capsid and is named for antigens it contains (e.g.: “H1N1.” = Spanish flu 1918) - infection/immunization with influenza virus results in production of antibodies that react with HA and NA glycoproteins → when antibodies bind to HA or NA, virus is blocked from either attaching or releasing and is effectively neutralized, stopping infection process - host immunity to a given virus strain diminishes as strain mutates (surface proteins mutate) because of antigenic drift - gradually introduced changes by mutations (no proof reading) → slight changes in bases - humans usually still immune to changed virus, but lower - reinfection with mutated strain → last year’s influenza vaccine may work only poorly against this year’s crop of influenza viruses → vaccine always contains several strains of viruses - new vaccines each year → host immune system produces specific antibodies for new surface proteins (antigens) - cladogram → based on similarity in sequence of RNA genome - HIV (human immunodeficiency virus) → retrovirus (RNA) - transmitted through infected body fluids → leading to disease acquired immunodeficiency syndrome (AIDS) - envelope + surface envelope proteins - enzymes: reverse transcriptase, integrase, protease - genome of all retroviruses contains 3 genes: - gag = structural proteins - pol = reverse transcriptase and integrase → synthesis and integration of viral DNA into the host genome + generation of capsid proteins - env = envelope proteins → binding/attachment + entry into host cells - mutations in env gene = HIV evolves: - can use different cell types in human as hosts - becomes resistant to antiretroviral drugs → combination of 2/more drugs needed - CD4+ cells - type of blood cells (mature T helper cells - central for immune system) → very susceptible to HIV virus (primarily infects, destroys them) - highest know mutation rate of all viruses; reasons: - reverse transcriptase → converts ssRNA to DNA (does not proofread/correct errors) - more error-prone than DNA polymerases = many mutations → can lead to emergence of new HIV strains that  may be more/less virulent, more/less transmissible, more/less able to evade immune system or antiviral drugs - cytidine deaminase → enzyme made by host (protection enzyme → attacks RNA) - converts C into U = mutation (can also increase infectivity - easier attachment, more virulency) - person can be infected by more strains → combinations of genes = new strains - recombination = exchanging gen. material with other viruses or its host cell → new genes/traits which can increase its adaptability - short generation times - 1 person is infected by 1 strain → many new genetically different strains because of mutations inside body (low gen. time → high rate of mutations) - most infections chronic, not curable - antiviral compounds/drugs only help keep concentration of virus low - prevent replication → inhibition of reverse transcription (for retrovirus) - target viral protein enzymes → inhibition of viral protease - block fusion of HIV with T lymphocyte membrane - prevent attachment - block active side of virus (influenza - neuraminidase) MEMBRANES Functions 1. boundary → separation of interior and exterior = protects cells from their environment mechanically and chemically (selectively permeable) 2. controlled metabolite transport (integrated proteins) → maintains differences in concentrations of many substances between intracellular and extracellular environment 3. signal reception and transmission → transfers extracellular signals into interior of cell + produces signals 4. enzymatic reactions → accumulation of important enzymes (eg. oxidative phosphorylation reactions occur on mitochondrial membranes…) 5. contact with other cells → cell fusion and tissue formation; communication with ECM 6. anchor for cytoskeleton → maintains shape of organelles; provides basis for movement process The basis of cell membranes - lipid bilayers - membranes are composed of: - lipids (phospholipids - most abundant, glycolipids, sterols) - proteins - small amounts of carbohydrates (in form of glycolipids and glycoproteins) - phospholipid → amphipathic nature: to glycerol backbone (3-carbon alcohol) hydrophobic (non polar tails) + hydrophilic part (polar head - form hydrogen bonds) attached - response of phospholipid molecules to water → phospholipids spontaneously organise themselves so that hydrophobic tails shielded from water (hydrophobic tails point inward, away from aqueous environment; hydrophilic heads point outward): - in contact with water (on surface) → monolayer (heads dissolved in water, tails sticking out) - mixing with water → bilayer (hydrophobic tails attracted to each other) - phospholipid bilayer is (thermodynamically) stable structure → bonds between polar heads surrounding water molecules + hydrophobic interactions between tails (weak, but huge number of interactions) - need for continuity of phospholipid bilayer → formation of closed structures = vesicles - bilayer sheets not very stable (hydrophobic tails exposed to water on edges) → sealed compartment (energetically favorable - avoids exposure) - micelle (heads outside, tails inside) evolves into liposome/vesicle (also internal aqueous