Kaplan Biochem Flashcards by Gail I

in alpha amino acids, both the … and … groups are bound to the alpha carbon

amino; carboxyl

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not all amino acids have to have the amino and carboxyl groups .. –> GABA has the amino group on the gamma C

on the same C

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… amino acids: the 20 alpha amino acids encoded by DNA

proteinogenic

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only nonchiral/non-optically active amino acid: …

glycine

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all chiral amino acids used in eukaryotes are … amino acids
all except cysteine have … configuration
cysteine is ..

L
S
R

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nonpolar, nonaromatic aas: 
... 
... 
... 
... 
... 
... 
... --> cyclic, conformationally strained

glycine
alanine
valine
leucine
isoleucine
methionine
proline

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aromatic aas:
…
…
… —> polar

phenylalanine
tryptophan
tyrosine

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polar aas: 
... 
... 
... 
... 
... - has thiol that can participate in ... bonds

serine
glutamine
asparagine
threonine
cysteine; disulfide

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in cysteine, sulfur is larger and less electronegative than O –> leaves Cys susceptible to …

oxidation

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amide groups for Gln and Asn do not … – amides are relatively …

become charged; neutral

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acidic aas:
…
…
the negative charges on the anion forms of these aas form at … (…) –> these are the only 2 amino acids that have … on the side chains at physiological pH

aspartic acid
glutamic acid
physiological pH; 7.4; negative charges

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basic aas:
…
…
…

lysine
histidine
arginine

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pKa of histidine imidazole group is close to ….; at physiological pH, one N from the imidazole is … and the other is not

physiological pH; protonated

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all aas with … are hydrophilic –> more likely to be found on protein surface
… and … are also hydrophilic

charged side chains (acidic and basic aas)

asparagine; glutamine

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all nonpolar aas are … the rest have both … and …

hydrophobic; hydrophobic and hydrophilic character

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(three and one letter abbreviations)

alanine

ala, A

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(three and one letter abbreviations) arginine

Arg, R

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(three and one letter abbreviations) asparagine

Asn, N

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(three and one letter abbreviations) aspartic acid

Asp, D

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(three and one letter abbreviations) Cysteine

Cys, C

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(three and one letter abbreviations) glutamic acid

Glu, E

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(three and one letter abbreviations) glutamine

Gln, Q

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(three and one letter abbreviations) glycine

Gly, G

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(three and one letter abbreviations) Histidine

His, H

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(three and one letter abbreviations) Isoleucine

Ile, I

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(three and one letter abbreviations) leucine

Leu, L

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(three and one letter abbreviations) Lysine

Lys, K

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(three and one letter abbreviations) Methionine

Met, M

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(three and one letter abbreviations) Phenylalanine

Phe, F

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(three and one letter abbreviations) Proline

Pro, P

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(three and one letter abbreviations) Serine

Ser, S

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(three and one letter abbreviations) Threonine

Thr, T

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(three and one letter abbreviations) Tryptophan

Trp, W

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(three and one letter abbreviations) Tryosine

Tyr, Y

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(three and one letter abbreviations) Valine

Val, V

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amino acids are …: they have both basic (amino) and acidic (carboxylic) groups that makes them able to either accept/donate a proton

amphoteric

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in general: at low pH, ionizable groups tend to be …

at high pH, ionizable groups tend to be …

protonated; deprotonated

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pKa is the point at which the concentration of the protonated and deprotonated species are … –> …

equal; [HA] = [A-]

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pH most groups will be …

pH > pKa –> most groups will be …

protonated

deprotonated

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all aas have at least … pKas bc they have 2 groups that can be protonated/deprotonated (amino and carboxyl)
pKa for carboxyl group is around …
pKa for amino group is around …

2
2
9-10

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at physiological pH, the carboxyl group will be … and the amino group will be …

deprotonated; protonated

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…: has both positive and negative charge but is electrically neutral as a whole –> … ions
exist in water as …

zwitterion; dipolar; internal salts

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…: pH at which the molecule is electrically neutral
average of the … values
aas with acidic side chains have relatively … isoelectric points and those with basic side chains have relatively … isoelectric points

isoelectric point
two nearest pKa values
low; high

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…: small peptides, up to 20 residues

oligopeptides

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peptide bond formation occurs as a …/… reaction
has partial … character due to … which restricts its ability to rotate
by convention, peptides are drawn with … to the left and … to the right and are read from left to right

condensation; dehydration; double bond; resonance; N-terminus; C-terminus

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hydrolysis of peptide bonds in living organisms is …

e.g. trypsin and chymotrypsin –> cleave at specific peptides

enzymatically catalyzed

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the secondary, tertiary, and quarternary structures a protein adopts is that which is most … in a given environment

energetically favorable

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primary sequence of a protein can be determined by … – most easily done by … from which the protein derives

sequencing; sequencing the DNA

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…: peptide chain coils clockwise around central axis –> …

alpha-helix; right-handed

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alpha helix
stabilized by … between carbonyl oxygen and amide H … residues away
side chains point … helix core
significant secondary structure of …

intramolecular H bonds
n+4
away from
keratin

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…: either antiparallel or parallel

beta pleated sheets

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beta sheets stabilized by both … and … H-bonds

intramolecular; intermolecular

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due to its cyclic nature, proline would introduce a … in the peptide chains when in the middle of alpha helices or beta sheets
only in alpha helices for something that will ..
Tends to be found at the … in a beta pleated sheet and at the start of an alpha helix

kink; cross cell membrane; turns

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… proteins: have structures that resemble sheets or long strands
e.g. …
tend to serve … purposes

fibrous;
collagen
structural

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… proteins: tend to be spherical (like a globe)
e.g. …
can be hormones, enzymes, etc. –> have more … than the other category of proteins

globular
myoglobin
diverse roles (other category is fibrous)

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…: intermediate states of protein folding

molten globules

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when a solute dissolves in a solvent, nearby solvent molecules form a

solvation layer

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when hydrophobic substances dissolve in water, water cannot … effectively and so water molecules must arrange themselves into a more … structure to maximize H bonding –> results in an …
this is the basis for the … that largely influence protein folding

hydrogen bond; ordered; unfavorable decrease in entropy; hydrophobic effect

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when hydrophilic substances dissolve in water, …

entropy is increased

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quarternary structure roles:
can be more stable, by … of the protein complex
can reduce amount of … needed to … protein complex
can bring … close together
can induce … (as in hemoglobin) or … effects

reducing the surface area; DNA; encode; catalytic sites; cooperativity; allosteric

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… proteins: derive part of their function from prosthetic groups

conjugated

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… are permanently attached cofactors that can be organic molecules (e.g. vitamins) or metal ions – necessary for enzyme function

prosthetic groups

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…: proteins with lipid prosthetic groups
…: proteins with carb prosthetic groups
…: proteins with nucleic acid prosthetic groups

lipoproteins
glycoproteins
nucleoproteins

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denaturation of proteins is often irreversible

can be caused by …, …, …

heat; solutes; pH

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… is the individual amino acid Cys. … is when two of them form a disulfide bond

cysteine; cystine

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peptide bond is thermodynamically …., but hydrolysis doesn’t occur spontaneously in the cell because the … is too high, such that hydrolysis is …

unstable; activation energy; kinetically unfavorable

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… are needed to catalyze peptide bond hydrolysis

enzymes

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N amino acids –> … peptide bonds

n - 1

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… angle: angle of rotation of single bond between N and alpha C
… angle: angle of ration of single bond between carboxyl C and alpha C

phi

psi

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Gabriel synthesis of amino acids:

