Biology 101- Exam #1

• The Scientific Method:

1. IDEAS give rise to…2. HYPOTHESES formulate…3. PREDICTIONS are tested by…4. DEDUCTIVE LOGIC allows one to set up…5. EXPERIMENTAL DESIGN gives rise to…6. EXPERIMENTAL RESULTS allow for…7. STRONG INFERENCES are the basis of…8. THEORIES (allows for new ideas; AKA “Crisis Stage”)

• Paradigm: accepted theories that are based on fate.

• Placebo: a control used in an experiment that involves no treatment, but rather the use of measured deception.

• The most basic tool that a scientist can use is the school of thought.

• Deductive Reasoning: applies general principles to predict specific results. Used extensively in math and philosophy. (Ex: Eratosthenes’ estimation of the Earth’s circumference).

• Inductive Reasoning: the use of specific observations to construct general scientific principles. Used extensively in and is the definition of science. (Ex: Sir Isaac Newton and gravity).

• Experiment: the means of testing a hypothesis.

• Variables: factors that influence the processes of an experiment.

• Test Experiment: one variable is altered in a known way to test a particular hypothesis. All variables except the one being tested are kept constant.

• Control Experiment: all known variables are left unchanged.

• 7 Characteristics of ALL Organisms:

1. Hierarchical Organization2. Atoms-Molecules-Organelles-Cells-Tissues-Organs-Organism3. Sensitivity/Responds to Stimuli4. Growth, Development and Reproduction5. Regulation6. Homeostasis (maintain constant internal conditions)7. Evolutionary Adaptation

• Theory: 1. Explanation of a natural phenomenon based on general principles to unify concepts. 2. Body of interconnected concepts supported by experimental evidence that explains facts in some areas of study.

• Theory to a scientist indicates certainty; and theory to the public implies a guess or a lack of knowledge.

• Basic Research extends the boundaries of scientific knowledge.

• Applied Research is directed specifically toward the scientific community.

• Fundamental Properties of Life:

1. Cellular Organization2. Sensitivity3. Growth

- Metabolism: assimilation of energy that results in growth.- Creation of Carbon-Carbon covalent bonds.

4. Development5. Reproduction

- Pass traits from one generation to the next.- All living organisms ultimately die.

6. Regulation7. Homeostasis (everything stays the same).

• Potential Characteristics of Life:

1. Movement (not descriptive of only life).2. Sensitivity (some life is not apparently responsive).3. Death (meaningless concept).4. Complexity (describes nonlife also).

• ALL living organisms are chemical machines composed of molecules that continually undergo chemical reactions to become new molecules.

• Atoms: 1. Everything in the universe is composed of matter and ALL matter is made up of atoms. 2. Atoms are very difficult to study due to their extremely small size.

• Protons (positive +) and Neutrons (neutral +/-) have the same mass, but ONLY Protons have an electrical charge within the nucleus of an atom. Therefore, the net charge of the nucleus of an atom is positive.

• Structure of an Atom:

1. Composed of smaller subatomic particles.2. Protons: subatomic positively charged particles located within the nucleus.3. Neutrons: subatomic neutrally charged particles located within the nucleus.4. Electrons: subatomic negatively charged particles that travel in orbits around the

nucleus and equal the same number as the number of protons to balance the charge of an atom. Electrons dictate chemical activities of an atom. Electrons in the outer ring contain more energy.

• Atomic Number: equal to the number of protons that an element contains in its nucleus.

• Atomic Mass:

1. The mass of protons and mass of neutrons added together. 2. Mass is the amount of a substance.3. Weight is the force of gravity exerted on an object.4. Atomic mass is measured in Daltons.5. Protons and neutrons are roughly one Dalton each, but electrons are only 1/1840 of

a Dalton, which is essentially mass-less.

• Half-Life: the amount of time it takes for half of a substances atoms to decay. This is how radioactive decay is measured.

• ALL atoms of an element have the same atomic number (number of protons).

• Isotopes: “forms” of an element as it occurs in nature differing only in weight due to differing numbers of neutrons.

• Isotopes of an element can have the same number of protons, but differing numbers of neutrons.

• Unstable forms of isotopes can emit types of radioactive energy which has the potential to create harmful side effects, so exposure must be limited without proper protection.

• Ion: ANY charged atom in which the total number of electrons is NOT equal to the total number of protons.

• Anion: a negatively charged ion created when an electron is gained.

