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248 Cards in this Set

  • Front
  • Back
__ structure is when the primary and secondary configurations bend and fold into a specific 3d shape.
Tertiary Structure; tertiary structure is when the primary and secondary configurations bend and fold into a specific 3d shape
tertiary structure results from the interactions between the R groups of the different ______
amino acid residues, tertiary structure results from the interactions between the R groups of different amino acid residues
__ are covalent bonds that contriube to the stability of the 3d shape of the protein
disulfide bridges; disulfide bridges are covalent bonds that contribute to the stability of the 3d shape of a protein
R group interations in tertiary structures include __ , ___,___, and ____
disulfide bridges, ionic interactions, hydrophobic interactions, and hydrogen bonds
In tertiary structure, carboxyl groups interacting with amino groups is an example of __ interactions
ionic; in tertiary structures, when carboxy groups interact with amino groups, that is an example of an ionic interaction
__ structure refers to the structure of proteins containing more than one polypeptide chain (subunit)
quaternary structure; quaternary structure refers to the structure of proteins containg more than one polypeptide chain
___ proteins contain only amino acid residues
simple; simple proteins only contain amino acid residues
Conjugated proteins also contain other components called __ groups
prosthetic groups; Conjugated proteins contain prosthetic groups
Hemoglobin (hb) is an example of a __ protein with a quaternary structure
conjugated protein; hemoglobin is an example of a conjugated protein with a quaternary structure
Protein folding occurs during synthesis in the __
ER; protein folding occurs during synthesis in the ER
Interactions between the ____ --both attraction and repulsion play a role in the folding process
side chains; interactions between the side chains--both attraction and repulsion play a role in the folding process
Chaperones called ____ proteins assist in the protein folding
heat shock proteins; chaperones called heat shock proteins assist in the protein folding
__ is the 1 degree component of plaque in Alzheimer's disease
amyloid plaque; amyloid plaque is the 1 degree component of plaque in alzheimer's disease
__ of a protein results in the loss of its characteristic native structure and function
denaturation; denaturation of a protein results in theloss of its characteristic native structure and function
Extreme temperatures denature proteins, so most proteins are biologically active b/w __ and __ degree celcius
Extreme temperatures denature proteins, so most proteins are biologically active b/w 0-40 degrees celcius
Strong acids/bases can denature proteins by affecting the ____
salt bridges; strong acids/bases can denature proteins by affecting the salt bridges
organic solvents and ___ can cause protein denaturation by disrupting hydrophobic reactions
detergents; organic solvents and detergents can cause protein denatuation by disrupting hydrophobic reactions
reducing agents such as __ and b-mercaptoethanol, disrupt disulfide bridges and cause protein denaturation
urea; reducing agents such as urea and b mercaptoethanol, disrupt disulfide bridges and cause denaturation
__ concentration can cause denaturation b/c it binds amino acids ionizable groups followed by h20 solvation and precipitation
salt concentration; salt concentration can cause protein denaturation
___ ions disrupt salt bridges, bind sulfydryl groups, and cause denaturation
heavy metal ions; heavy metal ions can disrupt salt bridges, bind sulfydryl groups, and cause denaturation
__ disrupts hydrogen and salt bridges
mechanical stress; mechanical stress disrupts hydrogen and salt bridges and can cause denaturation
8 things that cause protein denaturation
strong acids/bases; extreme temperatures; organic solvents; detergents; reducing agents; salt concentration; heavy metal ions; and mechanical stress
Protein denaturation is a precursor for _____
protein digestion; protein denaturation is a precursor for protein digestion
In ____, the 3d structure is broken and the protein loses its native structure. (uncoiling of protein)
protein denaturation; in protein denaturization, the 3d structure is broken and the protein uncoils
The amount of __ released when an acid is dissoved in water determines the strength of the acid
