FINAL EXAM Biochem Flashcards

Question

Classify thymine, uracil, adenine, and guanine as pruines or pyrimidines

Answer 1

thymine - pyrimidine adenine- purine uracil - pyrimidine guanine- purine

Answer 2

NB's : A, T, U,G,C nucleoside break down: adenine + ribose sugar --> adenosine, adenine + deoxyribose sugar --> deoxyriboadenosine , guanine + ribose sugar --> guanosine, cytosine + ribose sugar --> cytidine , uracil + ribose sugar --> uridine, thymine + ribose sugar --> thymidine Nucleoside is a nitrogenous base (ie: adenine) attached to a ribose sugar. Nucleotide; a nuceloside with on to three phosphates attached. A phosphodiester bond links the 3' carbon of (deoxy) ribose to the 5' carbon of the next nucleotide's (deoxy)ribose.

Answer 3

DNA: deoxyribonucleic acid , double stranded RNA: ribonucleic acid, single stranded

Answer 4

DNA: 3 and 2 bps ; Chargffs rules: In doubled stranded DNA: the % A = % T and the %G = %C. RNA: 2 bps only

Answer 5

DNA : double helix that is 3 to 5 A ( angstromes) long., the two DNA strands are antiparallel and the resulting helix is right- handed. Contains A, B and z forms; contains major and minor grooves. DNA strands may be separated (denuatured) by heating. ( separation of strands by breaking weak forces holding them together.

Answer 6

DNA duplex separation heating ( separation of stands by breaking weak forces holding them together) The melting temp of DNA is sequence and length dependent.

Answer 7

DNA denaturation occurs when UV light absrobance due to hyperchromatic effect. The more UV absorbance, the more DNA is denatured

Answer 8

DNA stability and stacking length; The melting temperature of DNA is sequence and length dependent GC base pairs contribute more to base stacking interactions than AT base pairs.

Answer 9

Central dogma: DNA is replicated --> transcription --> RNA --> translation --> protein. Codons are three nucleotide sequences that specify an amino acid or stop translation. The codon sequence, in a particular reading frame, corresponds to the polypeptide sequence.

Answer 10

Normal hemoglobin b gene, Hemoglobin b protein, Normal hemoglobin b gene, hemoglobin protein. Sickel cell anemia is a genetic disease arising from an A to T point mutation in the DNA that alters the amino acid sequence and properties of the translated protein.

Answer 11

20 amino acids: Hydrophobic amino acids: Alanine (Ala, A); Valine (Val,V); Phenylananine (Phe, F); Tryptophan (Trp, W); Leucine (Leu, L); Isoleucine (IIe, I); Methionine (Met, M). Polar amino acids: Serine (Ser, S); Threonine (Thr, T); Tyrsoine (Tyr, Y); Cysteine (Cys, C); Asparagine (Asn, N); Glutamine (Gln, Q); Histidine (His, H); Glycine (Gly, G); Charged amino acids: Asparatae (Asp ,D) ; Glutamate (Glu, E); Lysine (Lys, K); Arginine(Arg, R).

Answer 12

L : D : Use in proteins:

Answer 13

Hydrophobicity of an amino acid: the hydrophobic effect is the driving force for protein folding and results in the burial of most hydrophobic resides in the interior of proteins. Polar amino acids: polar residues often reside on the surface of proteins or hydrogen-bonded in the interior. Charged resides tend to reside on the surface of a protein or as an ion-pair (salt-bridge) in the interior.

Answer 14

isoelectric point: the pH at which the molecule has no net charge, if the solution pH is above the pI, then the molecule will be negatively charged, if the solution pH is below the pI, then the molecule will be postively charged.

Answer 15

polypeptide bonds consist of :

Answer 16

N-term: amino terminus C-term: carboxyl terminus Peptides are synthesized from the amino terminus (N-term) to the carboxy terminus (C-term) and sequences are usually written in that direction. Within a polypeptide, only the N-term, C-term, and certain amino acid side chains are ionizable. ex: His, Glu, Asp, Cys ( C-term). Tyr, Lys, Arg (N-term)

Answer 17

N-Ca (phi) & Ca-C(W) : bonds that may rotate to angles to avoid steric clashes Ca-C(W) : peptide bond that has a partial double-bond character and does not rotate. sigma bonds can only twist to a few angles avoiding steric clash.

Answer 18

disulfide bonds and cross links: disulfide bonds may form between nearby Cys side chains, either within a polypeptide or btwn two polypeptide, in an oxidizing environment. (outside the cytosol).

Answer 19

Types of Chromatography: IEC : uses a stationary phase containing charged groups to bind proteins of opposite charge. Contains beads: DEAE and CM ( Cation exachange column) , buffer = nonstationary, moves through, separates based on affinity of charge and stationary = affinity for charge of beads , non sationary = low affinity --> move with buffer solution off column. A column with postively charged resin, ex DAEA (anion exchange column), will bind negatively charged proteins, while postively charged proteins elute first. tightly bound proteins can be eluteed by increasing salt concentration or by changing the pH of the buffer alter the charge of the bound proteins , Gel Purification: size exclusion chromatorgraphy, SEC uses a stationary phase with small pores and channels in the beads that separate proteins based on size. Columns have a fractioonation range for separation. eg: 10-150 kDa, proteins larger than this range are excluded, from the pores and channels, and elute together at the void volume ( the volume of buffer, surrounding the column beads, that must be displaced by buffer running over the column). Proteins within the fractionation rage are separated from one another as they diffuse into different numbers of pores and channels depending on the size of the protein. Proteins smaller than this range elute together at the total pore volume (they can diffuse into all pores and channels). Affinity chromatography: takes advantage of the natural bininding properties of a protein (or of an engineered tag that extends the N or C term of the protein of interest. A protein with a His-tag ( 6 consecutive histadine residues) will specifically bind Ni2+-resin (this is not an ion exchange effect). SDS-PAGE: Ususally proteins are boiled in SDS before loading into well. SDS is a detergent that disrupts protein folding (removing shapre effects when migrating though the gel). , SDS also imparts a uniform negative charge to the protein (masking any intristic protein charge), the acrylamide polymer forms a tangled network that slows down proteins moving through the gel. Smaller proteind migrate through the gel faster than large proteins.

Answer 20

SDS-PAGE Fxns : Ususally proteins are boiled in SDS before loading into well. SDS is a detergent that disrupts protein folding (removing shapre effects when migrating though the gel). , SDS also imparts a uniform negative charge to the protein (masking any intristic protein charge), the acrylamide polymer forms a tangled network that slows down proteins moving through the gel. Smaller proteind migrate through the gel faster than large proteins.

Answer 21

Primary: Sequence of amino acids Secondary: localized conformation of polypeptide backbone Tertiary: 3 D struct of an entire polypeptide, including all its side chains Quatrinary: the spatial arrangment of polypeptide chains in a protein with multiple subunits.

Answer 22

alpha helicies: 3.6 residies/turns, nth carboonyl oxygen H-bonds to n+4th NH. Beta sheets: hydrogen bonding btwn the backbones of multiple beta-stands forms a stable beta-sheet. the side chains and carbonyls of consecutive resides alternate directions.

Answer 23

Domains: regions of a polypeptide that fold independently (ie: have their own hydrophobic core and have their own functions

Answer 24

Primary stabilizing structs: Hydrophobic resides on surface, interior charged resides tend to form ion pairs, major contributor = hydrophobic effect. Neighboring cysteines can form disulfide bonds within polypeptides or btwn separate polypeptides. Proteins that are misfolded may be targeted for degradation or refolded Secondary stabilizing structs side chains and carbonyls of consecutive residues alternate directions Tertiary stabilizing structs hydrophobic effect Quat stabilizing structs hydrophilic resides

Answer 25

misfoling results in diseases: Certain proteins can adopt a stable misfold conformation with higher beta sheets content. these misfolds proteins may aggregate into amyloid fibers with a beta sheet core. ex: alzhiemers disease and piron diseases such as scrapie and Creutzfeld-Jakob disease. prion diseases are caused by infections proteins. the misfolded protein (PrPsc) induced natively folded protein (PrPc) to adopt the misfolded conformations that are prone to aggregation

Answer 26

myoglobin: protein that carries oxygen in muscles; has a similar secondsary and tertiary structure to Hb alpha and Hb beta, but has different sequence hemoglobin: protein that carries oxygen in the blood, heterotetramer = 4 subunits that are not identical fxn of heme: a prostethic oxygen binding group, distal histadine prevents superoxide interactions, 6th oxygen interacts w/ ion -> interacts with another His, proximal His directly interacts w/ iron.

Answer 27

coopertivity: binding at one site influences binding at the other sites, usually postive, binding at one site aids or helps binding at another site. fractional saturation of venus and arterial pressure. importance of hemoglobin being cooperative: O2 binding at one subunit increases the affinity for O2 at the remaining subunits. The sigmoidal binding curve is characteristic of cooperative binding. myoglobin -> high affinity for oxygen and would have a hard time letting go. hemoglobic -> b/c of its high fractional context and lower affinity for oxygen, and can deliver higher amounts of oxygen,

Answer 28

R-state: has a high affinity for O2 and is the conformation favored by oxygenated hemoglobin, Hb behavior is modeled well by considering Hb as existing in equilibrium btwn all four subunits in the T-state and all four subunits in teh R-state. W/o O2, the equilibrium heavily favors T-state whearas at high pO2 the equilibrium heavily favors R-state hemoglobin. T-state: low affinity for O2 and is the conformation favored by deoxygenated hemoglobin, 35 residues are in contract at each of the a1b1 and a2b2 interfaces, while 15 residues are in contact at each of the a1b1 and a2b2 interfaces.

Answer 29

oxygen binding promotes the T state: in the absence of O2, T-state is favored due to the formation of salt bridges involving the C-term resides of the alpha and beta subunits., ionic interactions stabilize + and - state struct making it more favorable.

Answer 30

hemoglobin = no intermediate states b/c intermediate conformations btwn R-state and T-state are disfavored due to steric clashes. Formation of the Fe-O2 bond is very favorable and pulls the Fe2+ into the plane of the porphyrin ring (shortening the Fe-N bonds).

Answer 31

chemical equillibriums: Co2 + H2O = HCO3- + H+ ; Hb*H+ + O2 = Hb*O2+H+ ; N-term = 7.4; protonated N term --> +1 charge => allows participation ionic interactions -> stabilize T-state. Bohr effect: Hb binding H+ favors unloading O2 to the tissue that needs O2 the most. Muscle metabolism causes a pH drop in surrounding tissues, increasing [ H+] protonates the a-subunit N-term and the b-subunit His 146 side chain, favor the salt-bridge formation that stabilizes T state.

Answer 32

BPG affects hemoglobin: BPG binds and stabilizes the T-state of Hb. BPG binds in the central cavity of T-state Hb and contributes to further salt-bridge formation; w/o BPG, Hb would bind O2 too tightly to unload a significant fraction to the tissues. Physio importance of BPG at high alts: BPG increases to adapt to hight altitudes (the lower aterial pO2 at altitude is compensated by a lower fractional saturation at the venous pO2. Fetal Hb has a2y2 subunits. Fetal hemoglobin has stonger affinity for O2 relative to adult Hb binds BPG poorly, favors movement of O2 across the placental mbn. ( left shift in curve for affinity)

Answer 33

consequences of Hb mutation , rbc: sickle cell anemia is a genetic disease arising from a Glu6Val mutation on Hb beta, Sickeled cell may block small blood vessles, limiting O2 delivery and causing pain, organ damage, and destruction of red blood cells. Sickling is triggered bu factors that promote T state Hb (eg. high altitude and dehydration). A hydriophobic pocket is exposed on the b-subunit when Hb is in teh T-state. The pocket binds the exposed Val in neighboring Hb. Aggregation of Hb produces long, ridgid strands of Hb inside the red blood cells, these strands push on the cell mbn, deforming the cell into the sickle shape. homozygotes with mutation: heterozygotes with mutation:

Answer 34

Gen struct: Microfilaments, Intermediate filaments - intermediate diameter, microtubules - widest diameter, widely distributed. Actin monomers ('globular actin' or 'G-actin' polymerized to form 'filamentous actin' or 'F-actin' microfilaments Fxns: microfilaments help determine cell shape, allow some cells to move, and are part of the contractile apparatus in mucles. Actin = structure protein that can divide and form microfilaments. Mysoin: conventional myosin (myosin II) is a motor protein that helps contract actin filaments in muscles. dimer = two subunits, a helix, two alpha helixes wrapped around eachother.

