bch exam 2 sg flashcards

what is the goal of protein purification

to separate a protein of interest from other cell components while keeping it intact and active

why are proteins kept cold during purification

cold temperatures slows protein breakdown and helps preserve protein structure

why are protease inhibitors used during purification

they prevent proteases from breaking down the protein

why are reducing agents sometimes used during purification

they help prevent unwanted disulfide bond formation or help keep disulfides reduced

what does gel filtration chromatography separate proteins by

size

what is another name for gel filtration chromatography

size exclusion chromatography

in gel filtration, which proteins elute first

large ones

why do large proteins elute first in gel filtration

they cannot enter the pores of the beads so they travel around the beads and move through the column faster

why do small proteins elute later in gel filtration

they enter the pores of the beads, which slows them down

what does ion exchange chromatography separate proteins by

charge

what do cation exchange columns bind

positively charged proteins

what charge are the beads in cation exchange

negative, because they bind positively charged proteins

what do anion exchange columns bind

negatively charged proteins

what charge are the beads in anion exchange

positive, because they bind negatively charged proteins

how are proteins eluted from an ion exchange column

by increasing the salt concentration

why does salt cause proteins to elute in ion exchange chromatography

salt ions compete with the protein for binding to the charged beads

what does gel electrophoresis use to move proteins through a gel

an electric current

what happens to smaller molecules in gel electrophoresis

smaller molecules move faster and farther through the gel

what is the difference between native page and sds page

native separates by size and charge while keeping proteins folded. sds denatures proteins and separates mainly by size

what does sds do in sds page

sds denatures proteins and gives them a uniform negative charge

why does sds page separate mainly by size

sds coats proteins with a negative charge, so shape and original charge matters much less

what do b-mercaptoethanol or dtt do in sds page

they break disulfide bonds

what happens to quaternary structure in sds page

it is disrupted, so proteins are usually analyzed as individual subunits/monomers

in sds, which proteins travel farther

small proteins travel further

what does isoelectric focusing separate proteins by

isoelectric point, or pI

what is pI

the pH at which a protein has no net charge

what happens to a protein during isoelectric focusing

it moves through a pH gradient until it reaches the ph equal to its pI where its net charge is zero

what are the two steps of 2d gel electrophoresis

first, isoelectic focusing separate proteins by pI. then sds page separates them by mass

why is 2d gel electrophoresis useful

it separates proteins by two properties, charge/pI and size, giving better separation than one method

in ion chromatography, what is cation/anion exchange

c: positively charged proteins (charge and net) bind to negatively charged beads

a: opposite

sds steps

1. boil protein with sds to denature it and make it neg. can also add bme or dtt to break disulfide bonds

2. proteins will separate by size/mass and smaller ones will migrate fast

what is a pyranose ring

a six membered sugar ring

what is the most stable conformation of most pyranose rings

the chair conformation

why is the chair conformation more stable than the boat conformation

chair has less steric crowding and torsional strainb

why is b-D-glucopyranose especially stable

most bulky groups, including anomeric OH, are equatorial

does chair to boat conversion require bond breaking

no it only requires ring bending

what is mutarotation

the interconversion of a and b anomers through the open chain form in water

what are the approximate equilibrium amounts of D-glucose in water

about 36% a-D-glucose, 64% b-D-glucose, and trace open chain forms

why do a and b glucose coexist in solution

because the free anomeric carbin can open and reclose through the open chain form

which form is responsible for reducing sugar behavior

the open chain form

why is b-D-glucose more abundant than a-D-glucose

b-D-glucose is more stable because its anomeric OH is equatorial in the chair form

how do you determine D vs L in a fischer projection

look at the chiral carbon farthest from the carbonyl. OH on the right is D, on the left is L

what are enantiomers

non superimposable mirror images that differ at every chiral center

what are diasteriomers

stereoisomers that are not mirror images. differ and 2 C

what are epimers

diasteromers that differ at only one chiral carbon

what are anomers

epimers that differ only at the anomeric carbon

are epimers and anomers types of diastereomers

yes

what is a glycosidic bond

a bond between the anomeric carbon of one sugar and an OH or NH group of another molecule, with loss of water

what does a(1>4) mean

the anomeric C1 of the first sugar is alpha and connects to the c4 of the next sugar

