Chapter 2: The Chemistry of Life 2-1: The Nature of matter o Atoms- the basic unit of matter o Atomos (greek)

unable to be cut o Greek philosopher Democritus o The subatomic particles that make up at atoms are protons, neutrons, and electrons o Protons and electrons have the same mass o Protons = positive, neutrons= neutral, protons + neutrons= nucleus o Electron= negatively charged particles o Are attracted to the nucleus but stay outside because they are constantly moving o Element- pure substance that consists entirely of one type of atom o Isotopes- atoms of the same element that differ in the number of neutrons o Isotopes have the same number of electrons so they have the same chemical properties o Compound- substance formed by the chemical combination of two or more elements in definite proportions o Chemical bonds: o Ionic bond- formed when one or more electrons are transferred from one atom to another o Ions- positively and negatively charged atoms o Ions lose their atoms by giving it to another atom o Covalent bond- forms when electrons are shared between atoms o Molecule- the smallest unit of most compounds; structure that results when atoms are joined together by covalent bonds o Van der Waals Forces- intermolecular forces; when molecules are close together, a slight attraction can develop between the oppositely charged regions of attraction WHAT TO KNOW o Structure of an atom- protons + neutrons= nucleus; electrons revolving o Isotopes have the same chemical properties=> same number of electrons o Some isotopes are radioactive= their nuclei are unstable and break down at a constant rate over time o Covalent bond vs. ionic bond o Compound & relation to molecules (atoms make up molecules, molecules make up compounds) o SAME ATOM+ SAME ATOM= ELEMENT o DIFFERENT ATOM+ DIFFERENT ATOM (OR TYPES OF ATOM e.g. molecule)= COMPOUND o Van der Waals forces hold molecules together through the slight attraction developed between oppositely charged regions of attraction o Van der Waals forces vs. ionic bonds

o Ionic= stronger; both are intermolecular forces 2-2 Properties of Water: o Polarity- a water molecule is polar because there is an uneven distribution of electrons between the oxygen and hydrogen atoms o Cohesion- attraction between molecules of the same substance; negative attracts positive, positive attracts negative; molecules on the surface of water to be drawn inward thus creating beads on smooth surfaces o Adhesion- attraction between molecules of different substances; causes; graduated cylinder= adhesion between water molecules and glass molecules= CAPILLARY ACTION- one of the forces that draws water out of the roots of a plant and up into its stems and leaves o Adhesion + Cohesion = Meniscus in graduated cylinder o Mixture- material composed of two or more elements or compounds that are physically mixed together but not chemically combined o E.g. salt + pepper= mixture o Two types of mixture: Solutions- all the components are evenly distributed Solute- the substance that is dissolved Solvent- the substance in which the solute dissolves in (e.g.) water Water is the greatest solvent in the world Sugar (solute) + Water (solvent) = solution Suspensions- mixtures of water and nondissolved materials Oil + Water = suspension o pH scale- indicates the concentration of H+ ions in solution o Acid- any compound that forms H= ions in solution o Acidic solutions contain higher concentration of H+ ions than pure water and have pH values BELOW 7 o Base- compound that produces hydroxide ions (OH- ions) in solution o Basic, or alkaline, solutions contain lower concentration of H+ ions than pure water and have pH values ABOVE 7 o Buffers- weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH WHAT TO KNOW:

o o o o

Polarity due to water molecule structure Acid Vs. Basic in terms of H+ ions and OH- ions concentrations Difference between solution and suspension What pH measures

