Unit 1 Scientific Theory and Biomolecules
Laboratory Safety Skills • It is YOUR responsibility to protect yourself and other students by conducting yourself in a safe manner while in the laboratory. • It is also your responsibility to read the Flinn safety contract, sign it, and have it signed by a parent or guardian. • You will NOT be allowed to participate in labs until you return your signed safety contract AND pass the laboratory safety quiz.
General Guidelines of Laboratory Safety • Only perform experiments specifically assigned by your teacher. • Familiarize yourself with the investigation and all safety precautions before entering the lab. • Before beginning work, tie back hair, roll up loose sleeves, and put on any required personal protective equipment. • Always wear a lab apron and safety goggles. • No contact lenses allowed in the lab. • Know the location of all safety and emergency equipment used in the laboratory. • Immediately report any accident, incident, or hazard—no matter how trivial—to your teacher. • In case of fire, alert your teacher and leave the lab! • Do not have or consume food or drink in the lab. • Do not fool around in the lab. • Do not apply cosmetics in the lab. • Keep your work area neat and uncluttered. • Clean your work area at the conclusion of each lab period as directed by your teacher. • Wash your hands with soap and hot water after each lab period. Pg. 1024
Stages of Scientific Investigations • Collecting Observations • Observation is the basis of scientific research. • Observation is the act of noting or perceiving objects or events using the senses. • Asking Questions • Forming Hypotheses and Making Predictions • Hypothesis: an explanation that might be true—a statement that can be tested by additional observations or experimentation. • Prediction: the expected outcome of a test, assuming the hypothesis is correct. • Viewing Conclusions in Context
Stages of Scientific Investigations • Confirming Predictions • Experiment: a planned procedure to test a hypothesis. • Control group: a group in an experiment that receives not experimental treatment. • Independent Variable: the factor that is changed in an experiment. • Dependent Variable: the factor that is measured in an experiment. • Drawing Conclusions • Viewing Conclusions in Context
Scientific Explanations • Scientists build theories from questions, predictions, hypotheses, and the findings of their experiments. When related hypotheses consistently explain scientific events, a theory is formed. • Theory: a set of related hypotheses that have been tested and confirmed many times by many scientists. • Unites and explains a broad range of observations.
Atoms • Chemistry will help you learn about biology because organisms are chemical machines! • Atom: smallest unit of matter that cannot be broken down by chemical means. Made of: • Protons: positive, in nucleus • Neutrons: neutral, in nucleus • Electrons: negative, in electron cloud
Elements and Chemical Bonding • Atoms can join with other atoms to form stable substances. The force that joins atoms is a chemical bond. • Element: a pure substance made of only one type of atom • Differ in the number of protons in the nucleus • Compound: a substance made of the joined atoms of two or more different elements in known proportions • Represented by chemical formulas
Covalent Bonds • Covalent Bonds: form when two or more atoms share electrons to form a molecule • Molecule: A group of atoms held together by covalent bonds
Ionic Bonds • Sometimes atoms or molecules gain or lose electrons. • Ion: An atom/molecule that has gained or lost an electron • Ionic Bonds: a bond formed when ions of opposite charges are attracted • Found in table salt (Sodium Chloride, NaCl)
Hydrogen Bonds • Hydrogen Bonds: Bonds based on polarity of molecules which causes chemical attraction. • Bonds with an unequal distribution of electrical charge are called polar molecules. • Water molecules are polar and often form hydrogen bonds. • The different charges in each molecule makes the molecules attract each other.
Water in Living Things, Storage of Energy • 70% of your body is made up of water • Water absorbs heat slowly • Water retains energy well • Water absorbs heat more slowly and retains this energy longer than other substances, helping us maintain our body temperature. • Controlling body temperature is important part of homeostasis. • Homeostasis: the maintenance of a constant internal state in a changing environment.
Cohesion and Adhesion • Cohesion: an attraction between substances of the same kind. • Molecules of water are stuck together because of the hydrogen bonds between water molecules. • This is why water forms drops! • Adhesion: an attraction between different substances. • Water is attracted to other polar substances. • Capillary action is the process in which water molecules move upward through a narrow tube because the water sticks to the wall of the tube.
