Bio

The levels of organization of multicellular organisms and how they are related,The Cell: Basic Unit of Life Tissue: A collection of cells Organ: Collection of Tissues Organ System Collection of organs and auxiliary tissue What is an emergent property,A property thet a collection or complex system has, but the individual components do not 5 kingdoms,Fungi, Plantae, Animalia, Protists 3 Domains,Archea, Bacteria, and Eukaryotic Which elements are the most important for life?,Hydrogen, nitrogen, oxygen, sulfur, phosphorus, and carbon Atomic Structure,Protons and nutrons in the nucleus, electrons orbit in shells Atomic mass,protons plus the neutrons Atomic number,proton number Isotope,Atom that contains different number of neutrons than protons Electron configuration of oxygen, nitrogen, hydrogen, and carbon,Oxygen wants to make 2 bonds, nitrogen wants to make 3, hydrogen wants to make 1 and carbon wants to make 4 How does valence affect chemical bonding,Chemical bonding takes place so that atoms can vill valence shells. A full shell is more stable Two types of chemical bonds,Ionic and covalent Covalent bond,Sharing of electrons between two atoms Ionic bond,One atom donates an electron causing an opposite attraction How does hydrogen bonding work,Weak bonds that are made and broken easily. Hydrogen of a polar, covalent molecule has an attraction to a nitrogen of a similar molecule What makes some molecules polar,The more electronegativity an atoms has the more polar that it is. Atoms are non polar when electronegativity is equal and atoms are shared evenly The physical and chemical characteristics of water,Covalently bonded Polar molecule Occurs between hydrogen atom of one water molecule with oxygen of another 1/20th as strong as a covalent bond Why carbon based molecules are so diverse and how this diversity arrises,Carbon has 4 electrons in the outer shell and this allows for many possible configuration Shape determines the biological diversity Structures of functional groups commonly found in organic molecules,See notes How polymerization is accomplished,Accomplished through covalent bonding Takes place through dehydration This process can be reversed Dehydration,Removing a water molecule Hydrolisis,Adding a water molecule Recognize general structure of each macromolecule and its monomer,See notes and review online The functions of carbohydrates,Comprised of sugars and polymers of sugars Used for energy-simple sugars, storage of energy-starches, and structural components of cellulose and chitin , Monosaccharides,Simple sugars=monomers Usually have a chemical composition CxH2xOx Can exist as chains or rings Monosaccharides combine to form disaccharides Disaccharides,Formed b the dehydration reaction between two monosaccharides Bond between monosaccharides is called the glycosidic linkage Starches,Plants use for energy storage Cellulose,Most abundant organic compound on earth Plants use cellulose as a component of cell walls most animals cannot digest Starch vs Cellulose,Both has glycosidic linkage starch uses "a" configuration of glucose resulting in a helical molecule Cellulose uses "b" configuration of glucose which forms linear strands Biological function of lipids/fatty acids,Hydrophobic molecules Carboxyl group at one end Carbon/hydrogen chain which may or may not be saturated (Max # of hydrogens) Basis for hormones structure How fats are assembled,Three fatty acid chains bound to a glycerol backbone Also called triaclyglycerol Formed by dehydration reaction Fatty acids are bound to glycerol by ester linkage Fats,Used as a long term method of energy storage Animal fats tend to contain saturated lipids Plant fats contain unsaturated fat Saturated fats are linear molecules able to pack in more tightly and are solid at room temp Unsaturated fats (oils) have angles and do not pack in tightly. They are liquid at room temp. Structure and role of phospholipids,Major component of cell membranes Contain hydrophilic domain that contains phosphate (and other hydrophilic structure) Contains hydrophobic domain of lipid chains Structure and function of lipid bilayers,Protein channels are proteins that provide a passage through the lipid bilayer, and in the case of polar molecules, allows them to transport across the hydrophobic interior. Materials, such as sugars and ions, enter the cell this way. Various functions of proteins and why they are so versatile,Structural: collagen, keratin, silk, tubulin Storage: casein, ovalbumin Transport: hemoglobin Hormones: insulin Receptor: ASGPR Contractile: actin Defensive: antibodies Enzymatic:lysozyme and many others 4 levels of a protein structure,Primary Secondary Tertiary Quaternary Primary Structure of a protein,Order of amino acids within polypeptide Amino end to carboxyl end Secondary structure of a protein,Due to interactions of the backbone Stabilized by hydrogen bonds Parallel: oxygen and hydrogen making bonds Antiparallel: Same bonds but in opposite direction Alpha Helix stabilized by frequent polar R groups B pleated sheets are formed by polar R groups Tertiary Structure of protein,Due to side chain interactions Bigger folding events Hydrophobic: Nonpolar internalize Disulfide bridge Very stable bond forms between two cysteine residues Ionic bonds between acidic and basic Quaternary Structure of protein,Only seen in compound proteins Interactions maintained by polypeptide chains similar to the tertiary structure Hemoglobin is this but with 4 polypeptide chains 4 functional groups of amino acids,Nonpolar (hydrophobic):glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan and proline Polar (hydrophilic): serine, threonine, cysteine, tyrosine, asparagine and glutamine Electrically charged: Acidic: aspartic acid, glutamic acid Basic: lysine, arginine and histidines The amino and carboxyl termini and polarity of protein synthesis,Can tell one end of proteins from the other (Amino -> Carboxyl) General Structure of a nucleotide,5 Carbon nitrogenous base phosphate group, sugar pentose, and nitrogenous base Nucleic Acids,Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Polymer of nucleotides Store cellular information Molecules of inherited information Basis for genetics Often large, very complex molecules Serve as templates for proteins Help control regulation of cellular functions The structural and functional differences between DNA and RNA,Both are important for cell function DNA is double stranded and longer-lived RNA is single stranded and has shorter life Both can serve as a template for the synthesis of the other DNA to RNA is very common (transcription) RNA to DNA occurs only with retroviruses (reverse transcription) Both have 5'-3' orientations (5 prime to 3 prime) The structure of a double helix,Two strands that are anti parallel A-T (two bonds) G-C (3 bonds) Hydrogen bonds Since strands are complimentary they serve as a template for the opposite strand Inside is hydrogen bonds and outside is covalent bonds The Central Dogma of informational flow in cells,How information is stored in genes Info in DNA is used to make transcription to make RNA mRNA = Message RNA rRNA = transfer RNA Info in RNA is used to make a protein through translation DNA is long term storage RNA is short term Why organisms need energy input,Assembling compound structures requires the input of energy Potential energy exists as these structures are maintained The degradation of compound structures into simpler structures releases the stored energy The released energy may be used in the assembly of other compound structures Some energy is lost as heat, so food or solar energy needs to be added to the system Catabolism,Degradation of complex molecules into smaller ones Results in release of stored energy This energy can be used by anabolic pathways Anabolism,Anabolism Synthesis of complex molecules Requires the input of energy Energy is obtained by catabolic reactions Resultant molecules can be used in catabolic reactions How ATP is used for short term energy storage **,Adenosine triphosphate (ATP) is most significant Similar to nucleotide in RNA, but with 3 phosphates Similar to rechargeable batteries When free energy is present ADP acquires 3rd phosphate The bond between P2 and P3 stores energy as potential (battery charged) ATP is hydrolized to ADP +Pi and stored energy is released (battery depleted) Released energy drives cellular function (radio plays) Cycle repeats Phosphorylation of intermediates,The formation of complex molecules takes energy The hydrolysis of ATP releases energy The addition of a phosphate group from ATP can "activate" a molecule making it possible to form bonds that require energy Activated intermediates How enzymes function,Proteins that catalyze specific reactions Contain active site or pocket which modifies a molecule called the substrate into a product Returns to ready-form and is not "used-up" by the reaction Tend to perform only a single, specific reaction and not multiple reactions How inhibition occurs,The active site possesses a 3D structure which allows it to bind substrate Molecules that have a similar structure to the substrate may also bind the active site and prevent reaction-competitive inhibitor Other molecules may bind elsewhere on the enzyme and change the conformation of the active site-noncompetitive inhibitor Regulation,Feedback inhibition is very common The presence of high levels of a molecule will inhibit the pathway that synthesizes that molecule Like a thermostat Enzyme interactions,Enzymes often have active state and inactive state and require an interaction with another molecule to become active-activator Cooperative interactions-the interaction of a enzyme with one substrate increases the rate of binding to additional substrate molecules Prokaryotic Cells,All bacteria Most have cell wall No membrane-bound organelles Biochemical reactions take place in cytoplasm or cell membrane Typically very small Eukaryotic Cells,Protist, fungi, plant and animal cells Some have cell walls Possess membrane-bound organelles Biochemical reactions take place in specialized compartments Much larger than bacteria Why cells tend to be small,Cells obtain nutrients (gases, water other molecules) from the environment through the cell membrane High surface area:volume ratios maximizes the amount of cell/environment interaction Large cells would starve Structure of cell membranes,Lipid bilayer Integral proteins "float" in fluid Hydrophobid region of proteins reside in fatty acid layer of membrane Hydrophilic regions are on cytoplasmic and extracellular surfaces Membrane fluidity may be altered by adjusting fatty acid chains Function of cell membranes,Gatekeeper of cell Determines what goes in or out of cell Compartmentalization allows all membrane-bound organelles to remain distinct from cytoplasm Transport Actively move molecules into cell Signal transduction Environmental conditions trigger genetic and biochemical changes in cell via receptors Cell-cell communication and interaction Diffusion,Starts with a gradient System will eventually reach equilibrium (even distribution) Happens passively without selective barriers Many small molecules diffuse through cell membrane Osmosis,Requires a gradient and a selectively permeable membrane Water will move to area of