BIO101 Reviewer (Chapters 1-4)

CHAPTER 1 - Introduction to Biology Biology - study of life Properties of Living World Unity common traits rooted in the phenomenon of biological evolution Diversity- different types of environment where diverse forms of life have evolved Characteristics of Living Organisms Cells & Organization - organisms (organum, Latin) maintain an internal order separated from the environment - cell, simplest unit of an organism (Cell Theory) Energy Use & Metabolism - cells acquire energy & use it to maintain their internal order - cells use energy by catalyzing a variety of chemical reactions (metabolism) for breakdown of nutrients & synthesis of compounds Response to Environmental Changes - needed to survive - adaptations processes & structures by w/c organisms adjust to short or long-term changes Regulation & Homeostasis - to stay the same, Greek - process by w/c cells & organisms regulate their bodies to maintain stable internal conditions Growth & Development - Growth - more or larger cells - Development produces organisms w/ a defined set of characteristics Reproduction - needed to sustain life - DNA - genetic material; blueprint of life - genes contribute to the traits of organisms - Molecular gene expression - DNA -> RNA-> Polypeptide (largely responsible for the traits) Biological Evolution phenomenon that population of organisms change over the course of many generations Different Levels of Organization Atom - smallest component of an element - all matter is composed of atoms Molecules & Macromolecules - atoms bond w/ each other to form Organism - belonging to a particular species (related group of organisms sharing a distinct form & set of attributes) Population - group of organisms of the same species & environment Community - assemblage of populations Ecosystem - interactions of community of organisms w/ their environment Biosphere - all of the places on Earth where living organisms exist Two Mechanisms of Evolutionary Change Vertical Descent w/ Mutation progressions of changes in a series of ancestors (lineage) - new species evolve from pre-existing species by the accumulation of mutations (changes in the genetic material of an organism) o Mutation - changes in the genetic material of organisms o Natural Selection - mutation is more likely to increase in a population over many generations Horizontal Gene Transfer - genetic exchanges between different species - Tree of Life - vertical evolution; Web of Life vertical evolution and horizontal gene transfer Classification of Living Organisms Taxonomy- grouping of species 3 Domains of Life - Bacteria & Archaea - prokaryotic - Eukarya - eukaryotic; has a cell nucleus - 4 kingdoms: Animalia (has a nervous system; locomotion), Plantae (photosynthesis), Fungi (has a cell wall but cant carry out photosynthesis) & Protista Binomial - unique scientific name; GENUS (1st part) species (2nd part) Evolution - unifying concept in Biology Genome - complete genetic make-up of organism - acts as stable informational unit, provides continuity from gen. to gen. & acts as instrument of evolutionary change Biology as Scientific Discipline Science - observation, identification, investigation & theoretical explanation of natural phenomenon Scientific Method - standard approach to

Hypothesis - proposed explanation for natural phenomenon; based on previous observations & experiments Theory - broad explanation of some aspect of the world w/ a large body of evidence Knowledge - awareness & understanding of information Curiosity - key phenomenon that sparks scientific inquiry 2 Scientific Approaches Discovery-based science - collection & analysis of data w/o the need for preconceived hypothesis Hypothesis-testing - scientific method; used to test the validity of a hypothesis observation, hypothesis, experimentation, analyzation of data, accept/reject CHAPTER 2 - Chemical Basis of Life I Atoms Biochemistry - study of atoms & molecules in the context of living organisms Atoms - smallest unit of matter; each specific type of atom occurs as an element 3 subatomic particles - Protons - (+) charge; found in the atomic nucleus - Neutrons - no charge; found in the atomic nucleus - Electrons - (-) charge; found at regions at various distances from the nucleus Orbitals - regions surrounding the nucleus in w/c the probability of finding an electron is high - can hold a max. of 2 electrons - shapes: spherical (s-orbital) or dumbbell (p-orbital) - occupy energy shells/levels (innermost shell of atom - max. of 2 electrons; second shell - 1 (2s) & 3 (2p) orbitals; can hold 4 pairs of electrons) Valence electrons - electrons in the outer shell; available to combine w/ other atoms Atomic No. - number of protons; = no. of electrons Periodic table - rows ( indicate no. of energy shells); columns (indicate no. of valence electrons) Atomic Mass - atoms mass relative to the mass of other atoms - measured in daltons; 1 Da=1/12 the