Polarity • The polarity of water enables many substances to dissolve in water. • Solution: a mixture in which one or more substances are evenly distributed in another substance. • Non-polar substances such as oil do not dissolve well. • Ionic compounds and polar molecules dissolve best in water, because they are charged like the water. • When ionic compounds are dissolved in water, the ions become surrounded by polar water molecules.
Acids and Bases • While the bonds in water molecules are strong, sometimes these bonds break, forming a hydrogen ion (H+) and a hydroxide ion (OH-). H2O H+ + OH- • Acids: compounds that form hydrogen ions when dissolved in water and have a pH below 7 • Bases: compounds that reduce the concentration of hydrogen ions in a solution and have a pH above 7 • pH: a value used to express the acidity or alkalinity of a solution, this is the pH scale:
Organic Compounds • Most non-water matter in your body is made of organic compounds • Organic compounds contain carbon atoms that are covalently bonded to other elements such as H (Hydrogen), O (Oxygen) and other C (Carbon) atoms • Biomolecules: organic compounds that are important in the structure and function of living organisms. There are 4 biomolecules you need to know for this class: • Carbohydrates, Lipids, Proteins, and Nucleic Acids
Dehydration Synthesis and Hydrolysis • Dehydration Synthesis: A chemical reaction that builds up molecules by losing water molecules. • Hydrolysis: The process of splitting a compound into fragments with the addition of water; a kind of reaction that is used to break down polymers into simpler units, e.g. starch into glucose. • So, Dehydration Synthesis LOSES water, while Hydrolysis ADDS water! Which process is represented by the image below?:
Carbohydrates • Organic compounds made of carbon, hydrogen and oxygen atoms in the proportion of 1:2:1 • Carbohydrates are basically made of carbon and water! • Carbohydrates are built from single sugars called monosaccharides • Polysaccharides are chains or three or more monosaccharides. • Polysaccharides are macromolecules
Lipids • Lipids are nonpolar molecules that are not soluble or are mostly insoluble in water • Made of fatty acids attached to a glycerol • Include fats, phospholipids, steroids, and waxes. • Important in cell membranes • Fats store energy
Proteins • A large molecule formed by linked smaller molecules called amino acids • Amino acids contain Nitrogen, an important element for life! • Amino acids are the building blocks of proteins. • 20 different amino acids are found in proteins • Some proteins are enzymes and promote chemical reactions
Nucleic Acids • All of your cells contain nucleic acids • DNA and RNA are two common nucleic acids • Nucleic acids are long chains of smaller molecules called nucleotides • A nucleotide as three parts: a sugar, a base, and a phosphate group
Energy and Chemical Reactions Ch. 2.4
ATP • ATP Stands for Adenosine triphosphate • A single nucleotide with two extra energy storing phosphate groups (so why is it called ATP?) • Cells need a steady supply of ATP to function http://biochemisms.com/tag/atp/
Energy for Life Processes • Energy is the ability to move or change matter. • Exists in many forms: light, heat, chemical, mechanical, electrical; can be converted to other forms. • Energy can be stored or released by chemical reactions. • Chemical reactions are summarized by chemical equations, written: Reactants Products NaCl Na+ + Cl-
Energy in Chemical Reactions • In a chemical reaction, energy is absorbed or released when chemical bonds are broken and new ones are formed. • Some chemical reactions release energy • Other chemical reactions absorb energy • Metabolism: all of the chemical reactions that occur within an organism. • Most of our energy comes from the food we eat and digest! • When we digest food, chemical reactions convert the chemical energy in food molecules into energy our cells can use.
Activation Energy • Activation energy: the energy needed to start a chemical reaction • Example: a big rock rolling down the hill—to make it roll, you must first push it. The activation energy is a “push” for chemical reactions! • Enzymes are substances (mostly proteins) that increase the speed of chemical reactions (catalysts)
Enzymes • Most biochemical reactions (reactions that occur in cells) require activation energy to begin. • Chemical reactions can occur quickly and at the low temperature of our body because of enzymes. • Enzymes: substances that increase the speed of chemical reactions. Most enzymes are proteins. • Enzymes help organisms maintain homeostasis.