compartment) - differences, diversity between phospholipid layers: - different additional groups attached to phosphate group on head - differences in fatty acids → size (long or short - number of carbon atoms in fatty acid side chains of membrane lipids ranges from 16 to 20), saturated or unsaturated (one or more double bonds between carbon atoms) - composition of fatty acids in lipid bilayers = regulation of fluidity: - unsaturated fatty acids = lower melting points → membranes are fluid and flexible at T experienced by cell (high fluidity) - kinks in chains → prevent membrane lipids from packing together closely, maintaining fluidity - saturated fatty acids = higher melting points → make membranes stronger (more rigid) at higher T (low fluidity) - fit together tightly, making membrane denser and more rigid - higher T → reduced concentration of unsaturated fatty acids - lower T → reduced fluidity (more rigid) = cell increases concentration of unsaturated fatty acids (e.g.: cholesterol), phospholipid molecules come closer together (space in unsaturated fatty acids prevents molecules from packing too close together - maintain membrane fluidity) - homeoviscous adaptation → adaptation of cell membrane to maintain adequate fluidity (lipid composition of cell membrane can change as adjustment to changing T) → lake sturgeon - North American temperate freshwater fish - occupies some of most northerly distributions of any sturgeon species and experiences extended overwintering periods - when T decreases from 16 °C to 1 °C both mono and polyunsaturated fatty acids of phospholipids significantly increase; saturated fatty acids decrease → changes to fatty acid composition of its cell membranes allows fish to survive in cold conditions → winter wheat - higher percentage of unsaturated phospholipids → membranes don?t solidify during winter Lipid bilayers as barriers - hydrocarbon tails of both layers extend inward to form continuous hydrophobic interior = important role in determining permeability of membrane - permeability of biological membranes to molecules depends on size of molecules and their hydrophilic/hydrophobic nature - movements across cell membrane: - secretion: hormones, neurotransmitter substances, enzymes - procollagen → synthesized inside cell, assemblement into collagen fibers outside cell (mammals) - cell wall components - cellulose and hemicellulose → assembled to make plant cell wall outside cell - excretion: ammonia and urea - metabolic waste product (animals) - diffusion: small molecules - protein pumps: charged molecules (ions - e.g. Na+), trace elements - facilitated diffusion: nutritional molecules (sugars - glucose, amino acids, fatty acids, vitamins), nucleotides (transmembrane integral proteins) - mechanisms of movement across cell membrane: diffusion, osmosis, active transport, bulk transport (by vesicle) net movement = number of molecules moving in direction of forces minus number of molecules moving in other direction Simple diffusion → passive movement of particles from a region of high concentration to a region of low concentration (down concentration gradient) - occurs in both directions, but there is net movement from region of high to region of low concentration → results in equilibrium (equal concentration on both regions) - occurs because of kinetic energy (from continuous motion) of molecules = random movement disperse them towards places where there is fewer molecules - lipid bilayer (plasma membrane) permeable to: - solute - hydrophobic (non-polar, lipid soluble) uncharged molecules (benzene, O2, N2, steroids) - small polar uncharged molecules (H2O,CO2, ethanol, urea, glycerol, NH3) - lipid bilayer not permeable to: - charged molecules (ions - charge prevents from crossing nonpolar interior) - moderate to large polar uncharged molecules (glucose, sucrose - large size and polarity prevent from crossing) - diffusion of O2 and CO2 in alveoli and tissues (fast rate of diffusion) - O2 from oxygen rich air in alveoli down concentration gradient to blood in surrounding capillaries (gas exchange in lungs): alveoli → diffusion of oxygen through alveolar epithelium (pneumocyte cell) → extracellular matrix → endothelium → enter erythrocyte through phospholipid bilayer - O2 from capillary to individual cell tissues (metabolically active cells have lower concentration of oxygen) - internal respiration: O2 dislocates from hemoglobin → diffuses through phospholipid bilayer of erythrocyte → endothelium (inner cellular lining of blood vessels - arteries, veins, capillaries and lymphatic system) → extracellular matrix → plasma membrane → mitochondrial membranes = cellular respiration  - cytochrome c oxidase (mitochondrial protein in matrix) → oxidative phosphorylation = reduction of oxygen - binds to H+ protons to oxygen molecule forming molecule of water - same time in tissues CO2 diffuses from cells where concentration is higher to blood where concentration is lower → CO2 then carried to lungs - diffuses from blood to alveoli down concentration gradient - cornea → cells receive O2 from air via simple diffusion (no blood supply) - travels from air (high concentration of O2) → through fluid - tears (high