Biology Test One

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autotroph

Back 1

produces own food

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heterotroph

Back 2

consume external energy sources

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CHNOPS

Back 3

six most common elements in organic matter

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphate, Sulfur

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lineage

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changes in the program of an organism over time; allows evolution

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Linnaeus

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Swedish biologist established binomial nomenclature

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variability

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enables favorability to traits (eg hair length)

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heritability

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traits passed through genetics (eg height)

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fitness

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ability to produce offspring relative to others in the population

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biological imperative

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thrust your genes into the next generations

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Haekel

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added protista to plantae and animalia in 1866

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protista

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colonial single-celled organisms (eg algae)

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Robert Whittaker

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added monera (bacteria) and fungi in 1969

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Woese

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"scarred revolutionary" revolutionized taxonomy by organizing organism by biochemical similarity in ribosomal RNA

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domains

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of life: bacteria, archae, eukarya

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isotopes

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"equal places," are variants of an element by # neutrons

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atomic weight

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average of mass #s of naturally occuring isotopes by abundance %s

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radioactive isotope

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neutrons change into protons, changing the element (eg 14C --> 14N), helpful in fossil dating

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dalton

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unit of mass measuring atoms, equivalent to a proton or neutron

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orbital

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region in which up to 2 electrons surround the nucleus

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electron shell

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levels of orbitals

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valence shell

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outermost electron shell

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valence electrons

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electrons in the valence shell

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valence

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the # of unpaired electrons in an atom's valence shell (eg, oxygen's valence is 2)

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molecules

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substances held together by covalent bonds

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covalent bonds

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shared electrons; when attractive forces (electron-proton) overcome repulsive forces (electron-electron or proton-proton)

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electronegativity

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an atom's ability to attract electrons, affected by # protons and # electron shells; O > N > C = H

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nonpolar

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atoms in a covalent bond share valence electrons equally, with equal strength; uncharged

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polar

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imbalance in covalently bonded atoms' electronegativities; electrons shared unequally, closer to one atom than another; have partial charge

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partial charge

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∂ , of an atom in a polar covalent bond, due to electrons (and their charges) being more concentrated on one end of the bond, towards the more electronegative atom

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ionic

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a bond in which electrons transfer completely from one atom to another (forming ions); ions stick together due to opposite, full charges

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ion

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fully charged atoms due to extra or missing electrons

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cation

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positively charged ions (#protons > #electrons)

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anion

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negatively charged ions (#electrons > #protons)

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solvent

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dissolves solutes (breaks down covalent/ionic bonds between atoms of a molecule) to make a solution; water is good at this because it's polar

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hydrogen bonds

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the weak intermolecular attraction between partially charged H's and O's in water, to other H2O molecules or different (polar) substances

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hydrophilic

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substance that can dissolve in water; polar

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hydrophobic

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substance that does not dissolve in water; nonpolar

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hydrophobic reactions

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interactions between hydrophobic substances submerged in water; H2O forms stronger bonds with H2O, then with hydrophilic substances, not easily with hydrophobic substances

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cohesion

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when water stays together because of its strong hydrogen bonds

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adhesion

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when water "sticks" to any polar/charged solid surfaces

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surface tension

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minimizes surface area, acts like an elastic membrane, outputs reistance; eg surface water molecules have stronger bonds with each other, having fewer surrounding H2O molecules to share hydrogen bonds with than submerged water

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specific heat

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amount of energy required to raise 1 gram of a substance 1 degree Celsius

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heat of vaporization

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point at which a substance becomes gaseous; related to specific heat

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chemical reaction

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when atoms rearrange their bonds, either combining or breaking apart substances

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dissociation reaction

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when atoms of a molecule separate (eg 2H2O --> H3O + OH-)

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acids

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donate protons (ie Hydrogen atoms) in a chemical reaction

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bases

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accept protons (ie Hydrogen atoms) in a chemical reaction

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mole

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6.022 x 10^23; a named number like "dozen" which converts a certain mass of a substance to its # molecules to make up that amount of mass; 1 H atom x (6.022 x 10^23) = 1 mole of H

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molecular weight

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sum of atomic weights in a molecule (eg H2O = 1 + 1 + 16 = 18)

