Biob10 midterm 1.pdf

lOMoARcPSD|9498521 BIOB10 – Cell Biology Midterm o Cells response to stimuli, carry out mechanical activities a...

lOMoARcPSD|9498521 BIOB10 – Cell Biology Midterm o Cells response to stimuli, carry out mechanical activities and move Lecture 1 –  Use cell surface proteins for this = receptors - What is a cell? - Cells differ in many ways o Smallest unit of life o Obtain free energy in different ways o All living organisms are composed of cells  Phototrophic (sunlight) - What is Cell Biology?  Lithotrophic (inorganic chemicals in environment) o The study of cells at the microscopic and molecular level  Organotrophic (other living things and the organic chemicals they  Structure, function, and behaviour produce) - Why learn Cell Biology? o Some cells specialize in fixing nitrogen and carbon dioxide and other cells rely on o Biotechnology such cells/organisms o Forensics  Plants fix carbon dioxide o Medicine  Nitrogen-fixing bacteria help plants fix N2 - Society should make informed decisions - Types of Cells o GM plants? o Prokaryotes o Lab grown organs?  “Pro” meaning “before”, “Karyon” meaning “nucleus” o Human genome editing?  All bacteria o Fund basic science?  Unique Characteristics: - Discovering cells  Nucleoid – genetic material not bounded by a membrane o Robert Hooke (1665)  Structurally simpler  Examined cork under microscope  Less DNA than eukaryotes – typically, single circular chromosome  Cork is made up of “cells” (dead hollow cells)  No mitosis or meiosis – binary fission instead  Shape reminded him of a cell (room where a monk lived in a building) o Eukaryotes o Anton van Leeuwenhoek (1674)  “Eu” meaning true, “Karyon” meaning “nucleus”  Examined pond water under microscope  Protists, fungi, plants and animals  “Animalcules”  Unique Characteristics: o Matthias Schleiden (1938), Theodor Schwann (1839) & Rudolf Virchow (1855 –  Membrane bound nucleus – nuclear membrane proposed the Cell Theory:  Structurally more complex – internal organelles; complex  All organisms are composed of one or more cells cytoskeletal system  The cell us the structural unit of life  More DNA than prokaryotes  Cells can arise only by division from a pre-existing cell o Typically, several chromosomes composed of linear DNA - Universal Features of Cells molecules o Cells possess a genetic program and the means to use it (Genes to Proteins) o Non-coding regions contain gene regulatory functions  The Central Dogma – DNA to DNA synthesis (replication) to RNA  Division by mitosis and meiosis synthesis (transcription) to protein synthesis (translation) - Similarity between pro- and eukaryotes o Cells are capable of producing more of themselves o Genetic code is identical – information encoded in DNA  Ex. Mitosis and meiosis o Shared metabolic pathways – such as synthesis of ATP  Templated replication of their hereditary information o Shared structural elements – cell membrane o Cells carry out chemical reactions - The origin of Eukaryotic Cells  Proteins function as catalysts (typically) o Prokaryotic cells arose before eukaryotic cells – fossil record  Enzymes aid in cellular metabolic processes (use ATP) o Similarities noted between eukaryotes and prokaryotes o Cells can acquire and utilize energy  Did one arise from the other? (similar genetic code & metabolism)  Photosynthesis and respiration o “Endosymbiont theory”  All cells require ATP as a carrier of free energy  An endosymbiont is a combination of 2 cells living together in a symbiotic o All cells are enclosed by a membrane relationship; one cell lives “inside” the other cell  Nutrient in, waste out  “endo” meaning inside or within  Membrane transport proteins main this semi-permeable barrier o Eukaryotic cells may have originated as predators Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521 o Eukaryotic cells evolved from a symbiosis  Despite being an insect, has been used as a model for vertebrate  Begins with anaerobic cell (prokaryote) development  Invagination of other cells (bacterium’s) and overtime loss of membranes  9 days from egg to adult  Forming early aerobic eukaryotic cell  Cheaper and easier to breed than vertebrates - Types of Prokaryotes  Small genome with much lower frequency of gene duplication o Archea (archaebacteria) - Model Eukaryotes (3)  “extremophiles” – thermophiles that grow @ 80-105 degrees Celsius o Xenopus Laevis – frog and Danio rerio – zebra fish o Bacteria (eubacteria) – all other bacteria  Accessible models to understand cell fate and migration during  Cyanobacteria (most complex) development o Archea are actually closer to eukaryotes than eubacteria  Frog eggs are large and fertilized outside of the animal, so development o There are very many types of prokaryotes and have come about by different easy to follow modes of genetic innovation (examples include):  Zebrafish are transparent for the first 2 weeks of life so can actually watch  Spherical Cells behaviour of cells (Streptococcus)  Parts of their brain