Biochem Exam 1

Blood type A differs from type O in that type A has an extra

GalNAc

List some of the common and important disaccharides: Sucrose (maple sugar)

(Glc(alpha 1-2 Beta)Fru) Acetal and ketal bond at the same time Not a reducing sugar

Saxitoxin

(found in Red Tide, bacteria in sea/river water, bright red, makes water look blood red)-same effect as tetrodotoxin, would cause paralysis.

phosphodiglycerides

2 fatty acids, 1 glycerol, phosphate with polar head group. Membrane lipids, found in membrane. Polar head group shown in table below, outer surface of membrane. Example of a membrane lipid: phosphatidylcholine: polar head group choline. Diglycerides-Membrane lipids. The building blocks of membranes are 2 fatty acids esterified to a glycerol molecule with a polar head gropu

myoglobin and hemoglobin

2 major types of heme proteins Myglobin caries oxygen in muscle, monomer Hemoglobin oxygen in blood, tetramer Both cases heme in center of molecules

BPG

2,3-Bisphosphylglycerate Hemoglobin has oxygen binding curve, because this is a allosteric modulator in hemoglobin. Contains C1-carboxylic acid, C2 and C3-esteriphided to phosphate, highly negative (5 negatives) binds very tightly with hemoglobin and alter O2 binding No BPG-hyperbolic curve kind of like myoglobin, binds oxygen very efficiently In presence of BPG, takes on sigmoidal curve, hemoglobin holding only half saturation at 3 kPa, have to go to higher amount of oxygen to bind. At low oxygen pressure found in capillaries going through the tissue, hemoglobin releases oxygen. If there were no BPG, hemoglobin would not let go of oxygen. Higher elevation, lose some efficiency. BPG binds positive amino acids found in pocket inside hemoglobin where 4 tetramers come together. In pocket terminal amines on ends in pockets, lysine's and histidine's (partially charged) positively charged histidine's bind to negatively charged BPG

Non-standard amino acids

4-Hydroxyproline made from proline. Done after the fact, this is called modification, modified after protein is made such as 4 lysines=desmosine, found in elastin in skin, Selenocysteine S replaced by selenium In urea (not in proteins): ornithinie, citrulline

Define the peptide, y and f bond angles and explain the meaning of the Ramachandran Plot.

: alpha carbon is chiral with R group attached to it 3D shape of protein: rotation between C-C and C-N single bond, partial double bond character because of resonance, no free rotation between C-N bond by C=O (Peptide bond) we do have rotation in Psy angle alpha carbon of preceding amino acid and carbonyl carbon rotation in Phi angle bond between nitrogen and next alpha carbon bond. The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, setting up a small electric dipole. Virtually all peptide bonds in proteins occur in this trans configuration. 360 degrees of rotation makes a lot of possibilities. However, R groups bump into each other, not possible for 360 degrees. Ramachandran Plot shows which angles are possible, most are prohibited. Simplifies possible structures we can have. If you take all phi and psi angles for all amino acid residues except glycine, and enzyme pyruvate kinase and overlay them on a Ramachandran Plot you see there's a limit to angles possible

Alanine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

A (Ala)-Has 3 carbons

D-Tubocurarine chloride (Curare arrow poison)

Acetyl Choline Receptor inhibitor: also, a paralytic because it blocks acetyl choline receptors which are very important, particularly in neuromuscular junctions so muscles would be unable to contract-flaccid paralysis.

Titration curve

Acidic conditions: amino acid fully protonated=carboxylic acid and ammonium form, fully protonated of Glycine pH < 2.34 At pH=pK1=2.34 we have a zwitterion: fully protonated 50:50 mixture. Zwitterion dominates from pK1=2.34 until pK2=9.60 where most biological activity is taking place (exception stomach) pK2=9.60 50:50 mix of zwitterion and deprotonated form where ammonium becomes amine and carboxylic acid becomes carboxylate Above pH=pK2=9.60 deprotonated form, amine and carboxylate pH near pKa=buffering zone, shallowest (flattest?) part of curve sharpest part of curve near pI Slide 36-titration curve for acetic acid. pKa=4.76 Henderson-Hasselbalch relates pH to ionization of acid or base Ratio of acid to base-important in pharmacology when we want to know what % of a molecule is in base form vs. acid form at any particular pH. pKa is a constant for a molecule. At pKa, we have a 50:50 ratio of 2 forms: acid and base Base/acid=1, log (1)=0, pH=pKa pH of 5 we can figure out ratio of acid and base If we are going to do this on left part of curve we do it for Acid (A-, HA) Right part of curve is base (B, BH+) Always base over acid

Describe the structure of agarose, hyaluronate, chondroitin-4-sulfate, keratin-sulfate and heparin (repeating disaccharides): Agarose

Agarose: (don't have to know exact structure)-used commonly as matrix for running DNA and RNA gels-know repeating disaccharide

Difference between glucose, mannose, and galactose t-Aldoses.

All 6 carbons, 4 chiral carbons differ on which side OH is on: Glucose: RLRR, Mannose: LLRR, Galactose: RLLR

Difference between glceraldehyde, erythrose, and ribose.

All aldoses have an aldehyde. Glyceraldehyde-3 carbon, erythrose-4 carbon, ribose (DNA)-5 carbon.

Steroids

All steroids are derived from cholesterol (also a steroid) 6 classic examples, 4 fused rings common to all of them One molecule, Vitamin D3 we don't think of as a steroid is derived from a steroid dihydrocholesterol. One of those 4 rings is broken to from Vitamin D3 molecule.

Acid-Base Properties of Amino Acids

Amino Acids are both an acid and a base. Amino Acids can act as a buffer within 1 pH unit of its pKa. Amino acids have at least 2 pKa's

D vs L

Amino acids are chiral, left handed and right handed. 99% of the time we talk about left handed form. You may see d from time to time, but mostly we talk about L amino acids. If we can take amino acids and put the most oxidized portion on top, the least oxidized portion on bottom and compare it to the sugar glyceraldehyde, as it turns out L-alanine has a similar configuration as L-Glyceraldhyde. So we determine what L and D is by how it compares to L-Glyceraldhyde. Most sugars are in the right handed confirmation, most amino acids are in the left handed confirmation.

zwitterion

Amino acids exist in the zwitterionic form. Amino acids-amine group and carboxylic acid, at pH 7.4 bases are proton acceptors and acids are proton donors, therefore basic amine group will take a proton away from the acid group. At pH 7.4 amino acids are really what we call zwitterions. Amine actually ammonium and carboxylic acid is carboxylate. We have a +, and - on the same molecule makes this ionic but neutral (cancels out the overall charge). The other important feature is the side group R: differentiates all 20 amino acids

Eicosanoids

Another important lipid are those derived from Arachidonic acid C20 molecule. These are the prostaglandins, thromboxane's, and leukotrienes. just cyclized forms of arachidonic acid:

Negatively charged Amino Acids

Aspartate and Glutamate, Carboxylic side groups. At pH 7.4 (which is above their pKa's) they will be carboxylates. (D, E)

Fructose vs. Glucose

Fructose is almost identical to glucose except fructose has a ketone in position 2 instead of an aldehyde group in glucose.

