Exam 1 (Exam 1&2&Final Comp+Misc)

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Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE?

(1) Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. (2) The majority of autotrophs on Earth require aerobic respiration in order to survive. (3) Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration.

Answer the following questions about the graph shown above and record the set of answers in the correct order. 1. The protein with the lowest dissociation constant (Kd) is protein (A or B)? 2. The protein with the highest affinity for oxygen is protein (A or B)? 3. The protein most likely to bind oxygen cooperatively is protein (A or B)? 4. The protein most likely to be an oxygen storage protein is protein (A or B)? 5. The protein most likely to be hemoglobin is protein (A or B)? 6. The protein most likely to be myoglobin is protein (A or B)?

(1) protein A (2) protein A (3) protein B (4) protein A (5) protein B (6) protein A

partioning

* "logp"

quartenary structure

*an arrangement of protein subunits *examples: Myoglobin(Mb - oxygen storage), Hemoglobin(Hb -oxygen transport)

hydrophobic interactions

*beta sheets are destabilized in water. *beta sheets are formed in "drg" (anhydrous) regions of the folded protein

affinity chromatography

*can separate molecules based on protein-ligand binding *the stationary phase has a covalently bound group to which a protein in the mobile phase can bind. *uses a mobile phase and a stationary phase to separate proteins.

exopeptidace

*cuts C terminal AA *cuts N terminal AA

quaternary protein structure definiton

*multimers(dimers, trimers..) form a large non-covalently bound proteins. *sometimes nature uses -S-S- disulfide bonds to covalently connect monomers

hydrophobic collapse

*nonpolar amino acids are driven together to push water out of the way to form molten globule.

secondary protein structure definition

*polypeptides from 4-20+ AAs that form common motifs. (motifs: alpha-helix, beta sheets)

cleavage of disulfide bond

*reductive change using mercaptanace *beta-mercaptoethanol *p-mercaptoethanol *oxidative cleavage

size elcusion chromatography

*separates molecules by size *the stationary phase contains cross-linked polymers with different pore sizes. *uses a mobile phase and a stationary phase to separate proteins.

What is the approximate net charge of the molecule shown below at pH 7?

-1

What is the approximate net charge of the molecule shown below at pH 7? +1 0 −2 −1 None of these answers are correct.

-1

For the reaction A↔B, ΔG°' = -28.5 kJ/mol At steady-state in cells at 37 °C, [A] is 0.05 mM and [B] is 15 mM, calculate ΔG for the A↔B reaction. (Note: Use the alternative convention that the biochemical standard state is defined at 37C.)

-13.8kJ/mol

Calculate the delta G value for the conversion of 2-phosphoglycerate to phosphoenolpyruvate by the enzyme at 25 degrees C when the concentration of 2-phophoglycerate is 10 times higher than the concentration fo phosphoenolpyruvate. The biochemical standard free energy change for this reaction is 1.7 kJ/mol

-4.0 kJ/mol

Which of the following process are driven by the hydrophobic effect

-Separation of oil and vinegar in salad dressing -Formation of a protein dimer through leucine and valine residues -Protein folding of a globular protein that transports fatty acids -The formation of limonene droplets on the surface of a mixed drink

pH=

-log of h+ or of Ka

Calculate the DeltaEo' of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table below.

1.25

Given that the approximate bond length of O-H in water is roughly 1 Å, what is the approximate distance each proton "hops" between molecules?

1.5 A

what leads to protein folding theories

1.disulfide bond direct folding. 2. hydrophobic interactions 3. h bonding leads to 3/4 structure

The process of condensation reduced the size of DNA by

10,000 fold

residues per helix

12 residues/helix

Given a pH gradient differential measured across the inner mitochondrial membrane of an aquatic animal is found to be 25 times lower inside the mitochondrial matrix as compared to the inter-membrane space, what is the energy requirement to transport 1 H+ across the membrane, from the mitochondrial matrix side tot he intermembrane space, at 10 C with a membrane potential of 50 mV

12.4 kJ/mol

The HindIII-DNA complex that is shown in this molecular structure contains amino terminus/termini and carboxy terminus/termini. An amino terminus sequence KSALEKLLSL is associated with a(n) . Use the sequence view from the dropdown menu and determine the location of KSALEKLLSL within the folded polypeptide.

