Biochemistry Exam by vivi 2

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allosteric protein

-protein in which the binding of a ligand to one site affects the binding properties of another site on the same protein. -ligands that induce conformation change are called modulators -

^^The higher the energy of the cell the more inhibited pyruvate kinase becomes. Indicators of high energy levels within the cell are high concentrations of ______________________________________

ATP, Acetyl-CoA, Alanine, and cAMP.

What are the products of the ETC?

ATP, oxidized NAD+ ions, H2O

_________ and _____________ (a biosynthetic product of pyruvate) act as allosteric inhibitors of pyruvate kinase.

ATP; alanine

ATP

Adenosine triphosphate (ATP) is a high-energy compound. It fuels biochemical reactions in the cells. It's responsible for charging our metabolic engines, allowing our muscles to move and our brains to think, It supplies our enzymes with the energy they need to catalyze chemical reactions.

Aerobic Respiration

Aerobic respiration, or cell respiration occurs in the presence of oxygen,

Anabolic pathways

Anabolic pathways build new molecules out of the products of catabolism, and these pathways typically use energy. The new molecules built via anabolic pathways (macromolecules) are useful for building cell structures and maintaining the cell.

This energy-requiring process forms larger molecules by joining together smaller molecules

Anabolism

______________uses those small _________ mol. and the________ produced during _____________ to to macromolecules.

Anabolism; building block; energy; catabolism

Glycolysis is an

Anaerobic process.

free heme molecules

-reaction of oxygen at one of the two "open" coordination bonds of iron can result in the irreversible conversion of Fe2+ to Fe3+.

During glycolysis, fructose and galactose enter the liver and are phosphorylated at carbon number

The basal glucose transporters present in nearly all cells have a Km for glucose of around_________ much less than the average blood glucose concentration.

1 mM,

What are the reactants of glycolysis?

1 molecule of glucose, 2 molecules of NAD-, and 2 molecules of ATP

_____________________is most affected by __________, ______________ and ________________________

Metabolism; nutrition; hydration; physical activity **When lacking any of these, metabolism is decreased.

A deficiency in vitamin B12 would directly affect which enzyme used in nitrogen metabolism?

Methionine synthase

The ultimate source of methyl-groups for SAM (S-adenosyl-methionine) and cobalamin stems from which molecule?

Methyl-THF

7 of the 10 reactions in the glycolytic pathway have free energy values close to 0. What does this tell us about the reactions? a) they are not near equilibrium reactions b) they are not control points for pathway regulation c) they are reversible reactions d) all of the above e) none of the above

A fatty acid designated w-3 a) has 3 double bonds b) is saturated c) has a double bond 3 carbons from the alpha carbon d) has a double bond 3 carbons from the end of the chain e) contains a triple bond between two carbon atoms

For a step in a reaction pathway to serve as a control point it should be ___________ a) irreversible b) endergonic c) far from equilibrium d) both A and C e) all of the above

In the mitochondria NADH and QH2 are essentially oxidized by ___________ since it is the ferminal electron acceptor. a) carbon dioxide b) hydrogen peroxide c) ozone d) oxygen

Linoleate is an essential fatty acid in mammalian diets because mammalian cells ___________. a) synthesize it from arachidonate b) do not use this acid for biosynthesis c) can use it to synthesize eicosanoids d) do not have a desaturases that acts beyond the carbon-9 position

Much of the stability of the double-stranded DNA structure is the result of a) hydrogen bonding between purines b) the phosphodiester backbone c) the angle of the planes of the bases with respect to the helix axis d) the stacking interactions between base pair

Regions of DNA that are most easily unwound have a) about half G and half C b) alternating A and G c) Greater G:C content d) Greater A:T content

The citric acid cycle oxidizes pyruvate, and some of the pathway intermediates are starting materials for many biosynthetic pathways. This means that the citric acid cycle is ____________ a) amplifying b) catabolic c) anabolic d) amphibolic

The expression Vmax = K2[E]total applies when a) [S] is low, and the kinetics are first order in [S] b) [S] is low, and the kinetics are zero order in [S] c) [S] is high, and the kinetics are first order in [S] d) [S] is high, and the kinetics are zero order in [S] e) generally valid as long as Michaelis-Menten kinetics are obeyed

The metal ions in metalloenzymes are firmly bound at the active site of the enzyme. In catalase and cytochromes they are found attached to ___________ a) sulfur clusters b) phosphate c) vitamins d) hemes

Transcription termination a) occurs at certain DNA sequences where the elongation complex is unstable b) sometimes requires a specific protein, rho, which facilitates disassembly c) often occurs near pause sites d) all of the above

Transfer of the phosphoryl group from PEP to ADP is an example of a) mutase reaction b) isomerization c) dehydrogenase d) substrate-level phosphorylation

What type of bond links the monomers of the polysaccharide? a) carbohydrate ester bond b) glucotide bond c) aldo-keto bond d) glycosidic bond e) epimeric bond

Which is not a property of RNA polymerase? a) polymerizes in the 5'-3' direction b) catalyzes the formation of phosphodiester linkages c) polymerizes a reaction assisted by pyrophosphate hydrolysis d) has exonuclease proof-reading abilities

You are sequencing a protein sample via Edman degradation, and after the first round of degradation, you identify amino acids derivatives. Which of the following are reasonable explanations for this result? a) the sample is impure and contains multiple different proteins b) the protein is composed of several different subunits c) the protein is partially degraded d) all of the above e) none of the above)

the initial velocity of an enzyme reaction (v0) describes) a) the concentration of the enzyme at maximal velocity b) the concentration of substrate at maximal velocity c) the concentration of both at the start of the reaction d) the rate of the reaction when the substrate and enzyme are first mixed

what information can be gained by comparing the sequences pf proteins that have the same or similar function in different species? a) to determine evolutionary relationships and relatedness of species b) to determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins c) to locate highly variable residues which contribute little to the structure and function of the protein d) all of the above e) none of the above

which statement explains the cleaning action of soap on greasy dishes? a) the soap changes the water-solubility of the grease so that it is easily dissolved by the water b) the soap hydrates the grease with its polar head groups and holds it in suspension c) the soap chemically breaks down the grease into smaller, more water-soluble molecules d) the grease is trapped inside the hydrophobic interior of micelles made of soap molecules e) the soap protonates the grease, increasing its pKa, and thus the forward rate constant, k1, for dissolution

These events occur during the reactions of the citric acid cycle except: a. ATP production b. NADH and FADH2 production c. Carbon dioxide formation d. Water molecule formation

d water molecule formation

Glucose is used for a. Structure b. Energy storage c. Quick energy d. All of the above

d. All of the above

Proteins are necessary for which of the following? a. Muscle structure b. Immune system function c. Neurotransmitter production d. All of the above

d. All of the above

Unlike bacterial mRNA, eukaryotic mRNA must undergo __________ before it may be used for translation a) splicing b) capping c) polyadenylation d) export to the cytoplasm e) all of the above

What is the major driving force for protein folding? a) the hydrogen bonds that stabilize alpha helices and beta sheets b) van der waals forces c) ionic forces (salt bridges) d) covalent bonds, like disulfide bonds between cysteine residues e) the increase in the entropy of the solvent when the protein folds

Isomerization ribulose-5-phosphate

Ribulose-5-phosphate can then be isomerized by phosphopentose isomerase to produce ribose-5-phosphate. Ribose-5-phosphate is one of the main building blocks of nucleic acids. PPP is the primary source of production of ribose-5-phosphate.

Ions and water

Secreted by epithelial cells. The mechanism is the same as in pancreatic ductal cells. Secretin stimualtes ion and water secretion by the bile ducts just as it does in the pancreatic ducts.

Which of the following is a driving force for the exergonic reaction involving the second irreversible step in glycolysis?

Separation of negative charge occurs when the gamma phosphate is removed from ATP and transferred to fructose-6-phosphate (F6P).

Which of the following is a driving force for the exergonic reaction involving the second irreversible step in glycolysis?

Separation of the negative charge occurs when the gamma phosphate is removed from ATP and transferred to fructose-6-phosphate.

catalytic triad

Ser195 is linked to His57 and Asp102 in H-bonding network

Pyruvate produced in glycolysis can be used in the __________

TCA cycle

Difference between RNA and DNA

The hydroxy group on 2 prime carbon indicates RNA.

If phosphofructokinase (PFK)-1 is inhibited, which direction will the reaction catalyzed by glucose-6-phosphate isomerase (G6PI or PGI) proceed?

Toward glucose-6-phosphate

michaelis-menten equation

Vo = Vmax/2

In the Cori cycle, gluconeogenesis occurs in _______ and glycolysis in _________ a) liver; muscle b) liver; liver c) muscle; muscle d) muscle; liver

Pause sites are regions ________ sometimes causing transcription to stop completely. a) rich in GC base pairs b) rich in AT base pairs c) without palindromic sequences d) where Nus A is not present

Shifting of the reading frame by one nucleotide results in ___________ a) the production of a completely different protein that is likely non-functional b) a substitution only at the first amino acid c) the generation of homologous proteins d) a protein that has one less or one more amino acid

The carbonic acid (H2CO3)/bicarbonate (HCO3-) conjugate pair maintain the pH of blood plasma at 7.4. What is the ratio of bicarbonate to carbonic and in the blood? (pKa of H2CO3 = 6.4) a) 10 b) 1 c) 0.1 d) 1:1 e) insufficient data given to solve this problem

The net effect of the eight steps of the citric acid cycle is to a) completely oxidize an acetyl group to carbon dioxide b) convert pyruvate to succinate c) produce NAD+ and Q d) produce B ATP for every pass through the cycle

Which is not true about the lac repressor? a) its genes is part of the lac operon and is transcribed along with lacZ, lacA, and lacY. b) when it binds to DNA, it forms a loop-type structure. c) it likely blocks both RNA polymerase binding as well as transcription initiation d) it binds to DNA by interaction of an alpha helix with the major groove

Which will be different for a catalyzed reaction versus an uncatalyzed reaction? a) activation energy b) ground state energy c) free energy change d) all of the above

What is oxidation-reduction?

a chemical reaction in which an atom or ion loses electrons to another atom or ion

Where is most ATP made?

a majority of ATP is produced in the ETC

The bond that links to amino acids together is called

a peptide bond

What condition is required in the cell for pyruvate to be converted to acetyl CoA

aerobic

The NH3 produced in muscle degradation of amino acids and other nitrogenated compounds is transported through blood to the liver using ______ as a carrier

alanine

which of the following AAs would you expect to produce a similar sickling effect if substituted for Val alanine leucine lysine phenylalanine arginine

alanine leucine

The amino acid pool is

all the amino acids within the tissue and body fluids

Like PFK, pyruvate kinase is regulated both by _________________ effectors and by _________________modification (phosphorylation).

allosteric; covalent

PFK is___________________inhibited by ATP, so glycolysis is slowed when cellular ATP concentrations are ________

allosterically ; high

Name the two classification of secondary structures found in proteins

alpha helix beta sheet

Which enzyme removes the amine group from an amino acid? What is it's coenzyme?

aminotransferase; coenzyme = PLP

What is formed when an amino acid has it's amine group removed?

an alpha-keto acid

Each amino acid contains

an amine group and a carboxyl group

What are the symptoms of hyperammonemia?

an intoxicated person: slurred speech, confusion, stumbling gate, etc.

A cutthroat trout during the winter will be relatively rich in _________, allowing it to live in the icy cold waters of Yellowstone lake a) arachidonic acid b) unsaturated fatty acids c) saturated fatty acids d) eicosanoids e) all of the above

Adenylate and AMP each contain ________ phosphate group(s) a) 0 b) 1 c) 2 d) 3 e) none of the above

Alanine, valine, leucine, and isoleucine are important in 3D structure because they a) are branched b) are highly hydrophobic c) are highly hydrophilic d) attract water molecules

Amino acids with non-ionizable side chains are zwitterions when they are a) in any solution b)in solutions with pH>pKa value of their acidic group and pH<pKa value of their basic group c)in solutions with pH>pKa value of their acidic group and pH>pKa value of their basic group d) in solutions with pH<pKa value of their acidic group and pH<pKa value of their basic group e)in solutions with pH<pKa value of their acidic group and pH>pKa value of their basic group

Three phosphorous groups are connected by __________ to each other, and there are also side _______ connected to the phosphorous atoms.

oxygens; oxygens

What causes hyperammonemia, generally?

pathologies of the liver

A small chain of amino acids is called a

peptide

What biomolecule is formed at very high levels in the blood of PKU patients?

phenylalanine

what 2 AAs would be resonable candidates for the pocket-Val-6 interaction

phenylalanine leucine.

What is the most common intracellular buffer?

phosphate

What reaction generates Co2

phosphoenolpyruvate carboxylkinase

Which enzyme in glycolysis is responsible for catalyzing the "committing-step"?

phosphofructokinase

Which enzyme in glycolysis is responsible for catalyzing the rate-limiting step?

phosphofructokinase (PFK)

The ATP can power needed reactions by losing one of its ____________groups to form ______,

phosphorous; ADP

It is essential to stimulate the metabolic rate through other means such as routine _____________

physical activity

Transketolase is ........

responsible for the cleaving of a two carbon unit from xylulose-5-P and adding that two carbon unit to ribose-5-P thus resulting in glyceraldehyde-3-P and sedoheptulose-7-P.

Which enzyme-catalyzed reaction in glycolysis generates H20?

rxn catalyzed by enolase.