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molarity

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# moles of a substance in a solution per 1 liter

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pH

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concentration of protons in a solution; a scale of 1-14, where each integer represents a power of 10; affects polarity and therefore the chances for certain chemical reactions to occur

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buffers

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substances that offset changes in pH due to chemical reactions in a cell/tissue; maintains homeostasis

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ammonia

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NH3

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reactant

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initial molecules in a chemical reaction (left)

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product

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resulting molecules in a chemical reaction (right)

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chemical equilibrium

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dynamic but stable state of a substance undergoing spontaneously reversible chemical reactions (<-->)

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system

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a closed set of interacting elements

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endothermic

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heat absorbed during a chemical reaction

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exothermic

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heat released during a chemical reaction

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energy

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the capacity to do work or supply heat

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potential energy

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stored energy

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kinetic energy

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energy of motion

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chemical energy

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potential energy stored in bonds (distance of shared electrons from a nucleus, highest in nonpolar covalent bonds)

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thermal energy

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kinetic energy of molecular motion

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temperature

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how much thermal energy an object's molecules possess

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heat

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transferred thermal energy between contacting objects of different temperatures

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first law of thermodynamics

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energy is conserved; cannot be created nor destroyed

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spontaneous

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chemical reactions which are able to proceed on their own without continuous external influence

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nonspontaneous

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chemical reactions which require continuous external influence to proceed

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entropy

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amount of disorder in a system, represented by an italic S

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second law of thermodynamics

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entropy increases in an isolated system

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prebiotic soup model

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atmospheric gasses synthesized certain molecules (or came from meteorites), condensed with rain, and accumulated in oceans

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surface metabolism model

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dissolved gasses formed organic and complex molecules with minerals from deep-sea vents

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photons

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packets of light energy, can scatter electrons which breaks covalent bonds

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ozone

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O3, an atmospheric gas which prevents photons from reaching the Earth's surface

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free radicals

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fragments from photon dismemberment, have unpaired valence electrons

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catalyst

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a substance that speeds up chemical reactions by providing appropriate chemical environment for reactants to interact effectively; orients reactants

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organic molecules

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contain carbon bonded to other elements

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carbon

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C, atomic # 6, has 4 valence electrons, structures organic molecules

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functional groups

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amino, carboxyl, carbonyl, hydroxyl, phosphate, sulfhydryl; groups that characterize many substances by providing specific structures and functions

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amino functional group

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R--NH2, acts a base

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carboxyl functional group

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R--COOH-, acts as an acid

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carbonyl functional group

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R--COH or R--CO--R, aldehydes and ketones, help for larger molecules

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hydroxyl functional group

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R--OH, alcohols, highly polar so helps make compounds more soluble in water, acts as a weak acid

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phosphate functional group

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O

R--OPO- store lots of chemical energy

O-

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sulfhydryl functional group

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R--SH, can form disulfide (S--S) bonds that contribute to protein structure

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free energy

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amount of energy that is available to do work, represented by an italic G

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enthalpy

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total energy in a molecule represented by an italic H in formulas; potential energy (heat content) + surrounding's effects (pressure, volume)

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delta

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Δ, represents change

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Gibb's free-energy exhange

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determines whether a chemical reaction is spontaneous; ΔG = ΔH - TΔS

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exergonic

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spontaneous reactions, increases entropy, ΔG < 0

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endergonic

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nonspontaneous reactions, decreases entropy, ΔG > 0

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energetic coupling

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endergonic and exergonic reactions facilitate each other with the exchange of free energy

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redox reactions

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reduction-oxidation reactions; when an atom/molecule loses or gains electrons; OIL RIG

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electron carrier

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acts as both an electron donor and receptor to relocate H2

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ATP

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adenosine triphospate; lots of potential energy (in its 3 phosphate groups, nonpolar, electrons at farthest edges of valence shells)

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kcal

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kilocalorie; energy it takes to raise 1 kilogram of water 1 degree Celsius

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substrate

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target molecule that interacts with a catalyst as a reactant

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phosphorylation

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phosphate group is added to a substrate