… is alkylated using base, then …, and then …. to yield amino acid

N-phthalimidomalonic ester;
hydrolyzed
decarboxylated

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strecker synthesis of amino acids:
starting materials: …, …, …/…
aldehyde reacts with … to yield an … … is added to the imine to yield … which is hydrolyzed to form the alpha amino acid

ammonia; KCN; aldehyde; ketone

ammonia; imine; KCN; alpha-amino nitrile

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…: catalyze redox rxns –> transfer of electrons between molecules
…: electron donor
..: electron acceptor
… or … tend to be of this class
enzymes that have oxidase in their names use … as the final electron acceptor

oxidoreductases 
reductant 
oxidant 
dehydrogenases; reductases
oxygen

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dehydrogenases remove a … –> removing …

hydride; electrons

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…: catalyze movement of functional groups between two molecules
…: catalyze transfer of a phosphate group

transferases;

kinases

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…: catalyze breaking of a compound into two molecules by addition of water
tend to be named only for their …
…: cleaves a phosphate group from another molecule

hydrolases; substrate

phosphatase

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…: catalyze cleavage of a single molecule into two products; don’t require water
synthesis of two molecules into a single molecule can also be catalyzed by a lyase –> …

lyases; synthases

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…: catalyze rearrangement of bonds within a molecule

isomerases

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…: catalyze addition/synthesis rxns, often require ATP

ligases

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enzymes don’t alter the … for a reaction and do not change the … of a rxn. they only affect …

free energy change; equilibrium; rxn rates

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… theory suggests that enzyme’s active site is already in the appropriate conformation for the substrate to bind –> no … necessary to form enzyme substrate complex

lock and key; conformational change

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… model: conformational change of the enzyme is necessary for substrate binding to occur

induced fit

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…/…: nonprotein molecules that bind to the active site of an enzyme and participate in catalysis

cofactors; coenzymes

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…: enzymes without their cofactors

…: enzymes containing their cofactors

apoenzymes

holoenzymes

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…: generally inorganic molecules/metal ions –> …

directly participate in enzymatic rxn

cofactors; minerals

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…: small organic groups –> … and derivatives of these

coenzymes; vitamins

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water-soluble vitamins: … and …

fat-soluble vitamins: …, …., …, …

B; C

A; D; E; K

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fat-soluble vitamins regulated by … – quantify ability of a molecule to dissolve in a polar/nonpolar environment

partition coefficients

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coenzymes act as a … molecule

carrier

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cofactors and coenzymes tend to be … and usually carry a charge by …, …, or …
usually in …, … concs in the cells

small; ionization; protonation; deprotonation

low; tightly regulated

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…: all enzymes bound to substrate

saturation

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reaction rate can no longer increase once … is achieved –> enzyme working at …

saturation; maximum velocity

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can only increase vmax by increasing

enzyme concentratio

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… describes relationship between rate of reaction, enzyme, substrate, and product concs
equation: … or …

michaelis-menten

v= (v_max[S])/(K_m+[S]) or v= (k_cat[E]*[S])/(K_m+[S])

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Km is the substrate concentration at which …. (velocity is …)

half of the enzyme’s active sites are full; half-maximal

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Km is … –> lower Km = … affinity of enzyme for its substrate –> … conc of substrate required for 50% enzyme saturation
Km cannot be altered by changing …/… …

Michaelis constant; higher; lower; enzyme/substrate concentration

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when [S] < Km –> rxn rate … when substrate is added

increases a lot

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when [S] > Km and approaches Vmax –> rxn rate … and is … by addition of substrate

slows; not really affected so much

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Vmax = …

[E]*kcat

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kcat is … –> measures number of substate molecules converted to product, per enzyme molecule per second
… –> catalytic efficiency of an enzyme

turnover number

Kcat/Km

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... = double reciprocal of michaelis-menten; allows for easier graphical analysis of enzyme kinetics 
X-int = ... 
Y-int = ...

lineweaver-burk
-1/Km
1/Vmax

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…. michaelis-menten plot indicates cooperativity among substrate binding sites (like Hgb)

sigmoidal

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enzymes have … state and … state
in …, binding of substrate to one subunit promotes … transition of the other subunits, thus increasing their … for the substrate

low-affinity tense; high-affinity relaxed

cooperativity; T–> R; affinity

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enzymes showing cooperative kinetics tend to be … enzymes in pathways
cooperative enzymes subject to … and …, competitively and allosterically

regulatory; activation; inhibition

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…: indicates degree of cooperativity

Hill’s coefficient

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Hill’s coefficient
> 1 –> … –> affinity … in other subunits when substrate binds to one subunit
< 1 –> … –> affinity … in other subunits when substrate binds to one subunit
= 1 —> …

positively cooperative; affinity
negatively cooperative; decreases
no cooperativity

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enzyme activity = enzyme … = enzyme …

velocity; rate

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enzyme catalyzed rxns occur at an …
rates tend to double for every … increase until optimal is reached
optimal for human body is …

optimal temp
10 degree C
37 degrees C

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optimal pH for enzymes that circulate and function in human blood is … –> …

physiological pH; 7.4

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pH < 7.35 –> …

acidemia

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in vitro, altering … can disrupt hydrogen and ionic bonds, changing the … of the enzyme, or … it

salinity; conformation; denaturing

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…: enzyme regulation facilitated by products further down a pathway
…: more rare scenario in which intermediates that precede the enzyme regulate it
…/… –> once there is enough of a given product, we turn off the pathway that creates the product

feedback regulation
feed-forward regulation
feedback inhibition/negative feedback

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…: competitive, noncompetitive, mixed, uncompetitive

reversible inhibition

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… inhibition: occupancy of the active site by a competitor of the substrate
overcome by …
… is not altered, bc if enough substrate is added, it will outcompete the inhibitor and be able to run at the same one
… –> substrate conc has to be higher to reach half max velocity

competitive; adding more substrate
Vmax
increases apparent Km

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…: inhibitor binds to allosteric site, inducing change in enzyme conformation
cannot be overcome by adding more substrate
bind equally well to … and …
… decreases bc there is less enzyme available to react
… stays the same bc active forms of enzyme retain same affinity for the substrate

noncompetitive inhibition
enzyme; enzyme-substrate complex
Vmax
Km

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… inhibition: can bind to either enzyme/enzyme-substrate complex –> has a different affinity for each
if it were to have the same affinity, it would be a … inhibitor
bind at an …

mixed;
noncompetitive
allosteric site

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mixed inhibition:
alter value of Km
if preferentially binds to enzyme-substrate complex, Km would … bc it would cause the enzyme to bind more … to the substrate
if preferentially binds the enzyme without the substrate, Km would …

decrease; tightly

increase

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mixed inhibition:
Vmax is …, again bc there is less enzyme available to react
on lineweaver-burk, intersection occurs at …

decreased; point that is not on either axis

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... inhibition: bind only to enzyme-substrate complex 
Km ... 
bind to ... site 
... Vmax 
shows as ... on lineweaver-burk

uncompetitive 
decreased
allosteric 
decreases 
parallel lines

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…: active site made unavailable for prolonged period of time/ enzyme is permanently altered

irreversible inhibition

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regulated enzymes
…: allosteric inhibitors/allosteric activators can bind to enzyme
…: can be activated/deactivated by …/…
…: covalent attachment of sugar molecules

allosteric enzymes
covalently modified enzymes; phosphorylation; dephosphorylation
glycosylation

