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139 Cards in this Set
- Front
- Back
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Glucose
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6-carbon aldohexose sugar that is an important energy source in living organisms and is a component of many carbohydrates
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Cellulose
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polymer of glucose with beta1,4 glycosidic bonds. It is an insoluble substance that is the main constituent of plant cell walls and of fibers such as cotton.
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fatty acid
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A monocarboxylic acid usually with an even number of carbon atoms; R-COOH where R is an alkyl group
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saturated fatty acid
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Molecule that contains no carbon-carbon double or triple bond
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unsaturated fatty acid
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Molecule that contains one of more carbon-carbon double or triple bond
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triacylglycerol
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– A naturally occurring ester of three fatty acids and glycerol that is the chief constituent of fats and oils
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phosphoglyceride
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type of lipid molecule found predominantly in membrane; composed of glycerol linked to two fatty acids, phosphate, and a polar group
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nucleophilie
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An atom or group with an unshared pair of electrons that is involved in a displacement (nucleophilic substitution) reaction
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leaving group
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outgoing nucleophile that leaves with its electron pair
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a nucleotide -- ATP adenonine triphosphate
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The energy carrier molecule
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Anhydride
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A molecule containing two carbonyl groups linked through an oxygen atom
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ATP sturcture
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ribose sugar, nitrogenous base adenine, 2 phosphoanhydrides and 1 phosphoester
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phospho ester and phosphoanhydride
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P-O-"R" and P-O-P
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3 main functions of carbs
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1.energy source glycogen in liver and muscles
Liver- breaks down glycogen polymer to glucose monomer transported to the organs via the blood stream in between meals and at sleep (sleep large amount goes to the brain) skeletal muscle- provides energy for syntesis of ATP for muscle contractions 2. cartilage structure (knee articulating) 3.cell-cell communication (bind to the outer surface of proteins to let the neighboring cells know whats happening) |
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Oxidation and Reduction
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oxidize = loss of Hydrogen
reduction = gain of hydrogen |
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peptide bond
polypeptide |
An amide linkage in an amino acid polymer
more than 50 amino acid linkages |
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Amine plus a carboxylic acid makes what bond
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peptide bond -- amide bond N-H
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Hydrolysis
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A chemical reaction in which molecules are cleaved by water
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Standard amino acid structure
alpha carbon |
20 amino acids commonly found in polypeptides; consist of a specific R-group, an amino group, and a carboxyl group attached to the same α-carbon atom.
alpha carbons attched to the R side chain and seperates the two functional groups |
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ATP functions
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energy source and monomeric unit of nucleic acid polymer
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elimination reaction
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A chemical reaction in which a double bond is formed when atoms in a molecule are removed
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addition reaction
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A chemical reaction in which one molecule is added to another
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dehydration reaction
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– A chemical reaction that involves the loss of water from the reacting molecule
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hydration reaction
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A type of addition reaction in which water is added to a carbon-carbon double bond
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redox reaction
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A transfer of electron from a donor to an electron acceptor
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oxidizing agent
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Atom or group reduced (GAIN H) during an oxidation/reduction reaction
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reducing agent
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Atom or group oxidized (LOSE H) during an oxidation/reduction reaction
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NADH
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Reduced form of Nicotinamide adenine dinucleotide. It is a coenzyme that is involved in electron transfer in a class of enzymes called dehydrogenases
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Oxidized molecule
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molecule that donated electrons
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Hydride ion
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- Is the anion of hydrogen, H−, or a compound in which one or more hydrogen centers have nucleophilic, reducing, or basic properties.
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metabolic pathway
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Series of chemical reactions occurring in a cell
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anabolic pathway
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Small precursors are used to generate large complex molecules
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catabolic pathway
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complex molecules are degraded into simple products
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Glycolysis
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10-reaction pathway that degrades glucose to two pyruvates to generate energy
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signal transduction pathway
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A pathway that permits a cell to receive and respond to signals from its environment
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DNA
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a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. DNA consists of both coding (genes) and noncoding (controlling the synthesis of proteins) sequences.
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RNA
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RNA is a nucleic acid that is involved in the expression of genetic information. It is a fundamental component in protein biosynthesis.
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autotrophs
chemoautotrophs photoautotrophs |
are organisms that transform energy of the sun through photosynthesis or various chemicals through chemosynthesis into chemical bond energy.