2-3 Carbon Compounds: o Carbon compounds can bond with many other elements and themselves o Macromolecules- formed by polymerization in which large compounds are built by joining smaller ones o Monomers- smaller units o Polymers- large compounds made of monomers o Monomers can be different or same (e.g. like beads in necklace or link in watch) o Four groups of organic compounds found in living things are carbohydrates, lipids, nucleic acids, and proteins o Carbohydrates- made up of carbon, hydrogen, and oxygen; Living things use carbohydrates as their main source of energy, Plants & some animals sometimes use for structural purposes; breakdown of sugar= carbohydrates or starches o Monosaccharide- single sugar molecules

o Polysaccharides- large macromolecules formed from monosaccharide

o Lipids- made from carbon and hydrogen atoms; used to store energy, make up important parts of biological membranes and waterproof coverings Tiglycerol (lipids)

o Nucleic acids- macromolecules containing hydrogen, oxygen, nitrogen, carbon, and phosphorous; polymers assembled from individual monomers known as nucleotides; store and transmit hereditary or genetic information

o Nucleotides- 5-carbon sugar, phosphate group, and a nitrogenous base o Two types: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) o Proteins- macromolecules that contain nitrogen, carbon, hydrogen, and oxygen; polymers of amino acids; amino acids- compounds with an amino group (-NH2) on one end with a carboxyl group (-COOH) on the other end o Some proteins control the rate of reactions and regulate cell processes. Some are used to form bones and muscles. Other transport substances into or out of cells to help fight disease. Monopeptide:

Dipeptide:

Polypeptide

WHAT TO KNOW: o The four groups of organic compounds: carbohydrates, lipids, nucleic acids, and proteins o The functions of the organic compounds

o The properties of carbon allowing carbon to form different macromolecules 2-4 Chemical Reactions and Enzymes: o Chemical reactions- process that changes or transforms one set of chemicals into another o Reactants- elements or compounds that enter into a chemical reaction o Products- elements or compounds produced by a chemical reaction o Chemical reactions always involve changes in the chemical bonds that join atoms in compounds o Energy is released or absorbed whenever there is chemical reactions (chemical bonds form or are broken) o Chemical reactions that release energy often occur spontaneously. Chemical reactions that absorb energy will not occur without a source of energy o Activation energy- energy that is needed to get a reaction started o Catalyst- substance that speeds up the rate of chemical reaction o Enzymes- proteins that act as biological catalysts; speed up chemical reactions that take place in cells by LOWERING ACTIVATION ENERGIES; lock and key! o Substrates- the reactants for enzyme catalyzed reactions o How do enzymes work? 1. Substrates (Glucose & ATP) bind to enzyme in an active site 2. Substrates converted into products 3. Products (Glucose-6-phsophate & ADP) are released o Enzymes are affected by changes in temperature (work best at 37 degrees C) o Enzymes play essential roles in regulating chemical pathways, making materials that cell need, releasing energy, and transferring information WHAT TO KNOW: o o o o What happens during chemical reactions to chemical bonds The roles of energy in chemical reaction Enzymes and their importance How enzymes work

Chapter 7: Cell Structure and Function 7-1 Life is Cellular: o Microscopes allowed Robert Hooke to discover cells o Cells- the basic unit of life o Cell theory: 1. All living things are composed of cells 2. Cells are the basic units of structure and function in living things 3. New cells are produced from existing cells o Different types of microscope: light microscope= proteins and viruses, transmission electron microscopes (TEM)- uses wavelengths= cell structures

& large protein molecules & thin samples of cells and tissues, scanning electron microscopes (SEM)- pencillike beam of electrons = scanned over the surface of specimen o Cells fall into two broad categories: o Eukaryotes- cells that contain nuclei; genetic material is separated from the rest of the cell in a nucleus; contain dozens of structures and internal membranes; highly specialized; plants, animals, fungi, and protists o Prokaryotes- cells that do not contain nuclei; genetic cells not in a nucleus; smaller; less complicated; they grow, reproduce, respond to the environment, and some even move by gliding along surfaces or swimming through liquids WHAT TO KNOW: o o o o o The statements that make the cell theory The difference between prokaryotic cells and eukaryotic cells The processes use to produce a TEM and a SEM Structures that all cell have The invention of the microscope and its benefits on the cell theory