What are Eicosanoids

signaling molecules made by oxidation of 20-carbon fatty acids. They exert complex control over many bodily systems, mainly in inflammation or immunity, and as messengers in the central nervous system. They are derived from either Omega 6 or 3 Fatty acids.

the cetral iron atom has _____ bonds, ____ to nitrogen atoms in porphyrin, one to a _____ residue, and one to oxygen

six four histidine

The first rxn in glycolysis converts glucose to ________, and is catalyzed by ____________________?

glucose - 6- phosphate hexokinase

Which enzyme in glycolysis is responsible for "trapping" glucose in the cell?

hexokinase

^^^^It is thus most active when glucose is very ______________ in the portal vein, immediately after consumption of a carbohydrate-rich meal.

high; It has a high Vmax, allowing the liver to effectively remove excess glucose, and minimize hyperglycemia after eating. Glucokinase is not inhibited by G6P.

also in metabolism, the _____________________ are used to make ______________ones

smaller molecules; larger

In the____________, the action of ____________________ is opposed by the action of ___________________________, which hydrolytically removes phosphate in a futile cycle.

liver; glucokinase; glucose-6-phosphatase

Glucokinase, found in the _____________________and _______________ b cells, requires a much _____________ glucose concentration for maximal activity.

liver; pancreatic; higher

sort the following into lock-and-key model, induced-fit model, or common to both. 1. substrate binds to the enyzme at the active site, forming an enzyme-substrate complex. 2.enzyme active site has a rigid structure complementary to that of the substrate. 3.substrate binds to the enzyme through noncovalent interactions. 4. enzyme conformation changes when it binds the substrate so the active site fits the substrate.

lock-and-key model: 2 induced-fit model: 4 common to both: 1, 3

hill equation for pressure

log(θ/1-θ) = nlog(pO2) -nlog (P₅₀^n)

P₅₀ as function of pH

low pH : P₅₀ ~ 35 torr high pH: P₅₀ ~ 22 torr * in tissues pH is low and CO2 is high

Hexokinase has a ______ Km (________________) for glucose, so it permits initiation of ______________even when blood glucose levels are relatively low. However, its _____________ is relatively low.

low; high affinity; glycolysis; Vmax

ATP is a ___________and __________process

making and breaking Use of food energy in the mitochondria can convert the ADP back to ATP so that the energy is again available to do the needed work.

Where in the cell does the TCA cycle occur?

matrix of the mitochondria

Consequently, weight loss and weight maintenance are directly related to healthy ____________

metabolism.

What organelle does respiration take place?

mitochondria

Where does beta oxidation of medium chain fatty acids occur?

mitochondrial matrix

Nitrogen metabolism is essential for all the following biological molecules, EXCEPT __________.

monosaccharides

Nitrogen metabolism is essential for all the following biological molecules, EXCEPT __________.

monosaccharides -Nitrogen metabolism refers to the synthesis and degradation of molecules containing nitrogen atoms. All molecules listed contain nitrogen atoms, except carbohydrates.

What 2 waste products are excreted as urea?

nitrogen and CO2

order of HbS aggregation in sickle-cell anemia

no aggregation 1.[O2] decreases due to exercise or high altitude 2.R state Hb shifts to T state Hb 3. Val interacts with the 'pocket' of a beta chain on another HbS 4. additional T state HbS interact with the growing aggregation to form insoluble fiber. sickled red blood cell

Which enzyme catalyzed reaction generates an NTP?

none

What do we call the amino acids that human beings can synthesize?

nonessential

Metabolism is regulated by.......

nutrition, physical activity,

if a person were deficient in vitamin b12, which enzyme catalyzed reaction would be directly affected?

odd chain fatty acid degradation

The oxidation phase of the PPP is ________ responsible for the production of the NADPH to be used in anabolic processes.

solely

what do amylose, amylopectin, glycogen, and cellulose all have in common?

starches

Name two classes of protein in the body

structural enzymes

What are the reactants of the Krebs cycle?

the 2 molecules of pyruvic acid from glycolysis

Because Glucose is split to yield two molecules of D-Glyceraldehyde-3-phosphate, each step in the "Pay Off" phase occurs ______________ per molecule of glucose.

twice

Glutamate can enter the mitochondrial matrix and initiate removal of excess nitrogen by the __________ cycle.

urea

What are the 2 end products of the urea / ornithine cycle?

urea and arginine

Catabolism: Summary

or destructive metabolism. This is the process that breakdown molecules to obtain energy.

ATP has an _________________ as a____________

ordered carbon compound; backbone

decreased metabolism can cause

our body to store excess fat in reserve.

Where is the medium chain acyl-coa synthetase located?

outermembrane of the mitochondria

What are the reactants of the ETC?

oxygen and ADP

Why is oxygen so important in cellular respiration?

oxygen is the electron acceptor in cell respiration

Under the normal conditions in the body, each of these ___________has a ___________charge,

oxygens ; Negative

substrate product equilibrium constant

Keq = [P]/[S] ∆G'° = -RTlnK'eq

Amino acid carbon skeletons can be used to synthesize ________ or ________

Ketones or Glucose

if a person were deficient in vitamin b3, which enzyme catalyzed reaction would be directly affected?

L-3-hydroxyacyl-CoA dehydrogenase

A person who is lactose intolerant is deficient in which enzyme's activity?

Lactase

Which major metabolic product is produced under anaerobic conditions by muscle cells during intense exercise

Lactate

What is the function of the Cori cycle

Lactate produced by glycolysis is transported from the skeletal muscle to the liver for gluconeogenesis, where the glucose produced can travel back to the skeletal muscle.

Which carbohydrate does not come from plant sources

Lactose

What is the primary organ site for detoxification?

Liver

A blood sample has high concentrations of alanine transaminase (ALT). What could this indicate?

Liver tissue damage -ALT is a transaminase specific to liver cells. Liver tissue damage will cause ALT to be released from liver cells and enter into the bloodstream. Asp transaminase (AST), in contrast, is expressed in many tissues types, such as heart, liver, kidney, brain, and red blood cells.

Kd units

Which carbohydrate is formed from 2 glucose molecules?

Maltose

Average blood glucose levels typically around ________ but can go as high as _________ immediately after a rich meal.

5 mM, 12 mM

General reversible binding of protein to ligand equilibrium constant

Ka = [PL]/[P][L] Ka = association constant

Concentration

The epithelial cells of the gallbladder absorb ions and water in an iso-osmotic fashion.

cooperative binding of oxygen in Hb

-For a protein with n binding sites: P + nL ↔ PLn Ka = [PLn]/[P][L]^n θ = [L]^n/([L]^n +Kd) log(θ/(1-θ)) = nlog[L] -logKd Kd = [L].₅^n

Second Step

-G-6-P is converted to Fructose-6-phosphate by Phosphoglucoisomerase (Class: Isomerase)

Anabolism

(builds) uses those small building block mol. and the energy produced during catabolism to to macromolecules.

The enzymes responsible for catalyzing these three steps,

#hexokinase (or glucokinase) for step 1, # phosphofructokinase for step 3, # and pyruvate kinase for step 10, are the primary steps for allosteric enzyme regulation.

affectors

*H+ is an allosteric affector *CO2 is an affector *BPG is a TRUE affector

Chylomicrons (CM)

- transport dietary lipids to tissues - has the highest TAG concentration and lowest cholesterol concentration - lowest density and large size "oil tanker" - starts in small intestine and travels to liver

High Density Lipoproteins (HDL)

- transport of cholesterol from peripheral tissues to liver; excess cholesterol goes back into the liver to turn into bile salts - smallest size but most dense - transport of cholesterol directly or indirectly via other lipoproteins to the liver - reservoir of co-activating apoproteins

What is the overall yield or consumption of ATP for one turn of the urea cycle?

- 3 ATP -The urea cycle is an energetically expensive pathway. Initially two ATP molecules are required to synthesize carbamoyl phosphate. Then a third ATP is used to react citrulline and Asp in the reaction catalyzed by arginosuccinate synthetase. In all, three ATPs are directly consumed in this pathway.

ApoA-I

- co-activating apoprotein - activates PCAT (reverse transport of cholesterol) - anchors HDL to cells and activates transporter which pumps cholesterol into HDL

ApoCII

- co-activating apoprotein - activates lipoprotein lipase (LPL) - helps anchor VLDL or CM to the endothelial cell surface via heparin sulfate - stored in HDL

ApoE

- co-activating apoprotein that acts like a structural protein - used for endocytosis if chylomicron remnant and IDL - picked up from HDL while lipoprotein particle is in circulation - mediated import of IDL and CM remnants into the liver

Lipoproteins

- contain hydrophobic TAG and esterified cholesterol on the inside - coated with phospholipids and cholesterol monolayer - transport lipids through the body in the bloodstream

ApoAI

- structural apoprotein - associated with HDL - view as a marker for reverse transcription of cholesterol - holds and deposits ApoCII and ApoE - aka ApoA-I, ApoA, or ApoAII

ApoB100

- structural apoprotein - associated with VLDL, IDL, and LDL - created from full length ApoB100 mRNA - view as marker for lipoprotein carrying endogenous fats

Apo48

- structural apoprotein - associated with chylomicrons - viewed as a marker for lipoprotein carrying dietary fats - created from RNA editing of ApoB100 mRNA

Electrons want to be with protons

- the negative charges repel each other.

Low Density Lipoproteins (LDL)

- transport of cholesterol to the liver and other tissues - contains the highest cholesterol concentration and a low TAG [most cholesterol and cholesterol esters] - has two fates: endocytosed into the liver where it supplies cholesterol for bile synthesis or is endocytosed into extra hepatic tissue where it acts like a cholesterol deliver system - high levels in blood cause elevated risks of cardiac diseases due to decreased tissue uptake

Very Low Density Lipoproteins (VLDL)

- transport of synthesize or re-synthesized lipids to tissues - smaller size than CM but greater density - deliver de novo TAG to peripheral tissues - start in liver and can return to liver or be transported to peripheral tissues (extrahepatic tissues - delivery of cholesterol) - formed in the ER around ApoB100 and secreted through Golgi via COPII vesicles

Intermediate Density Lipoproteins (IDL)

- transport to liver or conversion to LDL - has two fates: endocytosed in the liver or converted to LDL through hepatic lipase

Third Step

-**Committed step: this reaction after making fructose -1, 6 biphosphate MUST go FORWARD. Fructose-6-phosphate is phosphorylated by ATP via the enzyme Phosphofructokinase (Class: Transferase) to yield D-Fructose-1,6-bisphosphate

BPG

-2,3-bisphosphoglycerate -interaction of BPG with Hb is an example of heterotropic allosteric modulation. -increases P₅₀ to ~ 22 torr of deoxyHb

What is the overall yield or consumption of ATP for one turn of the urea cycle?

-3atp

Cl effect

-Cl⁻ stabilizes the H⁺ on Val which causes the release of H⁺ -example of how H-bonding can be modulated by outside molecules.. Cl⁻ effectors. Val-C-NH₃⁺ --- Cl⁻ ---2(NH2)⁺C-Arg (plus is shared between the 2 NH2)

Fourth Step

-D-Fructose-1,6-bisphosphate is then cleaved into two, three carbon molecules; Dihydroxyacetone phosphate (DHAP) and D-Glyceraldehyde-3-phosphate (G-3-P)(GLAP) by the enzyme Fructose bisphosphate aldolase (Class: Lyase)

T → R transition

-Perutz proposed that transition is triggered by changes in the positions of key amino acid side chains surrounding the heme. -deoxy Hb undergoes a 15° rotation. -DeoxyHb → OxyHb: His94⁺- - - ⁻Asp146 →→→salt bridge broken →→His94⁺ ⁻Asp146 Arg141 - - - Asp126 →→ Arg141⁺ ⁻Asp126 (arg141 and asp126 are in α1)

Phase 1: Priming Step

-Requires ATP ****(2) -Glucose is substrate -First reaction is catalyzed by Hexose Kinase -***Regulatory Step (The enzyme can be regulated)

T state Hb

-Tense, stabilized by a greater number of ion pairs. -P₅₀ = 63 torr -when O2 binding in T state it triggers change in conformation to the R state.

prosthetic group

-a coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein.

covalent catalysis

-a transient covalent bond is formed between the enzyme and the susbstrate A-B + X → A-X +B → A+X +B

phases of chymotrypsin

-acylation phase: peptide bond is cleaved and an ester linkage is formed between the peptide carbonyl carbon and the enzyme -deacylation phase: the ester linkage is hydrolyzed and the nonacylated enzyme is regenerated.

lyases

-addition of groups to double bonds, or formation of double bonds by removal of groups

cofactor

-additional chemical component required by enzyme for activity -ex: Fe2+, Mn2+, Zn2+

Transition state theory

-affected by thermodynamics, concentration/orientation, temperature. -thermo: highly exergonic: very slow, ∆G is huge. -conc./orientation: collision frequency.. H2 and O2.. if axis parallel no rxn, if axis perpendicular rxn goes. -temp: collision rate αv =√3KT/m k -boltzman

Hill plot

-allows you to see immediately that a protein is or is not cooperative in binding.

blood saturation

-arterial blood: hemoglobin is ~96% saturated -venous blood: hemoglobin is ~64% saturated

-association constant -provides a measure of the affinity of the ligand for the protein. -units of M⁻¹ -a higher Ka value corresponds to a higher affinity of the ligand for the protein.

Bohr Effect

-at relatively low pH and high CO2 concentration the affinity of Hb for oxygen decreases as H+ and CO2 are bound, and O2 is released to the tissues. -in capillaries of the lungs, as CO2 is excreted and the blood pH rises, the affinity of Hb for oxygen increases and bind more O2. - at equilibrium: HHb⁺ + O₂ ↔ HbO₂ + H⁺

why can you use hemoglobin to transport oxygen..