H+; the amount of hydrogen released when an acid is dissoved in water determines the strength of the acid
The more free H+ ions, the __ the acid
stronger the acid; the more free hydrogen ions, the stronger the acid
hydrogen concentration is expressed as the ___
molarity; hydrogen concentration is expressed as the molarity
M=moles/L
Molarity; Molarity equals moles per liter
___ denotes the number of moles of a given substance per liter of solutions
Molarity; Molarity denotes the number of moles of a given substance per liter of solution
The ____ ion is the most important ion in biological systems due to its effects on protein structure and biological reactions
H+; hydrogen ions are the most important ions in biological systems due to its effects on protein structure and biological reactions
Acids are proton ___
donors; acids are proton donors
Protons, hydrogen ion, and H+ are all the same; interchangeable terms; ie proton donor= hydrogen ion donor= H+ donor
TRUE
Bases are proton ___
acceptors; bases are proton acceptors
Bases accept protons=accept H+= accept hydrogen ions
TRUE
bases want to become more positive and therefore accept H+
TRUE
acids want to be more negative therefore they want to get rid of their positive H+ charges
TRUE
Stomach acid and battery acid are ___
strong acids; stomach acid and battery acid are strong acids with a ph of 0-2
lemon juice and vinegar are ___
weak acids; lemon juice and vinegar are weak acids with a ph of 3-6
pure water is __ with a ph of 7
neutral; pure water is neutral with a ph of 7
bicarbonate solution is a __
weak base; bicarbonate solution is a weak base with a ph of 8-11
NaOH, and oven cleaner (KOH) are ___
strong bases; NaOH and KOH are strong bases with a ph b/w 12-14
__ acids and bases completely dissociate
strong; strong acids and bases completely dissociate
Organic acids are __ acids and thus only partially dissociate
weak acids; organic acids are weak acids and thus only partially dissociate
The acid dissociation constant
Ka
__ represents the strength of an acid
Ka
The greater the Ka, the __ the acid
stronger; the greater the Ka, the stronger the acid
Ka=[H+] [A-]/[HA]
TRUE
Acids are defined by __ concentration
H+
H+ is not found free in solution and instead combines with a water molecule to form __
H30; H+ is not found free in solution and instead combines with a water molecule to form H30
H3O+ is a ___ion
hydronium ion; H3O+ is an hydronium ion
The ph of 7 is considered neutral at 25 degrees celsius b/c at theis ph the concentration of h3o equals the concentrations of OH- in pure water
TRUE
kw=[h+] [oh-]=1*10^-14
water constant
pH= -log [H+]
TRUE
pKa=-log Ka
TRUE
the smaller the pKa value, the __the acid
stronger; the smaller the pKa, the stronger the acid
Used in predicting properties of buffer solutions sued to control pH of reaction mixtures
henderson-hasselbalch equation
pH=pKa+log [A-}/[HA]
henderson hasselbalch equation
A --solution is one which resists changes in ph when small quantities of an acid or base are added to it
buffer solution
an acidic buffer has a ph of less than ___
7; an acidic buffer has a ph of les than 7
a __ buffer has a ph of more than 7
basic; a basic buffer has a ph of more than 7
Ways the body regualtes ph
1. Buffers 2. Co2 eliminated by the lungs 3. Acids and bases eliminated via kidneys
blood ph must be kept close to __
7.4
blood ph above 7.4=___
alkalosis
blood ph below 7.4=___
acidosis
body must get rid of __ moles of acid/day (mostly C02)
-15
ph changes charges on molecules, especially---
proteins
__ is when measured amounts of base are added to a measured amount of acid
titration
where ph=pka is called the xxx
inflection point; the inflection point is the point where ph=pka of acid
at the xxx ph changes very slowly as more base is added
inflection point; at the inflection point ph changes very slowly as more base is added
buffering region is -- ph unit above and below the inflection point
1; the buffering region is 1 ph above and below the inflection point
__ is an intracellular physiological buffer
phosporic acid; phosphoric acid is an intracellular physiological buffer with a ph of 7.2
__ is an extracellular blood buffering system
carbonic acid; carbonic acid is an extracellular, blood buffering system
dissolved co2 forms __ which reacts to produce bicarbonate ion (HCO3-)
carbonic acid; dissoved co2 forms carbonic acid which produces hco3
there is a direct relationship b/w blood ph and lung ____.