structure resemble human brain structure (can  Rod-shaped Cells be used to examine neurological disorders) (Escherichia coli, Vibrio - Model Eukaryotes (4) Cholerae) o Mus musculus – mouse  The Smallest Cells  Most used vertebrate model; rapid, easy breeding; mutants resemble (Mycoplasma, Spiroplasma) human conditions  ~500 genes o Human genome and study of human genetic disorders  Spiral Cells (Treponema  Notes that 2 people differ in 1-2 out of every 1000 nucleotides = huge Pallidum) variation - Types of Eukaryotic Cells  Provides clues to how different people manifest the same mutations and o Unicellular – protists (example) genetic conditions very differently  Everything that this - Cell Differentiation organism needs to survive is o Humans go through ~250 cell differentiation events done by one cell o The process by which an unspecialized cell becomes a specialized one (fertilized o Multicellular – humans (example) egg to human being)  Different activities are o Differentiation occurs primarily through signals received by the cell from its carried out by different environment types of specialized cells, o The type of signals received depends upon the location of the cell within the “cell differentiation” embryo - Model Eukaryotes (1) o Changes in cell morphology (appearance) o Yeast is a single-celled eukaryote o Express “cell-specific” genes – unique proteins but “housekeeping” proteins will  Easy to grow, Small genome, mutants available for almost every gene be the same as other cells  Many components interchangeable between yeast and humans o Organelles stay the same, but their number and location may differ greatly  Pathways and processes studied in yeast can be extrapolated to humans and other multicellular eukaryotes - Model Eukaryotes (2) o Arabidopsis thaliana – weed  Produces thousands of offspring per plant in 8 weeks o Caenorhabditis elegans – worm  Has helped us understand controls over cell division and cell death o Drosophila melanogaster – fruit fly  Used for vertebrate development Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521 - Study cells through Cell Culture  Related to the refractive index of the medium that the lens is o Cells are grown outside the body “in vitro” operating in  Simplified, controlled environment  Theta = half the angular width of the cone of rays (maximum  In conditions similar to their regular living conditions width is 180 degrees) o Cells are grown in plastic flasks filled with defined media  n = the refractive index of the medium o Primary Culture: obtained directly from the organism  lambda = the wavelength of light used (for white light typical 0.53  Mostly embryonic tissues (easy to handle and disassociate into specialized micrometers is commonly assumed) cells really quickly) o multiple different stains can be used to see more detail in specimen  Divide ~25-100 times in culture = passages (will die after and require new o Dark-field microscopy extraction of cells)  Unstained specimens are used (even living) o Cell Line: primary cultures that have undergone genetic modifications to allow  Light is applied in an oblique direction (at an angle so most of the light is them to grow indefinitely in culture not entering our eyes)  Can occur spontaneously (mouse cells)  Light will be bent in a specific way by the specimen reaching the objective  Tumour tissue can be used (HeLa cells) = transformed cells lines seeing those following regions o Plastic or glass provides solid surface on which the cells adhere and divide  Cell with very dark background and certain regions can be seen - Cell Culture in the Lab: 2-D cell culture o Phase contrast & differential interference contrast o Temperature, carbon dioxide levels, and humidity levels are monitored  Unstained specimens - Cell Culture in the Lab: 3-D cell culture  Incident light used (white) o Significant number of cells that do not adhere to anything as they are free floating  Waves that go through the specimen will go in different ways through (e.g. inside lining of your stomach, intestines, bladder) different parts of the specimen  One side line the organ and the other in water  Due to regions of differing refractive index (changing phase of  Solution was growing cells in a gel like culture (like jello) light)  Total embedment – cells are 100% gelled in ECM  Picked up by phase contrast system  Overlay –are attached on one side to culture media with diluted ECM on  DIC – rate of change of these refractive index/phases are taken into the other consideration (how much darker/lighter) - Advantages of Cultured cells o Stains used in light microscopy o Cells can be obtained in large quantities  Preparation of cells: o Most cultures constitute only one type of cell  Fix cells – immobilizes the material in cells to preserve structure o Important cell biological phenomena can be studied using cultured cells  Stain cells – dye makes structure more visible  Cell movement; cell division  Mount on slides to view o Cells