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activated substrate

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phosphorylated substance that acts as an intermediate that allows two other substances to be exergonically reacted

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amino acids

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20 building block molecules for proteins

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monomer

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"one part" single molecular subunit (eg amino acid, nucleotide)

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polymer

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"many parts" several monomers bonded together (eg protein, carbohydrate)

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polymerization

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linking of monomers into polymers

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macromolecules

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very large molecules (a type of polymer) made of smaller molecules, nonspontaneously formed

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condensation reaction

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aka dehydration reaction: water is a product (opposite of hydrolysis), polymerization is this type of chemical reaction

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peptide bond

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C--N covalent bond that results from a condensation reaction, ACTS as a double bond

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residue

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a molecule linked by peptide bonds

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n-terminus

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amino terminus (NH3+), start on left

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c-terminus

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carboxyl terminus (COO-), end on right

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ogliopeptide

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a smaller peptide chain of <50 amino acids; called just a "peptide"

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polypeptide

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50+ amino acids

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protein

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any chain of amino acid residues, but technically only the complete, functional molecules

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primary structure

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unique sequence of amino acids in a protein

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secondary structure

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alpha-helix and beta-pleated sheets; are the folds created by hydrogen bonds between R-groups

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tertiary structure

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overall shape of a protein, can also include interactions between R-groups and backbone via hydrogen bonds, hydrophobic interactions, van der Waals interactions, disulfide bonding, and ionic bonding

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quarternary structure

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shape of proteins that contain multiple polypeptides

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dimer

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"two parts", proteins with 2 polypeptide subunits

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tetramer

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"four parts", proteins with 4 polypeptide subunits

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macromolecular machines

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groups of multiple proteins that assemble into one structure to perform a specific function (eg ribosome)

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denature

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unfolded proteins, done by treating protein with compounds that break disulfide bonds, disrupts function of protein

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molecular chaperones

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proteins that facilitate folding (usually after heat-shock or for basic activity regulation in enzymes)

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prion

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alternate "normal" (ie, inactive) protein shapes which make other proteins adopt the dysfunctional shape. fatal disease (eg mad cow disease, spongiform encephalopathies)

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catalyze

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speed up chemical reactions

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enzyme

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a protein that acts as a catalyst, large and globular, often end in -ase, flexible and dynamic; stabilize reactions to lower activation energy

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active site

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where substrates bind to enzymes and where catalysis occurs

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induced fit

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conformational change of an enzyme when substrate(s) bond at the active site; stabilizes transition state

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transition state

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climax of catalysis, when substrate(s) bind through hydrogen bonds and R-groups interact

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activation energy

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kinetic energy requires to catalyze substrates' reactions

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initiation

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step 1 of enzyme catalysis: orient reactants non-randomly

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transition state facilitation

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step 2 of enzyme catalysis: stabilize reaction by lowering activation energy

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termination

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step 3 (of 3) of enzyme catalysis: products released from enzyme as they do not fit in active site

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saturation kinetics

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as substrate levels increase, so does enzyme activity, until substrate levels approach, meet, and exceed enzyme levels, which then function at maximum efficiency

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cofactors

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a type of enzyme helper made of inorgainic ions (eg Zn2+, Mg2+, Fe2+); reversibly interacts with enzymes

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coenzymes

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a type of enzyme helper made of organic molecules that reversibly interact with enzymes (eg NADH, FADH2)

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prosthetic groups

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a type of enzyme helper made of non amino acids *permanently* attached to enzymes (eg retinal), often attached to active site

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competitive inhibition

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regulatory molecule is similar in size and shape to substrate, so will occupy active site, thus inhibiting the chemical reaction, and competing with the substrate for enzyme interaction

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allosteric regulation

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regulatory molecule binds at non active sites, changing the shape of the enzyme and allowing or preventing it to function properly

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RNA world hypothesis

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suggestion that life began with a nucleic acid, not proteins because they can replicate themselves

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nucleic acid

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a polymer made of nucleotides

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nucleotide

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a monomer which contains a phosphate group, a 5-carbon sugar, and a nitrogenous base

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purines

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adenine & guanine (have 9 atoms)

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pyrimidines

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cytosine, uracil, and thymine (have 6 atoms)