-because hemoglobin is a tetramer and undergoes a conformation change -O2 binding to individual subunits of Hb can alter the affinity for O2 in adjacent subunits. - the first O2 that interacts with deoxyhemoglobin binds weakly because the subunit is in T state. -after first O2 binding Hb goes from T to R and makes it easier for addition O2 to bind and so on to the next subunit.

myglobin vs hemoglobin in oxygen storage

-because of hyperbolic binding curve for oxygen Mb is relatively insensitive to small changes in concentration of dissolved oxygen and functions well as an oxygen-storage protein. -hemoglobin functions better as an oxygen-transport protein

mixed inhibitor

-binds at site distinct from substrate active site but it binds to either E or Es.

uncompetitive inhibitor

-binds at site distinct from the substrate active site and, unlike a competitive inhibitor, binds only to the ES complex.

ATCase

-binds when too much CTP -makes it go from R to T to stop synthesis of CTP -CTP synthesis depends on [ATP] through feedback regulation. -ATP is an allosteric regulator of ATCase -increase CTP, increase ATP

other pathway for CO2 alimination

-carbonylation R-NH₂ + CO₂ → R-NH-COO⁻ + H⁺ (salt bridge reformed) *salt bridge is a pH dependent process

urease

-catalyzes hydrolysis of urea

DNA polymerase

-catalyzes the polymerization of nucleotides to form DNA

competitive inhibitor

-competes with the substrate for the active site of an enzyme -reversible

holoenzyme

-complete, catalytically active enzyme together with its bound coenzyme and/or metial ions.

coenzyme

-complex organic or metalloorganic molecule required by enzyme for activity. -act as transient carries of specific functional groups. -most are derived from vitamins

-dissociation constant -reciprocal of ka -units of M -when L is equal to kd, half the ligand-binding sites are occupied. -lower value for kd corresponds to a higher affinity of ligand for the protein. -kd is equivalent to the molar concentration of ligand at which half the available ligand-binding sites are occupied and at this point the protein is said to reach half-saturation with respect to ligand binding.

binding energy, ∆Gb

-energy derived from enzyme-substrate interaction. -major source of free energy used by enzymes to lower the activation energies of reactions.

rate of enzymatic reaction is affected by?

-enzyme -substrate -effectors -temperature

what does an enzyme do

-enzymes represent a special case of proteins that bind and chemically transform other molecules.. they catalyze reactions.

fetal Hb

-fetal Hb must have a higher affinity for O2 than adult. -fetal Hb synthesizes γ subunits rather than β. -fetal Hb has much lower affinity for BPG than adult Hb.

cooperative binding

-form of allosteric binding -the binding of one ligand affects the affinities of any remaining unfilled biding sites. -sigmoid binding curve is diagnostic of cooperative binding. -permits a much more sensitive response to ligand concentration.

ligases

-formation of C-C, C-S, C-O , and C-N bonds by condensation reactions coupled to ATP cleavage.

allosteric enzymes

-function through reversible, noncovalent binding of regulatory compounds.

allosteric effectors

-generally small metabolites or cofactors.

sickle-cell anemia

-genetic disease where individuals inherit the allele for sickle-cell hemoglobin from both parents. -unusually large number of immature cells -blood contains many long, thin, crescent-shaped erythrocytes. -when Hb from sickle-cells is deoxygenated it becomes insoluble and forms polymers that aggregate into tubular fibers. -the insoluble fibers are responsible for the deformed sickle shape. -results from a single amino acid substitution, a Val instead of a Glu residue at position 6 in the two β chains. -capillaries become blocked -Hb content of their blood is only about half of normal value. -sickle cells are very fragile they rupture easy resulting in anemia. -

reaction coordinate ground state

-ground state is the bottom of products and reactants. -catalysts enhance reaction rates by lowering activation energies

transferases

-group transfer reactions

stabilizing ES complex

-hydrogen bonds -hydrophobic and ionic interactions

hydrolases

-hydrolysis reactions (transfer of functional groups to water)

catalytic or active site definition

-in an enzyme the binding site is called a catalytic site or an active site.

V₀ equation

-intial rate

metal ion catalysis

-ionic interactions between enzyme-bound metal and substrate can help orient the substrate for reaction or stabilize charged reaction transition states. -mediate oxidation-reduction reactions by reversible changes in the metal ion's oxidation state. -pka shifters

protein ligand binding points, involving kd.

-kd is equivalent to the molar concentration of ligand at which half the available lingand-binding sites are occupied and at this point the protein is said to reach half-saturation with respect to ligand binding. -the more tightly a protein binds to a ligand, the lower the concentration of ligand required for half the binding sites to be occupied and thus the lower the value of kd.

modulators

-ligands tha induce conformation change are called modulators. -may be either inhibitors or activators. -O2 is both a ligand and an activating homotropic modulator.

Myoglobin.. heme

-myoglobin has 153 amino acid resides and 1 molecule of heme. -8 α-helical segments -heme related His: His⁹³

what does hemoglobin transport

-nearly all the oxygen required by cells from lungs to tissues. -~40% of the total H+ and 15% to 20% of the CO2 formed in the tissues to the lungs and the kidneys.

nh less than 1

-negative cooperativity -the binding of one molecule of ligand impedes the binding of others.

nh greater than 1

-positive cooperativity -Hb -binding of one molecule of ligand facilitates the binding of others.

chymotrypsin

-protease- enzyme that catalyzes the hydrolytic cleavage of peptide bonds. -specific for peptide bonds adjacent to aromatic AA residues(Trp, Phe, Tyr) -example of general acid-base and covalent catalysis -enhances the rate of peptide bond hydrolysis by a factor of at least 10⁹ . -a transient covalent acyl-enzyme intermediate is formed. -two phases: acylation phase, deacylation phase. -also catalyzes the hydrolysis of small esters and amides.

BGP interaction with Hb

-reduces the affinity of Hb for oxygen. -HbBPG + O₂ ↔ HbO₂ +BPG -BPG binds at a site distant from the oxygen-binding site and regulates the O2-binding affinity of Hb in relation to the pO2 in the lungs. -site of BPG binding is in the cavity between the β subunits in the T state. -cavity is lined with positively charged amino acids residues that interact with the negatively charged groups of BPG. -only one BPG is bound to each Hb tetramer. -BPG lowers Hb affinity for O2 by stabilizing the T state. -transition to the R state narrows the binding pocket for BPG precluding BPG binding.

R State Hb

-relaxed -P₅₀ = 0.43 torr -oxygen has a higher affinity for Hb in R state. -oxygen binding stabilizes the R state.

reason of sickle-cell anemia

-single amino acid substitution -Val instead of Glue -at position 6 in the 2 β chains.

binding site

-site on protein where ligand binds. -its complementary to the ligand in size, shape, charge, and hydrophobic or hydrophilic character.

Hill Equation

-slope: nh (Hill coefficient) -hill coefficient: measure of the degree of cooperativity. -if nh =1, ligand binding is not cooperative -if nh is greater than 1, positive cooperativity(Hb) -nh less than 1, negative cooperativity.

acid-base catalysis

-specific: catalysis that use only H+ and OH- ions present in water . -general: proton transfers mediated by other classes of molecules -general only occurs when the unstable reaction intermediate breaks down faster than the protons can be transfered to or from water.

treatment of hemoglobin with with urea

-tends to cause the tetramer to disassemble into αβ dimers. -dimers stay intact with hydrophobic interactions predominating at the interfaces, but also some hydrogem bonds and a few ion pairs(salt bridges)

hemoglobin structure

-tetrameric protein containing four heme prosthetic groups. -adult Hb contains 2 types of globin: 2 α and 2 β chains. -features interactions between unlike subunits: α₁β₁ and α₂β₂ interact strongly.

O2 binding to free heme

-the axis of the oxygen molecule is positioned at an angle to the Fe-O2 bond (a). -when CO binds to free heme the Fe, C, and O atoms lie in a straigh line (b).

induced fit

-the binding of protein and ligand is often coupled to a conformational change in the protein that makes the binding site more complementary to the ligand, permitting tighter binding. -its the structural adaptation that occurs between the protein and ligand.

Heme in Hb/Mb

-the coordinated nitrogen atoms help prevent conversion of the heme iron to the ferric (Fe3+) state....The Fe2+ state binds oxygen reversibly while the Fe3+ state doesnt bind oxygen. -in heme attacted to proteins, binding to oxygen is prevented by keeping the heme deep inside the protein structure, keeping the two open coordination bonds restricted. -one open coordination bond is occupied by a side chain nitrogen of a His residue.

substrate definition

-the molecules acted upon by enzymes are called substrates rather than ligands.

nh = n

-theoretical upper limit of nh is reached when nh=n -binding would be completely cooperative meaning all binding sites on the protein would bind ligand simultaneously, an no protein molecules partially saturated with ligand would be present in any conditions. -this lime is never reached in practice -nh is always less than the actual number of ligand-binding sites in the protein.

irreversible inhibition

-those that bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme's activity.

His⁶⁴ myoglobin importance...

-too far away to coordinate with the heme iron but it does interact with a ligand bound to heme. -His⁶⁴ called distal His and it doesn't affect the binding of O2. -may preclude the linear binding of CO, providing one explaination for the diminished binding of CO to heme in Mb/Hb. -because of His⁶⁴ CO is forced to bind at an angle which weakens the binding of CO to Mb/Hb

oxidoreductases

-transfer of electrons (hydride ions or H atoms)

isomerases

-transfer of groups within molecules to yield isomeric forms

heterotropic

-when modulator is a molecule other than the normal ligand.

homotropic

-when normal ligand and modulator are identical.

H+ binding in Hb

-when protonated, the residue His¹⁴⁶ forms one of the iron pairs to Asp⁹⁴ -stabilizes the T state.

Muscle and fat cells express a third type of glucose transporter, with a Km around _________.

5 mM The level of expression of this transporter on the cell surface is rapidly regulated by insulin.

which of the following statements about hemoglobin and myoglobin structure are true: 1. molecular oxygen binds reversibly to Fe2+ in a heme. 2. each iorn atom can fomr six coordination bonds: 2 of these are formed between iron and oxygen. 3. by itself, heme is not a good oxygen carrier. it must be part of a larger protein to prevent oxidation of the iron atom. 4. each hemoglobin or myoglobin molecule can bind four oxygen molecules. 5. both Hb and Mb contain a prosthetic group called heme, which contains a central iron atom. 6. heme is composed of an organic protoporphyrin component and a metal atom. 7. Hb is a heteroteteramer, where as Mb is a monomer.

1, 3,5,6,7

Which of the following statements about enzymes are true: 1. Catalysis occurs at the active site, which usually consists of a crevice on the surface of the enzyme. 2. Generally, an enzyme is specific for a particular substrate. For example, thrombin catalyzes the hydrolysis of the peptide bond between Arg and Gly. 3. An enzyme yields a specific product, whereas a nonbiological catalyst may produce more than one product, and side reactions may occur. 4. Nonbiological catalysts and enzymes tend to have a similar degree of reaction specificity. 5. A substrate must bind to the active site before catalysis can occur.

1,2,3,5

which of the following are characteristics of allosteric enzymes. 1. may have binding sites for regulatory molecules that are separate from active sites. 2. generally have more than one subunit. 3. tend to have a hyperbolic curve V0 vs. [S]. 4. interconvert between a more active form and less active form. 5. conform to Michaelis-Menten kinetics.

1,2,4

identify the true statements regarding the heme group of Mb and Hb: 1. heme group is conjugated. 2. the t state of Hb has lower affinity for O2 than the R state because the Fe-Nporphyrin bonds are lnger 3. the globin chains of Mb and Hb prevent the oxidation of Fe2+ to Fe3+ 4. Mb contains one heme group. 5. the cooperativity of oxygen binding in Hb arises from electronic interactions between heme groups. 6. a heme group contains 4 pyrrole rings, which are linked via methene bridges. 7. the iron in the heme group can form six bonds, the fifth is with an imidazole ring of a histidine and the sixth is with oxygen.

1,2,4,6,7

which statements are true: 1. one HIS residue abstracts a proton from the substrate at pH 6.0 whereas the other donates a proton. 2. The RNAse reaction is an example of metal ion catalysis with a positvely charged metal. 3. There are two HIS residues, and both are deprotonated below pH 4.2. 4. Both HIS residues are deprotonated at pH higher than 6.5 5. The substrate is affected by the change in pH, and is inactive(+ charged) when pH is above ~6.0.

1,4

Phosphofructokinase is regulated by which of the following?

1. Allosteric inhibition 2. Allosteric activation 3. Product inhibition

Aerobic respiration _____________ ATPs and _____ require oxygen

38 does

What are the 3 carriers of nitrogen, and what distinguishes each?

1. Glutamate: 1 amine group transferred moves WITHIN cells aminotransferase-makes glutamate glutamate dehydrogenase-opposite 2. Glutamine 2 amine groups transferred moves BETWEEN cells 3. Alanine from muscles

which ligand binds tightest: 1. ligand A, with kd =10⁻⁹ M 2. ligand B, with kd = 10⁻³ M 3. ligand C, with a percent occupancy of 30% at 1µM 4.Ligand D, with a percent occupanct of 80% at 10µM

1. Ligand A.

Depending on relative needs of a cell for ribose-5-phosphate, NADPH, and ATP, the Pentose Phosphate Pathway can operate in various modes, to maximize different products. ........3 Scenarios are........

1. Ribulose-5-phosphate may be converted to ribose-5-phosphate, a substrate for synthesis of nucleotides and nucleic acids. -The pathway also produces some NADPH. 2. Glyceraldehyde-3-phosphate and fructose-6-phosphate, formed from the 5-carbon sugar phosphates, may be converted to glucose-6-phosphate for reentry into the linear portion of the Pentose Phosphate Pathway, maximizing formation of NADPH. 3. Glyceraldehyde-3-phosphate and fructose-6-phosphate, formed from the 5-carbon sugar phosphates, may enter Glycolysis, for synthesis of ATP. The pathway also produces some NADPH.