can be induced to differentiate in culture o Cultured cells can be used to test the activity of drugs  Example – Feulgen stain (stains DNA)  Also, hormones of growth factors  Tissues: embed and section first  Microtome is like a “meat slicer” – works on super thin structures of tissue embedded in wax to than be placed on glass slides Lecture 2 –  Slides can be then immersed in different stains - Bright field light microscopy o Example – Haematoxylin & Eosin staining (H&E) o Microscopes produce enlarged images of an object  Haematoxylin stains nucleic acids (blueish) and Eosin stains proteins o Cells are placed on a stage between the light source and our eyes (pinkish) o View light that is diffracted by the cells  Used in the brain structure to compare normal brain to CJD brain o Resolution: the extent to which details of a specimen are retained in the image - Electron microscopy (EM)  The resolution of a microscope depends on both the wavelength of light o Uses electrons as “light” source and the numerical aperture of the lens system (resolution = 0.61 x lambda /  Short wavelength n x sin theta) o Image formed when electrons pass through a specimen  Numerical aperture impacts the light gathering capacity of a lens o Provides much greater resolution o The resolution of a microscope is inversely proportional to the wavelength of its  Related to the angle of the cone of light entering the lens light source Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521  The longer the wavelength – the poorer the resolution - Stem cells for cell replacement  Light – constant wavelength o Stell cells:  Electrons – wavelength varies with speed  Undifferentiated cells  Speed controlled by accelerating voltage applied in scope, very  Can self-renew short wavelengths possible = very high resolution  Can differentiate into 2 or more cell types o Electron beam is filled by Tungsten wire filament or cathode (electron source) o Most organs in humans contain stem cells o Passes through magnets rather than lenses  Adult stem cells - Transmission Electron Microscope (TEM) o Transplantation of such cells to specific areas could be future therapy o Specimens have to be fixed, embedded & sectioned - Embryonic stem cells (ES) o Stained with heavy metal solutions o Are derived from human embryos  These bind to cellular macromolecules o IVF clinics  Glutaraldehyde – cross links proteins o Are pluripotent = capable of differentiating into EVERY cell type in the body  Osmium tetroxide – stabilizes lipids and proteins o Can be cultured for extended periods o Metals scatter electron path o Phenomenal resource for cell replacement therapy o Image of scattered electrons is caught on photographic emulsion or recorded o ES-derived oligodendrocytes – spinal cord injury patients using a high-resolution digital camera o Problems:  Parts of the image that appear dark are regions where electrons have been  Immunologic rejection (not a problem with adult stem cells) scattered away by metal atoms  Ethical/political debates - Cryoelectron (Tomography – implies image processing) Microscopy - Customizing ES cells o Not fixed in chemicals but using rapid freezing – cryofixation o Changing the genetic makeup of the cells to match that of the patient who needs o Prepare sample -> Freeze Grid -> Collect images -> Image processing -> the cell transplant reconstruction -> reconstruction -> structural analysis -> model  Water in the sample is supercooled into a noncrystalline state called vitreous ice o Multiple images can be combined to increase resolution - Freeze fracture and freeze etching techniques o Cells are rapidly frozen in low temperature liquids o Knife edge used to strike frozen cells o Fracture plane spreads from point of initial contact splitting cells into 2 o Cellular structures deviate the place of fracture either upward or downward – irregular surface – etching removes thin layer of ice o Deposit heavy metals on top of this fracture surface to get a “replica” of the plane o Carbon is then deposited over the metals to cement them in place o This metal-carbon replica is viewed by EM  Freeze etching maybe an extra step where water is removed before viewing - Scanning electron microscope (SEM) o Specimens prepared by careful drying procedures o After drying, coated with carbon and metals o Image is formed by electrons reflected back by the specimen  Referred to as “backscattered” electrons o Gives surface view of cells, tissues and whole animals o Problems:  A 3-D quality to the image  Creating an embryo just as a source of ES cells o Best used for viewing extensions or processes that cells use to interact with the  Major ethical questions environment - Reprogramming to induce stem cells  Viewed typically on a video screen o Induced pluripotent cells (iPS cells)  = reprogrammed somatic cells by introduction of specific genes into them Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521  Do away with the need for human oocytes/embryos  Polymers form