Midterm Review AP Bio

Chapter 1 Material INTRODUCTION: TEN THEMES IN THE STUDY OF LIFE

Positive and Negative Feedback positive feedback-A physiological control mechanism in which a change in some variable triggers mechanisms that amplify the change. negative feedback-A primary mechanism of homeostasis, whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation.

Positive and Negative Feedback

Scientific method Although science rarely conforms exactly to this protocol of steps, inquiry usually involves posing and testing hypotheses. OBSERVATION: My flashlight doesnt work. QUESTION: Whats wrong with my flashlight? HYPOTHESIS: The flashlights batteries are dead. PREDICTION: If this hypothesis is correct EXPERIMENT: and I replace the batteries with new ones, PREDICTED RESULT: then the flashlight should work.

Chapter 2 Material THE CHEMICAL CONTEXT OF LIFE

Atomic structure Proton - A subatomic particle with a single positive electrical charge, found in the nucleus of an atom. Neutron - An electrically neutral particle (a particle having no electrical charge), found in the nucleus of an atom. Electron - A subatomic particle with a single negative charge; one or more electrons move around the nucleus of an atom.

Atomic structure Isotope - One of several atomic forms of an element, each containing a different number of neutrons and thus differing in atomic mass. Valence electron - The electrons in the outermost electron shell.

Valence Electrons

Bonds Covalent Polar and non polar Ionic Cation and anion Hydrogen bonds

Covalent A type of strong chemical bond in which two atoms share one pair of valence electrons. Nonpolar covalent bond - A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity. Polar covalent bond - A type of covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

Ionic Compounds resulting from the formation of ionic bonds, also called a salt. Cation - An ion with a positive charge, produced by the loss of one or more electrons. Anion - A negatively charged ion.

More Vocab Electronegativity - The attraction of an atom for the electrons of a covalent bond. Reactant - A starting material in a chemical reaction Product - An ending material in a chemical reaction

Chapter 3 Material WATER AND THE FITNESS OF THE ENVIRONMENT

Properties of water Cohesion Adhesion Surface tension High specific heat High heat of vaporization Unusual phase change characteristics Versatile solvent Weak dissociation

Cohesion The binding together of like molecules, in this case water. Caused by hydrogen bonds Contributes to the to the transport of water against gravity in a plant

Adhesion Attraction between different kinds of molecules. Also caused by hydrogen bonds Adhesion of water to the walls of vessels helps counter the downward pull of gravity

Adhesion and Cohesion Water transport in plants. Evaporation from leaves pulls water upward from the roots through microscopic tubes called xylem vessels, in this case located in the trunk of a tree. Cohesion due to hydrogen bonding helps hold together the column of water within a vessel. Adhesion of the water to the vessel wall also helps in resisting the downward pull of gravity.

Surface Tension A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules. This bug is able to stand on the water because of SURFACE TENSION!!!

High Specific Heat Specific heat - The amount of heat that must be absorbed or lost for 1 gram of a substance to change its temperature by 1°C. Water has a high specific heat because it resist changes in heat Specific heat of water – 1 cal/g/°C Water will change temperature when it gains or loses a given amount of heat. Heat must be in order to break hydrogen bonds

Heat of Vaporization Quantity of heat a liquid must absorb for 1 gram of it to be converted from the liquid to the gaseous state. Caused by hydrogen bonds. Hydrogen bonds must be broken before a molecule can make their exodus from the liquid Evaporative cooling - property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous state. Organisms rely on heat of vaporization to remove body heat.

Unusual phase change characteristics Unlike most substances, ice, the solid form of water, is less dense then liquid water, so ice floats. Hydrogen bond keep at arms length from each other, make ice 10% less dense than liquid water.

Importance of Unusual phase change characteristics Oceans & lakes dont freeze solid surface ice insulates water below allowing life to survive the winter if ice sank… ponds, lakes & even oceans would freeze solid in summer, only upper few inches would thaw Life would not be the same without this property!

Versatile Solvent Solution - homogeneous, liquid mixture of two or more substances. Solvent - dissolving agent of a solution. Water is the most versatile solvent known. Solute - substance that is dissolved in a solution. Aqueous solutions - solution in which water is the solvent. Hydration shell - sphere of water molecules around each dissolved ion

Weak dissociation Hydrogen ion (H + ) - single proton with a charge of +1. Hydroxide ion (OH - ) - water molecule that lost a proton. H 2 O H + + OH – or 2H 2 O H 3 O + + OH – Concentrations of ions used to determine whether a substance is an acid or a base.