Chemical Bonds & Molecules Molecule - 2 or more atoms bonded together Molecular formula - consists of the chemical symbols & subscripts for all of the atoms present Compound - molecule composed of 2 or more diff. elements Covalent bond - strong chemical bond; atoms share a pair of electrons Electronegativity - measure of an atoms ability to attract electrons in a bond from another atom Polar covalent bonds - when 2 atoms with different electronegativities form a covalent bonds, the shared electrons are more likely to be closer to the atom of lower electronegativity Polar molecules - molecules containing significant numbers of polar bonds Nonpolar molecules molecules composed predominantly of nonpolar bonds Hydrogen bond - ability of one molecule to loosely associate with another molecule through a weak interaction Ion - atom or molecule w/ net charge from gaining or losing one or more electrons - cations (ions w/ + net charge); anions (ions w/ net charge) Ionic bond - occurs when cation binds to an anion Free radical - molecule containing an atom w/ a single, unpaired electron in its outer shell - can be either charged or neutral Chemical reaction - occurs when 1 or more substances are changed into other substances - requires source of energy (heat); causes atoms & molecules to vibrate & move (Brownian movement) - needs catalyst (substance speeding up a chemical reaction - will eventually reach equilibrium Properties of Water Solute - substances dissolved in a liquid Solvent - liquid which substances are dissolved in Solution - formed when solutes dissolved in solvent Aqueous solutions - solutions made with

Solute concentration - amount of solute dissolved in a unit volume of solution Molecular mass - sum of the atomic masses of all atoms in the molecule Vaporization - water from liquid to gaseous state Colligative properties - temperature at w/c a solution freezes or vaporizes - Heat of vaporization - heat required to vaporize 1 mole of any substance - Heat of fusion - heat required to cause a substance to change from liquid to solid state Anti-freeze molecules - produced by coldblooded animals Hydrolysis - process wherein water is used to break apart another molecule Dehydration - removal of water molecule in a reaction & formation of covalent bond Features of water - participate in chem. reactions - incompressible - has a very high heat capacity - Hydrogen-bonding properties of water (cohesion- molecules w/in a substance tend to noncovalently attract each other; adhesion - ability of water to adhere to another surface) - surface tension - measure of how difficult it is to break the interface between liquid & air Acids - molecules that release hydrogen ions in solution - Strong acid - complete dissociation when added to water (ex. HCl -> H + Cl) - Weak acid - some of the molecule will still remain when dissolved in water) (ex. H2CO3 -> H + H2CO3) Base - lowers H+ concentration; some release OH Solutions pH - concentration of H+ - acidic solution (pH is below 7); alkaline solution (pH is above 7); neutral solution (pH is 7) Buffer - minimize fluctuations in the pH of fluids; can raise or lower pH as needed CHAPTER 3 - Chemical Basis of Life II Carbon Atom & Study of Organic Molecules Carbon - provides atomic scaffold upon life is built Carbon-containing molecules - organic molecules Organic chemistry - science of studying carbon-containing molecules

Characteristics of Carbon - ability to form 4 covalent bonds w/ other atoms - carbon bonds may occur in linear, ringlike or highly branched configurations - ability to form both polar & nonpolar bonds (Hydrocarbons - molecules containing C-H bonds; nonpolar; insoluble in water) - carbon bonds are stable at diff. temperatures (shorter bond - stronger & more stable) Functional groups - groups of atoms w/ special chemical features that are functionally important - (amino, carbonyl - ketone & aldehyde, carboxyl, hydroxyl, methyl, phosphate, sulphate & sulfhydryl) Isomers - carbon-containing molecules existing in multiple forms - 2 structures w/ an identical molecular formula but different structures & characteristics - 2 types: Structural Isomers - same atoms; different bonding relationship Stereoisomers identical bonding relationship; differs in spatial positioning (geometric isomers cis-trans stereoisomers) (enantiomers - mirror images of each other) Classes of Organic Molecules Large molecules - polymer; linking of smaller molecules (monomer) Carbohydrates - composed of C, H & O atoms; Cn(H20)n - most of its C atoms are linked to a H atom or Hydroxyl group Sugars - small carbohydrates that taste sweet; source of energy of living organisms Monosaccharide - simplest sugars; most common type: pentoses (e.g. ribose & deoxyribose) and hexoses (e.g. glucose) Disaccharides - 2 sugars; (e.g. sucrose - composed of glucose & fructose, maltose & lactose) - Glycosidic bond - bond formed between 2 sugars Polysaccharides - many sugars - e.g. (used to store energy) starch plant cells & glycogen - animal cells; (structural role) cellulose - cell wall

