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443 Cards in this Set
- Front
- Back
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what is a theory
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a well substantiated explanation of some aspect of the natural world
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what is a hypothesis
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a guess as to why or how something happens
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what is reductionism
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the theory that a complex phenomenon can be explained by analyzing the simplest, most basic physical mechanisms
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what are the 4 important different atoms
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nitrogen, oxygen, hydrogen, carbon
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what is a valence shell
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the outermost energy shell of an atom, containing the valence electrons involved in chemical reactions of that atom
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what is a valence electron
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the electrons in the outermost electron shell
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what is valence
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the bond capacity of an atom generally equal to the # of unpaired electrons in the atom's outermost shell
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how is a covalent bond formed
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by the sharing of an electron pair between adjacent atoms
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what is an ionic bond a result from
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the attraction between oppositely charged ions (complete loss or gain of electron)
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what is a hydrogen bond
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a weak electrostatic attraction which can occur when a hydrogen atom is covalently linked to an electronegative atom in near proximity to another electronegative atom
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how are van der waals forces formed
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when 2 uncharged atoms are brought very close together, their surrounding electron clouds influence eachother
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what the the chemical bonds in biology from strongest to weakest
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-covalent bond
-ionic bonds -hydrogen bonding -hydrophobic interactions -van der waals interactions |
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what indicates the identity of atoms
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atomic & mass numbers
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what determines chemical reactivity
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# of electrons in valence shell of an atom
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What is Gibbs free energy change
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(delta H) - T(delta S)
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what is potential energy
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the energy stored by matter as a result of its location or spatial arrangement
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what is kinetic energy
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energy of motion
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what is energy
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the ability to do work
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what needs to happen for a chemical reaction to occur spontaneously
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the reactants must have more potential energy than the products/and or be more ordered than the products
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how does a water molecule have asymmetric polarity
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cuz the oxygen atom is electronegative and it attracts electrons
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what are the unusual properties of water
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-liquid water is more dense than solid water (no lattice forms)
-water has a large capacity for absorbing heat |
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what is oxidation
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losing electrons
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what is reduction
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gaining electrons
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what is molecular weight
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the sum of all the weights of all the atoms in a molecule
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what is dalton
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the atomic mass unit; a measure of mass for atoms
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what is mole
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the # of grams of a substance that equals its molecule weight
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what is molarity
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the number of moles of solute per liter of solution
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what is an acid
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a substance that increases H+ concentration of a solution
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what is a neutral solution
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when the concentration of H+ is equal to that of OH-
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What is pH equal to
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-log[H+]
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what does each pH difference signify
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a ten fold difference in H+ and OH- concentration
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what are buffers
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solutions in which the pH remains relatively constant when small amounts of acid or base are added
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what is a buffer solution usually made of
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a salt of strong base and weak acid
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what are trace elements
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elements required in minute amounts, but their lack can cause severe disorders
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what does matter consist of
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chemical elements in pure form and in combinations called molecules and compounds
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what is matter
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anything that takes up space and has mass
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what is an atom
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the smallest unit of matter that retains the properties of an element
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what are the subatomic particles of atoms
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protons, neutrons, and electrons
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what preserves the atomic structure
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the attraction between the nucleus and the electrons which keeps the electrons in the "vicinity" of the nucleus
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what are isotopes
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atomic forms of the same element with different number of neutrons
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how are radioactive isotopes valuable tools in biology?
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-they determine the age of samples
-serve as mutagenic and cytotoxic agents -they induce mutations in DNA -act as biological "tracers" |
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what is an orbital
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the 3D space (path) where an electron is found 90% of the time
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what is electronegativity
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a measure of an atom's attraction for electrons
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what does a chemical bond result from
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the attraction between oppositely charged ions
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what are compounds formed by ionic bonds called
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ionic compounds or salts
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what is a molecule's shape determined by
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the positions of its atom's valence orbitals
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what are chemical reactions
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the making and breaking of chemical bonds
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what are 4 of water's properties that facilitate an environment for life?
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-cohesive behavior
-ability to moderate temperature -expansion upon freezing -versatility as a solvent |
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what is cohesion
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the phenomenon that collectively, hydrogen bonds hold water molecules together
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what is adhesion
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that attraction between different substance
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what is surface tension
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a measure of how hard it is to break the surface of a liquid
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what is heat
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a measure of the TOTAL amount of kinetic energy due to molecular motion
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what does temperature measure
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the intensity of heat due to the AVERAGE kinetic energy of molecules
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what is evaporation
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transformation of a substance from liquid to gas
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what is heat of vaporization
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the heat a liquid must absorb for 1g to be converted to gas
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what is evaporative cooling
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when the remain surface cools as a liquid evaporates
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what is hydrophilic
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substances that dissolve in water
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what is hydrophobic
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substances that don't dissolve in water
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what is a colloid
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a stable suspension of fine particles in a liquid
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what is a hydration shell
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a sphere of water molecules that surround each ion when an ionic compound is dissolved in water
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what are solutions characterized by
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the concentration of the solute
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what is a molecule with an extra proton
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H3O, hydronium ion
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what is a molecule that lost a proton called
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a hydroxide ion (OH-)
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what do scientists use to describe whether a solution is acidic or basic
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the pH scale
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what is a solution in which the concentration of H+ is equal to that of OH- defined as
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neutral
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what is acid percipitation
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rain, snow, or fog with a pH lower than 5.2
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what does CO2, released by fossil fuel combustion contribute to
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-warming of the earth ("greenhouse effect"
-acidification of oceans (increasing protons drive the reaction towards carbonic acids, leaving less carbonate available for coral reef production) - |
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what is organic chemistry
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the study of compounds that contain carbon
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how many bonds can carbon form & why
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4 because it has 4 valence electrons (tetravalence)
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what does -ane mean
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carbon atoms are bonded with SINGLE bonds
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what does -ene mean
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carbon atoms are bonded with DOUBLE bonds
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how doe carbon chains vary?