Explain why the membrane has asymmetry.

Because outer and inner layer have slow flip flop diffusion, we can have asymmetry between outer and inner layer. Phosphatidylethanolamine found predominately on inner side, etc. Phosphatidylcholine and sphingomyelin found predominately found on outer layer. Phosphatidylinositol 4-phosphate found exclusively on inside of membrane. Not all membranes made the same. If you compared plasma membrane, mitochondrial membrane, and golgi membrane difference between total composition different in overall composition.

Bohr Effect

Bohr Effect similar to BPG binding, but directly related. Oxygen binding on hemoglobin changes in different ph. Higher pH, increase in oxygen binding activity. Lower pH, decrease in oxygen binding affinity. Oxygen binding affinity, has to do with histidine: slightly more acidic, more protonated histidine's, higher probability that negatively BPG will be bound to allosteric sight, decreases binding affinity of oxygen. Increasing amount of hemoglobin in T state. This is common in tissue, waste products from cell which are acidic. Lungs basic, carbon dioxide leaving and considered basic. Histidine's less likely to be positive, less BPG, more likely to be in R state. Oxygen binding curve shifts upward with higher pH

Cysteine (Polar, uncharged R groups: S, T, C, N, Q)

C (Cys)- Sulfur Group

Polar Amino Acids

C, S, T, K, R, H

From the abbreviated name of Gal(beta1-4)Glc, we know that:

C-4 of glucose is joined to C1 of galactose by a glycosidic bond.

Which of the following is an unsaturated acid?

C16:1

Which of the following is an Omega-6 fatty acid

C18:2 Delta 9, 12

1. Explain and give examples of cross-linking in a protein and how this increases protein strength.

Collagen: left handed helix, super coiled upon itself, 3 coiled in right handed triple helix, mostly glycine every third amino acid, followed by X and Y . Highly crosslinked by dehydrohydroxylysinonorleucine (derived amino acid made from 2 lysine's linked together) makes it stronger than steel. osteogenesis imperfecta-Ehlers-Danlos syndrom: Subistitude for Cys or Ser for Glysine cause loose joints, can be lethal, we don't have right 3d structure, can't form helices.

common amino acids the other "non-amino acid" chemicals that can be found at an active site.

Common features at active site: hydrogen binding, proton dotation or accepting: Glu, Asp, Lys, Arg, Cys, His, Ser Tyr commonly found Chymotrypsin breaks proteins. Serine active amino acid breaks bind. Participates by donating Hydrogen. Sometimes we have non-amino acid participants: metals for example. B vitamins also very common

Aspartate (Negatively Charged (D, E)

D (Asp)-pKa=3.65

parallel

Drawing on a flat sheet.

movement of material across membranes

Due to the fact that membranes can break or fuse, we have exocytosis where things are exocytosed out of the cell such as hormones, neurotransmitters, other molecules. Endocytosis is the opposite: macrophages get rid of bacteria. Unfortunately, bacteria can take advantage of this to get DNA into a cell. Sperm and Egg.

Glutamate (Negatively Charged (D, E)

E (Glu)-pKa=4.25. Remember that Glu is found at Position 6 of the beta-chain on sickle cell hemoglobin.

Glycine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

G (Gly)-only non-chiral R=H

Nonpolar Amino Acids

G, A, V, L, I, P, F, Y, W, M

catalyst

Enzymes speed up reactions that could take place on their own by a tremendous amount. 10^7 that means 10 million times faster, 10^9 trillion times faster, etc. Rate of chemical reaction: substrate to product like rolling a ball up to top of transition state, then it rolls down spontaneously. Blue line, less effort to get up smaller hills.

Glutamate Titration Curve

Example of amino acid which has a protonatable side chain: Glutamate has a R with a carboxylic group pK1-2.19, less than that fully protonated, both carboxylic acid and ammonium form, +1 charge between pK1=2.19 and pKR=4.25, zwitterion, 0 charge between 4.25 and pK2=9.67, -1 charge most common at pH 7.4 pI something between 2.19 and 4.35 3. Slide 40

Phenylalanine (Aromatic R groups: F, Y, W)

F (Phe)-Most non-polar of aromatics.

Olestra

Fake fat is real fat except fatty acids are esterified to table sugar, sucrose instead of glycerol. No calories because enzymes don't recognize it and break it down. Don't convert it to calories.

Formation of a peptide bond

Formed when 2 amino acids come together and kick out acids: Carbon of carboxylic group and Nitrogen of Amine and bring together, get peptide bond.

Describe the sphigolipidosis diseases and name some high profile examples listed in this lecture.

Gangliosides, molecular diseases where we are unable to break them down, collect in the lysosomes of the cells, especially brain cells. Unable to break down sugar portion of glycolipids.

Epimeric pair

Glucose & Mannose (Epimer-differ in 1 chiral center, all others identical: RLRR vs LLRR)

Starch (amylose)

Glucose held together by 1-4 bonds which are easily broken by an enzyme amylase. (Reducing end has H, Non-reducing end has O)

Describe the various glucose transporters found on various cell membranes.

Glucose transporters have many varieties. First, is glucose sodium symporter, glucose sucked out of lumen of intestine and sent into epithelial cells of intestine through a symporter: Glucose can come in, but only if sodium comes with it or you could say sodium whose concentration outside all cells is higher than inside of cell and wants to come in, allowed only if it brings glucose with it. So, energy that pulls glucose in is from sodium gradient which was created by sodium/potassium ATPase-primary active transport system. Sodium/glucose symporter secondary active transport. Another type of glucose transporter is the GLUT2, found on epithelial cell, which is a passive transporter, concentration of glucose in epithelial cell and in blood is the same. It equalizes the concentration on either side of the membrane, activity of this is pulling it into the cell in the first place but then it equilibrates with the blood and with the rest of the body.Table of cotransport systems. Must know one in red. Sodium/glucose found in intestine, but also in kidney.

glucose hemiacetal

Glucose: OH off of C5 is closest to Aldehyde C1 Can form where OH is pointing down-alpha OH pointing up-beta Sugars prefer hemiacetal ringed (6 member ring) structure, 99% Beta form is more stable

Reference compound for naming D & L isomers of sugars

Glyceraldehyde

triglyceride (aka triacylglycerol).

