BIOL 213: EXAM 1
141 Cards in this Set
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Why study cell and molecular biology?
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-cells are the fundamental unit of life
-all cells have similar chemistry (allows mechanistic understanding of cellular function and dysfunction)
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1st two tenets of Cell Theory proposed by
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Schleiden and Schwann
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third tenet of cell theory added by
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Louis Pasteur
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cell theory
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1. All organisms are composed of one or more cells
2. the cell is the smallest unit of life
3. cells can only arise by division from a pre-existing cell
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Features common to all cells
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-complex and highly organized
-DNA- genetic program for reproduction
-plasma membrane- selective barrier
-cytosol/cytoplasm
-ribosomes- protein synthesis
-respond to stimuli and adapt to their environment
-small
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two classes of cells (three evolutionary lineages)
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-prokaryotic- relatively simple, no nucleus
---bacteria and archaea
-eukaryotic- more complex, nucleus and other organelles
---animals, plants, fungi, protists
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eukaryotic cells contain _____ organelles
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membrane enclosed
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why is biological chemistry important?
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an understanding of the structures, properties and quantities of molecules associated with cells is essential to understanding biological function at any level
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why are moles important
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atoms and molecules are very small so a scale factor is generally used to describe quantities (mole)
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one mole is ____ individuals
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6 x 10^23 (avogadro's number)
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types of strong chemical bonds
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covalent and ionic
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types of weak chemical bonds
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hydrogen, hydrophobic interactions, Van der Waals Attractions
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covalent bond
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sharing of electrons
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ionic bond
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transfer of electrons
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Which type of bond is affected by water? why?
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ionic; weaker, can be pulled apart by polar water molecules
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hydrogen bond
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electrostatic interaction between a H held in a polar covalent bond and another atom (usually O or N) also held in polar covalent bond
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Hydrophobic interactions
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"water fearing" attraction between nonpolar molecules cause by repulsion from water. (phospholipid bilayer in cells)
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double bond (covalent)
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cannot rotate freely around the bond axis. This restriction has a major influence on the three-dimensional shape of many macromolecules
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an ionic bond can be considered
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a very polar covalent bond
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van der Waals Attractions
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weak interaction caused by transient electrical charges, dependent on the distance between atoms
-in large numbers can be significant in the attraction between macromolecular surfaces
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-OH group is called a
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hydroxyl group
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C=O group is called a
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carbonyl group
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-COOH is called
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a carboxyl group
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hydrophilic
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water loving
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hydrophobic
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water hating
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The acidity of a solution is defined by
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the concentration of H+ ions it possesses.
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pH=
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-log[H+]
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is a solution of pH 4 more acidic or alkaline than a solution of pH 6
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more acidic; by 100 fold
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acid
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any molecule capable of releasing (donating) a hydrogen ion (proton)
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strong acids vs. weak acids
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strong acids lose their protons quickly
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base
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any molecule capable of accepting a hydrogen ion (proton)
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strong bases vs. weak bases
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strong bases dissociate readily in water
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buffers
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weak acids and bases that can release or take up protons near pH 7, keeping the environment of the cell relatively constant under a variety of conditions.
-consists of a mixture of a weak acid and its conjugate base, or a weak base and its conjugate acid
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why are many of the acids and bases important in the cell weak?
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partial dissociation, reversible
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methyl
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-CH3 (nonpolor hydrocarbon)
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hydroxyl
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-OH (alcohol)
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carboxyl
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-COOH (weak acid)
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carbonyl (ketone and aldehyde)
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C=O
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Amino
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-NH2 (weak base)
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Amide
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O=C-NH2 (carbonyl + amine)
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Phosphate
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PO3 (ester and anhydrides)
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Sulfhydryl
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-SH (forms disulfide bonds)
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cells consist of 70% water, and 30% chemicals such as
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ions, small molecules (4%)
phospholipids (2%)
DNA (1%)
RNA (6%)
proteins (15%)
polysaccharides (2%)
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most sugars have the same general formulas (CH2O)n hence the name carbohydrate:
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most sugars have 3-7 carbons, with 6 carbon sugars (hexoses) being especially important.