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-length
-branching -double-bonds -rings |
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what are hydrocarbons
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organic molecules consisting of only carbon and hydrogen; have a lot of chemical potential energy
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what are structural isomers
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they have different covalent arrangements of their atoms
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what are geometric isomers
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they have the same covalent arrangements by different spatial arrangements
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what are enantiomers
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isomers that are mirror images of eachother
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what are functional groups
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the components of organic molecules that are most commonly involved in chemical reactions
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what are the 7 most important functional groups
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-hydroxyl group (OH)
-carbonyl group (-C-) -amino group (NH2) -carboxyl group (COOH) -sulfhydryl group (HS) -methyl group (CH3) -phosphate group (PO4) |
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what are the carbonyl compounds
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-ketone (internal carbon)
-aldehydes (terminal carbon) |
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what can amines act as
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bases; can pick up a proton from the surrounding solution
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what is ATP
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adenosine triphosphate: a phosphate molecule that is the primary energy-transferring molecule in the cell
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what is a polymer
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a high molecular weight compound consisting of long chains that may be open, closed, linear, branched, or cross-linked.
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what are the polymer chains composed of
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repeating units, called monomers
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what are examples of monomers
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-monosaccharides (simple sugars)
-acetate -amino acids -nucleic acids (nucleotides) |
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what are examples of polymers
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-glycogen (animals)
-cellulose (plants) -fats/lipids -proteins -DNA -RNA |
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what is a condensation reaction
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monomer in, water out
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what is hydrolysis
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water in, monomer out
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what are the types of carbohydrates
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-monosaccharides (single)
-oligosaccharides (few) -polysaccharides (many) |
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what is a carbohydrate
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carbon hydrate or hydrated carbon atoms
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what is the general empirical formula for carbs?
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(CH2O)n
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what determines the strength of the glucose bond?
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where the OH group is
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what is an alpha glucose ring structure
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the OH is below the plane
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what is a beta glucose ring structure
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the OH is above the plane
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when is a disaccharide formed?
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when a dehydration reaction joins 2 monosaccharides; this covalent bond is called a glycosidic linkage
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how is a maltose formed
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glucose+glucose
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how is sucrose formed
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glucose+fructose
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what is the structure and function of a polysaccharide determined by
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its sugar monomers and the positions of glycosidic linkages
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what is starch
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1-4 linkage of alpha glucose monomers (reactive, digestible, helical shape)
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what is cellulose
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1-4 linkages of beta glucose monomers (unreactive, indigestible)
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what is starch used for
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energy storage in plant cells
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what is glycogen used for
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energy storage in animal cells
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what is cellulose used for
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structural support in cell walls of plants and many algae
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what is amylose
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the form of starch that is composed of long, unbranched chains of glucose units which are joined by means of alpha (1-4) glycosidic bonds
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what is amylopectin
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the form of starch that is composed of long, unbranched chains of glucose units which are joined by means of alpha (1-4) and alpha (1-6) glycosidic bonds
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what is glycogen
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a highly branched homopolysaccharide of D-glucose units that the major form of storage of carbohydrate in animals
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what is chitin?
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structural polysaccharide, found in the exoskeleton arthropods
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what are lipids
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a diverse group of hydrophobic molecules
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what are the most biologically important lipids
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-neutral lipids (fats & oils)
-phospholipids -steroids |
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what are fats constructed from
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glycerol & fatty acids
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what is glycerol
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a 3-carbon alcohol with a hydroxyl group attached to each carbon
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what is a fatty acid
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a carboxyl group attached to a long carbon skeleton
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what is a saturated fat
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a fatty acid chain that has no double bonds (C=C)
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what is an unsaturated fat
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a fatty acid chain that has double bonds (C=C)
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what do waxes contain
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fatty acids combined with other alcohols and hydrocarbons
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what is a phospholipid
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2 fatty acids (hydrophobic)and a phosphate group (hydrophillic) attached to glycerol
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what is amphipathic
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hydrophobic and hydrophillic
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what do phospholipids arrange themselves to form when placed in aqueous environment
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phospholipid bilayer or phospholipid micelle
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what are steroids
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lipids characterized by a carbon skeleton consisting of 4 fused rings
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what are sterols
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steroids with a polar -OH group on one end and a non-polar hydrocarbon on the other end (amphipathic)
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what does trans fat come from
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commercial hydrogenation of oils
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what are the 2 types of nucleic acids
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deoxyribonucleic acid (DNA) & ribonucleic acid (RNA)
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what is DNA
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the genetic material that organisms inherit form their parents; contains the info cells require to function (genes that code for proteins)
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what is RNA required for
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gene expression
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what are the components of nucleotides
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-nitrogenous base
-pentose sugar -phosphate |
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what are the 2 families of nitrogenous bases
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-pyrimidine: single 6-membered ring
-purine: single 6-membered ring fused to a 5-membered ring |
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what are sugars
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poly-hydroxyaldehydes or ketones
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what are the most common sugars
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hexoses (glucose) and pentoses (ribose)
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what bond is a nitrogenous base covalently linked to the ribose sugar though
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N-beta-glycosyl bond
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what are adjacent nucleotides joined by
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covalent bonds
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what structure does the DNA molecule have
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double helix; 2 polynucleotides spiraling around an imaginary axis
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what are the pairing in DNA
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adenine-thymine
guanine-cytosine |
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what are the bases from 2 strands of DNA held together by
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hydrogen bonds
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what is base pairing used to
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-preserve information
-repair mistakes -transfer info |
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what is the primary structure of DNA
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single strand of ribonucleotides linked by phosphodiester bonds
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what is the secondary structure of RNA
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stem-loop hairpins may form by internal H-bonding
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What does the RNA have instead of thymine
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uracil
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what are protein functions
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-structural support
-storage -transport -cellular communications -movement -defense against foreign substances |
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how many amino acids do cells use
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20
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what is an amino acid
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central carbon carboxyl group, amino group, side chain, and H attached
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What are the different things that side chains contain
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-carbon and/or hydrogen
-ring structures -sulfur -hydroxyl groups -amide groups |
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what is a protein
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a polymer of amino acids linked to one another by peptide bonds
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what does a functional protein consist of
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one or more polypeptides twisted, folded, and coiled into a unique shape
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what determines a protein's 3D conformation?
