Biology: Characteristics of Living Systems, Proteins, and Cell Structure - Prof. Arthur L., Study notes of Biology

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 7 characteristics of living systems cellular organization ordered complexity respond to stimuli growth, development, reproduction energy utilization homeostasis evolutionary adaptation  Unifying themes in bio Cell theory, molecular basis of inheritance (continuity of life, DNA, genome), relationship between structure&function (f depends on s), evolution, emergence of novel properties  What determines net movement of ions Relative concentrations, voltage difference, state of gate  7 categories of Protein Function enzyme catalyst, defence (use shape to recognize foreign microbes and cancer cells), transport, support, motion (muscles contract through sliding motion of actin and myosin), regulation (hormones), storage (Ca and Fe bond to storage proteins)  Cells exhibit basic structural similarities Centrally located genetic material, cytoplasm, plasma membrane,  Cells membranes consist of 4 components Phospholipid bilayer, transmembrane protein, interior protein network, cell surface markers  Key functions of proteins with membranes Transport, enzymes, cell surface receptors, cell surface identity markers, cell to cell adhesion, attachment to cytoskeleton  1 st^ Law of Thermodynamics – energy cannot be created or destroyed  2 nd^ Law of Thermodynamics – disorder in the universe in continuously increasing Active transport – low to high concentration, requires ATP Atomic Energy Levels – higher the level the more energized the electrons Acid – increases the hydrogen ion concentration, lowers pH Actin – lies below membrane, mechanical strength, muscle contraction, cell movement, locks centrioles in place in cytokinesis, polar Amylose- simplest starch structure Amylopectin- branched polysacc. Adhesion- H 2 O attracts to other polar molecules, capillary Aquaporin- water channel Area to Volume ration- cell volume increases more rapidly than surface area Amino acid- amino group, carboxyl group; specific order determines protein function and structure, 5 types 1. Nonpolar (--CH 2 , -CH 3 ) 2. Polar uncharged (-OH –R group with O) 3. Charged (acid/base can ionize) 4. Aromatic (organis C ring with alternating single/double bond) 5. Special functions ATP – the energy currency of cellular metabolism in all organisms Base – absorbs and therefore reduces the hydrogen ion (H+) concentration, increases pH Bulk transport- endo and exocytosis Buffer- resists change in pH Carbohydrate – an organic compound consisting of a chain or a ring of carbon atoms to which hydrogen and oxygen atoms are attached (CH 2 0) Carrier proteins – actively or passively transport molecules across membrane Catalysts – used to lower the amount of activatio needed to initiate a reaction Cell theory – all organisms consist of one or more cells, which are the smallest living things, and that all cells come from pre-existing cells Centrioles – barrel shaped organelles found in animals (line up the poles in cell division Cellulose- structural material, polymer of beta glucose, main component of cell walls, not easily broken down/digested Chromatin- DNA packaging Centrioles- Centrosomes- microtubule organizing centers Channel Proteins – passively transport molecules across membrane Cilia – responsible for movement, small and there’s lots of them Chloroplasts – energy and metabolism in plants, double- membrane structures, divide by binary fission, more complex than mitochondria Cohesion- H 2 O attracts to other H 2 O, surface tension Chitin- structural material in arthropods and fungi, modified cellulose, exoskeleton Chaperone protein- help proteins fold correctly Coupled/Counter transport - sodium-potassium pump Cytoskeleton – actin, microtubule, intermediate filament Deductive reasoning – general to specific Domain- functional units with larger structure, help proteins fold Denaturation- protein changes shape/ unfolds if environment is altered Dissociation- protiens with quaternary structure may dissociat without losing tertiary structure, not the same as denaturation Endergonic – reaction that requires input of energy Endocytosis – plasma membrane envelops food particles and fluids Endosymbyosis- prokaryote engulfed another cell to evolve into eukaryotes Exocytosis –opposite of endocytosis Exergonic – reactions that release free energy as heat Extracellular matrix – surrounding animal structures Emergent properties- result from the way in which components interact, can’t be deduced by just looking at parts (cell doesn’t tell about whole animal), arise at each higher level of organization, can’t be predicted from lower levels Electronegativity- atoms affinity for electrons (increase across period, decreases down group) Facillitated Diffusion – carrier mediated transport process Flagella – used in movement, one and very long FAD- electron carrier Fatty acid- long hydrocarbon chain with carboxylic acid, glycerol (3C polyalcohol) Fluid-mosaic model – mosaic of proteins floats in or on the lipid bilayer, cell-cell recognition Functional group – a molecular group that attaches to a hydrocarbon that confers chemical properties or reactivities Glycogen- like starch in animals, insoluble starch with branched amylose Glycolipids – cell identity markers, tissue recognition Glycoproteins – cell identity markers, “self” recognition Golgi Apparatus – sort and package “UPS center” gets a vesicle from the ER goes to GA cis- receive trans- discharge Gram negative – multilayered cell wall (doesn’t retain purple dye) Gram positive – thick single- layered peptiglycan cell wall Glycosomes – convert lipids to carbs *only in plants Gated channel- can open/close in response to stimulus Homeostasis – The maintenance of a relatively stable physiological environment in an organism; usually involves some form of feedback or self regulation Hypertonic – higher osmotic concentration (always goes here, leaves hypo) Hypotonic – lower osmotic concentration (leaves hypo goes to hyper) Hydrophobic exclusion- H 2 O forces hydrophobic portions of molecules together Hydrolysis – a reaction that breaks a bond by addition of water (opposite of dehydration) Ion channel- hydrated interior Isotonic – same osmotic concentration Isomer- same formula, different structure 1. Structural- difference in C skeleton 2. Stereoisomer- differ in how groups attached to C skeleton are arranged a. enantiomer- mirrorimage D-dextrorotatory L- levorotatory Intermediate Filament – “cables” for structure stabilizes the inner nuclear membrane, cell-cell adhesion, cell-matrix adhesion, twined together in overlapping arrangement Inductive reasoning – specific to general Lipid – a nonpolar hydrophobic organic molecule (non water soluble) can fold like proteins to keep nonpolar portions away from aqueous environment Lysosomes – contain hydrolytic enzymes, digestive vesicle, acidic Mitochondria- “powerhouse” energy and metabolism in animal cells (sugar  ATP) Microtubule – cellular movement, cell organization, “tracks” for vesicles, chromosome movement, 13 protein protofilaments Microbodies- membrane enclosed vesicles, glyoxisome