Answer 35

Steps of myosin movement: a myosin head bound to an actin subunit of the thin filament, ATP binding alters the conformation of the myosin head so taht it releases actin. --> rapid hydolysis of ATP to ADP + Pi triggers a conformational change that rotates the myosin lever and increases the affinity of myosin for actin --> Myosin binds to an actin subunit farterh along the thin filament --> Binding to actin causes Pi and then ADP to be released. AS the rxn products exit, the myosin lever returns to its original postion, this causes thin filaments to move relative to the thick filaments (the power stroke). --> ATP replaces the lost ADP to repeat the rxn cycle. physio importance: Filaments associated:

Answer 36

struct of keratin: Two long a helices wrapped around one another to form a coiled coil. Each helix has a repeating seven amino acid sequence where the 1st and 4th residues of each repeat are hydrophobic and form the interface btwn helices Keratin is a structural protein that assembles into intermediate filaments bundles and is present in hair, wool, nails, claws, quills, hooves, and the outer layer of skin. fxn of keratin: aa sequence related to fxn: Diaulfide bonds btwn dimers help strengthen keratin microfibrils

Answer 37

Activation energy of rxn: Ea or Delta G++ = the energy to go from the ground state to teh transition state., barrier can delay rxn from occuring due to high activation energy. effects of enzymes on thermodynamics: the sign of Delta G rxn (not Delta G ++) determines whether a process is spontaneous or not, the magnitude of delta G++ determines the rate of the rxn. Catalysts increased the rate of rxn by lowering delta G++ ( delta D rxn is unchanged). kinetics of the forward and reverse rxns

Answer 38

substrate: Substrate binding occurs in a pocket or cleft on the surface of the enzyme. the substrate is held in place by electrostatic, hydrogen bonding, Van der Waals, and hydrophobic interactions. binding pocket is not fully formed until the protein is more flexible --> strains towards the stransition state. active site: name usually descibes fxn, enzyme commision (EC) number assigns unique four level number eg (EC) to classify a rxn, we must consider both the forward and reverse direction, classification gepends only on the net rxn (not the mechanism). Forces allowing enzyme substrate binding: enzymes speeds up both forward and reverse rxns.

Answer 39

oxireductase: either have a redox cofactor present or disulfide formation ex: NAD+/NADH, NADP+/NADPH, FAD/FADH2, FMN/FMHN2, Q/QH2 transferase: swap fxnal groups btwn subrates hydrolase: use water to break a bond or condense to eliminate water lyase: break bonds w/o the use of redox activity or water and produce an extra double bond (or ring) in the products isomerase: rearrange fxnal goups in a substrate, but keep the chemical formula the same ligase: use ATP energy to connect two other substrates.

Answer 40

cofactor: a small organic molecule or metal ion that is required for enzymatic activity coenzyme: are organic cofactors cosubstrate: are coenzymes that tansiently assoicate woth then enzyme prosthetic group: are coenzymes that are tightly associated with the enzyme Apoenzyme: an enzyme w/o its required cofacotrs (inactive) holoenzyme: an enzyme w/ its required cofactors (active)

Answer 41

Acid-base: H+ is transferred btwn an enzyme and the substrate ; RNASE A is an example of an acid-base catalysis with histadine residues transferring H+ with the RNA substrate covalent catalysis: a stable intermediate is formed when the enzyme covalenty binds to the substrate. Mech: acetoacetate decarboxylation --> nonenzymatic path (CO2 product) --> enoate formation --> H+ addition --> acetone formation. Acetoacetate with RNH2 in and OH- out creates a schiff base formation (imine) CO2 product --> rearragment intramolecular reaction --> H+ in --> imine --> OH in and RNH2 out --> acetone metal ions: can stabilize negative charges that form in the transition state. eg. decarboxylation of dimethyloxaloacetate, can sheild charges that might repel the attacking group, can promote nucleophilic attacks through ionization of water., can participate in redox reactions. proximity and orientation effects: Reactants must come (promxinity) with the proper spatial relationship (orientation) for the reaction to occur transition state stabilization: The more tightlly an enzyme binds to the transition state, relative to the substrate, the greater the rate acceleration of the catalyzed rxn.

Answer 42

pH dependency: RNase A is an ex of acid-base catalysis with histidine residues trasnferring H+ with the RNA substrate; A stable intemediate is formed when the enzyme covalently binds to the substrate

Answer 43

lock and key fit models: specificty pocket only binds certain amino acids, positioning the peptide bond for cleavage by catalytic triad.

Answer 44

Catalytic triad: Asp, His, Ser fxns of residues in catalysis: breaksdown proteins, Prancreatic proteases, subtilisin, catalytic triad

Answer 45

pocket specificity of serine proteases and peptide bonds:

Answer 46

convergent evolution: divergent evolution: protein relations based on strucutre :

Answer 47

serine proteases evolutionary relations:

Answer 48

goals of chymotrypsin rxn: Interaction of Ser and His generates a strongly nucleophilix alkoxide ion on serine; the ion attaccks the peptide carbonyl group, forming a tetrahedral acyl-enzyme. This accompanied by formation of a short lived negative charge on the carbonyl oxygen of the substate, which is stabilized by hyrdrogen bonding in the oxyanion hole.

Answer 49

zygomens: are secreted into the small intestine and cleaved by other proteases so that they acquire a conformation where the specificity pocket and oxyanion hole are available for catalysis, fxns : inhibitors in the blood stream and pancreas bind the proteases active site to inhibit any proteases that are active outside the small intestines; synthesized as inactive precursors

Answer 50

velocity depends on substrate concentration: the hyperbolic shape of the rate dependence on [S] is due to the formation of an enzyme-substrate complex.

Answer 51

reaction velocity: (v) = d[P]/dt = -d[S]/dt rate of reaction: (v) = d[P]/dt = -d[S]/dt Michaelis constant (KM): k-1+k2/k1, the substrate concentration that gives Vo=Vmax/2 turnover number (kcat): Kcat/Km is the specificity constant ( a measure of catalytic efficiency) specificity constant (catalytic efficiency): maximal velocity (Vmax): Vmax=k2[E]t where k2=kcat =turnover and [E] is the total enzyme concentration; k2(or kcat) represents the number of catalytic cycles that each active site undergoes per unit time. substrate: Michaelis-Menten complex: hyperbolic relationship velocity as a fxn of substrate concentration product:

Answer 52

assumptionso of M-M kinetics: only valid when 1) measurements are made before much product has formed (so we can ignore E+P-- ES and ignore product inhibition. E+S k1=k-1 ES --> K2 E+P, 2) there is only one rxn substarate, 3) the rxn occurs in a single step, 4) binding is not cooperative. affect on kinetic measurements:

Answer 53

L-B equation and plots:1/observed rate vs 1/[S], its easier to estimate the Vmax on a lineweaver-burk reciprocal plot

Answer 54

irriversibe inhibitors: a reaagent that permanently associates w/ an enzyme inactivating it, is an irreversible inhibitor.

Answer 55

competitive: competes with the substrate for binding at the enxyme's activue sites; alpha is the degree of competitive inhibition, Ki is the inhibitor constant ( the dissociation constant for EI= E+I, a low Ki indicates a good inhibition (tight binding) Vmax stays the same, Km increasses by a factor of alpha, best competitive inhibitors minic the transition state for the rxn. inosine: KI = 3*10-4 M , 1,6-dihydroinosine KI= 1.5*10-13 M ( very strong competitive inhibitor fortune enzyme. uncompetitive: only bind to the enzyme-substrate complex, Lowers Km and Vmax by the same factor (a') noncompetitive: is a special case of mixed inhibition where a=a' >1, binds away from the enzyme active site and does not affect substrate binding. mixed: affects both Vmax abd Km, a mixture of competitive inhibition. allosteric : enzymes exhibit cooperativity , binding at one site affects the substrate affinity at other sites. inhibitors shift the sigmoidal curve to the right. regulators affect the activity of multisubunit enzymes by stabilizing the R-state (high activity stabilized by ATP, higher velocity, regulation purine and pyrimidine nucleotide production or T-state (low activity stabilized w/ CTP lower, stabilizes inactive conformation of substrate rxn.

Answer 56

degree of inhibition : uncompetitive : alpha prime is degree of uncomp inhibition a' = km w/o inhibition / (apparent) km with inhibitor or a'= Vmax w/o inhibitor /(apparent) Vmax w/ inhibitor pure competitive: a > 1 a'=1; mixed : a > 1 and a'>1

Answer 57

competitive inhibitors and substrate/product or a rxn: competitive inhibitors frequently resemble the substrate or product of a reaction and that competitive inhibitors that mimic the transition state frequently bind with very high affinity to an active site (which can be exploited in rational drug design).

Answer 58

allosteric effector stabilization of R/ T states: regulators affect the activity of multisubunit enzymes by stabilizing the R-state (high activity stabilized by ATP, higher velocity, regulation purine and pyrimidine nucleotide production or T-state (low activity stabilized w/ CTP lower, stabilizes inactive conformation of substrate rxn.

Answer 59

enzyme activity regulation w/o inhibitors: 1) rate of synthesis and/or degradation, 2) Localization 3) release of co-activators such as Ca2+ 4) Covlalent modification (eg. phosphylation or zygomen cleavage.

Answer 60

effects of HIV: HIV reverse transcriptase is very error prone (it is not as specific as most polymerases when incorporating a nucleotide) Viruses have high mutation rates --> increase resustance development to treatments. The error-prone nature of HIV reverse transcriptase means it may incorporate chain-terminator nucleotide drugs such as AZT and ddC. AZT and ddC prevent DNA polymerase from incorpating additional nucleotides, human polymerases are more discriminating and rarely incorporate these drugs. Nevirapine is a noncompetitive inhibitor that binds to a hydrophobic pocket away from the active site. HIV-1 protease cleavage sites (cleavage occurs during maturation); HIV protease has some unique recognition sites that aren't recogized by human proteases. Saquuinavir and ritonavir are competitive inhibitors of the HIV protease that mimic the transition state of the rxn.

Answer 61

systemic naming of fatty acids... : Unsaturated fatty acids have at least one double bond in the hydrocarbon tail. Water soluable end (delta end), fat soluable end (omega end) The symbole name gives the ratio of the number of carbons to the number of double bonds, as chain length increases, so does the melting point (mp) of the fatty acid; tempurature must increase to overcome the great van der Waals interactions. Symbol names: eg 6,9,12-octadecrienoate is 18:8n-6 or 18:3delta 6,9,12 (if cis or trans is not explicitly identified, assume cis for biological fatty acids n-6 or n-3 gives the postion of the last double bond ( where n is the number of carbons in the fatty acid), n-3 fatty acids are omega-3 fatty acids, n-6 fatty acids. Additional bonds are always spaced three carbons apart.