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the sequence of amino acids
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what are typical protein secondary structures
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a coil called an alpha helix and a folded structure called a beta pleated sheet
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what determines protein secondary structure
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interactions between backbone constituents
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what determines protein tertiary structure
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interactions among various side chains (R groups)
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what reinforces the protein's conformation
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strong covalent bonds called disulfide bridges
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what are the 4 different R-group interactions
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-hydrogen bonds
-ionic bonds -hydrophobic interactions -van der waals forces |
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when the quaternary structure of a protein result
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when 2 or more polypeptide chains form one macromolecule
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what is sickle-cell disease
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an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
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what can cause a protein to unravel
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-alterations in pH
-salt concentration -temperature |
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what is denaturation
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loss of a protein's native conformation
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how do scientists determine a protein's conformation
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using x-ray crystallography and nuclear magnetic resonance spectroscopy
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what are chaperonins
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protein molecules that assist the proper folding of proteins
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where has protein misfolding been implicated
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-cystic fibrosis
-Alzheimer's -Parkinson's |
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what does the cell theory state?
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-all organisms are made of cells
-the cell is the functional unit of life, the simplest collection of matter than can live -all cells are descended from earlier cells |
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what are the basic features of all cells
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-plasma membrane
-semifluid substance called cytosol -chromosomes (carry genes) -ribosomes (make proteins) |
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what is the basic structural and functional unit of every organism
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-prokaryotic (bacterial & archaea)
-eukaryotic (protists, fungi, animal, and plants) |
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what is a prokaryote
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a simple, unicellular organism that lacks a discrete nucleus surrounded by a nuclear membrane, and that contains its genetic material within a single chromosome
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what is eukaryotic
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DNA exists in chromosomes, in a nucleus that is bounded by a membranous nuclear envelope
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how big are prokaryotic cells
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.5-5 micrometers
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how big are eukaryotic cells
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10-100 micrometers
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what are the 3 most common shapes of prokaryotic cells
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-spheres (cocci)
-rods (bacilli) -spirals |
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what is an important feature of prokaryotic cells & why
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cell wall- it maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment
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what is peptidoglycan
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a network of sugar polymers cross-linked by polypeptides (found in bacterial cell walls)
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what is a capsule
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an outer sticky, jelly-like coat made of lipo-poly-saccharide
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what is the gram-stain used for
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scientists to classify many bacterial species into gram-positive and gram-negative groups based on cell wall composition
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what is gram negative bacteria
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had less peptidoglycan and an outer membrane that can be toxic, and they're more likely to be antibiotic resistant
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why are cells so small?
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a large surface area (cell membrane) is needed for the cell to interact with the environment
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how big are most plant and animal cells
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10-100 micrometers
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what happens in a light microscope
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visible light passes through a specimen and then through glass lenses, which magnify the image (1000 times)
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what is the minimum resolution of a light microscope
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200 nanometers
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what is the magnification range of a light microscope
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40-1000 times
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what is the total magnification of a light microscope
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ocular magnification times objective magnification
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how do electron microscopes work
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they use magnets to focus electron beams. the electrons then directed to photographic film to produce an image
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what is the resolving power of electron microscopes and why
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.2 nm because they have shorter wavelengths
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what are the 2 basic types of electron microscopes used to study sub-cellular structures
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-scanning electron microscopes
-transmission electron microscopes |
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what do SEMs do
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focus a beam of electrons onto the surface of a specimen, providing images that look 3D
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what do TEMs do
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focus a beam of electrons through thin sections of a specimen
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what does cell fractionation do
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it takes apart and separates the major organelles from one another by size, using high speed centrifuges
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what is homogenization
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any mechanical shearing
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what is homogenate
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anything that was left after the cells were pulvarized
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what is the centrifuge speed for larger cells
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low speed
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what speed is nuclei on in centrifuges & why
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low because its big
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what speed id mitochondria on in centrifuges
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low speed
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what is the plasma membrane
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the membrane at the boundary of every cell that acts as a selective barrier, thus regulating cells chemical composition
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what is the nucleus
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the genetic library of the cell; biggest and most conspicuous organelle
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what is chromatin
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the complex of DNA and protein that makes up the eukaryotic chromosome
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what is the nucleolus
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a region in the nucleus active in the synthesis of ribosomal RNA and ribosome assembly
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what is the nuclear envelope
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the double membrane in eukaryotes that encloses the nucleus separating it from the cytoplasm
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what is the nuclear lamina
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the nuclear side of the envelope containing protein filaments that maintain the shape of the nucleus
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what is the nuclear pore complex
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the multi protein structure forming a channel through the nuclear envelope allowing selected molecules to move between the nucleus and cytoplasm
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what is a ribosome
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a particle composed of rRNA & ribosomal proteins that associated with mRNA and catalyzes the synthesis of protein
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where do ribosomes carry out protein synthesis
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-in the cytosol (free ribosomes)
-on the outside of the endoplasmic reticulum (bound ribosomes) |
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what does the endomembrane system do
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it regulates protein traffic and performs metabolic functions in the cell
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what are the components of the endomembrane system
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-nuclear envelope
-endoplasmic reticulum -golgi apparatus -lysosomes -vacuoles -plasma membrane |
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what is the endoplasmic reticulum
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a networkd of membranous tubules and sacs within the cystoplasm of eukaryotic cells, where lipids and synthesized and membrane bound proteins and secretory proteins are made.