greater solvent concentration The common methods by which molecules get inside of a cell,Membrane pumps, facilitated diffusion active transport Membrane Pumps,Can be used to remove unwanted molecule from cytoplasm Can also be used to form a gradient across the membrane which can drive cytoplasm Facilitated diffusion,An integral protein helps molecules across the membrane Often acts as a revolving door (carrier) or tunnel (channel) Greater specify in which molecule it lets through Active transport,Cell expands energy to make molecule or atom inside often forms gradient to accomplish this Goes from lower concentration to higher 3 Forms of membrane facilitated uptake,Major ways cels acquire samples from environment Phagocytosis Pinocytosis Receptor Mediated endocytosis Phagocytosis,"Cell eating" Amoebae or macrophages Cell produces pseudopod to surround large object Pinocytosis,"Cell sipping" Very delicate Samples outside material and brings in very small volumes Receptor Mediated endocytosis,Rearrangement of cell membrane that brings the cells inside Receptors bind to molecules The structure and function of the nucleus and its components,Command center of the cell Where DNA as chromosome is located Membrane bound Only found in eukaryotes Nuclear membrane with perinuclear space in between Very important for cell function (allows separation from DNA) Storage carbohydrates,Polysaccharides=many monomers in one polymer Glucose is most common monomer used Starches =plants use for energy storage Amylose is unbranched chain of glucose monomers Glycogen=animals use glycogen as medium-term energy storage Glycogen is highly-branched polymer of glucose monomers Cells contain enough glycogen for approximately one day's activity Synthesis of polypeptides,Polypeptide is synthesized by dehydration reaction Chain grows from amino terminus to carboxy terminus Chain has a repetitive backbone with variable side groups R groups frequently interact with others What is cellular uptake and what are the 3 major forms,Cellular Uptake Major ways that cells acquire large samples from environment Phagocytosis, Pinocytosis, and Endocytosis Phagocytosis,Phagocytosis-"cell-eating" or engulfment Amoebae or macrophages Cell produces pseudopod to surround large object Pinocytosis,"cell drinking" Vesicle forms and brings in liquid Endocytosis,receptor mediated A specific receptor-target interaction triggers Forms coated pit and vesicle Structure and function of ribosomes,Synthesize protein via translation Use mRNA as template or blueprint Comprises two subunits-60S and 40S Very complex structures made up of many small proteins The location of Ribosomes,Found at several locations but perform one function On outer surface of nuclear membrane On Rough Endoplasmic Reticulum Free in cytosol The two types of Endoplasmic reticulum and their respective functions,Complex mass of membranes with cytoplasm of cell Extension of nuclear membranes and perinuclear space Two varieties Rough-coated with ribosomes Smooth-no ribosomes Complex structure with: Tubules-thin tubes of membrane Cisternae-large holding vats Rough Endoplasmic reticulum,Ribosomes synthesize excreted proteins Stored in cisternae or vesicle Modify proteins Glycosylation of proteins Delivery of membrane associated proteins Often interacts with the Golgi Smooth endoplasmic reticulum,Tissue-specific uses Storage of carbohydrates Detoxification reactions in liver Synthesizes much of the new membrane material Modification of existing molecules What is the golgi and what is its structure,Complex collection of membrane Has polarity Cis and trans surfaces Responsible for secretion Very prominent in cells that serve secretory functions-such as epithelial cells Modifies structures previously synthesized in the ER How the ER reacts with golgi,Synthesis in ER but modification in Golgi Similar to an assembly line Options packages are added in Golgi Sequential passage through cisternae (cis to trans) Each cisternae contains different enzymes Function of golgi,Cis face is nearer the nucleus of cell Cis face is often adjacent to ER Trans face is nearer the cell membrane Activity is directional Starts at cis face and moves to trans The process of cell renewal and how it is accomplished,Cells and their molecules age and become less effective An important cellular function is renewal Old molecules and organelles are recycled New phospholipids are produced for the membrane Toxic molecules need to be collected and detoxified Sometimes a cell needs to commit suicide Called autolysis or apoptosis Glyoxysomes,Specialized peroxisomes found in plant seeds Recognize appropriate signals and begin to degrade stored fat in seed Fat is converted to sugars which allows seedling to sprout Once photosynthesis starts, glyoxysomes degrade Lysosomes,Contains digestive enzymes used to degrade macromolecules or organelles Originates in ER but enzymes are activated in Golgi Important in macrophages Used to degrade organelles Peroxisomes,Contain enzymes to collect free hydrogen and oxygen and combine into H2O2 (peroxide) Peroxide is also toxic so they contain enzymes to degrade into water and oxygen molecules Catalase experiment in lab Peroxisomes are formed by aggregation of lipids and proteins (not formed in ER) Many are found in liver cells Degrade alcohols into peroxide then into water and oxygen Cell death and its biological uses,Sometimes used in development of organism Hand development Certain cells are programmed to die at appropriate times Defense against viral or intracellular bacterial infections Self-destruct Apoptosis is often accomplished by leaky or popping lysosomes