AP bio unit 1

water

-polar molecule

-polar colvalent bonds

-oxygen end is partial negative and the hydrogens have a partially positive end

-cohesive

polar covalent bonds

-opposite ends of the molecule have opposite charges

cohesion

-H bonding between H2O creates it (sticky)

-allows for the movement of water against gravity

-high surface tension -water moves up a tree by transpiration (helped by ____)

adhesion

-H2O molecules form H bonds with other substances
~capillary action
~meniscus
~water climbs up fiber

solvent

-water is the universal one
-polar water molecules will surround the (+) and (-) ions causing the ions to separate and dissolve
-dissolve solutes and create aqueous solutions

hydrophilic

-some molecules have an affinity for water

-polar and ionic molecules

-ex: cotton, cellulose, paper

hydrophobic

-some substances do not have an affinity for water

-nonpolar and non ionic substances

-ex: fat, glycerol, oils

floats

-less dense when it is solid, water ______

-forms crystal lattice structure

-important because oceans and lakes do not freeze solid ~insulates water below ~seasonal turnover of lakes

specific heat

-the amount of heat that must be absorbed or lost for 1g to change its temperature by 1C

-water had high _____ due to H bonding

-resists change in temp

-moderates temp on earth

evaporative cooling

-organisms use to regulate their temperature

-ex: sweating

-water evaporates through a surface, cooling occurs

acidic

If [H+]>[-OH]

basic

If [-OH]>[H+]

pH scale

-how acidic or basic a solution is

-pure water, only 1 molecule in every 554 million is dissociated

-most biological fluids have 6-8

-each unit represents a 10-fold difference in H+ and -OH concentrations

neutral

-If concentration of 2 ions is equal

carbon

-all life mostly based on this element

-important due to its electron configuration
~able to make 4 stable covalent bonds (tetra valence)
~very versatile

-tetravalence allows them to be strung together in chains

hydrocarbons

-combinations of C and H

-nonpolar ~not soluble in water ~hydrophobic -stable

-very little attraction between molecules -gas at room temp

isomers

-molecules with the same molecular formula but different structures
-different chemical properties -different biological functions

structural isomers

-differ in covalent arrangement of atoms

geometric isomers

-same covalent relationships by different spatial arrangements

enantiomers

-isomers that are mirror images of each other
-structural differences create important functional significance

functional groups

-substitute other elements for hydrogen -parts of organic molecules that are involved in chemical reactions -give organic molecules distinctive properties -affect reactivity ~make hydrocarbons hydrophilic ~increase solubility in water

macromolecules

-by joining carbon to other elements, we form the basis of life
-smaller organic molecules join together to form larger molecules

polymer

-a long molecule consisting of similar or identical building blocks
-blocks known as monomers
-joined through covalent bonds
-dehydration synthesis

synthesis

-joins monomers by "taking" H2O out
-one monomer donates -OH
-other monomer donates H+
-together these form H2O
-requires energy and enzymes
-condensation reaction

digestion

-use H2O to breakdown polymers
-reverse of dehydration synthesis
-cleave off one monomer at a time
-H2O is split into H+ and -OH
-requires enzymes
-releases energy
-hydrolysis

carbohydrates

-composed of C, H, O
-function: energy, raw materials, energy storage, and structural storage
-monomer: sugars

sugars

-all have carbonyl group and multiple hydroxyl groups

-location determines whether it is an aldehyde or ketone

-most names end in -ose -classified by number of carbons

-when in solution, 5C and 6C structures form rings

monosaccarides

-simple one monomer sugars

-ex: glucose

disaccharides

-2 monomer sugars

-ex: sucrose

polysaccharides

-large polymer sugars
-ex: starch

sugar polymers

-costs little energy to build

-easily reversible=release energy

-function: energy storage (starch in plants and glycogen in animals) and structure (cellulose in plants and chitin in arthropods and fungi)

starch vs. cellulose

-differ in the position of the hydroxyl group on Carbon 1 -S____ has an alpha configuration (normal bonding of glucose monomers)

-C________ has a beta configuration (every other glucose monomer is upside down)