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what is smooth ER
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its involved in lipid synthesis, carbohydrate metabolism, detoxification, and calcium storage; it lacks ribosomes
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what is rough ER
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its involved in the synthesis of membrane bound proteins and secretory proteins (hormones, digestive enzymes) which are distributed by transport vesicles
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what is the golgi apparatus
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the shipping and receiving center
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what are the functions of the golgi apparatus
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-modifies proteins and lipids made in the ER, and sorts and packages them into transport vesicles
-manufactures certain macromolecules, like the cell wall polysaccharides in plants and extracellular matrix glycosaminoglycans in animal cells |
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what are lysosomes
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digestive compartments
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what is Tay-Sachs disease caused by
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a mutation in gene encoding an enzyme that digests gangliosides, a fatty acid found in brain and nerve cells
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what are vacuoles
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diverse maintenance compartments
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what are food vacuoles formed by
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phagocytosis
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what are contractile vacuoles
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pump excess water out of cells & found in many freshwater protists
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what is tonoplast
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membrane that surrounds the central vacuole
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what do central vacuoles do
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hold organic compounds and water
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what are mitochondria
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the sites of cellular respiration
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what are chloroplasts
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the sites of photosynthesis
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what does chloroplast structure include
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-thylakoids, membranous sacs
-stroma, internal fluid |
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what is peroxisome
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a membrane bounded organelle that uses molecular oxygen to oxidize organic molecules
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what are the functions of peroxisome
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-detoxification of alcohols and other compounds
-breaking down fatty acids |
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what is the cytoskeleton
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a network of fibers that organizes structures and activities in the cell
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what does the cytoskeleton do
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-helps to support the cell and maintain its shape
-interacts with motor proteins to produce motility -may help regulate biochemical activities |
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what are the 3 networks that comprise the cytoskeleton
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-microfilaments
-intermediate filaments -microtubules |
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what are microtubules and their functions
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hollow rods that shape the cell or guide the movement of organelles or separate the chromosome during cell division
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what are kinesin
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motor molecules that move various types of vesicles along microtubule tracks
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what do cilia do
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circulate fluids, move egg into oviduct, line air passages to sweep out mucus containing bacterial, pollutants, etc.
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what are flagella required for
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cell motility
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what is the common ultrastructure of cilia and flagella
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a core of microtubules, called an axoneme, sheathed by the plasma membrane & a basal body that anchors the cilium and flagellum
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what is dynein
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a motor protein which "walks" along the microtubules, causing them to bend
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what happens in isolated doublet microtubules
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dynein produces microtubule sliding
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what happens in normal flagellum
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dynein causes microtubule bending
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what are microfilaments and their role
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solid rods built as twisted double chain of actin subunits. their role is to bear tension, resisting pulling forces within the cell
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what are microfilaments formed by
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actin subunits
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what is actin
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the most abundant intracellular protein in a eukaryotic cell
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what do microfilaments that function in cellular motility contain
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the protein myosin in addition to actin
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what do crosslinker actin-binding proteins do
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they induce discrete microfilament arrangements
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what drives amoeboid movement
|
localized contraction brought about by actin and myosin
|
|
|
what is cytoplasmic streaming
|
a circular flow of cytoplasm within the cells
|
|
|
what drives cytoplasmic streaming in plant cells
|
the actin myosin interactions and sol-gel transformations
|
|
|
what do intermediate filaments do
|
they support cell shape, fix organelles, including the nucleus, in place, and are more permanent than MT and MF
|
|
|
what is made of the protein keratin
|
skin, nails, and hair
|
|
|
what are vimentins
|
the type of IF found in fibroblasts (connective tissue)
|
|
|
what are the extracellular structures that help coordinate cellular activities
|
-cell walls of plants
-the extracellular matrix of animals -intercellular junctions |
|
|
what does the cell wall of plants do
|
-protects the plant cell
-maintains its shape -prevents excessive uptake of water |
|
|
what is the cell wall of plants made of
|
cellulose microfibrils embedded in a matrix of other highly branched polysaccharides and protein
|
|
|
how is the primary cell wall material
|
relatively thin and flexible
|
|
|
what is the secondary cell wall like
|
wood, between the plasma membrane and primary cell wall, much thicker
|
|
|
what is the middle lamella
|
thin layer of sticky polysaccharides between primary walls of adjacent cells
|
|
|
what is the plasmodesmata
|
channels between adjacent plant cells
|
|
|
what is the extracellular matrix
|
complex network of polysaccharides and glycoproteins secreted by cells
|
|
|
what does the extracellular matrix form
|
the mass of skin, bones, tendons
|
|
|
what are the functions of the extracellular matrix
|
-protection
-support -adhesion -movement -regulation |
|
|
what are integrins
|
membrane proteins that connect ECM to cytoskeletal-associated proteins
|
|
|
what happens at tight junctions
|
membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
|
|
|
what do desmosome (anchoring junctions) do
|
fasten cells together into strong sheets
|
|
|
what do gap junctions (communication junctions) do
|
provide cytoplasmic channels between adjacent cells
|
|
|
what happens at tight junctions
|
membranes of neighboring cells are pressed together (fuse), preventing leakage of extracellular fluid
|
|
|
what are tight junctions
|
cells that line the stomach, intestine, bladder
|
|
|
where are desmosomes common
|
in tissues that stretch like skin, and in cells that line organs and cavities
|
|
|
what is the plasma membrane
|
the boundary that separates the living cells from its surroundings, it exhibits selective permeability, allowing some substances to cross it more easily than others
|
|
|
what do membrane lipids include
|
phospholipids and sterols (cholesterol & phytosterols)
|
|
|
what is a simple membrane
|
a phospholipid bilayer
|
|
|
what model did H Davson and J. Danielli propose
|
a sandwich model in which the phospholipid bilayer lies between 2 layers of globular proteins
|
|
|
What did Singer and Nicolson propose about the membrane
|
that it is a mosaic of proteins dispersed and individually inserted into the phospholipid bilayer, with only the hydrophilic regions exposed to "water"
|
|
|
what is the fluid mosaic model
|
membrane proteins are embedded in the lipid bilayer, and float freely
|
|
|
what does the fluid mosaic mean
|
membrane fluidity: membrane lipids drift laterally and even "flip flop"
|
|
|
what is fluorescence photobleaching used for
|
to visualize the lateral movement of lipids
|
|
|
how does fluorescent photobleaching work?
