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Hypervariable region

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is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat (in the case of nuclear DNA) or have substitutions (in the case of mitochondrial DNA). Changes or repeats in the hypervariable region are highly polymorphic

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Immunoglobulin G (IgG)

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are antibody molecules composed of four peptide chains-two heavy Y chains and two light chains. Each IgG has two antigen binding sites. IgG is considered the monomer. Involved in secondary immune response.

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Cooperativity

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is a phenomenon displayed by enzymes or receptors that have multiple binding sites where the affinity of the binding sites for a ligand is increased positive cooperativity, or decreased, negative cooperativity, upon the binding of a ligand to its binding site.

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Amphipathic

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describes a chemical compound that is both hydrophilic, and lipohilic (fat loving) Soaps and detergents are examples.

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In terms of what type of polymer it is, myoglobin is a

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monomer

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In terms of what type of polymer it is, Hemoglobin is a

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Heterotetramer with two alpha subunits and two beta subunits.

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The oxygen binding curve for myoglobin is____.

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hyperbolic

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The oxygen binding curve for hemoglobin is______

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Sigmodal

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A sigmoidal oxygen binding curve indicates what?

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cooperative binding

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Cooperative binding is

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Allosteric regulation is

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the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site (that is a site other than the protein's active site)

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True or False. Proteins can have domain structures that may behave independently or exhibit degrees of interaction.

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true

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Describe IgG in terms of what type of polymer it is

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IgG is a tetramer with two identical light chains and two identical heavy chains.

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True or False. Only heavy chains have variable and constant regions.

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False, both the Light chains and heavy chains have variable and constant regions.

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In IgG how many hypervariable regions are within the variable regions?

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three

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How does the constant and variable regions fold

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As separate domains

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Enzymes do what

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they catalyze reactions that take place in a cell

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Enzyme activity can be measured by?

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the rate of product formation or substrate breakdown.

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Enzymes speed up a reaction by ____ the activation energy but not the ______ ______ ______ change.

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lowering, overall free energy

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True or false-Enzymes do not change equilibrium

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true

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Activation energy can also be lowered by...

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-stabilizing the transition state,
-straining the susceptible bond to make it easier to break,
-holding substrates in close proximity and proper orientation
-forming a covalent bond with a reactant that destabilizes another bond
- acting as a proton donor or acceptor

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The Michaelis constant (Km) is...

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the substrate concentration required to achieve 1/2 Vmax and provides a measure of the affinity of the enzyme for substrate

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Vmax is observed when...

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all enzyme molecules are in the ES complex

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ES complex=

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Enzyme Substrate complex

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A high Km indicates... a low Km indicates...

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weak affinity... strong affinity

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What are the two generally accepted mechanisms for enzyme substrate binding.?

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1. Lock and Key-the active site shape is similar to the substrate shape.
2. Induced Fit- the active site changes shape after substrate binding to fit the substrate

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Metabolic pathways are often controlled at...

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a few key committed steps, usually at a branch point

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Regulatory enzymes exhibit _____ kinetics and are influence by ______ effectors.

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Sigmoidal kinetics, allosteric

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Positive effectors of enzyme activity ____ the Km, _____ Vmax, or both

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lower, increase

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Negative Effectors of enzyme activity ____ the Km, ____ the Vmax, or both.

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increase, decrease

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The _________ transmits information (signals) across the cell membrane

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the G protein signal system

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Proteins can function as...

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in structure, as ligands, receptors, membrane transporters, molecular motors, antibodies, and/or enzymes

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What are the two components of the G protein signal system?

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-A G protein coupled receptor that responds to external signals,
- a G protein complex that transfers the signal from the receptor to an intracellular molecule or complex

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In an enzyme activity assay what happens?

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Substrate is added to the enzyme sample and either the amount of product produced or the amount of substrate depleted is measured.