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regulated enzymes:
…: enzymes that are secreted in an inactive form; these must be activated
have .. domain and … domain
… domain must be removed/altered to expose the active site

zymogens; catalytic; regulatory

regulatory

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active sites create … for the rxns that the enzyme catalyzes in that it essentially closes around the substrates, preventing interference from compounds outside of the enzyme

microenvironments

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regulation of enzymes by phosphorylation is favorable for the following reasons:
creates … that can disrupt old interactions and form new ones. can modify active site to allow for better interactions with substrate

negative oxygen grants active site … properties that allows enzyme to interact with substrate in a more stabilizing way

net negative charge

hydrogen bonding

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regulation of enzymes by phosphorylation is favorable for the following reasons:
the speed at which phosphorylation occurs is adjustable by the cell –> … is adjustable

… is abundant in the cell – regulation by phosphorylation occurs …, not really .. since there isn’t much ATP there

kinetics

ATP; intracellularly; extracellularly

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regulation of enzymes by phosphorylation is favorable for the following reasons:
…: activated kinases can be used to regulate many rxn pathways, which can allow for amplification

amplification effects

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regulation of enzymes by phosphorylation is favorable for the following reasons:
releases large amount of …
phosphorylation is reversible using …

free energy

phosphatases

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catalytic efficiency is limited by the rate at which the enzyme and substrate actually … to form the …

come together; enzyme-substrate complex

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non competitive inhibition … the turnover number of the enzyme

reduces

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structural proteins generally have … secondary structure and a … – a repetitive organization of secondary structural elements together sometimes referred to as a motif

highly repetitive; supersecondary structure

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structural proteins:
… gives it a fibrous nature
…: trihelical fiber (three left-handed helices that form an overall right-handed helix) –> makes up most of the … of connective tissue and provides … and ..

regularity

collagen; extracellular matrix; strength; flexibility

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structural proteins:
…: part of extracellular matrix of connective tissue; provides stretch and recoil
…: intermediate filament in epithelial cells; contribute to mechanical integrity and function as regulatory proteins

elastin

keratin

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structural proteins:
…: makes up microfilaments and thin filaments in myofibrils –> most abundant protein in eukaryotic cells
… and … side allows motor proteins to travel … along actin filament

actin
positive; negative
unidirectionally

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structural proteins:
…: makes up microtubules which provide structure, chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein
has …: negative end of a microtubule is located adjacent to the …, positive end in … of a cell

tubulin

polarity; nucleus; periphery

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… proteins: display enzymatic activity, acting as ATPases to power … change necessary for motility
interact with …/…

motor; conformational

actin; microtubules

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(motor proteins) …: motor protein that interacts with actin; thick filament in myofibril; involved in cellular transport
has head and neck; neck movement contributes to …

myosin; sarcomere contraction

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(motor proteins) .. and …: motor proteins associated with microtubules; have 2 heads, one of which is always attached to tubulin

kinesins; dyneins

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(motor proteins) …: align chromosomes during metaphase and depolymerize microtubules during anaphase
bring vesicles toward … end of microtubule
in neurons, kinesins bring neurotransmitters toward … end –> towards …

kinesins
positive
positive
synaptic terminal

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(motor proteins) …: involved in sliding movement of cilia and flagella
bring vesicles toward … end of microtubules
in neurons, bring neurotransmitters towards … end –> back toward …

dyneins
negative
negative
soma

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…: transport or sequester molecules by binding to them

Hgb, calcium-binding proteins, DNA-binding proteins (transcription factors), etc

binding proteins

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binding proteins contd

when sequestration of a molecule is goal, binding protein has … across a …

high affinity; variety of concentrations

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binding proteins contd:
transport proteins tend to have varying affinity depending on … –> whether it needs to ../… its target to maintain a steady-state

environment

bind; unbind

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…: proteins on most cell surfaces that assist in binding the cell to the extracellular matrix/other cells

cell adhesion molecules

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cell adhesion molecules contd:
all … proteins
…: glycoproteins that mediate calcium-dependent cell adhesion –> different cells have …

integral membrane proteins
cadherins
type-specific cadherins

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cell adhesion molecules contd:
…: group of proteins that all have two membrane-spanning chains, alpha and beta, involved in binding to and communicating with the extracellular matrix
important for …
can promote .., …, etc

integrins
cellular signaling
cell division; apoptosis

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cell adhesion molecules contd:
…: bind to carbs that project from other cell surfaces –> form the weakest bonds of the cell adhesion molecules (that is, this one compared to cadherins and integrins)
important in ….

selectins; host defense

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immunoglobulins:

… and … interactions hold heavy and light chains together

disulfide linkages; noncovalent interactions

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…: cells receive and act on signals; take advantage of either existing gradients or second messenger cascades
proteins participate by acting as .., … for facilitated diffusion, …, and …

biosignaling 
extracellular ligands
transporters 
receptors 
second messengers

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….: proteins that create specific pathways for charged molecules
allow for …

ion channels

facilitated diffusion

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ion channels:
…: unregulated –> based solely on conc gradient
…: gate is regulated by the membrane potential change near the channel (e.g. nonspecific sodium-potassium channels work in sinoatrial node of heart to bring cell back to threshold when voltage drops)
..: requires the binding of a ligand to open/close the channel

ungated channels
voltage-gated channels
ligand-gated channels

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ion channels contd:
kinetics of transport can be derived from …–> Km here would refer to … at which transporter is functioning at half of its maximum velocity

michaelis-menten

solute conc

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…: membrane receptors that have catalytic activity when ligands bind

enzyme-linked receptors

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enzyme-linked receptors:
…: anchors receptor to cell membrane
…: stimulated by ligand to induce a conformational change that activates catalytic domain

membrane-spanning domain

ligand-binding domain

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enzyme-linked receptors:
binding of ligand initiates a …
…: contains monomer and when ligand binds, they dimerize and this dimer can phosphorylate other enzymes

second messenger cascade

receptor tyrosine kinases

…: integral membrane proteins involved in signal transduction

G-protein coupled receptors

G-protein coupled receptors:
have … membrane spanning alpha helices
use a … protein – intracellularly linked to guanine nucleotides
ligand binding … of receptor for G protein, activating the protein

Yeah 7
heterotrimeric G protein
increases affinity

G-protein coupled receptors:
Gs –> stimulates …, … [cAMP]
Gi –> inhibits …., … [cAMP]

adenylate cyclase; increasing

adenylate cyclase; decreasing

G-protein coupled receptors:

Gq –> activates …, which cleaves … from the membrane to form PIP2 which is cleaved into … and …

phospholipase C; phospholipid; DAG; IP3

G-protein coupled receptors:

IP3 can open .. –> increases … in the cell

calcium channels

[Ca2+]

G-protein coupled receptors:
G proteins have …, …, and … subunits
… subunit binds GDP in its inactive form and is complexed with the other two subunits
when a ligand binds, GDP is replaced with … and the … subunit dissociates –> this subunit …/… …

alpha; beta; gamma
alpha
GTP; alpha
activates/inhibits adenylate cyclase

…: crushing, grinding, or blending tissue of interest into an evenly mixed solution

homogenization

… can isolate proteins from smaller molecules before other isolation techniques are used

centrifugation

both …. and … can be used for native/denatured proteins

electrophoresis; chromatography

electrophoresis subjects compounds to an electric field to move them according to … and …

net charge; size

…: directly proportional to electric field strength (E) and net charge on the molecule (z) and is inversely proportional to a frictional coefficient (f), that depends on mass and shape of migrating molecules

migration velocity

migration velocity: v =

Ez/f

…: porous gel that allows for separation based on size and charge
molecules will move fastest if they are …, … charged, or placed in a …
molecules will move slower/not at all if they are … and .., electrically …, or in a …

polyacrylamide gel;
small; highly; large electric field
bigger; convoluted; neutral; small electric field

…: used for analyzing proteins in native states
limited by the fact that there are varying … and … ratios of proteins that may cause multiple proteins to experience same level of migration

polyacrylamide gel electrophoresis

mass-to-charge; mass-to-size

polyacrylamide gel electrophoresis

most useful in comparing size/charge of proteins known to be …

similar in size

polyacrylamide gel electrophoresis
SDS-PAGE:
sodium dodecyl sulfate is used to make charge for all proteins …, such that … is the differentiating factor
it disrupts … interactions

uniform; molecular mass

noncovalent interactions

polyacrylamide gel electrophoresis
…: separation of proteins based on isoelectric point
mix of proteins is placed in a gel with a … (acidic at …, and basic at …, … in the middle)
when proteins reach part of gel, where the pH = pI, the protein becomes …, and thus stops moving

isoelectric focusing
pH gradient; anode; cathode; neutral
electrostatically neutral

… allows for isolated proteins to be immediately available for identification and quantification

chromatography

chromatography:
the more similar the compound is to its surroundings, the more it will … and move … through its surroundings
preferred over electrophoresis when … are beings separated

stick to; slowly; large amounts of protein

chromatography:
sample is placed on … (aka …). a … phase is run through, allowing the sample to run through (…) the stationary phase

solid stationary phase; adsorbent; elute

chromatography:
if sample has high affinity for stationary phase, it …
if it has high affinity for mobile phase, it …

won’t move much

will move quickly

chromatography:
… amount of time a compound spends in the stationary phase
…: separation of compounds within the stationary phase that results from varying retention times

retention time

partitioning

chromatography:

common properties used for separation: …, …, …

charge
pore size
specific affinities

(column chromatography) column filled with … as adsorbent

… and … determine migration velocity

silica/alumina beads

size; polarity

(column chromatography) less polar the compound the … it elutes through the column
solvent drips out at the end of the column and different fractions that leave the column can be collected. these fractions contain … that differentiate them

faster

bands

(column chromatography) … + … is kept and the solvent is …
can be used to separate and collect … besides proteins (e.g. nucleic acids)

solvent; compound of interest

macromolecules

(ion-exchange chromatography) beads in column coated with …
after all other compounds have moved through the column, a … is used to elute the charged molecules that have stuck to the column

charged substance;

salt gradient

(size-exclusion chromatography) … of various sizes are used
… get stuck in these and thus move more slowly
size of pores can be varied so that molecules of … can be fractionated
common approach in protein purification is to use an … followed by a …

porous beads
small compounds
different molecular weights
ion-exchange column; size-exclusion column

(affinity chromatography)
coating beads with … that binds protein/specific antibody to the protein, such that protein is … in column
common stationary phase molecules include … (used in separation of genetically engineered proteins with histidine tags), …, …, …

receptor 
retained 
nickel 
antibodies
antigens 
enzyme substrate analogs

(affinity chromatography) once protein is retained, it can be eluted by washing column with …
eluents can also have specific … or … that disrupts bonds between ligand and protein of interest
drawback: recovered substance can be …

free receptor
pH; salinity level
bound to the eluent

protein structure can be determined through … and …
… more common and reliable –> measures e- density on a high resolution scale; can also be used for nucleic acid – generates … that can be used to determine structure

X-ray crystallography; nuclear magnetic resonance spectroscopy
diffraction pattern

… can be used to determine the primary sequence of small proteins:
for sequences of up to …-… aas
selectively and sequentially removes … of the protein, which is subsequently analyzed using …

Edman degradation
50-70
N-terminal aa
mass spec

… (…, …, …) can also selectively cleave proteins, creating smaller fragments that can be analyzed via Edman or electrophoresis
positions of … and .. cannot be determined by these methods since they reduce protein to primary structure

proteases; chymotrypsin; trypsin; cyanogen bromide

disulfide links; salt bridges

…are determined by following the process of a known rxn, often accompanied by a …

activity levels for enzymatic samples; color change

… can be used for proteins, since they have aromatic side chains
drawback: sensitive to contaminants

UV spec

proteins cause … changes with certain rxns
… (BVA) assay
… reagent assay
… protein assay –> more reliable and simpler

colorimetric;
bicinchoninic acid
Lowry reagent
Bradford

bradford protein assay:
mixes protein with … dye, which turns blue in presence of protein
higher protein conc = larger conc of …
samples of known protein concs are reacted with the bradford reagent to create a … that is then used to determine unknown protein concs
not very accurate when more than one proteins present

coomassie brilliant blue
blue dye
standard absorbance curve

…: basic structural units of carbs

simplest monosaccharides are trioses - 3-C sugars

monosaccharides

…: carbs with an aldehyde as their most oxidized functional group
…: carbs that have ketones as their most oxidized functional group

aldoses

ketoses

carbonyl C in carbs is always … ( if aldehyde) or … (if ketone), because it is the most oxidized

C-1; C-2

aldehyde C/ketone C can participate in … –> sugars in these linkages are …

glycosidic linkages; glycosyl residues

simplest ketose: …

dihydroxyacetone

…: determined by the three dimensional arrangement of the groups attached to the chiral C
enantiomers have … absolute configs

absolute configuration

opposite

number of stereoisomers = …, where n is the number of chiral Cs

2^n

not all carbs labeled as D have … optical rotation and not all that have L are … this is just for …
optical activity is determined …

+; -
glyceraldehyde
optical activity

Fischer projections:
horizontal lines are …, vertical lines are …
in this projection, D-C have their highest numbered OH group on the … and L-carbs have their highest numbered OH group on the …

wedges; dashes

right; left

…: same sugars, in different optical families –> configuration at every chiral center is switched

enantiomers

…: two sugars that are in the same family, but are not identical and are not mirror images of each other –> only configurations at some chiral Cs are switched

diastereomers

…: diastereomers that differ only in the configuration of one chiral C

epimers

a compound can have only one …, but can have multiple ..