Products of gluconeogenesis

4 ADP 2 GDP 4 NAD+ 6 Pi Glucose

What 3 reactions does PLP catalyze?

1. Transamination of Amino Acids 2. Racemization 3. Decarboxylation (when a nitrogen transfer is involved, otherwise TPP)

What are the 2 sources of nitrogen for the urea cycle?

1. carbamoyl phosphate 2. aspartate

transition states analogs are usually... 1. competitive inhibitors 2. noncompetitive inhibitors. 3. uncompetitive inhibitors.

1. competitive inhibitors.

What is the order of events in cellular fatty acid oxidation?

1. fatty acid oxidation 2. carnitine shuttle 3. beta-oxidation

two principles which provide explaination for how enzymes use noncovalent binding energy.

1. much of the catalytic power of enzymes is ultimately derived from the free energy released in forming many weak bonds and interactions between an enzyme and its substrate. this binding energy contributes to specificity as well as to catalysis. 2. weak interactions are optimized in the reaction transition state; enzyme active sites are complementary not to the substrates per se but to the transition states through which substrates pass as they are converted to products during an enzymatic reaction.

What is the sequence of event from start to finish in beta-oxidation?

1. oxidation 2. hydration 3. oxidation 4. thiolysis

predominant physical and thermodynamic factors contributing to ∆G, the barrier to reaction

1. reduction in entropy 2. solvation shell of H-bonded water the surrounds and helps to stabilize most biomolecules in aqueous solution 3. the distortion of substrates that must occur in many reactions 4. the need for proper alignement of catalytic functional groups on the enzymes. -binding energy can be used to overcome all of these barriers.

What are the 5 basic steps for breakdown of amino acids?

1. remove amino group 2. take amino group to liver for nitrogen excretion 3. entry into mitochondria 4. prepare nitrogen to enter urea cycle 5. urea cycle

steps of chymotrypsin

1. when substrate binds, the side chain of the residue adjacent to the peptide bond to be cleaved nestles in the hydrophobic pocket on the enzyme, positioning the peptide bond for attack. 2. interaction of Ser195 and His57 generates a strongly nucleophilic alkoxide ion on Ser195, the ion attacks the peptide carbonyl group, forming a tetrahedral acyl-enzyme, accompanied by formation of a short-lived negative charge on the carbonyl oxygen of substrate, which is stabilized by hydrogen bonding in the oxyanion hole. 3. collapse of tetrahedral intermediate, re-formation of a double bond with carbon displaces the bond between carbon and the amino group of the peptide linkage, breaking the peptide bond. the amino leaving group is protonated by His57 facilitating its displacement. 4. incoming water molecule is deprotonated by general base catalysis, generating strong nucleophilic hydroxide ion. attack of the hydroxide on the ester linkage of the acyl-enzyme generates a second tetrahedral intermediate, with both oxygen in the oxyanion hole again taking on a negative charge. 5. collapse of the tetrahedral intermediate forms the second product, a carboxylate anion and displaces Ser195. 6. diffusion of the second product from the active site regenerates the free enzyme

The net cost of gluconeogenesis

4 ATP 2 NADH 2 GTP

Given these phases of aerobic respiration list the phases in order 1. Acetyl-coenzyme A formation 2. citric acid cycle 3. Electron-transport chain 4. Glycolysis

4 Glycolysis 1 acetyl-coenzyme A formation 3 Citric Acid cycle 2 Electron transport chain

Wherein a eukaryotic cell does glycolysis occur?

cytosol

Glycolysis has _____ different steps

Hexokinase performs step ____of glycolysis in most tissues, including__________and __________.

1; muscle ; brain

Before the payoff phase of glycolysis can begin, the cell needs to invest _____ ATP

How many CO2 molecules are released during one round of the Citric Acid Cycle?

Glycolysis has ____ phases

2 -There is an "input" of energy in phase 1

what are the products of the Krebs cycle?

2 ATP, 6 NADH, 2 FADH2, 4CO2

What are the products of glycolysis?

2 molecules of pyruvic acid, 2 molecules of NADH, and 4 molecules of ATP

What is the 2nd step in the urea cycle?

2 parts: 1. An ATP is used to convert Citrulline into citrullyl-AMP intermediate. 2. Which condenses with aspartate, i.e. the 2nd source of nitrogen) to form argininosuccinate.

What is used in gluconeogenesis

2 pyruvate 4ATP 2 GTP 2 NADH 6 H2O 2 H+

The net products of glycolysis are __________.

2 pyruvates (Pyr), 2 ATP, and 2 NADH

The net products of glycolysis are

2 pyruvates, 2 ATP, 2 NADH

Which of the following interactions can contribute to the intrinsic binding energy during enzymatic catalysis: 1. permanent covalent bonding 2. electrostatic interactions 3. nucleophilic attack by serine 4. hydrogen bonding 5. van der waals interactions

2, 4, 5

Anaerobic respiration produces _____________ ATPs and _____________ as a waste product

2, lactic acid

What effects are produced by an enzyme on the general reaction below S ↔ P k1→ k2← 2. the activation energy for the reaction is lowered. 3. the rate constant for the reverse reaction (k2) increases. 4. ∆G for the reaction decreases. 5. The formation of the transition state is promoted. 6.The concentration of the products is increased.

2,3,5

Step 4 Pay off

2-Phosphoglycerate is then converted to phosphoenolpyruvate (PEP) by Enolase. H2O, potassium, and magnesium are all released as a result.

How many common amino acids are there?

There are a total of __ amino acids and _______ are considered essential

20;9

A disaccharide is _____ monosaccharides joined together covalently by a

2; Glycosidic bond

Step 3 Pay off

3-Phosphoglycerate is then converted into 2-Phosphoglycerate by Phosphoglycerate mutase in preparation to yield another high energy molecule

How many total ATP are made from the complete oxidation of 1 glucose molecule to CO2 and H2O

How many carbon atoms do each of the following molecules contain? 1. Glucose- 6- phosphate 2. Glyceraldehyde-3-phosphate 3. Pyruvate

6 3 3

How many carbon atoms do each of the following molecules contain? 1. Glucose-6-phosphate (G6P) 2. Glyceraldehyde-3-phosphate (GAP) 3. Pyruvate (Pyr)

6, 3, and 3

6-phospho-D-gluconate is oxidized by NADP+ in the presence of ______________________________________ which yields ribulose-5-phosphate

6-phosphogluconate dehydrogenase

Glucose-6-phosphate dehydrogenase deficiency

600 million people are affected by this disease. Occur mainly in Africa, Asia and the Meditteranean. Affects 1 out of 10 African American males in the US. G6PD Deficiency is an inherited genetic disorder. It cannot pass from one person to another.

How many molecules of FADH, NADH, and acetyl coa are produced by beta oxidation of a 17 fatty acid (ODD)

7, 7, 7

cutting of one bond with the accompanying rearrangement is sufficient to liberate about _______________________________________

7.3 kilocalories per mole = 30.6 kJ/mol. This is about the same as the energy in a single peanut

What is the normal pH of the blood?

7.35-7.45

How many cycles of beta oxidation are required to metabolize a 20 acyl-coa?

suppose that an arginine residue in the active site of an enzyme was mutated to alanine. as expected, the alanine mutant was inactive, suggesting that the arginine residue was critical to the catalytic mechanism. which mutantion is most likely to restore wild-type level of activity to the alanine mutant. a to e a to k a to m a to y a to s

A TO K

What is a buffer?

A buffer is an aqueous solution that has a highly stable pH. If you add acid or base to a buffered solution, its pH will not change significantly. Similarly, adding water to a buffer or allowing water to evaporate will not change the pH of a buffer.

The energy released by oxidation of glucose is stored as

ADP

Step 5 Pay off

ADP is once again phosphorylated, this time at the expense of PEP by the enzyme pyruvate kinase to yield another molecule of ATP and pyruvate. This step is regulated by the energy in the cell.

Step 2 Pay off

ADP is then phosphorylated at the expense of 1,3-Bisphosphoglycerate by the enzyme Phosphoglycerate kinase (Class: Transferase) to yield ATP and 3-Phosphoglycerate (3-PG)

Uric acid is an intermediate in the breakdown of __________.

AMP

Uric acid is an intermediate in the breakdown of __________.

AMP -Uric acid is an intermediate in the degradation of purine bases and, therefore, of the options given, only AMP contains a purine. UTP contains a pyrimidine nitrogenous base. Gln and Arg are amino acids.

Hexosekinase requires........

ATP

PFK is inhibited by high concentrations of

ATP

Phosphofructokinase (PFK) -1 is inhibited by high concentrations of __________.

ATP

The energy currency of the cell is

ATP

A deficiency in vitamin B6 would directly affect which enzyme used in nitrogen metabolism?

Alanine transaminase -Vitamin B6, which is pyridoxine, is a precursor to pyridoxal phosphate (PLP), which is a coenzyme needed by transaminases, like alanine transaminase and other enzymes that alter the alpha, beta, or gamma carbons of amino acids. Dihydrofolate reductase is part of the synthesis of tetrahydrofolate and would be affected by a deficiency in folic acid, or vitamin B9. Glutamate dehydrogenase uses NAD(P)H, which requires niacin, or vitamin B3, as a precursor. Methionine synthase requires THF and Vitamin B12.

Monosaccharides are

Aldoses and ketoses

The two kinds of monosaccharides are

Aldoses, Ketoses

Phospholipids and cholesterol

Also secreted into bile by hepatocytes, and are included in the micelles with the products of lipid digestion. Like the bile salts, phospholipids are amphipathic and aid the bile salts in forming micelles. The hydrophobic portions of the phospholipids point to the interor if the micelle, and the hydrophilic portions dissolve in the aqueous intestinal solution.

Summary of Glycolysis

Although four ATP molecules are produced, the net gain of glycolysis is only two ATP because two ATP molecules are used during the "Priming Step". Red blood cells depend on glycolysis as their sole source of ATP in order to survive, because they do not have mitochondria. Cancer cells and stem cells also use glycolysis as the main source of ATP (process known as aerobic glycolysis, or Warburg effect).

Which class of biomonomer does ornithine belong?

Amino acid

Which class of biomonomer does ornithine belong?

Amino acid -Ornithine is classified as an amino acid, although it's not one of the 20 amino acids because it is not incorporated into proteins via translation. Ornithine does have the correct connectivity to be an amino acid with an amino group attached to the alpha-carbon of a carboxylic acid. Monosaccharide are polyhydroxy-ketones or aldehydes and do not have any nitrogen atoms. Fatty acids have hydrocarbon chain attached to the alpha-carbon of a carboxylic acid and they also do not contain nitrogen atoms. Sterols possess a unique steroid nucleus and they also do not contain nitrogen. Nucleotides are made of phosphate, ribose sugar, and a nitrogenous base (either purine or pyrimidine).

Which of the following is not a direct product of ammonia assimilation?

Arg

Which of the following is not a direct product of ammonia assimilation?

Arg -Since ammonia is toxic to cells, this molecule must be readily converted to other molecules. There are a number of reactions that assimilate ammonia, the products of which can be Asn, Gln, Glu, or carbamoyl phosphate. Arginine is not one of these products.

What is the fourth step of the urea cycle?

Arginine breaks into urea and ornithine. Urea is transported to the kidneys for excretion, and ornithine is recycled throughout the urea cycle.

What is the third step of the urea cycle?

Argininosuccinate breaks into fumarate and arginine. Fumarate becomes an intermediate in the Aspartate-arginino-succinate shunt of the citric acid cycle.

Ejection of bile

Begins within 30 minutes after meal is ingested. The major stimuli is from CCK, in respons to aa/peptides, fatty acids.

Bilirubin

Bilirubin, a yellow colored byproduct of hemoglobin metabolism is the major bile pigment, the spleen (reticuloendothelial) will degrade hemoglobin, yielding bilirubin, which is carried in blood bound to albumin. The liver extracts bilirubin from blood and conjugates it with glucoronic acid to form bilirubin glucuronide, whoch is secreted into the bile. This is also called conjugated bilirubon, is secreted into the intestine as a component of bile. In the intestinal lumen conjugated bilirubin is converted back to bilirubin then into urobilinogen by intestinal bacteria. A portion is recycled to the liver, and a portion is excreted in the urine, and a portion is oxidized to urobilin and stercobilin, the compounds that give stool its dark color.

How are the syntheses of cobalamin and SAM (S-adenosylmethionine) analogous?

Both of them nucleophilically attack the 5' carbon of ATP.

How are the syntheses of cobalamin and SAM (S-adenosylmethionine) analogous?

Both of them nucleophilically attack the 5' carbon of ATP. -Cobalamin and SAM are covalently bound to the nucleoside of ATP. The synthesis of these two different molecules requires nucleophilic attack at the 5' carbon of the ribose and the three phosphates are cleaved. Only these two molecules are known to attack ATP at this specific atom.

Kd equations

Kd = [P][L]/[PL] [PL] = [P][L]/kd θ = [L]/([L]+kd) -when L is equal to kd, half the ligand-binding sites are occupied.

Order the Lipoproteins from Largest Size to Smallest Size

CM > VLDL > LDL > HDL

Which of the following is not a product of glycolysis: CO2 NADH ATP Pyruvate

CO2

primary pathway for CO2 alimination

CO2 +H2O →→→→HCO3⁻ (aq)+ H⁺(aq) carbonic anhydrase *carbonic anhydrase leads to drop in pH

what catalyzes the "committing step" in fatty acid oxidation?

Carnitine shuttle

What is the function of cholic acid in TAG digestion?