Glycerol + 3 fatty acids

Glycolipid

Glycolipid are based on sphingosine molecules, ceramide oligosaccharide group attached, group of sugars,

O, A, B and AB blood types

Glycolipids Blood cells can be identified as O, A, or B depending on which of these oligosaccharides are found on the outside of that cell. If we have cells with O Antigen it has Glc-Gal-GalNAc-Gal Fuc A Antigen is the same as O, with an additional GalNAc (Galactose N Acetate)(attached to terminal Gal B Antigen is the same as O, with an additional Gal attached to terminal Gal AB=mixture of A & B antigens together A very interesting phenomena is that a bacteria that recognizes the o group antigens is able to cause trouble with stomach ulcers, therefore people with type o blood have a risk for ulcers that's 7 times higher than people with A or B

N-linked.

Glycoprotiens-Proteins that have a oligosaccharide attached to it- a bunch of sugars attached to it. Attached in an n link, nitrogen of this amino acid asparagine, is attached to the oligosaccharide. Sugars attached to proteins. If glycoproteins is O-linked, it's one of the serine or threonine, one of the alcohol amino acids.

O-linked

Glycoprotiens-Proteins that have a oligosaccharide attached to it- a bunch of sugars attached to it. Attached in an n link, nitrogen of this amino acid asparagine, is attached to the oligosaccharide. Sugars attached to proteins. If glycoproteins is O-linked, it's one of the serine or threonine, one of the alcohol amino acids.

Histadine (Positively charged R groups, Polar & Basic: K, R, H)

H (His)-neutral at pH 7.4, positively charged only at more acidic pH's pKR=6.00

Chitin

Hard substance making up exoskeleton of insects, looks just like cellulose except polymer of glucose and acetate, but also beta 14 bonds.

Aldose sugars

Have an aldehyde.

protein denaturation

Heat a solution containing proteins, we can measure protein unfolding using UV light or circular dichroism. As it unfolds, amino acids let go out of inner and absorbs more UV light. Plotted as a function of nature of protein. Halfway up is the Tm Value-melting temperature. Apomyoglobin more stable, melts at higher temp than ribonuclease. Adding salts denatures: Guanidine hydrochloride, increase concentration, increase rate of unfolding Once unfolded, cannot spontaneously fold back

Describe the formation of an acetal or ketal.

Hemiacetals can react with additionoal alcohals to form acetal (difficult, split out water, but more stable once they form) Ketose is similar. Two glucose: hemiacetal on carbon number 1 reacting with alcohol on C4 (not spontaneous, enzyme is going to direct specification). Form acetal linkage, this is a disaccharide because we have 2 sugars, and this disaccharide is a glucose that we call alpha 1,4 glucose. Glucose 1 in alpha position (because OH is coming down) reacts with OH on other Glucose's C4. This is also a reducing sugar because on the right side on the right sugar, we still have a hemiacetal OH on C1 which can still open up into an aldehyde.

hemoglobin F to hemoglobin A

Hemoglobin variants: HbF and HbA F fetus, higher oxygen binding/affinity doesn't bind it as tightly, takes oxygen from mother's hemoglobin. Decreases overall efficiency to deliver oxygen to tissues. Major shift from HbF to HbA, beta subunit differs substituted for gamma subunit. HbA2 found in all of us, higher elevations express more A2 (halfway between F and 2) slightly increases amount of O2 hemoglobin can grab in lungs. Otherwise altitude sickness.

cooperativity

Hemoglobins binding affinity can be graphed in hill curve: log of bidning percentage theta, and if you take that and divide it by 1-theta and take log of that number and plot it against parital pressure of oxygen, increase binding on hemoglobin with increase on pO2, at certain pt. on hemoglobin low-affinity state has change in affinity, high affinity though is linerar. Hemoglobin I a tetramer, Low -affinity circle with L, high affinity square with L. once it has 2 ligands or oxygens it will bind more even more strongly

membrane lipids.

Here are some of the molecules we find in membranes. Glyceralphospholipids which are based on the 3-carbon glycerin molecule with 2 fatty acids attached and a polar head group. Listing of the different variations of the polar head group. Sphingolipids which are based on the sphingosine molecule which acts as both 3 carbon backbone and first fatty tail along with 2nd fatty acid attached with an amid group and then the various polar head groups attached to this molecule. Notice that the glycolipids tend to be sphingolipids. Cholesterol, sphingolipids and the glycerophospholipid are the major types of molecules found making up membranes.

Describe the repeating disaccharide found on the cell wall of Gram Positive Bacteria.

Heteropolysaccharide: On the outer side of the membrane we find on gram positive bacteria are a bunch of sugars which make gram positive bacteria gram positive. They stain positively to the gram stain. Structure found on the outside of cell making it a cell wall: peptidoglycan: repeating saccharides (GlcNAc & Mur2Ac) keep repeating and then are connected to each other by cross bridges which are made up of peptides, hence the name peptidoglycan. Penicillin prevents the synthesis of the peptide cross-links leaving the cell vulnerable to osmotic lysis.

Histidine Titration Curve

Histidine: +2, +1, 0, -1 pI halfway between 6 and 9.17: 7.59 much more basic than gluatamate pK tell you 50:50 ratio of titration Example: pH=3.5+log (1/10)=2.5

Homopolysaccharides vs. heteropolysaccharides

Homopolysaccharides are made up all of the same type of sugar (starch, cellulose, and chitin) Heteropolysaccharides are made up 2 or more types of sugar

Isoleucine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

I (Ile)-Branched Chain

Define and explain the activity at the active site of an enzyme.

Induced fit: amount of energy to break a stick in half. Take enzyme stickase, induced fit, binding site not complimentary to stick, complimentary to transition state, break stick easier. Where reaction takes place, once substrate bound reaction can take place.

Ouabain (AKA Arrow Poison)

Sodium-potassium ATPase inhibitor: prevents cells from becoming depolarized, very serious affect in all cells, especially muscle and nerve cells which require polarization to function.

Hemiacetal vs. hemiketal

If an alcohol is going to react with an aldehyde, it's most likely going to react with the one closest to it.

liposome

If we extend this bilayer out far enough, they can wrap around themselves into liposomes, which is basically our cell. We have the outer layer which is the outside of the cell and the inner portion is the space inside the cell. All protected by a lipid bilayer-membranes are made of bilayers. Bilayer thickness: 60 angstroms thick. Critical micelle concentration of detergent SDS: 1 millimolar. Bilayer concentration: 1 micromolar. This means formation of cells spontaneous, membranes very stable and spontaneous structures.

aquaporin

Important membrane channel aquaporin, let's membranes become semi-permeable to water. Aquaporin is a protein that crosses the membrane 6 times (transmembrane, serpentine receptor). We take each one of these proteins and cluster it with 4 other proteins that are the same. The 4 of them together-tetramer-forms aquaporin channel created by space between 4 proteins, barrel shape. Water can squeeze through the small pore formed. We've known about semi-permeable membranes for years, but it was very recently that we figured out how this takes place: explained by 2003 Nobel Prize winners in Chemistry Do not need to know all aquaporins, but do need to know they are important for water to move across membrane for important metabolic and physiological functions.

