Biochemistry Test 2 Flashcards
What is meant by the “native conformation” of a protein?
Native Conformation: proteins in their normal, functional state
What forces influence protein folding and stability?
Hydrogen Bonding, hydrophobic effect, ionic interactions
How do different R groups contribute to folding?
-Packing of Hydrophobic amino acids away from water favors protein folding
-Polar groups contribute hydrogen bonding and ion pairs to protein folding
-Individual van der Waals interactions are weak but combine to promote folding
Why is the peptide bond describes as rigid and planar?
-due to resonance between the carboxyl oxygen and the amide oxygen
-cannot rotate around the C=O bond
-partial double-bond character of C-N peptide bond prevents rotation, limiting range confirmations
What are the phi and psi angles, what carbon do they surround, and how do these angles determine protein folding?
-3 dihedral angles:
-phi: between -180 and +180 degrees
-psi: between -180 and +180 degrees
-many phi and psi values are prohibited by steric interference
-both phi and psi angles cannot both=0 degrees
-omega: +/- 180 degrees for trans
-The phi angle is the angle between the alpha carbon atom and the nitrogen while the psi angle is the angle between the alpha carbon and the carbon of the carbonyl group.
What do the levels of protein structure refer to?
-Primary: sequence of amino acids
-Secondary: describes the spatial arrangement of the main-chain atoms in a segment of a polypeptide chain
-Tertiary: fold into larger, complex structure
-Quaternary: two or more proteins together
What are the most common secondary structural forms?
-Alpha Helices
-Beta Sheets/Strands
Descibe Alpha Helices.
-simplest arrangement, max number of H bonds
-interacts with itself for stability via H bonds
-backbone wound around an imaginary longitudinal axis
-R groups protrude out from the backbone
Describe Beta Sheets/Strands
-backbone extends into a zigzag
-Beta Strand: single protein segment
-Beta Sheet: several strands in Beta conformation side by side
-antiparallel or parallel
What are the major classes of proteins based upon structure?
-Fibrous Proteins: arranged in long strands or sheets
-Globular Proteins: folded into a spherical or globular shape
-Membrane Proteins: embedded in hydrophobic lipid membranes
-Intrinsically Disordered Proteins: lacking stable tertiary structures
What are some examples of fibrous proteins and what do they do?
-Fibrous proteins are arranged in long strands or sheets
-Keratin; tough, insoluble protective structures of varying hardness and flexibility
-Fibron: soft, flexible filaments
-Collagen: high tensile strength, without stretch
What is an example of a globular protein?
Enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins
What advantage would an intrinsically disordered protein domain offer to a protein?
facilitates a protein to interact with multiple binding partners
What disease does protein misfolding or aggregation contribute to?
-amyloid fiber: protein secreted in a misfolded state and converted to an insoluble extracellular fiber
-amyloidosis diseases: type 2 diabetes, Alzheimer’s disease, Huntington disease, and Parkinson’s disease
What is the function of a heme group?
-heme group: protein-bound prosthetic group; serves as a binding site for molecular oxygen
-myglobin, hemoglobin, cytoglobin
How does the heme group bind to oxygen?
-the heme group uses Fe2+ to bind O2 reversibly
-Fe3+ does NOT bind O2
What is the basic structure of a globin?
highly conserved tertiary structure of eight alpha-helical segments
What is a ligand?
a molecule that binds to another
What is binding equilibrium?
Whar is the dissociation constant and how does that value affect binding affinity?
-Dissociation Constant (Kd): reciprocal of Ka; equilibrium constant for the release of a ligand\
-lower Kd=higher affinity
How does the pressure of oxygen in the body relate to the affinity of hemoglobin and myoglobin for binding to oxygen?
- Partial pressure of O2 is easier to measure than O2. The less saturated hemoglobin is and the
lower the partial pressure of oxygen in the blood is, the more readily hemoglobin binds to
carbon dioxide.
What is an allosteric protein? And what are homeotropic vs heterotropic modulators?
-Allosteric Protein: binding of a ligand to one site affects the binding properties of another site on the same protein
-Homotropic Modulators: ligands that bind to an allosteric protein to include a conformational change
-Heterotropic Modulators: modulator is a molecule other than the normal ligand
What does it mean for enzymes to be biological catalysts?