Cholic acid is an amphipathic lipid that breaks large lipid globules into smaller lipid droplets. it is a main component of bile salts it is produced in the liver it is stored in the gallbladder

Which lipoprotein particles primary function is to transport dietary TAGs?

Chylomicron

Order the lipoprotein particles from smallest to largest

Chylomicron > VLDL > LDL > HDL

The 6-carbon molecule that is formed by the addition of acytyl CoA to ocaloacetate is

Citrate

Dietary fiber is

Complex Carbohydrates Cellulose Divided into soluble and insoluble

What is step 1 of the urea cycle?

Condensation of Ornithine with carbamoyl phosphate to form citrulline.

Which metabolic step is irreversible? What consequence does that have for gluconeogenesis?

Conversion of pyruvate to Acetyl CoA - less efficient

Hexosekinase

Converts Glucose to Glucose-6-Phosphate

Where does the final reaction, generating urea, take place in a eukaryotic cell?

Cytosol

Nature uses the D or L form of carbohydrates

Step 1 Pay off

D-Glyceraldehyde-3-phosphate is phosphorylated at the 1 carbon by the enzyme Glyceraldehyde-3-phosphate dehydrogenase to yield the high energy molecule 1,3-Bisphosphoglycerate (BPG)

RNA can turn back into

DNA via Reverse Transcription

CTP used in

DNA/RNA synthesis

general enzyme-catalyzed reaction.

E + S ↔ ES ↔ E + P

The reaction N2 + 3 H2 ← → 2 NH3 is thermodynamically favorable. However, the activation energy barrier is very high. Which of the following is not a method used by the nitrogenase complex enzyme for overcoming this barrier?

Energy is released when the two enzymes (dinitrogenase and dinitrogenase reductase) bind due to a lowering of entropy.

Energy is released when the two enzymes (dinitrogenase and dinitrogenase reductase) bind due to a lowering of entropy. -The two enzymes of the nitrogenase complex need to associate in order to pass electrons through and reduce N2 to ammonia. This association has an entropic cost and therefore does not release energy. All other answer choices are correct. Binding of ATP, hydrolysis of ATP, and passing electrons in a favorable direction all release energy that helps lower the activation energy of this reaction.

Catabolic reactions makes _________or released as ________

Energy; heat

_________ and _______ are involved in catalyzing the glycolytic reactions

Enzymes; ATP

Pyruvate kinase is activated by ________________ in the ___________.

F-1,6-BP; liver

In the third step, _____________ is converted to ___________________________ by the enzyme ____________________

F-6-P; Fructose-1,6-bisphosphate; Phosphofructokinase (Class: Transferase)

T/F All amino acids are essential amino acids

False

T/F The major excretory product of amino acid catabolism is ammonia

False

T/F Methionine is the only amino acid that contains sulfur.

False- cysteine also does

T/F Protein synthesis is decreased during periods of growth.

False- increased during periods of growth

For long-term storage, glucose is converted to _________ while for short-term storage glucose is converted to

Fat, glycogen

What are reasons as to why fats comprise the majority of reserved energy, as opposed to carbohydrates?

Fats, specifically fatty acids, contain more, not fewer, reduced carbons (by weight) than carbohydrates; therefore, fats release more energy upon oxidation than carbohydrates. Fatty acid tails are less branched than glycogen (carbohydrate storage) and take up less space for storage. Furthermore, carbohydrates are covered in hydroxyl groups that attract and require a lot of water for solvation, whereas fatty acids are extremely hydrophobic and do not require as much water solvation.

under normal conditions the central atom of heme is....

Fe2+

which of the following are bound to Hb when Hb is in R state. CO2 Fe2+ Fe3+ oxygen BPG

Fe2+ oxygen

Regulation of Glycolysis:

Flux through a metabolic pathway can be regulated in several ways: 1. Availability of substrate 2. Concentration of enzymes responsible for rate-limiting steps 3. Allosteric regulation of enzymes 4. Covalent modification of enzymes (e.g. phosphorylation)

Some cells are dependent on glycolysis.....

For certain cells in the brain and eye, glycolysis is the only ATP generating pathway.

In the second step, ___________________________is converted to ____________________________by enzyme _______________________.

G-6-P; Fructose-6-phosphate; Phosphoglucoisomerase (Isomerase)

Why does the process of fatty acid activation yield AMP and 2pi instead of ADP and 1pi?

Hydrolysis of ATP. ADP pi does not release enough energy to synthesize the thioester bond in an irreversible manner

Which of the following processes is involved in using proteins as a source of energy?

Keogenesis

What is the mechanism for glutamine synthetase's conversion of glutamate into glutamine, and what happens to glutamine after this conversion?

G.S. uses ATP to phosphorylate the gamma carboxyl, then replaces the phosphate with an ammonium group (nitrogen) forming glutamine. Glutamine can now move between cells to the liver where glutaminase hydrolyzes the ammonia off as ammonium, and converts glutamine back into glutamate.

Glucagon

Glucagon is a different peptide hormone secreted by the pancreatic a cells. Its secretion is stimulated by low blood glucose levels, and its general effect is to oppose the action of insulin.

The process by which amino acids and glycerol can be converted to glucose is called

Gluconeogenesis

Starches are polymers made exclusively from

Glucose

The most common monomer of carbohydrate is

Glucose

______ is the substrate in Priming Step

Glucose

Sucrose is a disaccharide made up of

Glucose and fructose

Hexosekinase can be regulated if the level of __________________ is ______.

Glucose-6-Phosphate ; high

if the level of______________________is HIGH, it will ____________the function of______________

Glucose-6-Phosphate ; high; hexosekinase

****Regulation:

Glucose-6-phosphate Dehydrogenase is the committed step of the Pentose Phosphate Pathway. This enzyme is regulated by availability of the substrate NADP+.

Which of the following enzymes does NOT catalyze an irreversible reaction in glycolysis?

Glucose-6-phosphate isomerase (G6PI or PGI)

Glycolysis is a process that breaks________ and makes ___________, also produces ______

Glucose; pyruvate; ATP

A deficiency in vitamin B9 would directly affect the synthesis of which amino acid?

Gly

A deficiency in vitamin B9 would directly affect the synthesis of which amino acid?

Gly -Vitamin B9, which is folic acid, is the precursor for tetrahydrofolate (THF) and a reduced carbon carrier (i.e., carrying methyl and methylene groups, which are reduced carbons). THF accepts a methylene from Ser and in turn Gly is synthesized. THF is also required for the synthesis of Met, Glu, dTMP, purines, and formate.

Which amino acid is not chiral?

Glycine

Excess glucose in the body following a meal can be stored in the liver as this is for use in the near future:

Glycogen

Skeletal muscle cells derive most of their energy from

Glycogen

The carbohydrate storage polysaccharide made by animals is

Glycogen

Where does each step take place?

Glycolysis occurs in the cytosol of the cell; the Krebs Cycle and the ETC take place in the mitochondria

What are the 3 steps of aerobic cellular respiration?

Glycolysis, the Krebs Cycle, and the Electron Transport Chain

The bonds between carbohydrate monomers are called

Glycosidic

Order the Lipoproteins from Highest Density to Lowest Density

HDL > LDL > VLDL > CM

Disorders associated with Glucose-6-phosphate dehydrogenase deficiency

Hemolytic Anemia: Abnormal breakdown of red blood cells (RBCs) either in the blood vessels or elsewhere in the body. Cataract: Cataracts are cloudy areas in the lens of the eye that can cause changes in vision.

Which enzyme in glycolysis is responsible for "trapping" glucose in the cell?

Hexokinase

The first reaction in Primary step is catalyzed by ___________

Hexosekinase *Is a transferase)

****________________________ (low blood sugar) causes phosphorylation, which in this case renders the enzyme _________________.

High glucagon; inactive

residues involved in chymotrypsin

His⁵⁷ Ser¹⁹⁵ Asp102

His in myoglobin heme

His⁹³- binds to iron, His64 stabilizing O2 binding site

The concentration of these three enzymes in the cell is regulated by hormones that affect their rates of transcription

Insulin Glucagon

Insulin

Insulin is a peptide hormone secreted by pancreatic b cells in response to sudden increases in blood glucose levels, such as after a carbohydrate-rich meal. It is also secreted in response to increases in amino acid levels in the blood, The general effect of insulin is to promote the storage of energy when food is available in abundance.

**Hormonal influence summary

Insulin upregulates the transcription of glucokinase, phosphofructokinase, and pyruvate kinase, while glucagon downregulates their transcription. These effects take place over a period of hours to days, and generally reflect whether a person is well-fed or starving.

Apoproteins

Integral: stay associated with the particle and act as the address labels Peripheral: are co-factors involved in lipid metabolism and maybe moved between particles EXCEPTION: ApoE and ApoA-I

In the 2-compartment model for water in the body, water partitions into

Intracellular and extracellular

Anaerobic normally in ______________

It occurs mostly in prokaryotes

The ultimate source of methyl-groups for SAM (S-adenosyl-methionine) and cobalamin stems from which molecule?

Methyl-THF -The root source for all methyl groups, transferred by either SAM or cobalamin, originates from methyl-THF (as shown in the diagram below—note that methionine is a precursor to SAM). Biotin is also a carbon carrier; however, this coenzyme is important for transferring oxidized carbons (i.e., CO2) whereas SAM, cobalamin, and THF are reduced carbon carriers (CH2 or CH3).

What is the pathway for alanine mediated transfer of nitrogen, and which tissue is this method associated with?

Muscle tissue is broken down into amino acids, and the nitrogen from these aminos is transferred to glutamate. Alanine aminotransferase transfers the nitrogen to alanine (derived from pyruvate through muscle glycolysis), leaving alpha-ketogluterate, and sending alanine to the liver. Alanine from here is converted back to pyruvate for gluconeogenesis, having it's nitrogen attached onto another alpha-ketogluterate by alanine aminotransferase which forms glutamate. Glutamate is then sent to the urea cycle.

units of Ka

M⁻¹

k units of second order reaction

M⁻¹s⁻¹

In the liver arginine stimulates which enzyme to process glutamate, and to what is glutamate processed by this enzyme?

N-acetyl-glutamate synthetase; N-acetyl-glutamate

Diazotrophs convert __________ into NH3 in a process called __________.

N2; nitrogen fixation

Diazotrophs convert __________ into NH3 in a process called __________.

N2; nitrogen fixation -Diazotrophs convert N2 into NH3 in a process called nitrogen fixation. Nitrogen fixation reduces N2 to NH3, the form of nitrogen used by organisms to build biomolecules containing nitrogen (i.e., amino acids and nucleotides). Carbon fixation is the conversion of inorganic carbon (carbon dioxide) into an organic carbon form. NO3- can also be reduced to NH3, but is performed by a number of plants and bacteria where diazotrophs are rare. The urea cycle is the pathway used to eliminate excess nitrogen. Denitrification is oxidation of NH3 to N2.

Vitamin B3, also know as niacin, is a precursor for __________.

NAD+

WHat is reduced in each round of beta-oxidation?

NAD+ and FAD

As glucose is oxidized to pyruvate (Pyr), where are the electrons from glucose stored?

NADH

As glucose is oxidized to pyruvate, where are the electrons from glucose stored.

NADH

In oxidative deamination, an amine group is removed from an amino acid (usually glutamic acid) leaving ammonia and keto acid. In this process _________ is formed which can enter the electron transport chain.

NADH

The electron-carrier molecules that are used in electron-transport chain to generate additional ATP are

NADH and FADH2

In this oxidative pathway,___________ is the electron acceptor, yielding ______________.

NADP; NADPH

^^^^^The main molecule in the body that makes anabolic processes possible is _____________.

NADPH The PPP is the main source of synthesis for NADPH.

All organisms can convert __________ to organic nitrogen (nitrogen bound to a carbon), but few organisms can make this same molecule from __________.

NH3; N2

All organisms can convert __________ to organic nitrogen (nitrogen bound to a carbon), but few organisms can make this same molecule from __________.

NH3; N2 -All organisms can convert NH3 to organic nitrogen (nitrogen bound to a carbon), but few organisms can make this same molecule from N2. Reduced nitrogen is extremely important, as this is the usable (reactive) form of nitrogen used in organisms to synthesize molecules containing nitrogen (like amino acids and nucleotide bases).

The sources of nitrogen in urea are __________.

NH4+ and Asp

The sources of nitrogen in urea are __________.

NH4+ and Asp - Urea has two nitrogen atoms, one of which stems from carbamoyl phosphate that is generated by NH4+ and CO2. The second nitrogen is supplied by the amino of Asp. The carbon atom of urea originates from CO2. Arg is the final carrier of these atoms, when arginase catalyzes the cleavage of Arg into urea and ornithine using water (one of the oxygens in water is the oxygen in urea).

The reaction N2 + 3 H2 ← → 2 NH3 is thermodynamically favorable. However, the activation energy barrier is very high. In diazotrophs, what enzyme is responsible for overcoming this barrier?

Nitrogenase complex

Does glycolysis require oxygen?

No.

Which enzyme-catalyzed reaction in glycolysis directly consumes O2?

None of the enzyme-catalyzed reactions in glycolysis directly consumes O2

Which enzyme-catalyzed rxn in glycolysis directly consumes O2?

None of the enzyme-catalyzed reactions in glycolysis directly consumes O2.

Which enzyme-catalyzed reaction in glycolysis generates CO2?

None of the enzyme-catalyzed reactions in glycolysis generates CO2

Which enzyme-catalyzed reaction in glycolysis generates CO2?

None of the enzyme-catalyzed reactions in glycolysis generates CO2.

Which enzyme-catalyzed reaction in glycolysis generates FADH2?

None of the enzyme-catalyzed reactions in glycolysis generates FADH2

Which enzyme-catalyzed reaction in glycolysis generates NAD+?