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transport protein
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is a type of protein that actively transports materials across a cell membrane.
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structural protien
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contributes to cell or tissue structure.
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enzyme catalytic protein
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enzyme is a protein formed by the body that acts as a catalyst (speeds up) to cause a certain desired reaction.
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POlypeptides are made up of three proteins
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transport, structural, enzyme catalytic
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3 macromolecules
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The largest biomolecules in living organisms are the nucleic acids, proteins, and polysaccharides. A nucleic acid is a macromolecule formed from the polymerization of nucleotides. They store genetic information (DNA) and mediate the protein synthesis (RNA). A protein is a macromolecule composed of one or more polypeptides that serve as catalysts and structural elements. They are tools that perform tasks to sustain living processes. A polysaccharide serves structural and energy source functions.
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Prokaryote
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Single-celled organism lacking a nucleus
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Eukaryote
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Composed of cells that have a nucleus and membrane-bound compartments
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Oraganelle
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subcellular compartment specialized for a specific task
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Hydrophilic
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Molecules that possess positive or negative charges that interact with water.
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hydrophobic
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Molecules that possess few electronegative atoms and do not interact with water
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lipid bilayer
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Biological membrane composed primarily of two layers of phospholipids
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polar head group
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hydrophilic charged or uncharged polar group in a phospholipid
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hydrocarbon group
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– A hydrophobic group such as the fatty acids in a phospholipid
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peripheral protein
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A protein that is not embedded within the membrane but is attached to a membrane protein or lipid
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integral protein
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embedded in the membrane
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signal transduction pathway
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The process that organisms use to receive and interpret information
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ligand
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molecule that binds to a protein or receptor
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plasma membrane
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A phospholipid bilayer that is inside the cell wall of bacteria and the phospholipd bilayer that surrounds eukaryotic cells
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endomembrane system
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Extensive set of interconnecting internal membranes that divide the cell into function compartments
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Mitochondrion
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An organelle possessing two membranes in which aerobic respiration occurs
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apoptosis
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genetically programmed series of events that lead to cell death
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nucleus
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eukaryote
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lyosomes
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membrane-enclosed sacs containing hydrolytic enzymes..store old proteins and used for remodel of bones
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endoplasmic reticulum
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long pathway through the membrane
rough er- ribosomes for protein synthesis smooth er- stores and releases Ca2+ for muscle contraction and stores lipids for synthesis in the liver |
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cell membrane
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keeps the cell from outside contents and the organelle from the outside with is help by cytoskeleton and cystol
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Nucleus
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main genome of the cell. where DNA RNA and ribosomes are synthesized
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Mitochondrion
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has its own dna. where energy yielding oxidation reactions occur. The synthesis of ATP using oxygen aerobic process
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golgi apparatus
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flattened membrane vesicles that secretion of proteins and reaction where sugars bind to other cell components. vescicles bumming
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eukaryotes
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plasma membrane, nucleus, cytoskeleton(organelle) nucleolus, mitochondria, endoplasmic reticulum,
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prokaryotes
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single-celled organism, just a plasma membrane
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signal transduction
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Signal transduction is the mechanisms by which extracellular signals are received, amplified, and converted to a cellular response. The first phase is reception where the signal molecule binds to and activates a receptor on the membrane surface, causing transduction. Transduction is the second phase where there is a change in the receptors 3D-shape, triggering the response. The response is the third phase inside the cell where there is a cascade of events that involves covalent modification of proteins and results in changes such as enzyme activity, gene expression, and motion.
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lyosomes
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A lysosome is a saclike organelle that’s capable of degrading most biomolecules. This degrading process is called autophagy and plays a role in the receptor-mediated endocytic pathway. Lyosome’s also are involved in a variety of secretory processes. For example, osteoclasts can fuse with the plasma membrane and release enzymes onto the bone surface to aid in bone resorption.
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plasma membrane protein transporters
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The plasma membrane proteins play role of transportation by channel and carrier proteins. Channels and carriers regulate the passage of ions and molecules in and out of the cell. They also respond to stimuli, have cell-cell contact, and catalytic functions.
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Rough and Smooth ER
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. Smooth endoplasmic reticulum contains no ribosomes and is involved in lipid synthesis and biotransformation processes. Rough endoplasmic reticulum has ribosomes bound to its external surface. It is the synthesis of membrane proteins and proteins for export from the cell.
