1Biology 181 Chapter One The Science of Biology Biology- Study/Science of life & life processes Properties of Living

g Things 1) Made of 1 or more cells 2) Reproduce, grow, develop 3) Assimilate energy & materials 4) Maintain homeostasis- constant internal conditions (pH, Salt, Temp) 5) Organization- molecule > organism *Side note: Entropy- The tendency to become disordered 6) Responds to stimuli 7) Evolve (individual organisms DO NOT evolve, populations evolve) Science- A way of studying the world through observation & experiments Scientific Method (Scientists think deductively & inductively) a. Deductive reasoning- logic that flows from the general to the specific b. Inductive Reasoning- logic that flows from the specific to the general 1) Make observations of some phenomenon 2) Make a hypothesis to explain the observations 3) Do experiments to test hypothesis a. Testing H - Null hypothesis (to rule out the hypothesis) b. Testing HA Alternate Hypothesis i. A successful experiment is one in which one or more of the alternative hypotheses is demonstrated to be inconsistent with the results & is thus rejected. c. Controls i. Used as a comparison to rule out H ii. & Account for other variables iii. Usually try to test 1 variable at a time 4) Evaluate the hypothesis in light of the experimental results 5) Do more experiments w/ new information & create new hypothesis *Side note: Anecdotal Evidence- hearsay medical evidence (my aunt used X & it fixed Y) Chapter two Chemistry Definitions: Matter - has mass, occupies space Atoms - the smallest particle of pure matter that still contains the chemical properties of that particular matter Has: protons nucleus, +1 charge, weigh 1 amu Neutrons nucleus, 0 charge, weigh 1 amu
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Electrons orbitals, -1 charge, weigh 1/1800th amu - The closer an electrons orbit to the nucleus, the lower its energy level Element - a pure form of matter made up of only one type of atom Molecule 2 or more atoms, chemically combined Compound substance, a pure form of matter made of molecules containing 2 or more different types of atoms combined in definite proportions & structure Ions charged atoms or molecules. Atoms in which the number of electrons does not equal the number of protons. Isotope 2 or more atoms of the same element w/ different # of neutrons (carbon dating) Atomic # - the number of protons in a given atom/or element Carbon Example: 12= total # in Nucleus of protons & neutrons 12 C Extra Neutrons Increase the number in the nucleus 13 C isotopes 14 C

Electronegitivity relative attraction for electrons of a particular atom or element Charges Always Neutralize. Energy Level The distance away from the nucleus. Orbital rings. When an electron absorbs energy, it moves to high energy levels, farther from the nucleus. When an electron releases energy, it falls to lower energy levels, closer to the nucleus. Oxidation the loss of an electron *see sodium Reduction the gain of an electron

Bonds & Interactions

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1.Ionic Compounds (bonds) substance made of oppositely charged ions. (Stuff

on opposite sides of periodic table-Valence Electrons) Strongest bond, form crystals

2.Covalent Bonds shared pairs of electrons (not as strong as ionic)

These are shared electrons between H & O

The amount of bonds created equals the amount of electrons needed to become a whole atom (carbon 4, Hydrogen1, oxygen 2)
3.Hydrogen Bonds intermolecular attractions between polar molecules (not as

strong as covalent) Because the hydrogen & oxygen atoms of water share electrons unequally, a partial charge separation occurs. Each water atom acquires a positive & negative pole & is said to be polar. Polar opposite ends are different (like batteries)
4. Hydrophobic Interactions (Exclusion) water forces NON-

polar molecules together (for example water & oil. Water forces oil together & oil floats to the top because it is less dense.) Hydrophilic groups like water (polar) Hydrophobic groups dont like water (nonpolar) Because the opposite particle charges of polar molecules attract one another, water tends to cling to itself & to other polar molecules while excluding nonpolar molecules. Special Properties of Water H2O 1) Polar that leads to the rest of the properties 2) Forms h-bonds w/ itself & other polar molecules 3) Forces non polar groups/molecules together 4) Dissolves polar & ionic substances well, it is a good solvent 5) Has a high specific heat heat capacity a. Heat is a quantity, temp is a property Hydrogen bonds will form & break but you need to heat it up
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to get groups moving (bubbling, boiling water is the bonds forming & breaking)

6) Has a high heat of vaporization you need to get it really hot to vaporize 6) Ice Floats (ice also insulates & is less dense thats why it floats) 7) Can act as an acid & base a.Acid any substance that increases the concentration of Hydrogen Ion solution b.Base Any substance that reduces the concentration of hydrogen Ion Solution c.pH = --log[h+] - Log [10 -2] - [-2] 0---------------------7---------------------14 pH=2 Acid Neutral base Difference between pH3 & pH5 is: 10 3 - 10 5= 102= 100 times greater acid 8)Water Ionizes Because its covalent bonds occasionally break, water contains a low concentration of hydrogen (h+) & hydroxide (OH-) ions, the fragments of broken water molecules. Chapter 3 Basic Organic Chemistry Biological Molecules Chemical compounds that contain carbon Hydrocarbons nonpolar Biological Molecules consisting only of carbon & hydrogen, Example: Propane gas:

Functional Groups Act as units during chemical reactions & give specific chemical properties to the molecules that possess them

These groups tend to act as units during chemical reactions & confer specific chemical properties on the molecules that possess them. Amino groups, for example, make a molecule more basic, while carboxyl groups make a molecule more acidic.