Explain why fatty acids form micelles.

In order to understand how membranes form, need to understand fats in water. If we take a fatty acid: Polar head group-hydrogen bonds in water, tail hydrophobic. Shell of water molecules must surround it for it dissolve in water. This shell is what we call surface tension-unstable situation. Fatty acids and water create surface tension (oil and water do not mix). If we have 3 fatty acids in water, we have 3 times the amount of surface tension. 3 times more unstable, unless they cluster together: diminishing the amount of surface tension. This is a hydrophobic interaction where the fatty acids are pushed together to minimize surface tension. The best situation is a micelle: all the tails cluster together in center all polar head groups are on outside. Micelles are then soluble in water. This is how soap works. Soap is fatty acids, oil and grease dissolve to the inside of micelle. And because the micelle itself is water soluble, we can then solubilize things that are not soluble in water.

List some of the common and important disaccharides: Lactose milk sugar

In this case carbon 4 is on sugar 4 on left is flipped, making it a galactose instead of glucose. The acetal bond between C1 on sugar left and sugar on right is in Beta position-bond is coming up from C1 on left, Galactose Beta 1-4 Glucose This is also a reducing, because hemiacetal on C1 on right.

Explain how ATP synthesis in the mitochondria is active transport in reverse.

In this simple model of the electron transport chain, we have NADH produced by metabolism (citric acid cycle for example), succinate (also citric acid cycle). These can pass their electrons onto proteins imbedded in membrane of mitochondria. Matter of fact it's got a 2-membrane system, so we're talking about the inter-mitochondrial membrane that we're talking about. And when it puts these electrons in, it pumps protons out of the matrix and into the outer membrane space. There's a protein called an ATPase which normally pumps protons across the membrane, but in this case the proton concentration from the electron transport chain is so high that these protons push across the membrane through this channel and instead of ATP involved in pushing protons across, the protons push ATP synthesis. So in many ways this is an ATP primary active transport system running in reverse

Lysine (Positively charged R groups, Polar & Basic: K, R, H)

K (Lys)-Amine side group pKR=10.53

Fructose-Reducing Sugar

Ketones cannot be oxidized easily, therefore you'd think fructose would not be a reducing sugar. Even though fructose is a ketone, it is a reducing sugar because it can isomerize to glucose or mannose, this happens very slowly at room/body temp, but is very rapid when heated in the test tube.

beta-lactam antibiotics

Know that the beta-lactam antibiotics work by blocking the peptidoglycan formation of cell wall formation in bacteria. You will be expected to know that these include penicillin. Know the names of these drugs, how they work, and that they are on the list of the top 300 drugs that you are expected to know for your clinical classes. There will be a biochemistry question on the mechanism of this class of drugs. There will be no more than one question on the names of these drugs since you will be tested on that in other classes.

Leucine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

L (Leu)-Branched Chain

Describe how membrane composition affects the thermal properties of membrane fluidity.

Lower the temp, fluidity decreases & vice versa. Therefore, we can vary what membrane lipids are in a membrane so that fluidity stays about the same. E. coli will change its composition of its membrane depending on what temperature it's cultured in because it wants the same fluidity no matter the temp.

3 positively charged amino acids

Lysine, Arginine (2 positively charged) and histidine sometimes positively charged when it's in more acidic solvent. pKR is pKa of side group is 6 for histidine, which is near the pH 7.4. Neutral at pH 7.4, negatively charged only at more acidic pH's. (K, R, H)

Methionine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

M (Met)- Sulfur, non-polar, thioether.

isopreneoids

Made up of repeating 5 Carbo, n units, ex. beta carotene, we metabolize it and we convert it to vitamin A, necessary for visual pigments found in retina in eye. Vitamin E another important isopreneoid, acts as an antioxidant, primarily found dissolved in membranes of our cells. Vitamin K: necessary for blood clotting (Warfarin: a blood anticoagulant inhibitor against vitamin K) Ubiquinone (coenzyme Q) antioxidant found in mitochondrial membrane part of electron transport chain.

fluidity of membrane proteins.

Membrane bilayer itself predominately made of lipids. However, if you were to isolate the membrane and weight it, you'd find 50% of mass is bilayer (above and below too, but anchored somehow). Lipid fluidity is not only for the lipids in the membrane, but also for the proteins which are not anchored down. Experiment: HumSince proteins can float around in 2D, that could create a problem for cells that don't want proteins floating around: nerve cells that certain channels or receptors that we want at certain locations in the cell. Anchored in place using cytoskeleton elements with ankyrin proteins and skeletal proteins such as spectrin and actin found just inside the membrane to anchor things in placean cells fused with mouse cells, after a while they homogenized.

Glycolipids

Membrane of all of our cells are made up a fatty material. Either phosphoglycerallipids or sphingolipids. Sphingolipids are fatty material that makes up much of the membranes of our cells, but we can glycolipids, sugar molecules attached to these lipid molecules of the membrane. When this happens, the sugar portion is pointing on the outside of that cell membrane and it can tell it much about the properties of that cell.

Describe and differentiate the three major types of membrane proteins.

Membrane proteins can be classified in 3 varieties: o Integral proteins: proteins imbedded in the membrane o Transmembrane proteins: which cross all the way through membrane o Peripheral proteins: associated with membrane but not embedded

fluid mosaic model of the membrane

Model consists of glycerophospholipids (AkA Phosphodiglycerides), sphingolipids (commonly glycolipids-sugar molecule attached as polar head groups), sterols (predominately cholesterol, also embedded in membrane-help stabilize fluidity of membrane), and proteins (commonly found embedded in membrane, often transmembrane proteins-cross all the way through the membrane).

Explain why carbon monoxide is toxic.

Molecule shifts in shape because heme being puckered in deoxy state once we bind oxygen becomes flat and moves histidine F8, dramatic shape change in molecule. sabatoge: Bind carbon monoxide, binds much stronger to heme than iron. Small amounts of CO2 will win over oxygen we have excess of 1% from car exhaust ect. Smokers as much as 10% Met hemoglobin Fe3+ does not bind oxygen Cyanide binds met hemoglobin and not oxyhemoglobin, cytocrhomes of our mitochondrial very tightly, but does not bind hemoglobin tightly, anecdote for cyanide poisoing changes Fe 2 to Fe 3, cause hemoglobin to bind cyanide so it doesn't get in brain cells.

unsaturation

More unsaturation we have, the more liquid something is. Butter 40 unsaturated, solid. Olive oil 70% unsaturated, liquid at room temp. unsaturated fatty acid, especially cis, has a kink, can't pack the materials together.

Describe the effect of high CO2 on hemoglobin.