enantiomer; diastereomers

carbs can undergo intramolecular rxns to form cyclic … and …
carbonyl C becomes chiral –> … C
…: OH on C1 is trans relative to CH2OH group
…: OH on C1 is cis relative to CH2OH group

hemiacetals; hemiketals
anomeric
alpha-anomer
beta-anomer

… rings: six-membered rings

… rings: five-membered rings

pyranose

furanose

…: useful for describing 3D conformation of cyclic structures
groups on the right in a Fischer projection will point … on a Haworth projection

Haworth projection

down

in water, hemiacetals will cycle between the … and … forms (bc of hydrolysis of the hemiacetal and then reformation of the ring) –> this allows it to spontaneously change its conformation as … or … –> …

open; closed
alpha; beta;
mutarotaiton

mutarotation can be catalyzed by …/… and leads to mixture of alpha and beta anomers at …
… anomer of glucose is more stable, so equilibrium is …% alpha and …% beta –> hydroxyl is … in eta

acid; base 
equilibrium concs
beta 
36; 64
equatorial

in the open-chain forms, carbs can be …
aldehyde oxidation yields …
aldehydes are considered … bc they can be oxidized

oxidized
aldonic acids
reducing agents

any monosaccharide with a hemiacetal ring is a … sugar

oxidation of aldose in ring form yields … –> cyclic ester with carbonyl group on the anomeric C – … is a lactone

reducing
lactone
vitamin C

reagents that detect presence of reducing sugar –> … and …
…: silver nitrate is mixed with NaOH to produce …, which is dissolved in ammonia to produce [Ag(NH3)2]+ –> produces .. when aldehydes are present, indicating that sugar is reducing sugar
…: aldehyde group is oxidized, yielding a red precipitate of …

Tollen's; Benedict's 
Tollen's 
silver oxide 
silvery mirror
Benedict's
Cu2O

… can be used to test for glucose, because it doesn’t react with other reducing sugars

glucose oxidase

more reactive oxidizing agents (e.g. dilute nitric acid) will oxidize the aldehyde and the primary alcohol to ..

carboxylic acids

… are also reducing agents –> can be … to form … and subsequently oxidized

ketose sugars; tautomerized; aldoses

…: rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond
…: compound with a double bond and an alcohol group

tautomerization

enol

…: when aldehyde group is reduced to an alcohol

alditol

…: contains a hydrogen that replaces a hydroxyl group on that sugar (e.g. deoxyribose)

deoxy sugar

carbs can react with carboxylic acids and their derivates to form …

estes

esterification is similar to … of carbs, wherein a phosphate ester is formed

phosphorylation

hemiacetals react with alcohols to form …
the subsequent C-O bonds are … bonds and the acetals are …
This rxn is essentially how we make larger saccharides
same happens with hemiketals to form …

acetals
glycosidic bonds
glycosides
ketals

glycoside formation is a … rxn, and breaking a glycosidic bond therefore requires …

dehydration rxn

hydrolysis

glycosides derived from furanose rings = …

glycosides derived from pyranose rings= …

furanoses

pyranosides

formation of an alpha or beta glycosidic linkage is nonspecific in that the anomeric C on one monosaccharide can react with … –> glycosidic linkages are thus described by the … of the Cs between which the bond is formed along with the … of the anomeric C

if a glycosidic bond is formed between two anomeric Cs, the … of both anomeric Cs must be in the name (e.g. alpha, alpha-1,1 linkage)

any of the alcohols on another monosaccharide
numbers
configuration

configuration

important disaccharides: …, …, …

sucrose; lactose; maltose

sucrose: ….
lactose: …
maltose: …

glucose-alpha-1,2-fructose
galactose-beta-1,4-glucose
maltose: glucose-alpha-1,4-glucose

…: long chains of monosaccharides linked by glycosidic bonds
…: polymer of just one type of monosaccharide
…: made up of more than one type of monosaccharide

polysaccharides
homopolysaccharide
heteropolysaccharide

polysaccharides:
polymer formation can be …/… since glycosidic bonding can occur at multiple OH groups
…: when an internal monosaccharide in a polymer forms at least 2 glycosidic bonds

linear; branched

branching

important polysaccharides:

…: main structural component of plants, present in their cell walls

cellulose

cellulose:
… –> beta-1,4 polymer of D-glucose
humans can’t digest it because we don’t have …
acts as a source of … for humans –> draws water into gut

homopolysaccharide
cellulase
fiber

…: linked alpha-D-glucose monomers

starches

plants store starch mostly as .. –> … linkages

amylose; alpha-1,4

…: type of starch that is branched via alpha-1,6 linkages (Still has alpha-1,4 on the “main’ chain)

amylopectin

starches:
… is used to test for presence of starch
enzymatically broken down to be used as ..
… cleaves amylose at nonreducing end to produce maltose
… cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, glucose
… help degrade amylopectin

iodine 
energy source
beta-amylase
alpha-amylase 
debranching enzymes

…: carb storage unit in animals; highly branched

glycogen

glycogen:
like starch, but has more …
branching optimizes …, makes it more … as well and allows more …

alpha-1,6 glycosidic bonds
energy efficiency; soluble
glucose storage

glycogen:
enzymes can work on many sites within the molecule at the same time since it’s so …
…: cleaves glucose from nonreducing end and phosphorylates it to form glucose-1-phosphate

highly branched

glycogen phosphorylase

highly branched structure of amylopectin (same for glycogen) decreases … between polysaccharide polymers and increases interaction with the …, which makes it more soluble

intermolecular bonding; surrounding solution

membrane lipids are … –> both hydrophobic and hydrophilic

amphipathic

…: have phosphate and alcohol that comprise polar head group, joined to hydrophobic fatty acid tail by phosphodiester linkages

phospholipids

phospholipids:
fatty acids are attached to a backbone to form … region
classified according to the ….
glycerol forms …/…
sphingolipids have a … backbone (not all sphingolipids are phospholipids)

hydrophobic tail
backbone
phosphoglycerides; glycerophospholipids
sphingosine

fatty acid tails of phospholipids vary in degree of … and … –> these behaviors determine behavior

saturation; length

…: no pi bonds, greater van der Waals forces, more stable structure –> solids
…: contains double bonds, which kink the fatty acid chain –> . liquids
… make up more fluid portions of the phospholipid bilayer

saturated fatty acids
unsaturated fatty acids
unsaturated phospholipids

glycerophospholipids contain …. backbone and are bonded to a polar head group and to two fatty acid tails
named according to their … (e.g. phosphatidylcholine has a choline head group)
important to …, …, and …

glycerol
head group
cell recognition; signaling; binding

the cell surface antigens on RBCs that dictate blood type are …

sphingolipids

sphingolipids are involved in biological recognition at the

cell surface

sphingolipids have …/… backbone

many sphingolipids are phospholipids bc they contain a … linkage, but some contain … linkages to …

