biochemistry Flashcards

9279415066	disulfide bond	thiol group of Cys can be deprotonted and can occasionally undergo oxidation with another thiol group	0
9279417681	condensation reaction	reaction in which a water molecule is eliminated	1
9279420543	peptide bond	amide bond linking the two amino acids	2
9279427991	residues	remaining portions of amino acids	3
9279432383	microenvironment	side chain's immediate neighbors, can alter polarity and tendency to lose or accept a proton	4
9279437184	primary structure	sequence of amino acids in a polypeptide, seldom assumes linear extended conformation	5
9279440122	secondary structure	local folding arrangement of the polypeptide backbone, exclusive of the side chains, electrons are somewhat delocalized/two resonance forms, partial double bond character therefore no rotation around the CN bond	6
9279447478	a helix	exhibits a twisted backbone formation polypeptide backbone twists in a right handed helix carbonyl oxygen of each residue forms a hydrogen bond with the backbone NH group four residues ahead atoms of backbone are in Van der Waals contact	7
9279489261	b sheet	multiple polypeptide strands strands can be arranged in two ways parallel b sheet: neighboring chains run in same direction antiparallel b sheet: neighboring chains run in opposite directions	8
9279495132	irregular secondary structures	polypeptide does not adopt a defined secondary structure in which successive residues have the same backbone conformation	9
9279500689	tertiary structure	three dimensional shape of the protein, includes its irregular and regular secondary shape and spatial arrangement of all its side chains	10
9279505564	domain	polypeptide segment that has folded into a single structural unit with a hydrophobic core 1. core of domain is usually richer in regular secondary structure 2. irregular secondary structures are found in the surface	11
9279720907	ion pair	when two charged residues of opposite charges interact electrostatically	12
9279726682	hydrogen bonding	helps fine tune the folded formation folded conformation stabilized by the hydrophobic effect	13
9279734682	molecular chaperones	certain small proteins require assistance of proteins	14
9279738017	processing	additional steps beyond polypeptide folding	15
9279742429	intrinsically unstructured proteins	highly flexible extended segments rich in hydrophobic amino acids	16
9279755390	quaternary structure	spatial arrangement of all chains subunits: individual polypeptide chains	17
9279759805	heme	polypeptide chain plus the iron containing porphyrin derivative	18
9279767658	prosthetic group	an organic compound that allows a protein to carry out some function that the polypeptide alone cannot perform	19
9279778409	Y (fractional saturation)	proportion of the total myoglobin molecules that have bound O2	20
9279781728	saturation	when all the molecules have bund O2	21
9279783672	hemoglobin	heterotetramer containing two alpha chains and two beta chains	22
9280845257	cooperative binding	hb's four heme groups are not independent but communicate with each other in order to work in a unified fashion	23
9280851521	deoxyhemoglobin	hb without any bound O2	24
9280855033	oxyhemoglobin	hb with bound O2 the Fe moves into the center of the porphyrin plane	25
9280859288	Tense	deoxyhemogobin, reluctant to bind to oxygen because Fe atom lies outside the heme plane	26
9280860717	Relaxed	oxyhemoglobin, much more oxygen binding	27
9280865410	allosteric proteins	proteins with multiple binding sites where the binding of a small molecule (ligand) to one site alters the ligand binding affinity for the other sites	28
9280871556	Bohr Effect	reduction of hb's oxygen binding affinity when the pH decreases increasing pH=more O2 binding	29
9280967657	BPG	binds in the central cavity of tense hb, the presence of this stabilizes the deoxy conformation of hemoglobin and helps hb let go of oxygen	30
9280972765	microfilaments	actin filaments, support the plasma membrane and determine cell shape f-actin: polymerized actin g-actin: globular monomeric form	31
9280982173	treamilling	net rate of addition of subunits to one end of a microfilament that matches the net rate of removal of subunits at the other end	32
9280985531	intermediate filaments	diameter of 100A, example keratin, exclusively structural proteins and are intermediate in thickness b/w the microtubules and the microfilaments	33
9280991306	microtubules	diameter of about 240A, cytoskeletal fibers built from small globular protein subunits, thin and flexible rod ex. tubulin construct cilia and flagella and align and separate pairs of chromosomes during mitosis	34
9281000056	protofilament	assembly of a microtubule that begins with the end to end association of tubulin dimers to form a short linear blank	35
9281007136	coiled coil	basic structural unit of an intermediate filament, dimer of helices that wind around each other ex. keratin	36
9281019972	hydrolysis	cleavage by water (breaks down peptide bonds)	37
9281024407	transition state	point of highest energy, considered an intermediate between reactants and products	38
9281026300	oxidoreductases	oxidation reduction reactions	39