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Golgi appartus
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The Golgi appartus is involved in the processing, packing, and distribution of cell products to internal and external compartments of the cell. These products may be protein or lipid molecules. In plants, the functions of the Gogli appartus include transport of substances into the cell wall and expansion of the plasma membrane during cell growth.
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Smooth ER in hepatocytes
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Smooth ER in hepatocytes perform biotransformation and synthesis of the lipid components of very-low-density lipoproteins. Biotransformation reactions convert water-insoluble metabolites and xenobiotics into more soluble products that can be excreted. The smooth ER also is involved in the structure and function of striated muscle. The sacroplasmic reticulum extends throughout the muscle cell and is a reservoir for calcium that triggers muscle contraction.
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Lyosomes and melanocytes
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The lysosomes of the bone-remodeling cells called osteoclasts can fuse with the plasma membrance and release enzymes onto the bone surface to aid in bone resorption. Lyosomes are also platelets that release a-granules that contain adhesive protein ligands. In melanocytes, which are cells in the basal layer of the skin, melanin accumulates in vesicles called melanosomes.
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Polar
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Uneven distribution of electrons in a molecule
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Hyrdrogen bond
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Occurs when electron-deficient hydrogens of one water molecule are attracted to the unshared pairs of electrons of an oxygen atom in another water molecule
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Electrostatic interaction
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Occurs between two opposite partial charges or full charges
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Salt bridge
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Forms as a result of attraction between positively and negatively charged amino acid side chains
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Dipole
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Molecules in which charge is separated
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Heat of fusion
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The energy required to melt a solid
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solvation sphere
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– Shells of water molecules that cluster around both positive and negative ions
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amphipatic
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– A molecule that contains both polar and nonpolar groups
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Micelle
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Formed when amphipathic molecules are mixed with water with the polar surface exposed to water and the nonpolar surface internalized
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Acid and bases
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. Acid – A species that donate protons
4b. Base – A species that accept protons 4c. Weak acid – Acid that does not completely dissociate in water 4d. Weak base – Base that does not completely dissociate in water 4e. Conjugate base – The deprotonated product of the dissociation of an acid |
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buffer
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Often composed of weak acids and their conjugate bases to help maintain a relatively constant hydrogen ion concentration
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pH and pKa
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pH- the negative log of the hydrogen ion concentration
pKa – the negative log of the dissocation constant, Ka |
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Kind of interactions
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. Lactic and ammonium ions have ionic interactions
16c. H20 would have a dipole moment 16e. CH3 CH3 would not have a dipole moment 17a. NaCl – No micelle 17b. CH3COOH – No micelle 17c. CH3COO-NH4+ = No micelle |
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CH3 (CH2) 10COO- NA+
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A Micelle forms when these molecules are close together because one end of the molecule is polar and one is nonpolar.
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Acid types
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. HCl – This is a strong acid because it can be fully ionized
b. H2PO4- - This is a weak acid because it is only partially ionized c. CH3COOH – This is a weak acid because it is only partially ionized d. HNO3 – This is a strong acid because it can be fully ionized e. HSO4- – This is a weak acid because it is only partially ionized |
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Hyperventilation
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Hyperventilation drives the transfer of carbon dioxide from the blood. During this process the equilibrium is shifted to the left and consumes protons, thereby making the blood more alkaline. Alkaline means the pH is greater than 7 (more basic).
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aliphatic hydrocarbon
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Nonaromatic hydrocarbons
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neurotransmitter
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Substances released from one nerve cell that influences the function of a second nerve or muscle cell
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asymmetric carbon
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A carbon that is bonded to four different functional groups
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chiral carbon
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carbon that is bonded to four different functional groups
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stereoisomers (cis and trans)
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Molecules that differ only in the spatial arrangement of their atoms
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isoelectric point
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pH where an amino acid is electrically neutral
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peptide bond
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The bond formed when the α carboxyl group of one amino acid reacts with the amino group of another
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disulfide bridge
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Occurs when two cystene amino acids form a disulfide bond
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alpha carbon
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The carbon atom in an amino acid that is bonded to an amino group and a carboxyl group
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hydrophobic amino acid
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– An amino acid with a nonpolar side chain
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types of amino acids
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Valine, Leucine, Isoleucine, methionine, and phenylalanine occur inside proteins because they are hydrophobic, meaning they do not interact with the water molecules. Arginine, Lysine, Aspartic acid, and glutamic acid occur near the outer surface of proteins because they are hydrophilic, meaning they interact with the water molecules. Glycine and alanine are hydrophobic amino acids so they would occur inside proteins. Glutamine is hydrophilic because of its polar side chain that interacts with hydrogen bonds, meaning it would occur on the outer surface of the protein.
