biochem exam 4 review

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__ ______ nucleotide synthesis forms nucleotide bases from component parts.

De novo

Ribonucleotides Are Precursors to:

Deoxyribonucleotides

____________ is a removal of small molecules from a solution of a macromolecule by their diffusion through a semipermeable membrane into a buffered solution

Dialysis

Radioactive‑labeling experiments can yield estimates of the amount of glucose 6‑phosphate metabolized by the pentose phosphate pathway (PPP) and the amount metabolized aerobically by the combined action of glycolysis, the pyruvate dehydrogenase complex, and the citric acid cycle. A researcher has a tissue sample and two radioactively labeled glucose samples, one labeled with C14 at C‑1 and the other labeled with C14 at C‑6. What is the rationale for the experiment? A) In the PPP, C‑1 of glucose 6‑phosphate becomes C‑1 of ribose 5‑phosphate. B) Aerobic glucose metabolism reduces NAD+, whereas the PPP reduces NADP+. C) Aerobic glucose metabolism is oxidative, whereas the PPP is completely nonoxidative. D) Glucose 6‑phosphate is only metabolized by the PPP. E) Aerobic glucose metabolism decarboxylates C‑1 and C‑6, whereas the PPP only decarboxylates C‑1.

E) Aerobic glucose metabolism decarboxylates C‑1 and C‑6, whereas the PPP only decarboxylates C‑1.

Nitrogen is a component of which molecules? A) Amino Acids B) Lipids C) Nucleotides D) Disaccharides E) Both A and C

E) Both A and C

What is/are the primary transport form(s) of ammonia in our body? A) ATP B) Glutamine C) It is soluble in water and does not need a specific transport form D) Glutamate E) Both B and D

E) Both B and D

Insulin Signaling Is Terminated by the Action of ____________

Phosphatases

The Proteome Is the Functional Representation of the __________

genome

The resulting buildup of acetyl-CoA increases __________________ by activating _____________ __________________.

gluconeogenesis pyruvate carboxylase

This cleavage yields _________-__-_______________, which is converted by _______________________ to ___________-__-______________.

glucose 1‑phosphate phosphoglucomutase glucose 6‑phosphate

what is this?

glucose 6-phosphate

in glycogen degradation, glucose-__-phosphate is converted to glucose-___-phosphate

glucose-1-phosphate --> glucose-6-phosphate

Complete the reactions showing the transfer of glucose to a growing glycogen chain. Choose the correct reactant or product to complete each equation. __________-__-__________ ----phosphoglucomutase--> glucose-1-phosphate

glucose-6-phosphate

in glycogen synthesis, glucose-__-phosphate is converted to glucose-__-phophate

glucose-6-phosphate --> glucose-1-phosphate

Complete the balanced equation for the synthesis of alanine from glucose. glucose + 2 ADP + 2 Pi + 2 NAD+ + 2 ____________ --> 2 alanine + 2 a-ketoglutarate + 2 ATP + 2 NADH + 2H2O + 2H+

glutamate

____________ serves as a nitrogen source for biosynthesis reactions, such as the synthesis of amino acids from a-ketoacids

glutamate

Ammonium ion is incorporated into an amino acid through:

glutamate and glutamine

_______________ _________ catalyzes the incorporation of ammonia into a-ketoglutarate to generate glutamate

glutamate dehydrogenase

___________ is a versatile nitrogen donor

glutamine

_____________ __________ incorporates another nitrogen into glutamate in an amidation reaction to form glutamine

glutamine synthetase

what is a key regulatory enzyme in nitrogen metabolism?

glutamine synthetase

The synthesis of nucleotides requires several amino acids. Identify each amino acid as a precursor in the synthesis of purines, pyrimidines, both purines and pyrimidines, or neither purines nor pyrimidines. Purines

glycine

in de novo biosynthesis of purines, the purine ring builds up following the addition of three carbons from:

glycine

Epinephrine binding to receptors in muscle or liver cells induces breakdown of __________.

glycogen

PKA activation leads to activation of enzymes that release glucose from ___________.

glycogen

These PKA enzymes activate thousands of _________-degrading enzymes in the liver tissue.

glycogen

glucose can be stored for later use as

glycogen

2) enzyme __________ ________ is the basic enzyme in glycogen synthesis

glycogen synthase

glycogen is synthesized by

glycogen synthase

the _________-____________ enzyme forms a new branch point during glycogen synthesis.

glycogen-branching

Glycogen is broken down at its free nonreducing ends. The reducing end of a glycogen molecule is not available for enzymatic degradation, because it is bound to _________.

glycogenin

_______ starts a new glycogen chain

glycogenin

__________, the small protein, is the primer for the molecule synthesis and is located in the core.

glycogenin

Steroid hormones are synthesized from cholesterol in _______ and _________ glands.

gonads adrenal

the overall goal of fatty acid synthesis is to attach acetate unit (2-carbon) from malonyl-CoA to a __________ _______ and then reduce it

growing chain

G-proteins

heterotrimeric (aBY) membrane-associated guanosine-binding proteins that bind GTP (active form) or GDP (inactive form)

The nonoxidative phase reactions convert pentose phosphates to ________ phosphates, allowing the oxidative reactions to continue.

hexose

the nonoxidative phase of the pentose phosphate pathway converts pentose phosphates to _______ __________, which allows the oxidative reactions to continue

hexose phosphates

Citrate is the indicator of ______ energy in the cell.

high

Many proteins lose their activity in the presence of ______ salt.

high

in electrophoresis, the gel matrix _________ mobility of proteins according to their size and shape.

hinders

In 2D gel electrophoresis, _____________ separation reflects differences in pI

horizontal

Nuclear receptor

hormone binding allows the receptor to regulate the expression of specific gene

Where does fatty acid synthesis occur in the cell?

in the cytoplasm

cAMP is low: 2 catalytic subunits are bound to two regulatory subunits; complex is _______________

inactive

Ethanol consumption inhibits gluconeogenesis by causing an increase in the concentration of NADH. NADH is a substrate for malate dehydrogenase, the enzyme that produces malate. An accumulation of malate favors the activity of malic enzyme. Thus, an increase in NADH concentration increases the enzymatic activity of malic enzyme. The increase in NADH after ethanol consumption favors an _________ in the NADPH concentration and ____________ fatty acid synthesis. Therefore, ethanol consumption in an otherwise fasting state __________ the risk of hypoglycemia.

increase stimulates increases

Epinephrine binding to receptors in heart cells _____________ heart rate.

increases

4) glycogen synthase can make only 1,4 glycosidic bonds. it cannot create alpha 1,6 bonds. benefits of branching: a) it ________ solubility of glycogen b) it __________ number of terminal residues Alpha 1,6 bonds are made by ___________ ________________ enzyme.

increases increases ___________ _________ enzyme

In uncontrolled diabetes, the combination of low insulin and high glucagon levels results in the __________ of fatty acid synthesis.

inhibition

A high level of citrate, which also indicates a sufficient energy supply, ________ carbohydrate fragmentation and diverts the carbohydrate that has been fragmented from combustion to the formation of _________.

inhibits lipids

in de novo biosynthesis of purines, The first intermediate with a full purine ring is:

inosinate (IMP)

The receptors for _______ and epidermal growth factor are prototypes of the (receptor tyrosine kinases) family

insulin

an example of an enzyme-linked receptors

insulin receptor

an example of other membrane receptors

integrin receptors

the reaction of the synthesis of UDP-glucose is subsequently rendered __________ by the hydrolysis of pyrophosphate

irreversible

which one is uracil?

Nonphotosynthetic organisms rely on the pentose phosphate pathway for generating biosynthetic reducing power. First, the _______________ ____________ phase converts ____________ __-_____________ to __________ __-__________, generating _________ in the process.

irreversible oxidative glucose 6‑phosphate ribulose 5‑phosphate NADPH

______________ _______________ regulate the entire signaling process.

Feedback pathways

___________ is supplied in the form of N10-formyltetrahydrofolate

Formate

The epinephrine-initiated pathway is shut down in a variety of ways: 2) Gα has inherent GTPase activity that cleaves the bound GTP to GDP. The Gα bound to GDP spontaneously reassociates with the βγ subunits, terminating the activity of the __ __________.

G protein

Nonoxidative Phase Recycles R-5-P to

G-6-P

The activation of a few ______ leads to the activation of few adenylyl cyclase enzymes.

GCPRs

Note that ATP is used to phosphorylate _____ precursor, while GTP is used to phosphorylate _____ precursor.

GMP AMP

G Proteins Spontaneously Reset Themselves Through:

GTP hydrolysis

in de novo biosynthesis of purines, Synthesis begins with reaction of 5-phosphoribosyl 1- pyrophosphate (PRPP) with:

Glu

What is the source of N in amino acid synthesis?