concentration of O2) → cells on outer surface of cornea (low concentration of O2 = cellular respiration) - diffusion of O2 from maternal blood (uterus chorion microvilli) to fetal blood and diffusion of CO2 from fetal to maternal blood Integral peripheral proteins in membranes - proteins concentrate on surface of membranes → more enzymes can bind → high metabolic activity of membrane (higher than in cytosol) - membrane proteins differ in location, structure, function and are asymmetrically (unevenly) oriented across lipid bilayer - structures of membrane proteins = globular (round) - not fibrous: - integral proteins → permanently embedded within plasma membrane - how?: amphipathic molecules → between phospholipids = hydrophobic part, hydrophilic part sticks interact with hydrophilic heads or aqueous environment (out of membrane) - transmembrane proteins (most) → spans entirety of cell membrane - integral monotopic proteins → attached to only one side of membrane and do not span whole way across - glycoproteins = attached oligosaccharides - transmembrane channel protein/pump (usually hydrophilic) → ions, lipids, amino acids - transport proteins (no channel) - peripheral proteins → temporarily attached/anchored to lipid bilayer (hydrophilic heads) or other integral proteins (hydrophilic region) - hydrophilic surface (can be easily extracted/removed) - lipoproteins → hydrophobic/lipid part (unit with fatty acid) - functions: - transport proteins → facilitate movement of molecules in and out of cell - channel proteins (usually hydrophilic) → transmembrane proteins that form channels/pores for passage of (polar) molecules - passive transport (down concentration gradient) - facilitated diffusion of hydrophilic particles - specific size and polarity → selective passage - carrier proteins → undergo conformational change to transfer molecules from one side of membrane to other (active transport) - pumps → ATP hydrolysis = active transport - shape change (confirmation) to transport substance from one side to another - selective - movement of ions against concentration gradient - cell-to-cell recognition (‘name tags’ for cells) → short living connection  - essential, especially in functioning of immune system → helps to distinguish between self and non-self cells (detection of foreign cells) - interaction of cells to form tissues → tissue recognition with specific glycoproteins - based on type of protein (muscle cells binds to another muscle cell) - receptors for chemical signals, binding sites for molecules - hormones (hormone receptors, e.g. insulin receptor), neurotransmitters - binding of these molecules often triggers chain of intracellular reactions - hormone receptors 1. binding of hormone (signaling molecule) 2. changes conformation of integral protein (also on inside) = change of shape 3. signal transduction = relaying message to cytoplasmic protein (3 relay molecules in transduction) → conformational change - g-proteins → transduce hormone’s message (signal) to interior of cell (inside cell activates other molecules) 4. activation of cellular response → activation of enzymes, gene transcription, transport of metabolites - enzymes → show enzymatic activity and catalyse reactions (e.g. glucose-6-phosphatase - membrane-bound enzyme found in ER) - help in cell adhesion to other cells or to environment - membranes of adjacent cells attach with help of transmembrane proteins = long living connections (gap and tight junctions between groups of cells in tissues and organs) - activation of enzymes, gene expression - immobilized enzymes can concentrate on membrane (e.g.: small intestine) → organization as team in sequential arrangement → metabolic pathway (e.g. mitochondria) - active side exposed to substances in adjacent solution - cell-to-cell communication (receptors for neurotransmitters at synapses) - nerve cells → ion flow = communication - synapse → sites of transmission of electric nerve impulses/signals between two neurons or neuron and gland or muscle cell 1. action potential → depolarization of presynaptic membrane 2. opening of voltage-gated channels → trigger influx of Ca2+ 3. elevated Ca2+ concentration causes synaptic vesicles to fuse with presynaptic membrane → release neurotransmitters into synaptic cleft (space between axon of one neuron and dendrites of another) 4. neurotransmitter binds to ligand-gated ion channels in postsynaptic membrane → triggers opening - play role in cell motility - function of membrane proteins depends orientation - roots → pump proteins oriented and concentrated in a way that enables uptake of water and potassium ions from soil into root cells - epithelial cells?  - importance of membrane proteins in medicine - bacteria + membrane viruses use membrane to attach to host - drug → blocks/masks surface membrane proteins - binds to CCR5 → virus (HIV) cannot bind; does not interfere with CD4 Osmosis → passive net movement of free water across partially permeable membrane from area of lower to area of higher solute concentration - only occurs where there are substances dissolved in water - osmotically active solutes → become surrounded by hydrating coat in water (bound water) - usually concentration of solutes tends to be higher within cell than outside, resulting in net movement of water into cell - organic substances: sugars - glucose, sucrose; amino acids; polypeptides, proteins - inorganic ions: Na+, K+, C –, NO3–organic substances (sugars,) and inorganic - reduced tendency for random movement by dissolved substances and their surrounding water molecules - hydration shell makes it difficult for ions to pass through membrane → channels - diffusion of water: high concentration of free water → low concentration of free water - osmotic pressure (highest with salt) → pulls water - lowers water potential (how much free water there is) - higher the osmotic pressure → lower the water potential - occurs until water potential is equal on both sides of partially permeable membrane (dialysis tube) - random movement of water molecules continues, no net movement - membrane is impermeable to solutes → differences in solute concentration cause differences in water concentration - osmolarity of solution → total concentration of osmotically active solutes - units: osmoles or milliosmoles (mOsm) - normal osmolarity in human tissue: 300 mOsm - isotonic solution = same osmolarity as tissue - hypotonic solution = low osmotic pressure (e.g.: distilled water) - lower osmolarity as tissue - hypertonic solution = high osmotic pressure (e.g.: sucrose solution) - higher osmolarity as tissue - animal cells = no cell wall → lyse in hypotonic solution; shrink in hypotonic solution (indentations - crenellations) - cells of terrestrial animals bathed in extracellular fluid - isotonic to cells - marine animals → sea water usually isotonic to tissues - freshwater fish problem: water always goes inside fish - a lot of effort to equal excess water (hypotonic environment) - seawater fish problem: seawater trying to suck water out of them - effort to retain water - tissues/organs to be used in medical procedures must be bathed in solution with same osmolarity as cytoplasm to prevent osmosis - saline solution (0.9 %) - can be safely introduced to patient's blood system via intravenous drip - washing wounds and skin abrasions - keeping areas of damaged skin moistened prior skin grafts  - basis for eye drops - frozen to consistency of slush (reduces energy, enzyme activity and metabolism → lower rate of decay) for packing hearts, kidneys,...that have to be transported to hospital where transplant operation is to be done - proterozoic cells → adaptation to perform osmoregulation: less permeable cell membrane for water + contractile vacuole (squeeze → water expelled) - plants, fungi, prokaryotic cells → rigid cell wall - inelasticity - hypotonic environment = turgid cell (normal) → high water pressure inside (turgor pressure) - hypertonic environment = plasmolyzed cell - plasmolysis (wilting of plants) → cytoplasm and cell membrane shrink, pull away/detached from cell wall - isotonic environment = flaccid cell - plasmolysed bacterial and fungi cells → useful for food preservation - high sugar/salt content = addition of osmotically active cells - movement of water across membrane: - simple diffusion - hydrophobic interior of lipid bilayer doesn’t allow polar H2O molecules to pass through easily → facilitated diffusion via aquaporins = much faster transport of H20 molecules - particles move through specific channels (only H2O can pass) - quaternary protein with four monomeric subunits - each subunit has water channel → aquaporin molecule has 4 identical water channels - water channels are lined with specific hydrophilic side chains (amino acid residues) which allow passage of water molecules but not of ions - positive charges of amino acids in channel prevent protons (H+) and ions from passing through - at narrowest point, channel in aquaporin only slightly wider than water molecules → water molecules pass through in single file - bidirectional → water can flow in either direction: into interior or out to exterior of cell depending on concentration gradient - aquaporins are involved in absorption of water from soil to root - water travels between cell walls; between concentric cell layers (epidermis, cortex, endodermis, stele) - apoplast pathway (apoplastic route) → water moves through intercellular spaces and cells walls of root cortex (passive diffusion) - symplast pathway (symplastic route) → water passes from cytoplasm to cytoplasm through plasmodesmata - transcellular pathway → transports molecules by passing them through apical, basolateral membranes and cytoplasm via passive diffusion, active transport, or endocytosis - advantage: regulation of what and how fast flows - involved in reabsorption of water in kidney (high concentration of aquaporins) - if kidney would not perform this function, one would excrete about 180 L of urine per day (+have to drink equal V of water) Facilitated diffusion → passive transport (no ATP), down concentration gradient - when you need to increase rate of molecules; when size or polar nature of molecules prevents them from crossing cell membrane - specific channel proteins → water molecules, large polar solutes (glucose, sucrose) → aquaporins → ion channels - highly selective → different channels needed for different