AP Bio Review 1 - 4 main properties of water and how water works, and 7 main functiol ghroups PDF

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4 main properties of water and how water works, and 7 main functiol ghroups in biology like carboxyl,methane etc... with drawn our chemical strucutres...

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AP Bio: Chemistry and Macromolecules: Polar Vs Nonpolar Molecules: Polar:  Asymmetrical shape, have unequal sharing of electrons resulting in “polarity” or separation of charges. Nonpolar:  Symmetrical shape, atoms have similar or equal electronegativity and electrons remain equally shared. Covalent bonds are the inter-molecular forces that hold the H20 molecule together while Hydrogen bonds hold water molecules together. Water’s polarity:  Allows for it to make hydrogen bonds easily which helps with nutrient transport  Makes it possible to conduct electricity very well (*electricity is flowing electrons)  Allows for a single water molecule to bond with 4 other water molecules. Emergent Properties of Water:  Cohesion: refers to water molecule binding to other water molecules. This property is made possible because of hydrogen bonds. Adhesion: refers to water molecules binding to something other than a water molecule. Also because of hydrogen bonds. EX: water binding to cell wall  Surface Tension: the measure of how difficult it is to stretch or break the surface of a liquid. Specific heat: the amount of energy needed to heat a substance 1 degree Celsius.  Temperature moderation: evaporative cooling: putting heat energy into water (it takes a tremendous amount of E to break hydrogen bonds) causing the water to evaporate and carry the heat energy away from the body, thus providing a cooling of the organism as heat energy leaves. Ice: hydrogen bonds are stable. Liquid water: hydrogen bonds constantly break and reform. Humidity, water vapor in the air, decreases the effect because water can’t evaporate into the air as it is already full of water vapor.  Expansion upon freezing: A. Water condenses down to 4% Celsius; after that, the colder it gets, the more it expands. The HYDROGEN bonds move outward to 90⁰angles from original position of 105 ⁰ . This movement “pushes” the water molecules farther apart and thus it becomes less dense.  Versatility as a solvent: water is polar so it allows other molecules to dissolve. Solvent: due to polarity of water a solute can be dissolved in water. (this makes transportation easier) Molecular Shape and Function:  4 ways that carbon skeletons can vary: length, double bond position, branching, and presence of rings. Isomers: same molecular formula, but different arrangement in atoms. Structural Isomers: Differ in:   Covalent arrangement of atoms. Location of double bonds. Ex: butane and isobutane Cis-Trans isomers (geometric): differ in arrangement of atoms around double bond. Double bonds do not permit rotation of atoms. **Double bonds must be present Enantiomers: isomers that are mirror images of each other. Shape difference due to asymmetric carbon. Carbon attached to different atoms/group of atoms. 

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Functional Groups: chemical groups directly involved in chemical reactions, each has certain properties that cause it to react in a characteristic way.  Hydroxyl group:  Carbonyl group:

 Carboxyl group  Amine group

 Sulfhydryl group  Phosphate group  Methyl group

Importance of Carbon:  Usually associated with living elements  Helps make organic mkolecules like : Carbohydrates, lipids, protiens, nucleic acid ** to be organic, carbon needs to be bonded to hydrogen. How structure of carbon allow it to form so many diverse molecule:  Can bond in 4 different directions with up to 4 atoms  Can form single, double, and triple bonds  Can form different carbon skeletons. Hydrocarbon tails of phospholipids:  Hydrocarbons are important parts of the cell memebrane (the tails od phospholipids). All hydrocarbons are extremely hydrophobic because they are nonpolar molecules. Functional properties or organic molecules are determined through the functional groups that are attached to the carbon skeleton Macromolecules: big molecules made up of many small molecules.  Carbohydrates, lipids, protens, nucleic acid Momomer: 1 small molecule Polymer: a long chain molecuole made up of a repeated pattern of monomers linked by covalent bonding. Synthesis: build things up, put monomers togethe  polymer (macromolecule) Digestion: Break things down Macromolecules decompose  get monomers back. Smallr molecules bind to form a larger oe through Dehydration Synthesis

Dehydration synthesis (reaction): joining of 2 molecules following removal of water Ex : C6H12O6 + C6H12O6  C6H22O11 + H2O

Hydrolysis Reaction: when water is added to break a bond. (larger molecules break down into smaller ones)

Macromolecules Formed dehydration synthesis. Macromolecules Broken down  hydrolysis reaction Carbohydrates are called: saccharides *** short term food/energy storage Monosaccharides: 1 monomer ex: glucose, fructose, and galactose Disaccharides: 2 monomers ex: sucrose, maltose, lactose Polysaccharides: 2+ monomers ex: starch cellulose glycogen. Monosaccharides serve as building material, anything that ends in -use must be a sugar.] Sugar monomers differ by having different skeletal structures The covalent bond between monomers is called glycosidic linkage, it means “sugar bond” Numbered carbons: the smaller the number the less amount of energy 2 types of Carbs: Simple sugars: monosaccharides, disaccharides Complex sugars: polysaccharides Polysaccharide Function: Energy storage – fuel Ex: starches- energy storage molecule in plants. Glycogen store energy in animals Linear and branched polysaccharides: Linear: energy storage slow release Branched: energy storage fast release/ fast digestion Polysaccharide diversity-isomers: Glucose in starch- we can digest, glucose in cellulose we cannot digest. Cellulose: a carb found in plant cell wall, building blocks for plants. Chitin: fibrous substance made from polysaccharides that for the exoskeleton of some animals and fungi cell walls. Lipids: 3 types Fats, Phospholipids, and Steroids 2 main parts in lipids, 3 carbon glycerol molecule (alcohol) and 1 fatty acid (long hydrocarbon tail)