Glu or Gln

In isoelectric focusing, if a mixture of proteins is placed in a gel with a pH gradient and an electrical field is applied, proteins will migrate until they reach their _____________ _________, the pH at which they have no net charge.

isoelectric point

Ribulose 5-phosphate, generated by the oxidative phase, is _________ into ribose 5-phosphate.

isomerized

what is the major metabolic fate of glucose 6-phosphate?

it will be converted into pyruvate from glycolysis for the citric acid cycle or the pentose phosphate pathway

The isoelectric point is where proteins are ___________ soluble.

least

nitrogen-fixing bacteria in root nodules of

legumes

When proteins are separated by binding via affinity chromatography, protein mixture is added to a column containing a polymer-bound ligand specific for the protein of interest. The protein of interest is eluted by the ________ solution while the unwanted proteins are washed through the column.

ligand

Epinephrine binding g to receptors in adipose cells induces _________ _________________.

lipid hydrolysis

glycogen storage occurs mainly in the ________ and _________

liver and muscle

in de novo biosynthesis of nucleotides, nucleotide pools are kept ______, so cells must continually synthesize them. this synthesis may actually limit rates of transcription and replication.

low

(in column chromatography) Proteins with a _________ affinity for the solid phase will wash off first; proteins with ___________ affinity will retain on the column longer and wash off later.

lower higher

Most proteins in mammals contain all 20 amino acids. If even one essential amino acid is absent from the diet, protein degradation occurs to such an extent that more nitrogen is excreted than ingested, a condition called negative nitrogen balance. Why does the increase in amino acid degradation lead to an increase in nitrogen excretion?

Increase in protein degradation will lead to an increase of free amino acids. Since amino acids cannot be stored, amino acids will have nitrogen removed and incorporated into urea, which will be excreted

in the de novo pathway for purine nucleotide synthesis: ________________ (IMP) is the common intermediate

Inosinate

_______________ ____________ allows separation of proteins in a gel on the basis of their relative amounts of acidic and basic amino acids.

Isoelectric focusing

the sources that supply NADPH for fatty acid synthesis are:

malate glucose 6-phosphate

When proteins are separated by size via size exclusion, protein molecules separate by size. ___________ molecules pass more freely, appearing in the earlier fractions.

Larger

________ phosphatases contribute to signal termination by converting PIP3 into PIP2

Lipid

The Formation of _________ ___ Is the Committed Step in Fatty Acid Synthesis and occurs in two steps

malonyl CoA

the three stages of fatty acid synthesis: 2) Activation of acetyl CoA in the cytoplasm to form

malonyl CoA

The committed step in fatty acid synthesis is the formation of __________ _____ in a reaction catalyzed by ____________ ______ ________________ ___.

malonyl CoA acetyl CoA carboxylase 1

acetyl CoA is carboxylated to form _________ _____ and is catalyzed by __________-_____ _______________

malonyl CoA acetyl-CoA carboxylase

Glucagon inactivates acetyl‑CoA carboxylase, inhibiting the production of __________-_____.

malonyl-CoA

In the cytosol, acetyl-CoA is converted to _________-___, a three-carbon compound.

malonyl-CoA

In 2D gel electrophoresis, individual protein spots can be cut out of the gel and identified by _______ ___________________.

mass spectrometry

nucleotides are the universal currency of:

metabolic energy

Fatty acid synthesis requires the cooperation of various ___________ ____________ located in different cellular compartments

metabolic pathways

glycogen can also be made by the recycling of glucogenic __________ like lactate or certain amino acids

metabolites

Citrate, synthesized in the ____________, is transported to the cytoplasm and cleaved by ATP-citrate lyase to generate _________ _____ for fatty acid synthesis.

mitochondria acetyl CoA

SDS PAGE Separates Proteins by __________ __________

molecular weight

The first lane shows a set of standard proteins (of known Mr), serving as: These marker proteins can be used to estimate the molecular weight of an unknown protein (lane 2).

molecular weight markers

The electrophoretic mobility of a protein on an SDS polyacrylamide gel is related to its ______________________.

molecular weight, Mr

Steroids are ____ polar than cholesterol

in de novo biosynthesis of nucleotides, Glu provides:

most amino groups

At a higher pH, proteins will carry a ____________ charge.

negative

SDS gives all proteins a uniformly ____________ charge.

negative

With cation exchangers, proteins with more ___________ net charge move faster and elute earlier.

negative

The inside of the cell is typically ___________ charged compared with the outside: Vm -50 to -70 mV.

negatively

an example of a ligand-gated ion channel

nicotinic acetylcholine receptor

When organisms die, microbial degradation of their proteins return ammonia to the soil, where nitrifying bacteria again convert it to ________ and _________.

nitrite nitrate

The ____________ uses the electrons to reduce N2 to NH3 according to the following reaction.

nitrogenase

The _____________ complex is responsible for the fixation of N2 into NH3.

nitrogenase

Do fatty acid synthesis and degradation occur in the same location of the cell?

is ATP used in the nonoxidative phase?

Symbiotic nitrogen-fixing bacteria, or bacteroids (red), live inside the ___________ _____.

nodule cell

the _____________ _______ form a surface where the enzymes can work.

nonreducing ends

in animals, all three subunits of acetyl-CoA carboxylase are on ____ polypeptide chain

one

The membrane potential is largely due to assymmetric transport of cations by Na+K + ATPase. - 3 Na+_____ - 2 K+ __

out in

the three stages of fatty acid synthesis: 1) Transfer of acetyl CoA out of the mitochondria into the cytoplasm. Citrate is transported into the cytoplasm and cleaved into

oxaloacetate and acetyl CoA

Steroids are ___________ derivatives of sterols.

oxidized

When proteins are separated by charge through ion exchange, proteins move through the column at rates determined by their net charge at the ____ being used.

Deoxyribonucelotides mechanism: Two H atoms are donated by _______ and carried by proteins thioredoxin or glutaredoxin.

NADPH

Fatty Acid Synthesis requires reducing power obtained from _________ to go through reduction steps

NADPH

_______ Regulates Partitioning into Glycolysis versus Pentose Phosphate Pathway

NADPH

fatty acid synthase uses ________ as the electron donor

NADPH

stoichiometry of synthesis of palmitate (16:0) 2) Seven cycles of condensation, reduction, dehydration, and reduction... using ________ to reduce the B-keto group and trans-double bond

NADPH

the nonoxidative phase is used in tissues requiring more _________ than R-5-P, such as the ___________ and____________ ________.

NADPH liver and adipose tissue

oxidative phase of the pentose phosphate pathway generates:

NADPH and a pentose

glucose-1-phosphate is the substrate for

NDP-sugar pyrophosphorylase

The pathways for degradation of pyrimidines generally lead to ____ production and to ______ synthesis.

NH4+ urea

glycogen is a branched polymer of a(1-->__) linked glucose with a(1-->___) linkages every 12 to 14 glucose units.

a(1-->4) a(1-->6)

G protein-coupled receptors (GCPRs)

a-helical integral membrane proteins (7TM, or heptahelical, or serpentine receptors)

The source of carbon atoms for growing fatty acid chain is:

acetyl-CoA

Fatty acid synthesis begins with a preparatory step in which ___________-____ is transferred from __________ to the _______________. However, it cannot pass through the membrane, so it is transported as _________, which is cleaved to __________-______ and ___________________.

acetyl-CoA mitochondria cytoplasm acetyl-CoA oxaloacetate

Malonyl CoA is formed from:

acetyl-CoA and bicarbonate

UDP-Glucose is an __________ form of glucose

activated

1) glucose molecule needs to be ________, because glucose itself, or glucose-1-phosphate is not reactive enough to be attached to the growing glycogen chain. activation: glucose-1-phosphate interacts with UTP molecule to make _____-____________, which is much more active.

activated UDP-glucose

Effector enzyme in the plasma membrane is regulated by:

activated G-protein

Nucleotides are synthesized via the salvage pathway with:

activated ribose (PRPP) + base

cAMP is high: R subunits bind cAMP, undergo dramatic reorganization, and release C (catalytic) subunits in their __________ form

active

The function of the protein is called the:

activity

Epinephrine is a hormone made in __________ glands (pair of organs on top of kidneys).

adrenal

ribose phosphate pyrophosphokinase is a highly regulated _________ enzyme

allosteric

Most proteins in mammals contain all 20 amino acids. If even one essential amino acid is absent from the diet, protein degradation occurs to such an extent that more nitrogen is excreted than ingested, a condition called negative nitrogen balance. Why does the absence of a single essential amino acid lead to protein degradation?

amino acids are not stored; proteins are degraded to provide a source of the missing essential amino acid

Some amino acids can be made by simple transamination reactions which are catalyzed by:

aminotransferases (transaminases)

There is a short cut in nitrogen cycle that promote anaerobic ammonia oxidation (_____________). In this case Ammonia and NO2- is converted to N2. As much as 50 to 70% of the NH3 to N2 conversion in the biosphere may occur through this pathway, which went undetected until 1990s.

anammox

____________ Amino Acids Absorb Light in a Concentration-Dependent Manner

aromatic

Identify the metabolic precursors of three nonessential amino acids. You may need to reference a table of amino acids. The structures of some precursor molecules are given. *shows phenylalanine, serine, glutamate, aspartate, pyruvate, and oxaloacetate* Identify the metabolic precursor of asparagine.

aspartate

Plants and many bacteria can take up and reduce nitrate and nitrite to NH4. This ammonia is incorporated into AA by plants. Animals then use plants as a source of AA. This process is called:

assimilation

The catalytic domains of receptor tyrosine kinases adds a phosphate group to itself, also known as _____-_________________, which leads to a conformational change allowing binding and catalytic phosphorylation of specific target proteins. It also adds a phosphate group to a ____________ in specific target proteins.

auto-phosphorylation tyrosine

The results of a separation using two-dimension gel electrophoresis are shown here. Which protein has the highest molecular weight?

