Biochem Midterm 3 (copy)

NAG

Peptidoglycan:: consists of repeating ________ and NAM attached to crosslinked tetrapeptides, giving structural stability to bacterial cell walls, gram positive= thick peptidoglycan layer that retains stain in lab, gram negative= has additional thin outer layer so gram stain not retained and only counter stain seen.

Long

________ /branched fatty acids:: fatty acids that are oxidized in the peroxisome instead of the mitochondrial matrix (dont go through B oxidation in matrix because can not be transported)

oxidative phosphorylation

H /P transporter:: symport that imports Pi and H+ into the matrix, Pi is substrate for ________, makes movement of Pi favorable when paired with diffusion of H+ down its concentration gradient.

Glycosidic bonds

can be alpha or beta, occurs in glucose between the 1 and 4 carbons

Naming disaccharides

describe glycosidic bond by noting anomer along which carbons are linked, e.g

Starch

alpha(1-4) or alpha(1-6) linkage, used to store D-glucose in plants; amylose or amylopectin

Amylose

unbranched starch with alpha(1-4) linkages

Amylopectin

branched starch with alpha(1-4) and alpha(1-6) branches every 30 residues, produces nonreducing ends for enzymes to work at (no free anomeric carbon at branches), no need to mobilize glucose quickly in plants so fewer branch points

Glycogen

like amylopectin but branch points every 8-12 residues, stored in liver, more frequent branch points so easier mobilization of glucose

Cellulose

beta(1-4) linkage with second sugar flipped to line up the OH groups to H-bond with teh neighboring strand (provides stability for plant cell walls)

Chitin

beta(1-4) linkage with N-acetyl glucosamine that participates in h-bonding for increased fibril strength in exoskeletons

Glycosaminoglycan

linked to structural proteins of heteropolysaccharides of repeating uronic acid and hexosamine residues, found in extracellular space, make up connective tissue, have polar groups that attract H2O to help lubricate the tissue, negative charges repel each other upon compression for shock absorption

Peptidoglycan

consists of repeating NAG and NAM attached to crosslinked tetrapeptides, giving structural stability to bacterial cell walls, gram positive = thick peptidoglycan layer that retains stain in lab, gram negative = has additional thin outer layer so gram stain not retained and only counter stain seen

Glycoproteins

oligosaccharides linked to proteins that facilitate enzyme attachment, modifications, cell identifiers/attachment sites, o-linked = attached to Ser or Thr side chain in golgi n-linked = attached to Asn side chain in ER then finished in golgi

ABO blood type

O-linked oligosaccharide on cell surface , base of galactose+NAG+fucose serves as antigen structure for recognizing immunocompatibility, O is the universal donor since no additional monosaccharides, AB has 2 genes for glycosyltransferases so universal recipient, n-acetylgalactosamine added in A, no antibodies in AB to recognize the antigens

Anabolism

uses energy released by catabolism to synthesize new molecules e.g

Catabolism

releases energy by breaking down complex molecules, energy is then stored in cofactors for ATP for use in anabolism

Fuel priority

glucose/carbs are used as energy first, then lipids, then proteins as last resort

Lysosome

organelle with degradative enzymes that break down membrane and extracellular proteins due to being abnormal or because their concentration must be regulated (constant replacement)

Proteasome

multisubunit protease that targets intracellular proteins for degradation, B barrel structure, entry regulated by ubiquitin tag, ubiquitin ligase (looks for exposed hydrophobic core of protein) transfers ubiquitin to Lys residue of target protein on surface → at least 4-unit polyubiquitin because ubiquitin itself has exposed Lys to be recognized by proteasome cap → proteasome uses ATP to unfold the protein while filtering it through, then degrades it in inner beta chamber

B1(thiamine)

cofactor for pyruvate hydrogenase complex and alpha-ketoglutarate dehydrogenase, deficiency results in beriberi because no ATP production → lethargy and lower extremity blood pooling

Vitamin C (ascorbic acid)

cofactor for enzyme that hydroxylates proline in collagen (an oxidoreductase), deficiency causes unstable collagen (connective tissue) resulting in scurvy

Vitamin B3(niacin)

precursor for nicotinamides like NADH used to conserve energy, deficiency causes pellagra (diarrhea, dermatitis, dementia, death)

ubiquinone(Q)

lipid soluble cofactor that can carry 1 or 2 electrons, mobile

NAD/NADH

water soluble cofactor that can carry 2 electrons, mobile (nicotinamides)

NADP/NADPH

water soluble cofactor with phosphate that can carry 2 electrons, mobile

Flavins

FMN/FMNH2 or FAD/FADH2 derived from riboflavin (vitamin B2), prosthetic groups that can accept 1 or 2 electrons, hydrophobic