co2 pressure; there is a direct relationship b/w blood ph and lung co2 pressure
__ results in co2 trapped in lung tissue
pulmonary obstruction; pulmonary obstruction results in co2 trapped in lung tissue
A __ lower's blood hco3- concentration and thusly lowers blood ph
pulmonary obstruction; pulmonary obstruction lowers blood hco3- concentration and thusly lowers blood ph which causes acidosis and eventually death
__ in a solution contain weakly acidic carboxyl and weakly basic amino groups
amino acids; amino acids in a solution contain weakly acidic carboxyl groups and weakly basic amino groups
Buffers obey ___'s principle
le chatleier's principle
if a stress is applied to a reaction at equilibrium, the equilibrium will be displaced in the direction that relieves the stress
le chatelier's principle
At low (acidic) ph, both groups __
protenated; at a low ph, both groups are protonated
As ph increases, carboxyl group (COOH) DISSOCIATES h+ TO FORM ____ (COO-)
carboxylate; as ph increases, carboxyl group dissociates h+ and forms COO-
increasing ph results in converstion of H3N+ to __
H2N; increasing ph results in conversion of H3N+ to H2N
At isoelectric point (p1), amino acid is predominantly ___ form
dipolar; at isoelectric point (p1), amino acid is predominantly dipolar form
the 2 buffering regions
pk1 and pk2
pk1=
1=2
pk2=
2=3
protein is a __ molecule
polar; protein is a polar molecule
__ are catalysts that speed up reactions
enzymes
__ are not involved in the reaction, reduce the activation energy, are highly specific, and can be regulated
enzymes
enzymes are __
proteins
__ is what the enzyme is working on
substrate; a substrate is what the enzyme is working on
Enzyme contains special pocket where amino acid side chains create a 3d surface complementary to that of the substrates
active site
the number of molecules of substrate converted to product per enzyme molecule per second
Turnover number; the turnover number is generally 100-1000/second
___ and __ are nonprotein compounds that are needed for enzyme activity
coenzymes and cofactors; are nonprotein compounds that are needed for enzyme activitiy
Energy utilized by the body is obtained from the energy found in __
macronutrients
the SI energy unit is the
joule
__ is the energy needed to increase the temp of 1 gram of water by 1 degree celsius
calorie or kilocalorie
1 calorie=__ joules
4.18; 1 calorie = 4.18 joules
__ is the energy needed to incresae the temp of 1kg of water by 1 degree celsius
1 kcal or 1000 small calr
released energy is referred to as ____
free energy; released energy is referred to as free energy
Energy available to do work is known as ___ energy
free energy;
__ energy approaches zero as reaction proceeds to equilibrium.
free energy;
__ is the change in free energy of the reaction
delta G
Chem reactions have an energy barrier separating reactants from products callerd ___
activation energy
Free energy of products-Free energy of reactants=__
delta G of a reaction
if delta G negative then
exothermic
__ is energy releasing; net loss of energy and reaction goes as written from A-->B
exothermic
__ is energy requiring, net gain of energy and reaction does not go spontaneously from a-->b
endothermic
If delta G positive then
endothermic
if delta G is 0 then
reactants are in equilibrium
Intermediate formed during conversion of reactant to product
transition state;
Catalysts alter the ___
activation energy
____ binds substrate in a geometry resembling the activated transition state of the molecule
transition state stabilization; transition state stabilization binds substrate in a geometry resembling the activated transition state of the molecule
Amino acid side groupos participate in acid-base catalysis in which amino acids provide or accept protons
TRUE
Enzyme binds the substrate in position resembling the _____ of the molecule
activated transition state; enzyme binds the substrate in position resembling the activated transition state of the molecule
phosphate buffer___ the cell
inside the cell
Bicarb buffer___ the cell
outside the cell
___ converts co2 and h2o into h2co3
carbonic anhydrase
__ is the enzyme found in red blood cells
carbonic anhydrase
phosphate buffer___ the cell
inside the cell
Bicarb buffer___ the cell
outside the cell
___ converts co2 and h2o into h2co3
carbonic anhydrase
__ is the enzyme found in red blood cells
carbonic anhydrase
__ is the enzyme that controls the ph of blood
carbonic anhydrase
lungs eliminate ---
co2
liver excretes
acid
__ is the point at which you have equal concentrations of acid and conjugate base
pka; pka is the point at which you havve equual concentration of acid and conjugate base
pk1 refers to
COO-
pk2 refers to
NH3+
pk3 refers to
side chain
__ is only used when there is a side chain
pk3
alanine has no side chain and only has pk1 and pk2
TRUE
the average of pk1 and pk2 is the __
isoelectric ph
histidine has __pkas
3
minerals such as fe, zn, mn, fl, ni are __
cofactors
organic compoungs such as NAD, and FAD are __
coenzymes
__ are protein and non protein compunds
haloenzyme
alcohol dehydrenase and pyruvate dehydrogenase are examples of
haloenzyme
alcohol dehydrogenase needs _ as a cofactor