• Cation: a positively charged ion created when an electron is lost.

• Ionic Bonds: the loss or gain of electrons to cause a positive ion (cation) and a negative ion (anion) to attract each other and bond together.

• Covalent Bonds: sharing of one or more pairs of electrons so that a pair of electrons is shared for each covalent bond.

1. C—C is two carbons sharing one pair of electrons due to a single covalent bond.2. C=C is two carbons sharing two pairs of electrons due to a double covalent bond.

• Covalent bonds are very stable, but they require atoms to be in very close proximity to each other. A triple covalent bond is the strongest and atoms are able to share electrons with each other.

• Macronutrients: 99% of the most common elements that compose all life forms.

• Micronutrients: the remaining 1% of trace elements found in life forms which are specific to each species.

• Macronutrients Found in Life Forms ( CHNOPS ):

1. CARBON2. HYDROGEN3. NITROGEN4. OXYGEN5. PHOSPHORUS6. SULFUR

• Any substance or organism that contains carbon is considered organic.

• Radioisotopes: an atom with an unstable nucleus with differing numbers of neutrons.

• Radioactive Decay: occurs in certain radioisotopes that contain so many neutrons that they become “too heavy” and throw out subatomic particles from inside the nucleus. This is not normal because chemical reactions involve electrons being shared or exchanged.

• Three Main Types of Chemical Reactions:

1. Combination: A+B AB (Ex. Salt Lattice)2. Dissociation: AB A+B (Ex. Salt Ionization)3. Exchange: AB+CD AC+BD (Ex. Neutralization of acid by use of a base)

NaOH (lye) + HCl (hydrochloric acid) H2O (water) + NaCl (sodium chloride)

• Oxidation: loss of electrons to cause a positive charge.

• Reduction: gain of electrons to cause a negative charge.

• Chemical Reaction: the formation and breaking of chemical bonds within an atom.

• Moving electrons away from the nucleus requires energy. Therefore the electron has more potential energy.

• Moving electrons toward the nucleus releases energy. Therefore the electron has less potential energy.

• Octet Rule: (rule of 8) states that atoms want their outer valence shell full of electrons. K Ring= 2; L Ring= 8; M Ring= 8; N Ring=10.

• Reactant: the original, pre-reaction molecule.

• Product: molecules resulting from the chemical reaction.

• Inert: a molecule that has its outer ring/shell completely filled with electrons.

• Molecule: a stable group of atoms.

• To make sodium chloride (table salt), a sodium atom loses an electron to become Na+ and the Chlorine atom accepts the electron to become Cl-. The product is Na+Cl-.

• Sodium Chloride dissociates into ions when placed in water. (Ex. A 0.9% of Na+Cl- in a liter of IV fluid).

• pH Scale: quantifies the H+ (hydrogen) concentration of a substance. The scale goes from 0 (acidic) to 14 (basic/alkaline).

• A pH of 7 indicates neutrality of the H+ (hydrogen) and OH- (hydroxide) ions in a substance.

• The more H+ ions a substance contains, the more acidic it is. Therefore it has a lower pH on the scale. (< 7).

• The less H+ ions a substance contains, the more base/alkaline it is. Therefore it has a higher pH on the scale. (>7).

• Buffers: the pH of most body fluids is 7, so buffers minimize the changes in H+ and OH- by acting as reservoirs for H+ ions by donating extra H+ to solutions when concentration falls and taking excess H+ away from solutions when the concentration increases (Ex: Carbonic Acid/Bicarbonate in blood).

• Stomach buffers such as sodium bicarbonate and buffers within blood are used to help regulate drastic changes of the pH in the human body.

• Acids: chemicals which donate the hydrogen ion H+ and increase its concentration in a solution.

• Bases: chemicals which accept the hydrogen ion H+ and therefore decrease its concentration in a solution. This is usually called the Hydroxyl Ion.

• Strong Acids: acids which dissociate 100% completely all at one time. (HClH+Cl- ; 100% dissociation occurs all at once).

• Weak Acids: acids which dissociate a little at a time and therefore have a reservoir to draw upon when needed. (HAcH+Ac- acetic acid; only 3% of the HAc dissociates at a time).

• Strong Bases: bases which dissociate 100% completely all at one time.

• Weak Bases: bases which dissociate a little at a time and therefore have a reservoir to draw upon when needed.

• Solution: a mixture comprised of a solvent and solute.

• Solvent: a liquid (usually water) which dissolves the solute.