Metabolic degradation of nucleotides produces free _______ that can be recycled in salvage pathways.

bases

During purification, determination of the location of the protein of interest can be performed by tracking its ____________.

behavior

If a protein has a specific function (e.g., binding insulin), the fraction that binds insulin _____ after each purification step will contain the most of the protein of interest.

best

nucleotide derivatives participate in ______________ processes

biosynthetic

acetyl-CoA carboxylase has three subunits; one subunit has ______ covalently linked to Lys

biotin

glycogen can be made from excess ________ ___________

blood glucose

Smaller proteins move through the gel more rapidly than larger proteins and therefore are found nearer the ________ of the gel

bottom

Activation of the adenylate cyclase leads to the synthesis of the second messenger, ___________.

cAMP

Every active adenylyl cyclase enzyme makes several ________ molecules, thus activating several PKA enzymes.

cAMP

Many ___________ (e.g., malaria) lack de novo biosynthesis pathways and rely exclusively on salvage. Compounds that inhibit salvage pathways are promising _______________ drugs.

parasites antiparasitic

Centrifiguation is used to ________ precipitated protein.

pellet

The α‑1,4 linkages in glycogen are cleaved via _________________.

phosphorolysis

A protein was purified to homogeneity. The determination of the mass by gel‑filtration chromatography yields a value of 60 kDa.60 kDa. Chromatography in the presence of urea results in a 30 kDa30 kDa species. Repeating the chromatography in the presence of both urea and β‑mercaptoethanol, however, results in a single molecular species of 15 kDa.15 kDa. What do the data suggest about the structure of the protein? A) The 60 kDa protein is composed of multiple 15 kDa domains that hydrolyze upon treatment with an oxidizing agent. Some of the domains reassociate in the gel filtration column. B) The 60 kDa protein is composed of two 30 kDa subunits held together by disulfide bonds. Each 30 kDa subunit is composed of two 15 kDa subunits linked by noncovalent interactions. C) The 60 kDa protein is composed of two 30 kDa subunits linked by noncovalent interactions. Each 30 kDa subunit is composed of two 15 kDa subunits joined by disulfide bonds. D) The 30 kDa protein is composed of 15 kDa subunits held together by disulfide bonds. Treatment increases the protein's association with the gel‑filtration column and increases the apparent protein mass.

C) The 60 kDa protein is composed of two 30 kDa subunits linked by noncovalent interactions. Each 30 kDa subunit is composed of two 15 kDa subunits joined by disulfide bonds.

Consider an experiment where your goal is to isolate Bruton's tyrosine kinase (BTK) enzyme from a whole‑cell lysate. You have an affinity chromatography column with a tyrosine kinase inhibitor molecule covalently attached to the beads. The tyrosine kinase inhibitor binds and inhibits BTK. As a result of the experiment, you are able to elute BTK from the column, but in a mixture of other tyrosine kinases. Why are tyrosine kinases other than BTK present in the eluate? A) The kinase inhibitor has low binding affinity. B) BTK is inactive in the cell. C) The kinase inhibitor has low specificity. D) BTK is rapidly degraded during cell lysis.

C) The kinase inhibitor has low specificity.

Identify the true statements regarding α-1,6 linkages in glycogen. (Select) A) New α‑1,6 linkages can only form if the branch has a free reducing end. B) Exactly four residues extend from these linkages. C) The number of sites for enzyme action on a glycogen molecule is increased through α‑1,6 linkages. D) The reaction that forms α-1,6 linkages is catalyzed by a branching enzyme. E) At least four glucose residues separate α‑1,6 linkages.

C) The number of sites for enzyme action on a glycogen molecule is increased through α‑1,6 linkages. D) The reaction that forms α-1,6 linkages is catalyzed by a branching enzyme. E) At least four glucose residues separate α‑1,6 linkages.

Select the true statements about SDS‑PAGE, a method of separating proteins. Assume that SDS‑PAGE is performed under reducing conditions. (Select) A) Protein‑SDS complexes migrate toward the negative electrode. B) Sodium dodecyl sulfate binds proteins, resulting in protein‑SDS complexes that are similar in size. C) Protein‑SDS complexes have similar mass to charge ratios; therefore, separation is by size. D) Smaller proteins migrate faster through the polyacrylamide gel. E) Proteins are separated in a polyacrylamide gel matrix. F) Proteins are visualized using a dye that binds to the gel matrix, but not to proteins.

C) Protein‑SDS complexes have similar mass to charge ratios; therefore, separation is by size. D) Smaller proteins migrate faster through the polyacrylamide gel. E) Proteins are separated in a polyacrylamide gel matrix.

what type of regulation involves a common step for several pathways that is partly inhibited independently by each of the various end products?

cumulative feedback inhibition

serine, in turn, is metabolized to

cysteine and glycine

During the early stages of an enzyme purification protocol, when cells have been lysed but cytosolic components have not been separated, the reaction velocity versus substrate concentration is sigmoidal. As you continue to purify the enzyme, the curve shifts to the right. Draw both plots schematically and explain the results. A) This is an enzyme that displays Michaelis-Menten kinetics, and you purify away an inhibitor B) This is an allosteric enzyme, but you must use a Lineweaver-Burk plot to determine KM and Vmax correctly C) This is an allosteric enzyme, and during purification you purify away an activator D) This is an allosteric enzyme, and during purification you purify away one of the substrates E) This is an enzyme that displays Michaelis-Menten kinetics, but you must use a Lineweaver-Burk plot to determine KM and Vmax correctly

C) This is an allosteric enzyme, and during purification you purify away an activator

Fatty acid synthesis occurs in the:

cytoplasm

Which reaction is influenced by the molecule in the first question? Choose the enzyme that catalyzes the reaction. (This is the major controlling step.) A) transaldolase B) phosphopentose epimerase C) glucose 6‑phosphate dehydrogenase D) phosphopentose isomerase E) transketolase F) lactonase

C) glucose 6‑phosphate dehydrogenase

Which aromatic amino acid is nonessential? A) phenylalanine B) isoleucine C) tyrosine D) tryptophan E) threonine

C) tyrosine

The first step in pyrimidine synthesis is a three-step reaction to form __________ __________ catalyzed by carbamoyl phosphate synthase II (CPS II).

carbamoyl phosphate

in the de novo pathway for pyrimidine nucleotide synthesis: The C-2 and N-3 atoms in the pyrimidine ring come from _______________ ____________, whereas the other atoms of the ring come from ____________.

carbamoyl phosphate aspartate

Shuttle for Transfer of Acetyl Groups from Mitochondria to _________

cytosol

The results of a separation using two-dimension gel electrophoresis are shown here. Which protein or proteins have the highest pI value?

d and e

Steroids are carried through the body in the bloodstream, usually attached to ___________ ___________.

carrier proteins

__________ __________________ allows separation of a mixture of proteins over a solid phase (porous matrix) using a liquid phase to mobilize the proteins.

Column chromatography

Homogenization

cells are disrupted to form a homogenate, which is a mixture of all the components of the cell, but no intact cells

Gated ion channel

channel opens or closes in response to concentration of signal ligand or membrane potential

in electrophoresis, the electric field pulls proteins according to their ________.

charge

Steroids have the sterol nucleus but lack the alkyl chain found in ___________.

cholesterol

Many of the methods used in isolating molecules from cells involve some form of ____________________. It is commonly used for separation in which the protein is remain fully folded (in native conformation)

chromatography

Acetyl-CoA + oxaloacetate --citrate synthase--> citrate this reaction is a step of what metabolic process?

citric acid cycle

nucleotides can also function as enzyme _____________

cofactors

These signals cause changes in the cell's __________________ and ______________.

composition and function

Flow of ionic species across the membrane depends on its _____________ gradient and overall electrical potential.

concentration

For proteins and peptides with known extinction coefficients (or sequences), ______________ can be determined by UV-visible spectrophotometry

concentration

the reaction of fatty acid synthesis involves cycles of four enzyme-catalyzed steps: -___________ of the growing chain with activated acetate -___________ of carbonyl to -hydroxyl -________________ of alcohol to trans-alkene -__________ of alkene to alkane

condensation reduction dehydration reduction

At high salt concentrations, the solubility of proteins tends to ____________ as water molecules become bound to salt ions thereby allowing protein solutes to aggregate and precipitate.

decrease

step 2-4 of FAS I Rx: What is step 3?

dehydration

SDS - sodium dodecyl sulfate is a:

detergent

Salt can be removed from the protein solution by _________.

dialysis

The salt concentration at which a protein precipitates _______ from one protein to another

differs

Signal molecule ____________ from the receptor terminating the signal

dissociate

with the use of SDS, the native shape of proteins:

does not matter

Uridine diphosphate-glucose (UDP-glucose) is the glucose _______ in glycogen synthesis

donor

the fourth step of signal transduction is the response, which involves the activation (or sometimes inhibition) of the _______________.

effectors

Advantages of fatty acid synthase (FAS): -no diffusion of products/substrates between reactions, increasing __________ -______________ of energy -no release of growing ____________ product/substrate to the aqueous environment

efficiency conservation hydrophobic

Protein separation in analytical scale is commonly done by ______________.