by joining monomers – condensation reaction (water  A core set of transcription regulators defines and maintains the ES cell removed) state  Polymers are broken down into monomers – hydrolysis reaction (water is added) o Four types of biological macromolecules  Sugars – polysaccharides  Fatty acids – fats, lipids, membranes  Amino acids – proteins  Nucleotides – nucleic acids  Macromolecular assemblies – macromolecules form larger molecule using hydrogen bonds, Van der Waals forces, electrostatic interactions, hydrophobic forces - Carbohydrates o Monosaccharides (commonly referred to as sugars) o Aldoses have an aldehyde group at the end o Ketoses have an internal carbon double bonded to an oxygen o At least 5 carbons lead to formation of a closed ring structure (anomers – one formation, isomers – same chemical formula different structure) - iPS cells or ES cells can be differentiated into adult cell types o Alpha hydroxyl is hydroxyl on the bottom, beta hydroxyl is on top (can rapidly - Transdifferentiation: targeted reprogramming change) o Direct cell reprogramming = “Transdifferentiation o As soon as one sugar is linked to another, the alpha/beta form is frozen o One condition where this is successful: diabetes o Linked by covalent bonds: between Carbon-1 of one sugar and hydroxyl (OH) of  Type 1 Diabetes = Beta cells of pancreas is lost another sugar, generating C-O-C linkage between sugars  Beta cells make insulin o Disaccharides: 2 monosaccharides covalently bonded  Alpha cells in the pancreas can be transformed into beta cells  Energy storage (E.g. sucrose, maltose, lactose)  Through expression of 3 genes known to be important in differentiation of o Oligosaccharides: a small chain of sugars (oligo = a few) beta cells  Attached to lipids or proteins converting them to glycolipids and  Works on mice glycoproteins - The Tree of Life o Polysaccharides: a long chain of sugars bonded together o Archea and Eukaryotes share a common ancestor not shared by bacteria  Very large molecules with a structural or storage function (E.g. Chitin, o Archea actually share a lot of genes with eukaryotes that were thought to be cellulose, starch, glycogen) eukaryote specific  Glycogen – stores of chemical energy in most animals (branched  Suggesting only 2 domains of life (eukaryotes a subset of Archea) form a-4 and a-6 linkages) - Cell Chemistry and Macromolecules  Starch – stores of chemical energy in most plants (a1-4 linkage in o Reactions take place in an aqueous environment (cells are 70% water) twisting coil form) o Based overwhelmingly on carbon compounds  Cellulose – durable structural polymer (used in plant cell walls, b1-  Most are enormous polymeric molecules (macromolecules) 4 linkages & polymer of glucose) o Composed of complex reactions that allow cells to obtain and use energy o Sugar derivatives – hydroxyl groups of a simple monosaccharide such as glucose o Cells are formed of carbon compounds can be replaced by other groups  Certain combination of atoms, functional groups, occur repeatedly in cells  Chitin – polymer of N-acetylglucosamine (durable structural  Confer distinct physical and chemical properties (organic polymer used in exoskeletons of invertebrates with b1-4 linkage) chemistry) - Lipids  Ester bond = alcohol and acid o A large group of nonpolar biological molecules  Amide/Peptide bond = acid and amine  Composed mainly of C, H, O o Formation of biological macromolecules  Dissolve in organic solvents but not in water  Macromolecules are polymers of building blocks known as monomers Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521  Those with significant cell functions – fats, steroids, phospholipids,  They are used as specific signaling molecules in the cell (e.g. cyclic AMP glycolipids (cAMP)) o Fats = triacylglycerol = glycerol + 3 fatty acids  Fatty acids linked by ester bonds  Have long hydrocarbon chains with single carboxyl at the end Lecture 3 – o Presence of double bonds changes structure (fatty acids - Second Law of Thermodynamics vary in length o Cells take in energy from the environment and use it to generate order within it o No double bonds = saturated, double bonds = unsaturated o Many chemical reactions that create this order in cells, converts some of this  Stored as an energy reserve (fats and oils) through an ester linkage energy to heat to glycerol to form triacylglycerol (also called triglycerides) o Heat released then creates disorder in the cell’s environment, increasing entropy o Steroids and abiding by the second law  Large carbohydrate rings (Complex 4 rings) - How do cells obtain and use energy?  