• Solute: a substance (usually a salt) which is dissolved in a solvent.

• Neutralization: a chemical reaction which occurs between a strong acid and strong base. This always produces water and a salt precipitate. This is an example of an exchange chemical reaction.

• Periodic Table of Elements:

1. 92 naturally occurring elements2. Eight groups of repeating chemical properties

3. Based on the interactions of valence shell electrons4. Maximum of 8 electrons in outer shell of elements important to life

• Properties of Water Due to Hydrogen Bonds:

1. Water is POLAR in nature and is bent at an angle of 104.5°, therefore H20 is charged with a positive hydrophilic end (polar) and a negative hydrophobic end (nonpolar).

2. Water is the densest at 4°C, NOT at freezing. Ice at 0°C (32°F) floats in water at 4°C (37°F) because ice expands and is lighter.

3. Cohesion: polar water sticks to itself and other polar water molecules.4. Adhesion: polar water adheres to other polar (hydrophilic) molecules, but NOT to

nonpolar (hydrophobic) molecules.5. Water has a high surface tension due to cohesion of the molecules.6. Capillary Action: this is due to both cohesion and adhesion. This allows fluid to

move from roots to leaves or up a straw.7. Water is an excellent universal solvent.8. Water causes imbibitions of wood (causes it to swell and warp).9. Water has a higher specific heat, therefore it has a higher heat capacity. It takes a

lot of calories (amount of heat it takes to heat 1gm of water 1°C) to cause a temperature change in water.

10. Water is comprised as a lattice structure with each H20 molecule bonded to four other H20 molecules to form a tetrahedral lattice.

11. Water has a higher heat of vaporization, therefore it has a higher boiling point (higher temperature for a change from a liquid to steam vapor). This means that many chemical reactions can occur before water changes to a vapor.

12. Water has a higher heat of fusion which means a higher melting point. This means a higher temperature for a change of ice to a liquid (melting) or from liquid water to ice (fusion).

• Four Properties of Water are Affected by Dissolved Solutes:

1. Freezing Point: lowered by dissolved solutes.2. Boiling Point: raised by dissolved solutes.3. Vapor Pressure: increased by dissolved solutes.4. Osmotic Pressure: increased by dissolved solutes which is important for cells.

• Organic Molecules are formed by adding functional groups onto carbon chains, branches or rings.

• Five Main Types of Organic Molecules:

1. Hydrocarbons2. Carbohydrates3. Lipids (fats)4. Proteins5. Nucleic Acids

• Hydrocarbons:

1. The only organic molecule NOT unique to life.2. Only formed with Hydrogen and Carbon.3. The more reduced it is the more Carbon it contains.4. Contains a methyl group (CH3)5. May have double or triple bonds.6. Used primarily as an energy source.7. Also used to make plastics8. CH4=METHANE; C2H6=ETHANE; C3H8=PROPANE; C4H10=BUTANE

• Carbohydrates:

1. Saccharides=Sugars2. Carbon, Hydrogen and Oxygen as (CH2O) n.3. If the “n” is 3-7 it is a Monosaccharide4. Two monosaccharide’s= one Disaccharide5. Many monosaccharide’s= one Polysaccharide6. Polysaccharide’s can be used for energy (starch in plants and glycogen in the

animal liver) or structure (cellulose in plant cell walls and chitin in insects etc.)7. Alpha Linkage (storage) OH (Hydroxyl) group pointing Up8. Beta Linkage (structure) OH (Hydroxyl) group pointing Down9. The ring structure of a carbohydrate has one less Carbon

10. COH= an Aldehyde; COOH=a Carboxyl11. Anything –ose= a sugar12. Dehydration Synthesis/Condensation: water leaving to form a bond.13. Hydrolysis: adding water to break a bond.14. Aldehyde’s and ketones are involved in joining two monosaccharide’s together

to form a disaccharide bond.15. Reducing disaccharide: bond involves only one aldehyde or ketone of the two

monosaccharides.16. Non-Reducing Disaccharide: bond involves both aldehydes or ketones of the

two monosaccharide’s.17. Disaccharide bonds are formed by dehydration synthesis/condensation and

broken by hydrolysis.18. Monosaccharide’s either have a terminal aldehyde (glucose) or an internal

ketone (fructose).