electrophoresis

glycogen is degraded to glucose units for use in _________ production

energy

The Haber process, devised in 1910, allows for industrial fixation of nitrogen. Industrial synthesis of NH3 via the Haber process is one of mankind's most significant chemical processes. Mimicking biological nitrogen fixation (biomimetic nitrogen fixation) may yield significant __________ __________, or allow use of _____________ energy sources.

energy savings renewable

assay tells us how much __________ ___________ is present, not how much protein is present

enzyme activity

what type of regulation involves the committed step being catalyzed by two or more enzymes with differing regulatory properties?

enzyme multiplicity

an example of a G-protein coupled receptor

epinephrine receptor

G-protein coupled receptor

external ligand binding to receptor activates an intracellular GTP-binding protein, which regulates an enzyme that generates an intracellular second messenger

with the use of SDS, the rate of movement will only depend on size: small proteins will move _________.

faster

Fatty Acid synthesis is catalyzed by a single enzyme named ____________ _______ _________________, which contains __ different catalytic sites in one polypeptide chain.

fatty acid synthase 7

the synthesis of fatty acids is catalyzed by:

fatty acid synthase (FAS)

NADPH is an electron donor (reducing agent) -reductive biosynthesis of ________ ______ and __________ -repair of oxidative damage

fatty acids and steroids

Insulin is the biochemical signal for the _____ state.

fed

______________ __________ regulates amino acid biosynthesis. in _____________ _________, the final product in a pathway inhibits the enzyme catalyzing the committed step. *same blanks*

feedback inhibition

what type of regulation involves two pathways who have an initial common step, and one pathway is inhibited by its own product and stimulated by the product of the other pathway?

feedback inhibition and activation

Citrate acts as a positive effector for the _______ enzyme of fatty acid biosynthesis.

first

The pyrimidine ring is synthesized ______ and subsequently attached to an activated ________.

first ribose

Different proteins precipitate at different concentrations of salt based on the inherent ____________ of the specific protein.

polarity/hydrophobicity

in electrophoresis, the gel is commonly ________________, so separation of proteins via electrophoresis is often called polyacrylamide gel electrophoresis, or PAGE.

polyacrylamide

At a lower pH, proteins will carry a more ____________ charge.

positive

nucleotides function as activated _____________ of nucleic acids

precursors

the first step of signal transduction involves the release of the ___________ ________________ as a result of stimulus.

primary messenger

the second step of signal transduction involves the reception of the _____________ __________________. The signal molecule binds to the membrane receptor, which is usually a _____________________ _____________.

primary messenger transmembrane protein

3) enzyme glycogen synthase cannot start from scratch; it requires a _______ which is made by enzyme _____________. Glycogenin uses _____-___________

primer Glycogenin UDP-glucose

Accumulation of citrate will ________ Fatty Acid Synthesis

promote

Each band on the gel represents a different ___________

protein (or protein subunit)

The epinephrine-initiated pathway is shut down in a variety of ways: 1) Cyclic AMP phosphodiesterase converts cAMP to AMP, which does not activate ________ ________ ___.

protein kinase A

cAMP allosterically activates a variety of enzymes including cAMP-dependent _________________.

protein kinase A (PKA)

Coomassie blue binds to the ___________ but not to the gel itself

proteins

The ____________ is the entire set of proteins expressed and modified by a cell under a particular set of biochemical conditions.

proteome

Proteins in a complex mixture often require more than one _______________ to completely isolate the protein of interest.

purification

In de novo nucleotide synthesis, __________ _________________ synthesis is more complex, and the base is assembled on ____.

purine nucleotide PRPP

in de novo biosynthesis of nucleotides, Gly is precursor for:

purines

Specific Activity Describes the ________ of the Protein of Interest

purity

aminotransferases (transaminases) require the coenzyme ____________ __________, which is derived from vitamin B6

pyridoxal phosphate

In de novo nucleotide synthesis, _______________ _______ are built from bicarbonate, aspartate, and ammonia and then added to PRPP.

pyrimidine bases

in de novo biosynthesis of nucleotides, Asp is a precursor for:

pyrimidines

pyruvate

In addition to SDS, proteins may optionally be briefly heated to near boiling in the presence of a __________ agent, such as dithiothreitol (DTT) or 2-mercaptoethanol (beta-mercaptoethanol/BME), which further denatures the proteins by reducing disulfide linkages, thus overcoming some forms of tertiary protein folding, and breaking up quaternary protein structure (oligomeric subunits). This is known as reducing SDS-PAGE.

reducing

The _____________ provides high-energy electrons, in the form of ferredoxin, for reducing power.

reductase

step 2-4 of FAS I Rx: What is step 2?

reduction

step 2-4 of FAS I Rx: What is step 4?

reduction

Protein phosphatases _________ phosphates from the activated proteins in the insulin signal-transduction pathway, terminating the insulin signal.

remove

The epinephrine-initiated pathway is shut down in a variety of ways: 3) Epinephrine-β-adrenergic receptor interaction is ____________. Once the concentration of epinephrine falls, the receptor will no longer be active.

reversible

phosphoglucomutase catalyzed reaction is

reversible

Second, the ____________ _________________ phase results in the formation of two phosphorylated ______ sugars and one phosphorylated ______ sugar.

reversible nonoxidative C-6 C-3

2'C-OH bond is directly reduced to 2'-H bond without activating the carbon and is catalyzed by:

ribonucleotide reductase

the main products of the pentose phosphate pathway are

ribose 5-phosphate and NADPH

PRPP is synthesized from ribose 5-phosphate of PPP via:

ribose phosphate pyrophosphokinase

_______-__-_____________ can be used to generate ribose-5-phosphate for DNA/RNA.

ribulose-5-phosphate

The polypeptide hormone insulin is secreted when the blood is ______ in glucose.

rich

Most proteins precipitate out of solution at high salt concentrations, an effect called:

salting out

In contrast, __________ ____________________ recycle nucleotides by incorporating free bases released by nucleic acid degradation.

salvage pathways

Nucleotides can be ___________ from RNA, DNA, and cofactor degradation. In this case, preformed bases are recovered and attached to an activated ribose.

salvaged

the third step of signal transduction involves the transduction of the signal. Information that the signal has arrived is converted into other chemical forms. Transduction often comprises many steps. The signal is often amplified during the process. Cell increases the production of the ________________ ______________.

secondary messenger

serine

the glycolytic intermediate 3-phosphoglycerate is the precursor for

serine

Many of the steroid hormones are male and female _____ hormones.

sex

nucleotides are an essential component of __________-________________ pathways

signal-transduction

in de novo biosynthesis of nucleotides, bases are synthesized:

while attached to ribose

Which enzyme directly generates the majority of the acetyl‑CoA used in fatty acid synthesis? A) acyl‑CoA acetyltransferase B) malate dehydrogenase C) pyruvate dehydrogenase D) ATP‑citrate lyase E) citrate synthase

D) ATP‑citrate lyase

Which of the following is true? A) Membranes are lipid bilayers. B) Membrane lipids have both hydrophobic and hydrophilic properties. C) Many membranes are electrically polarized. D) All of the above. E) None of the above.

D) All of the above.

Symbiotic microorganism responsible for N2 fixation is:

Rhizobium

The primary messenger responsible for the "fight or flight" response: A) cAMP B) Insulin C) Epinephrine D) Glucagon E) Calcium ion

C) Epinephrine

One method for separating polypeptides utilizes their different solubilities. The solubility of large polypeptides in water depends upon the relative polarity of their R groups, particularly the number of ionized groups. The more ionized groups there are, the more soluble the polypeptide. Which polypeptide, (Ala−Asp−Gly)5 or (Asn−Ser−His)5 , is more soluble at pH 3.0?

(Asn-Ser-His)5

One method for separating polypeptides utilizes their different solubilities. The solubility of large polypeptides in water depends upon the relative polarity of their R groups, particularly the number of ionized groups. The more ionized groups there are, the more soluble the polypeptide. Which polypeptide, (Ala−Ser−Gly)5 or (Asn−Ser−His)5 , is more soluble at pH 6.0?

(Asn-Ser-His)5

(Glu)20

One method for separating polypeptides utilizes their different solubilities. The solubility of large polypeptides in water depends upon the relative polarity of their R groups, particularly the number of ionized groups. The more ionized groups there are, the more soluble the polypeptide. Which polypeptide, (Lys−Ala)3 or (Gly)20 , is more soluble at pH 7.0?

(Lys-Ala)3

Lipids Fulfill a Variety of Biological Functions:

-Energy storage -Constituents of membranes -Anchors for membrane proteins -Cofactors for enzymes -Signaling molecules -Pigments -Detergents -Transporters -Antioxidants

in the de novo pathway for purine nucleotide synthesis: AMP and GMP are synthesized from _____, ____________, ________, ____________, and __-______-_____________.