sphingosine/sphingoid
phosphodiester
glycosidic
sugars

…: any lipid linked to a sugar

glycolipid

…: simplest sphingolipid, has single H as head group

ceramide

..: major class of sphingolipids that are also phospholipids
have either phosphatidylcholine or phosphatidylethanolamine head group
head groups have … net charge
major components in plasma membranes of cells producing … –> … and … cells

sphingomyelins
no
myelin; oligodendrocytes; Schwann

…: sphingolipids with glycosidic linkages to sugars
NOT phospholipids
found on the outer surface of …

glycosphingolipids

plasma membrane

glycosphingolipids:
…: glycosphingolipids with a single sugar
…: glycosphingolipids with two or more sugars
…: no net charge at physiological pH

cerebrosides
globosides
neutral glycolipids

…: most complex sphingolipids
have polar head groups composed of oligosaccharides with one or more … (… acid)
have a … charge

gangliosides
N-acetylneuraminic acid; sialic
negative

gangliosides are … as well

important for …, …, and …

glycolipids

cell interaction, recognition, and signal transduction

…: esters of long-chain fatty acids with long-chain alcohols
function as protection:
for plants, prevent excessive … and protect against …
for animals, prevent … and act as a …

waxes
evaporation; parasites
dehydration; lubricant

lipids serve as coenzymes in the … and in … rxns

electron transport chain; glycosylation

lipids function as …. and …

hormones; intracellular messengers

…: lipids built from isoprene moieties (C5H8), and have carbons grouped in multiples of …
strongly scented
one terpene unit contains …

terpenes
five
2 isoprenes

… = two isoprene units (1 terpene unit)
… = 3 isoprene units (1.5 terpene units)
… = 4 isoprene units (2 terpene units)
… = 6 isoprene units (3 terpene units)
carotenoids are … (have 8 isoprenes, 4 terpenes)

monoterpenes 
sesquiterpenes
diterpenes
triterpenes
tetraterpenes

triterpenes – can be converted to … and other …

cholesterol; steroids

…: derivatives of terpenes that have been oxidized/rearranged
also strongly ..
named in the same way as terpenes, according to number of isoprene units

terpenoids

scented

… and … are precursors that feed into various biosynthetic pathways that produce important products

terpenes; terpenoids

…: metabolic derivatives of terpenes, have 4 cycloalkane rings fused together

steroids

steroids have … and …

functionality is determined by … status and … present

3 cyclohexane; 1 cyclopentane

oxidation; functional groups

…: steroids that act as hormones (e.g. testosterone)

steroid hormones

…: steroid that mediates membrane fluidity
…
at low temps, … membrane fluidity
at high temps, … membrane fluidity, preventing it from becoming too permeable

cholesterol
amphipathic
increases
decreases

cholesterol is precursor to some …, …, and …

steroid hormones; bile acids; vitaminD

…: 20-C molecules that are unsaturated carboxylic acids derived from arachidonic acid
contain one … C ring

prostaglandins

prostaglandins:
…/… molecules
regulate the synthesis of …
can have effects on … function, … cycle, and … associated with fever and pain

paracrine/autocrine signaling
cAMP
smooth muscle; sleep-wake; elevation of body temps

…: essential nutrient that is not adequately synthesized by the body and thus, must be obtained in a dietary manner

vitamin

lipid-soluble vitamins are stored in …
excess water-soluble vitamins are …
fat soluble vitamins are: …, …, …, and …

fat
excreted
A; D; E; K

vitamin A (carotene): unsaturated hydrocarbon plays a role in .., … and …, and … function

vision; growth; development; immune

vitamin A:
aldehyde form is … – component of light-sensing molecular system in the human eye
…: storage form of vitamin A, oxidized to retinoic acid – hormone that regulates gene expression during epithelial development

retinal

retinol

vitamin D (…): consumed/formed in … driven rxn

cholecalciferol; UV

vitamin D:
converted to … in liver and kidneys –> increases … and … uptake in intestines and thus promotes … production
lack of vitamin D is cause of is cause of … – impeded growth, underdeveloped bones in children

calcitrol; Ca2+; phosphate
bone
rickets

vitamin E: characterizes group of closely related lipids called … and … –> have a substituted aromatic ring with long isoprenoid side chain and are hydrophobic

tocopherols; tocotrienols

vitamin E:

…: biological antioxidants –> destroy free radicals to prevent oxidative damage

tocopherols

…: a group of compounds including phylloquinone and menaquinone
vital to posttranslational modifications required to form … - clotting factor in the blood

vitamin K

prothrombin

aromatic ring of vitamin K undergoes cycle of … and … during the formation of prothrombin
vit K is required to introduce … on some calcium dependent proteins

oxidation; reduction

calcium binding sites

…: lipids specifically used for energy storage

triacylglycerols

lipids are better than carbs for energy storage:
fatty acids are more … than sugars –> C in fatty acids have more …, and oxidation allows electrons to move from … to more … atom, which is stabilizing and releases energy

reduced
electron density
less electronegative
electronegative

oxidation of triacylglycerols yields … the energy per gram as carbs

twice

lipids:
triacylglycerols are … –> don’t require water for stability, which decreases their weight
dual benefit as … and …

hydrophobic

energy storage; insulation

… (…): three fatty acids bonded by ester linkages to glycerol
rare for all three fatty acids to …
… and … –> polar hydroxyl groups of the glycerol component and polar carboxylates of fatty acids are bonded together, …

triacylglycerols; triglycerides;
be the same
nonpolar; hydrophobic
decreasing their hydrophilicity

triacylglyerols:
deposits are seen in cells as … in cytosol – can be recruited when the cell needs additional energy to divide/survive
…: cells that store large amounts of fat, found primarily under the skin, around mammary glands, and int he abdominal cavity

oily droplets

adipocytes

triacylglycerols:
in plants, are present in seeds as ..
travel bidirectionally between … and … in the bloodstream
physical characteristics primarily determined by … of fatty acid chains

oils
liver; adipose tissue
degree of saturation

free fatty acids: unesterified fatty acids with a free …

circulate in the blood bonded noncovalently to ….

carboxylate group

serum albumin

…; ester hydrolysis of triacylglycerols using a strong base (such as lye-sodium or potassium hydroxide)
cleaves the fatty acid, leaving the … of the fatty acid and glycerol
fatty acid salt = …

saponification
sodium salt
soap

soaps act as … –> lowers surface tension at surface of a liquid, serving as detergent/…

surfactants

emulsifier

soaps act as surfactants:
with solutions that are in two separate phases, addition of soap would “combine” them into one phase, forming a … –> this is due to formation of …

colloid; micelles

…: tiny aggregates of soap with the hydrophobic tails turned inward and the hydrophilic heads turned outward, which allows for overall solvation

micelles

nonpolar compounds can dissolve in the … of the water-soluble micelle

hydrophobic interior

micelles are biologically important –> absorption of fat-soluble … and complex … like …
… and … secreted by gallbladder form micelles that increase SA available for lipolytic enzymes

vitamins
lipids; lecithins
fatty acids; bile salts

DNA is a … made of … –> polymer

polydeoxyribonucleotide; monodeoxyribonucleotides

nucleosides: a … bonded to a … and formed by covalently linking C-1’ of the sugar to the base
C atoms in the … are labeled with ‘ to distinguish from C atoms in …

pentose sugar; nitrogenous base

sugar; base

…: when one or more phosphate groups are attached to C-5’ of a nucleoside

nucleotides

molecules like ATP are high-energy compounds bc of the energy associated with the … between closely associated negative charges on the phosphate groups

repulsion

nucleic acids classified according to the … they contain –> ribose = …, deoxyribose (ribose with … OH replaced with H) = …

pentose
RNA
2’ OH
DNA

backbone of DNA is composed of alternating …. and … groups which determines its directionality –> always read from 5’ to 3’
nucleotides are joined by … bonds

sugar; phosphate; 3’-5’ phosphodiester bonds

phosphate group links … C of one sugar to the … phosphate group of the next incoming sugar in the chain
phosphates carry …, and thus so does DNA and RNA

