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1

the function of nearly all proteins depend on their ability to bind to molecules (ligands or substrates) with a

high degree of specificity

2

region of a protein that associates with a ligand

binding ste

3

protein-ligand interaction is mediated by

noncovalent bonds

4

protein-ligand interaction can be measured by

velocity, affinity (binding strength), and specificity (binding preference)

5

level of affinity and specificity depends on --

molecular complementaries

6

-- identify crucial ligand-binding sites

evolutionary tracing method

7

most common way two proteins bind with each other

surface-surface

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antibodies can directly -- or mark it for destruction

inactivate target protein

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T/F: antibodies can distinguish between proteins that differ by only one AA

true

10

foreign substance that elicits production of an antibody

antigen

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subunits/polypeptides of an antibody

2 heavy chains and 2 light chains

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the chains of an antibody are held together by

disulfide bonds

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each polypeptide chain of an antibody can be divided into 2 domains

variable and constant

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the -- domains interact with the antigen

variable

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ligand binding site in antibodies

hypervariable loop

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interaction between antibody and epitope of antigen is

complementary

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enzymes binds 2 molecules and -- them to encourage a reaction to occur between them

precisely orients

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binding of substrate to enzyme rearranges electrons in the substrate that --

favor a reaction

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enzymes strains the bound substrate molecule, forcing it toward a -- to favor a reaction

transition state

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enzyme that catalyze a hydrolytic cleavage

hydrolase

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break down nucleic acids by hydrolyzing bonds between nucleotides

nucleases

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break down proteins by hydrolyzing bonds between AA

proteases

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synthesize molecules in anabolic reactions by condensing two smaller molecules together

synthase

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join together two molecules in an energy-dependent process

ligase

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catalyze rearrangement of bonds within a single molecule

iosmerase

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catalyze polymerization reactions such as synthesis of DNA and RNA

polymerases

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catalyze the addition of phosphate groups to molecules

kinases

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hydrolyze ATP

ATPases

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GTPase

hydrolyze GTP

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dissociation rate

Koff * [AB]

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association rate

Kon * [A][B]

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dissociation rate = association rate at

equilibrium

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Vmax

all enzymes are used

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Km

substrate concentration at 0.5 Vmax

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low Km

enzyme binds to substrate very tightly

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enzyme's active site is made up of

catalytic site and binding pocket

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trypsin-like serene proteases' catalytic site

serine, histidine, aspartate, oxyanion hole

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trypsin-like serene proteases' catalytic site - serine

break peptide bond

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trypsin-like serene proteases' catalytic site - histidine

stabilize (accept proton)

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trypsin-like serene proteases' catalytic site - aspartate

orient histidine at right location by H bonding

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trypsin-like serene proteases' catalytic site - oxyanion hole

stabilize intermediates

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trypsin-like serene proteases' catalytic site - the binding site

is general

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trypsin-like serine proteases' catalytic site - has a -- binding pocket

side chain specificity

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Trypsin (Asp)

Arg and Lys (positive side chains)

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Chymotrypsin (Ser)

Phe, Tyr, Trp (large hydrophobic side chains)

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Elastase (Val)

Gly and Ala (small side chains)

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substrate of lysozyme

6-sugar oligosaccharide

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lysozyme breaks uses -- to break between the 4th and 5th sugar

glutamate and aspartate

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final products of lysozyme are

4-sugar oligosaccharide and a disaccharide

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proteins often use -- to carry functions that would be difficult using AA alone

small non-protein molecules

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change conformation --> change function examples

allosteric walking and ABC transporter

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enzymes in a common pathway are often --

physically associated with one another

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-- hold related enzymes

scaffold

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regulation of protein activity by kinase/phosphatase switch is an example of -- protein modification

covalent

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T/F: kinase can only turn on proteins

false

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Which amino acids are used in the kinase/phosphatase switch?

serine, threonine, tyrosine (hydroxyl group)

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receptro tyrosine kinase is activated by --

dimerization

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once RTK is active, they --

phosphorylate each other

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Src-type kinase as --

signal-integrating device

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refers to the changes of protein conformation and activity upon binding to a ligand

allosteric regulation

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allosteric regulation is an example of -- protein modification

noncovalent

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T/F: allosteric regulation can be positive or negative

true

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active PKA has lost its

catalytic site

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in allosteric regulation, the activity of an enzyme is either inhibited to activated by a regulatory molecule that binds to the allosteric site that is -- from the active site

distinct

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the binding to the allosteric site produces a -- of the active site either simulating or inhibiting the enzyme to catalyze a reaction

conformational change

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the binding of tryptophan changes the conformation of the --

repressor

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allosteric switch of calmodulin is

noncovalent

68

GTP bound

ON

69

GDP bound

OFF

70

GAP (GTPases Activating Protein)

help turn off faster

71

GEF (Guanine Exchange Factor)

help turn on faster

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when the amount of the -- is high it inhibits an enzyme that functions early in the reaction pathway

end product

73

three conformations of the acetylcholine receptor

unoccupied and closed
occupied and open
occupied and closed

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most stable form of the acetylcholine receptor

occupied and closed (inactivated)

75

tryptophan repressor is an examples of -- modification

noncovalent

76

when there's a lot of tryptophan, it will bind to the -- which binds to the DNA and turns it off

tryptophan repressor

77

enzymatic cleavage of a backbone peptide bond, resulting in the removal of residues from the polypeptide chain

proteolytic cleavage

78

proteolytic cleavage is a common mechanism for activating enzymes that function in

programmed cell death

79

proteolysis also generates active peptide hormones such as -- from larger precursor polypeptides

insulin

80

proteolytic cleavage -- inactivates or activates proteins

irreversibly

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Ubiquitin is a -- amino acid polypeptide that marks proteins for degradation

76

82

ubiquitin can be covalently linked to other proteins via a covalent bonds between an internal -- and its C-terminal

lysine on the substrate protein

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monoubiquitylation

histone regulation

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multiubiquitylation

endocytosis

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polyubiquitylation (Lys 48)

proteosomal degradation

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polyubiquitylation (Lys 63)

DNA repair

87

ubiquitin activating enzyme (E1) uses -- to attach ubiquitin to itself via a high energy thioester bond

ATP hydrolysis

88

E1 passes activated ubiquitin to --

E2 ubiquitin-conjugating enzymes

89

E2 works with E3 (ubiquitin ligases) which has the -- for the target protein

binding site