First semester study guide biology (5) Chemistry: H Protons + } same as the atomic number Electrons Neutrons O Nucleus

s (neutrons and protons) } atomic mass Electron configuration: 2-8-8-18-18-32-32. outer electrons are valence electrons Ionic Bonds: transfer of electrons from one atom to another. Covalent Bonds: sharing of electrons between atoms Nonpolar: equal sharing of electrons (hydrophobic: dont mix with water) Polar: unequal sharing of electrons (hydrophilic: love to mix with water) Isotopes: it is the same element, but it has a different number of neutrons H O

Hydrogen Bond

(10) Macromolecules: Carbohydrates (CH2O): give short term energy, 1:2:1 ratio Monosaccharides: 1 sugar unit. Ex. Glucose, fructose Dissacharides: two monosaccharides covalently bonded. Ex. Maltose, Sucrose Polysaccharides: made of glucose stuck together, chains of many sugar monomers. Ex. Cellulose, starch, glycogen, chitlin Lipids: (C,H,O) fatty acids, long chains attached to a carboxyl group. Saturated: each corner is a C. they stick to each other and are repelled by blood and build up inside you as plaque. They stack easily and are solid at room temperature. Come from animal fat Unsaturated: have one or more double bonds and are liquid at room temperature. Come from plant oils Cis: they dont stick together and they help remove sat fats Trans: stack together easily and with sat fats Phospholipids: phospholipids bilayer (head, tail, head, tail): head is hydrophilic, tail is hydrophobic Triglycerides: made from glycerol connected to three fatty acids Nucleic Acids: (C,H,O,N) Nucleotides are the monomers of nucleic acids. Nucleotides: made of sugar, a phosphate group, and a base. They make enzymes function Proteins: (C,H,O,N) monomers are amino acids. they do the most work of the macromolecules Amino acids: have an amino group, a carboxyl group and an R group (20 kinds which differs between them) Primary structure: bonds formed are peptide bonds Secondary Structure: called an alpha helix or beta sheet. Hydrogen bonds form between different parts of polypeptide chain which keeps it together when it coils Tertiary structure: R group bonds keep these together. Have a heme group each are helix and they form this shape because of amino acids Quaternary structure: polypeptide chain bonding. Hemeglobins: this whole thing is a protein Denaturation: a permanent thing that breaks weak bonds. Ph: extreme pH. Temperature: high temperature breaks bonds and proteins will change shape (3) Prokaryotes and Eukaryotes Prokaryotes: the simplest cells. Ex. Bacteria and archaea Eukaryotes: have a nucleus and they have little internal complexity. Ex. Plant and animal cells Cell Theory: A. all living things are made of cells. B. the cell is the basic building block of life. C. all cells come from preexisting cells.

(9) Cell Membrane: It is a phospholipids bilayer. It is a boundary layer which selectively controls the flow of substances Adhesion proteins: project outward from plasma membranes of multicelled species especially. They help cells of the same type stick together in the proper tissues. All in Communication proteins: of two adjoining cells match up, forming a direct channel between membrane: their cytoplasms. Signals through the channel. The channel is part of a gap junction between two heart muscle cells. Receptor proteins: docks for outside signals or substances that can make a cell change its activities. The cell may start making or secreting a protein, block a reaction, or get ready to divide. Recognition proteins: like molecular fingerprints. They identify each cell as self vs. nonself Membrane crossing mechanisms: diffusion across lipid bilayer, passive transport, active transport, endocytosis, exocytosis Active transport: net diffusion of solute against concentration gradient (from low to high), transport protein must be activated, ATP energy required, it transports ions. For muscle contraction and nerve cell function Passive transport: it goes from high to low through the concentration gradient, requires a transport protein, and does NOT require energy input. For simple sugars, monosaccharides, disaccharides, alcohols pass through Diffusion: net movement of molecules down concentration gradient (high to low) Osmosis: movement of water molecules from high to low water concentrations through a semi permeable membrane Tonicity: Hypertonic: more solutes, lower water concentration Hypotonic: fewer solutes, higher water concentration Isotonic: equal water and solute concentration (2) First Law of Thermodynamics: amount of energy stays the same, energy cant be created or destroyed, and it can be converted into something else Second Law of Thermodynamics: flows from high to low energy forms, heat is lowest quality form of energy, its random motion of molecules Endergonic: it requires an energy input; product has more energy than reactants Exergonic: energy is released; products have less energy than reactants Enzymes: they are catalytic molecules, they make things go faster, can be used again and again, works in forward and reverse, and they are very specific (fit with a certain substrate) Temperature: high temps denature enzymes so they cease to function pH: enzymes denature in an acidic environment (5) Photosynthesis: Light reactions Dark reactions Reactants: ADP, NADP+, H2O, sunlight Reactants: CO2, ATP, NADPH Products: ATP, NADPH, O2 Products: glucose, ADP, NADP+ Chloroplast: where photosynthesis occurs granum (stacks of thylakoids), two outer membranes, stroma (space between thylakoid stacks)