None of the enzyme-catalyzed reactions in glycolysis generates NAD+.

Which enzyme-catalyzed reaction in glycolysis generates FADH2.

None.

Which pair of molecules involved in the urea cycle can pass between the cytosol and the mitochondrial matrix?

Ornithine and citrulline -Ornithine, one of the products of arginase, can cross into the mitochondrial matrix to collect another nitrogen and carbon from carbamoyl phosphate. The resulting molecule, called citrulline, then passes into the cytosol where the second nitrogen for urea is contributed by an Asp molecule yielding arginosuccinate. After fumarate is cleaved from arginosuccinate, the resulting Arg molecule is cleaved into urea and ornithine via the arginase-catalyzed reaction.

PPP Phases

Oxidative / Non oxidative

general reversible binding of protein to ligand

P + L ↔ PL

What is PLP?

PLP = Pyridoxyl Phosphate attaches to the amine group being removed from an amino acid by aminotransferase to become pyridoxine phosphate.

What are the phases of detoxification? What enzymes are used?

PhaseI:Functionalization • Hepatic enzymes are responsible for the metabolism of xenobiotics by first activating them • Oxidation • Reduction • Hydrolysis • Hydration • PhaseII:Conjugation • active secondary metabolite with • Glucuronic acid • Sulphuric acid • Glutathione • Followed by excretion in bile or urine.

The three most important buffer systems in body fluids include the bicarbonate buffer system, the ____ buffer system and the protein buffer system.

Phosphate

Which enzyme in glycolysis is responsible for catalyzing the rate-limiting step?

Phosphofructokinase

Which enzyme in glycolysis is responsible for catalyzing the " committing-step"

Phosphofructokinase ( PFK)

If production of ribose-5-phosphate exceeds the needs of required ribose-5-phosphate in the organism.......

Phosphopentose epimerase then catalyzes a chirality rearrangement about the center carbon creating xylulose-5-phosphate. The products of these two reactions can then be rearranged to produce many different length carbon chains. These different length carbon chains have a variety of metabolic fates.

Why is it advantageous for glycolysis to proceed in 10 steps, rather than a one-step conversion of glucose, NAD+, and ADP to pyruvate (Pyr), NADH, and ATP?

Possessing many intermediates allows for molecules to enter and leave the pathway at different points.

Why is it advantageous for glycolysis to proceed in 10 steps, rather than in one-step conversion of glucose, NAD+, and ADP to pyruvate, NADH and ATP?

Possessing many intermediates allows for molecules to enter and leave the pathway at different points.

Which of the following is not a factor in the lifetime of a protein?

Post-translational phosphorylation

Which of the following is not a factor in the lifetime of a protein?

Post-translational phosphorylation -Post-translational phosphorylation is a mechanism for regulating enzyme activity but it is not a mechanism for determining a protein's lifetime. N-terminal sequence identity and PEST sequence enrichment are correlated to the half-life of a protein. Ubiquitination tags a protein for degradation by the proteasome.

The hormone aldosterone regulates the concentrations of _______ and ________ in the body.

Potassium ions and sodium ions

Hexokinase (HK) is down-regulated by which method?

Product inhibition

The necessary coenzyme for the transamination reaction is

Pyridoxal Phosphate (PLP)

The 3 carbon alpha ketoacid formed from the oxidative deamination of alanine is

Pyruvate

glocolysis produces _____________which is the end product of glycolysis

Pyruvate

two major conformations of hemoglobin

R State (relaxed) T State (tense) -oxygen will bind in either state but has a higher affinity for Hb in the R state. -when oxygen is absent T state is more stable

Specific tissue functions of Glycolysis

RBC's Rely exclusively for energy Skeletal muscle Source of energy during exercise, particularly high intensity exercise Adipose tissue Source of glycerol-P for TG synthesis Source of acetyl-CoA for FA synthesis Liver Source of acetyl-CoA for FA synthesis Source of glycerol-P for TG synthesis

Rate of ES breakdown

Rate of ES breakdown = k-₁[ES] + k₂[ES]

Rate of ES formation

Rate of ES formation = k₁([Et]-[ES])[S]

_______________ of just one of these phosphate groups from the end leads to the conversion from ________ to ________.

Removal; ATP; ADP

Fifth Step

Requires the molecule D-Glyceraldehyde-3-phosphate to continue Dihydroxyacetone phosphate is converted into D-Glyceraldehyde-3-phosphate by the enzyme Triose phosphate isomerase (Class: Isomerase)

The pentose phosphate pathway (PPP) is also responsible for the production of___________________________ which is an important part of nucleic acids.

Ribose-5-phosphate

______________ ions account for nearly 90% of the positively charged ions found in extracellular fluid

Sodium

_______ is the most common extracelluar cation, while _________ is the most abundant intracellular cation.

Sodium, potassium

What are the storage polymers

Starch, cellulose, glycogen

What is the difference between substrate-level phosphorylation and oxidative phosphorylation?

Substrate-level produces ATP molecules via transfer of a phosphate group

The side chain on an amino acid may include which element?

Sulfur

Gluconeogenesis is the

Synthesis of glucose from non-carbohydrate precursors

Biliary system

THe components of the biliary system are in the liver, gallbladder and bile duct, duodenum, ileum and portal circulation. The hepatocytes of the liver continiously sinthesize and secrete constitutents of bile. The components are: Bile salts Cholesterol Phospholipids Bile pigments Ions Water Bile flows out of the liver through the bile ducts and fills the gallbladder where it is stored. The gallbladder then concentrates the bile salts by absorption of water and ions. When chyme reaches the small intestine, CCK is secreted. CCK has two functions; stimulate contraction of the gallbladder and relaxation of the sphincter of Oddi. Causing stored bile to flow from the bladder to the lumen of the duodenum. In the small intestine the bile salts emulsify and solubilize dietary lipids. When lipid absorption is complete the bile salts are recirculated to the liver via the enterohepatic circulation. The steps involved are the absorption of bile salts from the ileum into the portal circulation back to the liver. The recirculation reduces the demand to produce new salts. Some bile salts are secreted to the feces.

The reaction N2 + 3 H2 ← → 2 NH3 is thermodynamically favorable. How can eukaryotes starve for nitrogen while surrounded by nitrogen?

The activation barrier is extremely high and therefore this reaction doesn't proceed at any appreciable rate.

The reaction N2 + 3 H2 ← → 2 NH3 is thermodynamically favorable. How can eukaryotes starve for nitrogen while surrounded by nitrogen?

The activation barrier is extremely high and therefore this reaction doesn't proceed at any appreciable rate. -Even though N2 is the most abundant molecule in the atmosphere and the reduction of this molecule to ammonia is thermodynamically favorable, the activation barrier is extremely high. Therefore, this reaction doesn't proceed at any appreciable rate unless an enzyme is present that can perform nitrogen fixation.

Oxidation Phase

The beginning molecule for the PPP is glucose-6-P which is the second intermediate metabolite in glycolysis

What is oxidized in each round of beta oxidation?

The beta carbon of the acyl chain

Part of the urea cycle takes place in the mitochondria, the other part takes place in the cytosol. Which takes place where?

The condensation of ornithine with carbamoyl phosphate to form citrulline occurs in the mitochondria. Everything else occurs in the cytosol.

Conjugating bile salts

The conjugation steps changes the pK of bile acids and causes them to become much more water soluble. Like this: pH of duodenal contents range between pH 3-5. Bile acids have pK of approximately 7. At duodenal pH most bile acids will be in their nonionised form, whoch is insoluble in water. Bile salts have pKs ranging between 1 and 4, at duodenal pH moste bile salts are in their ionised form A-, which is soluble in water. The critical property of bile salts is that they are amphipathic, meaning that the molecules have both hydrophilic and hydrophobic portions. Hydrophilic, negatively charged groups point outward from a hydrophobic portions. Hydrophobic steroid nucleus such that, at an oil water interface the hydrophilic portion of a bile salt molecule dissolves in the aqueous phase and the hydrophobic portion dissolves in the oil phase.

Which of the following statements concerning the malate-aspartate shuttle is true?

The cycle transports electrons from the cytosol to the mitochondrial matrix

Glycolysis is a 10-step pathway, in which reactions four through nine are reversible. With so many reversible reactions, how does the pathway have an overall directionality towards pyruvate (Pyr)?

The last step, catalyzed by pyruvate kinase (PK), is irreversible and it therefore keeps the concentration of phosphoenolpyruvate low and pulls all previous reversible reactions forward.

Glycolysis is a 10-step pathway, in which reaction four through nine are reversible. With so many reversible reactions, how does the pathway have an overall directionality towards pyruvate?

The last step, catalyzed by pyruvate kinase, is irreversible and it therefore keeps the concentration of phosphoenolpyruvate low and pulls all previous reversible reactions forward.

The main site for gluconeogenesis is

The liver

What is a monosaccharide?

The most basic units of carbohydrates. Made of 1 aldehyde and 1 ketone. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose (dextrose), fructose (levulose) and galactose

What determines the three-dimensional shape of a protein molecule?

The order and chemical properties of the amino acids

Which of the following statements INCORRECTLY describes the role of ATP in the reaction catalyzed by Gln synthetase?

The pyrophosphate released pulls the reaction forward upon the hydrolysis to 2Pi.

How is it possible for the rate and depth of breathing to affect hydrogen ion concentrations in body fluids?

The rate and depth of breathing does not alter hydrogen ion concentration in body fluids.

Which enzyme-catalyzed reaction in glycolysis generates h2O?

The reaction catalyzed by enolase

Which enzyme-catalyzed reaction in glycolysis generates H2O?

The reaction catalyzed by enolase (ENO)

What reaction yields NAD+

The reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase

If a person were deficient in vitamin B3, what enzyme-catalyzed reaction in glycolysis would be directly affected?

The reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase (GAPDH)

Which enzyme-catalyzed reaction in glycolysis generates NADH?

The reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase (GAPDH)

Which enzyme-catalyzed reaction in glycolysis generates NADH?

The reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase.

Which enzyme-catalyzed reaction in glycolysis generates an NTP - Nitrogenous base

The reaction catalyzed by pyruvate kinase

Which enzyme-catalyzed reaction in glycolysis generates an NTP (where N = any nitrogenous base)?

The reaction catalyzed by pyruvate kinase (PK)

Summary of Pentose Phosphate Pathway (PPP)

The reactions of the PPP takes place in the cytoplasm. PPP has both oxidative and non-oxidative phases. PPP generates NADPH. Provides cell ribose-5-phosphate (R5P) for the synthesis of the nucleotides and nucleic acids.

Why might it be advantageous to convert some of the pyrucate formed in glycolysis to lactate?

The reduction of pyruvate to lactate regenerates NAD+, which is a substrate for glycolysis.

Why might it be advantageous to convert some of the pyruvate (Pyr) formed in glycolysis to lactate?

The reduction of pyruvate to lactate regenerates NAD+, which is a substrate for glycolysis.

Phase 2: Pay off Step

The second phase of Glycolysis where 4 molecules of ATP are produced per molecule of glucose. Enzymes appear in red:

The difference between amylose and amylopectin are

The structure (branched vs linear)

Glycolysis

The word glycolysis is derived from two Greek words and means the breakdown of sugar (glycol). First stage of glucose metabolism *** Breaks down glucose and forms two molecules of 3 carbon pyruvate. Generates 2 ATP and 2 NADH.

Non-oxidative phase: Rearrangement Phase

There are two main classes of enzymes responsible for the rearrangement and synthesis of the different length carbon chain molecules. -Transketolase -Transaldolase

Of the 10 steps in the glycolytic pathway, three are essentially irreversible.

These are steps 1 (phosphorylation of glucose) 3 (phosphorylation of fructose-6-phosphate) and 10 (transfer of phosphate from phosphoenolpyruvate to ADP).

Explain the major role of glutamate and alpha ketoglutarate in amino acid biosynthesis and degradation

They lose or gain an amine group to generate energy and create NH4 or NADH

What is TPP?

Thiamine pyrophosphate (TPP or ThPP), or thiamine diphosphate (ThDP), is a thiamine (vitamin B1) derivative which is produced by the enzyme thiamine pyrophosphatase. Thiamine pyrophosphate is a coenzyme that is present in all living systems, in which it catalyzes several biochemical reactions. It was first discovered as an essential nutrient (vitamin) in humans through its link with the peripheral nervous system disease Beriberi, which results from a deficiency of thiamine in the diet.[1]

Glucose-6-P is oxidized in the presence of glucose-6-P dehydrogenase and NADP+.......

This step is irreversible and is highly regulated.

If PFK-1 is inhibited, which direction will the reaction catalyzed by glucose-6-phosphate isomerase proceed?

Toward glucose-6-phosphate

Most important part of ATP is the ________________

Triphosphate

Ammonia is detoxified to urea via the urea cycle in the liver

True

T/F Amino acid catabolism is increased during starvation

True

T/F Protein complementation combines foods containing proteins with different limiting amino acids in order to improve the protein quality of the diet.

True

T/F Proteins help keep fluids an pH balanced in the body

True

T/F The Urea cycle is regulated by an enzyme called CPS-1

True

T/f Alanine exists as a zwitterion at a pH7

True

Where is regulation centered for the urea cycle, and why?

Up or down-regulation of carbamoyl phosphate synthetase; requires 2 ATP to form carbamoyl phosphate from ammonium and bicarbonate.

Glutamate can enter the mitochondrial matrix and initiate removal of excess nitrogen by the __________ cycle.