|
1-label lipids with a fluorescent "tag"
2-focus a strong beam on a cell surface to bleach the label 3-watch how fast the label comes back from unbleached parts |
|
|
what must membranes be to work properly
|
fluid
|
|
|
what does cholesterol act as in membrane fluidity
|
a buffer, preventing unsaturated fats from becoming solid and saturated fats from becoming liquid
|
|
|
what are the 2 types of proteins
|
-integral proteins
-peripheral proteins |
|
|
when is the asymmetrical distribution of proteins, lipids and associated carbohydrates in the plasma membrane determined
|
when the membrane is built by the ER and golgi apparatus
|
|
|
what are transmembrane proteins
|
integral proteins that span the membrane
|
|
|
what are the functions of membrane proteins
|
-transport
-enzymatic activity -signal transduction -intercellular joining -cell-cell recognition -attachment to the cytoskeleton and extracellular matrix |
|
|
how do cells recognize eachother
|
by binding to surface molecules, often carbohydrates, on the plasma membrane
|
|
|
what molecules can dissolve in the lipid bilayer and pass through the membrane rapidly
|
hydrophobic molecules
|
|
|
what molecules have trouble crossing the membrane easily
|
polar molecules
|
|
|
what is passive transport
|
diffusion of a substance across a membrane with no energy investment
|
|
|
what is diffusion
|
net drift of molecules in the direction of lower concentration due to random thermal movement
|
|
|
what happens at dynamic equlibrium
|
as many molecules cross one way as cross in the other direction
|
|
|
what is osmosis
|
the diffusion of water across a selectively permeable membrane
|
|
|
what is the direction of osmosis determined by
|
a difference in total solute concentration
|
|
|
what direction osmosis
|
region of higher concentration to lower concentration
|
|
|
what is tonicity
|
the ability of a solution to cause a cell to gain or lose water
|
|
|
what is an isotonic solution
|
where the solute concentration is the same as that inside the cell; no net water movement across the plasma membrane
|
|
|
what is a hypertonic solution
|
solute concentration is greater than that inside the cell; cell loses water
|
|
|
what is a hypotonic solution
|
the solute concentration is less than that inside the cell; cell gains water
|
|
|
what is osmoregulation
|
control of water balance
|
|
|
what happens in facilitated diffusion
|
transport proteins speed movement of molecules across the membrane
|
|
|
what do channel proteins provide
|
hydrophilic corridors that allow a specific molecule or ion to cross the membrane
|
|
|
what are aquaporins
|
channel proteins that facilitate the passage of water
|
|
|
what are carrier proteins
|
transport proteins that bind to molecules and change shape to shuttle them across the membrane
|
|
|
what is a gated channel
|
a membrane channel whose permeability is regulated; facilitated or mediated transport system
|
|
|
what are the 2 major types of membranes that involve the opening of the channel
|
-voltage gated channel
-ligand-gated channel |
|
|
what is active transport
|
the movement of a solute across a biological membrane such that the movement is directed upward a concentration gradient
|
|
|
what is facilitated diffusion
|
passive diffusion
|
|
|
what drives the diffusion of ions across a membrane
|
the electrochemical gradient:
-chemical force -electrical force |
|
|
what is an electrogenic pump
|
a transport protein that generates the voltage across a membrane
|
|
|
when does cotransport occur
|
when active transport of a solute indirectly drives transport of another solute
|
|
|
what does bulk transport across the plasma membrane occur by
|
exocytosis & endocytosis
|
|
|
what happens in exocytosis
|
transport vesicles migrate to the membrane, fuse with it and release their contents
|
|
|
what happens in endocytosis
|
the cell takes in macromolecules by forming vesicles from the plasma membrane
|
|
|
what are the 3 types of endocytosis
|
-phagocytosis
-pinocytosis -receptor-mediated endocytosis |
|
|
what is metabolism
|
the totality of an organism's chemical reactions
|
|
|
what is metabolism
|
the totality of an organism's chemical reactions
|
|
|
what does a metabolic pathway begin an end with
|
it begins with a specific molecule and ends with a product
|
|
|
what do catabolic pathways do
|
release energy by breaking down complex molecules into simpler compounds
|
|
|
what do anabolic pathways do
|
consume energy to build complex molecules from simpler ones
|
|
|
what is bioenergetics
|
the study of how organisms manage their energy resources
|
|
|
what is energy
|
the capacity to do work
|
|
|
what are forms of energy
|
-heat
-chemical -electrical -mechanical -radiant |
|
|
what are the 2 states in which energy exists
|
-potential energy
-kinetic energy |
|
|
what is potential energy
|
stored energy/ energy of position
|
|
|
what is kinetic energy
|
energy of movement
|
|
|
what is thermodynamics
|
the study of energy transformations
|
|
|
what is the first law of thermodynamics
|
the energy of the universe is constant; energy can be transferred and transformed, but it cant be created or destroyed