-PRPP -glutamine -glycine -aspartate -N-formyl-tetrahydrofolate

Nucleotides are synthesized via the de novo pathway with:

-activated ribose (PRPP) -amino acids -ATP -CO2

selected biomolecules derived from amino acids:

-adenine -cytosine -sphingosine -histamine -thyroxine -epinephrine -serotonin -nicotinamide -3,6-dihydroxyindole

The intracellular levels of cAMP are regulated by the balance between the activities of two enzymes:

-adenylyl cyclase (AC) -cyclic nucleotide phosphodiesterase (PDE)

Nucleotides can be synthesized de novo ("from the beginning") from:

-amino acids -ribose 5-phosphate -CO2 -NH3

Receptor Tyrosine Kinases consists of:

-an extracellular ligand-binding domain -an intracellular catalytic domain -Extracellular and intracellular parts are connected by a single trans-membrane segment

Essential amino acids are amino acids that must be obtained through the diet. Non‑essential amino acids can be made biosynthetically. Classify the amino acids into either essential or non‑essential amino acids. Non-essential amino acids

-asparatate -glutamate -serine -glycine

in the de novo pathway for pyrimidine nucleotide synthesis: CMP and UMP are synthesized from ________, _____, and _________ ____________. The pyrimidine ring structure is constructed first, and then attached to PRPP.

-aspartate -PRPP -carbamoyl phosphate

amino acids that give rise to other amino acids from the citric acid cycle are:

-aspartate -threonine -glutamate

Categorize each characteristic of nucleotide synthesis as describing either de novo pathways or salvage pathways. De novo pathways

-assemble nucleotide bases from simple precursor compounds -produce carbamoyl phosphate or 5-phosphoribosylamine

Compare and contrast the de novo synthesis of purine and pyrimidine ribonucleotides. Move each phrase to the appropriate category. If a phrase does not describe either purine or pyrimidine ribonucleotide synthesis, move it to the "Neither" category. Purine ribonucleotide synthesis

-base assembled on ribose ring -inosinate (IMP) is an intermediate

-base is formed and then added to ribose ring -orotate is an intermediate

Pyrimidines are synthesized from _____________, _____________, and ___________, with _____________ often serving as the nitrogen donor.

-bicarbonate -aspartate -ammonia -glutamine

Place all eight of these steps of the insulin signaling pathway in the correct order. The abbreviation PIP2 is used for phosphatidylinositol 4,5‑bisphosphate, and PIP3 is used for phosphatidylinositol 3,4,5‑trisphosphate. Insulin is secreted --> Glucose enters cell

-binding of insulin to the a subunit of the insulin receptor -activation of insulin receptor tyrosine kinase -phosphorylation of IRS proteins -phosphorylation of phosphoinositide 3-kinase (PI-3K) -conversion of PIP2 to PIP3 -activation of PIP3-depdendent protein kinase B (PDK1) -activation of Akt -GLUT4 receptors transported to cell membrane

in the third step of signal transduction, examples of the secondary messengers that are produced are:

-cAMP -Ca2+ -PIP3

Classify the phrases. Does each phrase describe a kinase, a phosphatase, neither, or both? Kinases

-catalyze phosphorylation reactions -may use ATP as a phosphoryl group donor -PKA (protein kinase A) is an example

gated ion channels respond to:

-changes in the membrane potential -ligand binding to specific receptor sites

Arrange the four major steps in the elongation of fatty acid chains by fatty acid synthase. Binding of malonyl-CoA to ACP --> Butyryl group transfer from ACP to B-ketoacyl synthase

-condensation by B-ketoacyl synthase -reduction by B-ketoacyl reductase -dehydration by 3-hydroxylacyl dehydratase -reduction by enoyl reductase

Arrange the steps that occur during the first elongation cycle of fatty acid synthesis in chronological order. Reaction of malonyl CoA and acetyl CoA with ACP --> Reduction to form butyryl ACP

-condensation of acetyl ACP and malonyl ACP -reduction of a ketone on acetoacetyl ACP -dehydration to form crotonyl ACP

Match each role to the appropriate enzyme in the glycogen synthesis pathway. Glycogen synthase

-extends the glycogen chain -key regulatory enzyme -uses a primer

What are the steps of the nitrogen cycle?

-fixation -nitrification -assimilation -anammox

-glutamine -asparatate

The carbon skeleton precursors derive from three sources:

-glycolysis -citric acid cycle -pentose phosphate pathway

in the first step of signal transduction, examples of primary messengers are:

-hormones -pheromones -neurotransmitters

Cells receive signals from the environment beyond the plasma membrane. Types of signals include:

-hormones -neurotransmitters -light -touch -Pheromones

Classify the phrases. Does each phrase describe a kinase, a phosphatase, neither, or both? Neither

-in eukaryotes, transfer phosphoryl groups to acidic amino acids -catalyze reactions that are the reverse of dephosphorylation reactions

Nucleotides contain 3 components:

-nitrogenous base -sugar (pentose) -phosphate (at least one)

the major metabolic precursors from the citric acid cycle are:

-oxaloacetate -a-ketoglutarate

Classify each molecule based on whether or not it is an amino acid precursor. Precursors

-oxaloacetate -pyruvate -ribose 5-phosphate -phosphoenolpyruvate -erythrose 4-phosphate -a-ketoglutarate -3-phosphoglycerate

amino acids that give rise to other amino acids from glycolysis and pentose phosphate pathway:

-phenylalanine

the major metabolic precursors from glycolysis and the pentose phosphate pathway:

-phosphoenolpyruvate + erythrose 4-phosphate

important metabolites derived from amino acids:

-porphyrin rings (heme) derived from Glycine -phosphocreatine (from Gly and Arg) -glutathione -neurotransmitters and signaling molecules -cell-wall constituents -NUCLEOTIDES

the major metabolic precursors from glycolysis:

-pyruvate -3-phosphoglycerate

The nitrogenase complex consists of two components:

-reductase -nitrogenase

Classify the phrases. Does each phrase describe a kinase, a phosphatase, neither, or both? Both

-regulate the activity of other proteins

Categorize each characteristic of nucleotide synthesis as describing either de novo pathways or salvage pathways. Salvage pathways

-reincorporate preformed bases into nucleotides -require less ATP

Classify the phrases. Does each phrase describe a kinase, a phosphatase, neither, or both? Phosphatases

-remove phosphoryl groups from proteins -turn off signaling pathways triggered by kinases

-requires two or more ATP-dependent reactions -requires PRPP

the major metabolic precursors from the pentose phosphate pathway:

-ribose 5-phosphate

amino acids that give rise to other amino acids from glycolysis:

-serine

Match each role to the appropriate enzyme in the glycogen synthesis pathway. Glycogenin

-serves as a primer -autocatalysis -makes a polymer of 10 to 20 glucosyl units

A mixture of proteins can be separated. How they are separated are based on:

-solubility -charge -size -specific binding activity (affinity for a ligand)

Classify each molecule based on whether or not it is an amino acid precursor. Non-precursor

-succinate -glucose 6-phosphate -adenosine

what are the essential amino acids?

-threonine -lysine -isoleucine -valine -leucine -tryptophan -histidine

-tryptophan -threonine -valine -isoleucine

_______________ and _____________ are the strongest chromophores.

-tryptophan -tyrosine

-uses NADPH as a reducing agent

-valine -proline -tryptophan -leucine -tyrosine -methionine

gated ion channels play many important roles in the nervous system:

-voltage-gated sodium channels -nicotinic acetylcholine receptor -ionotropic glutamate receptor -gamma aminobutyric acid receptor A

A researcher resolves a mixture of peptides using isoelectric focusing. Order the peptides based on their relative positions in the immobilized pH gradient strip at the end of the experiment. Low pH --> High pH

1) Glu-Gly-Glu-Asp 2) Asp-Ala-Leu-Asp 3) Arg-Gly-Glu-Lys 4) Arg-Leu-Ala-Arg 5) Arg-Ala-Lys-Lys

Consider a mixture of four proteins with various molecular weights. A histone molecule weighs 15 kDa,15 kDa, a p53 molecule weighs 53 kDa,53 kDa, an actin molecule weighs 42 kDa,42 kDa, and an IgG molecule weighs 150 kDa.150 kDa. Arrange the molecules in order of their elution from a gel filtration column. Elutes first --> Elutes last

1) IgG (150kDa) 2) p53 (53kDa) 3) actin (42 kDa) 4) histone (15 kDa)

Some glucose produced by gluconeogenesis is stored in the body as glycogen. Order the steps of glycogen synthesis. Not all descriptions accurately describe glycogen synthesis; therefore, not all the descriptions will be used.

1) UDP-glucose pyrophosphorylase catalyzes the reaction of glucose-1-phosphate and UTP and UDP-glucose and PPi 2) Pyrophosphatase converts PPi and water into two Pi 3) Glycogen synthase adds a glucose unit from UDP-glucose to glycogen, producing a larger glycogen molecule and UDP

each chain of a glycogen particle has __-__ glucose residues

12-14

Fatty Acid Synthesis leads to the production of a single product, and no intermediates are released. The final product is ___ carbon saturated fatty acid.

Elongation of the fatty acid chain stops at ____ carbon atoms, after ___ cycles, as the free fatty acid is released.

16 7

Which are purines? *shows various 1 and 2 ring structures 1-5*

2, 4

Proteins typically have UV absorbance maxima around 275-_____ nm.

280

In ________________________, proteins are separated in one direction by isoelectric focusing. This gel is then attached to an SDS-PAGE gel and electrophoresis is performed at a 90 angle to the direction of the isoelectric focusing separation.

2D gel electrophoresis

Thousands of cellular proteins can be resolved using this technique:

2D gel electrophoresis

serine, cysteine, and glycine are formed from what glycolytic intermediate?