Biochemical standard state

has o and ‘ above symbol, 298K, [H+] = 1.0x10^-7, [H2O] = 55.5M, 1 atm

Chemical standard state

only o above symbol, 298K, 1M for everything, 1 atm

Mass action ratio

ratio of concentrations of products over reactants (usually embedded in the ln term)

Energy currency

store energy in ATP (alpha = closest, beta, gamma = farthest phosphate), thioesters(hydrolysis of sulfhydryl bond like in acetyl-CoA releases energy) *thioesters have less resonance than O esters because S is larger than O

Pathway regulation

control flux through pathway by adjusting rate of a reaction with a large free energy change (the irreversible steps) e.g

Glycolysis

convert glucose to pyruvate, which can then go through the citric acid cycle and the electron transport chain to yield free energy, many steps so cell can recover energy in smaller more manageable amounts, no O2 required, produces 2 ATP, 2NADH, and 2 pyruvate per glucose molecule (1st half requires 2 ATP per glucose, 2nd half yields 4 ATP per glucose), occurs in cytosol

Glycolysis intermediates

glucose→ glucose-6-phosphate(G6P) → fructose-6-phosphate → fructose-1-6-biphosphate → GAP and dihydroxyacetone phosphate → 2GAP → 2 1,3-biphosphoglycerate + 2NADH → 3-phosphoglycerate + 2ATP → 2 2-phosphoglycerate → 2 phosphoenolpyruvate → 2 pyruvate + 2 ATP

Glycolysis enzymes

hexokinase → phosphoglucose isomerase → phosphofructokinase-1 → aldolase → triose phosphate isomerase → glyceraldehyde-3-phosphate dehydrogenase (GAPD) → phosphoglycerate kinase → phosphoglycerate mutase → enolase → pyruvate kinase

Hexokinase

phosphorylates glucose, which prevents it from leaving cell and reducing intracellular [glucose] in muscle cell compared to blood, favors glucose import with gradient, phosphate prevents GLUT from binding glucose

Enzyme mechanism

determined through alanine scanning (replace active site residue with alanine to see if reaction still occurs), transition state analogs (will bind better to active site and reduce product formed), radiolabels (show how carbons rearrange from reactant to product), iodoacetate (inhibitor of cysteine peptidases like GAPD)

Lactate

pyruvate is reduced to lactate by pyruvate dehydrogenase to reoxidize NADH to NAD+ (rapid consumption of NAD+ during exercise at GAPD step, occurs under anaerobic conditions

Ethanol

produced via fermentation (anaerobic in yeast) in which pyruvate decarboxylase removes carboxylate (Co2) to produce acetaldehyde, then alcohol dehydrogenase converts it to while using NADH

Gluconeogenesis

convert pyruvate into glucose, uses same enzymes as glycolysis except at steps 1,3, and 10

Gluconeogenesis enzymes

glucose-6-phosphatase instead of hexokinase, fructose biphosphatase instead of phosphofructokinase-1, pyruvate carboxylase (consumes ATP) and phosphoenolpyruvate carboxylase (consumes GTP) instead of pyruvate kinase

Gluconeogenesis regulation

occurs at fructose biphosphatase step (step 3), inhibited by fructose-2,6-biphosphate and allosteric activator of PFK-1 (ensures opposing pathways dont occur simultaneously) (produced by PFK-2)

Glycogen synthesis

phosphoglucomutase converts G6P to G1P → G1P activated by UTP to form UDP-glucose + PPi (PPi hydrolyzed to power rxn) → glycogen synthase links alpha-1-4 glucose units and UDP functions as leaving group

Glycogen branching enzyme

moves 7 residues from main chain to form new branch

Glycogen phosphorylase

enzyme that uses phosphorolysis to break alpha-1,4 and produce G1P monomers

Debranching enzyme

moves three residues to main chain and then cleaves alpha-1,6 branch point

Warburg effect

cancer cells use glycolysis much more than other cells so treat cancer by inhibiting glycolytic enzymes

Pyruvate dehydrogenase

links glycolysis to citric acid cycle by converting pyruvate to acetyl-CoA, contains E1, E2, and E3; has substrate channeling so easier to regulate enzymes together with E2 lipoamide linker with Lys that swings between active sites, minimize side reactions; pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH

E1

decarboxylation of pyruvate and transfer of acetyl group to lipoamide, intermediate stabilized by ring structure of thiamine pyrophosphate cofactor

E2

transfer of acetyl group to CoA → acetyl-CoA

E3

dihydrolipoamide is reoxidized using NAD+ and FAD to restore the enzyme

Citric acid cycle

converts 2C acetyl groups to CO2 (final step of fuel oxidation), takes place in cytosol of prokaryotes and mitochondria of eukaryotes, cyclical; acetyl-CoA + GDP + Pi + 3NAD+ + Q + 2H2O → 2CO2 + CoA + GTP + 3NADH + QH2; steps 1, 3, and 4 are irreversible, * substrate level phosphorylation