3’; 5’

negative charge

distinct 5’ and 3’ ends gives DNA backbone …

5’ end of DNA will have an …/… group bound to C’5’ of the sugar, while 3’ end has a … on C-3’ of the sugar

polarity
OH/phosphate
free OH

purines: have … rings in their structure
two purines in nucleic acids are …and …
PURe As Gold

adenine; guanine

pyrimidines: have only … ring in their structure
…, …, and …
CUT the PYe

one

cytosine; thymine; uracil

purines and pyrimidines are … heterocycles

aromatic

aromaticity qualifications:
compound is …, …, and…
compound has … pi electrons –> … rule
stable due to delocalization of electrons, and thus, are pretty unreactive

cyclic; planar; conjugated

4n+2; Huckel’s

Bc of …, nucleic acids are very stable –> why they are ideal for storing genetic information

aromatic nature

Watson-Crick model: presented 3D structure of DNA and indicated that DNA is a …
…: two linear polynucleotide chains of DNA are wound together in a spiral orientation along a common axis
two strands of DNA are …

double helix
double helix
antiparallel

…. is on the outside of the helix with the … on the inside

sugar-phosphate backbone; nitrogenous bases

…: A always with T and G always with C

G and C have … H bonds, which makes the G-C interaction stronger than A-T which only has … H bonds

complementary base pairing

3; 2

The … and the … between bases provide stability to the double helix structure

H bonds; hydrophobic interactions

…: total purines will be equal to total pyrimidines overall, since %A = %T and %G = %C

Chargaff’s rule

most DNA is a … helix –> ….-DNA
makes a turn every 3.4 nm and has … bases within that span
has … and … between the interlocking strands that are often the site of protein binding

right-handed helix; B
10
major and minor grooves

…-DNA –> zig-zag appearance, left-landed helix

4.6 nm and contains … bases within that span

Z-DNA; 12

Z-DNA:
high … conc or high … conc can contribute to the formation of this form of DNA
No … contributed to it yet bc its unstable and hard to research

G-C; salt

biological activity

Double helix of DNA can be denatured by conditions that disrupt …. and …
none of the … links between nucleotides in the backbone of the DNA break during this process
achieved via …, …, and chemicals like … and …

H bonding; base-pairing
covalent
heat; alkaline pH; formaldehyde; urea

denatured single stranded DNA can be … if denaturing condition is slowly removed
important for … and detection of specific DNA sequences

reannealed

PCR

…: DNA with known sequence
can be added to mix of target DNA sequences, and when it binds to target, may provide evidence of gene of interest –> …

probe DNA; hybridization

DNA of chromosomes is wrapped around a group of small basic proteins called … to form chromatin

histones

two copies each of the histone proteins …, …, …, and … form a histone core and about 200 bp of DNA are wrapped around the protein complex to form a …
the last histone, …, seals off the DNA as it enters and leaves the nucleosome, stabilizing the structure further

H2A; H2B; H3; H4
nucleosome
H1

… create more organized and compacted DNA

nucleosomes

histones are an example of … –> proteins that associate with DNA
most others are .. soluble and tend to stimulate processes like transcription

nucleoproteins

acid

during interphase, DNA is … such that replication is more efficient
small percent of chromatin remains compacted and is therefore transcriptionally silent –> …: tends to have … sequences
…: dispersed chromatin that contains genetically active DNA

uncondensed
heterochromatin; highly repetitive
euchromatin

DNA replication cannot extend to the …, or else sequences and info will be lost with each round of replication
solved by a …: simple repeating unit (TTAGGG) at end of DNA

end of a chromosome; telomere

telomeres are progressively shortened but can be replaced with …, which is more expressed in rapidly dividing cells
telomeres have second function: high … content creates strong strand attractions at end of chromosomes to prevent …

telomerase
GC
unraveling

…: region of DNA found in center of chromosomes and act as sites of constriction
composed of … and is made up of repeat sequences that have a high GC content
during cell division, sister chromatids can remain connected at the … until separated during anaphase

centromeres
heterochromatin
centromere

…/…: set of specialized proteins that assist DNA polymerases

replisome; replication complex

DNA replication:

DNA unwinds at … and generation of new DNA proceeds in …, creating …. on both sides of the origin

origins of replication; both directions; replication forks

… origins of replication in eukaryotes

multiple

as replication forks move toward each other and sister chromatids are created, the chromatids remain

connected at the centromere

… unwinds DNA in replication

helicase

… bind to unraveled DNA 🧬, preventing reassociation of the DNA strands of degradation by nucleases

single-stranded DNA-binding proteins

helicase unwinding causes … – wrapping of DNA on itself as the helical structure is pushed further toward telomeres during replication
… relive this torsional strain and prevent strand breakage by working ahead of helicase and making small cuts in one/both of the strands and later reseal the cut strands

positive supercoiling; DNA topoisomerases

parental strands serve as templates for the generation of new daughter strands –> … process bc one parental strand is retained and bonded to a new daughter strand

semiconservative

DNA polymerase reads the DNA template from … to … and synthesizes from … and …

3’; 5’; 5’; 3’

leading strand is the parental … strand and is the strand that is copied in a … fashion

3’; 5’; continuous

lagging strand: copied in a direction …; the parental … strand
must be copied in small strands called … DNA polymerase must go back and fill in gaps

opposite the direction of the replication fork; 5’ to 3;

Okazaki fragments

dna polymerase cannot make new strands so a … synthesizes a short …
these short sequences are constantly being added to the lagging strand bc each Okazaki fragment must start with a new primer
leading strand only requires one in theory (in reality, there are a few)

primase; RNA primer

as new phosphodiester bonds are made in dNA, a free … is released

pyrophosphate (PPi)

DNA polymerase …/…, …, and … synthesizes daughter strands and RNA primers are then removed by DNA polymerase …/… and replaced by DNA polymerase …/DNA polymerase …

III; alpha, delta, and epsilon
I/RNAse H
I; delta

… seals the ends of the DNA molecules together to create one continuous strand of DNA

DNA ligase

bacterial chromosome is closed, double-stranded circular DNA with a … origin of replication. There are … replication forks that move away from one another and then eventually meet, resulting in production of two identical …

single; circular DNA molecules

Five “classic” DNA polymerases in eukaryotic cells:
DNA polymerases …, …, and… work together to synthesize both the leading and lagging strands: DNA polymerase … also fills in the gaps left behind when RNA primers are removed

alpha; delta; epsilon

delta

Five “classic” DNA polymerases in eukaryotic cells:

DNA polymerase … replicates mitochondrial DNA

gamma

Five “classic” DNA polymerases in eukaryotic cells:

DNA polymerases … and …. are important to the process of DNA repair

beta; epsilon

Five “classic” DNA polymerases in eukaryotic cells:
DNA polymerases … and … are assisted by the … protein, which assembles into a trimer to form the … – strengthens the interaction between DNA polymerases and the template strand

delta; epsilon; PCNA; sliding clamp

DNA polymerase cannot complete synthesis of 5’ end and so chromosome becomes shorter –> fixed by …

telomeres

cancer cells proliferate excessively bc they divide without … and aren’t subject to normal controls on proliferation
can migrate by … or … – migration to distant tissues via bloodstream/lymphatic system

stimulation

local invasion; metastasis

…: mutated genes that cause cancer

mostly …-related proteins

oncogenes

cell cycle

oncogens:
…: named after sarcoma; abnormal alleles encode proteins that are more active than normal proteins and promote rapid cell cycle advancement –> mutation in 1 copy is enough to promote tumor growth –> …

Src; dominant

…: oncogenes before they are mutated

…: mutated genes that cause cancer that normally would function to stop tumor progression

proto-oncogenes

antioncogenes

antioncogenes:
… or … are tumor suppressor genes that code for proteins that inhibit the cell cycle/participate in DNA repair
promote cancer by losing their … activity
…

P53; Rb
tumor suppression
recessive

DNA polymerase proofreads DNA strands. mismatched nucleotides tend to be … and the polymerase can recognize this and fix the error

unstable

to differentiate between template and parent strands such that the polymerase knows which nucleotide should actually be there:
parent strand existed longer and tends to be more heavily …

methylated

…. lacks proofreading ability and this is what closes the gaps between Okazaki fragments, not polymerase, so mutations in the … strand are more likely than for the other strand

DNA ligase; lagging

cells have machinery in the … phase of the cell cycle for mismatch repair (bc this is where the cell checks to ensure that DNA has been replicated properly)
enzymes encoded by genes … and … detect and remove errors in replication
… and … are the genes for prokaryotes

G2
MSH2; MLH1
MutS; MutL

UV light induces formation of …, which interferes with normal gene expression and replication and distorts double helix
removed by … repair mechanism –> proteins scan DNA and recognize legion. … makes nicks in the phosphodiester backbone on both sides of the abnormality and removes it. …. fills in the gaps. nick is sealed using …

thymine dimers 
nucleotide excision 
excision endonuclease 
dna polymerase 
ligase

thermal energy can be absorbed by DNA and can lead to …, which converts cytosine to …

deamination; uracil

…: detection systems that exist for small, non-helix distorting mutations in bases
affected base is recognized and removed by a …, leaving an …/…, or .., site

base excision repair
glycosylase
apurinic/apyrimidinic; abasic

base excision repair contd:
the apurinic/apyrimidinic (AP) site is recognized by an … that removes the damaged sequence from the DNA and DNA polymerase and ligase fill in gap and seal the strand

AP endonuclease

… allows a DNA fragment from any source to be multiplied either by cloning or PCR
means of analyzing and altering genes and proteins
…
… of genetic diseases
…
can provide a source of a specific protein

recombinant DNA tech
genetic testing
prenatal diagnosis
gene therapy

DNA cloning:

Desired DNA is inserted into a …, forming a … This is usually a plasmid

vector; recombinant vector

DNA cloning contd:
bacteria with recombinant DNA is then … and the non-recombinant bacteria are killed off with …
recombinant bacteria must be …
bacteria can then be left to express the gene or lysed to reisolate that gene depending on what is needed

grown in colonies; antibiotics

antibiotic resistant

insertion of DNA into a plasmid can be facilitated by … –> enzymes that are bacterial in origin and cleave … DNA at specific sequences
…: the 5’ to 3’ sequence of one strand is identical to the 5’ to 3’ sequence of the antiparallel strand

restriction endonucleases; palindromic

palindromic

some restriction endonucleases yield … which allow the fragment to be inserted directly into the vector when the vector is cut with the same restriction enzyme

sticky ends

…: large collections of known DNA sequences

DNA libraries

… contain large fragments of DNA, and include both coding (exon) and noncoding (intron) regions of the genome

genomic libraries

… (…) libraries are constructed by reverse transcribing processed mRNA and thus lacks … –> aka … libraries

cDNA; complementary DNA; introns; expression

only … can be used to reliably sequence specific genes and identify disease-causing mutations, produce recombinant proteins, or produce transgenic animals

cDNA libraries

…: joining of complementary base pair sequence –> DNA-DNA recognition or DNA-RNA recognition
uses two single stranded sequences
part of PCR and southern blotting

hybridization

PCR: ... DNA 
requires ..., ..., and ... 
requires ... to denature DNA 
uses ..., which doesn't denature under the high temp conditions
amount of DNA is ... each cycle

amplifies 
primers; nucleotides; DNA polymerase 
heat 
taq polymerase
doubled

… can be used to separate DNA

… is used to separate DNA by size

gel electrophoresis

agarose gel

gel electrophoresis:

often used while performing a … - used to detect the presence and quantity of various DNA strands in a sample

southern blot

gel electro/southern blot
DNA cut by restriction enzymes and separated by gel electro
DNA fragments transferred to a membrane that is … with copies of a … sequence, which binds to its complementary sequence to form double-stranded DNA
probes are labeled with …/… proteins

probed; single-stranded DNA

radioisotopes; indicator

…: contains a hydrogen at both C-3’ and 2’ –> once incorporated into a dNA strand, polymerase can no longer add to chain
… DNA strands –> useful for DNA sequencing

dideoxyribonucleotides

terminates

…: offers potential cures for inherited diseases; involves transferring a normal copy of a mutated gene into the affected tissues
requires efficient … –> tend to be modified …
drawback: randomly integrated DNA poses risk of integrating near and activating a host …

gene therapy
gene delivery vectors
viruses
oncogene

transgenic mice are altered at their … by introducing a cloned gene into ova or embryonic stem cells

germ line

…: introduced cloned gene

transgene

transgenic mice:
can be used to study … from early embryonic development
can be developed by microinjecting a .. into nucleus of newly fertilized ovum such that gene (hopefully, but rarely) incorporates into DNA. this is then implanted in a … offspring would have transgene and would pass it onto offspring. not as useful for studying … diseases bc number of copies of the gene that insert into genome cannot be controlled

disease processes
cloned gene
surrogate mother
recessive

transgenic mice:
other method: using … lines –> cloned genes can be introduced in cultures
stem cells injected into … and implanted into surrogate mothers – blastocyst has stem cells containing the transgene and the original blastocyst cells that lack the transgene –> offspring will be …

embryonic stem cell
blastocysts
chimera

transgenic mice:
other method contd:
chimeras can be bred to produce mice that are … for the transgene and … for the transgene

heterozygous; homozygous

…: mice in which a gene has been intentionally deleted to study human diseases

knockout mice

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