Answer 62

packing and imf's affects: IMFs --> SA increases due to chain lengths + van der waals interactions increase mp important in how they are placed + interactions w/ other bio molecules unsaturated biological fatty acids usually have cis double bonds. The highly ordered packnig of fatty acid chains is disrupted by the presence of cis double bonds. low m.p of unsaturated fatty acids < higher m.p saturated fatty acids (within the biological range of fatty acid lengths), each additional double bond lowers Tm Fatty acids are usually carried as glycerol esters (triacylglycerols) rather than free fatty acids. polar character ester linkages but overall molecule is nonpolar.

Answer 63

cis db's: advantages of more saturated v unsaturated fatty acids :

Answer 64

cholesterol fxn: Cholesterol and other steriods have a four-ring core sturecture, cholesterol is a major component of animal membranes that helps maintain fluidity and integrity. cholesterol also serves as a precoursor for steroid hormones, vitamin D, and bile salts. stored in hydrophobic form --> as cholesterol ester (hydroxyl group + lipid)

Answer 65

tryglycerides:

Answer 66

vitamins: essential molecules that we cannot synthesize and must obtain in our diet. Vitamin A: important for visual perception, deficiency results in night blindness. Lipid soluable. Vitamin D: important for calcium homeostasis, deficency results in rickets, a disease characterized by deformed bones and stunted growth Vitamin E: had antioxidant activity; hydrophobic, partions into mbns reacts w/ reactive oxygen species preventing modification of fatty acids tails --> mbn modification. Vitamin K: a cofactor for an enzyme that modifies glutamate residues on blood clotting proteins, defiviency in excessive/prolonged bleeding , lipid soluable

Answer 67

glycerolphospholipids: a glycerol backbone with fatty acids esterified to the first two carbons and a polar phosphate derivative head group attached to the third carbon sphingolipids: consist a (dihydro)sphingosine backbone with a single fatty acid attached via an amide linkage and a sugar or polar phosphate derivative head group.

Answer 68

two tailed lipids form extended lipid bilayers because: mbn lipids must have the correct geometry to stack correctly without forming voids

Answer 69

integral proteins: have hydrophobic peptide regions embedded in the lipid bilayer and these proteins reqiure strong detergents to isolate mbn proteins: peripheral mbn proteins: associate with the polar head groups of membrane lipids or with the exposed regions of other mbn proteins, may be isolated with other mild solutions lipid-linked proteins: insert a hydrophobic anchor into the mbn, can be 1) myristoyl group ( C 14:0) attached to an N-term Gly via an amide linkage; 2) a palmitoyl group ( C 16:0) reversibly attached to a Cys side chain via a thioester linkage. 3) an isoprenoid group linked to a C-term Cys via a thioether linkage 4) a glycosylphosphatidylinsitol (GPI) group linked to the C-term of the protein

Answer 70

integral mbn proteins span hydrophobic regions of bilayer beta barrels or transmbn helices:

Answer 71

fluid mosaic model: proposes that lipids and proteins may freely move laterally but cannot flip-flop through the layer by themselves, the cytoskeleton may be restrict some proteins to particular regions of the membranes. eg: Protein A is anchored to a cytoskeleton filament. Protein B is fenced in by cytoskeleton filaments.

Answer 72

features of lipid bilayer: mbns have polarity. inside of a mbn is different, in both lipid and protein composition from the outside, both lipids and proteins facing the extracellular space are frequently glycosylated, integral mbn proteins are always oriented in the same direction ; translocases are proteins that move mbn lipids from one side of the mbn to the other. lipid movment form leaflet to leaflet:

Answer 73

Na+ concentrations: high outside, low concentrations inside K+ concentrations: high inside, low concentrations outside negatively charged (-70 mV),

Answer 74

free energy for a moving substance across mbn: the plasma mbn is mostly impermeable to Na+ but allows some K+ to leak across the mbn; K+ movement reaches equilibrium with a high [K+] inside the cell (favoring K+ efflux) and a negative mbn potential ( favoring K+ influx), this is the major contribution to the cell's resting mbn potenial

Answer 75

movment of Na+ and K+ across mbn during AP: stimulus orginates where the axon leaves the neuronal cell body. stimulus opens Na+ channels in the mbn --> VG Na+ channels open Na+ influx results in depolarization from -70 to +55 mV, closing of VG Na C's results in opening of VG K+ channles results in efflux of K+ restoring resting potential --> occurs multiple times @ nodes of ranvier as AP propagates down axon.

Answer 76

porin structure: proteins that form an open channel in the mbn of bacteria and certain organells to allow the passage of small solutes. effects on selectivity: certains organells to allow the passage of small solutes

Answer 77

K+ channel strucutre and selectivity: K+ channels are much more selective for K+ than Na+, the last third of K+ channels is a selectivity filter that is too narrow for large ions and too wide for smaller ions such as Na+, when K+ moves into the filter, it looses favorable interactions w/ water, but gains favorable interactions with the residues lining the filter (selectivty filter) --> smaller ions (eg. Na+) do not interact favorably w/ the selectivity filter as the energy for desolvation cannot be compensated by interactions with the selectivity filter.

Answer 78

stimuli affecting gated channels: 1) changes in mbn potential, 2) changes in pH, 3) binding of a specific ligand 4) phosphorylation, 5) temperature, 6) mechanical pressure affects on channel structure: mechanosensitive channels

Answer 79

aquaporin selection for water transport: aquaportin channel contains two Asn residues that disrupt the hydrogen-bonding chain of passing H2O molecules: hydrophobic residues lining the channel force H2O into an orientation that hydrogen bonds with the asparagrines the size of the channel is optimized for a single chain of H2O and a positvely charged Arg residue disfavors entry of H3O+

Answer 80

uniport: move a single substance across mbn, eg: glucose transporter allows glucose to move down its concentration gradient ; Glucose binding changes the conformation, so that the transporter opens on the opposite side of the mbn. symport: moves two different substances across the mbn in the same direction, eg: Na+-glucose transporter uses the energy of Na + moving down its concentration gradient (into the cell) to drive glucose import into the cell agonist the [ glucose] gradient. antiport: move two different substances across the mbn in opposite directions, eg: Na+/K+-ATPase uses the energy of ATP to move three Na+ out of the cell and two K+ into the cell against their concentration gradients, primary active transport: the use of ATP to drive transport secondary active transport: movement of an ion down its electrochemical gradient, to move another substance across the mbn passive transport: facilitated diffusion: using a protien to bind and move a molecule or ion across the mbn exocytosis: AP at axon terminal --> VG Ca2+ to open --> Ca2+ concentration influx results in synaptic vesicles w/ the plasma mbns so that the NT Ach is released into the synaptic cleft (exocytosis) --> Ach binding to receptors on the surface of the muscle cell leads to muscle contraction. Signal is short lived b/c Ach remaining in the synaptic cleft is rapidly degenerated. endocytosis:

Answer 81

glucose transporter fxns: NC 104

Answer 82

Importance of Na+/K+ - ATPase for gradient establishment: NC 104

Answer 83

transport across mbns via vesicle fusion: NC 104

Answer 84

SNAREs fxn: the favorable formation of a four-helix coiled-coil pulls the vesicles into the target mbn 1) Zipping: as the vessicle approaches its target mbn, the SNAREs being zipping together from their N-termini , which draws the two mbns toward eachother to form trans-SNAREs complexes 2) Hemifusion: as docking proceeds, the increased curvature and lateral tension induce the approaching bilayer leaflets to fuse, exposing the bilayer interior 3) the two bilayer leaflets that where orgionally farthest apart are brought together to form a new bilayer 4) fusion pore formation: continuing SNARE-induced lateral tension causes mbn breakdown, resulting in the formation of a fusion pore; 5) the fusion pore expands as the now fused mbn relaxes --> cis-SNARE complexes.

Answer 85

RTK: GPCR: 7 transmbn helices with a ligand binding region on the extracellular face and a G protein binding region on the intracellular face.

Answer 86

GPCR activation: Ligand binds --> conformation change in GCPR --> Ga releases GDP and binds GTP (switches on) --> Ga-GTP dissiciates from the Gby subunits (both Ga and Gby may activate other proteins). --> Ga has intrinsic GTPase activity and hydrolyses GTP to GDP+Pi (switches off) --> Ga-GDP reassociates with the Gby subunits. GPCRs are associated with G-proteins, heterotrimic intracellular proteins w/ a,b, and y subunits. The Ga subunits has a guanine nucelotide binding site

Answer 87

epi role in body & signal pathway: Epinephrine is an agoinsit for the B2 adrenergic receptor (a GPCR) effects: increase HR, vasodialtion of blood vessels in essential organs. mobilize fuels -> liver (glycogen) + fat tissue. As long as Ga*GTP is present, AC will keep making more cAMP (amplification signaling). ATP--> cAMP + PPi, Ga*GTP activates adenylyl cyclase (AC), AC produces cAMP. PKA (Protein Kinase A): has two regularoty subunits and each subunit binds 2 cAMPs, Once cAMP has bound , the catalytic subunits dissciate and can transfer a phosphate from ATP to a Ser or Thr side chain on target proteins involved in fuel metabolism.

Answer 88

signal pathway regulation: are not linear, they can have branching or cross talk as multiple pathways intersect, multiple steps allow multiple levels of regulation to fine tune the signaling response. Turning off signaling pathways: Phosphodieasterase hydrolyse cAMP (PKA regulatory subunits reassociate with the catalytic subunits). Process: Ga converts GTP to GDP + Pi and reassoicates with Gby; Arrestin binds the GCPR and prevents further activation of the G-protein.

Answer 89

second messengers: cAMP its a signaling molecule that is procuded by AC ( Adenenylyl cyclase) fxn: amplification of signaling)

Answer 90

signal amplification: making a signal stonger which recruits more protein kinase A and produces a greater response within a cell.

Answer 91

RTKs pathway activation: Ligand binding to EC domain of an RTK dimer induces a conformation change in the cytosolic domains. Cytosolic domain of one monomer moves close enough to the cytosolic domain of the other monomer to phosphorylate Tyr resides (swithcing receptor on). --> RTK activation induces a kinase cascade where one kinase activates the next kinase in a chaon --> activation at each step amplifies the signal. Some activated RTKs can recruit binding protein to transmit a signal, while other RTKs directly phosphorylate kinases.

Answer 92

Ras pathway: monomeric G-Protein (homologous to Ga that is activated by adaptor protiens once tha adapter recognizes phosphoTyr on an RTK with a growth factor ligand bound. Ras exchanges GDP for GTP ( activating RAS), Ras initiates a kinase cascade that regulates the expression of genes that are important for cell growth and division.

Answer 93

lipid homone stucture: many lipid hormones move inside the cell to activate intracellular receptors. hydrophobic character allows them to move through the mbn. Phospholipids --> Phospholipase A2 (blocked by cortisol-like steroids)--> Arachidonate --> converted to compound ligand activation of IC receptors is either autocrine ( same cell) or paracrine (neighboring cell) .

Answer 94

phospholipids to prostagladins steps: Arachidonate --> Cyclooxygenase (COX) (blocked by aspirin, ibuprofen (targets of postglandins which inhibit their effect) --> postglandins --> inflammatory and pain response. COX enzymes then convert the arachidonate to prostaglandins that promote a pain and inflammatory response.

