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Cell theory 1.

robert hooke uses weak microscopes composed of same fundamental building blockcell cell - highly organized compartment that is held with plasma membrane in watery solution all cells arise from previous cells all organisms made of cells all cells are connected by common ancestry natural selection - survival of fittest- more offspring

Tree of life 1.3

eukaryotic- have membrane bound nucleus prokaryotic-free floating nucleus/genetic material phylogeny- tribe sourceactual genealogical relationships studied rRNA, used it to compare the ribonucleotide order phylogenetic tree-- shows relationships among species more similar - closer together on tree 3 domains: BACTERIA, ARCHAEA, EUKARYA

Doing Biology 1.4

Hypothesis, prediction, tests, observations, results need control group to be accurate+ repetition

Building Blocks of Chemical Evolution 2.1

O>>N>C-H make up 96% of organisms theory of chemical evolution- simple compounds in ancient atmosphere + ocean- complex substances electrons(much smaller than protons) - negative charge atomic number- number of protons( positive charge) isotopes- same element diff mass number( prot+ neut) electrons move around in regions called orbitals each orbital-2 electrons grouped into electron shell 1,2,3............ valence- unpaired electrons in outer shell atom is stable when valence shell filled-- uses Chemical bonds covalent- shared electrons electronegativity- amount of nrg want eIonic bonds- transfer of electrons cation- positive charge polar bonds- unequal sharing of electrons

anion- negative charge

double bond- share 2 triple- share 3 CH4-tetrahedron H20- bent molecular formula- numbers and types of atoms in mlcl structural formula-shows the bonds ball and stick - shows angles space filling models-actual representative of model

Early oceans and properties of water 2.2

most important to life - water water- solvent (dissolves substances into solution) polar so makes hydrogen bonds between other water mlcls hydrophillic- water loving hydrophobic- water hating cohesion- binding with like molecules adhesion- binding with unlike molecules(not straight if held in a cup - meniscus) surface tension- elastic membrane formed from cohesion and adhesion Density- liquid > solid high capacity for absorbing heat

acids - proton donor base - proton acceptor ph= -logH H= antilog(-ph) Buffers- maintains pH by becoming weak base or acid

Importance of Carbon 2.4

carbon- most versatile atom because of 4 valence electrons can from many covalent bonds contains C- organic no C- inorganic functional groups- attaches to C and gives characteristics * refer page 41

What do proteins do 3.1

Proteins are used for: Defense- antibodies destroy disease Movement- motor and contractile proteins moves the cells Catalysis- speed up a chemical reaction using enymes Signalling- peptide hormones carry and receive signals Structure- gives mechanical support Transport- Passage of specific molecules/ions

Amino Acids and Polymerization 3.3

Amino acids- 21 types that make up proteins carbon attaches to amino group (NH2), carboxyl group(C-OOH), H and R group Hydrophobic R groups (nonpolar) cannot form h bonds with water polar or charged R groups can form H bonds with R groups ( hydrophillic) *Refer p 49 If R groups are not charged/ polar the chemical behaviour depends on size/ shape Structural isomers- same atoms but different order of bonds Geometric isomers- same atoms but diff arrangements of atoms around dbl bond Optical isomers- same atoms but diff arrangements around C atoms amino acids are called monomers lots of them are called polymers polymerization- joining of amino acids protein- macromolecule and a polymer polymerize through condensation reactions AKA dehydration synthesis- monomers in water out hydrolysis- water in monomer out C of carboxyl group combines with N of amino groups peptide bond forms ( as strong as dbl) when a.a are linked by peptide bonds into chain they are called residues resulting molecule is polypeptide peptide bonded backbone a.a always numbered starting from N terminus single bonds beside peptide bonds - flexible and rotates <50 - oligopeptide/ peptide

>50- protein

What do proteins look like 3.4

Proteins serve diverse functions because of their diverse size and shape underlying structure of protein - same 4 lvl of organization Primary structure- unique sequence of amino acids 21^n fundamental to function and to determine higher lvls of protein structure Secondary structure- Created by H bonding between carboxyl group + amino group not by R group forms- alpha helix and beta pleated sheets formation depends on primary structure esp the geometry of a.a increase stability and define shape

