biochemistry exam 2

why are proteins kept cold and treated with protease inhibitors during purification

cold temps can slow protein degradation and denaturation, while protease inhibitors prevent proteins from being broken down

what does size exclusion chromatography separate proteins by, and which proteins elute first

it separates by size. large proteins elute first becuase they cannot enter the pores in the beads

what does ion-exchange chromatography separate proteins by

charge

what binds in cation exchange versus anion exchange chromatography

cation: positively charged proteins bind negatively charged beads

anions: negatively charged proteins bind positively charged beads

how are proteins released from an ion exchange column

by increasing salt concentration, so salt ions compete with the proteins for binding

how does affinity chromatography isolate a specific protein

a specific ligand is attached to the beads. the target protein binds, while other proteins wash through. a competing ligand releases the target protein

what is the difference between native PAGE and SDS PAGE

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

what do SDS and reducing agents do in SDS page

SDS denatures proteins and coats them with negative charge. B-mercaptoethanol or DTT breaks disulfide bonds

which proteins travel farther in SDS page

smaller proteins move faster and farther through the gel

what are the two steps of two dimensional gel electrophoresis

1. isoelectric focusing separates by pI/charge

   1. SDS PAGE separates by mass

compare xray crystalography and NMR

xray studies a protein crysal and gives a detailed but mostly statis structure. nmr studies proteins in solution and is better for dynamics, but is harder for large proteins

what is AlphaFolds main limitation and why is the proteome important

alphafold predicts a likely static structure but may not show dynamics, alternate states, or ligand binding, the proteome reflects wha the cell is actually doing because proteins carry out cellular functions

why is protein folding described as marginally stable

the folded and unfolded states are close in energy, so the protein stays stable but can still move and change shape during funtion

begin carbohydrates

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what is the difference between a monosaccharide, oligosaccharide, and polysaccharide

a mono is one sugar unit, an oligo has about 2-10 units, and a poly is a long chain of many sugar units

what is the difference between an aldose and a ketose

an aldose has an aldehyde at the end of its chain, usually C1. a ketose has a ketone wihthin the chain, usually at C2

how do you determine whether a sugar is a D or L in a fischer projection

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

what is a chiral center

a carbon attached to four different groups, allowing different three dimensional arrangements

what are enantiomers, epimers, and anomers

enantiomers are mirror images, epimers differ a one chiral carbon, and anomers differ only at the anomeric carbon

what is the anomeric carbond

the carbon that was the carbonyl carbon before the ring formation. usually c1 in aldoses and c2 in ketoses

for a D sugar, how do you identify alpha vs beta

alpha has the anomeric OH pointing doen, while beta has it pointing up

what are a hemiacetal and a hemiketal

a hemicetal forms when an alcohol reacts with an aldehyde. a hemiketal forms when an alcohol reacts with a ketone

what is mutarotation

the interconversion between alpha and beta anomers through the open chain form in water

what makes a sugar reducing

it has a free anomeric carbon that can open into the linear carbonyl form

what is a glycosidic bond

a covalent bond connecting the anomeric carbon of one sugar to an OH or NH group on another molecule

compare maltose, lactose, and sucrose

maltose is glucose a(1>4) glucose; lactose is galactose b(1>4) glucose; sucrose connects glucose and fructose through both anomeric carbons and in nonreducing

compare starch and glycogen

both store glucose and have a(1>4) chains with a(1>6) branches. glycogen is more highly branches and is the animal storage form

why is cellulose structural rather than a stroage carbohydrate

its b(1>4) bonds create straight chains that hydrogen bond together into strong fibers

what is glycosaminoglycan or GAG

a long, negatively charged chain of repeating disaccharides that attracts water and helps lubricate or cushion tissues

compare glycoproteins and proteoglycans

glycoproteins are mostly protein with shorter branched sugar chains. proteoglycans are ostly carbohydrate, with long GAG chains attached to a core protein

compare cellulose and chitin

cellulose is made of b(1>4) linked glucose and is found in plant cell walla. chitin is made of b(1>4) linked N-acetylglucosamine and is found in fungal cell walls and arthropod exoskeletons

what is the difference between N-linked and O-linked glycosylation

N-linked sugars attach to the amide nitrogen of asparagine. O-linked sugars attach to the hydroxyl group of serine or threonine

what is peptidoglycan and how does it differ in gram positive and gram negative bacteria

peptidoglycan is a sugar and peptide mesh that strengthens bacterial cell walls. in pos, there is a thick layer of pdn. neg has a thin layer between two membranes

what are the main functions of heparin, hyaluronate, and chondroitin sulfate

heparin is an anticoagulant. hyaluronate helps lubricate joints and is found in the eye. chondroitin sulfate is found in cartilage and connective tissue

why does glycogens branching matter

more branches create more nonreducing ends, allowing many glucose units to be released quickly at the same time

what does a(1>4) mean

the anomeric carbon C1 of the first sugar is in the alpha configuration and is linked to C4 of the next sugar

what does B(1>4) mean

the anomeric carbon C1 of the first sugar is in the beta configuration and is linked to C4 of the next sugar

what does a(1>6) mean

the anomeric carbon C1 of one sugar is alpha and links to C6 of another sugar, usually creating a branch

what do the numbers in a glycosidic bond name tell you

they show which carbon atoms are connected. for example, 1>4 means C1 of the first sugar bonds to C4 of the second

what is a tautomer

a structure that can rapidly convert into another form by moving a hydrogen and shifting a double bond