Most CO2 released becomes bicarbonate and proton in blood itself, some will bind to hemoglobin by binding to amino terminal residue, making carbamino terminal residue. Released proton to solution, tissue blood more acidic, decrease oxygen binding. Carbamino hemoglobin, deoxyhemoglobin less likely to bind oxygen.

Ketose sugars

Most ketose have ketone on 2nd carbon. Only 1/2 as many ketose as aldose because #2 ketone carbon is not chiral. (Dihydroxyacetone, Fructose)

Right-handed sugar

Most sugars are right-handed: second to last OH is on the right hand side.

Movement of something across the membrane can be described by graphs/mathematics that are the same as enzyme kinetics

Movement of something across the membrane can be described by graphs/mathematics that are the same as enzyme kinetics. Moving something across the membrane: a lot of resistance, particularly if something has a hydration shell-water does not pass through a membrane. If we use a transporter we facilitate diffusion, requires less activation energy. We can define this using Mcalis menton kinetics or linereverbit kinetics instead of Km we have Kt and what we're catalyzing is movement across the membrane.

movement of material across membranes

Movement of substances across membrane without breaking it can be as simple as simple diffusion: a steroid that is lipid soluble. Other things such as ions which are polar and have a charge need help such as an ionophore which can dissolve in membrane and can also bind ion. If it binds ion before it dissolves in membrane it can carry it through. A similar process is a channel embedded in the membrane: ion channel. Similarly facilitated diffusion can let ions and water and glucose, facilitated diffusion, very selective pores in membrane. Primary active transport: something can cross into membrane only using only ATP and usually against concentration gradient. Secondary active transport: something comes in through channel along with something else. This something else was either pumped in or pumped out by ATP involving process (doesn't require ATP, but one of the substrates did require ATP).

2. Differentiate between the oxygen binding curves for myoglobin and hemoglobin

Myoglobing binding curve: y axis percent bound=theta like percent, xaxis partial pressure of oxygen in kilapascals. Compared with oxygen binding for myoglobin and hemoglobin Hemoglobin takes longer time to be saturated delivers to tissue Myoglobin has higher affinity, takes from tissue Hemoglobin can be found in several states: high-affinity, low-affinity, and transition from low- to high- affinity state (sigmoidal) PO2 in lungs in pink grab oxygen in lungs and in tissue, hemoglobin will let go.

Asparigine (Polar, uncharged R groups: S, T, C, N, Q)

N (Asn)-Amide of Asp

List some of the common and important disaccharides: Trehalose (honey, mushrooms)

Not a reducing sugar Glucose (Glc(alpha 1-2alpha)GLc) Glucose

Reduced sugar

Not all sugars have aldehydes or ketones on them.

2. Describe the naming system for fatty acids and the meaning of "omega-3" and "omega-6".

Omega always the last carbon away from carboxylic acid, always have cis double bonds. Omega 3 means theres a double bond 3 carbons from the last carbon. First double bond 6 carbons away from the last carbon is an omega 6

sugars found in the extracellular matrix

On the outside of the cell in the extracellular matrix, collagin, etc and proteoglycan=sugars and proteins. Proteoglycan aggregates are intimidating, but nothing more than proteins and repeating disaccharides. Central core-repeating disaachharide Hyaluronate has attached to it proteins which are attached via the linker proteins. Protein branches coming off repeating dissacharide core and then almost like leaves off branches we have more repeating disaccharides. Keratan sulfate and chondroitin sulfate as the repeating dissachardes coming off of these. Commonly found in connective tissuse, highly hydrated like sponges or cushions.

Oxidized sugars aka acidic sugars

Oxidize glucose C6, carboxylic acid where OH used to be-glucuronate Oxidize Glucose C1, carboxylic acid where aldehyde used to be-Gluconate which can form rings: lactone. pic of D-Gluconate & D-Glucono-delta-lactone

Deoxy sugars

Oxygen is missing. D-Ribose has an OH where Deoxy-D-Ribose has CH2.

Proline (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

P (Pro)-only non-flexable, onlgy ringed amino acid using the amine.

Antiparallel

Parallel beta sheet, still has complimentary hydrogen bonding, -119 phy +113 in psy. Still has a pleat, alpha helices flattened into sheet.

Amylopectin and glycogen (found stored in our liver)

Polymers of glucose, they have branch points are alpha1-6 occasionaly a sugar will have a linkage to other glucose besides just alpha 1-4 linkages. Amylopectin and glycogen have a very similar structure; they are both made of alpha glucose molecules and have 1,4 and 1,6 glycosidic bonds. Glycogen has more branches than amylopectin though.

4 levels of protein organization

Primary: amino acid sequence held together by covalent bonds Secondary: alpha helix or beta sheets held together by hydrogen bonds Tertiary: polypeptide folding held together by covalent and non-covalent bonding Quaternary structure: Assembly of multiple units, 2 or 4, sometimes more come together to form fully functioning protein complex

alpha-helix

Proteins form either helix or sheet 3 different types helices: collagen triple heli, left handed alpha helix (rare), most common: right-handed alpha helix Right handed Alpha helix accounts for ~25% of all amino acids found in proteins, highest percentage. Elucidated by Linus Pauling and Robert Corey We know psi angle is ~ -45-50 degrees, phi angle ~ -60 Minimizes steric hindrance and maximizes hydrogen bonds within protein. Hydrogen bonding between every forth amino acid within alpha helix, forms helix w/rise of 3.6 residues per turn, H of N and carbonyl oxygen are hydrogen bonded. R groups on alpha helix all pointed outward away from center, hole down center of helix

glycoprotein

Proteins that have a oligosaccharide attached to it- a bunch of sugars attached to it. Attached in an n link, nitrogen of this amino acid asparagine, is attached to the oligosaccharide. Sugars attached to proteins. If glycoproteins is O-linked, it's one of the serine or threonine, one of the alcohol amino acids. Proteins, such as glycoproteins which have a mano6phosphate on their surface are targeted for the lysosome. Sugar group on surface of proteins, important for cell to know where is this sugar supposed to go. All lysosome proteins are glycoproteins with mano6phosphates, proteins that don't belong in lysosome will not have this marker on it. In addition to being sorted to the lysosome, other sorting takes place inside the golgi apparatus. Addition of these sugars and other modifications takes place in the golgi apparatus. Oligosaccharides can be used for protein targeting.

Glutamine (Polar, uncharged R groups: S, T, C, N, Q)

Q (Gln)-Amide of Glu

Arginine (Positively charged R groups, Polar & Basic: K, R, H)

R (Arg)-Guanadino Side group pKR=12.48

Henderson-Hasselbalch Equation

Relates pH to the ionization of an acid or base.