|
|
|
what is the second law of thermodynamics
|
every energy transfer or transformation increases the entropy (disorder) of the universe
|
|
|
where does energy flow from
|
the sun
|
|
|
how do spontaneous processes occur
|
without energy input, they can happen quickly or slowly
|
|
|
what must happen for a process to occur without energy
|
it must increase the entropy of the universe
|
|
|
what do scientists need to do to whether a reaction occurs spontaneously
|
they need to determine energy changes that occur in chemical reactions
|
|
|
what must happen for a chemical reaction to be spontaneous
|
the reactants must have more potential energy than the products and/or be more ordered than the products
|
|
|
what is a living system's free energy (G)
|
energy thats available to do work when temperature & pressure are uniform, as in a living cell
|
|
|
what is free energy
|
a measure of a system's instability, its tendency to change to a more stable stable; higher G to lower G
|
|
|
what is equilibrium
|
a state of maximum stability
|
|
|
what is an exergonic reaction
|
energy outward; reaction proceeds with a net release of free energy and is spontaneous
|
|
|
what is an endergonic reaction
|
reaction absorbs free energy from its surroundings and is not spontaneous
|
|
|
what is a defining feature of life
|
that metabolism is never at equilibrium
|
|
|
what are the 3 main kinds of work that cells do
|
-mechanical
-transport -chemical |
|
|
what is energy coupling
|
the use of an exergonic process to drive an endergonic one
|
|
|
what are the 3 types of cellular work powered by
|
hydrolysis of ATP
|
|
|
what are enzymes
|
proteins (usually) that carry out most catalysts in living organisms
|
|
|
what is activation energy
|
the initial energy needed to start a chemical reaction
|
|
|
how do enzymes catalyze reactions
|
by lowering the activation barrier
|
|
|
what is a catalyst
|
a chemical agent that speeds up a reaction without being consumed by the reaction
|
|
|
what do enzymes end in
|
-ase
|
|
|
what is a substrate
|
the reactant that an enzyme acts on
|
|
|
what is an enzyme-substrate complex
|
when the enzyme binds to its substrate
|
|
|
what is the active site
|
the region on the enzyme where the substrate binds
|
|
|
what is induced fit
|
that many enzymes change shape when they bind to the substrate
|
|
|
what is the "lock and key"
|
that the shape of an enzyme active site allows a specific substrate to fit
|
|
|
how does the active site lower activation energy barrier?
|
by
-orienting substrates correctly -straining substrate bonds -providing a favorable microenvironment -covalently bonding to the substrate |
|
|
what is acid-base catalysis
|
enzyme side chains transfer H+ to or from the substrate- a covalent bond breaks
|
|
|
what is covalent catalysis
|
a functional group in a side chain bonds covalently with the substrate
|
|
|
what is metal ion catalysis
|
metals on side chains gain or lose electrons
|
|
|
what environmental factors affect enzyme activity
|
-temperature
-pH |
|
|
what are cofactors
|
nonprotein enzyme helpers, usually metal ions, (minerals) found in the active site participating in catalysis.
|
|
|
what are coenzymes
|
nonprotein organic molecules required for proper enzymatic activity, vitamins B2, and B3 "store" energy containing electrons, vitamin B6 in amino acid metabolism, and B12 in DNA, fatty acid metabolism
|
|
|
what are inhibitors
|
molecules that bind to an enzyme to decrease enzyme activity
|
|
|
what are competitive inhibitors
|
they bind to the active site of an enzyme, competing with the substrate
|
|
|
what will nullify the effect of the competitive inhibitor?
|
increasing the substrate concentration
|
|
|
what does a noncompetitive inhibitor do
|
it binds to the enzyme at a different site (allosteric site) and distorts the active site
|
|
|
what is allosteric regulation
|
a protein's function at one site is affected by binding of a regulatory molecule at another site, called an allosteric site
|
|
|
what are the 2 forms in which allosteric enzymes exist
|
-active form
-inactive form |
|
|
what do allosteric inhibitors do
|
stabilize the inactive form of the enzyme, inhibiting activity
|
|
|
what do allosteric activators do
|
stabilize the active form of the enzyme, promoting enzyme activity
|
|
|
what is oscillation
|
conformational changes in an allosteric enzyme
|
|
|
what are allosteric regulators attractive for
|
drug candidates for enzyme regulation
|
|
|
what is feedback inhibition
|
the switching off of a metabolic pathway by its end product
|
|
|
what does feedback inhibition prevent
|
the cell from wasting chemical resources by synthesizing more product than is needed
|
|
|
how do animals obtain energy?
|
some by eating plants and some animals feed on other organisms that eat plants
|
|
|
what does photosynthesis generate
|
O2 & organic molecules which are used in cellular respiration
|
|
|
what do cells use to regenerate ATP
|
chemical energy stored in organic molecules
|
|
|
what is the most important source of chemical potential energy in cells?