Answer 95

COX-2 specific inhibitors: Aspirin and ibuprofen inhibit both COX1 and COX2 --> reduced pain and inflammation through COX2 inhibition, but increase the risk of stomach ulcers through COX-1 inhibition. (if taken constantly) Drugs such as Celebrex are designed as inhibitors of COX-2, but cannot bind COX-1 due to a steric clash. (for more chronic pain)

Answer 96

naming of sugars: use common name for sugars (eg glucose or can indicate the number of carbons and whether the sugar is an aldehyde or ketone (eg aldohexose) ex: Glyceraldehyde --> aldotriose; Dihyroxyactone --> Ketotriose; ribose--> aldopentose; Glucose --> aldohexose; Fuctose --> ketohexose). number of carbons: when numbering the longest carbon chain, the anomeric carbon is assigned the lowest possible number. Anomeric carbon has two bonds with an electronegative element such as oxygen or nitrogen. aldehyde or ketone; chirality: type of rings: 5 or 6 member rings; 5 membered ring = 'furanose' and 6 membered ring ='pyranose' anomer: has two carbon bonds with an electronegative element ie: oxygen or nitrogen. reducing sugars: Fehling's test and Benedict's test both Use Ca2+ solutions (deep blue) that are reduced to Cu+ (forming CuO2, a deep red ppt.) in the presence of aldehydes and alpha-hydroxyketones. Sugars that react with oxidizing agents are called reducing sugars, whereas those that do not are nonreducing sugars. A sugar that has an anomeric carbon with a free hydroxyl in the ring form will be an aldehyde or an a-hydroxyketone in the open chain form and is a reducing sugar.

Answer 97

D-glucose characteristics; in the standard Fischer orientation, a D-sugar has the -OH group to the right of the stereocenter furthest from the anomeric carbon L-sugars have the -OH group to the left of anomeric carbon. enantiomer of D-glucose is L-glucose. the C5 epimer of D-glucose is L-idose.

Answer 98

enantiomers: molecules that are non-superimposible mirro images of one another, most biological sugars are D-enantiomers. epimers: diastereomers that differ only by the stereochemistry of a single carbon center (stereocenter). ex: D-glucose and D-galactose are C-4 epimers of one another. signficance of anomeric carbon: standard Fischer projection of sugar has the anomeric carbon at the top.

Answer 99

chiratlity of carbons: Haworth projections are used to represent the stereochemistry of sugars in their ring form. In standard Haworth orientation, the ring oxygen is at the back and the anomeric carbon is to the right. If the last stereocenter's -OH group closes the ring, then a D-sugar will have the next carbon above the ring and an L sugar will have the next carbon below the ring. If the ring-forming hydroxyl is to the right in the standard Fischer projection, then the next carbon will be above the ring. In solution, sugars are mostly in the ring form (although monosaccharides quickly convert btwn the ring and staight chain conformations), At a given amount, a soln of D-glucose ia ~ 36 % a-anomer and ~64 % b-anomer. ( has OH in eq postion in chair = more stable); A D-sugar with the anomeric hydroxyl below the ring is called the a-anomer (above the ring is b-anomer); an L-sugar with the anomeric hydroxyl below the ring is called the b-anomer (above the ring is the a-anomer).

Answer 100

glycosidic bonds: formed when the anomeric carbon is joined to another group (making the sugar non-reducing) systemic naming of disaccharides or triglycerides: describing the glycosidic bond by noting the anomer along with which carbons are linked eg: sucrose is a Alpha-D-glucopyranosyl-91-2)-b-D-fructofuranose.

Answer 101

structural features of homopolysaccharides: starch: glucose stored in plants, can be either an unbranched polymer called amylose (only a(1-->4) linkages or a branched form = amyliopectin that has a(1-->4) linkages along with a(1--> 6) branch points every ~ 30 resides. glycogen: glucose stored in animals, similar structure to amylopectin, but branch points are every 8 to 12 residues. cellulose: primary component of plant cell walls, straight chains with extensive H-bonding strengthening the fibrils. b(1-->4 ) linkage chitin: primary component in exoskeletons; straight chains have extensive H-bonding b(1-->4) linkage of N-acetylglucosamine. all are HOMOPOLYSACCHARIDES b/c they are made of the same monosaccharide residues.

Answer 102

struct fnx of: conncetive tissue such as cartilage, skin, and tendons include proteoglycans: structural proteins linked to glycosaminoglycans (GAGs). These gycosaminoglycans are heteropolysaccharides consisting of repeating uronic acid and hexosamine resides. heteropolysaccharides: glycosaminoglycans, peptidogluycan: the polar groups on glycosaminoglycans attract H2O to help lubricate tissue, while negative charges repel each other upon compression to act as shock absorbers. Peptidoglycan consists of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) repeating units attached to cross-linked tetrapeptides.

Answer 103

roles of glycoproteins: Wide variety of oligosaccharides = modifications possible, b/c they can serve as unique cell ID's N and O -linked oligosaccharides on proteins: N-linked oligosaccharide is attached to an Asn side chain. O-linked oligosaccharide is attached to a Ser or Thr side chain. ( ecf on mbn is glycolated (from Ch 8). Wide variety of oligosaccharides = modifications possible, b/c they can serve as unique cell ID's

Answer 104

ABO blood groups produced: Differences in a few active site residues of a glycosyltansferase result in a different sugar being added to the O antigen in A- and B- type individuals, O--> type indivduals dont have a fxnal version of this glycosyltransferase so no sugar is added. ABO blood type is determined by part of a O-linked oligosaccharide on the cell surface. A, B and O blood types: A = anti-B antibodies in plasma, A antigens on RBC, Compatible A,O bloodtypes. B= anti-A antibodies in plasma, B-antigen in RBCs, Compatable B,O bloodtypes. AB = no antibodies, A and B antigens, AB+ is universal recipient, compatable with A,B,O,AB blood types. O= Anti-A and Anti-B Antibodies in Plasma, no antigens in RBC, compatable with O (O is the universal donor)

Answer 105

anabolism: building complex molecules at the expense of energy catabolism: breaking down larger molecules

Answer 106

bioploymers hydrolyzation by intestinal enzymes: Enzymes hydrolyze biopolymers into smaller products that may be absorbed by the intestine. energy 70-80 % come from nutrients main energy comes from sugar. W/o constant supply of energy --> break down glycogen and once glycogen is gradually depleated --> fat is then broken down. Starvation leads to break down of proteins --> N as energy.

Answer 107

order of fuel availabilty:

Answer 108

proteins degraded by lysosomes: lysosomes are organells containing digestive enzymes that primarily breakdown extracellular or mbm proteins. increase pH of 7 prevents enzymes activation if they fall outside cell. proteins degreaded by proteasomes: multisubunit protease that targets intracellular proteins. core regonizes which proteins are meant to be degraded and which aren't based on specific structure binding steps for degradation by proteasome: Ubiquitin ligase transfers a small protein, = ubiqutin to a Lys residue of the target protein. --> once four or more ubiquitins have been added, the end cap subunits of the proteasome recognize the target protein for degradation. Proteasome --> A chain of ubiquitin molecules targets a protein to the proteasome --> the polypeptide is unfolded as it enters the proteasome --> protease active sites inside the proteasome cleave the polypeptide into small peptides that diffuse away. Proteins may be degraded b/c they are abnormal or b/c their concentration must be regulated

Answer 109

Water soluable vitamins: Vitamin C: an antioxidant that acts as a cofactor for the enzyme the hydroxylates proline residues in collagen. deficency = scurvy Vitamin B1 = thiamine is a cofactor for the pyruvate dehydrogenase complex and a-ketoglutarate dehydrogenase; Vitamin B1 deficiency leads to beriberi --> characterized by weakness and leg swelling. Vitamin B3 deficiency leads to pellagra, characterized by diarrhea, dermatitis, dementia, and death. (ordered from most to least funny --> 5 D's),. Cells have high rates of metabolism.

Answer 110

Redox cofactor properties: NAD+/NADH: Niacin is a precoursor for NAD(P)+/NAD(P)H. Vitamin B3 deficiency leads to pellagra, characterized by diarrhea, dermatitis, dementia, and death. (ordered from most to least funny --> 5 D's),. Cells have high rates of metabolism. NADP+/NADPH: Nicotinamide adenine dinucleotide (NAD+/NADH) is a water soluable 2e- carrier, the phosphorylated form (NADP+ / NADPH) is generally used as a redox cofactor in biosynthetic pathways. Q/QH2: Ubiquinone or Coenzyme Q (Q or CoQ) is a lipid soluable 1(QH*) or 2e- (QH2) carrier. FMN/FMNH2: Ubiquinone is a mobile electron carrier that often receives electron from an FADH2 or FMNH2 porstentic group, these flavins are dervied from Vitamin B2 (riboflavin). Flavins are prosthetic groups that can carry 1 or 2 e- FAD/FADH2: Ubiquinone is a mobile electron carrier that often receives electron from an FADH2 or FMNH2 porstentic group, these flavins are dervied from Vitamin B2 (riboflavin). Flavins are prosthetic groups that can carry 1 or 2 e-

Answer 111

Free energy change: delta G not is free energy change under chemical standard state conditions : 298 K, 1 atm and all [1M]. free energy change under biochemical standard state conditions (same asv chemical standard state except [H+] = 1x10-7 and [H2O] =55.5 M equillibrium constant: Keq = [C]ceq [D]deq / [A]aeq [B]b eq mass action ratio: Q = [C]c [D]d / [A]a [B]b , used when the concentrations at equilibrium.

Answer 112

classes of molecules used as energy currency by cell: energy may be stored in reduced cofactors, phosphoanhydride bonds (eg ATP) or thioester bonds (eg Acetyl-CoA). Energy currency is used in chemical reactions to make the overall process favorable (negative delta G).

Answer 113

reversible steps in metabolic pathway: a metabolic pathway with a postive delta G irreversible steps in metabolic pathway: a metabolic pathway with a negative delta G effects on pathway regulation: metabolic pathways are often regulated at steps with a negative delta G (irreversible step), steps with a delta G near zero are reversible and the direction of the net reaction depends on the concentrations of reactants and prodcuts. some opposing pathways may share reversible enzymes (but require different enzymes at any irreversible steps). An irreversible step generally occurs early in a metabolic pathway (often the 1st step) in order to commit a metabolite to the pathway. Keq less than 1 => reactants are favored as Delta G not = would be (+) , little changes in the [ ] amt of rxns and products will change the favorably of the rxn.

Answer 114

glycolysis: occurs in the cytosol of cells; two stages of glycolysis: 1) rxns 1-5 -> Glucose --> G-3-P 9 requires 2 ATPs) 2) reactions 6-10 G-3-P --> pyruvate (yeilds 4 ATP). Net yeild = 2 ATP + 2 NADH ; under anaerobic conditions (from muscles) : 2 NADH --> heat ; under aerobic conditions (from cytsol to mitochondrial matrix) : 2 NADH --> ~ 5 ATP

Answer 115

advantages of hexokinase phosphorylate glucose : Phosphorylating six carbon sugars prevents the sugars from leaving the cell and reduces the intracellular [glucose] so that the [glucose] gradient favors import. Hexokinase rxn is irreversible.

Answer 116

alanine screening of active site Lys or Asp eliminates enzymatic activity. the gene for a protein is modified to test the importance of a specific residue. When the codon for Lys is changed to Ala, and activity of the expressed protein is measured, there will be not activity since Lys is essential to the form the Schiff base. transition state analongs: enediolate transition state analogs, 2-phosphoglycolate and phosphoglycohydroxamate, bind more tightly to TIM than either GAP or DHAP. radiolabels: iodoacetate: the presence of an active site Cys is suggested by inactivation of the enzyme by iodoacetate, carboymethlcysteine is then isolated when the protein is separated into individual amino acids.