ions (sodium channel, magnesium channel, chloride channel…) - e.g.: Mg channel right charge and diameter only for Mg2+ ions - selectivity due to: - binding sites of hydrophilic amino acid side chains lining channel being highly ion-specific - size of pore acting as size filter → gated channels = open/close in response to stimulus - ligand-gated (chemical) channels → open in response to ligand binding → neuron activity: - membranes of dendrites → opened ligand-gated ion channels (ligand binds) allow Na+ ions to enter cell → depolarization of membrane - number of channels that open depends on concentration/amount of ligand in surrounding space → creates graded potential (initial change in membrane potential) - graded potentials (initial change in membrane potential) summate at axon hillock (area dense with voltage-gated channels) → if summed graded potentials reach threshold potential (-70 mV to -50 mV) → voltage-gated Na+ channels open in all-or-nothing response (either all open or none open) - membrane becomes very permeable for Na+ ions → rapid influx of Na+ ions (specific quantity) = triggers action potential → further depolarization of membrane (+30mV) - action potential - nerve signal → travels along axon as sodium channels open sequentially, ensuring signal moves forward - when action potential reaches nerve terminal, it triggers opening of voltage-gated calcium channels → influx of calcium ions facilitates release of neurotransmitters into synaptic cleft, allowing signal to jump to next neuron (another dendrite) or target cell - synapses → small gaps between neurons (communication between neurons or neurons and muscle cells) - action potential carried by neuron cannot cross synapse → message must be transduced (changed) from electrical signal into chemical signal, which can diffuse across synapse - neurotransmitters (acetylcholine - ACh) → group of chemicals that cross synapse this way - nicotinic acetylcholine receptors (neurotransmitter gated ion channel) → 5 transmembrane subunits arranged symmetrically; present at skeletal neuromuscular junctions - binding site for acetylcholine between two of subunits → binding causes conformational change = opens pore/channel  - between subunits cations (positively charged ions) can pass → Na+ diffuses into postsynaptic neuron, changing its voltage (depolarization - interior more positive) - voltage-gated potassium? channels to open - binding of acetylcholine is reversible - when it dissociates from receptor, conformational change caused by binding is reversed and pore in receptor is closed (Na+ cannot pass anymore) - agonist = activates channels; antagonist (closes) - nicotine = agonist of nicotinic acetylcholine receptors (can activate) - skeletal muscles → causes muscle contraction - autonomic nervous system (basic functions of internal organs) → can cause increases in heart rate, blood pressure, adrenaline release - central nervous system → increased alertness and attention, decreased appetite, reduced anxiety and depression, elevated mood, improved concentration… - addiction = long-term overstimulation of receptors → body gets used to presence of nicotine, receptors adapt by becoming less sensitive to it (more nicotine needed for same effect) - voltage-gated (electrical) channels → open in response to changes in membrane potential (neurons) - every living cell separates charge on surface of membranes = membrane potential (-70mV - inside more negative) → changes due to stimulus = gated ion channels open/close - potassium (K+) channels = selectivity filter - specificity → only K+ ions can pass - other too large to pass pore or too small to make bonds with amino acids in narrower part of pore → cannot remove their water molecules (e.g.: Na+ too small to make contact) 1. K+ with hydrating molecules 2. breaking of bonds between K+ and water 3. formation of temporary bonds between K+ and amino acids lining narrowest part of channel pore = selectivity filter 4. hydrating coat forms again (backbone carbonyl oxygens form precisely fitting cage, replacing water molecules of hydration sphere) - channels composed of four α- subunits (span cell membrane: pore-forming domain, lateral window, central cavity) and 4 β-subunits (just inside of cell membrane) - each of 4 subunits has voltage sensor domain (respond to changes in membrane potential) + pore forming domain (with selectivity filter) - ball and chain theory of action → each channel has four balls (positive charge) and chains, one of them passes through lateral window and binds in hydrophobic binding pocket of pore’s central cavity = inactivation of pore - states of potassium voltage gated channels (126):  1. closed: polarized membrane (rest membrane potential: -70 mV) → outer surface of axon (portion of nerve cell = neuron that carries nerve impulses away from cell body) more +, inner more - charge (closed K+ channels) 2. open: nerve impulse → membrane potential changes (threshold to action potential) = depolarization (-50 mV → +30 mV) → flow/influx of ions through pore (membrane on inside becomes more +, on outside more –) → diffusion of K+ ions out of axon = repolarization 3. inactivated: ball moves inside channel = closes pore → remains that way until membrane potential returns to rest membrane potential (e.g. with pumps) → channel closes again, ball goes out - refractory period → impossible to stimulate another nerve response (time interval required to recover from action potential before generating the next one) - nerve impulses, muscle contractions = changes in membrane potential - mechanical channels → open by mechanical stress over a wide dynamic range of external mechanical stimuli which stretch membrane (light - light receptor in retina, sound, heat, electrical stimulation, compression) - molecules move in both directions, important net movement - structure of channel proteins makes membranes selectively permeable by allowing specific ions to diffuse through when channels are open → specific transport/carrier proteins = transmembrane integrated proteins that bind large, charged particles - cannot pass phospholipid bilayer with simple diffusion - presence of transported particle (molecule binds) → change of conformation (3D structure) = open → transfer molecule; absence of particle = closed - no pore, movement of particles depends on changing of structure - highly specific → sites specific for solute or class of solutes - glucose transporters (GLUT) → helps in transport of glucose into red blood cell (RBC) down concentration gradient - different tissues = different versions of transport proteins, channels: - liver → removal of excess glucose from blood - pancreatic islet (contain hormone producing cells), intestine → regulation of insulin release - muscle, fat, heart → activity increased by insulin (regulating glucose levels in blood on surface of muscle cells?) - brain (neuronal) → basal glucose uptake - intestine, testis, kidney, sperm → fructose transport 1. between meals = ↓ concentration of insulin → glucose transporters stored within cell membrane vesicles in cytoplasm 2. after meal = ↑ concentration of insulin → insulin reaches and interacts with receptor on target cell → binds → changes conformation of receptor → changes another signaling molecule → vesicles move to surface and fuse = increase number of glucose transporters in plasma membrane  3. insulin level drops → no more insulin bound to receptor = cell doesn’t need receptors → glucose transporters removed from plasma membrane by endocytosis = formation of small vesicles → fuse with larger endosome 4. patches of endosome with glucose transporters bud off → vesicles ready to return to surface when insulin levels rise again…cycle - facilitated diffusion of glucose from maternal to fetal blood - mitochondria need to uptake ATP → antiporter adenine nucleotide translocase (2 particles, opposite direction) - movement of ADP into and exit of ATP out of mitochondria - simple diffusion rate = linear - facilitated diffusion rate = transport proteins concentrated in membrane speed up diffusion of substrates, but reach maximum rate (same in enzymatic reactions) → number of transport proteins available limits rate (max. = all transporters occupied) Active transport → substances move against concentration gradient = cell must use metabolic energy (usually released by breakdown of ATP) - transport of molecules coupled with E-releasing/exergonic reaction (spontaneous reactions where E is released into surrounding environment) - e.g. breakdown of ATP - role: concentration of molecules/substrates - out → in (many substances cell needs occur in low concentrations in surroundings outside plasma membrane); in → out (less common) - plants → nitrate ions, K+ ions must be taken from very dilute solutions in soil to build their proteins - muscle cells → actively take in Ca2+ ions to enable them to contract - absorption in gut - removing secretory or waste materials from cell into extracellular fluid (kidney tubules → formation of urine) - nerve fibers → propagation of an impulse: pump K+ ions in and Na+ ions out to build up store of potential E or electrical potential used to transmit a nerve impulse - taking up essential nutrients (e.g. uptake of glucose from lumen of intestine to epithelial cells lining small intestine) - maintaining right concentrations of ions in cells (e.g. helps red blood cells maintain internal sodium and potassium levels) - protein pumps → globular membrane proteins that span lipid bilayer and hydrolyze ATP directly - molecule/ion enters pump protein → ATP causes conformational change of protein shape = space opens up → transport of particles to create and maintain concentration gradients - after molecule passes to other side of membrane, protein moves back to original shape - highly specific - types of proteins based on number and direction of transported particles (passive or active transport): - uniport → one particle can pass in one direction - cotransport → two particles can pass - symport → both particles in same direction - antiport → particles in opposite direction - primary/direct active transport (pump) - requires ATP directly → transport proteins = ATPases or ATPase pumps - integral protein pumps use energy from ATP hydrolysis to move ions/large molecules across cell membrane - against concentration gradient - secondary/indirect active transport (cotransport) - transport