what does b (1>4) mean

the anomeric c1 of the first sugar is beta and connects to c4 of the next sugar

for d sugars, how do you identify a vs b in a haworth projection

a has the anomeric OH or bond down; b has it ip

what do the numbers in glycosidic bonds tell you

they tell which carbons are cnnected

why is sucrose nonreducing

both anomeric carbons are involved in the glycosidic bond, so there is no free anomeric carbon

what makes a disaccharide reducing

it has at least one free anomeric carbon

what is an aldose

a monosaccharide with an aldehyde group at the end of the C chain, usually at c1

what is a ketose

a monosaccharide with a ketone group eithin the carbon chain, usually at c2

what is an aldohexose

a six carbon sugar with an aldehyde group, like glucose

what is a ketohexose

a six carbon sugar with a ketone group, like fructose

where is the anomeric carbon in an aldose

usually c1 bc c1 was the carbonyl carbon

where. isthe anomeric carbon in a ketose

usually c2 bc c2 was the carbonyl carbon

what does an aldose form when it cyclizzes

a cyclic hemiacetal

what does a ketose form when it cyclizes

a cyclic hemiketal

what is a tautomer in carbohydrates

a structure that can interconvert with another form by moving a hydrogen and shifting a double bond

where does OH go in the cyclic structure if it is on the right side of a fischer projection

it points down

how do you number a cyclic aldose

start at the aldehyde carbon and go clockwise

how do you number a cyclic ketose

start at the carbon above where the c=o should be, usually a ch2oh

where does the O go in a haworth projection

top right

if the penultimate carbon in a haworth projection is pointing up, is it d or l

D

for a D sugar, what makes it alpha or beta

OH on C1 is down makes it alpha, up is beta

for a L sugar, what makes it alpha or beta

alpha is OH up on C1, beta is down on C1

what is a monosaccharaide

a single sugar unit that cannot be broken down into simpler sugars under mind conditions

what is an olgosaccharide

a short chain of abou 2-10 monosaccharides linked by glycosidic bonds

what is a polysaccharaide

a long carbohydrate polymer made of many monosaccharides, usually 11 or more

what makes a sugar reducing

it has a free anomeric carbon, meaning that carbon is not locked in a glycosidic bond

what makes a disaccharide nonreducting

both anomeric carbons are involved in the glycosidic bond, so neither sugar can open into the linear form

why does a free anomeric carbon matter

it allows the sugar ring to open into the open chain form, which can act as a reducing agent

if the anomeric c is free, not bonded in the glycosidic bond, what is it

reducing sugar

basic structure of a fatty acid

a long hydrocarbon tail with a terminal carboxyl group

what charge does a fatty acid usually have at biological pH

the carboxyl group is deprotonated, so it usually has a negative charge

what does amphipathic mean

a molecule has both a polar/hydrophillic region and a nonpolar/hydrophobic region

what does omega classification describe

the position of the first double bond counted from the methyl/tail end of the fatty acid

what does omega 3 mean

the first double bond is 3 carbonds from the methyl end

what does omega 6 mean

the first double bond is 6 carbons from the methyl end

what are essential atty acids

fatty acids humans cannot synthsize enough of, so they must come from diet

what are examples of omega three fatty acids

a-linoleic acid, epa, and dha, linoleic acid,

how many C do linolic and a linolic acids have

18

what is a saturated fatty acid

a fatty acid with no carbon-carbon double bonds

what is an unsaturated fatty acid

a fatty acid with one or more carbon carbon double bonds

When Incorporated into phospholipids, the saturation of the fatty acid tail directly regulate what

Cell membrane fluidity

what does polysaturated mean

the fatty acid has multiple double bonds

why are saturated fats usually solid at room temp

their straight chains pack tightly, creating stronger intermolecular forces

why are unsaturated fats usually liquid at room temp

cis double bonds create kinks, preventing tight packing

what does 18:2 mean in fatty acid notation

it has 18 carbons and 2 double bonds

structure of a phospholipid

a sat and unsat fatty acid connecting to a head made of a phosphate group and glycerol backbone

what is triacylglycerol or TAG

a glycerol molecule attached to three fatty acid chains

what type of bond connects fatty acids to glycerol in TAGs

ester bonds

what is the main function of TAGs

long term energy storage

where are TAGs stored in animals

in adipocyted, which are fat cells

why do TAGs store more energy han carbs or proteins

fatty acid tails have highly reduced carbons that release lots of energy when oxidized

how are TAGs transported through blood

in lipoproteins