Serine (Polar, uncharged R groups: S, T, C, N, Q)

S (Ser)-Alcohol group

Describe the 3-D shape change in hemoglobin that results from oxygen binding and specifically the effect this has on the heme. T & R

Shift in affinity, caused by shift in 3D state, 15 degree shift from : T state (taut) to R state (relaxed). T state low oxygen affinity, R state high oxygen affinity. Heme itself bound in center is associated with 2 amino acids: directly coordinated with Fe is proximal histidine, distal histidine not coordinated with iron, but with H that is coordinated to Fe. Distal and prximal hold onto Fe and oxygen In T state, no oxygen. Iron bound to 5 other atoms, 4 in heme and 1 in proximal histidine. Puckered In R state in a plane, pulled slightly changes state of molecule. Small move in histideine F8 will amplify change in entire protein Compare amino acid sequence myoglobin, alpha and beta of hemoglobin, significant diffferneces, but shape is still very similar. Highly conserved, identical amino acid sequences, but other than that not lined up or similar (except in polarity). histidines hold on to iron and oxygen. 15 degree shift between T & R.

explain why sickle cell hemoglobin is less water soluble than normal hemoglobin

Sickle Cell Anemia-amino acid is no longer where it's supposed to be on beta chain. Valine (neutral) instead of glutamate (negative). Valine less water soluble because it's less charged. Sickle cell form fibrous crystals that cause the cell Valine is found at Position 6 of the beta-chain on sickle cell hemoglobin Microscopic examination of blood cells: characteristic sickle shape Hemoglobin has a negative charge overall, therefore in electrophoresis gel it moves toward positive electrode, normal hemoglobin moves faster than sickle cell-not as negative Young child experiencing severe abdominal pain, swelling of hands and feet, fever, fatigue, paleness, and shortness of breath. Retina signs of deterioration and evidence of trouble seeing, yellowing of skin and eyes Lab tests: low hemoglobin 7.8g/dL (normal range 12-16) Hematocrit 23.4% (normal 41%-53) Bilirubin 2.3 mg/dL (normal .2-1)

hemoglobin S to hemoglobin A

Sickle Cell hemoglobin S-protein precipitating inside red blood cell not flexible causing it to elongate, clog arteries. Hemoglobin precipitating because of single amino acid substitution: glutamate changed to valine, less polar beta chain at position 6: hydrophobic pocket on surface, hemoglobins cluster together, elongated filaments. Common in equatorial areas. Decreases possibility of contracting malaria. Increase survival advantage. If both parents have it, 1 in 4 chance.

Explain how the sodium-potassium ATPase generates membrane potentials in cells.

Sodium potassium ATPase found in almost every cell: drives sodium out and potassium into cell. Concentration: sodium higher outside, potassium higher inside because of sodium/potassium ATPase. However, it's asymmetric: pumping 3 Na+ out for 2 K+ that come in. 3 positive charges out and 2 positive charges in: net effect- inside of cell negatively charged relative to outside of cell. Electrophysiology defines outside cell voltage of zero, potential difference across membrane makes inside -150 to -170mV. So, in review, sodium/potassium ATPase in one conformation can bind 3 Na+ ions and then it becomes phosphorylated by ATP. The phosphorylated version of this molecule opens to the other side of the membrane letting 3 sodium ions out. Also exposes 2 K+ binding sites. When they bind, it's accompanied by the dephosphorylation of the protein which then changes its conformation back to its original conformation, opening to the inside, allowing the 2 potassium ions to enter the cell. Process starts over.

glucose transporters in the human genome

Sodium/glucose symporter important secondary active transport system. All the other glucose transporters in body are all passive transport systems: equilibrate concentrations inside and outside. 12 different varieties; need to know the first 5. GLUT1 found on just about every cell. GLUT2 unique to liver, pancreas, and intestine. GLUT3 is found on neurons. GLUT4-very important-found on muscle, fat, and heart and these are the ones that are insulin sensitive transporters. GLUT5 important for transporting fructose rather than glucose (but it can still transport glucose). GLUT 4 transporters are insulin sensitive: in this system, insulin will bind to its receptor and once it binds a series of second messenger cascade events induces the movement of vesicles inside the cell to the surface of the cell. Interesting about these vesicles is that the contain the GLUT4 transporters in their membranes. When these vesicles fuse with the plasma membrane, the vesicles become part of the plasma membrane and increase the concentration of the GLUT4 transporters. Therefore, the rate at which glucose can come through membrane, Vmax increases, rate of glucose increases rate it enters the cell: via an insulin induced process. When insulin is no longer present, the vesicles spontaneously pinch off the membrane and go back to being vesicles again.

how enzymes speed up reactions

Speed up ligation reactions joining to substrates together, 10^5 increased rate just by holding 2 molecules near each other. (Restricted rotation, reaction rate increases 10^8)

sphingolipid

Spingolipids, another variation of membrane lipids. Based on a molecule called Sphingosine: tail which looks like a fatty acid, 3 more carbons which functionally are the same as the 3 carbon backbone, only in reverse, are the first 3 carbons of the sphingosine molecule and they serve as the backbone in place of glycerol. Attached to C2 is fatty acid with amide bond instead of ester. Phosphate group as in other ones an polar head group like we saw before Sphingolipid, 3 carbon backbone continuous with first tail sphingosine. Polar head groups shown in table, including sugars: glycolipids are generally based on these sphingosine molecules.

Cellulose

String of glucose linked by beta 14. We do not possess enyzmes that can break beta 14.

Amino Sugars

Sugars that have N instead of O, Galactosamine, Galactose with NH2 in position 2 Mannosamine is a mannose that has NH2 in position #2.

Threonine (Polar, uncharged R groups: S, T, C, N, Q)

T (Thr)-Alcohol group

Oxidized sugar

Take the aldehyde group and oxidize it to a carboxylic acid. Sugars that can undergo an oxidation are called reducing sugars: Used to be a test for diabetes test was urine sample + copper + base + heat brick red precipitate. Reducing sugar-copper became reduced, sugar glucose became oxidized reducing sugars in the urine were present if brick red precipitate.

List the forces that hold the 3 and 4 structures together.

Tertiary structure-protein folding, how proteins fold upon itself 1. Differentiate between fibrous and globular proteins. Myoglobin, predominately alpha helix with a few beta blends folded together into globular shape Alpha-Keratin: Structural or fibrous protein very strong, water insoluble, water insoluble side groups, strength and flexibility, forms an alpha helix right handed, coils upon itself to form coiled coil, come together to form protofilaments and then profibribl held together by cross-linked with disulfide bonds. hair, nails, wool, claws, quills, horns, hooves, skin. curly vs straight hair is placement of disulfide bonds. Restructure hair: reducing agent, curl, oxidize Permanent waving of hair

Explain why diglycerides form bilayers.

The fact that fatty acids form micelles imply that they are conical in shape. Diglycerides-general membrane lipids, they have 2 tails and are generally cylindrical in shape. As a consequence, instead of forming micelles, they will form bilayers where they are tail to tail with the polar head groups on top and bottom.