3-phosphoglycerate

the committed step in serine synthesis is catalyzed by ___________________ _________, which is inhibited by serine

3-phosphoglycerate dehydrogenase

How many times do these four steps repeat to elongate malonyl‑CoA into a 1010‑carbon fatty acid?

A diagram of the reactions of the first round of fatty acid synthesis (lipogenesis) is shown. How many cycles of the synthesis pathway are needed to produce lauric acid, C11H23COOH?

Complete conversion of ribose-5-phosphate to glucose-6-phosphate requires __ _____ to make 5 G6P.

6 R5P

A protein has a molecular mass of 400 kDa when measured by gel filtration (sizeexclusion chromatography). When subjected to gel electrophoresis in the presence of SDS, the proteins gives three bands with molecular masses 180, 160, and 60 kDa. When electrophoresis is carried out in the presence of SDS and dithiothreitol, three bands are again formed, with molecular masses of 160, 90, and 60 kDa. Determine the subunit composition of the protein (How many subunits? What is molecular weight of each?).

: the protein has 4 subunits: 160 kDA, 60 kDA, and two 90 kDa subunits linked by disulfide bonds

Signal transduction is part of a cell's response to an external signal. Although signal transduction pathways can differ in their details, there are some common elements. Select the six statements that accurately describe signal transduction pathways. A) A receptor may pass on a signal by interacting with another protein or by acting as an enzyme. B) A second messenger carries a signal from a tissue or organ to a target cell. C) Signal transduction cascades, often involving protein kinases, amplify a signal intracellularly. D) A ligand, such as a hormone, binds to a specific cell surface receptor on a target cell. E) A ligand phosphorylates protein residues, ending the signaling cascade inside the cell. F) A receptor changes conformation upon binding, transmitting a signal across the cell membrane. G) A second messenger may carry a signal from the cell membrane to an organelle. H) Signal transduction cascades directly transmit a single stimulus to a single target. I) Phosphatases remove phosphoryl groups from polypeptides, regulating a cell's response.

A) A receptor may pass on a signal by interacting with another protein or by acting as an enzyme. C) Signal transduction cascades, often involving protein kinases, amplify a signal intracellularly. D) A ligand, such as a hormone, binds to a specific cell surface receptor on a target cell. F) A receptor changes conformation upon binding, transmitting a signal across the cell membrane. G) A second messenger may carry a signal from the cell membrane to an organelle. I) Phosphatases remove phosphoryl groups from polypeptides, regulating a cell's response.

Lipogenesis, or fatty acid synthesis, occurs in several cycles. A diagram of the reactions of the first cycle of fatty acid synthesis is shown. Select all of the true statements. A) Acetyl‑SCoA is used to produce malonyl‑SCoA. B) Each cycle lengthens the fatty acid chain by three carbon atoms. C) The growing fatty acid chain is bound to an acyl carrier protein (ACP). D) Malonyl‑CoA adds a two‑carbon group to the growing fatty acid chain with each cycle. E) The reactions of lipogenesis include, but are not limited to, condensation, reduction, and dehydration. F) The first cycle of lipogenesis yields CO2CO2 , one NADP+NADP+ , and an acyl group attached to ACP.

A) Acetyl‑SCoA is used to produce malonyl‑SCoA. C) The growing fatty acid chain is bound to an acyl carrier protein (ACP). D) Malonyl‑CoA adds a two‑carbon group to the growing fatty acid chain with each cycle. E) The reactions of lipogenesis include, but are not limited to, condensation, reduction, and dehydration.

Which protein is to be retained the longest on a size-exclusion chromatographic column? Cytochrome C (human): MW = 13,000; Number of AA = 104; Number of polypeptide chains = 1 Myoglobin: MW = 16,890; Number of AA = 153; Number of polypeptide chains = 1 Serum Albumin: MW = 67,000; Number of AA = 585; Number of polypeptide chains = 1 Apolipoprotein B: MW = 513,000; Number of AA = 4,536; Number of polypeptide chains = 1 A) Cytochrome C B) Myoglobin C) Serum Albumin D) Apolipoprotein B

A) Cytochrome C because it is the smallest

Select the results that occur from having few or no α‑1,6 linkages in glycogen. A) Glycogen synthesis would slow down. B) Maintaining proper blood sugar levels would be more difficult. C) Glycogen degradation would be faster. D) Glycogen solubility would increase.

A) Glycogen synthesis would slow down. B) Maintaining proper blood sugar levels would be more difficult.

Which of the subunits, when activated, associates with adenylyl cyclase (adenylate cyclase) and enables it to assume a more catalytically active conformation? A) Gα B) Gβ C) Gγ D) Gβγ

A) Gα

Which molecule binds to a membrane receptor that has intracellular kinase domain? A) Insulin B) Epinephrine C) cAMP D) Ca++ E) Estrogen

A) Insulin

Glucose is mobilized for ATP generation in muscle in response to epinephrine, which activates Gαs.Gαs. Cyclic AMP phosphodiesterase is an enzyme that converts cyclic AMP (cAMP) into AMP. How would an inhibitor of cAMP phosphodiesterase affect glucose mobilization in muscle? A) It would maintain high cAMP levels and elevate glucose mobilization. B) It would reduce cAMP levels and inhibit glucose mobilization. C) It would increase AMP concentration, thereby increasing glucose mobilization. D) It would increase cAMP levels, which would inhibit glucose mobilization.

A) It would maintain high cAMP levels and elevate glucose mobilization.

The net equation for the oxidative reactions of the pentose phosphate pathway is glucose−6−phosphate + 2NADP+ + H2O ⟶ ribulose−5−phosphate + 2NADPH + CO2 + 2H+ glucose−6−phosphate + 2NADP+ + H2O ⟶ ribulose−5−phosphate + 2NADPH + CO2 + 2H+ Select true statements about the pentose phosphate pathway. A) Products of the pentose phosphate pathway contribute to reductive biosynthesis reactions. B) Glucose is a precursor of the pentose phosphate pathway. C) Pentose phosphate pathway activity is high in rapidly dividing cells. D) NADP+NADP+ is oxidized to NADPH in the pathway.

A) Products of the pentose phosphate pathway contribute to reductive biosynthesis reactions. B) Glucose is a precursor of the pentose phosphate pathway. C) Pentose phosphate pathway activity is high in rapidly dividing cells.

Which protein would show up as the band at the top of an SDS PAGE gel after electrophoresis? Why? Cytochrome C (human): MW = 13,000; Number of AA = 104; Number of polypeptide chains = 1 Myoglobin: MW = 16,890; Number of AA = 153; Number of polypeptide chains = 1 Serum Albumin: MW = 67,000; Number of AA = 585; Number of polypeptide chains = 1 Apolipoprotein B: MW = 513,000; Number of AA = 4,536; Number of polypeptide chains = 1 A) Cytochrome C B) Myoglobin C) Serum Albumin D) Apolipoprotein B

D) Apolipoprotein B because it is the largest

You prepare a cell line that overexpresses a mutant form of epidermal growth factor receptor, or EGFR, in which the entire intracellular region of the receptor has been deleted. Predict the effect of overexpression of this construct on epidermal growth factor (EGF) signaling in this cell line. What will be the effect of the overexpression of this truncated receptor? A) EGFR will activate other proteins without dimerization, causing uncontrolled cell growth. B) EGFR will not form a dimer in the presence of EGF, stopping normal cell growth. C) EGFR will be unable to bind its ligand, blocking the signal and stopping cell growth. D) EGFR will form a dimer, but the kinases will not be activated and the signal will stop.

D) EGFR will form a dimer, but the kinases will not be activated and the signal will stop.

What is the name of 16 carbon saturated fatty acid? A) Arachidonic acid B) Stearic acid C) Linoleic acid D) Palmitic acid E) Myristic acid

D) Palmitic acid

What is pI (Isoelectric point)? A) The pH at which a molecule does not have any electric charge B) The negative log of hydrogen ion concentration of an aqueous solution C) The pH of maximum electrolytic mobility D) The pH at which a solute has no net electric charge and does not move in an electric field E) -log(pK1+pK2)/2

D) The pH at which a solute has no net electric charge and does not move in an electric field

Suppose a team of researchers sequences the genome and measures the proteome of a human skin cell and a human kidney cell. Will there be a greater difference between the genome or the proteome between these two cells? A) The genome is more different between the two cells than the proteome due to the differences in tertiary structure of the chromosomes. B) The proteome is the genetic material in a prokaryotic cell, and thus these cells do not have a proteome because they are eukaryotic. C) The genome is more different between the cells than the proteome because gene expression varies between the two cells. D) The proteome is more different between the cells due to differences in gene expression and post-transcriptional processing of mRNA. E) Each gene codes for a specific protein, so there is no difference between the genome and the proteome of the two cells.

D) The proteome is more different between the cells due to differences in gene expression and post-transcriptional processing of mRNA.