Tertiary structure- created from interactions between R groups causes peptide bonded backbone to bend and phone 3d shape of polypeptide hydrogen bonds between R group and carboxyl when hydrophobic chains are close to each other makes van der waals interaction(weak chrg) covalent bonds between sulfur containing R groups makes disulfide bond ionic bond form between full opposing charges Quaternary structure- combination of several polypepties held together by interactions of R groups, bonds, peptide backbone protein with 2 polypeptide called dimers *refer p 59 protein structure is hierarchical. Higher lvls based on previous ones folding is spontaneous in some cases- bonds that occur makes mlcl more stable so it can be exergonic denature- protein can be unfolded and no longer functional folding facilitated by specific protein called molecular chaperones proteins function depends on shape; shape depends on folding

Enzymes 3.5
brings substrates together in precise orientation into a transition state and finally products activation energy- nrg required to reach transition state need kinetic energy to reach the state so higher temp - faster catalyst - lowers activation energy can increase rxns up to trillions times faster enzymes bring reactants together and stabilize transition states. Proposed theory - lock and key substrate fits into active site of enzyme actual- induced fit theory enzyme changes shape slightly to bind substrate interactions with R groups at active site lowers activation nrg *refer p 64 enzyme catalysts - initiation(precise collision), transition state facilitation(lower nrg), termination(products less affinity so releases) Cofactors and organic mlcls called coenzymes help with enzymes they stabilize transition state enzymes are regulated by mlcls that change the protein structures competitive inhibition- slows down rxn by competing with substrates allosteric regulation- mlcl binds with enzyme and changes the shape of it substrate concentration low - increases in linear fashion substrate concentration high- levels out at max speed (saturated) pH and temperature affects enzyme for better or for worse

Lipids 6.1
carbon containing compound which are non polar and hydrophobic can still dissolve in liquids with non polar organic compounds mlcls that contain only H and C - hydrocarbons non polar fatty acid- type of compound consists of hydrocarbon chain bonded to carboxyl group key building blocks of lipids Lipids defined by solubility so structures varies fats- 3 fatty acids linked to glycerol thru dehydration synthesis joined by an ester linkage page 101 AKA triglycerides

fats are not polymers and fatty acids arent monomers steroids- differ from others cuz they have cholesterol ( 4 ring structure) phospholipid- glycerol +phosphate group+ 2 isoprenes or fatty acids makes up plasma membrane membrane forming lipids have polar, hydrophilic region and non polar hydrophobic region amphipathic- contains both hydrophilic and phobic elements. Phospholipids and cholesterol responsible for membrane

Phospholipid bilayer 6.2

micelles- tiny droplets created when hydrophilic head face water and phobic forced together most phospholipids form bilayers b/c too big for micelles phobic heads face towards each other sandwiched by philic heads short tails- micelles long tails- bilayer forms spontaneously because it is more stable than free floating artificial membranes - liposomes permeability- tendency to allow substance to pass thru lipid bilayers- selevtive permeability small, non polar molecules- fast large, polar- slow or none unsaturated- double bonds exist saturated- no double bonds higher permeability - lower permeability - liquid at rtp - solid at rtp phospholipid molecules are in constant lateral movement while small molecules move in /out

Diffusion and Osmosis 6.3

diffusion-solutes go towards lower concentration gradient because of entropy it is spontaneous osmosis- movement of water towards lower gradient when solute cannot move *they both want to establish equilibrium hypertonic-more solute on outside than inside hypotonic-more solute inside than outside isotonic- same amount

Membrane proteins 6.4

proteins that are amphipathic (R groups) can be inserted into lipid bilayer nonpolar amino acid inside interior while polar on outside fluid mosaic model- proteins embedded in bilayer used scanning electron microscope to see surface of bilayer integral membrane proteins/ transmembrane proteins - proteins that are in interior and exterior peripheral membrane protein- found on one side proteins are not staticthey move around detergent- isolates proteins for in-depth studies transport proteinschannels,transporters, and pumps facilitated diffusion via channel proteins- ions flow through protein down electrochemical gradient protein is therefore called ion channel channel proteins- proteins that allow particular type of ion to pass aquaporins- allow water to cross membrane 10x faster extremely selective gated channels- open or close to mlcl to a change in electrical charge passive transport- powered by diffusion along electrochemical gradient facilitated diffusion via carrier proteins- aided by carrier proteins/transporters change shape to bind substrate and then releases substrates

active transport by pumps- transport against electrochemical gradient proteins are called pumps sodium potassium pump- Na inside + P outside K outside inside releases P lipid layer + protein makes internal environment diff from outside