(plants fatcarbs), peroxisome (removal of electrons and H=) Microfilaments- part of the cytoskeleton, made of solid rods of globular proteins Monosaccharide- energy storage, 6C Motif- similarities between dissimilar proteins Microbodies – lysosomes, peroxisomes, glyoxycomes NAD+ - electron carrier in many cellular processes Nucleotides (CHONP) – 1 phosphate for every sugar, long polymer of nucelotides, pentrose, phosphate group, organic nitrogeneous base Nucleic acid- chain of 5C sugars linked by phosphodiester bonds with nitrogeneous base protruding from each sugar Nucleolus- ribosome manufacturing Nuclear envelope- phospholipid bilayer, nuclear pores Nitrogeneous bases- purine (adenine and guanine) and pyramidines (cytosine, thymine (DNA) and uracil (RNA)) Oxidation – the loss of an electron by an atom Osmosis – NUMBER OF SOLUTES NOT THEIR SIZE, water across membrane Osmotic pressure- cytoplasm pressing against cell membrane, force needed to stop osmotic flow Passive transport- no energey expended, high to low concentration Primary structure – the specific amino acid sequence of a protein Phylogenic tree- pattern of decent, evolutionary history of a gene Phagocytosis – endocytosis when the cell takes in little particles Phospholipid bilayer – foundation of a cell’s membrane bilayer b/w two layers of globular proteins Polysaccharide- energy storage, structural components

1. Starch= alpha 2. Cellulose=beta Polyunsaturated- fatty acid with more than one double bond Peptidoglycan – makes up the cell wall: carbohydrate matrix Peroxisomes – metabolize fatty acids and rid cell of toxic peroxides Proteins bonds (CHON) = peptide bond covalent bond between 2 amino acids, dehydration reaction, partial double bond means no rotation Protein- olymer of amino acids Pinocytosis – endocytosis, material taken in is liquid Peroxisomes – contains enzymes that catalyze the removal of electrons and associated hydrogen atoms Polymer- long molecule built by linking large number of monomers, built by dehydration, broken by hydrolysis Quartenary – 2 + polymers combine to make a functional group Quanta- steps in energy, move electron closer to nucleus = release energy Reduction – the gain of an electron by an atom Rough ER- protein synthesis Secondary structure – formation of pleats or helixes, hydrogen bonds b/w adjacent peptide bonds Starch – an insoluble polymer of glucose, chief food storage of plants Saturated- has all H atoms possible, no double bonds Sodium-potassium pump – 3 sodium to 2 potassium, they go in opposite directions Smooth ER- modify foreign substances to make them less toxic Tertiary Structure – fold on themselves, hydrophobic exclusion Transmembrane proteins – the proteins that float in the lipid bilayer, hydrophobic centers and hydrophilic ends Triglyceride – an individual fat molecule, composed of a glycerol and three fatty acids Universal solvent- hydration shell forms around solute ions so they can’t bond to othe solutes Unsaturated – has double pairs b/w carbon atom

 Vacuoles- Membrane-

bound sacs for storage, digestion, and waste removal