Answer 117

Fates of pyruvate: pyruvate is reduced to lactate so the that NADH can be reoxidized to NAD+. NAD+ is then used in the GAPDH rxn to cont glycolysis. ( in animals) ( in yeast) -> Pyruvate is decarboxylated to acetalaldehyde which is then reduced to ethanol so that NADH can be reoxidized to NAD+. Pyruvate dehydrogenase: pyruvate may be converted to acetyl-CoA which is then oxidized further in the citric acid cyle or used in lipid synthesis. Pyruvate carboylase: Pyruvate may be converted to oxaloacetate which can be used for amino acid or glucose biosynthesis.

Answer 118

humans metabolizing methanol: ethanol = alcohol dehydrogenase ( NAD+ -> NADH,H+ is produced via reducing reaction) acetaldehyde = avetaldehyde dehydrogenase , ( OH - NAD+ forms NADH, H+ ) Acetate; energy currency tells liver cells to produce collagen and fatty acids --> liver disease (cirrhosis & triglycerides).

Answer 119

gluconeogensis: energetically expensive. Costs : 4ATP + 2 GTP + 2 NADH, occurs primarily in the liver. Steps 1, 3 , and 10 in gluconeo have a substantial drop in free energy => irreversible -> separate pathway in gluconeogenesis are bypassed which results in hydration of phosphates ( break phosphoester (via hydrolysis) glycolysis regulation: high concentrations of glycolytic products such as ATP and PEP inhibition further glycolysis, while molecules that indicate a low energy charge in the cell such as AMP and ADP activate glycolysis. F-2-6- bisphosphate is produced by PFK-2 ( as opposed to PFK-1, which is the glycolysis enzyme that makes F-1,6,-bisphosphate, aka FBP, step 3 glycolysis). F26BP is an allosteric activator of PFK-1 amd inhibitor of the gluconeogensis enzyme FBPase-1 . Ensures that the opposing pathways do not run simultaneously.

Answer 120

glycogen synthesis: phosphoglucomutase interconverts G6P and G1P --> G1P is activated by UTP to form UDP-glucose and PPi. the subsequent hydrolysis of PPi drives the rxn forward. (irreversible). 2 phosphates come off at and get hydrolyzed by inorganic pyrophosphate, 2 broken + 1 formed = favorable. --> 3) glycogen synthesis links glucose units via a(1-> 4) and UDP functions as a leaving group. Glycogen branching enzyme moved 7 residues from the main chain to form a new branch. glycogenolysis: Glycogen phosphorylase use phosphorolysis to break a(1->4) bonds and produce G1P monomers. When a branch has only 4 glucose residues, a debranching enzyme moves 3 residues to the main chain and then cleaves the a(1->6) branch point. Phophorylated sugars cannot cross the plasma mbn so G6P is converted to glucose for export.

Answer 121

pentose phosphate pathway; Depending on the cellular requirements for ribose or NADPH, different paths may be used. Path 1: the oxidative path, irreversible. produces NADPH and ribulose-5-phosphate (Ru5P) which may be reversibly converted to ribose-5-phosphate (R5P) Path 2: the carbon rearrangement path. Two F6P + one GAP are rearranged through a series of reversible reactiosn to Ru5P. Path 3: of the cell needs NADPH but not ribose, then G6P may be converted to Ru5P through the oxidative path and Ru5P is converted to GAP and F6P by reversing the carbon rearrangement path.

Answer 122

Cancer and the warburg effect : cancer cells have rates of glycolysis 10 x normal cells. inhibiting glycolysis harms cancer cells more than regular cells. glycolytic enzyme target of chemotherapy: FdG is metabolized by HK, but cannot be metabolized by PGI.

Answer 123

pyruvate dehydrogenase complex: a multienzyme that links glycolsysis to the citric acid cycle.

Answer 124

advantages of multienzyme complexes : 1) the product of one activate site quickly moves to the next active site. PDC is an example of substrate channeling where the intermediates are never released into solution. 2) easier to regulate all enymes together, 3) Minizes side rxns. substrate channeling: PDC is an example of substrate channeling where the intermediates are never released into solution.

Answer 125

citric acid cycle: occurs in the mitochondria, the mitochondrial matrix contains the pyruvate dehydrogenase complex and most of the enzymes of the citric acid cyle. Acetyl-CoA enters the citric acid cycle from the pyruvate dehydrogenase complex, amino acid catabolism, or fatty acid oxidation, steps 1,3, and 4 are irreversible, step 6 has an FAD prosthetic group. FADH2 transferase 2e- to Q producing QH2 at this step. acetyl-CoA + 3NAD+ +Q +GDP + Pi + 2H2O --> 2 CO2 + CoA + 3 NADH + QH2 + GTP. Step 1: Citrate synthase + step 8 : malate dehydrogenase. ( favorable combined with favorable) the citrate synthase rxn has a lrg enough (negative) free energy change to pull the malate dehydrogenase rxn forward. Regulation: 1) Substrate availabilty of acetyl-CoA and oxaloacetate (OAA), 2) Allosteric activation by Ca2+ (steps 3 and 4) and ADP (step 3), 3) Allosteric inhibition of isocirtrate dehydrogenase (step 3) by ATP. 4) Product inhibtion (NADH, citrate, and succinyl-CoA) , 5) Feedback inhibition (NADH and succinyl-CoA). Key idea of citric acid cycle: Intermediates of the citric acid cycle serves a precoursors for a variety of anabolic patheays through cataplortic rxns (anaplerotic rxns replenish citric acid cycle intermediates).

Answer 126

acontinase step of citric acid cylcle: Citrate is prochiral -> the hydroxyl group is always moved to the carbon originating from the oxaloacetate and not the carbon from the acetyl-CoA.

Answer 127

malate dehydrogenase step forward despite unfavorable standard free energy change for rxn: Step 1: Citrate synthase + step 8 : malate dehydrogenase. ( favorable combined with favorable) the citrate synthase rxn has a lrg enough (negative) free energy change to pull the malate dehydrogenase rxn forward.

Answer 128

Radiolabels used to track carbons through citric acid cycle: Carbons used to make CO2 originate in oxaloacetate, not acetyl-CoA, track carbons using radioactive isotopes to see where acetyl-CoA is used and where OAA is used via radiocarbon traces.

Answer 129

anaplerotic : consequence of catabolic process.; rxns that increase the number of intermediates, cataplerotic: taking out/ reducing intermediates out of pathway, rxns that reduce # of intermediates.

Answer 130

intrepretations of calculations: e = reduction potential ( the affinity of a substance for electrons) eo' = standard reduction potential electrons flow spontaneously from the substance with the lower reduction potential to the substance with the higher reduction potential.

Answer 131

struct of mitochondria: the inner mbn of mitochondria contains all the complexes for oxidative phosphorylation, the outer mbn is very porous, while the inner mbn is impermeable to most small molecules and ions intermembrane space = cytosol. complexes of oxdiative phosphorylation: reduced cofactors donate electrons to an electron transport chain that generates a H+ gradient. this gradient is used to generate ATP.

Answer 132

thermodynaic driving force of ATP/ADP transporter: H+/Pi transporter: ATP is produced in the matrix, so it must be exported to the cytosol while ADP is imported into the matrix in order to make more ATP. ATP and ADP are moved using an antiporter driven by the inner mbn potential (negative on the matrix side of the mbn). Pi is imported along with a H+ using a symporter driven by the H+ gradient (lower [H+] in matrix).

Answer 133

malate/aspartate shuttle: net effect is one fewer NADH in the cytosol and one additional NADH in the matrix. NADH is too lrg to transported efficently in the matrix.

Answer 134

NADH dehydrogenase: Complex I is a proton pump driven by NADH oxidation, in complex I (aka NADH dehydrogenase), 4H+ are translocated into the intermbn space for every 2 e- that pass through the complex. NADH + H+ +Q --> NAD+ + QH2 Complex I , a H- ion is trasnferred from NADH to FMN. FMN then passes the electrons ( one at a time) to a series of 8-10 iron-sulfur clusters until they reach Q. NADH has to give 2e- at a time. NADH is a water soluable, mobile 2e- carrier. Flavins are prosthetic group that can carry 1 and 2e-. Fe-S clusters are obligate 1e- carriers using cystines and inorganic sulfure to corrdinate Fe2+/Fe3+ Ubiquinone is a lipid soluable, mobile 1 or 2 e- carrier.

Answer 135

Complex II in citric acid cycle: a) from succinate dehydrongenase (complex II) in the citric acid cyle (succinate +FAD -> Fumarate + FADH2) , b) fatty acid oxidation (acyl-CoA dehydrogenase rxn), c) from glycerol-3-phosphate (mitochondrial dehydrogenase rxn.

Answer 136

Complex III: Ubiquinol (QH2) donates 2 electrons to complex III (aka cytochrome bc1), ultimately reducing cytochrome c (cty c) , a mobile (single) electron carrier, 4H+ are translocated into the intermbn space for every 2e- that pass through complex III. Comples #4: Two cytochrome c proteins each donate 1 electron to complex IV (aka cytochrome c oxidase), ultimately reducing the terminal electron acceptor O2. 2H+ are translocated into the intermembrane space for every 2e- that pass through complex IV.

Answer 137

cytochromes heme-containing proteins: Cytochromes are proteins with a heme group that are obligate single electron carriers. a,b, and c denote the type of side groups on the heme. oxidative phosphoralation is regulated only by the availability of NADH and QH2.

Answer 138

chemiosmotic model: A combination of the H+ imbalance 9due to e- transport), and the negative charges on the matrix side of the mbn, results in an electrochemical gradient that favors H+ moving into the matrix.

Answer 139

Complex V: (f1,F0ATP): The F1 soluable portion includes 3a and 3b subunits. --> Each of the b subunits has ATP synthase activity. F0 mbn-spanning portion includes the a subunit, where H+ enter and exit, and a c-ring. The c-ring consists of 8-15 subunits that each bind a H+ to help rotate the ring. Protons move down their gradieent by passing through ATP synthase The y subunit extends from F0 to F1 and rotates 120 deg once enough strain has built up from the c-ring rotation. Experimentally, we observe 1 ATP produced for every 4 H+ translocated in the electron transport chain (no matter how many subunits are in the c-ring) 1) L: ADP+Pi are bound, 2) ATP is formed 3) O:ATP is released, 120 degree rotation of the y subunit forces the b-subunits into one of threee conformations. One full rotation of the the y subunits produces 3 ATP (1 ATP/b subunit)

Answer 140

P:O ratios: the ratio of phosphorylations (ADP+Pi --> ATP) to oxygen atoms reduced (1/2 O2 + 2H+ + 2e- --> H2O) is the P:O ratio. use for ATP yeilds: NADH oxidation translocases 10 H+ (4H+ in comples I + 4H+ in complex III + 2H+ in complex III + 2H+ in complex IV , 10 H+ x( 1 ATP/4H+) = 2.5 ATP QH2 oxidation translocases 6 H+ (4H+ in complex III + 2H+ in complex IV) 6H+ x (1ATP/ 4H+) =1.5 ATP ie: the P:O ratio of NADH is 2.5 and of QH2 is 1.5

Answer 141

uncoupling oxidative phosphorylation: Venturididin and oligomycin block the H+ channel in ATP synthase. blocking the H+ channel causes the electron transport chain to slow down as the H+ gradient gets too sleep (it doesnt stop electron transport completely since some H+ can leak across the mbn. Dintrophenol (DNP) dissipates the electrochemical gradient and generates heat. uncouplers such as 2,4-dinitrophenol (DNP) carry H+ across the mitchondrial inner mbn (down the H+ gradient) w/o passing through ATP synthase.