-causes differences in organisms' ability to digest it (S easy, C hard)

cellulose

-major component of plant walls -most abundant organic compound on Earth

-herbivores have evolved a mechanism to digest it

-most carnivores have not evolved

-undigested roughage

lipids

-functions: long term energy storage and concentrated energy, cushions organs, and insulates body

-not a true polymer and not large enough to be a macromolecule

-big molecules made up of smaller subunits -not a continuous chain

-all mix poorly in water (hydrophobic) -include waxes, pigments, fats, pils, phospholipids, and steroids

-structure: glycerol (3 Carbons) and a fatty acid chain

triacylcglycerol (triglyceride)

-three fatty acid chains linked to a glycerol -combine by an Ester linkage (hydroxyl and carboxyl)

-dehydration synthesis

saturated fats

-all carbons are bonded to hydrogens -there are no carbon to carbon double bonds

-long, straight chain -most animals fats

-solid at room temp. (contributes to cardiovascular disease, atherosclerosis)

unsaturated fats

-contains carbon to carbon double bonds in the fatty acids

-C=C double bonds in the fatty acids

-plant and fish fats

-vegetable oils

-liquid at room temp (the kinks made by double bonded C prevent the molecules from packing tightly together)

-mono- and poly-

phospholipids

-structure: glycerol + 2 fatty acids + PO4 (negatively charged)

-contains a head and a tail region

-fatty acids tails are hydrophobic

-PO4 head is hydrophilic

-in water, assembles into a bubble (forms a bilayer)

-create a barrier for water and define "outside" vs. "inside"

-make up the cell membrane

steroids

-structure: carbon skeleton of four fused rings with different chemicals attached

-with a different functional group attached you create a new one

-ex: cholesterol and sex hormones

cholesterol

-important cell component -animal cell membranes

-helps keep membrane fluid, flexible and mobile

-precursor of all other steroids ~including vertebrate sex hormones

-high levels in blood may contribute to cardiovascular disease

proteins

-most structurally and functionally diverse group

-function: involved in almost everything ~enzymes (pepsin, DNA polymerase) ~structure (keratin, collagen) ~carriers and transport (hemoglobin, aquaporin) ~cell communication (signals and receptors) ~defense (antibodies) ~movement (actin and myosin) ~storage (bean seed) -structure: ~monomer amino acids ~polymer polypeptide

-can be one or more polypeptide chains folded and bonded together -large and complex molecules

-complex 3D shape

amino acids

-structure: central carbon (alpha carbon)

-amino group -carboxyl group (acid)

-R group (side chain) ~variable group ~different for each ~confers unique chemical properties -physical and chemical properties based on R groups attached

peptide bonds

-covalent bond between NH2 (amine) of one amino acid and COOH (carboxyl) of another
-C-N bond

protein structure

-a polypeptide chain that has been folded, twisted and coiled into unique shapes
-performed as soon as the polypeptide is formed by creating bonds between parts of the chain
-the specific structure determines the function

primary structure

-unique sequence of amino acids
-amino acid sequence determined by gene (DNA)
-slight change in amino acid sequence can affect protein's structure and its function

secondary structure

-localized folding or pleating of parts of the protein chain
-result of H bonds between repeating structures of polypeptide
-weak bonds
-α helix and β pleated sheets

tertiary structure

-whole molecule folding
-interactions between distant amino acids
-hydrophobic interactions
~cytoplasm is water-based
~nonpolar amino acids cluster away from water
-H bonds and ionic bonds
-disulfide bridges
~covalent bonds between sulfurs in sulfhydryls (S-H)
~anchors 3D shape

quaternary structure

-more than one polypeptide chain bonded together
-only then does polypeptide become functional protein
-hydrophobic interactions

denaturation

-although proteins fold as they are made, under certain conditions, these proteins will not fold properly
-can be caused by heat, change in pH, change in solution, or salinity
-will be inactive
-some proteins will be able to regain their original structure by removing the elements

nucleic acid

-function: genetic material
-stores information; genes, blueprint for building proteins
-transfers information; blueprint for new cells and next generation
-monomer: nucleotides