Versatile Solvent Solution - homogeneous, liquid mixture of two or more substances. Solvent - dissolving agent of a solution. Water is the most versatile solvent known. Solute - substance that is dissolved in a solution. Aqueous solutions - solution in which water is the solvent. Hydration shell - sphere of water molecules around each dissolved ion

Hydrophilic and Hydrophobic Substances Hydrophilic - having an affinity for water. Substances are ionic or polar. can dissolve in water or absorb water. Ex: Cotton, salt Hydrophobic - Having an aversion to water; tending to coalesce and form droplets in water. Substances are non-ionic or non-polar. Ex: Oil, fat

Acids and Bases Acid – substance that increases the hydrogen ion concentration of a solution Base – substance that decreases the hydrogen ion concentration of a solution. if [H + ] = [ - OH], water is neutral if [H + ] > [ - OH], water is acidic if [H + ] < [ - OH], water is basic

pH Scale pH - measure of hydrogen ion concentration pH=–log [H + ] Ranges from 0-14 When the pH<7, the substance is acidic. The lower the number the more acidic the substance is. When the pH=7, the substance is neutral. When the pH>7, the substance is more basic The higher the number the more basic the substance is.

Chapter 4 Material CARBON AND THE MOLECULAR DIVERSITY OF LIFE

Isomers One of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types of isomers are: structural isomers, geometric isomers, and enantiomers.

Isomers structural isomers - Compounds that have the same molecular formula but differ in the covalent arrangements of their atoms geometric isomers - Compounds that have the same molecular formula but differ in the spatial arrangements of their atoms. Enantiomer -Molecules that are mirror images of each other.

Functional groups Hydroxyl Carbonyl Carboxyl Animo Sulhydryl Phosphate

Hydroxyl -OH Organic compound with OH = Alcohols Names typically end in –ol Ethanol

Carbonyl C=O O double bonded to C if C=O at end molecule = aldehyde if C=O in middle of molecule = ketone

Carboxyl –COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids

Amino -NH 2 N attached to 2 H compounds with NH 2 = amines amino acids NH 2 acts as base ammonia picks up H + from solution

Sulfhydryl –SH S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins

Phosphate –PO 4 P bound to 4 O connects to C through an O lots of O = lots of negative charge highly reactive transfers energy between organic molecules ATP, GTP, etc.

Characteristics of carbon Its organic Has a total of 6 electons 4 of which are valence electrons It is tetravalent most versatile building blocks of molecules Little tendency to form ionic bonds H HH C H

Chapter 5 Material THE STRUCTURE AND FUNCTION OF MACROMOLECULES

H2OH2O HO H HH Condensation Reaction (dehydration) connects monomers to form polymer also known as dehydration reaction requires energy requires enzymes

Hydrolysis hydro = water lysis = break releases energy requires enzymes

Carbohydrates A sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides). smallest carbohydrates are sugars sugar monomer = monosaccharides (CH 2 O) provide fuel and carbon sources Ex. glucose, fructose, galactose

Carbohydrates 5 properties of sugars (1.) carbonyl group (aldose or ketose) (2.) 3 – 7 carbon chain (3.) arrangement around asymmetric carbons (4.) major nutrients for cells (5.) carbon skeletons are used to synthesize other organic molecules

Carbohydrates sugar polymer = polysaccharide monomers are joined by glycosidic linkage A covalent bond formed between two monosaccharides by a dehydration reaction. covalent bond formed by dehydration reaction

Storage Polysaccharides STARCH used in plants (stored in plastids) allows plant to store excess glucose sugar can be withdrawn later by hydrolysis reactions GLYCOGEN used in animals (stored in liver / muscle cells) hydrolysis releases energy in times of need bank depleted in ~ one day

Structural Polysaccharides CELLULOSE component of tough walls in plants most abundant organic compound on Earth polymer of glucose in plants, grouped into units called microfibrils building material for plants enzymes for digesting starch cannot hydrolyze beta linkages Humans mostly cant digest, but abrasion of digestive tract triggers release of mucus some microbes can digest cellulose cows harbor bacteria in rumen termites also host necessary bacteria CHITIN

Lipids common property: little or no affinity for water

Lipids Fats store large amounts of energy macromolecule constructed from: glycerol fatty acid triacylglycerol = fat composed of 3 fatty acids to one glycerol via ester linkages fat characteristics: 1. insoluble in water 2. different fatty acids lead to variation in fat molecules saturated no double bonds in tail unsaturated one or more double bonds in tail

Lipids Phospholipids similar to fats, but have 2 fatty acid tails instead of 3 3 rd hydroxyl group is joined to a phosphate group, which has a negative charge hydrocarbon tail = HYDROPHOBIC phosphate group forms head = HYDROPHILIC when clustered in water, form micelles at the surface of a cell, phospholipids arrange in a bilayer

