AP Biology Test: UNIT 1

Structure of Water and Hydrogen Bonding 1.1

Matter

anything that has mass; all three states

Elements

composed of only one type of atom; CHNOPS

Atom

smallest unit of matter that retains properties of an element; has protons, neutrons, and electrons

Isotopes

atoms of same element but different number of neutrons; some isotopes are radioactive but can decay to go back to stable form

Uses of Isotopes

radioactive dating uses the half life of certain isotopes; can be used as tracers

Compounds

two or more elements bonded together to create a full valence shell

Ionic bonds/compounds

form salts; when atoms transfer electrons to one another which consists of partially charged ions; can usually dissociate in water

Covalent bonds/compounds

form "molecules"; don't dissociate in water but require a chemical reaction

Nonpolar molecules

atoms share electrons equally; ex) fats and oils; hydrophobic

Polar molecules

atoms don't share electrons equally; ex) water; hydrophilic

"Like dissolves like"

polar dissolves polar and nonpolar dissolves nonpolar

Molecular Shape

key to the cells function; molecules with a similar shape can perform similar functions

Hydrogen Bonding

water is a very polar molecule allowing it to form hydrogen bonds; bonded to N, O, or F which causes hydrogen to take up strong partial positive; hydrogen bond is just an attraction but is easily broken

Properties of Water (due to Hydrogen Bonding)

cohesive and adhesive (cling to other polar surfaces); high surface tension; high specific heat (absorbs a lot of thermal energy without change in temperature); high heat of vaporization (has to absorb a lot of thermal energy to break hydrogen bonds so that it can evaporate into vapor); water expands when it freezes (because of hydrogen bonds); universal solvent because of its polarity

Hydrogen and Hydroxide Ions

acids increase [H+] and lower [OH-] and bases do the opposite

the pH scale

acidic<7, basic/alkaline>7

Organic Molecules

carbon-containing molecules that exist because of living things

Carbon Atom

will form 4 covalent bonds because of its 4 valence electrons; bonds are very stable; long hydrocarbon chains (nonpolar/hydrophobic) can be formed between carbon atoms which can be either ring or branching structures

Functional Groups

clusters of specific atoms bonded to the carbon skeleton with special structures and chemical properties; chemical groups can replace one of the hydrogens bonded to the hydrocarbon chain;

Macromolecules

consist of many repeating molecules (monomers) bonded together to make a polymer

Synthesis of Macromolecules

dehydration synthesis which forms a covalent bond which results in the production of a water molecule

Degradation of Macromolecules

hydrolysis is when a water molecule is used to break a covalent bond; polymers --> monomers

Macromolecules Background Info

carbon atoms form the backbone of macromolecules; there are four classes; all (except lipids) are polymers

Carbohydrates

short term energy storage and provide building material to cells and organisms; composed of carbons, hydrogens, and oxygens in a 1:2:1 ratio; monomers are called monosaccharides

Disaccharides

two monosaccharides bonded together by dehydration synthesis; covalent bond is called a glycosidic linkage; lactose intolerant people lack the enzyme lactase which breaks down lactose

Polysaccharides

polymers of monosaccharides; two main types: structural and storage; plants store in form of starch and animals in form of glycogen both made of glucose monomers which can be broken by hydrolysis to give the organism energy; also used for cell walls and chitin (exoskeleton)

Starch vs. Cellulose

structure of a polysaccharide is determined by its sugar monomers and the position of its glycosidic linkages; structure--> function; there are two ring structure for glucose (a and b) and starch is made up by all a and cellulose is all b which gives them distinct 3d shapes

Protiens

functions: defense, transport, cellular communication, movement and structural support; composed of CHONS; all protiens made up of smaller monomers called amino acids which bond to form polymers called polypeptides

Amino Acids

20 different ones; each amino acid has an amine group, carboxyl group, and an R group connected to a central carbon; differ in properties due to the variable R group

variable R group

some are nonpolar (hydrophobic); some are polar (hydrophilic); some are ionic (have overall positive or negative charge) also hydrophilic

Polypeptides

amino acid monomers are linked together through dehydration synthesis forming peptide bonds; peptide bonds are formed between carbon bond of one carboxyl group of one nucleotide and the nitrogen group of one amine group of another nucleotide; polypeptides have two ends: amino terminus (N) and carboxyl terminus (C); new amino acids are added to the carboxyl terminus