- Ester bond - hydroxyl group is linked to carboxyl group by removal of H20 molecule (dehydration) - Saturated fatty acid - C atoms in a fatty acid are linked by a single covalent bond - Unsaturated fatty acid - C atoms in a fatty - Electron Microscope -a uses an covalent acid are linked by double electron beam bond (Types of Oils - fats high in unsaturated - Electron Microscope: TEM (Transmission Electron Microscope) fatty acids beam of electrons is transmitted through a sample, has -the best resolutionacids & Phospholipids glycerol, 2 fatty of any phosphate group (linked to the 3rd microscope; SEM (Scanning Electron hydroxyl group of glycerol) Microscope) - utilizes electron beam to - Amphipathic produce a 3D image of the surface of the sample) - 4 fused rings of carbon atoms Steroids - Sterols Structure Overview of Cell - steroids w/ hydroxyl group; cholesterol Cell structure - relies on 4 critical phenomena: Waxes - lipids that are secreted by plants matter, energy, organization & information & animals - their a simple structure; Prokaryotesontohave surface - a membrane- enclosed nucleus; 2 lack contain 1 or more hydrocarbons & long structures & Archaea categories: Bacteriathat resemble a fatty acid Structure of typical bacterial cell: - nonpolar; repel water - Plasma Membrane - important barrier Proteins - first rank; external environment & between cell & its composed of C, H, N O atoms and smallregion of theothercontained - Cytoplasm - amounts of cell elements (S) w/in the p lasma membrane - Aminostructures buildingbacterial of protein - acids - in the blocks cytoplasm (structure: C + amino grp. carboxyl (nucleoid atom region where + DNA is grp. located; ribosomes - involved in protein + H atom + side chain) - 20 amino acids - nonpolar (Glycine, synthesis) Alanine, Valine, Leucine, Isoleucine, Proline, - Cell Wall - supports & protects the Phenylalanine, Tyrosine, Tryptophan, Cysteine plasma membrane; porous & Methionine); - outer gelatinous covering of - Glycocalyx Polar uncharged (Serine, Threonine, Asparagine & water; (capsule Glutamine); Polar bacteria; traps charged thick glycocalyx) (Aspartic acid, Glutamic acid, very Histidine, Lysine & - pili (allows prokaryotes to - Appendages Arginine) - Peptide bond - bond formed between attach to surfaces); flagella (allows a carboxyl & aminoswim) prokaryotes to group - Polypeptide - resulting molecule when - Proteins important in the architecture amino acids are joined by peptide bonds (ends inside the cytoplasm of bacterial of the resultingcell division;amino terminus cells (FtsZ - molecule: free amino -group; carboxyl terminus - free MreB cell polarity; CreS - cell shape) carboxyl group) Eukaryotes - include protists, fungi, plants Protein Structures at 4 Progressive Levels & animals Primary DNA is housed acid a nucleus - its - linear amino in sequence; determined by membrane-bound genes (organelle compartment-w/ a irregular or repeating Secondary specific structure & folding patterns; 2 types: helix & sheet function) Tertiary - compartmentalization (many - exhibits 3D shape of a single polypeptide; separating the cell to final structure of a organelles functional protein for some different regions Quaternary of Animal/Plant polypeptides General Structure - 2 or more Cell (protein subunits) each adopting a PLANT CELLS LACK lysosomes, centrioles tertiary & flagella structure & then assemble w/ ANIMAL CELLS LACK cell wall, central vacuole & chloroplasts The Cytosol - region outside the organelles but inside the plasma membrane