Enzyme Specificity • Substrate: a substance on which an enzyme acts during a chemical reaction. • Enzymes act ONLY on specific substrates. • For example, amylase, an enzyme in your saliva, assists in the breakdown of starch to glucose in your food. • Enzymes often end with the letters “ase” so we can figure out that “amylase” is an enzyme even if we’ve never heard of it before! • An enzyme’s activity is determined by the shape of the enzyme.
Enzyme Specificity • Typically, an enzyme is a large protein with one or more deep folds on the surface. • Active sites: pockets in the folds on enzyme surfaces. • The substrate of the reaction fits into the active site. • An enzyme acts only on a specific substance because only that substrate fits into the active site.
Inhibition: Competitive and Non-Competitive Enzyme function can be inhibited (restrained or checked)in two main ways: • Competitive Inhibition: inhibitor that fills the active site of an enzyme and stops the normal substrate from binding (biology-online.org). • Non-Competitive Inhibition: Enzyme inhibition in which the inhibiting substance does not compete with the normal substrate for the active site on the enzyme but inhibits reaction by combining with the enzyme-substrate complex after the complex is formed (medical-dictionary.thefreedictionary.com)
Factors in Enzyme Activity • Enzymes operate most efficiently within a certain range of temperatures or in a certain pH. • Temperatures outside the normal range can break of strengthen some bonds between amino acidsinthe enzyme (usually made of protein), changing the shape. • If the shape is changed, the active site may also change and the substrate will be unable to bind. • pH also impacts enzyme activity. A pH that is too low (acidic) or too high (alkaline) can also break bonds between amino acids, changing the shape of the protein.
Digestion Ch. 39.2
Breaking Down Food • Before your body can use the nutrients in food you eat, the large food molecules must be broken down. • Digestion: the process of breaking down food into molecules the body can use.
Starting Digestion • Digestion of food begins in your mouth. • Teeth rip and chew food and mix food in with saliva. • Saliva contains amylases. • Amylases: enzymes that begin the breakdown of carbohydrates such as starch, into monosaccharides (single sugars). • Food then passes through the pharynx into the esophagus.
The Esophagus • Esophagus: a long tube that connects the mouth to the stomach. • No digestion takes place in the esophagus. • Food is moved through the esophagus through peristalsis. • Peristalsis: successive rhythmic waves of smooth muscle contractions in the esophagus that moves the food toward the stomach.
The Stomach • The stomach is a saclike organ that stores food temporarily and mechanically breaking down food and chemically breaking down proteins. • When food enters the stomach, it secretes gastric juice, a mixture of hydrochloric acid and pepsin. • Pepsin: a digestive enzyme that breaks protein strands into chains of amino acids.
The Small Intestine • Food passes into the small intestine is where carbohydrates are broken down into monosaccharides, proteins into amino acids, and lipids into fatty acids and glycerol. • Fats are digested by pancreatic enzymes called lipases, but are first treated with bile which emulsifies the fats (turns them into little drops). • Absorption of nutrients occurs in the small intestine through the lining of the small intestine on projections called villi.
The Large Intestine • Components of food that are not for energy production are considered wastes. • Wastes move into the large intestine, also called the Colon. No digestion takes place in the colon. • Most of colon’s contents are dead cells, mucus, digestive secretions, bacteria, and yeast. • Balancing water absorption is an important function of the colon.
The Liver’s Role in Digestion and Metabolism • The liver plays several roles in human digestion and metabolism even though food never enters the liver. • The Liver’s Role in Digestion • Secretes bile, which aids in the emulsification of fat and promotes the absorption of fatty acids and fat soluble vitamins A, D, E, and K. • The Liver’s Role in Metabolism • The liver stabilizes blood sugar by converting extra sugar to glycogen for storage. The liver then breaks down the glycogen when needed. • The liver also modifies amino acids. • Fat-soluble vitamins and iron are stored in the liver. • The liver monitors the production of cholesterol and detoxifies poisons. If the liver cannot make something non-toxic, it stores it.