"Lateral" and "Flip-Flop" diffusion.

The reason we call it the fluid mosaic model is because it is fluid, but it's fluid in only 2 dimensions. We have lateral diffusion (depicted by red arrow) able to move anywhere laterally within bilayer (at least one half of the bilayer), however it's not allowed to flipflop to the other side of the bilayer (going from inner leaf to outer leaf or vice versa happens very slowly).

"mad-cow's disease"

The running hypothesis is that proteins assume the lowest energy conformation possible. This would imply that protein flding is entirely spontaneous. For the most part (up to 70%) this may be true. One exception to this idea is that the path to the most stable conformation is not easily achieved. As a protein folds, it doesn't go from high energy to lowest energy possible in 1 fell swoop, it goes through steps, 1 conformation to next, energy barrier, works its way down and another energy barrier, works to lowest energy possible, for most proteins lowest energy, however, some proteins have high energy barriers, may settle in. Example: prion we use in our cells as chaperone protein, if it gets corrupted in can lead to Mad Cow Disease. This prion protein is in an active confirmation on one of shoulders of higher energy, never goes to lowest energy, but if it refolds to lowest energy it's pathological and becomes a toxin. One frightening example of this possibility is the new idea of prions. These are proteins that when normal are not in the most stable conformation. If achaperone protein helps it refold into a more stable protein it looses its function. The theory is that this new more stable protein is also the chaperone that refolds the next protein. This means that if you are infected with a prion, it corrupts all of the similar proteins and then those proteins corrupt others. This makes prions an infectious toxin. They are not alive like viruses and they don't reproduce themselves but they are still very infectious. Ex. Kuru, Creutzfeldt-Jakob disease, Scrapie (in sheept) and Mad Cow Disease. causes degeneration of brain cells looks like sponge, wholes all over the place: Bovine Spogiform Encephalopathy. Prions not living, inadvertently becomes low energy confirmation, still contains some enzymatic activity to fold other prion proteins into low energy confirmation then they precipitate out in the cell, clog up cells machinery and cause cell to die

Steroids top 300

There are a large number of steroid drugs. For biochemistry, you will be required to recognize the steroid nucleus and thus be able to classify these drugs as steroid drugs. You will need to know the names and applications of these drugs.

cis-Proline & Beta Turns

There are factors that determine alpha vs. beta: especially R group. If you take a domain within the protein and look at predominance of specific amino acids, it's correlated with structure it likes to be in. Beta turn=domain breaker, change domains, don't tend to fold as well as other ones: proline and glycine most important. Nearly 1/3 of all amino acids in the Beta-turns of globular proteins are cis-PRO. The beta-turn involves 4 amino acids and makes a 180 degree turn. Proline is a domain breaker, find in beta turns: 1/3 of all amino acid in Beta turns of globular cis proteins. Beta turn involves 4 amino acids and makes a 180 degree turn.

protein renaturation

This is not true of all proteins, some proteins are permanently inactivated when they are denatured. Ribonucluesase is an enzyme that has disulfide bonds. When these bonds are reduced (broken) and the nezyme is denatured using urea it looses activity. When the urea is dialyze away and the disulfide bonds are permitted to reform, bonds are permitted to reform, the enzyme regains its activity. Ribonuclease (stabilized by disulfide bonds) add urea and mercaptoethanol it will denature, but if you remove urea and mercaptoethanol, it can fold back to its original form, very rare.

Transferases

Transferase transfer one group from another: adoMet extra methyl group it can transfer from norepinephrine to epinephrine

fatty acids

Typically 12-24 carbons long (counting the carboxylic acid carbon, but can be as short as 2 and as long as 30).

Glucuronates

Useful in helping to excrete less than water soluble molecules such as drugs and toxins including bilirubin which is the break down product of heme from hemoglobin, bilirubin is not very water soluble, we can get rid of it by conjugating it to glucuronate becomes direct bilirubin and is water soluble and can be excreted from the boy. Indirect is the non-conjugated from and is found generally associated with protein albumin within the blood. Glucuronates are commonly used to increase water solubility of target molecules to facilitate excretion from the body.

Describe ligand gated channels.

Using model of classical action potential and synapse of a nerve cell. When an action potential comes down a neuron, it causes depolarization of the cell membrane. When depolarization gets to the end of axon terminal, it not only opens the voltage gated Na+ channels at the terminal, but it's also opening calcium channels which are found at the terminal end. When calcium concentration increases inside the terminal, it induces the fusion of neurotransmitter containing vesicles from that terminal and the transmitter then gets in the synapse where it binds to ligand gated channels that open & allow ions into the cell, thus depolarizing the postsynaptic cell. Once we're in postsynaptic cell, this local depolarization caused by opening of a ligand gated channel will trip the voltage gated sodium ion channels that are next to it letting more sodium in and therefore we've induced a cascade of events that allow depolarization of the postsynaptic cell and a wave a depolarization to propagate from there.

Valine (Nonpolar, aliphatic R groups: G, A, V, L, I, P, M)

V (Val)-Branched Chain

List and describe some of the drugs and toxins that affect the above mechanisms.

Vanadate- looks just like phosphate and interferes with the P-type ATPase systems, therefore it's a P-type ATPase inhibitor.

plasmalogen

Variation of diglyceride. Membrane lipids, plasmalogen. Instead of 2 ester groups, one of them is an ether-linked alkene. Example: platelet-activating factor

Tetrodotoxin

Voltage-gated sodium channel inhibitor (Puffer fish): prevents action potential from propagating down a nerve because we're not letting sodium in via the voltage-gated sodium channels.

Tryptophan (Aromatic R groups: F, Y, W)

W (Trp)-W because it is the largest amino acid

Adding charges on proteins

We can add charges on proteins because so few have charges (terminal +1 and -1 cancel each other out).

2. Describe the hydropathy plot for a membrane protein and explain what this plot implies

We don't have good techniques to tell which proteins are embedded or cross through the membrane. Not even electron microscopy can see this. We can extract proteins out of the structure and elucidate their amino acid structure and look at the sequence and from the sequence we can figure out is it likely that this is a transmembrane protein? For this we're going to talk about the hydropathy plot and how we can read it. The hydropathy plot plots the water soluble vs. the insoluble. The bottom part of the plot is hydrophilic amino acids, which ones are water soluble? The top part of the plot plots hydrophobic amino acids, most likely to be embedded in the membrane. If we take the first part of this protein, starting with amino acid one, this is the part that is outside the membrane: hydropathy index less than 1, not likely to be in membrane. Next section which is embedded in membrane, it's mostly hydrophobic amino acids and this plot makes it very clear to predict which proteins are in the membrane and which amino acids in that protein are embedded through the membrane. Lastly you can see the portion that's out of the membrane, water soluble. We can use this to look at media receptors. There's a very important one called a Serpentine Receptor aka heptahelical receptor. It's called this because it has 7 helices which all cross the protein, snakes its way through the membrane 7 times. Transmembrane proteins must have a series of hydrophobic amino acid side chains in the regions that it crosses through the membrane.

isotonic hypertonic hypotonic

What does this mean for a cell? If it's placed in a situation where outside has different pressure than inside, we're going to have various effects. If we have a hypertonic solution (b) where the pressure outside is higher than pressure on inside, it's going to shrink. If we have hypotonic solution, cell will burst: osmotic pressure inside the cell is greater than osmotic pressure outside the cell. This has to do with the number of solute molecules inside vs. outside. The larger the number we have inside, the more pressure inside.