RNA

-nucleic acid
-single helix
-controls protein synthesis

DNA

-nucleic acid
-double helix
-controls its own synthesis and protégé's as well as instructions for reproduction from one generation to the next

nucleotides

-made up of three parts
-nitrogen (C-N ring)
-pentose sugar (5C)
~ribose in RNA
~deoxyribose in DNA
-phosphate (PO₄) group
-two types: purines and pyrimidines

purines

-double ring N base
-adenine (A) and guanine (G)

pyrimidines

-single ring N base
-cytosine (C), thymine (T), uracil (U)

phosphodiester bond

-new base added to sugar of previous base
-polymer grows in one direction

metabolism

-the totality of an organism's chemical reactions
-each reaction will follow a pathway
-what manages the material being used and formed and the energy needed for the changes

metabolic pathway

-a specific molecule is altered resulting in a product (needs enzymes in order to be changed)

catabolism

-breaking down of complex molecules to simpler compounds
-releases energy
-known as hydrolysis or digestion

anabolism

-uses energy in order to form bonds/ molecules
-go through biosynthetic pathways
-dehydration synthesis

bioenergetics

-the study of how organisms manage their energy resources

energy

-the capacity to cause change

kinetic energy

-the energy of an object due to its motion

light energy

-energy from the sun that cane converted to solar energy, or chemical energy through photosynthesis

thermal energy (heat)

-energy associated with the random movement of atoms and molecules

potential energy

-energy not in use, but that an object possesses due to its location or structure

chemical energy

-the potential of a substance to undergo a chemical reaction and transform, thus releasing energy

thermodynamics

-the study of energy transformation

First Law of Thermodynamics

-energy is constant
-can change forms, but cannot be created or destroyed
-just like matter
-"principle of conservation of energy"

Second Law of Thermodynamics

-all energy transformations increase the entropy of the universe
-entropy is the measure of disorder or randomness

free energy

-measures the portion of a system's energy that can perform work while temperature and pressure are uniform
-shows if a process or change will be spontaneous or if energy is needed for a change to occur
~negative=spontaneous
~positive or 0=not spontaneous

exergonic reactions

-release of free energy from a chemical reaction
-ex: digesting polymers

endergonic reaction

-chemical reaction that requires an input of energy
-absorbs free energy from surroundings
-ex: building polymers

cell work

-3 main types
~mechanical (muscle contractions)
~transport (diffusion/transport)
~chemical (endergonic reactions)
-coupling reactions to save energy

energy coupling

-use exergonic (catabolic) reactions to fuel endergonic (anabolic) reactions
-allows for the energy that organisms need to live

ATP

-adenosine triphosphate
-modified nucleotide
-adding phosphates is endergonic
-P groups unstable, excellent energy donor

phosphorylation

-released P can transfer to other molecules
~destabilizing them

enzymes

-speed up reactions by lowering the energy barrier
-regulate the movement of molecules through metabolic pathways
-a catalytic protein
-needed by all reactions for completion
-do not change ∆G
-hasten a reaction that would occur eventually
-selective, determine which chemical processes will occur at any time
-substrate specific
-catalyze reactions only at the active site
-unchanged by a reaction
-can catalyze or anabolize a substrate (work towards equilibrium in reactants and products)

catalyst

-a chemical agent that changes the rate of a reaction without begin consumed by the reaction

energy of activation

-makes the reactants unstable, increases the speed of the reactant molecules, and creates more powerful collisions
-the amount of energy necessary to push the reactants over an energy barrier
-at the summit the molecules are at an unstable point, the transition state

∆G

-the difference between the free energy of the products and the free energy of the reactants

cofactors

-nonprotein enzyme helpers
-bind permanently to the enzyme or reversibly
-ex: zinc, iron, and copper

coenzymes

-organic cofactors include vitamins or molecules derived from vitamins

inhibitors

-binding prevents enzymes from catalyzing reactions
-binding involving covalent bonds, often irreversible
-if weak, reversible

competitive inhibition

-if the inhibitor binds to the same site as the substrate, it blocks the substrate

noncompetitive inhibition

-if the inhibitor binds somewhere other than the active site, it blocks the substrate
-binding causes the enzyme to change shape, rendering the active site unreceptive at worst or less effective at catalyzing the reaction