of substance requires energy stored in form of concentration gradient of other substance (typically created by primary active transport) → indirect use of ATP - diffusion of other solute across membrane drives secondary transport - transport of 1 molecule/ion in 1 direction (uniport): Ca2+ ATPase → maintains low concentration of cytoplasmic Ca2+ - plasma membrane Ca2+ pump: pumps Ca2+ ions out of cell (e.g.: pond water, blood plasma) - sarcoplasmic and endoplasmic reticulum Ca2+ pumps: moves Ca2+ into ER lumen - secondary active transport: Na+-Ca2+ exchange transporter - movement of Na+ down concentration gradient energizes transporter → that E secondarily moves Ca2+ against electrochemical gradient - primary/direct active transport of 2 substances in opposite directions (antiport): Na+- K+ pump (Na+- K+ - ATPase) → exchange transporter (3 Na+ out and 2 K+ in) - enables animal cell to maintain higher Na+ outside and higher K+ inside cell → electrochemical gradient - sets and maintains intracellular concentration of Na+ and K+ - generates transmembrane electrical potential - helps establish and maintain voltage across membrane (resting membrane potential of nerve cells) → -50 mV to -70mV - plays important role in re-establishing membrane potential after passage of nerve impulse - brain cells use up to 20% of ingested energy for maintenance of membrane potential - required for: - electrical excitability (electrical signaling in neurons) - cellular uptake of ions, nutrients and neurotransmitters - regulation of cell volume and intracellular pH - Na+-K+ pump alternates between two shapes with different affinities for each - transmembrane pump with 3 binding sites for sodium, 2 for potassium 1. 3 cytoplasmic Na+ bind to sodium-potassium pump = high affinity for Na+ 2. Na+ binding site stimulates phosphorylation by ATP (hydrolysis of ATP to ADP and phosphate group → phosphate group attaches to pump) 3. phosphorylation leads to change in protein shape (conformational change) = reduced affinity for Na+ (Na+ released outside)  4. new shape has high affinity for K+ → 2 K+ ions bind on extracellular side and trigger release of phosphate group (detaches) = high affinity for K+ 5. loss of phosphate group restores protein’s original shape (conformational change again) → pump again opens to interior of cell = low affinity for K+ 6. K+ is released → high affinity for Na+ again…cycle - indirect (secondary) active transport of 2 substances in same directions (symport) → sodium-dependent glucose cotransporters (glucose-sodium symporter) - role: glucose absorption 1. Na+K+ pump constantly pumps Na+ outward to maintain Na+ gradient (low Na+ concentration in cell) → gradient drives glucose uptake 2. Na+ has tendency to diffuse into cell → Na+ ion and molecule of glucose simultaneously bind to binding site on Na+-dependent glucose cotransporter = conformational change → glucose is cotransported with Na+ in same direction across apical plasma membrane (in microvilli) into epithelial cell (2Na+/1 glucose) 3. glucose moves through cell to basal surface, where it passes to blood via GLUT2 (passive glucose uniporter) - in small intestine (epithelial cells) and proximal tubule of nephrons in kidney - after digestion, nutrient molecules (glucose, amino acids) need to be transported from intestinal lumen to epithelial cells lining small intestine against concentration gradient = E-requiring process (endergonic = non spontaneous reactions - E absorbed from surrounding environment) → E comes from simultaneous transport of Na+ ions - E-releasing/ exergonic process (ions transported down electrochemical gradient) - reabsorption of glucose by cells of nephron - filter blood in kidneys → as blood is filtered (with urea, waste material), large amounts of glucose and other useful substances are removed → glucose molecules in renal filtrate (filter in nephron) reabsorbed with help of Na+ dependent glucose cotransporters present on kidney epithelial cells, preventing loss of glucose - influx = flow of particles in; efflux = flow of particles out Facilitated diffusion, active transport → selective permeability in membranes Simple diffusion → permeability is not selective and depends only on size and hydrophilic or hydrophobic properties of particles Transport with vesicles → active bulk transport mechanism - when particles too large, cannot pass through channels or transport proteins (polysaccharides, antibodies, proteins, peptides) - fluidity of membrane = change shape, break, reform → formation of vesicles by pinching of small area of membrane (with fusion proteins) - endocytosis - membrane proteins and ATP needed - vesicle roles: - rejuvenating/remodeling plasma membrane - moving of materials within cells → endomembrane system  - transport of substances between cell and its surroundings - cytosis = movements of vesicles of matter (solids or liquids) across membrane - uptake into cell = endocytosis → phagocytosis (solid matter - cellular eating), pinocytosis (liquid matter - cellular drinking) or receptor mediated endocytosis - invagination of part of plasma membrane → fluid (with food particle) becomes enclosed when vesicle pinches off (engulfed