Enzymes are typically made of proteins and help to lower activation energy for reactions without changing the equilibrium for the reaction
What is a cofactor and what are some examples?
-Cofactor: 1+ inorganic ions
-Fe2+, Mg2+,Mn2+, or Zn2+
What is a coenzyme and what are some examples?
-Coenzyme: complex organic or metallorganic molecule that acts as transient carriers of specific functional groups
-Biocytin, Coenzyme A, Lipoate
What is an active site and what is a substrate?
-Active Site: provides a specific environment in which a given reaction can occur rapidly
-Substrate: the molecule that is bound to the active site and acted upon by the enzyme
What is a rate constant and when is it first order vs. second order? What are the units for first and second order reactions?
-Rate Constant: the rate of any reaction determined by the concentration of reactants
-First Order Reaction: rate depends only on the concentration of the substrate
-Units: s-1
-Second Order Reaction: rate depends on the concentration of 2 different compounds or the reaction is between 2 of the same molecules
-Units: M-1S-1
What does it mean to say that enzymes:substrate interactions are induced fit rather than a lock-and-key?
-Induced Fit: mechanism by which the enzyme itself undergoes a conformational change when the substrate binds, induced by multiple weak interactions with the substrate
The lock and key method infers that the enzyme and substrate are a perfect fit for each other, which is not true since the enzyme changes conformation for the substrate
What R-groups tend to participate in acid/base catalysis in enzymes? (examples)
Tyr, Ser, His, Cys, Lys, Arg, Glu, and Asp
Enzyme Kinetics
discipline focused on determining the rate of a reaction and how it changes in response to changes in experimental parameters
Initial Rate/Velocity
tangent to each curve taken at time=0; beginning of the reaction [S] is regarded as a constant
Maximum Velocity
the plateau like initial velocity region is close to the maximum velocity; is observed when virtually all the enzyme is present at the ES complex
Michaelis Constant (Km)
the substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity
Turnover Number (Kcat)
the number of substrate molecules converted to the product in a given unit of time on a single enzyme molecule when the enzyme is saturated
Specifictiy Constant (Kcat/Km)
the rate constant for the conversion of E+S–> E+P
What is the difference between pre-steady state vs steady-state in enzyme catalyzed reactions?
-Pre-steady state: initial transient period during which ES builds up
-Steady-State: period in which the [ES] and other intermediate remains constant
What is the Michaelis-Menten equation and what does it describe?
-Michaelis-Menten equation: rate equation for a one substrate enzyme catalyzed reaction
-V0=Vmax[S]/Km+[S]
What does a Michaelis-Menten plot illustrate?
What is a Lineweaver-Burk Plot and what does it illustrate?
For enzymes obeying the Michaelis-Menten relationships a plot of 1/initial velocity versus 1/[S] yields a straight line
What is irreversible inhibition?
bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme’s activity, or form a highly stable noncovalent association
What is allosteric modulation?
function through reversible. noncovalent binding of regulatory compounds called allosteric modulators (small metabolites or cofactors)
-reversible covalent modification
-binding of separate regulatory proteins
-removal of peptide segments by proteolytic cleavage
What are homotropic and heterotrophic modulators?
-Homotropic: regulation in which the substrate and modulator are identical
-Heterotropic: regulation in which the modulator is a molecule other than the substrate
What are some covalent modifications that modify protein activity?
Phosphorylation, Adenylation, Acetylation
What is a kinase and what is a phosphatase?
-Protein Kinase: catalyzes the attachment of phosphate groups to specific amino acid residues (Ser, Thr, Tyr, His)
-Protein Phosphatase: remove phosphate groups from the same target proteins
Zymogen
an inactive precursor of an enzyme
Proprotein/Proenzyme
precursors that are cleaved to form other proteins
Competitive Inhibition
-inhibitor looks like the substrate; competing for binding on active site
-Km goes up, Vmax stays the same
Uncompetitve Inhibition
-one binding pocket for substrate, one for inhibiotro, only binds when substrate is bound
-Km and Vmax both decrease proportionally
Mixed Inhibition
-inhibitor can bind with or without the substrate being bound
-can affect Km and Vmax in different ways depending on the type
-Km may increase or decrease
Noncompetitive Inhibition
-affects vmax but not km