Define the meaning of N-terminal and C-terminal

Within a peptide, the side that has full amine left over is called the N-terminal and Side with Carboxylate intact is called C-terminal.

Tyrosine (Aromatic R groups: F, Y, W)

Y (Tyr)-has an OH group, more non-polar than polar, but most polar out of aromatics.

Describe the structure of agarose, hyaluronate, chondroitin-4-sulfate, keratin-sulfate and heparin: Hyaluronate

a glucuronic acid, glucose and acetate repeating one right after the other.

Lyase

able to break a molecule apart. Break or addition of double bond when adding or removing a functional group

In glycoproteins, the carbohydrate moiety is always attached through which amino acid residues:

asparatine, serine, or threonine

ligase

brings 2 molecules together to form one laarger molecule creates C-C, C-N, C-O, or C-S bond.

Generalized Gangliosidosis

defect in Beta Galactosidase

Gaucher's disease

defect in Glucocerebrosidas

Tay Sachs disease

defect in Hexosaminidase A

Cystine

derived and non-standard amino acids. 2 s linked together: disulfide bridge

I-Cell Disease

failure to place a mannose-6-phosphate on the lysosomal enzymes

peptidoglycan

glycans cross-linked with peptides

heme group

hemoglobin center of it is heme (not just amino acids) and iron Fe atom in center

hydrolases

increases rate of hydrolysis

Isomerases

isomerizes the molecule

Glycolipid

lipid with oligosaccharide attached

Describe the structure of agarose, hyaluronate, chondroitin-4-sulfate, keratin-sulfate and heparin: Heparin

made up of 2 derived sugar that keep repeating themselves right after another. In knockout mice that lack the enzyme for placing the sulfates at the C2 position of IdoA are born without kidneys and have severe abnormalities in the skeleton and eyes.

Describe and name the various way which material can be transported across the membranes

membranes are self sealing which allows the to: reclose after puncture, fuse with vesicles, pinch off vesicles, this self sealing process allows for vesicles, exocytosis, endocytosis, fusion, viral infection, sperm and egg fusion, and cell division. Since membranes are held together by hydrophobic forces and not covalent forces, they're not that difficult to break open. Needles can go through them. If we break a membrane, it spontaneously heels itself. It's also able to do endocytosis, exocytosis, fusion, etc.

NSAID's

non-steroidal anti-inflammatory drugs are inhibitors to eicosanoids formation. Prostaglandin-pain, thromboxane-clot formation. Aspirin blocks both pain and clot formation.

primary and secondary active transport

o Primary active transport-movement using ATP to drive it across cell: X going out of cell o Secondary active transport-S can come into cell only if X comes with it, symport. Because X is coming with concentration gradient (high concentration outside because it was pumped out earlier using ATP requiring process), symporter now called secondary active transport because X is providing energy to bring S in, but X got it's energy because it was pumped out of the cell using ATP

Oxidoreductase

oxidation or reduction: adding or removing electrons (commonly H moves as well) FADFADH2 oxygenation of succinate to fumarate.

pI (isoeletric point)

pH at which a titratable molecule has no charge, neutral.

Glycoprotein

protein with oligosaccharide attached

proteoglycan

proteins with glycans attached

Proteoglycans

similar to glycoproteins, instead of having oligosaccharides attached to protein, we have repeating disaccharides-glycans attached to the proteins. Example of an O-link proteoglycan below.

Beta sheet

specialized, phi and psi angles are larger, ex: polyalanine beta sheet: phi angle: -139, psi angle +135. A normal flat sheet would have 180, 180, a little bit of a pleat to it, like a flat sheet with pleat in it, oscillates a bit. Stabilized by complimentary hydrogen bonding. Antiparallel-1 layer of amino acids running in 1 direction, another layer antiparallel other direction, looping around and coming back again.

Eastern diamondback rattler

venom (and indian cobra) contains phospholipase As which catalyzes the hydrolysis of fatty acids at the C-2 position of glycerophospholipids. One of the prominent phospholipid breakdown product of this reaction is lysolecithin (from phosphatidylcholine) which can act as a detergent if concentrations are high enough. Venom can turn our blood cells into detergents which disintegrate: lysing of red blood cells. the pain and inflammation caused by a snake bite can be treated with certain steroids which inhibit phospholypase A2 activity. What is the basis of this treatment? Commonly the second fatty acid in phosphatidylcholine is arachidonic acid. Reason it's painful and inflamed is because very commonly the 2nd fat for example on phosphatidylcholine is arachidonic acid which is converted into prostaglandins and thromboxane's. Prostaglandins responsible for pain and inflammation.

Anomeric Pair

α-D-glucose and β-D-glucose

uniport, symport, antiport

• If we move 1 thing across the channel: uniport. • If we require 2 things coming together at the same time: symport. • Two things that go in opposite: antiport. Very common for the symporter or antiporter to also be involved in secondary active transport.

osmotic pressure

• Osmotic pressure: Isotonic solutions • PV=nRT rearranged: P=RT (n/V) • n/V=molarity (M), P=RT(M) • We can use the same formula for pressures of a liquid against a membrane: • Π=RT(osM) • Not really interested in pressure against a membrane, interested in pressures on both sides of membrane balancing each other. We're going to concern ourself with calculation of osmolarity. Osmoalrity is equal to the number of ions in solution times the concentration of ions added together with all the other ions in solution. osM=i1c1+ i2c2+etc. • In general, we find for isotonic solutions (solutions where the pressure on outside of membrane and inside of membrane is pretty close to .32osM for humans) • What is the concentration (c) of each substance? • Example: sucrose i=1, NaCl i=2, CaCl2 i=3 • Osmolarity of CaCl2 is three times higher than its molarity, osmolarity and molarity of sucrose are the same.

3 very important types of ATPases:

• Plasma Membrane type (P type): Sodium/Potassium ATPase, Hydrogen/Potassium ATPase used to pump the protons into our stomach lumen which is what the proton pumps are in the stomach. • Vesicle Membrane type: found in bringing neurotransmitters into vesicles. • Energy Production type: we just talked about these, found in the mitochondria. These are the ones that run backwards. Instead of using ATP, it synthesizes ATP