What's Inside the cell 7.1

Prokaryotic cell- has few or no substructures separated from rest of cell by membranes usually smaller than eukaryotics 1-10um lack nucleus inside membrane- cytoplasm ( fluid part-cytosol) cell wall- resists pressure ( tough, fibrous layer that surrounds membrane) gives shape+rigidity glycolipids- lipids that contain carbohydrate groups chromosome- consists of large DNA mlcls with small # of proteins. abundant in prokaryotic makes proteins, RNAs, info for building rna - GENE chromosomes found in nucleoid ( usually in centre) 20% of cell volume DNA- double helix coils to be highly compact plasmids- (circular DNA)genes that are independent of chromosome ribosomes- manufacture proteins made up large RNA subunit, small RNA subunit and protein molecules flagella- power swimming/movement contains membrane bound storage containers can use photosynthesis organelles-membrane bound compartment contains enzymes or structures for specific job Cytoskeleton- contain long thin fibres that serve structural roles *page 129 Eukaryoticslarger than prokaryotics 5-100 um unicellular to extensively large organisms compartmentalization solves problem of taking long time to diffuse materials form 1 side to another nucleus- largest organelle and is highly organized surrounded by double membrane called nuclear envelope has pore like openings nuclear lamina- fibrous proteins that form a lattice like sheet inside nucleolus- RNA molecules found in ribosomes are manufactured Ribosomes- made of two subunits (large and small) subunit composed of proteins and RNA large- 3 RNA small- 1 RNA when they come together synthesizes proteins Endomembrane system- consists of Rough/Smooth ER and golgi appartus Rough Endoplasmic Reticulum- network of membrane tubules covered with ribosomes lumen- interior of network manufactures proteins by folding and other types of processing Smooth Endoplasmic Reticulum- long network with no ribosomes has enzymes that catalyze reactions with lipids manufacture site of phospholipids reservoir of Ca ions that signals activities in cell Golgi appartus- products of Rough ER pass here. Cis faces ER trans faces membrane Flattened membranous sacs called cisternae packages and processes proteins and sends them out

Peroxisomes globular organelles that have single membrane, grow and divide independently centres for oxidation reactions glyoxisomes- packed with enzymes that convert prod of photosynthesis into sugar Lysosomes- solid waste processing and materials storage in plants, fungi cells they are referred as vacuoles in animals they are digestive centers its lumen is acidic because enough hydrogen ions main pH of 5 each of these are specialized for breaking macromolecules digestive enzymes collectively called acid hydrolasis phagoctyosis- cell eating delivered inside membrane to lysosome autophagy- same eating damaged organelles are surrounded by membrane and recycled receptor mediated endocytosis- creation of lysosomes through binding of macromolecules, activation of proton pumps that lower pH and receiving digestive enzymes from golgi apparatus endocytosis- inside cell act/ taking in of material from outside of cell phagocytosis, receptor mediated endocytosis, pinocytosis( cell drinking) vacuoles are large compared with lysosomes and contain up to 80% of plant cell volume have enzymes specialized for digestive but most act as storage depots mitochondria- produces ATP(chemical energy required for work) up to millions may be present double membrane cristae- series of sac like mitochondria matrix- solution inside the inner membrane contains independent small chromosome grow and divide independently of cell manufactures own ribosome Chloroplasts- sunlight is converted to chemical energy double membrane thylakoids- single flattened vesicles grana- stacks of thylakoids stroma -region inside chloroplast contains independent genetic material divide independently cytoskeleton- major structural feature containing proteins and fibres cell wall- has an outer cell wall in addition to membrane in fungi, algae, plants rods or fibres composed of carbohydrate run thru stiff matrix made of proteins some plant cells create secondary cell wall called lignin lignin forms branching almost impossible for enzymes to attack organelle's membrane and its complement of enzymes correlate with function differential centrifugation- technique to isolate cell components for analyzing *refer p 137