2,2, alpha helix

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 x 10^2 mmol/sec and the catalyzed rate is 2.4 x 10^4 mmol/sec? 200 0.005 2.88 mc005-3.jpg 106 2

200

rare helices

3,10 2,2.7 pi

Calculate the pH of a solution that contains 3.9 x 10^-4M H+

3.41

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine?

35%

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine?

35%

What is the maximum number of covalent bonds a carbon atom can make?

What is the energy requirement to transport 3 moles Na+ from the inside to touside

41.2 kJ

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

5.5

If a sample of double-stranded DNA is determined to be 20% guanine, what percent of this DNA sample is purine nucleotide chemistry?

50%

Identify the phase of PCR amplification where DNA is denatured and the strands are separated.

Where would an amino acid be attached to the tRNA below? A B C D

A (3' at the top left of the strand, BCD are all at the bottom)

Identify the phase of PCR amplification where DNA is denatured and the strands are separated.

A - 95 degrees celsius

transformation (plasmid)

A process in which DNA is taken up by bacteria and incorporated into the genome or contained on a DNA plasmid. (p. 128)

transduction viral

A process in which a virus mediates the transfer of genetic material between host cells. (p. 129)

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine? A. 35% B. 70% C. 15% D. 30%

A. 35%

When DNA is transcribed into RNA, the __________ strand has the same base sequences as the RNA transcript. A. coding B. parallel C. mirror D. template E. antiparallel

A. coding

Chargaff's rule is that the amount of

A=T and the amount of C=G

Given the following common reactions, which are entropically favored?

ATP ⇒ ADP + Pi

Which of the following is/are functional groups contained in all amino acids:

Amino & Carboxyl Groups

which amino acids carry a charge at pH of 9

Aspartate, glutamate, cysteine, lysine, arginine

beri beri is what ?

B-1 deficiency called thiamine deficiency

For the figure shown below, which of the following is correct? Question Options A.The blue and yellow strands have a parallel orientation. B. The blue and yellow strands have an antiparallel orientation. C. The major groove is labeled A. D. The minor groove is labeled B.

B. The blue and yellow strands have an antiparallel orientation.

Which of the following pairs contain terms that would be considered synonyms of one another regarding DNA integrity? Choose one or more: A. denatured : annealed B. renatured : annealed C. denatured : renatured D. melted : denatured E. annealed : melted

B. renatured : annealed D. melted : denatured

Which suspect(s) should be further pursued? Base your answer on the DNA evidence alone. Choose one: A. suspect A only B. suspect B only C. both suspects A and B D. neither suspect A nor B

B. suspect B only

Consider the following microarray experiment: A single-stranded DNA sequence is attached to a microarray chip, and fluorescently labeled complementary RNA (cRNA) fragments (probes) prepared from mRNA isolated from a cell sample are incubated with the array chip under hybridizing conditions. Data specifically regarding the _________ are measured by this type of microarray. A. proteome B. transcriptome C. glycome D. genome

B. transcriptome

A common database tool used to determine homologous genomic sequences is called

Basic Local Alignment Search Tool.

All of the following are types of protein secondary structure EXCEPT

Beta helixes

sort the following as descriptions of alpha helices, beta sheets, beta turns, or all. -successive R groups point in opposite directions -1st residue hydrogen-bonded to 5th residue (that is, residue n is H-bonded to residue n+4) -all -NH groups point in the same direction -1st residue HB to the 4th residue(residue n is Hbonded to residue n +3) -contains -NH hydrogen bonded to c=o

Beta sheets: -successive R groups point in opposite directions alpha helices: -1st residue hydrogen-bonded to 5th residue (that is, residue n is H-bonded to residue n+4) -all -NH groups point in the same direction beta turns: -1st residue HB to the 4th residue(residue n is Hbonded to residue n +3) all: -contains -NH hydrogen bonded to c=o

As DNA unwinds and denatures, absorbance is predicted to a. remain the same. b. decrease. c. increase. d. vary unpredictably.

