Term
| Describe the composition of an amino acid |
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Definition
-H(a hydrogen atom)
-NH2 (an amino functional group)
-COOH (a carboxyl functional group)
-distinctive R group (side chain) |
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Term
| How is the identity of an amino acid's side chain (R group) related to its solubility? |
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Definition
| It affects the polarity, and thus the solubility of an amino acid in water.Nonpolar side chains lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic side chains tend to coalesce in aqueous solution. Polar or charged side chains interact readily with water and are hydrophilic. Hydrophilic side chains dissolve in water easily. |
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Term
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Definition
monomer in, water out
builds a polymer
requires an input of energy
endergonic reaction
non-spontaneous |
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Term
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Definition
water in, monomer out
breaks down polymers into monomers
energy is released
exergonic reaction
results in increase in entropy
spontaneous reaction |
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Term
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Definition
| the covalent bond formed by a condensation reaction between two amino acids, links the residues in peptides and proteins |
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Term
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Definition
| the sequence of amino acids in a polypeptide; stabilized by peptide bonds |
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Term
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Definition
| formation of ɑ-helices and β-pleated sheets in a polypeptide; stabilized by hydrogen bonding between groups along the peptide-bonded backbone, thus depends on primary structure |
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Term
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Definition
| overall three-dimensional shape of a polypeptide (includes contribution from secondary structures); stabilized by bonds and other interactions between R-groups, or between R-groups and the peptide-bonded backbone; thus, depends on primary structure |
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Term
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Definition
| shape produced by combinations of polypeptides (thus, combinations of tertiary structures); stabilized by bonds and other interactions between R-groups, AND between peptide backbones of different polypeptides; thus depends on primary structure |
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Term
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Definition
| polypeptide backbone is coiled; ribbon structure is coiled |
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Term
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Definition
| segments of a peptide chain bend 180 degrees and then fold in the same plane; ribbon structure is an arrow |
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Term
| How are alpha helices and beta sheets alike? |
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Definition
| -distance between residues that hydrogen-bond to one another is small and hydrogen bonding between sections of the same backbone is possible only when a polypeptide bends in a way that puts C=O and N-H groups close together, so in most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends |
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Term
| How can a change in the primary structure of a protein affect the overall conformation of the protein (remember the example of sickle cell anemia)? |
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Definition
| Because a protein's primary structure is fundamental to its function |
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Term
| Which levels of protein structure are present in all proteins? Explain. |
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Definition
| Primary structure is present in all other protein structures because it is fundamental (or is the foundation) to the higher levels of protein structure |
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Term
| How is the shape of a protein related to its function? |
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Definition
| Proteins can serve diverse functions in cells because they are divers in size and shape as well as in the chemical properties of their amino acid residues |
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Term
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Definition
-A covalent bond between two sulfur atoms, typically in the side chains of certain amino acids (e.g., cysteine)
-Often contributes to tertiary and quaternary levels of protein structure |
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Term
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Definition
| assist proteins with folding into their correct 3-D structures |
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Term
| What are some factors that can cause denaturation of a protein? Why does this occur? How does protein denaturation affect the function of the protein? |
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Definition
| Some factors that can cause denaturation of a protein are increase in temperature, change in pH of solution surrounding the protein, change in salt concentration of solution surrounding protein, and prions. This occurs because of a misfolding or the protein was not regulated which could cause the protein to become "infectious." |
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Term
| Explain how a protein co-factor is related to a protein's correct three-dimensional conformation. What are some examples of co-factors? |
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Definition
| Many proteins require co-factors to bind to proteins in order to reach 3-D conformation (ex: vitamins or ions) |
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Term
| What causes mad cow disease/variant Creutzfeldt-Jakob disease? Explain in detail, including an explanation of prions. |
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Definition
| Spontaneously proteins (prions) become denatured and form amyloids; then if someone/something eats nerve/brain tissue will get those prions |
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Term
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Definition
| the energy of a system that can be converted into work. It may be measured only through the change in free energy in a reaction. When the amount of energy changes say it has a decreased or negative charge, then it will become a spontaneous reaction |
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Term