particle) = food vacuole - phagosome → fusion with lysosome → digestion of particles with digestive enzymes (monomers - nutrients expelled to cytosol, not useful substances exocytosed out) - endocytosis mediated by protein clathrin (clathrin coded vesicles) - when molecule is too big to enter through membrane proteins: 1. clathrin becomes positioned on inner face of membrane 2. neighboring clathrin molecules bind to each other (polymerisation) to form a lattice of pentagons and/or hexagons - cage like structure 3. substance specifically binds on endocytosis mediated receptors on plasma membrane 4. clathrin coat helps plasma to become invaginated and eventually detach forming a sphere of membrane with clathrin cage around it acting as support 5. once vesicle is formed, clathrin coat breaks down (hydrolysis) back into individual pieces - macrophages (white blood cells) surround and engulf debris of damaged/dying cells or bacteria and viruses that enter tissues by pseudopodia and dispose of it - first line of defense in immune system - humans break down about 2 × 1011 red blood cells each day - absorption of proteins from mother’s blood (including antibodies) into fetus - export out of cell = exocytosis → vesicle fuses with plasma membrane, expelling its contents - e.g.: plasma cells (type of white blood cells) release antibodies into blood stream - e.g.: vesicles (endosomes) containing proteins and phospholipids released by GA fuse with plasma membrane discharging their contents outside - e.g.: release of neurotransmitters into synaptic cleft from neuron in response to given stimulus - occurs at synapses - presynaptic cell → neurotransmitters are released - postsynaptic cell → neurotransmitters bind to receptors to exert their effects - synaptic cleft → gap between presynaptic and postsynaptic cell that neurotransmitters move across once released 1. neurotransmitters contained within synaptic vesicles, concentrated at high density in ends of presynaptic neurons 2. arrival of action potential at presynaptic terminal (depolarization) → opening of presynaptic axon terminals →  synaptic vesicles move toward presynaptic membrane, fuse releasing neurotransmitters 3. neurotransmitters diffuse across synaptic cleft and bind to receptor molecules on postsynaptic membrane 4. receptor activation = opening/closing of ligand gated ion channels in membrane of postsynaptic neuron - alters cell’s permeability - depolarization → cell produces own action potential initiating electrical impulse - hyperpolarization → prevents generation of action potential by second cell 5. following receptor binding neurotransmitter is immediately deactivated by enzymes in synaptic cleft; may be taken up by receptors in presynaptic membrane and recycled (endocytosed) - constitutive secretion → occurs continuously in cells, depending on their function - regulated secretion → in response to trigger - when specific molecule binds (e.g. release of neurotransmitters) Structure and function of glycoproteins and glycolipids → sugars on surfaces of membranes attached to proteins or lipids - glycolipids → covalent bonding of carbohydrates to lipids - vital parts of cell membranes - amphipathic molecules, often restricted to external surface of cell membrane - carbohydrate groups are polar and extend into extracellular environment, non-polar lipid component lies embedded in bilayer - based on structure, classified into: - glycoglycerolipids or glycerol-based lipids - glycosphingolipids or derivatives of sphingosine (e.g. cerebrosides and gangliosides) - contribute to membrane stability → form hydrogen bonds with water molecules surrounding cell - glycoproteins → covalent bonding of oligosaccharides (short carbohydrate chains) to protein molecules - carbohydrate groups often protrude (stick out) into extracellular environment - functions of glycolipids and glycoproteins: 1. cell-to-cell recognition → ‘markers’ on cell surface, help cells of body recognise/distinguish each other + help cells of immune system recognise foreign cells - carbohydrates on extracellular side of cell membrane vary from species to species, from one cell type to another cell type in a single individual and on same cell type among individuals of same species  - red blood cells - blood typing → ABO system distinguishes all individuals based on different sugars attached to surface of erythrocytes - ABO gene → three types of alleles (i, IA, IB,) → encodes enzyme that modifies carbohydrate content (basic sugar) of red blood cell antigens (into either A or B sugar) 2. cell signaling → act as receptors for enzymes and other molecules - chemical signaling = receiving and transmitting chemical signals (important for signal recognition) 3. cell adhesion → binding of cells into tissues (recognition) 4. glycocalyx → sticky carbohydrate-rich layer on outer face of plasma membrane of animal cells (glycolipids and glycoproteins protrude out of cell surface) → cell signalling (signal for receptors, other molecules), cell adhesion, cell–cell recognition, helps in protecting cell surface - highly hydrophilic - attracts large amounts of water to cell’s surface (aqueous solution in gaps between carbohydrates) → helps cell?