|
electrons
|
|
|
why do electrons in ATP have high potential energy?
|
because of the 4 negative charges in its 3 phosphate groups repel eachother
|
|
|
what is energetic coupling
|
when the exergonic phosphorylation reaction is paired with an endergonic reaction
|
|
|
what are reduction-oxidation reactions (redox reactions)
|
class of chemical reactions that involve the loss or gain of an electron
|
|
|
what is an electron donor always paired with
|
a reactant that acts as an electron acceptor
|
|
|
when does an electron lose potential energy
|
when it shifts from a less electronegative atom to a more electronegative atom
|
|
|
what happens in cellular respiration
|
glucose is oxidized in a series of redox reactions. the partner that becomes reduced is called NAD+. 2 electrons and 1 proton from organic compounds are transferred to NAD+, reducing it to NADH.
|
|
|
what is FAD (flavin adenine dinucleotide)
|
A second electron acceptor
|
|
|
what does NAD+ represent
|
stored energy
|
|
|
how is NAD+ an electron shuttle?
|
-some enzymes harvest hydrogen atoms from energy rich molecules, and use NAD+ as a cofactor for these oxidation reactions
-in an oxidation-reduction reaction, 2 electrons and 1 proton are transferred to NAD+, forming NADH -NADH then diffuses away and is available to other molecules |
|
|
what is the partner that becomes reduced in cellular respiration
|
nicotinamide adenine dinucleotide (NAD+)
|
|
|
what is glucose?
|
a key intermediary in cell metabolism. cells use it to build fats, carbs, and other compounds. cells recover glucose by breaking down these molecules
|
|
|
what is the 4 step process for cellular respiration
|
-glucose is broken down to pyruvate
-pyruvate is processed to form acetyl-CoA -acetyl-CoA is oxidized to CO2 -compounds that were reduced in steps 1-3 are oxidized in reactions that lead to ATP production |
|
|
what is gycolysis
|
a series of 10 chemical reactions, its the 1st step in glucose oxidation
|
|
|
what happens in glycolysis
|
glucose is broken down into two 3-carbon molecules of pyruvate, and the potential energy released is used to phosphorylate ADP to form ATP. in the process, NAD+ is reduced to NADH, an electron carrier that donates electrons to more oxidized molecules
|
|
|
what are the 2 major phases of glycolysis
|
-energy investment phase
-energy payoff phase |
|
|
what is isomerase
|
an enzyme that rearranges a molecule into a structural isomer
|
|
|
what is substrate-level phosphorylation
|
the process by which a smaller amount of ATP is formed in glycolysis and the citric acid cycle. an enzyme transfers a phosphate group from a substrate molecule to ADP.
|
|
|
what is the energy payoff stage
|
the redox reaction that oxidizes the carbonyl carbon, and then uses the released energy to add Pi (substrate-level phosphorylation), creating an activated substrate & 2 ATP
|
|
|
what is NADH
|
an electron carrier that donates electrons to more oxidized molecules
|
|
|
what is coenzyme A
|
a cofactor, it accepts acetyl groups and transfers them to substrates
|
|
|
what does the citric acid cycle/Krebs cycle do
|
it oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH, per turn
|
|
|
what is the citric acid cycle
|
8 steps, each catalyzed by a specific enzyme. the acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate. the next 7 steps decompose the citrate back to oxaloacetate, making the process a cycle.
|
|
|
what is the krebs cycle regulated by
|
feedback inhibition by ATP & NADH
|
|
|
what happens in oxidative decarboxylation
|
NAD is reduced, and CO2 is released
|
|
|
what is the overall reaction for glycolysis and the krebs cycle
|
C6H12O6+10NAD++2FAD+4ADP+4Pi->6CO2+10NADH+2FADH2+4ATP
|
|
|
What is the NADH and FADH2 use for
|
to make more ATP
|
|
|
what happens during the 4th step in glucose oxidation
|
the high potential energy of the electrons carried by NADH and FADH2 is gradually decreased by molecules that participate in a series of redox reactions.
|
|
|
what is the electron transport chain
|
collection of molecules embedded in the cristae, the folded inner membrane of mitochondrion
|
|
|
what is the proton-motive force
|
the H+ gradient in electron transport
|
|
|
what is ATP synthase
|
an enzyme complex consisting of an ATPase "knob" component and a membrane-bound proton-transporting base component connected by a "stalk". It makes ATP from ADP & Pi
|
|
|
what is chemiosmosis
|
the use of energy in a H+ gradient to drive cellular work. the mitochondrion couple electron transport & energy release to ATP synthesis
|
|
|
what happens in the electron transport chain
|
electrons gradually lose their energy in a stepwise function, until they have low energy, and combine with oxygen to make water.
|
|
|
what is the energy flow sequence during cellular respiration
|
glucose->NADH->electron transport chain->proton-motive force->ATP
|
|
|
what happens in the absence of O2?