| Condensation reactions (anabolic-building complex molecules) |
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Definition
| monomer in, water out; builds a polymer; requires an input of energy; endergonic reaction; non-spontaneous reaction |
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Term
| Hydrolysis reactions (catabolic-breaking down complex molecules) |
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Definition
| water in, monomer out; energy is released; breaks down polymers into monomers; results in increase in entropy; spontaneous reaction |
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Term
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Definition
| amount of energy needed to start a reaction. Reactant molecules achieve enough energy to reach the activation energy level through the help of enzymes |
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Term
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Definition
| when bonds in reactants break and bonds in products form |
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Term
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Definition
-a reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction
-a surface on which a cell or organism sits |
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Term
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Definition
| the location in an enzyme molecule where substrates (reactant molecules) bind and react |
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Term
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Definition
| completely different site on the enzyme/substrate; doesn't involve active site |
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Term
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Definition
| a protein catalyst used by living organisms to speed up and control biological reactions; lower activation energy in reactions; very specific to the reactions they catalyze; contain an active site |
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Term
| How do enzymes lower the activation energy of a reaction? |
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Definition
-Initiation: Reactants bind to the active site in a specific orientation, forming an enzyme-substrate complex
-Transition state facilitation: interactions between enzyme and substrate lower the activation energy required
-Termination: products have lower affinity for active site and are released. Enzyme is unchanged after the reaction |
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Term
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Definition
| substrates cannot bind when a regulatory molecule binds to the enzyme's active site; inhibitor can be out competed by adding more substrate |
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Term
| Noncompetitive inhibition |
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Definition
| inhibitor molecule binds to allosteric site on enzyme; cannot be out competed by addition of more substrate |
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Term
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Definition
| concentration of substrate at half of the Vmax; with a competitive inhibitor, there is an increase; with a noncompetitive inhibitor it stays the same |
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Term
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Definition
| max velocity; with a competitive inhibitor it stays the same; with a noncompetitive inhibitor it decreases |
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Term
| What two functional groups are present on every amino acid? |
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Definition
| An amino group and a carboxyl group |
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Term
| Twenty different amino acids are found in the proteins of cells. What distinguishes these molecules? |
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Definition
| The atoms and functional groups found in the side chains |
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Term
| By convention, biologists write the sequence of amino acids in a polypeptide in which direction |
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Definition
| Amino to carboxy-terminus |
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Term
| Explain how water participates in the development of the interactions that glue nonpolar amino acids together in the interior of globular proteins |
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Definition
| Because the nonpolar amino acid residues are not able to interact with the water solvent, they are crowded together in the interior of a protein and surrounded by a network of hydrogen-bonded water molecules. This crowding leads to the development of van der Waals interactions that help glue the nonpolar side chains together |
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Term
| Provide an example of how a specific shape of a protein is correlated with its function |
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Definition
-The presences of an active site in an enzyme that is precisely shaped to fit a substrate or substrates in the correct orientation or a reaction to occur
-the doughnut shape of porin that allows certain substances to pass through it
-the cable shape of collagen to provide structural support for cells and tissues |
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Term
| A major theme in this chapter is that the structure of molecules correlates with their function. Use this theme to explain why proteins can perform so many different functions in organisms and why enzymes are such effective catalysts. |
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Definition
| Proteins are highly variable in overall shape and chemical properties due to variation in the compostion of R-groups and the array of secondary through quaternary structures that are possible. This variation allows them to fulfill many different roles in the cell. Diversity in the shape and reactivity of active sites also makes them effective catalysts |
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Term
| In a polypeptide, what bonds are responsible for the secondary structure called an alpha-helix? |
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Definition
| Hydrogen bonds that form between the core C=O and N-N groups on different residues |
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Term
| Where is the information stored that directs different polypeptides to fold into different shapes? |
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Definition
| The order and type of amino acids (i.e., the primary structure) contains the information that directs folding |
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Term
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Definition
| The position in an enzyme where substrates bind |
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