7-2 Eukaryotic Cell Structure: o Organelles- little organs o Cells are similar to factories
Job in the Factory Cell Organelle Function of the organelle

Shipping/Receiving Department

Plasma membrane

Regulates what enters and leaves the cell; where cell makes contact with the external environment

Chief Executive Officer (CEO)

Nucleus

Controls all cell activity; determines what proteins will be made; contains nearly all the cells DNA and with it the coded instructions for making proteins and other important molecules

Factory floor

Cytoplasm

Contains the organelles; site of most cell activity

Assembly line (where workers do their work)

Endoplasmic Reticulum (ER)

The site where lipid components of the cell membrane are assembled, along with

proteins and other materials that are exported from the cell

Workers in the assembly line

Ribosomes

Build the proteins

Finishing/packaging department

Golgi apparatus

Modify, sort, and package proteins and other materials from the endoplasmic reticulum for storage in the cell or secretion outside the cell

Maintenance crew

Lysosomes

Responsible for breaking down and absorbing materials taken in by the cell

Support beams (walls, ceilings, floors)

Cytoskeleton

Network of protein filaments that helps the cell to maintain its shape and move

Power plant

Mitochondria/chloropl asts

Transforms one form of energy into another

Storage room

Vacuoles

Saclike structures that store materials such as water, salts, proteins, and carbohydrates

o Nuclear envelope-surrounds the nucleus; composed of two membranes; nuclear pores that allow materials in and out o Chromatin- consists of DNA bound to protein o Chromosomes- distinct, threadlike structures that contain genetic information o Nucleolus-where the assembly of ribosomes begin o ROUGH ER= PROTEINS; SMOOTH ER= LIPIDS o Mitochondria- organelles that convert the chemical energy stored in food into compounds that are more convenient for the cell to use o Chloroplasts (plant cells)- organelles that capture the energy from sunlight and convert it into chemical energy in a process called photosynthesis

WHAT TO KNOW: o Functions of the organelles o The role of the nucleus 7-3 Cell boundaries: o Cell membrane- thin flexible barrier surrounding the cell; regulates what enters and leaves the cell; provides protection and support o Lipid bilayer- double-layered sheet in the composition of nearly all cell membranes o Cell wall (plants)- strong supporting layer around the membrane; provide support and protection o Cell membrane regulates the movement of dissolved molecules from the liquid on one side of the membrane to the liquid on the other side o Concentration- the mass of solute in a given volume of solution o Diffusion- more concentrated particles move to an area with less concentrated particles until reaching equilibrium o Equilibrium- the concentration of the solute is the same throughout a system o If substance is unequal on either side of the cell membrane, its particles will move towards the area here it is less concentrated o Diffusion depends upon random particles movements=>substances diffuse across membranes without energy o Osmosis- the diffusion of water through a selectively permeable membrane o Isotonic- same strength o Hypertonic- above strength o Hypotonic- below strength o Facilitated diffusion- protein channels in membranes allow particular substances to cross different membranes; NO ENERGY NEEDED o Active Transport- diffusion against a concentration difference; USES ATP ENERGY; carried out by transport proteins or pumps found in the membrane o Endocytosis- the process of taking materials into the cell by means of pockets of the cell membrane;

o Phagocytosis- cell eating; extension of cytoplasm to surround a particle and package it within a food vacuole o Pinocytosis- tiny pockets form vacuoles within the cell

o Exocytosis- the membrane of the vacuole surrounding the material fuses with the cell membrane, forcing the contents out of the cell

WHAT TO KNOW: o The functions and structures of the cell membrane & cell wall o The process of diffusion & osmosis o Difference between phagocytosis & pinocytosis