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Induced fit mechanism

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the active site changes shape after substrate binding to fit the substrate

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Domain

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Effector

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is a molecule that binds to a protein and thereby alters the activity of that protein. A modulator molecule binds to a regulatory site during allosteric modulation and allosterically modulates the shape of the protein. Can also be a protein that is secreted from a pathogen that alters the pathogen’s host organism to enable infection.

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Lock and key mechanism

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enzymes and the substrate possess specific complementary geometric shapes that fit exactly into one another. Since enzymes are flexible stuctures the active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme.

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Michaelis- Menton constant (Km)

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describes the rates of irreversible enzymatic reactions by relating reaction rate to the concentration of the substrate.

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Turnover number (Kcat)

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- is defined as the maximum number of molecules that an enzyme can convert to produce per catalytic site per unit of time and can be calculated as follows : Kcat=Vmax/[E]t

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Polyclonal antibody

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(or antisera) are antibodies that are obtained from different B cell resources. They are a combination of immunoglobulin molecules secreted against a specific antigen, each identifying a different epitope.

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Polyclonal antibody

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(or antisera) are antibodies that are obtained from different B cell resources. They are a combination of immunoglobulin molecules secreted against a specific antigen, each identifying a different epitope.

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G protein

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(guanine nucleotide binding proteins) are a family of proteins involved in transmitting chemical signals outside the cell, and causing changes inside the cell. They communicate signals from many hormones, neurotransmitters and other signaling factors.

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Sigmoidal curve

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a logistic function or logistic curve. It can model the S shaped curve.

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G protein- coupled receptors

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(also known as seven transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptor and G protein- linked receptors) comprise a large protein family of transmembrane receptors that sense molecules outside the cell and activate inside signal transduction pathways and ultimately cellular responses. (Only in eukaryotes)

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Substrate

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is a molecule upon which an enzyme acts. Substrate binds with the enzyme active site and an enzyme substrate complex is formed. The substrate is transformed into one or more products, which are then released from the active site.

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G protein signal system

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Transition state

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Heavy chain

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Variable region

answer

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Globular protein

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are one of the two main protein classes, comprising globe like poteins that are more or less soluble in aqueous solutions.

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Specific activity

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in biochemistry- it is the amount of product formed by an enzyme in a given amount of time under given conditions per milligram of total protein. (equal to the rate of the reaction multiplied by the volume of the reaction divided by the mass of total protein.

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Fibrous protein

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generally form connective tissue, tendons, bone matrices, and muscle fiber, is typically water insoluble and have long chains

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?-galactosidase

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is a hydrolase enzyme that catalzyes the hydrolysis of ? galactosides into monosaccharides. (Lactase is often confused as an alternative name for this but it is actually simply a sub class )

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domain

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is a part of a protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.

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pK

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is a specific type of equilibrium constant that measures the propensity of a larger object to separate reversibly into smaller components, as when a complex falls apart into its component molecule, or when a salt splits up into its component ions.

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monoclonal antibody

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are monospecific antibodies that are the same because they are made by identical immune cells that are all clones of a unique parent cell

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Homogenate

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its is when all constituents are all of the same nature

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Enzyme activity assay

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used to measure enzymatic activity

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True or False- Differences in myoglobin and hemoglobin function are explained by differences in myoglobin and hemoglobin tertiary structures

answer

False- they are explained by differences in QUATERNARY structures

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Ribonuclease and trypsin are

answer

proteins that catalyze chemical reactions

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Fingerprinting does what?

answer

provides a two dimensional separation and analysis of peptides.

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_____ are RNA catalysts

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Ribozymes

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____ assays are based on the fact that a substrate absorbs light of a particular wavelength.

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Colorimetric

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Enzyme activity can be altered by...

answer

phosphorylation, dephosphorylation, and allsoteric effectors.

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True or False- The term cooperativity embodies the idea that changes in the conformation of one subunit are communicated to the other identical subunits in any given molecule so that all of these subunits are in the same conformation

answer

True

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Phosphorylation

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is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes, causing or preventing the mechanisms of diseases such as cancer and diabetes- causes enzymes to become activated or deactivated (dephosphorylation)

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