|
glycolysis couples with fermentation or anaerobic respiration to produce ATP
|
|
|
what does fermentation consist of
|
glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis
|
|
|
what happens in alcohol fermentation
|
pyruvate is converted to ethanol in 2 steps, with the 1st releasing CO2
|
|
|
what happens in lactic acid fermentation
|
pyruvate is reduced by NADH, forming lactate as an end product, with no release of CO2
|
|
|
what do fermentation and aerobic respiration have in common
|
they both use glycolysis to oxidize glucose & other organic fuels to pyruvate
|
|
|
what are the differences between fermentation and aerobic respiration
|
the processes have different electron acceptors
|
|
|
what does cellular respiration produce
|
38 ATP per glucose molecule
|
|
|
what does fermentation produce
|
2 ATP per glucose molecule
|
|
|
what do obligate anaerobes do
|
carry out fermentation or anaerobic respiration
|
|
|
what are faculative anaerobes
|
yeast & bacteria which can survive using either fermentation of cellular respiration
|
|
|
what is beta oxidation
|
the way in which fatty acids are broken down
|
|
|
what is overnourishment
|
excessive intake of food energy with the excess stored as fat
|
|
|
what is insulin
|
the peptide hormone
|
|
|
what is glucagen
|
a peptide hormone that is synthesized by the alpha cells of the pancreas
|
|
|
what is glucagen's primary function
|
to increase levels of glucose in the blood
|
|
|
what is photoenergy
|
the process that converts solar energy into chemical energy
|
|
|
how do autotrophs sustain themselves
|
without eating anything derives from other organisms
|
|
|
how do heterotrophs obtain their organic material
|
from other organisms
|
|
|
are plants autotrophs or heterotrophs
|
autotrophs; they use the energy of the sunlight to make organic molecules from water & carbon dioxide
|
|
|
why is only 5% of the sun's energy that reaches the earth converted into chemical energy
|
-not all wavelengths absorbed
-much energy is lost during conversion of light energy to chemical energy, and during the carbon fixation reactions |
|
|
what are chloroplasts
|
highly structured, membrane rich organelles
|
|
|
what are thylakoids
|
internal vesicle-like structures; these are embedded with photosynthetic pigments like chlorophyll
|
|
|
what are grana (granum)
|
columns or stacks of thylakoids
|
|
|
what are stroma
|
semi-liquid surrounding thylakoids
|
|
|
what 2 sets of reactions does photosynthesis consist of
|
-light dependent reactions
-calvin cycle |
|
|
what does the light dependent reaction produce
|
O2 from H2O
|
|
|
what does the calvin cycle produce
|
sugar from CO2
|
|
|
what is the light dependent reaction & calvin cycle linked by
|
electrons
|
|
|
when are electrons released in the light dependent reactions
|
when water is split in 2 to form oxygen gas
|
|
|
what happens to the electrons release in the light dependent reactions
|
they're transferred to the electron carrier NADP+, forming NADPH
|
|
|
what does the calvin cycle use the electrons of NADPH and energy from ATP for
|
to reduce CO2 to make sugars
|
|
|
what is the electromagnetic spectrum
|
the entire range of electromagnetic energy, or radiation
|
|
|
what is light a form of
|
electromagnetic energy
|
|
|
what is wavelength
|
distance between crests of waves
|
|
|
what is a photon
|
a discrete amount of light energy
|
|
|
what happens when a molecule absorbs a photon
|
one of its electrons is elevated to a higher orbital
|
|
|
when are photons absorbed
|
when the energy of the photon is equal to the difference between the ground state and the excited state of the electron
|
|
|
is the excited state stable or unstable
|
unstable
|
|
|
what are pigments
|
substances that absorb visible light
|
|
|
what happens to wavelengths that aren't absorbed
|
they're reflected or transmitted
|
|
|
why do leaves appear green
|
because chlorophyll reflects and transmits green light
|
|
|
what are the 2 types of photosystems in the thylakoid membrane
|
photosystem II
photosystem I |
|
|
what is photosystem II best at absorbing
|
a wavelength of 680 nm
|
|
|
what is photosystem I best at absorbing
|
a wavelength of 700 nm
|
|
|
how are photosystem I & II similar
|
they both have chlorophyll a
|
|
|
how are photosystem I & II different
|
they are associated with different proteins, which affects their absorption spectra
|
|
|
what are the major steps in electron flow in photosynthesis
|
1)photosystem II absorbs light & electrons in chlorophyll are excited & transferred to the primary acceptor of photosystem II
2)an enzyme splits water into H+ & 1/2 O2. Electrons are transferred back to chlorophyll of photosystem II, reducing it. 1/2 O2 combines with another 1/2 O2 to make O2 which is then released 3)electrons pass from the primary acceptor of photosystem II through ETC, and release energy used to make ATP by phosphorylation 4)after ETC, electrons originating from photosystem II go to photosystem I to reduce it 5)photosystem I has already been excited by absorbing light and losing electrons to its primary acceptor |
|
|
What is the difference between ATP production in the mitochondria vs chloroplasts
|
mitochondria- oxidative phosphorylation, energy of electrons comes from food, ATP is made utilizing NADH
Chloroplasts-photophosphorylation, energy of electrons comes from sunlight, ATP is made without utilizing ATP |
|
|
what are the calvin cycle steps
|
1)carbon fixation- CO2 from the air is attached to CO2 receptor, RuBP sugar, catalyzed by the enzyme "RUBISCO" (most abundant protein). RuBP splits into 2 molecules of 3 phosphoglycerate
2)reduction- phosphorylation by ATP and reduction by NADPH. 6 molecule of glyceraldehyde 3-phosphate are made 3)other 5 molecules of G3P are used to recreate RuBP. More phosphorylation occurs using ATP from the light reactions |
|
|
what are the G3P molecules produced by the calvin cycle used for
|
to make glucose & fructose=sucrose
|
|
|
in rapidly photosynthesizing cells where sucrose is abundant, what is glucose temporarily stored in the chloroplast as?
|
starch
|
|
|
what does energy entering chloroplasts as sunlight get stored as
|
chemical energy in organic compounds
|
|
|
what does sugar made in the chloroplasts supply
|
chemical energy and carbon skeletons to synthesize the organic molecules of cells
|
