Scientific Theory and Biomolecules

• 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.

• 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

• 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

• 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

• 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.

Ch. 2.1, 2.2

• 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

• 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: form when two or more atoms share electrons to form a molecule
• Molecule: A group of atoms held together by covalent 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: 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.

• 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: 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.

• 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.

• While the bonds in water molecules are strong, sometimes these bonds break, forming a hydrogen ion (H + ) and a hydroxide ion (OH -
).
H
2
O  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:

Ch. 2.3

• 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: 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?:

• 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 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

•
– Amino acids contain Nitrogen, an important element for life!
•
•
•

• 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

Ch. 2.4

• ATP Stands for Adenosine triphosphate
• A single nucleotide with two extra energy storing phosphate groups (so why is it called A
T
P?)
• Cells need a steady supply of ATP to function http://biochemisms.com/tag/atp/

• 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 -

• 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: 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)

• 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.

• 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.

• 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.

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)

• 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 acidsin the 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.

Ch. 39.2

• 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.

• 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.

• 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 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.

• 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.

• 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 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 nontoxic, it stores it.