Urea

rate of reaction (V) for S → P

V = k[S] k: rate constant -first order reaction

rate of second order reaction

V = k[S₁][S₂]

In an ideally balanced human system water inputs would equal

Water outputs

As NADPH is utilized in reductive synthetic pathways, the increasing concentration of NADP+ stimulates the Pentose Phosphate Pathway, to replenish NADPH........

When the demand of NADPH slows, the level of NADP drops, the pentose phosphate pathway slows and glucose 6 phosphate is used to fuel glycolysis.

Would you expect synthesis of SAM (S-adenosylmethionine) to be affected by methotrexate?

Yes, because methotrexate inhibits the synthesis of tetrahydrofolate (THF) and THF carries the methyl-group for SAM. -Synthesis of SAM (S-adenosylmethionine) is expected to be affected by methotrexate because methotrexate inhibits the synthesis of tetrahydrofolate (THF) via competitive inhibition of dihydrofolate reductase. Since methyl-THF carries the methyl-group for SAM, methotrexate would also affect SAM synthesis.

Acyl-group-transfer reactions often involve which coenzyme? a) coenzyme A b) NAD+ c) cytochrome C d) all of the above

An operon is ________ a) a set of genes whose transcription is controlled by a single promoter b) the site of repressor binding c) a protein that activates the transcription of a whole class of genes d) a multisubunit complex responsible for the splicing of exons

During fasting, when glycogen supplies are depleted, ___________ become a major source of carbon for gluconeogenesis a) amino acids b) nucleic acids c) fatty acids d) lactate and pyruvate

Enzymes that catalyze the same reaction are called ________ a) isozymes b)complementary enzymes c) cofactors d) catalytes

In transamination an amine group is transferred to ________ to form a nonessential amino acid.

a. Alpha keto acid

sort the following into: acid-base catalysis, covalent catalysis, metal ion catalysis, or all. 1. catalyst retains its original form after reaction occurs. 2. a proton is transferred between enzyme and substrate. 3. a covalent bond forms between enzyme and substrate. 4. may use amino acids such as aspartate or lysine for protonation or proton abstraction. 5. may take part in interactions involving Fe2+. 6. Catalysts may participate in oxidation-reduction reactions by changes in the oxidation state. 7. uses a nucleophilic function group. 8. lowers the energy or stabilizes the transition state or intermediate. 9. a Zn2+ cofactor may properly orient the substrate in the active site through ionic interactions. 10. two-part catalytic process(for example, the chymotrypsin mechanism).

acid-base catalysis: 2, 4 covalent catalysis: 3, 7, 10 metal ion catalysis: 5,6,9 all: 8, 1

***PFK is allosterically _______________ by _______levels of ________. _______ overcomes the inhibitory effect of ATP

activated; high ; AMP; AMP

if a person were deficient in vitamin b2, which enzyme catalyzed reaction would be directly affected?

acyl-coa dehydrogenase

Disulfide bridges can form in proteins _____________ a) only between cysteine residues side-by-side in the protein sequence b) between cysteine residues that are close in 3D space, but not necessarily close in primary structure c) between 2 cysteine residues in proteins d) between any 2 methionines or cysteines e) only inside the cell where it is a reducing environment

Genes that encode for proteins that are need for basic metabolic processes (such as glycolysis) are called _______ genes a) essential b) housekeeping c) core d) cardinal

In eukaryotes the enzymes of the citric acid cycle are found in the ____________. a) cytosol b) mitochondria c) nucleus d) endoplasmic reticulum

Photorespiration in plants involves the _________ a) fixation of carbon dioxide to a four carbon acid b) light-dependent uptake of O2 catalyzed by rubisco, followed by the release of CO2 c) reduction of surface-exposed disulfides in the regulation of rubisco d) exclusive fixation of carbon dioxide at night by plants such as cacti

The glycolytic pathway oxidizes glucose to 2 molecules of pyruvate and produces a net of 2 ATP. ATP allosterically inhibits the Phosphofructokinase-1, that catalyzes the third step of glycolysis. This is an example of ____________. a) feed-forward activation b) feedback inhibition c) negative cooperativity d) competitive inhibition e) negative inhibition

The major driving force responsible for protein folding is a) the formation of hydrogen bonds in alpha helices and beta sheets b) the increased disorder in the surrounding solvent as the protein folds c) the resulting increase in the order of the protein d) the formation of multiple salt bridges between charged side chains like glutamate and lysine e) van der waals forces

The pKa values of glutamate's alpha carboxyl group, alpha amino group, and side chain are 2.1, 9.5, and 4.1, respectively. What is the isoelectric point of glutamate? a) 1.3 b) 3.1 c) 5.2 d) 7.9 e) 9.5

The processivity of E. coli DNA polymerase 3 holoenzyme accounts for all the following except a) the relatively small number of enzymes needed to replicate the entire chromosome b) the directionality of polymerization c) the rapid rate of polymerization d) the ability of a single holoenzyme to add many nucleotides to a growing DNA chain

What is the 5' -> 3' for an amino acid with the codon CAG? A) GAC b) CUG c) GUC D) CTG

Which of the following is not regulated in glycolysis? a) pyruvate kinase b) phosphoglycerate kinase c) hexokinase d) PFK-1

Which statement is not true about catabolic pathways? A) catabolic pathways generally provide a net release of energy b) catabolic pathways generally result in a net consumption of ATP c) catabolic pathways generally liberate smaller molecules from larger ones. d) catabolic pathways include the citric acid cycle e) catabolic pathways are usually oxidative, not reductive processes

Which statement is not true about catabolic pathways? a) they have a net release of energy b) they have a net consumption of ATP c) they liberate smaller molecules from larger ones d) they include the citric acid cycle

Which thermodynamic quantity is used to determine if a reaction in a cell is spontaneous? a) Delta G" b) Delta G c) Delta H d) Delta S

Why is DNA damage in human skin cells from exposure to excessive UV light not completely reverse by photoreactivation? a) DNA photolyase in humans is activated only under conditions of heat shock b) humans lack a photoreactivation repair mechanism c) the presence of histones greatly slows photoreactivation, thus humans depends primarily on other forms of DNA repair d) photoreactivation is specific for the removal of thymine dimers. Thymine dimers do not form in human DNA

the processivity of E. coli DNA polymerase 3 holoenzyme accounts for all the following except a) the relatively small number of enzymes needed to replicate the entire chromosome b) the directionality of polymerization c) the rapid rate of polymerization d) the ability of a single holoenzyme to add many nucleotides to a growing DNA chain

Typically, a person's________________ is the_____________ of energy use, representing ________________________ of the calories used each day.

basal metabolic rate; largest portion; two-thirds to three-quarters

What is the most significant plasma buffer?

bicarbonate

Composition of bile

bile salts 50%, bile pigments 2%, cholesterol 4%, phospholipids 40%. Bile also contains electrolytes and water which are secreted by hepatocytes lining the bile ducts. Total bile pool os approximately 2.5 g.

Mitochondria produce ___________ of ATP molecules every second

billions

Phosphorylation of pyruvate kinase is regulated by ___________________________ level, just like PFK.

blood glucose

Rapidly dividing cells such as those of________________________________________________________________________, use the pentose ribose 5-phosphate to make RNA, DNA and co-enzymes as ATP, NADH, FADH2 and coenzyme A.

bone marrow cells, skin and intestinal mucosa, and those of tumors;

Catabolic Pathways

breakdown of nutrient molecules (Food: A, B, C) into usable forms (building blocks), In this process, energy is either stored in energy molecules for later use, or released as heat

feedback inhibition

build up of the end product ultimately slows the entire pathway.

Decreased metabolism causes the body to....

burn fewer calories and less fat.

According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then a) the carboxylic acid is totally neutralized b) only salt forms are present c) pH = pKa d) pKa = log [proton acceptor/proton donor] e) the pH is neutral

Energy from electron transport reactions is stored as a ______________ gradient that is higher in the intermembrane space than in the mitochondrial matrix a) electron b) ATP c) proton d) NAPH

Facilitated diffusion (passive transport) through a biological membrane is a) generally irreversible b) driven by the ATP to ADP conversion c) driven by a concentration gradient d) endergonic e)all of the above

How are the termination codons different from other codons? a) they contain thymines b) the termination codon always codes for methionine c) they are not recognized by an tRNA molecules d) their conformations do not allow them to fit properly in the A site of the ribosome

In an enzyme reaction involving one enzyme and one substrate, the rate of the reaction depends on a) substrate concentration b) enzyme concentration c) both substrate and enzyme concentrations d) the enzyme concentration at first and the substrate concentration later on

In the adenylyl cyclase signaling pathway the second messenger(s) are ________ a) ATP and GTP b) protine kinase A c) cyclic AMP d) AMP e) GBy

Most of the energy released in citric acid cycle reactions is conserved in ________ a) GTP b) ATP c) NADH and QH2 d) ADP

Ten people are sitting in a row. Their objective is to whisper a secret from one person to the next all the way down the row. The first person whispers the secret to the second person and so on. After the third person, the second person notices the ninth person has fallen asleep in their chair, so she gets up, goes down the row and shakes person 9 awake. This example is similar to ________. a) allosteric control b) positive cooperativity c) feed-forward activation d) negative modulation

The Michaelis constant Km, is equal to the ___________. a) max velocity that any given enzyme reaction can achieve b) substrate concentration which gives the best enzyme assay for an enzyme reaction c) substrate concentration when the rate is equal to half its maximal value d) max velocity divided by 2

The compounds alpha-D-fructofuranose and B-D-fructofuranose are _________ a) enantiomers b) mutamers c) anomers d) conformational isomers

The sequence of glucose oxidation to lactate in peripheral tissues of lactate to the liver, formation of glucose from lactate in the liver, and delivery of glucose back to peripheral tissues is known as the _____________. a) glyoxylate cycle b) kreb's cycle c) Cori cycle d) gluconeogenesis cycle e) TCA cycle

The tetranucleotide AGTC (in DNA) has a free hydroxyl group on a) A b) A, G, T, and C c) C D) G, T, and C

the replication of DNA is ___________ because ______________ a) conservative; one strand of parental DNA is retained in each daughter DNA b) conservative; each daughter molecule has 2 new strands copied from the parental DNA template c) semiconservative; one strand of parental DNA is retained in each daughter DNA d) semiconservative; each daughter molecule has 2 new strands copied from the parental DNA template

what type of reaction is shown below? Amino acid + alpha-ketoglutarate <--> alpha-keto acid + Glutamate a) reductive amination b) oxidation c) Transamination d) Hydrolysis

Which of the following is the product of trans-deaminiatio reactions a. urea b. NH3 c. NH4 d. Carbonic acid

c. NH4

Which of these is not a consequence of vomiting? a. dehydration b. metabolic acidosis c. respiratory alkalosis d. metabolic alkalosis

c. respiratory alkalosis

Filling if the gallbladder

can be filled due to the closure of sphincter of Oddi

Which of the following is NOT a product of glycolysis?

carbon dioxide

Besides ATP the end products of aerobic respiration are

carbon dioxide water

What is the difference between anabolic and catabolic pathways?

catabolic reactions break down molecules and release energy by breaking down complex molecules to simpler compounds. Anabolic reactions build larger molecules from smaller ones, they consume energy to do this.

Which of the following terms is the total of all the breakdown processes in the body?

catabolism

Macro molecules made in anabolism may be used to make __________ in different _________

cell structure; tissues; And other macromolecules like PROTEIN

Which carbohydrate is not digestible and provides fiber or "roughage" in humans?

cellulose

An electrolyte is a) sugar b. fat c. charged molecule d water

charged molecule

rate (v) units

concentration/time

What is the Aspartate-arginino-succinate shunt of the citric acid cycle?

connects urea cycle and TCA by fumarate and oxaloacetate

For most tissues, then, glucose uptake proceeds at a fairly__________________ rate, regardless of the amount present in the blood.

constant

ATP is produced _________________________________ using the energy from the __________________________________

continuously throughout the day; breakdown of foods.

Where in the cell does glycolysis occur?

cytoplasm

Where does the final reaction, generating urea, take place in a eukaryotic cell?

cytosol

Where in a eukaryotic cell does glycolysis occur?

cytosol

Where in the cell does gluconeogenesis primarily occur.

cytosol

Which of the following statements about protein synthesis is false? a. limiting amino acids can halt protein synthesis b. nonessential amino acids can be made through transamination c. amino acids needed for protein synthesis come from the amino acid pool d. Essential amino acids can be made through transamination

d. Essential amino acids can be made through transamination

Select the best definition of an enzyme a. an enzyme is an amino acid that speeds up chemical reactions. b. an enzyme is a protein that is consumed in the diet and aids in chemical reactions. c. enzymes are proteins that speed up metabolic reactions and are destroyed in the process. d. enzymes are proteins that speed up metabolic reactions and are not destroyed in the process.

d. enzymes are proteins that speed up metabolic reactions and are not destroyed in the process.