• Lipids (fats):

1. One Glycerol + Three fatty acids = One Neutral Fat2. Since One glycerol contains three hydroxyl (OH) groups and each fatty acid

contains one carboxyl (COOH) group, three water molecules leave by condensation when each single OH (hydroxyl) of the fatty acid COOH (carboxyl) hooks up with one of the three H (hydrogen) ends of the OH (hydroxyl) groups of the glycerol to form one ester bond.

3. Ester bonds are broken by three water molecules being added by hydrolysis.4. The fatty acid part of the fat can either be saturated (carbons joined by SINGLE

bonds) or unsaturated (carbons joined by double or triple bonds).5. Several double or triple carbon bonds= polyunsaturated fats.6. Neutral fats are NON-polar.7. Fats can be made polar by replacing one of the fatty acids with a phosphate group

(PO4-3). Therefore One glycerol + 2 fatty acids + 1 phosphate= 1 phospholipid.8. Lipids (fats) can be used either for energy storage (oils, fats and adipocytes) or for

structure (waxes, steroid hormones, cholesterol and phospholipids in cell membranes).

• Proteins:

1. Proteins are the most common organic molecule and includes ALL enzymes.2. Proteins are made up of amino acids.3. There are 20 amino acids that make up proteins, these are classified by their R

group.4. Each amino acid contains a carboxyl (COOH) group which acts as a weak acid and

an amino (NH2) group which acts as a weak base.5. One water molecule leaves by condensation when the OH (hydroxyl) of the COOH

(carboxyl) group hooks up with the H of the NH2 (amino) group to form one polypeptide bond.

6. Peptide bonds are broken by the addition of water via hydrolysis.7. Proteins are also called polypeptide chains.8. Proteins are used mainly for structure.9. Proteins can be separated by chromatography or electrophoresis.

• Four Levels of Protein Organization:

1° Primary Structure : sequence of amino acids.

2° Secondary Structure : folding of polypeptide chains due to interactions of hydrogen bonds between adjacent amino acids; this produces an alpha-helix, beta-sheet or a cable called motifs.

3° Tertiary Structure : complex structure (globular) which results from further folding of the secondary structure due to spontaneous attractions/repulsions between the different negative/positive R groups.

4° Quaternary Structure : involves the interaction of two or more polypeptide chains with each other. (the two alpha and two beta chains of the oxygen carrying hemoglobin protein of blood, which produces the famous red cross symbol)

*Proteins denature in the reverse order (quaternary, tertiary, secondary & primary)*

• Denaturation and Renaturation of Proteins:

1. Denaturation: drastic changes in temperature and/or pH will cause a protein to unravel.

2. Renaturation: under certain conditions a denatured protein might be able to reform. This is why when you are sick you must break a fever ASAP.

• Attached to some proteins are non-protein substances called prosthetic groups (like the iron molecule in the middle of hemoglobin. Proteins with prosthetic groups are called conjugated proteins.

*** Nucleic Acids (DNA and RNA (Essay Question on Exam #1 ***

• Nucleic Acids :

- Makes up deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) which comprise genes.

- 1 five Carbon sugar+1 nitrogenous base+1 phosphate group = 1 nucleotide- Many nucleotides = DNA or RNA Helix.- Antiparallel Strains 3’ 5’ and 5’ 3’

• Deoxyribonucleic Acid (DNA): T-A and C-G

1. Five Carbon Sugar (Deoxyribose).2. Nitrogenous Bases: Thymine, Adenine, Cytosine and Guanine.3. Thymine always pairs with Adenine and Cytosine pairs with Guanine.4. Deoxyribose and Phosphate backbone.5. Double-Stranded Helix.

• Ribonucleic Acid (RNA): U-A and C-G

1. Five Carbon Sugar (Ribose)2. Nitrogenous Bases: Uracil, Adenine, Cytosine and Guanine.3. Uracil always pairs with Adenine and Cytosine pairs with Guanine.4. Ribose and Phosphate backbone.5. Single-Stranded Helix.

• ATP: Adenosine Triphosphate: used as a coenzyme in cells and if known as the molecular unit of currency of intracellular energy transfer.

• Main Differences in DNA and RNA :

1. The sugar in DNA (Deoxyribose) is LESS reactive due to C-H bonds.2. The sugar in RNA (Ribose) is MORE reactive due to C-OH (hydroxyl) bonds.3. Thymine is only found in DNA and Uracil is only found in RNA.4. Adenine, Cytosine and Guanine and found in both DNA and RNA.5. DNA is comprised of a DOUBLE Helix and RNA is a SINGLE Helix.