Answer 142

Cyanide effects: O2 consumption indicates that electrons are moving through the electron transoprt chain; Succinate produces QH2 ( at complex II) and QH2 is a source of eletrons in the electron transport chain ATP synthesis requires ADP + Pi and indicates that H+ are moving into the matrix through ATP synthase. Cyanide (CN-) blocks electron transport through complex IV, shutting down the entire electron transport chain and preventing the formation of a H+ gradient.

Answer 143

succinate added to mitochondria: Succinate produces QH2 ( at complex II) and QH2 is a source of eletrons in the electron transport chain

Answer 144

strcture/fxn of chloroplasts: Chloroplasts have inner mbn that surrounds the stroma (where the soluable enzymes are located) Within the stroma, flattened vesicles = thylakoids that contain the light harvesting complexes, the ETC and ATP synthase, teh thylakoid lumen has a low pH (high [H+] concentration and the H+ gradient drives ATP synthase.

Answer 145

chlorophylls: pigment that can absorb light at various wavelengths carotenoids: pigment that can absorb light at various wavelengths Photosynthetic pigments absorb light. The pigments are bound to proteins and the differing protein enviroments affect the wavelength of light absorbed. Absorbing a photon promotes an electron to a higher energy level (excited state) .

Answer 146

excited molecule energy loss: heat, light (fluroescence), excitation transfer, photooxidation relevance to photosynthesis: photosynthetic organisms have light-harvesting complexes consisting of pigments bound to proteins, The reaction center is a protein with a special pair of chlorophylls that has a lower excited state than the surrounding antenna chorlophylls.

Answer 147

antenna pigments funnel light energy to reaction center: antenna chlorophyll surround a rxn center and pass the energy of an absorbed photon from chlorophyll to chlorophyll until the energy is trapped by the reaction center. The excited reaction center has a low reduction potential allowing it to reduce the next electron carrier in the transport chain. An oxidized reaction center has a very high reduction potential allowing it to be spontaneously reduced by other electron carriers (water in the case of P680+ or plastocyanin in the case of P700+).

Answer 148

light reactions: the series of events from the oxidation of H2O through the production of NADPH and ATP. An electron transport chain generates a H+ gradient that drives ATP synthase. Photosystem II: P680 + hv --> P680* Excited P680* reduces phephytin (Pheo). P680* + Pheo --> P680+ + Pheo- Pheo- then passes an e- to a bound pastoquinone, PQa- ; PQa transfers an electron to the mobile plastoquinone: PQb; PQa - + PQb --> PQa + PQb-. Photosystem II has a P680 rxn center that is excited by photon energy, lowering the P680 reduction potential (e) so that it can transfer an electron to pheophytin. P680* has a high enough reduction potential that it is spontaneously reduced back to P680 by H2O in the oxygen-evolving complex (OEC) of PSII , PQBH2 carries 2e- away from PSII and toward cytochrome b6f. Overall, 4 Photons produce 4 photooxidations and 2PQBH2. 4H+ are effectivley translocated into the thylakoid lumen. photosystem I: The movement of 4e- through cytochrome b6f translocates 8H+into the thylakoid lumen and reduces 4 plastocyanins ( a mobile e- carrier); plastocyanin carries an electron to another photosystem (PSI) . Electrons move through PSI and reduce the mobile e- carrier ferredoxin. Free energy can be conserved by reducing NADP+ --> NADPH (noncyclic e- flow) or in the H+ gradient by transferring the e- back to cytochrome b6f (cyclic e- flow)

Answer 149

Z-scheme plots reduction potentials: H2O --> P680--> P680* --> Plastoquinone--> Cytochrome b6f --> plastocyanin --> P700 --> P700* --> Ferredoxin --> NADP+

Answer 150

C1F CF0-ATP synthase driving factors: CF1CF0-ATP synthase has a similar structure and function to mitochondrial ATP synthase, but is driven by a much larger pH gradient since thylakoid membranes are permeable to ions that prevent establishment of a potential across the membrane. ATP synthase driving factors: The thylakoid mbns is permeable to some ions so chloroplasts need a much larger pH gradient to compensate dor the lack of a charge difference across the mbn. Rxns occur: Mitochondrion, Chloroplast, bacterium

Answer 151

RuBisCO: ribulose Bisphosphate carboylase/oxygenase; regulated by pH, when the light rxns are occuring the stroma pH increases to activate rubisco. otherwise, rubisco is inactive to allow the cell to conserve ATP and NADPH

Answer 152

Calvin Cycle: RuBisCO fixes CO2 to form 3PG, which is then converted to GAP at the expense of ATP and NADPH. GAP is converted to Ru5P, Ru5P is then phosphorylated by ATP to get the RuBisCO substrate RuBP, the dark (light indep rxn occur in stroma) For every 6 GAP produced, one is removed from the cycle to serve as a precoursor for various biomolecules. The other five GAPs have their carbons rearranged to form three 5-carbon ribulose sugars.

Answer 153

digestion + absorption: bile salts emulsify dietary fats in small intestine, intestinal lipases degrade triglycerides, fatty acids and other breakdown products are taken up by the intestinal mucosa and converted into triglycerols, triacylglyerols are incorporated, with cholesterol and apoliproteins, into chylomicrons, chylomicrons move through the lymphatic system and bloodstream to tissues, lipoprotein lipase, activated by apoC-II in the capillary, converts triacylglycerols to fatty acids and glycerol, fatty acids enter cells, fatty acids oxidized as fuel or reesterified for storage. Transport: Chylomicrons transport dietary triglycerols from the intestine to adipose tissue and transport cholesterol to the liver, Low density lipoproteins (LDL or bad cholesterol) transport cholesterol to various tissues. high LDL --> high risk for athereosclerosis. High density lipoproteins HDL / good cholesterol, trasnport excess cholesterol back to the liver (HDL associated with decrease risk of athereosclerosis. Very low density lipoproteins (VLDL) transport triacylglycerols from the liver to other tissues, intermediate density lipoproteins (IDL) from as VLDLs lose triacylglycerols.

Answer 154

lipoproteins: struct and fxn --> Lipoproteins have a highly hydrophobic core of triacylglycerols and cholesteryl esters surrounded by proteins and amphipathic lipids such as cholesterol and phospholipids Roles of lipoproteins: fatty acids are actived for catabolism: linked to CoA via a high energy thioester bond at the expense of 2ATP equivalents

Answer 155

fatty acid removal: Long chain fatty acid (> 20 carbons) and branched fatty acids are oxidized in the perioxisome instead of the mitochondrial matrix. Acyl-CoA is too large to move into the matrix. Instead, the acyl group is esterified to carnitine for import to the mitochondrial matrix from the cytosol.

Answer 156

b-oxidation: Each round of beta ocidation consists of 4 rxns, there are 2 main oxidation steps The last round splits a 4-carbon acyl-CoA into two acetyl-CoAs. Each round of b-oxidation removes two carbons (as acetyl-CoA) from the activated end of the acyl-CoA. Each double bond in a fatty acid will reduce the energy yeild by 1 QH2 or 1 NADH depending on the position of the double bond. Odd-chainn fatty acids have approximately the same energy yeild (per carbon) as even-chain fatty acids.

Answer 157

carnitine transporter :

Answer 158

branched fatty acid & fatty acids that are 20 carbons or longer are oxidized in the peroxisome.

Answer 159

citrate transporter : ACC is activates by citrate which produces acetyl-CoA

Answer 160

fatty acid synthesis net rxn: Fatty acid sythesis (lipogensis) occurs in the cytosol, Acetyl-CoA is carboxylated in the cytosol by acetyl-CoA carboxylase (ACC) to from malonyl-CoA; glucagon/epinephrine signaling inhibits this step by phosphorylating ACC, insulin signaling acctivates this step by dephosphorylating ACC. FA Synth is a multienzyme with 6 different active sites that catalyzes 7 rxns, the usual product of fatty acid synthase is palmitate (16:0), elongases can extend palmitate to make longer fatty acids anddesaturases can introduce double bonds in fatty acids, Acetyl-CoA is extended, two carbons at a time ( from malonyl-CoA), by the fatty acid synthase multifxnal enzyme.

Answer 161

multiple active sites and flexible linker advantages: uses sibstrate channeling: acyl carrier protein (ACP) swings intermediates btwn active sites. Acetyl-Cys --> FA synthase ( Malonyl-CoA + 2 NADPH to CoA + 2NADP+ + CO2) --> 4 Carbon acyl-Cys (Malonyl-CoA + 2 NADPH to CoA + 2NADP+ + CO2) --> 6 carbon acyl-Cys --> 5 times (Malonyl-CoA + 2 NADPH to CoA + 2NADP+ + CO2) --> 16 carbon acyl- ACP --> FA synthase (thioesterase) --> Palmitate (16:0) + ACP.

Answer 162

fatty acid synthesis regulation: Acetyl-CoA carboxylase (ACC) is the primary regulation point for FA metabolism oxidation regulation: ACC is activated by citrate which produces acetyl-CoA ACC is inhibited by fatty acids ( the product of the pathway) the product of ACC, malonyl-CoA, inhibits acylation of carnitine ( so that fatty acid biosynthesis and fatty acid oxidation dont occur simultaneously).

Answer 163

ATP yeild for complete oxidation:

Answer 164

Ketogenesis: The CNS uses glucose as its primary fuel (fatty acids do not cross the blood-brain barrier efficiently) Ketogenesis occurs when blood [glucose] os low and glycogen is depleated (fasting) the liver responds by generating glucose through gluconeogenesis and using acetyl-CoA to make the ketone bodies acetoacetate and 3-hydroxybutyrate. Ketone bodies are converted back to acetyl-CoA in the CNS.

Answer 165

cholesterol synthesis: Assembled from acetyl-CoA units pathway inhibtion: the pathway can be inhibited at its rate-limiting step (HMG-CoA reductase) by competitive inhibitors (eg. Lipitor) called statins. rate limiting step: HMG-CoA reductase competitive inhibtor: Lipitor) called statins.

Answer 166

effects of statin on cholesterol and LDL levels: Statins mimic HMG-CoA and inhibit HMG-CoA reductase, HMG-CoA reductase is the rate limiting step of cholesterol biosynthesis, cells that cannot make enough cholesterol compensate by increasing production of LDL receptors, more LDL receptors results in more endocytosis of LDLs, fewer circulating LDLs reduces the risk of atherosclerosis.

Answer 167

Nitrogen cycle: N2 --> nitrogen fixation (nitrogenase) --> NH4+ --> nitrification NO2- (reversible via nitrate reductase) --> NO3- --> nitrification (reversible via nitrate reductase) --> N2 via denitrification. Diazotrophs are the only organisms taht produce the enzyme nitrogenase (fixates N2) N2 + 8H+ + 8e- + 16 ATP + 16 H2O --> 2 NH3 + H2+ 16 ADP + 16 Pi.

Answer 168

nitrogenase rxn: aKG + NH4+ NADPH + ATP --> Glu + NADP+ + ADP + Pi fixed nitrogen in diet of organisms: a combination of glutamine synthetase and glutamate synthase rxns results in the formation of an animo acid using ammonium as the nitrogen source. nitrogenase reaction is very energetically expensive and thus the enzyme is not produced by organisms that can obtain fixed nitrogen in their diet.

Answer 169

glutamine synthetase and glutamate rxn combo: a combination of glutamine synthetase and glutamate synthase rxns results in the formation of an animo acid using ammonium as the nitrogen source.

Answer 170

amino acids that serve as nitrogen carriers: Nitrogen may be incorporated into other biomolecules by incorporating the amino acid, or through transaminase rxns, transaminase enzymes swap the carbonyl group of alpha-keto acids with the amino group of amino acids.