Chargaff's rule is that the amount of a. A=GandtheamountofC=T. b. A=C=G=T. c. A=TandtheamountofC=G. d. A=CandtheamountofG=T.

Chromatin that consists of more condensed regions of mostly noncoding DNA are referred to as a. nucleosomes. b. histones. c. heterochromatin. d. euchromatin.

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand.

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand. *SEE #21* a. A b. B c. C d. Not enough information is included to determine the curve.

Foreign DNA fragments can be inserted into plasmids using a. promoters. b. cloning vectors. c. cloning sites. d. recombinant DNA.

Identify the phase of PCR amplification where DNA synthesis occurs. *SEE #62* a. A b. B c. C d. D

If HCO3mc135-1.jpg that is radioactively labeled with 13C is available, which carbon atom in the molecule below would ultimately be expected to be radioactive? A B C D

If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water? Choose one: A. The protein would demonstrate no change in water binding. B. The protein would bind water more tightly. C. The protein would not bind water and would lose antifreeze properties. D. The protein would have increased affinity for the phosphate backbone of DNA.

C- The protein would not bind water and would loose antifreeze properties

Which of the following would be an example of decreasing entropy?Choose one: A. Ice melting B. A catabolic pathway C. An anabolic pathway D. Flow of ions through a channel from higher ionic concentration to lower ionic concentration

C- anabolic pathway

For a circular, unbroken piece of DNA, which of the following is true? A. Increasing the twist also increases the linking number. B. Increasing the twist also increases the writhe. C. Decreasing the writhe increases the twist to keep the linking number constant. D. Decreasing the writhe also decreases the twist.

C. Decreasing the writhe increases the twist to keep the linking number constant.

Which of the following best describes monocistronic and polycistronic genes? Choose one: A. Monocistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while polycistronic genes are encoded in multiple different RNAs. B. Monocistronic genes are only prokaryotic, and polycistronic genes are only eukaryotic. C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein. D. Polycistronic gene products are interpreted by the ribosome, and monocistronic gene products are not.

C. Polycistronic genes are multiple genes under a single promoter that are transcribed into a single RNA, while monocistronic genes only encode a single protein.

Pyruvate decarboxylase converts pyruvate into

Carbon dioxide and acetaldehyde

Which of the following is true concerning cholesterol and plasma membranes? Choose one: A. At high temperatures, cholesterol inhibits membrane fluidity. B. High local concentrations of cholesterol increases membrane fluidity. C. Cholesterol inserts into the membrane via its non-polar planar rings. D. Cholesterol facilitates fatty acid packing.

Cholesterol inserts into the membrane via its non-polar planar rings.

Calculate the linking number for a B-DNA strand that contains 735 total base pairs. a. 50 b. 61 c. 67 d. 70

Genes found in prokaryotes that only contain a single coding sequence are referred to as a. exons. b. introns. c. polycistronic. d. monocistronic.

Less condensed, gene-rich chromatin is referred to as a. nucleosomes. b. histones. c. heterochromatin. d. euchromatin.

The ability to monitor the denaturation of DNA using absorbance is referred to as a. annealing. b. supercoiling. c. melting temperature. d. hyperchromic effect.

The proteins that bind to DNA in a sequence-independent manner are a. histones. b. single-stranded binding proteins. c. Lac repressor proteins. d. histones and single-stranded binding proteins.

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first?

D, +1

What mediates the binding of histone proteins to DNA? A. London dispersion forces B. hydrophilic interactions C. hydrophobic interactions D. ionic attractions

D. ionic attractions

On this graph, the curves shift to the right as the G-C content increases. This is because G and C are connected by Choose one: A. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. B. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher. C. two hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is lower. D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.

