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BIO 211 Chapter 3
Protein Structure & Function
49
Biology
Undergraduate 2
12/06/2010

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Term
Proteins are made of _______
Definition
amino acids
Term
Amino acids vary in structure and function because _________
Definition
their side chains vary in composition
Term
The structure of a protein can be analyzed at four levels that form a hierarchy— ________
Definition
the amino acid sequence, substructures called α-helices and β-pleated sheets, interactions between amino acids that dictate a protein’s overall shape, and combinations of individual proteins that make up larger, multiunit molecules.
Term
During enzyme catalysis, the reactants bind to ________
Definition
an enzyme’s active site in a way that allows the reaction to proceed efficiently
Term
To test whether the first steps of chemical evolution could have occurred on ancient Earth, Stanley Miller combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source
The products that resulted from Miller’s experiment included ________
Definition
hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.
Term
All proteins are made from just ______
Definition
21 amino acids
Term
All amino acids have a central carbon atom that bonds to ________, ________, _______, and ______
Definition
NH2 (an amino functional group); COOH (a carboxyl functional group); H; a variable side chain
Term
In water (pH7), the amino and carboxyl groups ionize to NH3+ and COO–, respectively, which helps ________
Definition
amino acids stay in solution and makes them more reactive
Term
Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are _____ than those with side chains composed of only carbon and hydrogen atoms.
Definition
more reactive
Term
isomers
Definition
molecules with the same molecular formula but different structures
Term
optical isomers
Definition
have the same atoms but differ in the arrangement of atoms, or groups, around a carbon atom that has four different groups attached
Term
amino acids ______ to form proteins. ________ reactions require energy and are not spontaneous.
Definition
polymerize; polymerization
Term
Monomers polymerize through ________, also known as ______, which release a water molecule.
Definition
condensation reactions; dehydration reactions
Term
In ________, water reacts with a polymer to release a monomer.
Definition
hydrolysis
Term
In the prebiotic soup,______ would predominate over ________ because it is energetically favorable.
Definition
hydrolysis; condensatio
Term
Condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a _______
Definition
peptide bond
Term
A polypeptide is _______ & has ________ (the N-terminus has a free amino group and the C-terminus has a free carboxyl group), and its side chains extend out from the backbone
Definition
flexible; directionality
Term
A protein's primary structure is _________
Definition
its unique sequence of amino acids
Term
Secondary structure of a protein results in part from _______
Definition
hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another.
Term
A protein's secondary structure increases its ________ — although each hydrogen bond is very weak relative to a covalent bond, the large number of hydrogen bonds makes these structures highly stable.
Definition
stability
Term
The tertiary structure of a polypeptide results from ________
Definition
interactions between R-groups or between R-groups and the peptide backbone
Term
R-group interactions include _________
Definition
hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds
Term
van der Waals interactions are ________. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability.
Definition
electrical interactions between hydrophobic side chains
Term
the bonding of two or more subunits produces _______ in a protein
Definition
quaternary structure
Term
Protein folding is often spontaneous, because _______
Definition
the hydrogen bonds and van der Waals interactions make the folded molecule more stable energetically than the unfolded molecule.
Term
catalyst
Definition
lowers the activation energy of a reaction by lowering the free energy of the transition state; do not change ΔG; not consumed in the reaction
Term
Substrates bind to the ________, and interactions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed.
Definition
enzyme’s active site
Term
R-groups in the active site may form short-lived covalent bonds that assist with the transfer of atoms or groups of atoms from one reactant to another. The presence of acidic or basic R-groups allows the reactants to gain or lose a proton more readily
Definition
Term
Enzymes induce the formation of the transition state to increase reaction rates. ______ have a low affinity for the active site and are therefore released from the enzyme.
Definition
Reaction products
Term
Enzyme catalysis has three steps: During initiation, ______; during transition state facilitation, ________; and during termination, ________
Definition
reactants are precisely oriented as they bind to the active site; interactions between the substrate and active site R-groups lower the activation energy; reaction products are released from the enzyme
Term
Some enzymes require _______ to function normally. These are either ______ or small organic molecules called ______. The cofactors usually are in _______ and are involved in transition state stabilization.
Definition
cofactors; metal ions; coenzymes; the active site
Term
Competitive inhibition occurs when _______
Definition
a molecule similar in size and shape to the substrate competes with the substrate for active site binding
Term
Allosteric regulation occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. Allosteric regulation either ______ depending on the way in which ________
Definition
increases or decreases enzyme activity; enzyme shape changes
Term
In enzymatic reactions, the rate of product formation increases linearly for a given increase in ______ at low substrate concentrations, but ______ at high substrate concentrations
Definition
substrate concentration; levels out
Term
* Enzymes with high substrate affinity rapidly achieve their maximum reaction rate as substrate concentration increases, whereas enzymes with low affinity for their substrate require ________ concentrations before they reach their maximum rate.
Definition
fairly high substrate
Term
Temperature affects the movement of substrates and enzyme; pH affects the enzyme's ________.
Definition
shape and reactivity
Term
Several observations argue that the first self-replicating molecule on Earth was a protein
Definition
(1) Amino acids were abundant in the prebiotic soup, (2) proteins are the most efficient catalysts known, and (3) a self-replicating molecule had to act as a catalyst for the assembly and polymerization of its copy.
Term
chemical evolution hypothesis
Definition
Complex organic compounds formed from water and atmospheric gases present on early Earth
Term
At which step of chemical evolution did life become possible?
Definition
evolution of an information-containing, self-replicating molecule
Term
What is one example of the many critical functions of proteins in organisms?
Definition
They impart mobility to cells and entire organisms.
Term
Monomers join to form polymers under what chemical conditions?
Definition
condensation
Term
What types of interactions are responsible for the secondary structure of a protein?
Definition
hydrogen bonds
Term
protein primary structure
Definition
The sequence of amino acids in a polypeptide
Term
quaternary structure of a protein
Definition
shape produced when two or more polypeptides associate to form a functional protein
Term
secondary structure of a protein
Definition
formation of a-helices and b-pleated sheets
Term
tertiary structure of a protein
Definition
overall three-dimensional shape of a polypeptide
Term
how do prions cause disease?
Definition
They cause changes in the shape of normal protein molecules that lead to disintegration of mammalian brains.
Term
In what important way does a competitive inhibitor differ from an allosteric inhibitor>
Definition
A competitive inhibitor binds to the active site, whereas an allosteric inhibitor binds to a site other than the active site.
Term
How does ATP provide the chemical energy to drive many endergonic reactions?
Definition
loses a phosphate group
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