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Biochemistry I > Biochemistry Test 2 > Flashcards

Biochemistry Test 2 Flashcards

1
Q

What is meant by the “native conformation” of a protein?

A

Native Conformation: proteins in their normal, functional state

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2
Q

What forces influence protein folding and stability?

A

Hydrogen Bonding, hydrophobic effect, ionic interactions

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3
Q

How do different R groups contribute to folding?

A

-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

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4
Q

Why is the peptide bond describes as rigid and planar?

A

-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

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5
Q

What are the phi and psi angles, what carbon do they surround, and how do these angles determine protein folding?

A

-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.

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6
Q

What do the levels of protein structure refer to?

A

-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

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7
Q

What are the most common secondary structural forms?

A

-Alpha Helices

-Beta Sheets/Strands

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8
Q

Descibe Alpha Helices.

A

-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

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9
Q

Describe Beta Sheets/Strands

A

-backbone extends into a zigzag
-Beta Strand: single protein segment
-Beta Sheet: several strands in Beta conformation side by side
-antiparallel or parallel

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10
Q

What are the major classes of proteins based upon structure?

A

-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

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11
Q

What are some examples of fibrous proteins and what do they do?

A

-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

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12
Q

What is an example of a globular protein?

A

Enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins

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13
Q

What advantage would an intrinsically disordered protein domain offer to a protein?

A

facilitates a protein to interact with multiple binding partners

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14
Q

What disease does protein misfolding or aggregation contribute to?

A

-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

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15
Q

What is the function of a heme group?

A

-heme group: protein-bound prosthetic group; serves as a binding site for molecular oxygen
-myglobin, hemoglobin, cytoglobin

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16
Q

How does the heme group bind to oxygen?

A

-the heme group uses Fe2+ to bind O2 reversibly
-Fe3+ does NOT bind O2

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17
Q

What is the basic structure of a globin?

A

highly conserved tertiary structure of eight alpha-helical segments

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18
Q

What is a ligand?

A

a molecule that binds to another

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19
Q

What is binding equilibrium?

A
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20
Q

Whar is the dissociation constant and how does that value affect binding affinity?

A

-Dissociation Constant (Kd): reciprocal of Ka; equilibrium constant for the release of a ligand\
-lower Kd=higher affinity

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21
Q

How does the pressure of oxygen in the body relate to the affinity of hemoglobin and myoglobin for binding to oxygen?

A
  • 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.
22
Q

What is an allosteric protein? And what are homeotropic vs heterotropic modulators?

A

-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

23
Q

What does it mean for enzymes to be biological catalysts?

A

Enzymes are typically made of proteins and help to lower activation energy for reactions without changing the equilibrium for the reaction

24
Q

What is a cofactor and what are some examples?

A

-Cofactor: 1+ inorganic ions
-Fe2+, Mg2+,Mn2+, or Zn2+

25
Q

What is a coenzyme and what are some examples?

A

-Coenzyme: complex organic or metallorganic molecule that acts as transient carriers of specific functional groups
-Biocytin, Coenzyme A, Lipoate

26
Q

What is an active site and what is a substrate?

A

-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

27
Q

What is a rate constant and when is it first order vs. second order? What are the units for first and second order reactions?

A

-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

28
Q

What does it mean to say that enzymes:substrate interactions are induced fit rather than a lock-and-key?

A

-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

29
Q

What R-groups tend to participate in acid/base catalysis in enzymes? (examples)

A

Tyr, Ser, His, Cys, Lys, Arg, Glu, and Asp

30
Q

Enzyme Kinetics

A

discipline focused on determining the rate of a reaction and how it changes in response to changes in experimental parameters

31
Q

Initial Rate/Velocity

A

tangent to each curve taken at time=0; beginning of the reaction [S] is regarded as a constant

32
Q

Maximum Velocity

A

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

33
Q

Michaelis Constant (Km)

A

the substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity

34
Q

Turnover Number (Kcat)

A

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

35
Q

Specifictiy Constant (Kcat/Km)

A

the rate constant for the conversion of E+S–> E+P

36
Q

What is the difference between pre-steady state vs steady-state in enzyme catalyzed reactions?

A

-Pre-steady state: initial transient period during which ES builds up
-Steady-State: period in which the [ES] and other intermediate remains constant

37
Q

What is the Michaelis-Menten equation and what does it describe?

A

-Michaelis-Menten equation: rate equation for a one substrate enzyme catalyzed reaction
-V0=Vmax[S]/Km+[S]

38
Q

What does a Michaelis-Menten plot illustrate?

A
39
Q

What is a Lineweaver-Burk Plot and what does it illustrate?

A

For enzymes obeying the Michaelis-Menten relationships a plot of 1/initial velocity versus 1/[S] yields a straight line

40
Q

What is irreversible inhibition?

A

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

41
Q

What is allosteric modulation?

A

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

42
Q

What are homotropic and heterotrophic modulators?

A

-Homotropic: regulation in which the substrate and modulator are identical
-Heterotropic: regulation in which the modulator is a molecule other than the substrate

43
Q

What are some covalent modifications that modify protein activity?

A

Phosphorylation, Adenylation, Acetylation

44
Q

What is a kinase and what is a phosphatase?

A

-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

45
Q

Zymogen

A

an inactive precursor of an enzyme

46
Q

Proprotein/Proenzyme

A

precursors that are cleaved to form other proteins

47
Q

Competitive Inhibition

A

-inhibitor looks like the substrate; competing for binding on active site
-Km goes up, Vmax stays the same

48
Q

Uncompetitve Inhibition

A

-one binding pocket for substrate, one for inhibiotro, only binds when substrate is bound
-Km and Vmax both decrease proportionally

49
Q

Mixed Inhibition

A

-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

50
Q

Noncompetitive Inhibition

A

-affects vmax but not km

Biochemistry I (6 decks)

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