Aconitase

stereospecific enzyme because citrate is prochiral, so hydroxyl group is always moved to C originating from oxaloacetate and not from acetyl-CoA (prochiral = can become chiral by moving group), carbons lost as CO2 originate in oxaloacetate

Malate dehydrogenase

step 8 of citric acid cycle that has positive deltaG, so pulled forward by favorable step 1 (citrate synthase)

Anaplerotic

reactions that replenish citric acid cycle intermediates

Cataplerotic

reactions that consume citric acid cycle intermediates

Glyoxylate pathway

pathway used by plants to convert acetyl-CoA into glucose, high demand for glucose cause them to convert fats to acetyl-CoA then get net synthesis of oxaloacetate, takes isocitrate straight to succinate (preserves carbons), generate glyoxylate with isocitrate lyase then malate synthase → malate → oxaloacetate → gluconeogenesis; 2 acetyl-CoA + 2NAD+ + Q → oxaloacetate + 2CoA + QH2 + 2NADH

Mitochondria

has a porous due to porins outer membrane and inner membrane that encloses the mitochondrial matrix with the intermembrane space composition same as cytosol

ATP/ADP transporter

antiport that exports ATP from matrix and imports ADP from intermembrane space, driven by inner membrane potential

H/P transporter

symport that imports Pi and H+ into the matrix, Pi is substrate for oxidative phosphorylation, makes movement of Pi favorable when paired with diffusion of H+ down its concentration gradient

Malate/aspartate shuttle

NAD+ cannot get across inner membrane, so oxaloacetate in cytosol converted to malate in cytosol and transported across to matrix, where it is converted to oxaloacetate then into aspartate, which is transported across to cytosol

Complex I (NADH dehydrogenase)

NADH binds matrix binding site and is oxidized, 2 electrons passed one at a time through FMN (2 electrons) then iron-sulfur clusters prosthetics to ubiquinone → ubiquinol, which can move through the lipid bilayer when fully reduced

Complex II (succinate dehydrogenase)

reduces ubiquinone to ubiquinol with FADH2, embedded in inner membrane and augments ubiquinol creation after complex I

Complex III (cytochrome bc)

receives 2 electrons from QH2 to ultimately reduce cytochrome c (mobile 1 electron carrier, peripheral, has heme prosthetic group with a,b,c heme side groups), 4H+ are translocated per 2 electrons

Complex IV (cytochrome c oxidase)

2 cytochrome c each donate 1 electron to this complex to ultimately reduce O2 to H2O, transfers 2 H+ to the intermembrane space per 2 electrons

Chemiosmotic model

combination of H+ gradient (matrix is alkaline) and electrical gradient with negative charge on matrix side favors movement of H+ into the matrix, which powers ATP synthase (complex V)

Complex V (ATP synthase)

F1 (soluble with 3 alpha and 3 beta subunits where each beta has ATPase activity) connects with gamma subunit to F0 (membrane spanning portion with alpha subunit where H+ enters and exits + c ring), c ring rotates past stationary alpha, causing gamma to rotate in 120 degree jumps → jumps between loose, tight, and open beta conformations, 3 ATP synthesized for every full c ring rotation

Loose

beta conformation of ATP synthase in which ADP + Pi bind

Tight

beta conformation of ATP synthase in which ADP + Pi condense to form ATP

Open

beta conformation of ATP synthase in which ATP is released

Uncoupling proteins

moves H+ down its concentration gradient so no ATP made (no longer functional ATPase), increases electron transport because trying to reestablish gradient by ETC, generates heat e.g

Cyanide

blocks electron transport through complex IV, prevents formation of H+ gradient because cytochrome c cannot be oxidized/regenerated, so nothing to accept electrons at complex III, so now QH2 cannot be oxidized, so nothing to accept electrons at complex I

Venturicidin and oligomycin

blocks H+ channels of ATP synthase so H+ gradient gets too steep

Chloroplast

site of photosynthesis, has inner membrane that surrounds the stroma, which contains flattened vesicles called thylakoids that have thylakoid membranes that contain thylakoid lumen = site of light-harvesting complexes, ETC, and ATP synthase; lumen has lower pH

Pigment

chlorophyll and carotenoid, absorb wavelengths depending on bound protein environment, shorter wavelength = blue/violet

Energy loss

electrons can undergo by losing the energy as heat, giving off a photon (fluorescence), exciton transfer (transfer energy to nearby pigment, distance-dependent e.g