 NON-POLAR Macromolecules Large, complex assemblies made of several functional groups. These are grouped into 4 major categories: Carbohydrates (Polymers), Lipids (Monomers), Proteins (Polymers), & Nucleic Acids (Polymers) Polymers - a long molecule built by linking together a large number of small, similar chemical subunits. (Joined by dehydration reactions) Monomers Subunits of Polymers Carbohydrates Store energy & provide building materials, Monosaccharides Simple Sugars, the simplest of the carbohydrates.

Disaccharides Two monosaccharides joined by a covalent bond. Sucrose= Glucose + Fructose 1,5 linkage by Dehydration Synthesis

Lactose= Galactose + Glucose 1,4 Linkage by Dehydration Synthesis

Maltose= Glucose + Glucose 1,4 linkage by Dehydration Synthesis Polysaccharides Macromolecules made up of monosaccharide subunits. Transport & Storage Carbohydrates A. Starches - Long chains of glucose connected by 1,4 linkages used for energy/sugar storage in plants. Some chains are branched. 100s1000s of monomers glucose polymers found in plants B. Glycogen - Long branched chains of glucose connected by a 1,4 linkages used as energy/sugar storage in animals serves as the animal version of starch. Structural Carbohydrates A. Cellulose (in plants) - Long chains of glucose connected by 1,4 linkages used to build cell walls in plants
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B. Chitin (in arthropods) Long chains of modified glucose connected by

1,4 linkages used to make cells of insects & crustaceans. resist digestion because most organisms lack the necessary enzymes. Lipids make membranes & store energy Phospholipids Form membranes, a composite molecule made up of glycerol, fatty acids, & a phosphate group. It contains a polar head & two nonpolar tails, forming the core of all biological membranes. Modified Triglyceride H OOOOOOO } Water Layer | O /////// H C O C /\/\/\/\/\ \\\\\\\ Oil Layer AKA | O /////// Phospholipid H C O -- C /\/\/\/\/\ /////// Bilayer O | \\\\\\\ OPOCH OOOOOOO } Water Layer O | H Phospholipid Triglyceride a fat consisting of a glycerol molecule & 3 fatty acids. Because Triglyceride molecules lack a polar end, they are not soluble in water. a. The Difference between Fats & Oils i. Longer chains of fatty acids are found in fats. The longer the fatty acid chain, the more interactions there are holding them together, so it takes more heat to melt them. ii. Unsaturated fatty acids are found in oils H H | O | O H C OH || H C O C /\/\/\/\/\ | HO C /\/\/\/\/\ | O H C OH Becomes H C O C /\/\/\/\/\ | | O H C OH C O C H C O C /\/\/\/\/\ H | H Glycerol + Fatty Acid = Triglyceride H H H H \C/ = Unsaturated Fat \C/ \C=C\ = Saturated Fat Other kinds of lipids include terpenes, steroids, & prostaglandins

b. Steroids the difference between steroids can be as little as 1 or 2 atoms

Dehydration Synthesis - for every subunit that is added to a macromolecule, one water molecule is removed. Hydrolysis The opposite of Dehydration Synthesis, a water molecule is added instead of removed. In this process, a hydrogen atom is attached to one subunit & a hydroxyl group to the other, breaking a specific covalent bond in the macromolecule. Proteins Perform the chemistry of the cell Functions: 1) Enzyme Catalysis 2) Defense 3) Transport 4) Support 5) Motion 6) Regulation 7) Storage Made of Amino Acids Proteins are polymers of Amino Acids. Each amino acid has unique chemical properties determined by the nature of the side group (indicated by R) covalently bonded to the central carbon atom. The 20 common amino acids are Amino Acids are grouped into five chemical classes, based on their side groups: Nonpolar amino acids, Polar uncharged amino acids, Charged amino acids, Aromatic amino acids, Special-Function amino acids Peptide Bond A covalent bond that links to amino acids. The Amino (NH3+) & Carboxyl (COO--) groups on a pair of amino acids can undergo a condensation reaction, losing a molecule of water & forming a covalent bond.

A peptide bond forms when the NH2 end of one amino acid joins to the COOH end of another. Because of the partial double-bond nature of peptide bonds, the resulting peptide chain cannot rotate freely around these bonds.