(5) Respiration: Glycolysis Krebs Cycle E.T.P. Reactants: 1 glucose, 2 ATP, 2 Reactants: 2 pyruvate, 6 NAD+, Reactants: 32 ADP, 8 NADH, 2 NAD+, 4 ADP 2 FAD, 2 ADP FADH2, oxygen Products: 2 ADP, 2 ATP, 2 Products: 4 CO2, 2 ATP, 6 Products: 32 ATP, 8 NAD+, 2 NADH, 2 pyruvates NADH, 2 FADH2 FAD, water *Oxygen is the final electron acceptor. Mitochondrion: has an inner and outer mitochondrial membrane, and an inner and outer compartment Ecology: (9) Populations: a group of individuals of the same species occupying a given area that interbreeds. Must be able to reproduce and have offspring. Population size is affected by immigration/emigration and births/deaths J curve: exponential growth S curve: logistic growth, the population levels out (carrying capacity) then fluctuates

Survivorship Curves: Type 1: (K strategy) large mammals, few offspring, parental carehumans, elephants Type 2: age/survivor not related, small mammalsmice, cats, birds, squirrels Type 3: (R strategy) die early on, few live to be old, mass offspring, no parental careinsects, fish, sea turtles Density Dependent: dependent upon density of population. Ex. Disease, resources, parasites, predators, competition Density Independent: NOT dependent upon density of population. Ex. Climate, pollution, weather, natural disasters (6) Communities: Neutral: 0/0 dont help or harm each other Commensalism: +/0 one benefits, other not helped or harmed. Ex. Shark and ramora Mutualism: +/+ both species benefit, have to help each other to survive. Ex. Insects and pollinating plants Competition: -/- both are harmed, take resources from each other Interspecific-between species Intraspecific-between members of the same species Predation/Parasitism: +/- one benefits while the other is harmed. Ex. Mistletoe, ticks, leeches Gauss principle: he studied competition One species was eliminated while the other did really well.

(1) Keystone species: Sea star and kangaroo rat, they increase biodiversity (2) Succession:

Primary: places with no life before or no life for years. Ex. Lichens, mosses Secondary: places with a community established that got wiped out. Ex. Weeds, grasses, annual plants (10) Ecosystems: Energy Pyramid: Primary producers: Photoautotrophs and algae Consumer: herbivores, Carnivores, omnivores, Parasites Decomposers: Fungi and Bacteria Detritivores: Invertebrates which feed on small animals

Top Tertiary consumer Secondary consumer Primary consumer Primary producer

10 percent 10 percent 10 percent 10 percent 1 percent

Food chain: linear sequence of who eats whom Food web: series of connected food chains Carbon Nitrogen Input: combustion, volcano, Input: N fixation, waste, respiration, decompostition ammonification, decomposition Output: photosynthesis, dissolves Output: leaching, denitrification in H2O (23) DNA: (9)Griffith: Phosphorous Input: erosion Output: runoff

He isolated two strains of Streptococcus pneumoniae; R cells were harmless, S cells were deadly, caused disease Hershey Created bacteriophages (virus that infects bacteria). They worked with radioactive sulfur and Chase: (protein) and phosphorus (DNA) and they allowed these labeled viruses to infect bacteria. They found that DNA contained genetic info, not protein Avery: He reported that the transforming substance was probably DNA. He found protein mixed with S cells could still function, but DNA mixed with S cells lost their transforming ability. Chargaff: Amount of adenine relative to guanine differs among species. A=T and G=C Franklin: She was an expert in x-ray crystallography. She knew that the helix width was 2 nm, distance between turns was 30 nm, and one base to the next base was 3 nm. Watson and They said that DNA consists of two nucleotide strands that run in opposite directions and Crick: are held together by hydrogen bonds between bases. A binds with T and C binds with G. (12)DNA structure: a double helix, each strand is a nucleotide which consists of deoxyribose, phosphate group, and a base (Adenine, Guanine, Thymine, or Cytosine) Replication: One nucleotide strand is copied in replication so there is one old and one new. Helicase, DNA polymerase, and ligase and the enzymes in replication Sequence of events: Helicase spreads outwards. Discontinuous assembly (lagging strand) moves towards the continuous assembly (leading strand) in the direction of 3 to 5 towards DNA polymerase in the replication bubble. Ligase fills the gaps between the Okazaki fragments which are the discontinuous assembly.