zinc; alcohol dehydrogenase needs zinc as a cofactor
pyruvate dehydrogenase needs __ as a coenzyme
NAD; pyruvate dehydrogenase needs NAD as a coenzyme
zinc is a --
cofactors
the protein portion of a haloenzyme is called__
apoprotein
apoprotein + coenzyme/cofactor=
haloenzyme
tightyly bound conezymes such as FAD have a ___group
prosthetic group
1 calorie=4.18 joules
TRUE
1kcal=4.184 kj
TRUE
a downhill reaction is __
exothermic
an uphill reaction is __
endothermic
free energy doesn't change with catalyst…catalysts only reduce activation energy
TRUE
part if the 3d protein strucutre where the substrate comes to bind
activation site
temperature, amount of substrate, and ph level affects __ speed
enzyme speed
__ results in a conformational change in the enzyme
substrate binding; substrate binding results in a conformational change in the enzyme
Factors affecting the reaction velocity include:
substrate concentration, temperature, and ph
the higher the substrate concentration the ___ the reaction
faster; the higher the substrate concentration, the faster the reaction
__ is the number of molecules of substrate converted to product per minute
V; velocity of reaction is the number of molecules of substrate converted to product per minute
velocity increases as substrate increases until ___ is reached
Vmax; velocity increases as substrate increases until maximum velocity is reached
__ reflects the saturation of enzymes binding sites with substrates
vmax; maximum velocity reflects the saturation of enzyme binding sites with substrates
velocity __ with temperature until vmax is reached
increases; velocity increases with temperature until vmax is reached
if temp increases too much, velocity will decrease due to ___
protein denaturation; if temperature increases too much, velocity will decrease due to protein denaturation
ph affects ionization of ___
active site; ph affects ionization of active site
optimum ph varies for different enzymes; for instance, alkaline phosphatase which is found in blood and tissues likes a ___ ph
high ph; alkaline phosphidase which is found in blood and tissue likes a high ph
pepsin, found in the stomach likes a __ ph
low ph; pepsin found in the stomach likes a low ph b/w 2-3
trypsin likes a __ ph
neutral; trypsin likes a neutral ph of 6.5
describes how reaction velocity varies with substrate concentration
michaelis-menten equation describes how reaction velocity varies with substrate concentration
the michaelis constant is
Km
Km reflect the __ of an enzyme for a substrate
affinity; km reflects the affinity of an enzyme for a substrate
km=
km=1/2 Vmax
every enzyme has a unique km
TRUE
__ predicts the velocity of a reaction
km; km predicts the velocity of a reaction
in the micahelis menton equation, the enzyme concentration remains constant, but the __ concentration is modified
substrate concentration; michaelis mention equation keeps enzyme concentration constant and modifies the substrate concentration
michaelis menten has a __ curve
hyperbolic, a hyperbolic curve represents michaelis-mention equation
a small km means the enzyme has a __ affinity for the substrate
high; a small km means the enzyme has a high affinity for the substrate b/c it only takes a little bit of substrate for reaction to reach 1/2vmax
large km means __ affinity b/w substrate and enzyme
low ; a large km reflects a low affinity b/w substrate and enzyme b/c it means it takes a lot of substrate to reach 1/2 vmax
__ occurs when inhibitor binds reversibly to active site of enzyme, therby competing with S for binding at that site
competitive inhibition; competitive inhibition occurs when an inhibitor binds reversibly to an enzymes active site and thusly competes with the substrate for that binding site
in competetive inhibition, __ is not affected
in competetive inhibition, vmax is not affected because can overcome inhibition by adding more substrate
in competetiive inhibition, __ increases
km; in competitive inhibition km increases
competitive inhibition increases km, does not change vmax, and shifts the curve to the __
right; competitive inhibition increases km, does not change vmax, and shifts the curve to the right
___ occurs when inhibitor and substrate bind at different sites on the enzyme
noncompetitive inhibition; noncompetitive inhibition is when inhibitor and substrate bind at different sites on the enzyme
vmax is __ by noncompetitive inhibition
decreased; vmax is decreased by noncompetitive inhibition
__ is not affected with noncompetitive inhibition
km; km is not affected by noncompetitive inhibition
___ inhibition slow the rate of reaction
noncompetitive inhibition; noncompetitive inhibition slows the rate of reaction
__ inhibition decreases vmax and 1/2 vmax, and does not affect km
noncompetitive inhibition
__ inhibition does not affect vmax, and increases km
competitive inhibition
___ inhibition does not affect vmax and increases km, __ inhibition decreases vmax and 1/2 vmax, and does not affect km;
competitive inhibition/noncompetitive inhibition; competitive inhibition does not affect vmax but increases km; noncompetitive inhibition does not affect km but decreases vmax.