Lipids Steriods carbon skeleton with 4 fused rings each ring has different functional groups Ex. cholesterol common component of animal cell membranes precursor of sex hormones

Proteins used for structural support, storage, transport of other substances, signaling from one organism to another, movement, and defense against foreign substances as enzymes, proteins regulate metabolism by speeding up reactions most structurally sophisticated molecules diversity stems from unique 3Dshape (conformation) all proteins are constructed from the same 20 amino acids

Proteins monomer = amino acid polymer = polypeptide protein = coiled and folded polypeptides physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid nonpolar = hydrophobic polar = hydrophilic acidic = usually (-)due to presence of a carboxyl group basic = have amino groups, which are usually (+)

Proteins amino acids are joined by dehydration reaction resulting covalent bond is called a peptide bond a proteins specific conformation determines how it works (based on linear sequence of amino acids and R groups) Ex. antibodies, enzymes

Levels of Protein Structure primary – sequence of amino acids Ex. Order of letters in word precision is required one substitution sickle cell disease secondary – polypeptide chain repeatedly folds or coils in patterns that contribute to the proteins overall conformation results from hydrogen bonds O and N of backbone are electronegative alpha helix Delicate coil held by Hbonds beta pleated sheet 2 or more regions lie parallel to each other

Primary

Secondary

Levels of Protein Structure tertiary – irregular contortions from interactions between R groups Ex. hydrophobic interaction – as polypeptide folds, amino acids with hydrophobic side chains usually end up in clusters at the core of the protein one theyre in the center, van der Walls interactions help hold them in place may be reinforced by disulfide bridges quaternary – overall protein structure that results from aggregation of polypeptide subunits Ex. collagen, hemoglobin

Tertiary

Quaternary

Levels of Protein Structure

Denaturation protein unravels and loses its native conformation (can return to original conformation)

Chapter 6 Material AN INTRODUCTION TO METABOLISM

Metabolism sum total of an organisms chemical reactions can be viewed as a road map enzymes route molecules through these streets, controlling the flow of traffic

Catabolic release energy by breaking down complex molecules to simpler molecules Ex. cellular respiration glucose à CO 2 + H 2 O downhill

Anabolic use energy to build complicated molecules from simpler ones Ex. protein synthesis uphill

EXERGONIC REACTIONS proceeds with net release of free energy ΔG = - … occurs spontaneously ENDERGONIC REACTIONS absorbs free energy ΔG = + … absorbs free energy

ATP cell does three main kinds of work: mechanical work (movement) transport work chemical work in almost all cases, immediate source of energy that powers work is ATP nitrogenous base adenine bonds to ribose with 3 phosphates (structure is very similar to a nucleotide) bonds between phosphate groups can be broken by hydrolysis bonds are relatively weak; instability allows energy yield all phosphate groups are negative

Enzymes ENZYMES ARE BIOLOGICAL CATALYSTS enzymes are extremely specific can distinguish isomers (i.e., selects specific disaccharide) sucrose + H 2 O glucose + fructose induced fit = as substrate and active site interact, substrate induces a change in enzyme shape to make the fit more snug binding of substrate and active site yields enzyme substrate complex substrate usually held by weak interactions once R groups of a few amino acids catalyze conversion, substrate is released enzyme emerges from reaction unchanged enzymes can catalyze forward and reverse reactions

Enzymes RATE OF REACTION 1. initial concentration of substrate 2. enzyme concentration (enzyme can be saturated) 3. temperature (optimal temperature for most human enzymes is 35 – 40 C) 4. pH (optimal pH is 6 – 8) pepsin (stomach)…pH = 2 trypsin (intestine)…pH = 8 COFACTORS = nonprotein helpers required by some enzymes for catalytic activity inorganic: metals organic: coenzyme (most vitamins)

Enzyme Inhibitors competitive resemble normal substrate; compete for active site (decreases productivity of enzymes) overcome by increasing substrate concentration as active sites open up, more substrate is available for inhibitors noncompetitive do not directly compete at active site bind to other parts of enzyme, changing the shape of the enzyme

Allosteric Regulation most allosteric enzymes are constructed from 2 or more polypeptide chains complex oscillates between two conformational states allosteric activator stabilizes active site (makes it active…ready to react) allosteric inhibitor stabilizes inactive form of enzyme (makes it inactive…no reaction) activity of an allosteric enzyme changes in response to fluctuating concentrations of regulators

Feedback Regulation switching off of a metabolic pathway by its end product (acts as inhibitor)