E.g. cholesterol – important animal plasma membrane component o Each cell carriers out millions of chemical reactions every second  Building blocks of many steroid hormones (e.g. testosterone)  Catalyze the oxidization of organic molecules in smalls steps allowing o Phospholipids useful energy to be harvested  Composed of glycerol + 2 fatty acids + phosphate + head group  This energy is stored in a small set of activated “carrier molecules”  Major component of plasma and organelle membranes which diffuse through the cell through sites in which they are  Hydrophilic (phosphate + head group) on one end and hydrophobic (fatty generated to sites in which biosynthesis will occur acid tails) on the other = amphipathic  Cells use carrier molecules like money to pay for reactions tht o Glycolipids would not otherwise occur  These compounds are similar to phospholipids but instead of having a phosphate group at the end there is a sugar group o Lipids form biological membranes  Arrange into a bilayer  Hydrophobic regions point inwards; hydrophilic regions on the outside - Nucleic Acids o DNA and RNA o DNA: genetic material; governs all cellular activities; codes for proteins required for the cell’s functions o RNA: many roles; central to the synthesis of proteins; regulates expression of genes; genetic material of some viruses  tRNA, mRNA, rRNA o Polymers of nucleotides – consists of nitrogen containing base, five-carbon sugar,  Vast majority of these chemical reactions only occur in cells under normal and one or more phosphate groups temperatures because of proteins known as enzymes o Polynucleotide strands  Catalysts increase the rate of reactions by lowering the activation energy  Nucleotides are joined by sugar-phosphate linkages required (for both forward/reverse reaction but enzymes are specific to  3’ hydroxyl attached to 5’ phosphate of the adjoining nucleotide maintain directionality)  Phosphodiester bond o Enzymes can speed up reactions, but cannot force energetically unfavourable ones  Sugar-phosphate backbone to occur o Pyrimidine (one ring structure) – uracil, thymine, cytosine  Delta G is a measure of the change in the amount of energy available to do o Purine (two ring structure) – adenine, guanine work o Other functions:  Favourable reactions decrease delta G (negative value) and increase  Carry chemical energy in their easily hydrolyzed phosphoanhydride bonds disorder (e.g. ATP)  Cell uses reaction coupling to drive energetically unfavourable reactions  They combine with other groups to form coenzymes (e.g. coenzyme A  We use the standard free energy change of reactions to predict the course (CoA)) of biological reactions Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521 o Glucose and other food we eat are broken down by stepwise oxidation reactions o Took a test tube with a perfectly folded enzyme to produce chemical energy in the form of ATP and NADH (ribonuclease), denatured it with chemicals and following a o These reactions also help produce many of the small molecules that are the few minutes it was re-folded and was functional again substrates for biosynthesis of macromolecules o Proteins may take several paths to get to the final folded o Macromolecules like glycogen and fats can be stored in cells as a major source of (native) state energy  Most proteins need help – chaperones = proteins that aid in the - Proteins folding of newly made proteins by preventing inappropriate o About 10000 proteins made in every mammalian cell interactions o Carry out almost all cellular functions: o Prevent inappropriate interactions with other cellular  Enzymes – accelerate chemical reactions in the cell components  Signaling – kinases, phosphates are involved o Bind hydrophobic segments of proteins  Hormones – long range messenger molecules o Are single proteins or a large protein complex with intricate  Growth factors structure  Membrane receptors – communication between cells o Secondary Structure  Cell movement – cytoskeleton  Conformation of portions of the polypeptide chain o Polymers of amino acids – 20 different types  Arranged to maximize the number of H-Bonds made between neighboring  Consist of an amino group and carboxyl group separated by alpha carbon amino acids – of peptide backbone only (has R group attached to it and this group provides variability)  Alpha – Helix o 4 categories of R groups:  Hydrogen bonding that links the C and O of one to the N and H of  Polar charged – can form ionic interactions another (between every fourth amino acids)  Polar uncharged – can form hydrogen bonds  Cylindrical twisting spiral  Nonpolar – mostly hydrocarbons (hydrophobic and usually in the core of  R group projects outward protein structure)  Beta – Pleated Sheets  Other (glycine, cysteine and proline)  Hydrogen bonds extend from one part of the chain to another o Peptide bonds: carboxyl group of one amino acid becomes attached to the amino  Polypeptide segments lie side by side group of another (amide linakge)  Can be antiparallel or parallel  Forms polypeptide chains = proteins  Travel N – C direction always - Protein Structure  Incorporating Proline in primary structure level o Primary Structure: specific sequence of amino acids  Found at the end of alpha helixes as a breaker  Determined by the sequence of the gene encoding the protein (DNA)  20 variations of proteins (20 