cyanide, carbonmonoxide, and heavy metals are examples of ___ binding
irreversible; carbon monoxide, cyanide, and heavy metals are examples of irreversible binding
noncompetitive and competitie inhibitors are examples of ___ binding
reversible; competitive and noncompetitive inhibition are examples of reversible binding
malonate and ethanol are examples of ___ inhibition
competitive inhibition; ethanol and melonate are examples on competitive inhibition
isoleucine, which is a feedback inhibitor is an example of __ inhibition
noncompetitive; isoleucine is an example of a noncompetitive inhibitor
__ is essential for coordination of metabolic processes
enzyme regulation
___ enzymes don't follow the michaelis-menton curve and instead have a sigmoid curve
allosteric enzymes; allosteric enzymes follow a sigmoid curve
regulated by either positive or negative effectors that bind to a site other than an active site; alter affinity of E or S or modifying maximum activity of enzyme
allosteric enzymes
__ effectors inhibit enzyme activity
negative effectors; negative effectors inhibit enzyme actiivity
__ effectors increase enzyme activity
positive effectors; positive effectors inhibit enzyme activity
there are homotropic and heterotropic effectors that regulate __ enzymes
allosteric; regulators of allosteric enzymes are either homotropic or heterotropic
if an allosteric enzyme has a ___ regulator, then S serves as the effector and is typically a positive effector
homotropic; S serves as the effector and is typically positive
if an allosteric enzyme has a __ regulator, then the effector may be different than S and is usually negative
heterotropic; the effector may be different than S and is usually negative
binding of asubstrate increases the affinity of other substrates; after 1st binds, the 2nd, 3rd, and 4th binds faster and faster; hemoglobin is an example
enzyme cooperativity
when the end product of enzyme catalyzed reactions will inhibit the activity of an earlier enzyme in the path
feedback inhibition; feedback inhibition is when the endproduct inhibits the activity of an earlier enzyme in the path
one way to increase the production of a metabolic end product is by increasing the amount of enzyme present
TRUE
__ is the synthesis of new enzymes in response to a temporary need of the cell
enzyme induction; enzyme induction is the synthesis of new enzymes inr esponse to a temporary need of the cell
___ allows the cell to adapt to environmental changes
enzyme induction; enzyme induction allows the cell to adapt to environmental changes
__ occurs by the addition or removal of phosphate groups
covalent modification; covalent modification occurs by the addition or removal of phosphate groups
__ is catalyzed by kinases and utilizes ATP as the phospate donor
phosphorylation; phosphorylation is catalyzed by kinases and uses ATP
__ is catalyzed by phophatases which cleaves phosphate groups from enzymes
dephosphorylation; dephosphorylation is catalyzed by phosphatases and cleaves phosphate groups from enzyms
The central theme of molecular biology is to describe thr flow of info from DNA through RNA to proteins
TRUE
genetic info is encoded in ___
dna
prior to cell division, new DNA is synthesized by complimetary pairing of ___ on 2 dna strands
nucleotide bases; prior to cell division new DNA is synthesized by complimentary pairing of nucleotide bases on 2 dna strands
__ is involved in decodig dna and translating this info to produce proteins
RNA; RNA is involved in decoding dna and translating the info to produce proteins
the 3 types of rna are
mRNA, tRNA, and rRNA
nucleic acids are polymers classified into two categories: ___ and __
Ribonucleic acid (RNA ) and Deoxyribonucleic acid (DNA)
__ is found mainly in cell cytoplasm
RNA; RNA is mainly found in cell cytoplasm