Structure of Protiens

a functional protein consists of one or more polypeptides precisely folded, twisted, and coiled into a unique conformation and they cant function properly until they are in that shape; four levels of protien structure

primary level

linear sequence of amino acids

secondary level

patters of the hydrogen bonding between amino acids causes regions of the polypeptide to form alpha helices and beta pleated sheets

tertiary level

final folding and overall 3-d shape of a polypeptide; determined by interactions of the R-group: hydrophobic interaction, hydrogen bonding, and ionic/covalent bonds;

quatenary level

consists of two or more folded polypeptides coming together (called subunits) to form a single, large, functional protein; only some proteins have this structure

Factors affecting Protein Structure: Mutations

a change in just one amino acid in a polypeptide can change the structure and therefore the function; dont always disrupt; changes primary structure so therefore changes all others

Factors affecting Protein Structure: Denaturation

physical and chemical conditions can affect the structure of a protein because can disrupt hydrogen bonding or R-group interactions causing a protein to change shape or unravel; doesn't change primary structure but changes all others; denatured protein is biologically inactive and doesn't work; can usually return to their functional purpose once environment conditions return to normal

Enzymatic Protiens

catalysts to accelerate chemical reactions within cells

Transport Proteins

embedded in the cell membrane that control the movement of substances in and out of a cell

Contractile and Motor Proteins

motor proteins: help cells move and help materials move inside; contractile proteins: found in muscles and are responsible for muscle contraction

Receptor Proteins

proteins that bind to chemical signals and initiate a cell response

Hormonal Signaling Proteins

many hormones are proteins that are released into the blood and bind receptors on cells throughout the body to regulate the activity of an organism

Defense Proteins

proteins such as antibodies assist the immune system in destroying viruses and bacteria and protecting organisms from infection

Structural Proteins

many long fibrous proteins play structural roles in organisms

Nucleic Acids

each nucleotide monomer is composed of three parts: a pentose (5-carbon) sugar, and a nitrogen containing (nitrogenous) base; the pentose sugar in RNA is ribose and in DNA is deoxyribose; carbon atoms are labeled 1' to 5'

Nitrogenous Base Families

Pyrimidines: one ring and include cystosine, thymine, and uracil

Purines: 2 rights with adenine and guanine

thymine only in DNA and uracil only in RNA

Polynucleotides

joined by dehydration synthesis; covalent bonds are formed between the 3' carbon of one nucleotide and then the 5' of another nucleotide called a phosphodeister linkage; polynucleotides have a hydroxyl (3') end and phosphate (5') end, so DNA and RNA have directionality, nucleotides are added to the 3' end

Structure of DNA and RNA

the side of DNA or a RNA strand is referred to as the sugar-phosphate backbone; DNA's two strands are held together between the hydrogen bonds between the nitrogenous groups of the two strands; some RNA are linear and some fold onto themselves; C w/ G (3 hydrogen bonds) and A w. U/T (2 hydrogen bonds); DNA strands are antiparallel (run opposite ways)

Adenosine Triphosphate (ATP)

nucleotide composed of adenosine, ribose, and 3 phosphate groups; high energy molecule due to the presence of the last phosphate molecule which is easily broken; this yields ADP and an inorganic phosphate, and energy to do cellular work

Lipids

diverse group of molecules unified by the fact that they are hydrophobic because they consist mostly of hydrocarbons and only a small number of polar functional groups; composed of CHOP; only class of monomers that don't form true polymers because they don't have monomers that can repeatedly bind to one another; most important are fats, phospholipids, and steroids

fats (triglycerides)

fats are made up of large nonpolar molecules called triglycerides; formed from the bonding together of four monomers: three fatty acid monomers bonded to one glycerol monomer; form covalent bonds called ester linkages; main function of fat is energy storage, also used for heat insulation in mammals.

saturated fats

fatty acid chains with all single bonds between the carbon atoms; usually solid at room temperature; ex) animal fat: butter

unsaturated fats

one or more fatty acid chain that has double or triple bond between carbon atoms; usually called oils and tend to be liquid at room temperature

phospholipids

one glycerol molecule linked to 2 fatty acids and a modified phosphate group; fatty acid tails are nonpolar and hydrophobic; modified phosphate group (head) is polar and hydrophilic; structural function is being the main component of all cell membranes; in water they aggregate to form a lipid bilayer;

steroids

carbon skeleton of 4 fused carbon rings; nonpolar molecules; some are components in cell membranes and some are hormones that regulate and control the body

hydroxyl group

adds to polarity: bonded -OH

Carbonyl Group

Adds to polarity: bonded -C- - O with double bond

carboxyl group

is found on every amino acid; bonded -COOH, acts as an acid

Amino Group

is found in all amino acids; bonded -NH2, acts as a base.

Sulfhydryl Group

covalent cross-links with other cysteines in the tertiary and quaternary protein structures: bonded -SH

Phosphate Group

energy releasing side group: -POOO

Methyl Group

Nonpolar: -CH3