Molecular Text 3.3

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Molecular Text 3.3
2015-01-20 14:43:46
Test One
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  1. a.       Enzymes must be efficient to avoid __. The rate at which cell metabolism proceeds can be measured by the __
    b.      The factor that limits reaction rate is now __; and, the rate will depend on the __
                                                                  i.      The cell can increase reaction rates without __ by doing what to form a large protein assembly known as a __; diffusion is then not limited
    • great disorder
    • rate of ATP utilization

    • diffusion
    • concentration of enzyme and substrate

    • raising substrate concentrations
    • bringing the various enzymes involved in a reaction sequence together

    multienzyme complex
  2. a.       Another way of increasing metabolic reaction rates is using __, which do what?
    b.      Because there are thousands of enzymes that form __, there are __ where different enzymes __; regulation is required at various levels.
    • intracellular membrane systems
    • segregate particular substrates and the enzymes that act on them into the same membrane-enclosed compartment, such as the ER or nucleus

    • webs of metabolic pathways
    • branch points
    • compete for the same substrate
  3.                                                               i.      At one level, the cell controls how many molecules of each enzyme it makes by regulating the __
                                                                ii.      The cell controls enzymatic activities by __
                                                              iii.      Enzymes can undergo __
                                                               iv.      __ occurs as well
    • expression of the gene that encodes that enzyme
    • confining sets of enzymes to particular subcellular compartments, enclosed by distinct membranes
    • covalent modification
    • Protein destruction
  4.                                                               i.      The most general process that adjusts reaction rates operates through a direct, reversible change in the __
                                                                ii.      Feedback inhibition: __

    1.       A molecule other than the __binds to an enzyme at a special __ outside the active site
    2.       It is negative regulation: prevents an enzyme from acting 
    activity of an enzyme in response to the specific small moelcules that it encounters

    a product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway

    • substrate 
    • regulatory site
  5.                                                               i.      Positive regulation: a regulatory molecule does what?
    1.       Occurs when a product in one branch of the metabolic network __
    stimulates the enzyme’s activity rather than shutting the enzyme down

    stimulates the activity of an enzyme in another pathway
  6. a.       Regulatory molecules often have __totally different from the __of the substrate of the enzyme. It is __
                                                                  i.      There is an __ and __ that recognizes the substrates and regulatory molecules, respectively
                                                                ii.      Conformational changes can occur: __ 
    b.      The effects of __ on protein follow from a fundamental chemical principle known as __. Whenever two ligands prefer to bind to the __, it follows from basic thermodynamic principles that each ligand must __
    • shapes 
    • shape 
    • allosteric regulation
    • active site and a regulatory site
    • binding at one of the sites shifts shapes
    • ligand binding
    • linkage
    • same conformation of an allosteric protein
    • increase the affinity of the protein for the other
  7.                                                               i.      Linkage operates in a negative way if two ligands __. In this case, the binding of the first ligand does what?
    b.      A single-subunit enzyme that is regulated by __ can decrease from 90% to 10% activity in response to a 100-fold increase in the concentration of an inhibitory ligand that it binds
                                                                  i.      The binding of a molecule of ligand to a single site on one subunit can promote an __ in the entire assembly that helps the neighboring subunits bind the same ligand
    • prefer to bind to different conformations of the same protein
    • discourages binding of the second ligand
    • negative feedback
    • allosteric change
  8. 1.       As a result, a __ occurs, allowing a relatively small change in __ in the cell to switch the whole assembly from an __ to an __ conformation
    b.      Principles involved in a cooperative “__” transition are the same for all proteins
    • cooperative allosteric transition
    • ligand concentration
    • almost fully active
    • almost fully inactive
    • all-or-none
  9. a.       An alternative to the induced fit model is a __, corresponding to __ and __ structures. This is __ between these two states, thereby changing the proportion of active molecules.
    b.      __ are begun by __, which has six regulatory and catalytic subunits; __forms two trimers, which face one another and are held by the __
    • symmetrical enzyme with only two possible conformations
    • enzyme on and enzyme off
    • all-or-none equilibrium

    • CTP production pathways
    • Aspartate Transcarbamoylase
    • catalytic 
    • three regulatory dimers
  10.                                                               i.      Binding of catalytic trimers causes an __, allowing __ to __
                                                                ii.      Binding of __ converts the enzymes to the __, from which the __
                                                              iii.      Each regulatory subunit has __, and CTP binding causes the two domains to move relative to each other, causing the__. __ form to stabilize the __
    • R conformation
    • regulatory to dissociate