7-4 The Diversity of Cellular Life o Unicellular Organisms- includes single celled organisms; MRS. GREN (movement, respiration, sensitivity, growth, reproduction, excretion, nutrition) o Multicellular Organisms- organisms that are made up of many cells o Cell specialization-cells throughout and organism that can develop in different ways to perform different tasks o E.g. Animal cells= red blood cells are specialized to transport oxygen; plant cells= guard cells regulate exchanges between leaves and the environment o The levels of organization in multicellular organisms are individual cells, tissues, organs, and organ systems o Tissues- group of similar cells that perform a particular function o Organs- many groups of tissues that work together o Organ system- a group of organs that work together to perform a specific function WHAT TO KNOW: o Multicellular organisms= cell specialization o Biological organizations in multicellular organisms o Unicellular vs. multicellular Chapter 8 Photosynthesis: 8-1 Energy and Life: o Plants and some other types of organisms are able to use light energy from the sun to produce food o Autotrophs- organisms that make their own food (e.g. plants) o Heterotrophs- organisms that obtain energy from the goods they consume o Adenosine triphosphate (ATP)- chemical compounds that cell use to store and release energy; like a fully charged battery o When cells have energy available: ADP + phosphate = ATP o Release energy = break the second and third phosphate o The characteristics of ATP make it exceptionally useful as the basic energy source of all cells o ATP: provides the energy that regulates the balance of ions on both side of the cell membrane; produces movement; synthesis of proteins, nucleic acids; Reponses to chemical signals (e.g. firefly lights) WHAT TO KNOW: o Ultimate source of energy for plants = SUN! o ATP and its role o Autotrophs vs. heterotrophs

8-2 Photosynthesis: An Overview o Photosynthesis- plants use the energy of sunlight to convert water and carbon dioxide into high- energy carbohydrates (sugar and starches) and oxygen o Van Helmont discovered the carbon in carbon dioxide is used to make sugars and other carbohydrates in photosynthesis o Joseph Priestly- found out that plants released oxygen o Jan Ingenhousz realized that light was necessary for plants to produce oxygen o The experiments performed by van Helmont, Priestly, and Ingenhousz led to work by other scientists who finally discovered that in the presence of lights, plants transform carbon dioxide and water into carbohydrates, and they also release oxygen Photosynthesis Equation:

o Photosynthesis uses the energy of the sunlight to convert water and carbon dioxide into high-energy sugars and oxygen o Photosynthesis also requires light and chlorophyll, a molecule in chloroplast o Pigments- light-absorbing molecules o Chlorophyll- plants principle pigment WHAT TO KNOW: o Scientists that contributed to the discovery of photosynthesis o The process of photosynthesis (reactants and products) o Why light & chlorophyll is necessary 8-3 The Reactions of Photosynthesis: o Inside a chloroplast: o Thylakoids- arranged in stacks known as granum (grana) o Photosystems- proteins in the thylakoid membrane organize chlorophyll and other pigments o Stroma- the region outside the thylakoid membrane; where the Calvin cycle takes place

o Cells use electron carriers to transport high-energy electrons from chlorophyll to other molecules o Nicotinamide adenine dinucleotide phosphate (NADP+)- accepts and holds 2 high-energy electrons along with a hydrogen ion. This converts the NADP+ into NADPH. The conversion is one way in which some of the energy of sunlight can be trapped in chemical form o Light-dependent reactions- produce oxygen gas and convert ADP and NADP+ into the energy carriers ATP and NADPH; not stable so cant store for long

o Calvin Cycle- plants use the energy that ATP and NADPH contain to build highenergy compounds that can be stored for a long time; The Calvin cycle uses ATP and NADPH from the light-dependent reactions to produce highenergy sugars o Water, temperature, and intensity of light can affect photosynthesis WHAT TO KNOW: o o o o Light-dependent reactions Reactions that make up the Calvin cycle How photosynthesis works Function of NADPH