Dipeptide for one, polypeptide for a chain

Protein Structure The shape of a protein determines the proteins function. Proteins consist of long amino acid chains folded into complex shapes. All the internal amino acids are nonpolar Levels of Protein Structure 1) Primary The specific amino acid sequence 2) Secondary The folding of the amino acid chain by hydrogen bonding into the coiled alpha ( ) helix & beta ( ) pleated sheet. (Coils & sheets) Local areas of order within a single polypeptide chain. a) Motifs Super secondary structure Other characteristic folding such as the motif, & the turn motif that many proteins use to bind the DNA double helix. (Folds & creases) Structural themes among similar proteins of function 3) Tertiary The final folded shape of a globular protein (single polypeptide chain), which positions the various motifs & folds nonpolar side groups into the interior. (Three dimensional shape) a. Domains Proteins that are encoded within genes that are typically 100 to 200 amino acids long, that fold into a structurally independent functional unit, defines function 4) Quaternary A proteins subunit arrangement. When 2 or more polypeptide chains associate to form a functional protein, the individual chains are referred to as subunits of the protein. Denaturation Occurs when a protein changes shapes, or unfolds, & can be caused by a change in environmental pH, temperature, or ionic concentration, renders a protein biologically inactive
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Nucleic Acids long polymers of repeating subunits (nucleotides) connected by phosphodiester bonds 1) DNA Stores Genetic Material (Double-stranded helix- 2 anti-parallel complementary strands held together by hydrogen bonds between bases on opposite strands.) a. Uses Ribose that is De-oxidized (deoxyribose) b. Uses A, C, G, T (Adenosine, Cytosine, Guanosine, & Thymine) c. A & T Form 2 hydrogen Bonds d. G & C Form 3 hydrogen Bonds e. PSPSPSPS A G C T T C G A SPSPSPSP 2) RNA To assist in utilizing (decoding) genetic info a. mRNA Messenger RNA, copy of DNA genetic info b. rRNA (Ribosomal) part of the machinery for making proteins c. tRNA Transfer RNA, brings amino acids to ribosomes for protein synthesis d. Catalytic RNA Newly discovered Ribozome i. RNA uses A, C, G, U (Adenosine, Cytosine, Guanosine, & Uracil) Purines Adenine & Guanine Pyrimidines Cytosine, Thymine/Uracil Chapter Five Cell Theory Cell Theory: 1) All living things are made of 1 or more cells 2) The Cells is the basic Unit of Life 3) New Cells can only come from existing cells Why are cells so small? 1) Structural Ridgidity 2) Surface area to volume ratio, want high surface area compared to volume 3) Basically the smaller they are, the more efficient Two Basic Categories of Cells Prokaryotic Cell Prokaryotes Bacteria, Archae Bacteria
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Eukaryotic Cell Eukaryotes Plants, Animals, Fungi, Protists

No Nucleus No Membrane Bound Organelles Organelles Have Circular Chromosomes Smaller (1-10 Micrometers)

Have Nucleus Many Membrane Bound Have Linear Chromosomes Larger (10-100 micrometers)

Generic Prokaryote Capsule Jell like coating, Helps Stick to surfaces Plasma Membrane Phospholipid Bilayer, keep inside in/outside out

Cell Wall Cellulose/Chitin/peptide glycan, Protect cell & give it structure Flagella Made of proteins, helps cell move or bring water to it Cytoplasm Jell like goo that organelles float in Ribosomes Complexes of rRNA & rProteins (2 subunits), site of protein synthesis Circular Chromosome DNA, 5 million base pairs Generic Eukaryotic Nucleus double membrane bound organelle Membrane has small pores called nuclear pores Double membrane & pores make up Nuclear Envelope Where chromosomes are kept Chromosomes are linear & have lots of protein on the DNA, Protein Coated

Cytoskeleton Protein scaffolding inside the cell Non-Membrane Bound Made of 3 types of fibers: 1) Actin Filaments (contractile motion) 2) Intermediate Filaments (primarily structural) 3) Microtubule (Transport & movement within the cell & some motionFlagella/Cilia) Lysosomes Single membrane bound bags of digestive enzymes Low pH Acid, used to break down food & old organelles Endoplasmic Reticulum Membrane bound channels (network of channels) throughout the cytoplasm Smooth ER Site of Lipid Synthesis Rough ER Site of protein synthesis (modify & package protein to move throughout the cell) Ribosomes stick to it

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Golgi Apparatus Single membrane sacs used for modification & shipping of proteins for export from the cell Flagella & Cilia hair like structures that help move the cell or move water to the cell Made of proteins (microtubules) Ribosomes Site of protein synthesis Non-Membrane Bound Made of rRNA & Proteins Micorbodies Single membrane bound vesicles used to hold certain enzymes & processes Centrioles Non-membrane bound bundles of microtubules used to organize other microtubules as in cell division They have DNA, not found in plant cells Mitochondria Double membrane bound organelles Site of cellular respiration Have circular DNA Chromosome PLANTS Chloroplasts Double membrane bound organelles Site of photosynthesis Have circular DNA chromosome Central Vacuole Single membrane bound sac of water & small molecules (sugar, salt, pigments) Cell Wall Gives the cell structure & protection Made of cellulose in plants Made of chitin in Fungi

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