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Serotonins amino acid precursor and dopamines amino acid precursor
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Serotonin’s amino acid precursor is tryptophan. Dopamine’s amino acid precursor is tyrosine.
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supersecondary structure
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Combinations of α-helix and β-pleated sheet secondary structures
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denaturation
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Process of structure disruption
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protein family
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A group of protein molecules that are related by amino acid sequence similarity
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protein superfamily
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A large group of distantly related proteins ( For example: The globin superfamily includes the hemoglobins and myoglobins, which bind oxygen in blood and muscle cells, respectively, and the cytoglobins, which bind oxygen in the brain
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fibrous protein
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– Long, tough rod-shaped molecules often insoluble in water
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globular protein
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Compact spherical molecules that are usually water soluble
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prosthetic group
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A nonprotein component of a protein
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apoprotein
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A protein that lacks its prosthetic group
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salt bridge
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An electrostatic interaction in proteins between ionic groups of opposite charge.
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oligometer
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A multisubunit protein in which some or all subunits are identical
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allosteric transition
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The ligand-induced conformational change in a protein
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protein denaturation
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- Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent or heat.
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chaperonin
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a family of molecular chaperones of the Hsp60 (60 kDa) family of heat shock proteins
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secondary structure
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Localized arrangement of α-helices and β-pleated sheets of adjacent amino acids
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B pleated sheet
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form when two or more polypeptide chains of β strands line up side by side
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protein structure
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A protein is composed of one of more polypeptide chains. A polypeptide is a polymer containing more than 50 amino acid residues. A peptide is a polymer with fewer than 50 amino acid residues.
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structure of bonds
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Amino acid sequence – Primary structure
18b. β – pleated sheet – Secondary structure 18c. Hydrogen bond – Inter- and intra- chain hydrogen bonds between N-H groups and carboxyl groups of peptide bonds are secondary structure. Hydrogen bonds formed between polar side chains are tertiary and quaternary structure. 18d. Disulfide Bond – Tertiary and quaternary structure |
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Heat denaturation
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This denaturation agent acts as hydrogen bonding in secondary and tertiary structure.
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strong acid
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This denaturation agent acts as hydrogen bonding and salt bridges in secondary and tertiary structure.
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pI values
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Amino acids with basic side groups such as lysine, arginine, or tyrosine would contribute to a high pI value
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protein folding
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The force of protein folding is the requirement to achieve a low-energy state despite the decrease in entropy that occurs as the protein’s three-dimensional structure becomes more ordered. Key considerations include the energy associated with different bond angles and bond rotation, the chemical properties of the amino acid side chains, and interactions between side chains. Of the noncovalent interactions that are possible, hydrophobic interactions are particularly important.
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catalyst
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A substance that enhances the rate of a chemical reaction but is not permanently altered by the reaction
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transition state
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In catalysis, the unstable intermediate formed by the enzyme that has altered the substrate so that it now shares properties of both the substrate and the product
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substrate
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The reactant in a chemical reaction that binds to an enzyme active site and is converted to a product
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activation energy
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threshold energy required to produce a chemical reaction
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active site
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the cleft in the surface of an enzyme where a substrate binds
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cofactor
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The nonprotein component of an enzyme (either an inorganic ion or a coenzyme) required for catalysis
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coenzyme
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A small organic molecule required in the catalytic mechanism o a certain enzyme
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apoenzyme
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The protein portion of an enzyme that requires a cofactor to function in catalysis
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holoenzyme
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A complete enzyme consisting of an apoenzyme plus a cofactor
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velocity
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The rate of a biochemical reaction; the change in concentration o a reaction or product per unit time
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reaction order
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The power to which its concentration term in the rate equation is raised
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turnover number
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The number of molecules of substrate converted to product in each second per mole of enzyme
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inhibitor
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A molecule that reduces an enzyme’s activity
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competitive inhibitor
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An inhibitor molecule that competes with the substrate for occupation of the active site
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irreversible inhibition
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form of enzyme inhibition in which an inhibitor permanently impairs an enzyme, usually through biding via a covalent bond
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