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polysaccharides function as
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stores of chemical energy and durable biological structural materials
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Glucose- two ring conformations
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alpha and Beta
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monosaccharides are formed into polysaccharides by
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condensation reaction (gives off water)
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polysaccharides broken up by
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hydrolysis (consumes water)
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cells contain four major families of organic molecules
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sugars, fatty acids, amino acids, nucleotides
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sets of molecules with the same chemical formula but different structures are called
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isomers
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mirror-image pairs of molecules are called
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optical isomers
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monosaccharides can be linked by covalent bonds called
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glycosidic bonds
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sucrose
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glucose + fructose
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prefix oligo-
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macromolecules made of a small number of monomers (3-50)
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polymers
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contain hundreds or thousands of subunits
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glucose has a central role as
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an energy source for cells
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fatty acids and lipids ____ in water
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insoluble
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lipids or fats are not really ______ but are ______
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not really polymers of fatty acids, but are formed by condensation reactions.
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Functions of fatty acids and lipids
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structural: cell membranes
Energy Storage: triacylglycerols
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fatty acids
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long, unbranched hydrocarbon chains with a single carboxyl group on the end
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Amphipathic molecule
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hydrophilic end (carboxyl) and hydrophobic end (hydrocarbon)
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fatty acids typically have ____ number of carbons
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an even (14-20) number of carbons
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carbon #1 in fatty acid associated with
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carboxylic group
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saturated tails
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no double bonds between its carbon atoms and contains maximum possible number of hydrogens
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unsaturated tails
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one or more double bonds along their length
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micelle
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formed by fatty acids in water; spherical
e.g. triacylglycerols in cytoplasm
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monolayer
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formed at surface of water by fatty acids
-phospholipids and glycolipids form self-sealing lipid bilayers that are the basis for all cellular membranes
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fatty acids are stored as
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an energy reserve through an ester linkage to glycerol to form triacylglycerol (fat)
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what determines the properties of fat?
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the chain length and level of saturation
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phospholipid
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glycerol + 2 fatty acids + phosphate group linked to another hydrophilic molecule
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triacylglycerols vs. phospholipids (in water)
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triacylglycerols are predominately hydrophobic; phospholipids are strongly amphipathic
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proteins are
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polymers of amino acids
-formed by condensation reactions
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functions of proteins
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-enzymatic
-signaling
-structural
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peptide bonds formed by
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condensation reactions that link one amino acid to the next
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functionality of proteins derives from
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side groups:
-acidic or basic
-polar or nonpolar
-other features
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amino acid side chains (R groups)
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-profound influence on structure/function of proteins
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side chains (R groups) classified as
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-charged (acidic, basic)
-uncharged polar (hydrophilic)
-nonpolar (hydrophobic)
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pyrimidines
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Cytosine, Thymine, Uracil (5 membered ring)
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Purines
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Adenine, Guanine (6 membered ring + 5 membered ring)
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nucleotide
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base + pentose + phosphate
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nucleic acids are polymers of
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nucleotides (formed by condensation reactions)
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functions of nucleic acids
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-storage and transmission (expression) of genetic information
-nucleotides also function as energy carriers and as signaling molecules
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nucleotides are joined together by
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a phosphodiester linkage to form nucleic acids. condensation reaction
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nucleic acids have structural polarity:
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the 5' end has a free phosphate group, the 3' end has a free hydroxyl group
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central dogma of biology
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replication--> transcription -->translation
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sequence defines.... which defines....
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structure; function
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noncovalent bonds specify
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structure and intramolecular interactions
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pyrimidines
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Cytosine, Thymine, Uracil (5 membered ring)
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Purines
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Adenine, Guanine (6 membered ring + 5 membered ring)
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nucleotide
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base + pentose + phosphate
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nucleic acids are polymers of
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nucleotides (formed by condensation reactions)
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functions of nucleic acids
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-storage and transmission (expression) of genetic information
-nucleotides also function as energy carriers and as signaling molecules
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nucleotides are joined together by
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a phosphodiester linkage to form nucleic acids. condensation reaction
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nucleic acids have structural polarity:
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the 5' end has a free phosphate group, the 3' end has a free hydroxyl group
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central dogma of biology
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replication--> transcription -->translation
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sequence defines.... which defines....