9281026302	transferases	transfer of functional groups	40
9281028089	hydrolases	hydrolysis reactinos	41
9281028090	lyases	group elimination to form double bonds	42
9281030026	isomerases	isomerization reactions	43
9281030027	ligases	bond formation coupled with ATP hydrolysis	44
9281032834	-Delta G	reaction is spontaneous and thermodynamically favorable but the height of the DG determines how fast reaction actually occurs	45
9281036187	+Delta G	reaction is nonspontaneous and reaction goes uphill	46
9281038806	catalyst	decreases the activation barrier (DG)	47
9281043275	cofactor	participates in catalysis when the amino acid side chains of an enzyme cannot provide required catalytic groups	48
9281049762	coenzymes	organic molecules that may be derived from vitamins	49
9281079359	cosubstrates	form of coenzyme, enter and exit the active site as substrates do	50
9281081869	prosthetic group	a tightly bound coenzyme that remains in the active site between reactions	51
9281089888	acid base catalysis	proton is transferred between the enzyme and a substrate usually to reduce unfavorable character of the transition state, catalytic activity of these are sensitive to changes in pH	52
9281097891	covalent catalysis	second major chemical reaction mechanism used by enzymes,bond forms between catalyst and substrate during formation of the transition state	53
9281103450	metal ion catalysis	occurs when metal ions participate in enzymatic reactions by mediating oxidation-reduction reactions or by promoting the reactivity of other groups in the enzyme's active site through electrostatic effects	54
9281122895	lock and key	model that suggests the catalytic residues must be precisely aligned in the active site so a certain amount of surrounding structure is required to hold them in place	55
9281128507	transition state stabilization	because the transition state is complementary in shape and charge with the active site getting to transition state increases stability	56
9281133136	close proximity	increases reaction rates by increasing the frequency of collisions that can lead to a reaction	57
9281135789	induced fit	upon binding substrates some enzymes undergo a pronounced conformational change so that they almost fully enclose the substrate	58
9281147072	multisubstrate reactions	biochemical reactions that involve more than one substrate, either oxidation reduction reaction or transferase reactions	59
9281150791	random mechanism	substrates can bind in any order as long as they both end up in the active site at the same time	60
9281152892	ordered mechanism	enzymes in which one substrate must bind before the other follow	61
9281155239	ping pong mechanism	one substrate binds and one product is released before the other substrate binds and the second product is released	62
9281157769	multistep reactions	each step of this process has characteristic forward and reverse rate constants	63
9281162604	nonhyperbolic reactions	enzymes that do not obey MM rate equation	64
9281162605	allosteric enzyme	in blank the presence of a substrate at one active site can affect the catalytic activity of the other active sites	65
9281172220	cooperative behavior	occurs when the enzyme subunits are structurally linked to each other so thata substrate-induced conformational change in one subunit eliicts conformational changes in the remaining subunits	66
9281187965	irreversible	any reagent that covalently modifies an amino acid side chain in a protein is potentially this	67
9281193201	suicide substrates	type of irreversible compound, enter enzyme's active site and begin to react, just as a normal substrate would but are unable to undergo the complete reaction and become stuck in the active site	68
9281223394	competitive inhibition	ost common form of reversible inhibition, it is where the inhibitor is a substance that directly competes with a substrate for binding to the enzyme's active site	69
9281234043	product inhibition	product of a reaction occupies the enzyme's active site thereby preventing the binding of additional substrate molecules	70
9281288526	noncompetitive inhibition	inhibitor binds to a site on the enzyme other than the active site and elicits a conformational change that affects the structure or chemical properties of the active site	71
9281324477	mixed inhibition	inhibitor affects substrate binding so the KM appears to increase or decrease, the inhibitor binding to the enzyme alters its conformation in such a way that both the Vmax and Km are affected although not necessarily in the same way	72
9281329362	uncompetitive inhibition	multisubstrate reaction where an inhibitor can bind to the enzyme after one substrate has bound in a way that prevents the reaction from continuing and yielding product	73
9281342562	feedback inhibitor	when concentration in the cell is sufficiently high it shuts down its own synthesis by blocking an earlier step in its biosynthetic pathway	74
9282780504	competitive inhibitor		75
9282788703	noncompetitive inhibitor		76
9282804222	uncompetitive inhibitor		77
9282807942	competitive inhibitor		78
9282809514	noncompetitive inhibitor		79
9282814227			80