NOTE: Lipids do NOT form polymers, they are big molecules made up of smaller sub units, not a continuing chain. Lipids are synthesized through dehydration synthesis with the 3 fatty acid linked to the glycerol through Ester linkage: a carboxyl group of the fatty acid paired with a hydroxyl group of the glycerol molecule. Saturated Fat: Linear molecule  All C bonded to H  No C=C double bonds, long straight chain, most animal fats, solid at room temp,  Contributes to cardiovascular disease (atherosclerosis) = plaque deposits. Unsaturated Fat: Branching molecule:  C=C double bonds in the fatty acids  plant and fish fats, vegetable oils, liquid at room temperature  the kinks made by double bonded c prevent the molecules from packing tightly together Polyunsaturated Fats: have numerous double or triple bonds in the fatty acid portion, liquids at room temp, from pants Hydrogenated/ Trans fats: oils turned solid by adding hydrogen and by breaking the double or triple bonds in order to transform it into a saturated fat. Phospholipids are most commonly found in the cell membrane: phospholipid bilayer Phospholipids: hydrophilic heads, hydrophobic tails  can self-assemble into “bubbles” Bubble= micelle  can form a phospholipid bilayer, early evolutionary stage of cell Steroid structure: 4 fused C rings.  Different steroids created by attaching different functional groups to rings diff structure= diff function  Ex: cholesterol, sex hormones. Cholesterol: important cell component  Animal cell membranes, precursor of all other steroids (including vertebrate sex hormones)  High levels in blood may contribute to cardiovascular disease  From cholesterol to sex hormone- change functional group. Function of lipids:  Stored in adipose tissue in animals for energy (long term energy)  2x carbohydrates  Concentrated in all H-C, Cushions organs, and insulates body. Nucleic Acids: Each nucleic acid monomer is called a nucleotide: structure of DNA nucleotide

DNA: double helix A (adenine)T (thiamine) C (cytosine) G (guanine) RNA: single strand: A (adenine) U (uracil) C (cytosine) G (guanine) Pyrimidines: has one 6-membered ring of carbon and nitrogen atoms (C, U, and T) Purines: are larger with 6-membered ring fused to 5-member ring. (A, G) DNA: occurs right before a cell divides. Protein Synthesis: DNA is transformed into single stranded mRNA which is then released from the nucleus through the nucleus port and it goes into the ribosome, the ribosome then reads the mRNA and produces the correct amino acid sequence. Whenever you see Phosphate group: start of backbone (5’) Whenever you see Hydroxyl group (OH): end of back bone (3’) (**CAN ALTERNATE) Benefits of DNA structure:  Permits easy replication  Provides a stable structure to maintain genetic sequences Functions of Nucleic Acids:  DNA directs and controls all activities of all cells like protein synthesis  RNA converts information from DNA to help in synthesizing proteins. Proteins:     

Enzymes: speed up chemical reactions ex: digestive enzymes breaks bonds in food molecules. Hormones: sends and receives chemical signals ex: insulin and nerve cells Transport: transport molecules ex: hemoglobin (in blood transports oxygen) Defense: identifies and fights infections ex: antibodies. Structural: support ex: collagen supports connective tissue, keratin forms hair, skin, nails,

 Can act like a base by accepting a hydrogen.  Gives each amino acid its distinctive function  acts like an acid because it can give off the hydrogen Carbon and Nitrogen: 2 atoms between peptide bond. 4 levels of protein structure:  Primary Structure: linear sequence of amino acids

 Secondary Structure: hydrogen bonds allow for overlapping and coiling to occur in the folding of the protein into 3d shape. All must be folded in order to work. Coiling is referred to as an alpha helix: (α), overlapping: Beta helix (β)  Tertiary Structure: 3d shape stabilized by interactions between size chains, hydrogen bonds, disulfide bridges, and hydrophobic interactions. Difference: hydrogen bonding is from the backbone in secondary structure while in tertiary you can have  hydrogen bonding only from the side chains.

 Quaternary Structure: 2 or more polypeptides woven together, hemoglobin has 4 polypeptides woven together. How is shape and structure of protein determined?  DNA had directions for Amino Acid sequences  Amino acid sequence determines 3d shape Function of proteins:  Form fits function, ex: exact match between antibody and flu virus. Denaturation: causes a protein to unravel and lose its function under conditions of high temp, pH changes, changes in salt concentration, organic solvents. Chaperonin protein complexes: provide shelter for folding polypeptides, keep new protein segregated from cytoplasmic influences. X ray crystallography used to observe protein structures

Nonpolar side chains: Hydrophobic mostly have carbons and hydrogens in R group, (inside of protein) Polar side chains: hydrophilic have oxygen and sulfur, polar molecules in R group (surface of protein) Ionic side chains (acidic or basic): will be on surface of proteins where they often neutralize each other and form salt bridges,...