Answer 171

transaminase rxn: transaminase enzymes swap the carbonyl group of alpha-keto acids with the amino group of amino acids. Ex: glutamate + Pyruvate rxn

Answer 172

essential AAs: necessary in diet nonessential AAs: not necessary in diet, only animals have biosynthetic pathways for some nonessential amino acids,

Answer 173

nitrogen in Nitrogenous bases from AAs: many signaling molecules dervied from AAs ex: Epi and Norepi Catechols, Serotonin, melatonin, Tyrosine, Dopamine, vasodilator (NO) derived from arginine. AAs are nitrogen precoursors of nitrogenous bases.

Answer 174

IMP = purine nucs UMP = precursor for pyrimidine nucleotides

Answer 175

fates of purine and pyrimidine nb's: Sodium urate has poor solubility and can crystallize in joints (gout) or form kidney stones. Purines are converted to uric acid (urate) and extreted in urine. Pyrimidine catabolism produces intermediates of fatty acid metabolism, in humans, nitrogen from pyrimidine catabolism ends up in the urea cycle.

Answer 176

gout and purine degradation: Sodium urate has poor solubility and can crystallize in joints (gout) or form kidney stones. Purines are converted to uric acid (urate) and extreted in urine.

Answer 177

aa precoursor for signaling molecules: structure of signaling molecule:

Answer 178

glucogenic : catabolized to precoursors for gluconeogenesis such as pyruvate and oxaloacetate ketogenic: catabolized to acetyl-CoA for use in ketogenesis or fatty acid synth.

Answer 179

ammonotelic: excrete nitrogen as ammonia ureotelic: excrete nitrogen as urea uricotelic organsisms: uric acid requires very little water to produce a paste but requires more energy to make. Using less water is an advantage to birds as it means less weight, using less water is an adv to animals in the desert as there is less water loss, uric acid/ urate is not very toxic so it can build up in eggs.

Answer 180

urea cycle: amino acids transfer their amino groups to alpha-ketoglutarate and oxaloacetate to form Glu and ASP, Asp and Glu donate their amino groups to ultimately form urea, incorporating NH4+ into urea requires some energy investment, but excretion only requires ~ 0.05 L or H2O/gram of nitrogen extreted

Answer 181

urea: polar and requires substantial water to eliminate in urine.

Answer 182

metabolic pathway expression: compartmentalized in different cell types, or in different regions of a given cell Liver --> Fed state --> glycolysis, Fasted state --> gluconeogenesis Kideny --> gluconeogenesis Adipose tissue --> fat storage (fed state), fat break down (lipolysis) in fasted state. Muscles --> glycolysis, store energy.

Answer 183

Cori Cycle: under anaerobic conditions, muscles produce lactate which is exported to the liver for gluconeogenesis. Liver then exports the glucose back to the mucles.

Answer 184

hormones: substances produced by one tissue that effect the fxn of other tissues throughout the body insulin: released by b-cells of pancreatic islets in response to high blood [glucose]. it signals fuel abundance promoting fuel storage while limiting the release of stored fuels. glucagon: released by a-cells of pancreatic islets in response tp low blood [glucose]. it signals stored fuel release epinephrine: released by adrenal medula in response to fight or flight situations. epi and glucagon have similar effects on liver cells (promote gluconeogeneis and glycogen breakdown), muscle cells do not have glucagon receports or the enzymes for gluconeogenesis, in muscle cells, epi promotes glycolysis and glycogen breakdown. conditions which stimulate release of hormones: types of cells that produce each hormones:

Answer 185

effect of hormones on glucose (GLUT4): insulin receports initates a signaling cascade with various intracellular effects including fusion of vesicles, containg GLUT 4 transporter, w/ plasma mbn glycogen synthase: insulin signaling activates phosphatases that dephosphorylate both glycogen synthase (activating it) glycogen phosphorylase: insulin signaling activates phosphatases that dephosphorylate glycogen phosphorylatse (inhibiting it) triacylglycerol synthesis and breakdown: glycolysis: gluconeogenesis: fatty acid synthesis: b-oxidation: effects on catabolic pathways: effects on anabolic pathways:

Answer 186

Causes and treatments of Type I and II diabetes: A disorder of fuel metabolism characterized by high blood [glucose], affects ` 10 % of Americans, Type I: juvenile onset --> no insulin: autoimmune disease that kills pancreatic b-cells, treated with insulin injections Type II: adults onset --> insulin resistance: underlying cause unknown, but closely linked to obesity and inactivity, treated with lifestyle changes (improve diet/exersize), drugs that lower blood [glucose], or bariatric surgery. Hyperglycemia leads to long term affects such as cataracts, kidney failure, and cadio changes, acute affects include hypoglycemia (if too much insulin is injected) and ketoacidosis.

Answer 187

Steps of DNA replication: DNA is replicated in a semiconservative manner (one exsisting strand is present in new model. Proteins associate with a specific DNA sequence = origin of replication to open up an intital replication bubble. Helicase: Uses ATP to unwind the DNA helix single stranded binding protein: bind the single-stranded regions to prevent reannealing or nucleasse digestion of the DNA. Provides the reg struct so that sequences dont fold over DNA polymerase (I, III, ..., ... ): DNA Polymerase adds deoxynucleases to the free 3'OH of an esisting strand. DNA Pol III is the main polymerase used for replication. DNA pol delta does lagging strand synthesis and DNA pol epsilon does the leading strand. ( Most DNA polymerases have a proofreading fxn: the polymerase slows down due to the bulge causes by the mispairing and a 3'--> 5' exonuclease removes the misincorporated nucleotide. Sinse DNA polymerase extends DNA in the 5'-->3' direction, one strand is synthesized continuously ( leading strand) and the other strand is syntheszied in segements (Okazaki fragments (lagging strand). primase: introduces a short RNA primer that is complementary to the template stand. A 5' --> 3' exonuclease such as RNase H or DNA pol I removes the RNA primer from each Okazaki fragment. telomerase: the end shortening problem: linear DNA gets shorter adter a round of replication as the 5' RNA primer cannot be replaced by DNA. The soln: telomerase adds 5' TTAGGG repeasts to the 3' ends of human DNA. A reverse transcriptase that carries an RNA template that codes for a new repeat while base pairing with the previous repleat. Aster a found of replication, the shortened chromosome is missing repetitive DNA rather than essential genetic information. Cells that replicate indefinietly have telomerase activity, most cells stop expressing telomerases to protect against cancer. RNase H : A 5' --> 3' exonuclease such as RNase H or DNA pol I removes the RNA primer from each Okazaki fragment.

Answer 188

leading strand: 5'--> 3' direction strand (leading strand) DNA ( uninterrupted) lagging strand: strand that is synthezied in fragments. Okazaki fragments: smaller individual strands that synthesize the lagging strand.

Answer 189

telomeres struct and fxn: Linear DNA is susceptible to end-joining by the cell's DNA repair machinery or degredation by exonucleases. Ends of chromosomes adopt special structures called telomeres where a repleating sequencing of DNA folds into a loop and binds protective proteins.

Answer 190

mech for DNA polymerase rxn:

Answer 191

nucleosome struct and fxn: an enzyme the degrades nucleic acids,

Answer 192

proofreading activity of a polymerase: the polymerase slows down due to the bulge causes by the mispairing and a 3'--> 5' exonuclease removes the misincorporated nucleotide. Sinse DNA polymerase extends DNA in the 5'-->3' direction, one strand is synthesized continuously ( leading strand) and the other strand is syntheszied in segements (Okazaki fragments (lagging strand). accomplishment with fidelity of replication:

Answer 193

heterochromatin struct and fxn: is tightly packed (eg 30 nm fibre) and less transcriptionally active euchromatin struct and fxn: is lightly packed DNA (eg. beads-on-a-string) that is heavily transcribed

Answer 194

Characteristics: uncrontrolled cell division, results from accumulated mutations or modifications of DNA, origins: multiple dieases within multiple origins, Mutations may be induced by environmental factors (eg, sun smoke), genetic predisposition (eg. BRCA1), viral infection 9eg HPV, hep B) or spontaneous mutations.

Answer 195

UV light: promotes pyrimidine dimers (most frequently btwn thymines) benzopyrene : is oxidized in the liver and then forms an adduct with N2 of guanine, distorts helix, benzopyrene causes G--> T transversions. methylating agents: disrupt hydrogen bonding , transition G to A (purine to purine transition) ; reactive oxygen species:

Answer 196

transversion mutations: point mutations: a transversion is a mutation leading to a switch btwn purine and pyrimidine. a transition is a purine or pyrimidine to pyrmidine mutation. ex: guanine --> 8-oxoguanine caused by reactive oxygen species such peroxide and results in a G--> T transversion. a

Answer 197

abasic sites: thousands of bases are spontanrously hyrolyzed from ribose in our body each day , breaking glycosidic bond and taking off base pair bair, purines have more abasic site. deaminations: cytosine undergoes a demination rxn with water, H2O leaves behind an oxygen.

Answer 198

thymine vs uracil: DNA uses thymine instead of uracil so taht, if demination occurs, uracil is recognized as an error and can be removed.

Answer 199

base excision repair: cells that have specific glycosylases that recognize common erris, such as T-G pairs or uracil, and remove the incorrect bases. Ex: damaged base --> DNA glycosylase --> abasic site --> endonuclease --> Free hydroxyl group --> DNA polymerase + DNA ligase --> second phosphodiester bond with bp restored by enzyme leading sequence nucleotide excison repair: errors that significantly distort the helix are repaired by removing a segment of DNA surrounding the distortion. Ex: damaged nucleotide --> helicase--> endonuclease --> segment separation in need of repair --> DNA polymerase + DNA ligase --> repaired DNA strand. (Change of purine to pyrimidine. mismatch repair: scans newly synthesized stand and exices any segments with misincorporated nucleotides., Older strand is methylated , nonhomologous end-joining: broken DAN is recognized by Ku proteins, Ku proteins recruit a nuclease, that tims some nucleotides, and a DNA polymerase that adds some nucleotides, ligase connects the backbone , inherently mutagenix , radiation or free radicals can induce double-stand breaks in DNA. homologous recombination: 2nd chromosome is used as a template to repair the broken chromosone. Eg: An exonuclease toms the 5' ends at the break, --> One of the 3' ends invades a homologous segment of double stranded DNA --> DNA polymerase extends that 3' --> Resolution of the crossed -over structure yeilds two DNA segments with no breaks. alkyltransferases: transfer the methyl group to a cysteine (permanently inactivating the enzyme)

Answer 200

restriction enzymes : Type II restriction enzymes are isolated from bacteria and cut double stranded DNA within a defined recognition sequence that is usually palindromic. Complementray sticky ends allow reannealing and ligation of DNA fragments. recognition sites are directional (5' to 3'). product prediction of given DNA sequence:

Answer 201

role of restriction enzymes in prokaryotes: bacteria methylate restrtiction enzyme sites within their own genomic DNA to prevent cleavage, but the restriction enzymes will degreade viral DNA, organisms protecting genome from digestion:

Answer 202

cloning patterns of plasmids: Plasmids enginerred as cloning vectors , have origin of replication, have an antibiotic resistance gene to select for bacteria carrying the plamid, expression vectors also include transcriptional and translational control sequences, have a polylinker region (multiple cloning site) , a set of unique restriction enzyme sites that allow directional insertion of DNA fragments. plasmid engineering for recombinant protein expression: cut the gene and the vector using restriction enzymes that generate the same sticky ends, use gel electrophoresis to sparate unwanted fragments, use complementary sticky ends to anneal the gene inside vector, Cloning involves the recombination of DNA. A polypeptide od interest can be expressed by inserting a gene into a vector that may be replicated by the host organism.