__ is mainly found in cell nuclei
DNA; dna is found mainly in cell nuclei
__ make up nucleic acids
nucleotides; nucleotides make up nucleic acids
nucleotides are composed of 3 components:
nitrogen base, sugar, and phospate; nucleotides are made up of nitrogen base, sugar, and phosphate
a __ is just a base and sugar
nucleoside; a nucleoside is just a nitrogen base and sugar (does not have phospate group)
deoxyribonucleic acid does not have__
oxygen
nucleotides are composed of pyrimidines and purines, phosphate, and __
either ribose or 2-deoxyribose; nucleotides are composed of pyrimidines/purines, phosphate, and either ribose or 2-deoxyribose
__ is single stranded, contains ribose sugar, and has uracil instead of thymine
RNA; RNA is single stranded, has uracil instead of thymine, and contains ribose sugar
__ is double stranded, contains deoxyribose sugar, and has thymine
dna; dna is double stranded, has thymine, and contains deoxyribose sugar
the 3 pyrimidines are
cytosine, thymine, and uracil; cytosine, thymine, and uracil are the 3 pyrimidines
the 2 purine are
guanine and adenine; guanine and adenine are the 2 purines
there are __ pyrimidines and __ purines
3/2; there are 3 pyrimidines and 2 purines
__ structure has 2 rings
purine; purine's structure has 2 rings
nucleotide formation is a __ reaction b/c 2 h20 are released
condensation; nucleotide formation is a condensation reaction b/c 2 water molecules are released
in the formation of the nucleotide, the nitrogen base is in the __ prime position
1'; in nucleotide formation, the nitrogen base is in the 1 prime location
in the formation of the nucleotide, the phospate group is the the __ prime position
5'; in nucleotide formation, the phosphate group is in the 5' position
dna and rna are ___
polynucleotides
there is a ___ linkage b/w 2 nucleotides
phosphodiester linkage; linkage b/w two nucleotides is a 3' to 5' phosphodiester bond.
dna and RNA sequences are always read from __ prime to __ prime
5 prime to 3'; sequences are always read from 5'-->3'
in dna, A and __ always bond
T; in DNA adenine and thymine always bond
in rna A and __ bond
U; in RNA adenine bonds with uracil
C and __ always bond
G; cytosine and guanine always bond
human cells contain __ pairs of chromosomes
23
each chromosome contains one __
dna strand
dna strand coils around the __ proteins to form a nucleosome
histone; dna strand coils aroune the histone proteins to form a nucleosome
nucleosomes condense to form __
chromatin; nucleosomes condense to form chromatin
__ can fold back on itself
RNA; RNA can fold back on itself
___ syntheizes RNA
RNA polymerase; rna polymerase synthesizes RNA
transcription happends __ the nucleus
inside; transcription happends inside the nucleus
the __ controls protein synthesis inside the body
nucleus
the message that comes from the nucleus is the ___
amino acid sequence; the message that comes from the nucleus is the amino acid sequence
RNA is found mostly in the __
cytoplasm
__ is the formation of mRNA from DNA and occurs in the nucleus
transcription; transcription is the formation of mRNA from DNA and occurs in the nucleus
during transcription the info in the DNA is rewritten into __
Mrna
DNA unravels, and the available strand of DNA to be read is the ___ strand also known as the template or parent strand
sense strand; DNA unravels and the available strand of DNA to be read is the sense strand.
once produced by transcription, the ___ leaves the nucleus and goes into the cytoplasm
mRNA; once produced by transcription, the mRNA leaves the nucleus and goes into the cytoplasm
__ carries info to the ribosome where translation occurs
Mrna;Mrna carries info to the ribosome where translation occurs
translation occurs outside of the nucleus and on ___
ribosomes; translation occurs outside of the cell and on ribosomes