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structure; function
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noncovalent bonds specify
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structure and intramolecular interactions
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First law of Thermodynamics
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energy cannot be created or destroyed, but it can be converted from one form to another
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Second law of thermodynamics
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energy spontaneously tends to disperse
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entropy is
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dispersal of energy
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cells use energy to
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create and maintain order
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molecules of a living cells possess energy because
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of their vibrations, rotations, and movement through space, and because of the energy that is stored in the bonds between individual atoms.
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the free energy, G, measures
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the energy of a molecule that could in principle be used to do useful work at constant temperature (as in a living cell)
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energetically favorable reactions have
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a negative delta G
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delta G depends of
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the energy stored in chemical bonds and also on the concentration of the molecules in a reaction
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delta G =
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delta G* + RTln [products]/[reactants]
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delta G*, the standard free energy, reflects
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the intrinsic energy stored in bonds and is defined under standard conditions (25* C; 1 atm; 1 M concentration; pH7)
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at equilibrium, the forward and reverse ____ for a reaction are equal, but not necessarily the ____
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rates; concentrations
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Keq=
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[AB]/[A][B]
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the greater the value for Keq, the
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more negative delta G*
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delta G* and Keq values can be used to predict:
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1. ratio of reactants to products at steady state
2. direction of reactions
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2 different ways to couple reaction
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sequential "siphon" and activated carrier (ATP)
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activated carriers store energy in the form of...
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a transferable chemical group or as high-energy electrons
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NAD and NADP are electron carriers that
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facilitate oxidations and reductions
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Where do cells get the energy required to create and maintain order?
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environment:
-light (electromagnetic energy)
-food (chemical bond energy)
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Cells obtain energy from
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the oxidation of organic molecules
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oxidation
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loss of electron
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reduction
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gain of electron
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electron transfer often also involves
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a proton
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Hydrogenation
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reduction
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Dehydrogenation
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oxidation
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Reduced organic compounds yield
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more energy (electrons) for chemical work: fats>sugars
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enzymes increase the rate of reactions by
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reducing the activation energy
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KM
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the Michaelis' constant Intrinsic value; ability to 'grasp' substrate
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competitive inhibition
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interferes with active site of enzyme so substrate cannot bind
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noncompetitive inhibitor
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changes shape of enzyme so it cannot bind to substrate
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enzyme regulation- allosteric effects
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-more than one binding site
-binding of one ligand alters protein conformation, which changes activity
-can be positive or negative
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feedback inhibition
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inhibited when accumulated to certain level; provides balance
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conformational changes with nucleotide hydrolysis can be used to
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drive a motor protein
(muscle contraction, chromosome spindles, organelle movement)
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primary structure
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amino acid sequence
-joined through condensation reactions to form peptide bonds
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unstable folding leads to
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degradations or aggregation
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protein folding constrained by the formation of
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many weak noncovalent bonds
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protein folding in a cells is often assisted by
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molecular chaperones, or chaperonins
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secondary structure
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alpha helix and beta sheet
-stabilized by H bonds forming between the amino and carbonyl groups in the polypeptide backbone
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alpha helix
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the carbonyl group of one peptide bond is H bonded to the amino group of a peptide bond four amino acids away.
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alpha helix can span a membrane bilayer
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shielded from the hydrophobic lipid hydrocarbons (stable H bonding)
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B sheet ligand
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the polypeptide strands are extended, giving the backbone a pleated shape. These strands associate through hydrogen bonding between peptide bonds in different strands
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Tertiary structure
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the conformation formed by an entire polypeptide including alpha helixes, beta sheets, other loops and folds
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ligand
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anything that binds with a protein
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Quaternary Structure
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complex of more than one polypeptide
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extracellular proteins are often stabilized by
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covalent cross-linkages: disulfide bonds (Cystine)
these bonds do not change the conformation of a protein, just stabilize
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Test 1: Biol 213