Reaction center

protein with special chlorophyll pair that has lower excited state energy than the surrounding antenna chlorophyll (low reducing potential), surrounded by antenna chlorophyll that pass excited electron through exciton transfer to RC; reduced state has low reduction potential and oxidized state has high reduction potential

cytochrome b6f

receives 2 electrons from PQBH2, which transfers the electrons to plastocyanin (mobile 1 electron carrier on peripheral), similar to complex III, transfers 2 H+ per electron to lumen

photosystem I

P700+ accepts electron from plastocyanin → P700, which gets excited to P700* by photon, gives up electron to eventually ferredoxin (mobile peripheral single electron carrier that can do cyclic or non-cyclic)

Linear electron flow

ferredoxin reduces NADP+ to NADPH with 2 electrons (need 2 ferredoxin)

Cyclic electron flow

electrons from photo I return to cytochrome b6f → electrons transferred to plastocyanin to reduce photooxidized P700+ while plastoquinol cycles between the 2 plastoquinol binding sites (heightens H+ gradient)

Z-scheme

4 photons are absorbed at both photo I and photo II (8 total), P680 → P680* → plastoquinol → cytochrome b6f → plastocyanin → P700+ → P700 → P700 excited → ferredoxin → NADPH for linear or cytochrome b6f for cyclic

CF1-CF0 ATP synthase

driven by much larger pH gradient since thylakoid membrane is slightly permeable to ions, so need larger pH gradient to compensate for lack of charge gradient, thylakoid membrane has larger [H+] = 2-3 pH difference

Rubisco

used for carbon fixation in dark rxns (calvin cycle) to 3PG (converted to GAP later with ATP and NADPH), activated by higher stromal pH generated during the light reactions, otherwise inactive to conserve ATP and NADPH

Calvin cycle

3CO2 + 9ATP + 6NADPH → GAP + 9ADP + 8Pi + 6NADP+; * for every 6 GAP produced, one is removed to serve as a precursor for different biomolecules, the other 5 GAPs eventually form 3 5-C ribulose sugars (RuBP is substrate for Rubisco)

Photorespiration

under higher temps or greater pO2/pCO2, O2 competes with Co2 at Rubiscos active site, forming 2 2-phosphoglycolates and 1 3-phosphoglycerate, 2 2-phosphoglycolates converted to 3PG at expense of ATP and NADPH and loss of CO2 (allows use of excess free energy for carbon fixation when low in CO2)

C4 plants

concentrate CO2 in bundle sheath cells that express Calvin cycle enzymes surrounded by mesophyll cells to limit O2 entry into bundle sheath cells, mesophyll cells fix Co2 to make oxaloacetate and malate, malate transported to bundle sheath to provide CO2 for Calvin cycle, use 2 more ATP to fix each CO2 but can outcompete C3 plants in hot conditions by limiting photorespiration (malate converted to pyruvate in bundle sheath, producing CO2)

Lipid digestion

bile salts emulsify dietary fats in small intestine to form micelles, intestinal lipases degrade triacylglycerols, fatty acids and other breakdown products are taken up by intetinal mucosa and converted into triacylglycerols, which are incorporated with cholesterol and apolipoproteins into chylomicrons → chylomicrons move to tissues → lipoprotein lipase activated by apoC-II in capillary converts triacylglycerols to fatty acids and glycerol → fatty acids enter cells → fatty acids are oxidized or reesterfied for storage

Low-density lipoproteins (LDL)

transport cholesterol to tissues, associated with increased risk for atherosclerosis, highest cholesterol, lower triacyl (2nd lowest), 2nd highest protein content

High density lipoproteins (HDL)

transport excess cholesterol back to liver, decreased risk of atherosclerosis, highest protein, lowest triacyl, lower cholesterol

Very low density lipoproteins (VLDL)

transport triacylglycerols from liver to tissue, lowest protein content, lowest cholesterol, highest triacylglycerol

Intermediate density lipoproteins (IDL)

form as VLDLs lose triacylglycerols, 2nd highest cholesterol, intermediate level of protein and triacyl (lower protein than LDL, higher triacyl than LDL)

Lipoprotein

hydrophobic core of triacylglycerols and cholesteryl esters surrounded by proteins and amphipathic lipids e.g

Lipid activation

lipases split triacylglycerols into 3 acyl groups and glycerol, activated into acyl-CoA at expense of 2ATP, then imported to matrix by carnitine transporter

B-oxidation

one round yields 1 acetyl-CoA (removes 2 carbons from the acyl chain), but last round yields 2

Carnitine transporter

located in inner mitochondrial matrix, transports acyl-carnitine into matrix and transports carnitine out of matrix into cytosol, acyl is esterified to carnitine

Long/branched fatty acids

fatty acids that are oxidized in the peroxisome instead of the mitochondrial matrix (dont go through B oxidation in matrix because cannot be transported)

Citrate transporter

removes one acetyl-CoA from the matrix and produces one acetyl-CoA in the cytosol by combining it with oxaloacetate to form citrate

Elongase

enzyme that extends the length of fatty acids

Desaturase

enzyme that introduces double bonds to fatty acids