Nucleic Acids - storage, expression & transmission of genetic information - nucleotide (monomer); composed of a phosphate group, 5-C sugar & a single/double ring of carbon of C & N atoms (base) - phosphoester bond - phosphate group of 1 nucleotide is linked to the sugar of adjacent (polypeptide - unit of structure; protein - unit molecule ofclasses: 2 function) - requires ribosome & 2 RNA molecules DNA (Deoxyribonucleic acid) - stores (ribosome - site for polypeptide synthesis; genetic info mRNA - provides info; tRNA - carry amino - contains deoxyribose sugar acids, bind it to mRNA) - 4 bases: purine bases (adenine & * once entire polypeptide is made, it is guanine) & pyrimidine bases (cytosine released from the ribosome & thymine); (A-T & G-C pairing) Cytoskeleton - network of 3 different - Double helix (2 strands of nucleotides types of protein filaments: coiled) Microtubules hollow tubule; RNA (Ribonucleic acid) - decoding important in cell shape & organization; information into instructions for linking formed in the centrosome or amino acids to form a polypeptide chain microtubule-organizing center - contains ribose sugar - Single(centrioles pair of structures stranded perpendicular to each other found w/in - 4 bases: adenine, guanine, cytosine & the centrosome) uracil - Intermediate filaments - twisted - forms of RNA : mRNA (messenger filament; function as tension-bearing RNA) & tRNA (transfer RNA) - convert fibers that maintain cell shape & information contained in DNA into rigidity formation of new polypeptide - Actin filaments - spiral filament; CHAPTER 4 - General Features of Cells microfilaments; important in cell Cell Theory - Matthias Schleiden, Theodor strength and shape Schwann & Rudolf Virchow (every cell Motor from another cell)ATP as source of originates proteins - use energy - promote movement Cell Biology tostudy of individual cells and their - consists of 3 domains: head (site of interactions w/ each other ATP bonding & Endosymbiosis - process hydrolysis; a new by which causes movement & bend in thefusion of two organism originates from the hinge), hinge & tail (attached to other proteins) existing organisms - axoneme - arrangement containing Microscopy microtubules, motor protein enabling Microscope - magnification tooldynein & linking of structure & function of cells the studyproteins Nucleus & Endomembrane System Robert Hooke - studied cork; coined the Endomembrane system - larger network of term cell membranes enclosing the Zacharias Jansen - invented 1st compound nucleus microscope Vesicles - small membrane-enclosed spheres Max Knoll & Ernst of the invented the where other organelles Ruska - system pass 1st electron microscope materials to each other Anton Nuclear van Leeuwenhoek - invented envelope - doule-membrane simple enclosing the discovered blood structure microscope; nucleus cells & pores - provide passageway for Nuclear first to see sperm cells of animals theimportant parameters in microscopyof 3 movement of molecules in & out : Magnification - ratio between size of an the cell image produced inside the nucleus; Chromosomes - by microscope & actual size; Resolution - measure of clarity of an composed of genetic material & proteins object; Contrast - ability to by DNA a Chromatin - complex formed visualize & particular cell such protein structure

Nuclear matrix - inside the nucleus; filamentous network of proteins; Nucleus - organization, protection & expression of genetic material Nucleolus - region in the nucleus; where

- Rough ER - initial synthesis & sorting of proteins glycosylation attachment of carbohydrate to proteins & lipids - studded w/ ribosomes - Smooth ER - metabolic diverse processes; accumulation of calcium ions; synthesis & modification of lipids Golgi Apparatus - discovered by Camillo Golgi - composed of a stack of flattened membranes - 3 overlapping functions: secretion, processing & protein sorting - packages diff. types of proteins into secretory vesicles - proteolysis - cut proteins into smaller polypeptides; enzymes- proteases Lysosomes - found in animal cells; lyse or degrade macromolecules - Acid hyrdolases - found in lysosomes; enzymes that use water molecules to break a covalent bond - autophagy - eating of ones self; cellular material is enclosed in a double membrane (autophagosome) Vacuole - empty space; transport substances or store materials; for degradation - central vacuole - found in mature plant cells; (tonoplast - membrane of central vacuole) stores large amount of water, enzymes & inorganic ions; performs space-filling function (turgor pressure - pressure exerted on cell wall by the large size of the vacuole; helps maintain structure of plants & for expansion of its cell wall - for growth) - contractile vacuoles - found in freshwater organisms; expands as water enters the cell - phagocytic or food vacuoles - where some protists engulf their food Plasma Membrane - vital in cell signalling; vital role in animals - cell adhesion Semiautonomous Organelles - can grow and divide to reproduce themselves; depend on other parts of the cell for their internal components Mitochondria - thread granule; has an outer & inner membrane (highly folded to form projections called cristae; mitochondrial matrix - compartment inside inner membrane) separated by

- Has an inner & outer membrane too separated by an intermembrane space - thylakoid membrane - 3rd membrane; where light energy is captured; forms many fluid-filled tubules that tend to stack on top of each other to form a structure called granum (thylakoid lumen - enclosed by the thylakoid membrane ; facilitates process of photosynthesis) - stroma - compartment of chloroplast inside the inner membrane but outside the thylakoid membrane - specialized version of plant organelles known as plastids (chromoplasts - 2nd type of plastid; synthesize & store yellow, orange & red pigments; leucoplasts - 3rd type of plastid; lacks pigment molecules; Amyloplast - leucoplast that synthesize & store starch) Peroxisomes - discovered by Christian de Duve - consist of a single membrane that encloses a fluid-filled lumen - catalyze certain chemical reactions, those that breakdown molecules by removing H or adding O - usually contain enzymes involved in metabolism of fats & amino acids (catalase - enzyme in peroxisome that breaks down hydrogen peroxide to make water and oxygen gas) (glyoxisomes - contain enzymes needed to convert fats to sugars)