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Chapter 3
Review Questions
43
Biology
Undergraduate 2
07/10/2014

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Term
Describe the composition of an amino acid
Definition
-H(a hydrogen atom)
-NH2 (an amino functional group)
-COOH (a carboxyl functional group)
-distinctive R group (side chain)
Term
How is the identity of an amino acid's side chain (R group) related to its solubility?
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.
Term
Condensation reaction
Definition
monomer in, water out
builds a polymer
requires an input of energy
endergonic reaction
non-spontaneous
Term
Hydrolysis reaction
Definition
water in, monomer out
breaks down polymers into monomers
energy is released
exergonic reaction
results in increase in entropy
spontaneous reaction
Term
Peptide bond
Definition
the covalent bond formed by a condensation reaction between two amino acids, links the residues in peptides and proteins
Term
Primary structure
Definition
the sequence of amino acids in a polypeptide; stabilized by peptide bonds
Term
Secondary structure
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
Term
Tertiary structure
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
Term
Quaternary structure
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
Term
ɑ-helix
Definition
polypeptide backbone is coiled; ribbon structure is coiled
Term
β-pleated sheet
Definition
segments of a peptide chain bend 180 degrees and then fold in the same plane; ribbon structure is an arrow
Term
How are alpha helices and beta sheets alike?
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
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)?
Definition
Because a protein's primary structure is fundamental to its function
Term
Which levels of protein structure are present in all proteins? Explain.
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
Term
How is the shape of a protein related to its function?
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
Term
Disulfide bonds
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
Term
Molecular chaperones
Definition
assist proteins with folding into their correct 3-D structures
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?
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."
Term
Explain how a protein co-factor is related to a protein's correct three-dimensional conformation. What are some examples of co-factors?
Definition
Many proteins require co-factors to bind to proteins in order to reach 3-D conformation (ex: vitamins or ions)
Term
What causes mad cow disease/variant Creutzfeldt-Jakob disease? Explain in detail, including an explanation of prions.
Definition
Spontaneously proteins (prions) become denatured and form amyloids; then if someone/something eats nerve/brain tissue will get those prions
Term
Free energy
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
Term
Condensation reactions (anabolic-building complex molecules)
Definition
monomer in, water out; builds a polymer; requires an input of energy; endergonic reaction; non-spontaneous reaction
Term
Hydrolysis reactions (catabolic-breaking down complex molecules)
Definition
water in, monomer out; energy is released; breaks down polymers into monomers; results in increase in entropy; spontaneous reaction
Term
Activation energy (Ea)
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
Term
Transition state
Definition
when bonds in reactants break and bonds in products form
Term
Substrate
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
Term
Active site
Definition
the location in an enzyme molecule where substrates (reactant molecules) bind and react
Term
Allosteric site
Definition
completely different site on the enzyme/substrate; doesn't involve active site
Term
Enzyme
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
Term
How do enzymes lower the activation energy of a reaction?
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
Term
Competitive inhibition
Definition
substrates cannot bind when a regulatory molecule binds to the enzyme's active site; inhibitor can be out competed by adding more substrate
Term
Noncompetitive inhibition
Definition
inhibitor molecule binds to allosteric site on enzyme; cannot be out competed by addition of more substrate
Term
Km
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
Term
Vmax
Definition
max velocity; with a competitive inhibitor it stays the same; with a noncompetitive inhibitor it decreases
Term
What two functional groups are present on every amino acid?
Definition
An amino group and a carboxyl group
Term
Twenty different amino acids are found in the proteins of cells. What distinguishes these molecules?
Definition
The atoms and functional groups found in the side chains
Term
By convention, biologists write the sequence of amino acids in a polypeptide in which direction
Definition
Amino to carboxy-terminus
Term
Explain how water participates in the development of the interactions that glue nonpolar amino acids together in the interior of globular proteins
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
Term
Provide an example of how a specific shape of a protein is correlated with its function
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
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.
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
Term
In a polypeptide, what bonds are responsible for the secondary structure called an alpha-helix?
Definition
Hydrogen bonds that form between the core C=O and N-N groups on different residues
Term
Where is the information stored that directs different polypeptides to fold into different shapes?
Definition
The order and type of amino acids (i.e., the primary structure) contains the information that directs folding
Term
What is an active site?
Definition
The position in an enzyme where substrates bind
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