    CTP to regulatory dimers

    inactive T state

    substrates dissociate

    two domains

     T conformation

    • H bonds
    • T state
  11. a.       Proteins are regulated by __, such as covalent addition of a phosphate group, which can cause modification in two ways
                                                                  i.      Because each phosphate group carries __, the enzyme-catalyzed addition of a phosphate group to a protein can cause a major conformational change in the protein by __, which can affect the __ elsewhere on the protein surface, dramatically changing the protein’s activity. When a second enzyme removes the phosphate group, the protein returns to its original conformation and __
    • reversible binding of molecules
    • two negative charges
    • attracting a cluster of positively charged amino acid side chains
    • binding of ligands
    • restores its initial activity
  12.                                                               i.      An attached phosphate group can form part of a structure that the __. As a result, protein __ and __ very often drive the regulated __ and __ of protein complexes
    • binding sites of other proteins recognize
    • phosphorylation and dephosphorylation 
    • assembly and disassembly
  13. a.       Reversible protein phosphorylation controls the __, __, and __ of both enzymes and many other types of proteins in eukaryotic cells.
    b.      Protein phosphorylation involves the __ to the __
                                                                  i.      A protein phosphatase catalyzes the __; some are highly specific, whereas others have a broad range of proteins 
    • activity, structure, and cellular localization
    • enzyme-catalyzed transfer of the terminal phosphate group of an ATP molecule 

    hydroxyl group on a serine, threonine, or tyrosine side chain by a protein kinase

    reverse reaction of phosphate removal
  14. a.       The __ belong to a very large family of enzymes; and they have different __ on either end of the __, allowing __of a specific set of proteins it phosphorylates
    b.      Rapid addition and removal is important in allowing the phosphorylated proteins to do what?
    c.       Many extracellular signals involved in the complex networks of signaling pathways need to be both __ and __ by the cell
                                                                  i.      Individual protein kinases serve as __
    • protein kinases
    • amino acid sequences
    • kinase sequence
    • recognition 
    • switch rapidly from one state to another
    • integrated and amplified
    • input-output devices in the integration process
  15. a.       In general, specific sets of phosphate groups serve to __, while other sets can __. A __ provides a good example as kinases in this class phosphorylate __ and __and are central components of the __ in eukaryotic cells
                                                                  i.      Cdk proteins become active as a __ only when bound to a second protein called a __, which is only one of three distinct inputs required to __
    1.       In addition to cyclin binding, a __must be added to a specific threonine side chain, and a __elsewhere in the protein must be removed
    • activate the protein
    • inactivate it.

    • cyclin-dependent protien kinase
    • serines and threonines 
    • cell-cycle control system

    • Ser/Thr protein kinase
    • cyclin
    • activate the Cdk

    • phosphate 
    • phosphate
  16.                                                               i.      Cdk thus monitors a specific set of cell components—a __, __, and __—and acts as an __ that turns on if, and only if, each of these components has attained its appropriate activity state.
                                                                ii.      Sudden destruction of a cyclin immediately does what, and this triggers a specific step in the cell cycle 
    • cyclin, a protien kinase, and a protein phosphatase
    • input-output device

    shuts off its partner Cdk enzyme
  17. a.       The Src family of protien kinases is similar; the Src protein was the first __ to be discovered
                                                                  i.      These proteins contain a __ that becomes covalently linked to a __, which does what? After the N-terminal region are the __ and a __, followed by the __.            
    • tyrosine kinase
    • short N-terminal region
    • strongly hydrophobic fatty acid
    • holds the kinase at the cytoplasmic face of the plasma membrane
    • Src homology 3 (SH3) domain and a SH2 domain
    • kinase catalytic domain
  18.  i.      They normally exist in an __
    1.       Removal  of the__ and the binding of the __ by a specific activating protein turns it on
    b.      Protein activity can also be regulated with phosphate attached not to __ but to __
    • inactive conformation
    • C-terminal phosphate
    • SH3 domain
    • the protein
    • GTP.
  19.                                                               i.      Hydrolysis of GTP to GDP does what? These are __ and are controlled by __ that determine whether __ or __ is bound
                                                                ii.      There is a large family of __; in each, an important biological activity is controlled by a __that is caused by __ in a __ 
    • inactivates a protein
    • GTP-binding proteins
    • regulatory proteins
    • GTP or GDP