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pentoses

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sugars with 5 carbons

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hexoses

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sugars with 6 carbons

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ribose problem

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"how did ribose become the dominant sugar in prebiotic soup?"... minerals prefer to bond with ribose (think deep sea vents)

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phosphodiester bond

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polymerization/ condensation bond between hydroxyl (R--COOH-) and sugar of one nucleotide and phosphate of another (joins 5' and 3' to sugars); forms backbone

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xray crystallography

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seeing how DNA scatter radiation; used to identity DNA structure

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antiparallel

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side by side, but in opposite directions

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double helix

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coiled sugar-phosphate backbone on outside, N bases on inside

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complementary pairing

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purine-pyrimidine pairs AT/AU/GC

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template strand

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preexisting DNA sequence

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complementary strand

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new, opposite sequence

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hairpin

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most common secondary structure of RNA, stem and loop configuration

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ribosomes

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catalytic RNA molecules, can catalyze hydrolysis and condensation reactions for phosphodiester linkages (and also peptide bonds)

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RNA replicase

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enzyme that catalyzes replication of RNA

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amyloid

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clumps of insoluble fibrous protein

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plasma membrane

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aka cell membrane, separates life from nonlife with selective barrier to keep damaging compounds outside, allow entry of needed compounds, and allow more frequent collisions necessary for chemical reactions

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lipid

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catchall term for carbon-containing compounds found in organisms that are nonpolar and hydrophobic

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hydrocarbons

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molecules that contain only C and H, nonpolar

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fatty acid

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lipid with hydrocarbon chain and carboxyl (COOH-) functional group

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saturated

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a fatty acid with no carbon double bonds (C==C)

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unsaturated

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a fatty acid with at least one carbon double bond

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fats

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nonpolar molecules called triaglycerols or triglycerides composed of 3 fatty acids and glycerol

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oils

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polyunsaturated liquid triaglycerols (ie, fats with a lot of unsaturated fatty acids)

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glycerol

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a 3-carbon molecule

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ester linkage

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the connection between a fatty acid and a glycerol molecule

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steroids

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family of lipids characterized by bulky 4-ring structures

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phospholipids

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glycerol + phosphate group + 2 hydrocarbon chains (either fatty acids or isoprenoids), plus any small organic molecule

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amphipathic

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"dual sympathy" a molecule with both hydrophilic and hydrophobic parts (eg phospholipids)

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isoprenoid

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pure hydrocarbon chain, a type of fatty acid

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cholesterol

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big bulky rings with isoprenoid tail

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fluid mosaic model

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proteins operate embedded into membrane

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channels

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a type of transport protein, lined with pores (passive transport)

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carrier proteins

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a type of transport protein, aka transporter, binding induces a conformational change (passive transport)

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pumps

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a type of transport protein which uses energy (ATP) to move ions against electrochemical gradients

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aquaporins

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channels specific to H2O

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lipid bilayer

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two sheets of lipid molecules spontaneously aligned

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micelle

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spontaneously formed ring of fatty acids or simple hydrocarbons, all tails meet in center

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liposome

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a circular/spherical lipid bilayer often used to transport medicene

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planar bilayer

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a single bilayer line often used in artificial membrane to cross a gap between a plastic divider between two aqueous solutions

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permeability

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tendency of a structure to allow a given substance to pass through it, related to fluidity

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selective permeability

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some substances cross a bilayer much easier than others (small nonpolar, small uncharged polar, large uncharged polar, ions)

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solutes

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dissolved molecules and ions

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diffusion

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movement of solutes due to inherent kinetic energy (from high to low concentration)

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concentration gradient

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difference in concentrations causes net movement of solutes (high to low)

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osmosis

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diffusion of water (from low solute concentration to high solute concentration through selectively permeable membranes)

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protocells

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vescile-like structures that harbor nucleic acids

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hypertonic

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higher concentration than comparison (ie outside > inside, hypertonic to CELL), attracts osmosis

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hypotonic

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lower concentration than comparison (ie inside > outside, hypotonic to CELL), does not attract osmosis

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isotonic

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dynamically stable concentrations (ie inside = outside)