amino acids)  Geometry limits flexibility of the backbone  N = the number of amino acids in the chain  Introduce sharp kinks into a polypeptide backbone  Typical protein is over 100 amino acids long – infinite number od o Tertiary Structure sequences possible  Conformation of the entire protein  Interactions between R-groups in the protein  Sequence contains most of the information needed to specify 3-D shape and function of protein  Hydrophobic interactions, Van der Waals interactions, disulfide  Changes in the primary structure can have dire consequences for bridges protein function (e.g. sickle cell anemia – affects red blood cell  Non-covalent bonds that hold protein tertiary structure together – shape & therefore clogs arteries) electrostatic attractions, hydrogen bonds, Van der Waals o Glutamic replaced with valine and causes polar amino acid attractions to become hydrophobic (altering the shape of the beta-  3 Types: fibrous, globular, & intrinsically disorder proteins subunit forming a crystal shaped fiber)  Fibrous o Proteins must fold in order to have the next 3 levels of organization o Elongated shape, usually structural materials outside of  Christian Anfinsen: the linear sequence of amino acids in a protein cells contains all the information required for its 3-D conformation  Keratin, collagen (hair, skin, fingernails) o Form long strands or flattened sheets that resist shearing forces Downloaded by Aaravee K ([email protected])  lOMoARcPSD|9498521  Globular o Degradation pathways – lysosomes, autophagy, proteasomes (90% of protein o Compact shape, polypeptide chain folds into complex degradation in mammalian cells) shapes - Proteasomal Degradation o Usually have functions within the cell o Proteins suffer a death by a thousand cuts (chamber of “doom”)  Enzymes, hormones, most proteins o Catalytic subunits cut the peptide bonds recycling the amino acids  Intrinsically disordered o Proteasome degrades proteins for turnover (regulates life span) but also degrades o Loops or tails (or entire protein) remain disordered in misfolded proteins structure  Mark = ubiquitination o Contain repeated sequences of amino acids  Ubiquitin (Ub) = 76 residue protein o Have important functions (e.g. elastin) o Typically, multiple copies of Ub are attached to a protein tagged for proteasomal  Elastic fibres to prevent tissue breakage and allow degradation = polyubiquitination (4 or more Ub) tissues to stretch/relax without breaking any protein o Requires the activity of E1, E2, and E3 enzymes that work in sequence to bring structures about polyubiquitination  Modules or domains of proteins - Regulating Proteins: GTP binding  Can function in a semi-independent manner o Non-covalent binding to GTP can act as a “switch” to regulate protein activity  Can be swapped between proteins o GTP binding proteins = GTPases  Allows for unique protein activities o GTP bound = active = regulate the activity of target proteins (effectors) in this o E.g. move independently, bind to different molecules state  Domains can be constructed from alpha-helices, beta sheets or o GDP = in active various combinations of fundamental folding elements o The rate of GTPase activity differs between proteins o Quaternary Structure o GEFs and GAPs aid in regulating the “switch” that regulates these proteins  Linking of multiple proteins to form large complexes with multiple - Regulating Proteins: Phosphorylation “subunits” – multiprotein complexes o Phosphorylation is the most common covalent modification that is used to  Intermolecular interactions of R groups regulate protein activity  Disulfide bonds o The reversible addition of a phosphate group to the hydroxyl groups on the side chains of a serine, threonine or tyrosine residue  Noncovalent interactions (mostly) o The activities of kinases and phosphatases is hence the “switch”: - Proteins can be modified & regulated  Kinases – add phosphates o Cleaved into smaller polypeptides  Phosphatases – remove phosphates  “pro-form” cut into smaller fragments o Phosphorylation can alter the conformation and charge of a protein: o Sugar chains can be added  Can allow for protein-protein interactions  “glycoproteins”  Can allow for altered intrinsic activity (e.g. enzymes) o Lipids added  Can cause a change in the localization of a protein  Anchored to cell membranes  Can impact large signaling pathways in the cell o Metal/ions added o Individual protein kinases can act as microprocessors  Important for function  Integrate multiple upstream signals o Phosphate groups added  Signal integration is required for kinase activation  Signalling functions; alters structure or interactions o GTP or calcium binding  Alters protein activity o Degradation  Controls protein lifespan - Regulation by degradation o The lifespan of proteins differs a great deal  Few minutes = mitotic cyclins  Your whole life = crystallin in lens of the eye o Controlled by regulated degradation pathways Downloaded by Aaravee K ([email protected])