    • GTP-binding proteins
    • change in the protein’s conformation 
    • GTP hydrolysis
    • Ras-like domain
  20. a.       Motor proteins generate forces responsible for __ and the __ and __ of cells. They also power smaller-scale intracellular movements, helping to __, to move __within the cell and to move __ during the synthesis of a new DNA molecule
    • muscle contraction
    • crawling and swimming

    • move chromosomes to opposite ends of the cell during mitosis
    • organelles along molecular tracks
    • enzymes along a DNA strand
  21.                                                               i.      They move along tracks by undergoing a series of __ that are __; such movement uses free energy from other sources
    1.       To force the entire cycle to proceed in one direction, it is enough to make any change in shape __. Most proteins that can walk in one direction for a long distance achieves this motion by __
    • conformational changes
    • reversible


    coupling one conformational change to the hydrolysis of an ATP molecule bound to the protein
  22. a.       ATP hydrolysis releases __; and __ shifts a motor protein from conformation 1 to 2. It is then __, causing conformation 3 to occur. Release of the __ and __ brings about conformation 1. Thus, the cycle is one direction
    free energy

    ATP binding


    ADP and Pi
  23. a.       __ are important membrane-bound pump prtoteins because they function to export __ from the cytoplasm; they are __, with a pair of __ linked to a pair of __ located just below the plasma membrane
    b.      __ also exist; an example is __, which uses a proton gradient to produce ATP 
    • ABC transporters
    • hydrophobic molecules
    • tetramers
    • membrane-spanning subunits
    • ATP binding subunits
    • Rotary pumps
    • ATP synthase
  24. a.       Large proteins with several domains perform more __ than single-domain proteins
                                                                  i.      Each of the central processes in a cell is catalyzed by a __
    1.       In most such protein machines, an __ drives an ordered series of __ in one or more of the individual protein sububits, enabling the __ to __; allowing enzymes to move directly into position
    • elaborate functions
    • highly coordinated linked set of 10 or more proteins
    • energetically favorable reaction
    • conformational changes
    • ensemble of proteins
    • move coordinately
  25. a.       Protein machines with __parts make efficient use of genetic information, such as SCF ubiquitin ligase, which binds different “__” at different times in the cell cycle
                                                                  i.      Specific proteins are targeted for __ in response to specific signals, thereby helping to drive the cell cycle
    • interchangeable 
    • target proteins
    • rapid destruction
  26. a.       Proteins are only on when needed. Specific signals allow this. When certain __ bind to receptor proteins in the plasma membrane, they often recruit a set of other proteins to the __ of the plasma membrane to form protein __ that pass the signal on
                                                                  i.      Scaffold proteins do what?
    • extracellular signaling molecules
    • inside surface
    • protein machines

    link together a set of activating, inhibiting, adaptor, and substrate proteins at a specific location in a cell
  27.                                                               i.      Induced proximity explains what?
                                                                ii.      Cells change the locations of their proteins by __ in a variety of different ways, as part of a __, which allows __, thereby __ required for particular reactions in specific regions of the cell
    why slightly different forms of enzymes with the same catalytic site often have different biological functions

    • covalently modifying them
    • regulatory code
    • binding to particular scaffold proteins
    • clustering the proteins
  28.  i.      Scaffolds allow cells to do what?

     Some scaffolds link __ rather than __, __ and causing them to __ with each other in random orientations; this speeds up reactions by creating a __
    compartmentalize reactions even in the absence of membranes

    • unstructured regions of polypeptide chains
    • holding their bound proteins

    • tethering the proteins together
    • collide frequently

    very high local concentration of the reacting species
  29. a.       Aside from phosphorylation, there are other modifications that causes different regulatory events to occur. Each protein’s set of covalent modifications constitutes an important __, which causes a different set of __ as groups are added or removed
    b.      __is a term used to describe such research focused on the large-scale analysis of proteins, analogous to the term genomics describing the large-scale analysis of DNA sequences and genes
    • combinatorial regulatory code
    • protein behaviors

  30. a.       Biologists map binding interactions in two ways:
                                                                  i.      Genetics: __
                                                                ii.      Biochemical: __
    b.      Protein interaction maps are useful for identifying the __; they also need to be interpreted with caution because what? Those proteins displaying similar patterns of interactions in two protein interaction maps of crosspecies comparisons are likely to have the same function in the cell
    interactions between proteins in yeasts, nematodes, and fruit flies

    affinity tagging and mass spectroscopy

    likely function of previously uncharacterized proteins

    the same protein can be used as part of two different complexes with different functions