Answer 203

steps of reagents for Illumina sequencing: PCR: is a technique that amplifies any DNA sequence provided some sequence information is known on either side of the target DNA to be amplified, uses Cloning , making mutants, identifying pathogens. Consisits of three steps that are repeated until the desired degree of amplification is achieved, Need template DNA, dNTPs, primers that flank the sequence to be amplified, Mg2+ buffer, and a thermostable polymerase (eg. Pfu or taq). A thermocycler quickly changes the temp of the rxn mixture , 1) ` 95 deg cel --> DNA is dentured , 2) ~60 deg cel --> Primers anneal , 3) ~ 72 deg C --> DNA olymerase enxtends the primers, DNA is effectively doubled each cycle. Primers do not need to be perfectly complementary and can introduce restriction enzyme sites or change codons (site-directed mutagenesis) as the primer is incorporated into the amplified product. CRISPR-Cas9 gene editing system: Bacteria transcribe the viral segments and teh Cas9 protein uses the resulting guide RNAs to locate and destroy any complementary DNA sequences that might be present in an invading virus. Targeted genes may be inactivated by Cas9 as nonhomoglous end-joining (NHEJ) is inherently mutagenic,resulting in a nonfuctional protein product. Genes may be edited, by homology-directed repair, (HDR) after Cas9 cleavage, if replacement DNA is introduced, the cell will repair the cut DNA based on the replacement DNA sequence (that is modified to produce a desired protein sequence). plasmids that express Cas9, and contain DNA sequences that will produce guide RNAs against specific genes, may be used in research applications.

Answer 204

sequecing application to genone length DNA: Developed to sequence thousands of DNA fragments togethe. 1) DNA polymerase incorporates a complementary nucleotide into teh new DNA chain and unreacted nucleotides are washed away 2) the incorporated nucleotide is detected by its fluroescnece, then the fluroeescent group is removed 3) a new soln of nucleotides is introduced. Genomic DNA fragmented into manageable pieces and known sequences are attached to the ends of each fragment, Fragments are linked to solid support and amplifed in place so that a given spot on the solid support includes thousands of indentical copies of the fragment. Each cycle, dATP, dCTP, dGTP, and dTTP are added with each deoxynucleotide connected to a different fluorescent group . The complementary deoxynucleotide may be added to the 3' end of a primer but the fluorescent group prevents further extension. At each spot, the fluorescent color indicates which base was added to the growing strand opposite the unknown fragment and a computer records the identity of the nucleotide. Fluroescent group are chemically cleaved and washed away leaving a free 3' OH group before beginning the next cycle. Each spot corresponds to a different unknown fragment that may be sequenced by washing the same set of reagents over all spots in each cycle. Over lapping sequences from different fragments may be assesmbled to sequence entire genomes.

Answer 205

RNAP in E.Coli in euks: have single RNA polymerase (RNAP) RNAPI: Produceds ribosomal RNA (rRNA), rRNA includes structural and catalytic components of the ribosome (~80% of cellular RNA) RNAP II: produces messenger RNA (mRNA), mRNA codies for polypeptides ( ~5% of cellular RNA) RNAP III: produces rRNA and transfer RNA (tRNA), tRNAs deliver amino acids during translation ( ~15% of cellular RNA) RNA polymerase synthesizes new RNA stands from a DNA template.

Answer 206

upstream: from 5' to 3' , direction from which polymerase/ribosime has come. downstream: 3' to 5' direction of transcription template: strand of DNA that is continuosly trasncribed non-template stand: strand of DNA that is non-continuously trasncribed non-coding/antisense/negative/ template: The DNA strand that has a sequence complementary (except for the replacement of U with T) to the transcribed RNA; it is the template strand. Also called the antisense strand. coding/sense/positive/ coding: The DNA strand that has a sequence complementary (except for the replacement of U with T) to the transcribed RNA; it is the template strand. Also called the antisense strand. exon: A portion of a gene that appears in both the primary and mature mRNA transcripts. intron: A portion of a gene that is transcribed but excised by splicing prior to translation.

Answer 207

DNA sequences numbering: a gene segment of DNA that codes for a protein (Via mRNA) or another fxnal RNA, transcription produces RNA in the 5' to 3' direction w/ no primer required.

Answer 208

histones covalent modification: may increase or repress transcription affects on gene expression at modified region: acetylation of histone Lys residues typcially loosens the DNA-histone interaction and promotes transcription, other histone modifications, ie phorphorylation, methylation, and ubiquitination have varying effects on chromatin structure and transcription that depend on the specific residue being modified.

Answer 209

core promoters: Euks have a variety of upstream and downstream elements that may vary from gene to gene. general transcription factors bind some combination of these elements and recruit RNAPII to the start site.

Answer 210

Eukaryotic transcription initiation requires 6 highly conserved general transcription factors General transcription factors (GFTs) help RNAPII locate the transcription start site and open up the transcription bubble. TFIIA: assits TBP TFIIB: helps recruit TFIIF-RNAPII to the transcription start site. TFIID: includes the TATA-bindning protein (TBP) and TBP-associated factors (TAFs) that help recurit and locate Inr and DPE TBP: works with TFIIA TFIIE: recruits TFIIH which acts as a helicase to open up the transcription bubble TFIIF: increases RNAPII's affinity for the start site, enlongate the mRNA product, and bind the nontemplate strand to stabilize the transcription bubble. TFIIH: and mediator help phosphorylate the C-terminal domain of RNAPII

Answer 211

mediator complex: Activators are connected to the transcription complex in eukaryotes using a protein complex activators: proteins that increase the ability of RNAP to transcribe a gene repressors: proteins that decrease activity of RNAP silencers & enhacers: DNA sequences that help regulate transcription

Answer 212

RNAPII struct involved in elongation and proofreading transcripts: Phosphorylation of the C-terminal domain (CTD) allows RNAP II to dissociate from mediator and some of the general transcription factors so that it can make the full-length transcript.

Answer 213

transcription termination: transcription may be intrinsically terminated when RNAP transcribes a region that pulls apart the RNA-DNA hybrid helix when the RNA base pairs with itself to form a hairpin structure. Intrinsic transcription , spontaneously essembled and tugs on DNA --> break off, force from favorable base pairing U&A makes it easier for RNA to be released. Transciption may be terminated by a Rho protein factor that specifically binds a C-rich region on the transcript and bumps RNAP off the template.

Answer 214

operons: consisit of several genes under the control of one promoter that are transcribed as one mRNA. ( tryptophan = needs to express all 6 genes ). Eukaryotes: related genes may be grouped together under the control of the same regulatory elements but are transcribed separately. ( ingest tryptophan). advantages to prokaryotes:

Answer 215

5' caps fxn: eukaryotic mRNAs are capped at the 5' end by linking a guanosine residue to the emerging mRNA via a 5'-5' triphosphate linkage. 3' poly (A) tails fxn: Eukaryotic mRNAs are polyadenylated at the 3' end. poly(A) binding proteins protect the mRNA from degredation and help control the mRNA lifetime. splicing in eukaryotic transcriptional processing: introns are removed and exons are spliced together to form the mature mRNA product.Eukaryotic mRNA is transcribed with exons (expressed regions) that code for the polypeptide sequence, separated by introns (intragenic regions which are later removed).

Answer 216

cell determination of loc of exon splicing: Splicing occurs at conserved sequences at the exon-intron junction. Splicing occurs through two transesterification rxns catalyzed by an RNA-protein complex = spliceosome or catalyzed by the RNA itself. Most human structural genes undergo altnerative splicing where different processing of the transcript produces variant mature mRNAs.

Answer 217

rRNA: RNA can act as a ribozyme since it has catalytic functional groups and can adopt specific 3D structures. Note that some ribozymes are pure RNA, while others have protein components (that are not involved in catalysis). Some ribozymes involve self-cleavage reactions and thus cannot do multiple turnovers. RNA generally has multiple functional groups and adopts unique 3-dimesional conformations just like a protein enzyme.

Answer 218

codons: nucleotides grouped in sets of 3 , codon sequence in a particular reading frame corresponds with polypeptide sequence. recgonized by three-base anticodons in tRNA, mRNA is read by the ribosome in the 5--> 3 prime direction and protein synth proceeds from n-term to c-term, AUG is both the start codon and codes for methionine , UAG, UAA and UGA are stop (nonsense/termination) codons. DNA or RNA translation:

Answer 219

initiator codon: AUG is both the start codon and codes for methionine stop/nonsense codon:UAG, UAA and UGA are stop (nonsense/termination) codons.

Answer 220

frameshift mutations: insertions or deletions of a number of nucleotide (that isnt evenly divisible by 3. point mutations: involve a single base substitution, nonsense: the new codon codes for stop missense: the new codon codes for a different amino acid, silent: new codon codes for the same amino acid conservative missense mutations:(the new codon codes for a similar amino acid (eg. Leu --> IIe) or nonconservative ( the new codon codes for a dissimilar amino acid (eg.Glu --> Val) non-conservative point mutations: there are more codons for the most common amino acids, codons for the same or similar amino acids are grouped togther.

Answer 221

codon table organization:

Answer 222

tRNA struct and fxn: serve as adapters btwn mRNA and amino acids, teh tRNA anitcodon base pairs with the codon to read the mRNA while the CCA 3' acceptor stem is linked to the appropriate amino acid.

Answer 223

wobble hypothesis: the 5' anticodon postion experiences some flexibility (wobble) in its hydrogen bonding with the 3' codon position, some organisms have less than 61 tRNAs as some tRNA anticodons can read more than one codon, changes in the 3' codon base usually code for the same amino acid.

Answer 224

charged tRNA: aminoacyl-tRNA synthetases (aaRS) are enzymes that add the correct amino acid to a given tRNA. Each aaRS recognizes a specific amino acid along with all associated tRNAs for that amino acid. steps and enzymes required to charge tRNA:

Answer 225

ribosome =ribozyme --> struct: protein-RNA complex that catalyzes the formation of peptide bonds

Answer 226

A-site: amino-acyl site binds the incoming aminoacyl-tRNA P-site: binds the tRNA with the growing polypeptide chain (charged) E-site: exit site transiently binds teh exisiting deacylated tRNA (uncharged)

Answer 227

ribosme locates correct translation start site steps: initation factor 2 (IF-2) brings the charged initatior tRNA to the start codon in the P-site ( the A site is blocked by IF-1). if the correct codon-anticodon match is made, the ribosiome will shift its conformation to interact with the first two base-pairs and promote hydrolysis of the GTP bound to EF-Tu, EF-Tu GDP departs.

Answer 228

mech for ribosome's peptidyl transferase rxn: the amino acid in the A site attacks the ester bond in the P site --> EF-G (another G protein) bumps the peptidyl-tRNA from the A site to the P site (and the deacylated tRNA from the P site to the E site). --> Ribsome recycling factor (RRF), EF-G and IF-3 remove the deacylated tRNA and separate the ribosomal subunits in preparation for another round of peptide synthesis.

Answer 229

steps for synthesis of secreted and mbn proteins: the signal recognition particle (SRP) recognizes an N-terminal amino acid sequence (pos charged residue followed by several hydrophobic residues) and stops translation. SRP targets proteins to the ER for eventual secreation or for directional insertion to organelle mbns or the plasma mbn, Vesicles move from the ER to the Golgi complex and then from the Golgi to the target mbn to deliver proteins, Proteins may be modified inside the ER and the golgi appatatus (glycosylation and disulfide formation).