how can the same sugar form either a pyranose or furanose ring

it depends on which internal OH group attacks the carbonyl during ring formation

what does phosphorylase release from starch or glycogen

glucose 1 phosphate, not free glucose

why is heparin a strong anticoagulate

its many sulfate and carboxylate groups give it a very high negative charge

how do gram pos and gram neg peptidoglycan cross links differ

gram pos bacteria may use a pentaglycine bridge while gram neg bacteria often use a direct peptide cross link

lipids section

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major functions of lipids

energy storage, insulation, organ protection, membrane structure, homone production, signaling, and viamin absorption

what does amphiphatic mean

a molecule has both a polar, water attracting region, and a nonpolar, water repelling region

what is the basic structure of a fatty acid

a long hydrocarbon tail and a terminal carboxyl group

what is the difference between saturated and unsaturated fatty acids

saturated have no double bonds, unsaturated have one of more db

why are saturated fats usually solid and unsaturated fats usually liquid at room temp

saturated chains pack tightly. cis double bonds in unsat chains create kinks that prevent tight packing

what does a fatty acid notation such as 18:2 mean

it has 18 carbons and 2 dbs

what does omega 3 mean

the first double bond is three carbonds away from the methyl end of the fatty acid

what is an essential fatty acid

a fatty acid the body cannot make sufficiently, so it must be obtained from food

what is triacylglycerol, or TAG

one glycerol molecule attached to three fatty acids by ester bonds

why do fats store more energy than carbohydrates

their carbon atoms are more reduced, so oxidation releases more energy

what is the main role of TAG

long term energy storage, mainly in adipocytes

what are the three major membrane lipid types

glycerophospholipids, sphingolipids, and cholesterol

wha is a phospholipid

an amphipatic lipid with a polar phosphate containing head and nonpolar tail

difference between glycerophospholipids and sphingolipids

glycerophospolipids use glycerol as the backbone; sphingolopids use sphingosine

what is a ceramide

a fatty acid joined to sphingosine through an amide bond

compare cerebrosides, gangliosides, and sphingomyelin

cerebrosides have one sugar gangliosides have several sugars including sialic acid, and sphingomyelin in abundant in myelin

what does cholesterol do in cell membranes

it strengthens the membranes and buffers fluidity, limiting movement at high temperatures and preventing tight packaging at low temperatures

what important molecules are made from cholesterol

steroid hormones, bile acids, and vitamin D

what are bile acids and what do they do

detergent like cholesterol derivatives that emulsify dietary fats for digestion

what are eicosanioids and how do nsaids affect them

eicosanoids are signaling molecules made from polyunsaturated fatty acids. nsaids reduce inflammation by blocking prostaglandin synthesis

what is the charge of a fatty acid at biological ph

its carboxyl group is usually deprotonated so it has a negative charge

whcih positions of a triacylglycerol are lipases most likely to hyrolyze

the primary ester positions, especially sn 1 and sn 3

where are phosphatidylserine normally found in the plasma membrane

mainly in the inner leaflet

why are ceramides important

they are a major part of the skin barrier and help prevent water loss

what makes a ganglioside different from other glycosphingolipids

it contains several sugars, including at least one sialic acid

why can free cholesterol enter membranes but cholesteryl ester cannot

free cholesterol has a polar OH group and is amphiphatic, cholesteryl ester is fully hydrophobic

how are fatty acids transported in blood

bound to albumin

what does glucagon do to stored fat

it stimulates adipose tissue to break down tags and release free fatty acids into the blood

start membrane

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define amphiphatic

there is both a hydrophilic and hydrophobic region

why do phospholopids form bilayers in water

their hydrophilic heads face water while their hydrophobic tails cluster away from water

why do bilayers close into the vesicles

closing prevents hydrophobic edges from being exposed to water

what does semipermeable mean

the membrane allows some substances to cross more easily than others

which substances cross the lipid bilayer most easily

small nonpolar or hydrophobic molecules

which substances usually need transport proteins

ions and large or polar molecules

what is the fluid mosaic model

the membrane is a fluid bilayer in which lipids and proteins can move laterally

what increases membrane fluidity

shorter fatty acid tails and more cis double bonds

what decreases membrane fluidity

longer fatty acid tails and more saturated tailes

what does cholesterol do to membrane fluidity

it acts as a buffer: it decreases excess fluidity at high temperature and prevents tight packing at low temps

what is membrane asymmetry

the inner and outer leaflets have different lipid and protein compositions

where are phosphatidylcholine and phosphatidylserine mainly found

choline mainly in outer leaflet; serine is mainly in inner leaf

what is a lipid raft

a less fluid membrane region rich in cholesterol, sphingolipids, and saturated fatty acid tails

what is the purpose of lipid rafts

they cluster membrane proteins and can improve signaling or pathway activity

what is the difference between integral and peripheral membrane proteins

integral proteins are embedded in the bilayer; peripheral [proteins are loosly attached to the surface

what is a lipid anchored protein

a protein covalently attached to a lipid that holds it near the membrane

what is an amphitropic protein

a protein that can reversibly attach to and detach from the membrane

which amino acids are common in transmembrane regions

mostly hydrophobic amino acids

what structures commonly span membranes

alpha helices and b barrels

how can a membrane channel have a water filled pore

hydrophobic residues face the lipid bilayer, while hydrophobic residues face the pore

what does a flippase do

uses ATP to move certain lipids from the outer leaflet to the inner leaflet

what does a floppase do

uses ATP to move lipids from the inner leaflet to the outer leaflet

what does a scramblase do

moves lipids in both directions without ATP and reduces membrane asymmetry

what is passive transport

movement down a concentration or electrochemical gradient without energy input

what is the difference between simple and facilitated diffusion

simple diffusion occurs directly through the bilayer; facilitated diffusion uses a channel or carrier

why does facilitated diffusion saturate

there are a limited number of transport proteins