Which of these food groups is not considered a good source of protein? a. meat b. beans. c. milk d. fruit

d. fruit

The purpose of this is to _______________ production of NADPH when concentrations are high or the synthesis of_____________ is no longer necessary.

decrease; fatty acids

in ________ the central iron atom is dispaced 0.4A our of the place of the porphyrin ring system

deoxyhemoglobin

According to Chargaff's observations of nucleotide composition of DNA samples a) % of (G + C) + % of (A + T) = 100% b) A = T c) G = C d) %A + %G +%C + %T = 100% e) all of the above

Dilute amounts of acetic acid (CH3COOH, pKa = 4.76) are mixed in buffered solutions of pH = 2 and pH = 7 a) since it is an acid, it will be in the acidic form, and thus positively charged in both solutions. b) it will be present predominantly as a positively charged species at pH = 2 c) it will be present predominantly as a negatively charged species at pH = 2 d) it will be present predominantly as a positively charged species at pH = 7 e) it will be present predominantly as a negatively charged species at pH = 7

Enzyme activity can be modified by protein phosphorylation, i.e., by adding phosphate to the side chains of: a) tryptophan b) serine c) threonine d) tyrosine e) b, c, and d

Every third residue in collagen is invariably a glycine because glycine a) forms H-bonds which help stabilize the protein b) makes the protein rigid c) is required for hydroxylation d) forms covalent cross links e) allows tightly wound helix formation

How many fragments will result from the treatment of trypsin on the following protein? Gly-Lys-Ala-Thr-Trp-Arg-Val-Ser-Tyr-Gln-Lys-Ile a) 0 b) 1 c) 2 d) 3 e) 4

In the Holiday model describing recombination a) homologous sequences line up b) strands of DNA are nicked c) DNA strands associate with the homologous strand (strand invasion) d) strands rotate then are cleaved at the crossover point e) all of the above

The R group of an amino acid determines if it is a) hydrophilic or hydrophobic b) polar or nonpolar c) charged or uncharged d) an acid or a base e) all of the above

The excretory products of uric acid catabolism vary among organisms depending on their ability to ______________ a) tolerate the end-product b) remove the end-product to less toxic products c) solubilize the end product d) remove an end-product like ammonia to the environment e) all of the above

Complex carbohydrates a. include glycogen, cellulose, and starch b. consist of many glucose molecules bound together in long chains. c. can be energy storage molecules d. are polysaccharides. e.all of these

e. all of these

An abnormal accumulation of interstitial fluid is called

edema

When a molecule is oxidized what does it mean?

electrons are lost

TCA produces more ____________versus any other anaerobic pathway

energy (ATP)

Even when the body is at rest, it requires _________ for the basics, such as fuel for organs, breathing, circulating blood, adjusting hormone levels, plus growing and repairing cells.

energy;

The ATP provides the __________ to the _____________ to ___________ a reaction.

energy; enzyme; catalyze

Metabolism makes ____________and different _____________

energy; macromolecules

These bunched up negative charges want to ___________ , so there is a lot of ______ energy here

escape; potential

Amino acids that must be consumed in the diet are called

essential amino acids

When yeast synthesizes __________ from pyruvate (Pyr), it results in NADH being converted to NAD+, which is a coenzyme needed in glycolysis.

ethanol

When yeast synthesizes ____________ from pyruvate, it results in NADH being converted to NAD+, which is a coenzyme needed in glycolysis.

ethanol

Aerobic respiration is characteristic of__________________ when they have sufficient oxygen and most of it takes place in the ___________________

eukaryotic cells; mitochondria.

Fluid in the blood is classified specifically as _________ fluid

extracellular

In the 3 compartment model for water in the body, the__________ compartment is further divided into interstitial and plasma compartments

extracellular

When MR is high, _____is not stored as much in the body

fat

ATP is made from the energy we get from different________

foods

Catabolism is a reaction in which _______ are broken down to make building __________ of other _________, and __________ energy or releases it as _________

foods; blocks; smaller molecules; stores; heat ***Catabolism provides energy; This energy can be stored or released as heat.

At the end of aerobic respiration all six carbon atoms from the glucose molecule are

found in carbon dioxide molecules

NADH is produced

from the reduction of NAD

Central principle/dogma of molecular biology:

genetic information flows from DNA to RNA to protein Amino acids can't do anything without template from DNA DNA replicates its information (via many enzymes): REPLICATION DNA codes for mRNA during transcription : TRANSCRIPTION mRNA processed into proteins : TRANSLATION

What is an example of how gluconeogenesis is not the exact reverse of glycolysiss?

gluconeogenesis yields NAD+ glycolysis USES NAD+

If the alpha-ketoacid product from the transaminase reaction that uses alanine and alpha-ketoglutarate as substrates goes on to make glucose via the __________ pathway, then the amino acid carbon skeleton is considered to be __________.

gluconeogenesis; glucogenic

The brain relies almost entirely on _______ for energy production

glucose

The rate of entry of glucose into a cell is limited by the number of ___________________________on the cell surface and the ____________ of them for glucose.

glucose transporters; affinity The members of the glucose transporter family are expressed at different levels in different tissues.

What are the irreversible step of gluconeogenesis

glucose-6-phosphatase fructose 1,6-bisphosphatase pyruvate carboxylase+PEP carboxykinase

The first reaction in glycolysis converts glucose to __________, and is catalyzed by __________.

glucose-6-phosphate (G6P); hexokinase (HK)

Which of the following enzymes does NOT catalyze an irreversible reaction in glycolysis?

glucose-6-phosphate isomerase

Hexokinase is inhibited by the product of its reaction, _____________________________________

glucose-6-phosphate. This is a very important regulatory step, since it prevents the consumption of too much cellular ATP to form G6P when glucose is not limiting.

Which enzyme removes the nitrogen from glutamate in the liver, and what is the product?

glutamate dehydrogenase; alpha-ketoglutarate

Which enzyme removes nitrogen from glutamine in the liver? What is formed? Where in the liver cell does this process occur?

glutaminase; glutamate; the mitochondria

Which enzyme adds free nitrogen to glutamate to form glutamine (the principle nitrogen carrier)?

glutamine synthetase

Once NH3 is generated by the nitrogenase complex (or the urea cycle), the enzyme __________ uses ATP to catalyze the addition of NH3 to __________ to yield __________.

glutamine synthetase; Glu; Gln

Once NH3 is generated by the nitrogenase complex (or the urea cycle), the enzyme __________ uses ATP to catalyze the addition of NH3 to __________ to yield __________.

glutamine synthetase; Glu; Gln -Glutamine synthetase catalyzes the entry of nitrogen into metabolic pathways, by using ATP and ammonia to convert Glu to Gln (as demonstrated in the figure below). Glutamate dehydrogenase can also use ammonia to convert alpha-ketoglutarate to Glu. This reaction, however, is not popular in eukaryotes because glutamate dehydrogenase has a very low affinity for ammonia. As such, toxic levels of ammonia would be needed for this reaction to favor products.

if a person were deficient in vitamin b3, which enzyme catalyzed reaction would be directly affected?

glyceraldehyde-3-phosphate dehydrogenase

Finally the PPP can also be used to produce ______________________________________ which can then be fed into the ______and_________ cycles allowing for the harvest of energy.

glyceraldehyde-3-phosphate; TCA and ETC

Which of the following statements INCORRECTLY describes the role of ATP in the reaction catalyzed by Gln synthetase?

he pyrophosphate released pulls the reaction forward upon the hydrolysis to 2Pi.

prosthetic group of Hb and Mb is...

heme

Liver and pancreatic b cells have a distinct glucose transporter with a ___________ Km, around __________________.

high; 15-20 mM In these cells, then, the amount of incoming glucose is pretty much proportional to the amount of glucose in the blood. This allows the b cells to monitor blood glucose levels directly, and thereby regulate insulin secretion. It also insures that glucose is taken up rapidly by the liver only when it is abundant; in the fasting state, more glucose is delivered to other tissues (particularly the brain).

What reaction is catalyzed by lipoprotein lipase, or lipase?

hydrolysis of TAG in to fatty acid and glycerol

In most tissues glucose 6-phosphate is converted to pyruvate via glycolysis, However......

in some tissues Glucose-6-phosphate is oxidized to pentose phosphates by the pentose phosphate pathway (also know as hexose monophosphate pathway).

Enterohepatic circulation

in the ileum the bile salts are transported from the intestinal lumen into the portal blood by Na+/Bile salt cotransporters. The liver extracts the bile salts from portal blood and adds them to hepatic bile salt/acid pool. Therefore the liver must be replaced by synthesis. (600mg/day loss in feces). Bile acid synthesis is under negative feedback control from bile salts.

****NADPH and fatty acyl-CoA are strong negative __________________to this enzyme.

inhibitors (G6P dehydrodgenase)

^^^^It is also an ________________ step that is unique to the glycolytic pathway;

irreversible;

Glucose, lactose and galactose are all _____ each other, in that they all have the molecular formula C6H12O6

isomers of

What happens to a phophorylated molecule?

it can activate or deactivate the protein by changing the overall shape of the molecule

What is ATP synthase and what is its importance in cellular respiration?

it is an enzyme that can synthesize ATP from ADP by using a form of energy. It is important because it is linked to the ETS through the proton-motive force which allows protons back into the mitochondria

activation energy and rate constant

k = kT/h * e^ (-∆G/RT) the second k is boltzmann constant

relationship between Ka and kd

kd = 1/ka

During vigorous exercise, pyruvate produced by glycolysis is converted to

lactate

Metabolism breaks down ____________________ and makes _______________

large molecules; smaller molecules

The end results of the rearrangement phase is a variety of different ...........

length sugars which can be fed into many other metabolic processes. For example, fructose-6-P is a key intermediate of glycolysis as well as glyceraldehyde-3-P.

nh = 1

ligand binding is not cooperative

*****The enzymes reasonable for catalyzing the steps of the PPP are found most abundantly in the_______(the major site of gluconeogenesis) more specifically in the ____________

liver ; cytosol. The cytosol is where fatty acid synthesis takes place which is a NADPH dependent process.

Other tissues (___________,____________,__________________,) involved in _____________________________ or very active in the synthesis of _______________________and steroid hormones (liver, adrenal glands, gonads) require NADPH provided by the pathway.

liver, adipose, lactating mammary gland; fatty acid synthesis; cholesterol

organic ring component of heme is...

porphyrin

Hexokinase is down-regulated by which method?

product inhibition High glucose-6-phosphate (G6P) concentration inhibits hexokinase (HK). As glucose-6-phosphate (G6P) is the product of the hexokinase (HK)-catalyzed reaction, this is an example of product inhibition. Hexokinase (HK) is not a zymogen nor is it under phosphorylation control. Feedback inhibition would require phosphoenolpyruvate (PEP) or pyruvate (Pyr), which are end products/intermediates of glycolysis, to be inhibitory. Allosteric activation implies that the enzyme is up-regulated by a molecule that alters the shape of hexokinase (HK), causing the enzyme activity to increase. The major mechanism of regulatory control for glycolysis (on the left) and gluconeogenesis, a pathway that synthesizes glucose (on the right), are seen in the figure.

If a person were deficient in vitamin B7, which enzyme catalyzed reaction in gluconeogenesis would be directly affected?

pyruvate carboxylase

A transaminase (or aminotransferase) enzyme uses alanine and alpha-ketoglutarate as substrates to produce the products __________ and __________.

pyruvate; Glu

A transaminase (or aminotransferase) enzyme uses alanine and alpha-ketoglutarate as substrates to produce the products __________ and __________.

pyruvate; Glu -Transaminase enzymes catalyze the transfer of an alpha-amino group from an amino acid to an alpha-ketoacid. The products are a new amino acid and a new alpha-ketoacid (see the figure below). Alanine is the substrate amino acid whose alpha-amino group will be removed leaving a three carbon alpha-keto acid, pyruvate. Alpha-ketoglutarate accepts this amino group and is converted into Glu, the new amino acid.

Phosphofructokinase (PFK) catalyzes the_______________________step in glycolysis and is the most ________________control point.

rate-limiting ; important

Transaldolase is.......

responsible for cleaving the three carbon unit from sedoheptulose-7-P and adding that three carbon unit to glyceraldehyde-3-P thus resulting in erythrose-4-P and fructose-6-P.

Function of bile salts

the function depends on their amphiphatic properties, is to solubilize dietary lipids. Without the bile salts, lipids would be insoluble in the aqueous solution in the intestinal lumen and less amenable to digestion and absorption. In this regards, the first role of bile salts is to emulsify dietary lipids. The negatively charged bile salts surround the lipids creating lipid droplets in the intestinal lumen. The negative charges on the bile salts repel each other, so that the droplets dissperse, rather than blend theirby increasing the surface area for digestive enzymes. Without emulsification, lipids would clump into large blobs with little surface. Second role of bile salts is to form micelles, with the products of lipid digestion, including monoglycerides and fatty acids The core of the micelles contains these lipids, and the surface of the micelle is lined with bile salts. The hydrophobic portions of the bile salt molecules are dissolved in the lipid core of the micelle, and the hydrophilic portions are dissolved in the aqueous solution in the intestinal lumen.

why does chymotrypsin bind TPCK?

the phenyl group of TPCK is structurally similar to regular chymotrypsin substrate.

apoenzyme or apoprotein

the protein part of a holoenzyme

Metabolism

the sum of the chemical reactions that take place within each cell of a living organism. These chemical reactions provide energy for vital processes and for synthesizing new organic material. Metabolism is a necessary process, without which living organisms would die.

Anabolism: Summary

the synthesis of all compounds needed by the cells. It supports the growth of new cells, the maintenance of body tissues, and the storage of energy (fat storage) for future use.

What inactivates pepsinogen once it enters the duodenum?

the ~neutral pH

Pyruvate kinase is the __________ regulated enzyme of glycolysis.

third

^^^Secretion of insulin causes_________________ of these receptors from intracellular stores to the _________________________,

translocation; cell surface; This allows more efficient energy storage by these tissues when blood glucose is in excess.

Which type os fatty acid types must go to the peroxisome for initial degredation?

very long chain fatty acid degradation

How do humans obtain the amino acids that cannot be synthesized by the body?

we eat them

binding equilibrium... θ θ equations

θ = (binding sites occupied)/(total binding sites) θ = [PL]/([PL]+[P]) θ = [L]/([L] +(1/Ka))

θ for O₂ in myoglobin

θ = [O₂]/([O₂]+Kd) -kd is equal to the [O₂} at which half of the available ligand-binding sites are occupied. θ = [O₂]/([O₂]+[O₂].₅) θ = pO₂/(pO₂+P₅₀)

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