Chapter 9 Cellular Respiration 9-1 Chemical Pathways: o Calorie- the amount of energy needed to raise the temperature of 1 gram of water 1 degree Celsius; gradually release the energy from glucose and other food compounds o Glycolysis- pathway that release small amounts of energy

o Cellular Respiration- the process that releases energy by breaking down glucose and other food molecules in the presence of oxygen

o Glycolysis is the process in which one molecule of glucose is broken in half, producing two molecules of pyruvic acid o At the pathways beginning, 2 molecules of ATP are used up (investment) when Glycolysis is complete, 4 ATP molecule has been produced (gain)= ENERGY IS NEEDED o Nicotinamide Adenin dinucleotide (NAD+)- electron carrier; helps pass energy from glucose to other pathways in a cell o Fermentation- releases energy from food molecules by producing ATP in the absence of oxygen; converts NADH to NAD+ thus allowing glycolyssis to continue a steady supply of ATP o Anaerobic- not in air o The two main types of fermentation are alcoholic fermentation and lactic acid fermentation o Alcoholic fermentation produces carbon dioxide and alcohol o Lactic Acid Fermentation is produced in your muscles during rapid exercise when the body cannot supply enough oxygen to the tissues; unicellular organisms produce lactic acid as a waste product WHAT TO KNOW: o o o o o The process of cellular respiration The products of Glycolysis Two main types of fermentation Calorie The function of NAD+ vs. NADP+

Chapter 10 Cell Growth and Division: 10-1 Cell Growth o The larger a cell becomes, the more demands the cell places on its DNA. In addition, the cell has more trouble moving enough nutrients and wastes across the cell membrane and the organelles cant support the cell

SURFACE AREA= length*width* number of sides= cm2 VOLUME= length*width*height= cm3 Ratio= surface area divided by volume Volume increases more rapidly than the surface area, causing the ratio of surface area to volume to decrease o Cell division- the process by which a cell divides into two new daughter cells o o o o WHAT TO KNOW: o Why cells divide 10-2 Cell Division: o In prokaryotes; cells must copy its genetic information, then separate the contents of the cell into two parts o Cell division occurs in two main stages in eukaryotes: a. Mitosis- the first stage, division of the cell nucleus b. Cytokinesis- the second stage, division of the cytoplasm o Chromosomes- made up of DNA; carries the cells coded genetic info and proteins; not visible except in cell division o Before cell division, each chromosome is replicated, each chromosomes than consist of two identical sister chromatids o Centromeres- located near the middle of the chromatids or near the ends; chromatids attack onto the centromere o Interphase- in-between period of growth o Cell cycle- series of events that cells go through as they grow and divide; during the cell cycle, a cell grows, prepares for division, and then divides to form two daughter cells, each of which then begins the cycle o Mitosis= prophase, metaphase, anaphase, and telophase o Prophase- first and longest phase of mitosis; chromosomes become visible; centrioles (tiny structures located n the cytoplasm) separate and take up positions on opposite sides of the nucleus; this helps to organize the spindle (fanlike microtubule structure that helps separate the chromosomes) o Metaphase- second phase & lasts only a few minutes; chromosomes line up across the center of the cell; microtubules connect the centromere of each chromosomes to the two poles of the spindle o Anaphase- third phase; centromeres join the sister chromatids split, allowing the sister chromatids to separate and become individual chromosomes; chromosomes continue to move until they separate into two groups near the pole of the spindle; ends when the chromosomes dont move o Telophase- fourth and final phase; chromosomes begin to disperse into a tangle of dense materials; nuclear envelope re-forms around each cluster of chromosomes; spindle breaks apart; nucleolus becomes visible; thus ending mitosis o Cytokinesis- in most cells, the cytoplasm is pinched into two nearly equal parts; occurs at the same time as telophase

WHAT TO KNOW: o o o o o Main events of the cell cycle The four phases of mitosis and the process What happens during interphase Chromosomes Cell division for prokaryotic cells

10-3 Regulating the Cell Cycle: o Cyclin- a protein that regulate the timing of the cell cycle in eukaryotic cells o Cancer- cancer cells do not respond to the signals that regulate the growth of most cells WHAT TO KNOW: o Chemical that regulates the cell cycle o What happens when cells do not respond to the signals that normally regulate their growth