Starch is a polymer of glucose molecules in plants with a role analogous to that of glycogen in animals. Starch synthesis requires ADP‑glucose generated by ADP‑glucose pyrophosphorylase. The biochemical mechanism of ADP‑glucose pyrophosphorylase catalysis is similar to that of UDP‑glucose pyrophosphorylase. What is the driving force for the ADP‑glucose pyrophosphorylase reaction? A) production of ADP‑glucose B) production of pyrophosphate C) hydrolysis of ADP‑glucose D) hydrolysis of pyrophosphate

D) hydrolysis of pyrophosphate

Consider the images. *shows glutamate and arginine* Which is an intermediate in the biosynthesis of arginine from glutamate? A) glutamine B) urea C) oxaloacetate D) ornithine E) acyl‑adenylate

D) ornithine

Select statements that accurately describe receptor tyrosine kinases (RTKs). A) Some RTKs are dimeric in the presence of a ligand. B) A ligand binds to the extracellular domain. C) The structure includes a transmembrane helix. E) Ligand binding is required for autophosphorylation (cross‑phosphorylation). F) The intracellular domain has phosphatase domains. G) The α subunit contains seven α helices that span the membrane.

A) Some RTKs are dimeric in the presence of a ligand. B) A ligand binds to the extracellular domain. C) The structure includes a transmembrane helix. E) Ligand binding is required for autophosphorylation (cross‑phosphorylation).

Which two of the statements describing the synthesis of amino acids are accurate? (Select two) A) Synthesis of the amino acid alanine involves reduction, that is, the precursor is reduced; its degradation involves oxidation. B) Isoleucine is an essential amino acid and is synthesized in the human body by the transamination of α‑ketoglutarate. C) The carboxyl groups of all the nonessential amino acids are derived from glutamate. D) The carbon sources for nonessential amino acid synthesis include metabolic pathway intermediates and α‑keto acids. E) The synthesis of alanine from pyruvate, an α‑keto acid, involves the oxidation of pyruvate.

A) Synthesis of the amino acid alanine involves reduction, that is, the precursor is reduced; its degradation involves oxidation. D) The carbon sources for nonessential amino acid synthesis include metabolic pathway intermediates and α‑keto acids.

According to the table, size-exclusion (gel-filtration) chromatography could NOT be used to separate which protein mixture? Protein A = 12,500 Protein B = 13,200 Protein C = 13,500 Protein D = 25,200 Protein E = 36,900 Protein F = 78,400 A) proteins A, D, and F B) proteins C, E, and F C) proteins B, E, and F D) proteins A, B, and C E) All of the answers are correct.

D) proteins A, B, and C

the growing chain is initially attached to the enzyme via a _______________ linkage

thioester

step 1 of FAS I: elongation Note that malonylCoA and acetyl-CoA have already been attached to complex via _________ linkages to enzyme and have shed their CoA attachments. What is the type of reaction?

thioester condensation

Feedback inhibition is important for the regulation of many metabolic pathways. Which of the statements are examples of feedback inhibition? (Select) A) The beginning of glycolysis is inhibited by high levels of ATP in the cell. B) The production of tryptophan is halted by the presence of excess tryptophan. C) Arsenic binds to pyruvate dehydrogenase and inhibits the enzyme. D) An intermediate of glycolysis activates an enzyme downstream in the pathway. E) The lac operon is not transcribed when there is no lactose present.

A) The beginning of glycolysis is inhibited by high levels of ATP in the cell. B) The production of tryptophan is halted by the presence of excess tryptophan.

Which of the following amino acids can be phosphorylated? A) Tyrosine, serine, threonine B)Tyrosine, serine, tryptophan C) Serine, threonine, asparagine D) Histidine, serine, phenylalanine E) Tyrosine, methionine, tryptophan

A) Tyrosine, serine, threonine

The difference between a ribonucleotide and a deoxyribonucleotide is: A) a deoxyribonucleotide has an —H instead of an —OH at C-2. B) a deoxyribonucleotide has an —H instead of an —OH at C-3. C) a ribonucleotide has an extra —OH at C-4. D) a ribonucleotide has more structural flexibility than deoxyribonucleotide. E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.

A) a deoxyribonucleotide has an —H instead of an —OH at C-2.

Which of the molecules are used as second messengers in signal transduction pathways? (Select) A) cAMP B) Ca2+ C) adenyl cyclase D) insulin E) inositol triphosphate

A) cAMP B) Ca2+ E) inositol triphosphate

Identify two structural features of purines and pyrimidines. (Select) Purines A) contain four ring nitrogen atoms. B) contain only three ring nitrogen atoms. C) contain one heterocyclic ring. D) contain only two ring nitrogen atoms. E) contain two heterocyclic rings.

A) contain four ring nitrogen atoms. E) contain two heterocyclic rings.

Transketolase and __________ are specific to this pathway; the other enzymes also serve in the glycolytic or gluconeogenic pathways

transaldolase

what enzymes are specific to the nonoxidative phase of the pentose phosphate pathway?

transketolase and transaldolase

Olfaction is mediated by an enormous family of seven-______________-helix receptors

transmembrane

gated ion channels regulate ____________ of ions across cell membranes

transport

Identify two structural features of purines and pyrimidines. (Select) A) contain only two ring nitrogen atoms. B) contain two heterocyclic rings. C) contain four ring nitrogen atoms. D) contain one heterocyclic ring. E) contain only three ring nitrogen atoms.

A) contain only two ring nitrogen atoms. D) contain one heterocyclic ring.

Predict which product of the phosphoglucomutase reaction predominates when insulin levels are high. A) glucose 1‑phosphate B) glucose 1,6‑bisphosphate C) glucose D) glucose 6‑phosphate

A) glucose 1‑phosphate

Identify the enzymes that are required for the synthesis of a glycogen particle starting from glucose 6‑phosphate. (Select all) A) glycogenin B) phosphoglucomutase C) glycogen phosphorylase D) glycogen synthase kinase E) pyrophosphatase

A) glycogenin B) phosphoglucomutase E) pyrophosphatase

fatty acid synthase catalyzes a repeating four-step sequence that elongates the fatty acyl chain by ____ carbons at each step

two

how many phases are there of the pentose phosphate pathway?

two

the three stages of fatty acid synthesis: 3) Repetitive addition and reduction of _____ carbon units to synthesize C16 fatty acid. Synthesis occurs on an acyl carrier protein, a molecular scaffold.

two

Epinephrine is released in response to stress, and is a fight‑or‑flight hormone. Select all metabolic pathways that epinephrine stimulates. A) lipolysis in adipose tissue B) glycolysis in muscle C) gluconeogenesis in liver D) glycogen breakdown (glycogenolysis) in liver and muscle E) glycogen synthesis (glycogenesis)

A) lipolysis in adipose tissue B) glycolysis in muscle C) gluconeogenesis in liver D) glycogen breakdown (glycogenolysis) in liver and muscle

the catalytic domains of receptor tyrosine kinases have the:

tyrosine kinase activity

SDS micelles bind to proteins and facilitate __________.

unfolding

Select the structural features common to all membrane‑bound receptors. A) signal molecule binding site on the extracellular domain B) seven transmembrane helices C) intracellular domain undergoes structural changes upon extracellular ligand binding D) kinase domain

A) signal molecule binding site on the extracellular domain C) intracellular domain undergoes structural changes upon extracellular ligand binding

Unlike the genome, the proteome is not an ___________ characteristic of the cell.

unvarying

Pyrimidines to:

urea

Purines are degraded to:

uric acid

Gout is a form of arthritis, characterized by tender, swollen joints. Select the cause of gout. A) uric acid crystals accumulate in joints B) calcium pyrophosphate crystals accumulate in joints C) inflammation of joints due to a lack of purines in the diet D) inflammation of joints due to infection

A) uric acid crystals accumulate in joints

in de novo biosynthesis of purines, Adenine and guanine are synthesized as:

AMP and GMP

In 2D gel electrophoresis, _____________ separation reflects differences in molecular weight.

vertical

A balance is maintained by bacteria that reduce nitrate and nitrite to N2 under anaerobic conditions (denitrification). These bacteria use NO3- or NO2- as the ultimate electron acceptor (not O2) in electron transport chain to synthesize ______.

ATP

stoichiometry of synthesis of palmitate (16:0) 1) 7 acetyl-CoAs are carboxylated to make 7 malonyl-CoAs... using _______.

ATP

What is this molecule?

Acetyl-CoA

describe nitrogen fixation

the reduction of atmospheric nitrogen by nitrogen-fixing bacteria to yield ammonia

receptor

A membrane-bound or soluble protein or protein complex, which exerts a physiological effect (intrinsic effect) after binding its natural ligand

the intermediates in fatty acid synthesis is linked to:

Acyl Carrier Protein (ACP)

___________ can be used by most living organisms, but soil bacteria that derive their energy by oxidizing NH4 are so abundant, that nearly all NH4 reaching soil is oxidized to nitrate. This process is known as:

Ammonia nitrificaiton

When enzymes activate enzymes, the number of affected molecules increases geometrically in an enzyme cascade. This process is known as:

Amplification

The bacterium Methylophilus methylotrophus can use methanol and ammonia for protein synthesis. The glutamate dehydrogenase gene from E. coli was introduced into M. methylotrophus using recombinant DNA techniques. Under high ammonia conditions, the introduction of the glutamate dehydrogenase gene into M. methylotrophus resulted in an increase in protein yield. Select the statements that are reasonable explanations for the increased protein yield in the modified M. methylotrophus. A) Glutamate dehydrogenase has a high affinity for NH4+. Therefore, the rate of glutamate synthesis increases exponentially under high ammonia conditions. B) Glutamate is the source of amino groups for most amino acids. Therefore, an increase in glutamate concentration increases protein synthesis. C) Glutamate dehydrogenase has a low affinity for NH4+ and can only catalyze the formation of glutamate from α‑ketoglutarate and NH4+ when the concentration of NH4+ is high. D) Glutamate dehydrogenase incorporates NH4+ into glutamate and glutamine in a two‑step process. E) Both glutamate and glutamine play a key role in amino acid synthesis. An increase in levels of glutamate and glutamine increases protein synthesis.

B) Glutamate is the source of amino groups for most amino acids. Therefore, an increase in glutamate concentration increases protein synthesis. C) Glutamate dehydrogenase has a low affinity for NH4+ and can only catalyze the formation of glutamate from α‑ketoglutarate and NH4+ when the concentration of NH4+ is high.

In exercising muscle, glycogen degradation supplies the muscle with glucose‑6‑phosphate. In order to stimulate muscle glycogen degradation, protein phosphatase 1 (PP1) must be inhibited. Four of the five events are involved in the inactivation of PP1 in exercising muscle. Which event is not involved? A) Protein kinase A phosphorylates GM in the GM-PP1 complex, resulting in its dissociation. B) Insulin initiates a protein kinase cascade that utilizes glycogen synthase kinase. C) Phosphorylated PP1 inhibitor binds to PP1, facilitating glycogen degradation by phosphorylase a. D) Protein kinase A phosphorylates an inhibitor of PP1. E) Epinephrine initiates a cAMPcAMP signal transduction cascade that utilizes protein kinase A.

B) Insulin initiates a protein kinase cascade that utilizes glycogen synthase kinase.

Which molecule controls the rate of the pentose phosphate pathway? A) glucose B) NADP+/NADPH C) ADP/ATPADP/ATP D) ribose 5‑phosphate E) NAD+/NADH

B) NADP+/NADPH

If protein A has a pI of 3.1, protein B has a pI of 6.8, and protein C has a pI of 8.9, which protein would elute FIRST from a cation exchange column (negatively charged beads in the column) at pH 7? A) All three proteins would elute at the same time from the column B) Protein A C) Protein B D) Protein C

B) Protein A

Which of the outcomes could potentially result if a mutation in the gene encoding the Gα subunit eliminates its GTPase activity? Choose three outcomes. A) The cell would be unresponsive to molecules that act via cAMP . B) The concentration of cAMP in the cell would be continuously elevated. C) Gα would be activated for an extended period. D) Gα would be ineffective as a signal molecule (that is, it could not activate other proteins). E) The rate of GTP hydrolysis would increase. F) The signaling pathway could be activated for an extended period, possibly resulting in undesirable cell proliferation.

B) The concentration of cAMP in the cell would be continuously elevated. C) Gα would be activated for an extended period. F) The signaling pathway could be activated for an extended period, possibly resulting in undesirable cell proliferation.

An amino acid in a medium with a pH above its isoelectric point would have: A) a net positive charge B) a net negative charge C) a neutral charge D) either a net positive or net negative charge depending on the pKa value.

B) a net negative charge

Odorant receptors and 𝛽β-adrenergic receptors are 7TM receptors that initiate a signal cascade through G proteins. Which of the following steps is common between the signal-transduction cascade mediated by the odorant receptor and the signal-transduction cascade mediated by the 𝛽β-adrenergic receptor? A) an increase in intracellular levels of IP3 B) an increase in intracellular levels of cAMP C) an influx of cations into the cell D) activation of protein kinase A

B) an increase in intracellular levels of cAMP

A protein with a high percentage of aspartate and glutamate residues would be BEST purified and concentrated with which type of column? A) cation (negatively charged beads in the column) exchange B) anion (positively charged beads in the column) exchange C) size-exclusion chromatography D) affinity chromatography

B) anion (positively charged beads in the column) exchange

Purine bases, which have two rings, have a more complex synthetic pathway than do pyrimidine bases, which have one ring. As a result, purine synthesis requires more components than pyrimidine synthesis. Which amino acids contribute atoms to the purine structure in de novo purine synthesis? A) lysine B) aspartate C) histidine D) glutamine E) glycine

B) aspartate D) glutamine E) glycine

De novo nucleotide synthesis differs for purine and pyrimidine bases. However, some molecules are important precursors and intermediates in both pathways. Which intermediates are common to both purine and pyrimidine nucleotide synthesis? A) orotate B) aspartate C) formate D) glycine E) PRPP

B) aspartate E) PRPP

What are the roles of sodium dodecyl sulfate (SDS) in two‑dimensional electrophoresis? (Select) A) to preserve the structure of the bound proteins B) to denature proteins C) to cause bound proteins to have a large negative charge D) to cause bound proteins to have a large positive charge E) to preserve zero net charge of the proteins

B) to denature proteins C) to cause bound proteins to have a large negative charge

Which molecules directly participate in fatty acid synthesis by acting as energy sources? *select* A) NADH B) pyruvate C) ATP D) NADPH E) GTP F) acetyl‑CoA

C) ATP D) NADPH

What is this molecule? *shows four linked rings with hydrocarbons* A) cAMP B) UDP -glucose C) Cholesterol D) Sphingolipid E) Oxaloacetate

C) Cholesterol

A researcher labels C‑6 of glucose 6‑phosphate with C14C14 and adds it to a solution containing the enzymes and cofactors of the oxidative phase of the pentose phosphate pathway. What is the fate of the radioactive label? C14 appears at C‑6 of fructose 6‑phosphate. C14 appears in the CO2 evolved by the oxidative phase. C14 appears at C‑4 of erythrose 4‑phosphate. C14 appears at C‑7 of sedoheptulose 7‑phosphate. C14 appears at C‑5 of ribulose 5‑phosphate.

C14 appears at C‑5 of ribulose 5‑phosphate.

HCO3- (bicarbonate) is the soluble source of _______

CO2

Radioactive‑labeling experiments can yield estimates of the amount of glucose 6‑phosphate metabolized by the pentose phosphate pathway (PPP) and the amount metabolized aerobically by the combined action of glycolysis, the pyruvate dehydrogenase complex, and the citric acid cycle. A researcher has a tissue sample and two radioactively labeled glucose samples, one labeled with C14 at C‑1 and the other labeled with C14 at C‑6. To determine the relative activity of aerobic glucose metabolism compared with glucose metabolism by the pentose phosphate pathway (PPP), the researcher should compare the radioactivity of the _____ produced by the two samples.

CO2

biotin carries _____

CO2

Fatty Acid Synthesis is driven by the release of _____ in a decarboxylation step where ______ is used

CO2; ATP

Synthesis of AMP and GMP from:

IMP

_________ molecules are retained within the dialysis bag, whereas ________ molecules diffuse into the surrounding medium.

Protein small

_____________ are not salvaged in significant amounts in mammals.

Pyrimidines

Name the techniques described for separating cellular proteins: Proteins are separated on the basis of their ability to migrate in an electric field based on their size

SDS-PAGE

_________ __________________ is the process by which an extracellular signal is amplified and converted to a cellular response.

Signal transduction

Name the techniques described for separating cellular proteins: Proteins are chromatographically separated solely on the basis of size

Size-exclusion chromatography (gel filtration)

Fatty acid synthesis begins with the transfer of the acetyl group from acetyl-CoA to fatty acid synthase. ____-carbon groups, supplied by _________-___, are added to the growing acyl chain in a series of steps involving condensation, __________, and dehydration reactions.

Two malonyl-CoA reduction

______ + ATP --> _____ + ADP

UDP UTP

_____-____________ + (glycogen)n --> ______ + (glycogen)n+1

UDP-glucose UDP

In what biochemical process is this molecule involved? *shows UDP-glucose*

UDP-glucose is a precursor in glycogen synthesis

UDP-glucose is synthesized by

UDP-glucose pyrophosphorylase

glucose-1-phosphate + ____ --> _____-___________ + PPi PPi + H2O --> 2Pi

UTP UDP-glucose

______ ________ is the excreted end product of purine catabolism in primates and some other animals.

Uric acid

The ratio of activity to total protein concentration is called the:

specific activity

The signal molecule fits binding site on its complementary receptor; other signals do not fit. This is called:

specificity

an example of nuclear receptors

steroid receptors

insulin ________ glycogen synthesis by triggering a cascade of reactions leading to activation of ________ _________

stimulates glycogen synthase

Epinephrine mediates ________ response: mobilization of energy

stress

UDP-glucose is the ______ for glycogen synthesis

substrate

ribose-5-phosphate is a biosynthetic precursor of nucleotides. -used in DNA and RNA __________ -synthesis of some ___________

synthesis coenzymes

the fifth step of signal transduction is the _____________ of the signal. cells should be able to stop signaling processes to stay responsive to new signals.

termination

Protein purification requires a ______________ that determines whether the protein of interest is present.

test (assay)

the synthesis of glycine requires the cofactor

tetrahydrofolate

Differential centrifugation

the homogenate is then centrifuged at low speed to yield a pellet consisting of nuclei and a supernatant. This supernatant is then centrifuged at a higher centrifugal force to yield another pellet and supernatant. This process , is repeated several more times to yield a series of pellets enriched in various cellular materials and a final supernatant containing soluble cytosolic proteins

biochem exam 4 review

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