D. three hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.

If the concentration of aspartate in the cell decreased, what would be the predicted outcome? decreased concentration of fumarate increased concentration of argininosuccinate decreased concentration of citrulline increased concentration of arginine

Decreased concentration of fumarate

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4?

Diminished HCO-3 excretionMore CO2 exhaled (hyperventilation)

What is the "cost" of using the glycerol-3-phosphate shuttle instead of the malate-aspartate shuttle in terms of proton-motive force and ATP synthesis? (choose one correct answer).

For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis

In the second temperature phase of PCR, why does the temperature vary from 55 d Celsius to 65 d Celsius?

G-C content

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA

GLMK TYPDSTA

Which of the following is a GTPase?

Gsa

Which statement most accurately describes the structure and function of O2 transport proteins

Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell.

High AMP concentrations,Low ATP concentrations,The energy charge ratio is below 0.70

lambert-beers law with intensity

I0= intensity of incident light I = intensity of transmitted light

Which protein will be phosphorylated in a muscle cell in an obese individual with elevated serum levels of free fatty acids? protein kinase C insulin receptor IRS1 GLUT1

IRS1

Which of the following is true of sickle cell anemia?

It results in a hemoglobin that contains a hydrophobic amino acid on its surface

Predict how type I topoisomerases change the supercoil region

Lk = -1

Methionine

Met M Nonpolar Hydrophobic

In on type of hemoglobin mutant the amino acid change generates a strong ionic interaction stabilizing the T state conformation but only under conditions of lower pH, e.g., at pH 7.2 compared to pH 7.6. What effect would this mutation have on the amount of O2 delivered to the tissue and why

More O2 delivered to the tissue because the RT equilibrium would be shifted to the T state in tissues

given the partial sequence of a peptide: ILWANRMSHVLFAVEA which amino acid residues would you expect to be on the solvent-exposed surface once it folds into its native conformation

N,R,S,H,E

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace? NCCNCC CNCCNC NCONCO NCCONCCO

NCCNCC

What is the best name of the chemical analog labeled A in the figure below

PIP3

conjugation plasmid

Part of the bacterial mating process in which a donor bacterium transfers a copy of the plasmid to a recipient cell. (p. 128)

Why is more ATP obtained from the 12 carbons in the fatty acid dodecanoate, a fully saturated C12 fatty acid, than from the 12 carbons in two glucose molecules? A. The carbons from dodecanoate yield more NADPH and ADP than carbons from glucose. B. The glucose carbons require more water weight during cellular storage, which blocks energy conversion. C. The carbons in glucose are more oxidized (fewer electrons) than the carbons in dodecanoate. D. The glucose carbons are derived from CO2, whereas the carbon atoms in dodecanoate are from CO. E. The glucose carbons yield more NADH than carbons from dodecanoate, which yield more NADPH

The carbons in glucose are more oxidized (fewer electrons) than the carbons in dodecanoate.

Penicillin kills bacteria by inhibiting the biosynthesis of the cell wall. How does penicillin cause the inhibition? The transpeptidase of the bacteria binds to methicillin. The carbonyl carbon of the beta-lactam ring of penicillin binds to transpeptidase. The beta-lactam ring in penicillin is hydrolyzed. The glycine in transpeptidase binds to penicillin.

The carbonyl carbon of the beta-lactam ring of penicillin binds to transpeptidase.

Which of the following is an assumption made when using Michaelis-Menten kinetics?

The conversion of EP -> E + P is rapid

What would happen to a mutated ATP synthase enzyme where the proton binding aspartate residue on the c subunits was mutated to an alanine?

The enzyme would not make ATP in the presence of a proton gradient.

Oxygen binding is monitored for a solution of hemoglobin. During the experiment, the curve changes from sigmoidal to hyperbolic. Which of the following may be the reason for the change?

The protein dissociated into individual subunits

What characteristic is true for both RTKs and GPCRs?

The receptor undergoes a conformational change on activation.

How many fatty acids does each phospholipid contain?

Two

Kinase enzymes phosphorylate proteins in order to control their catalytic efficiency. Which of the following amino acids is targeted for phosphorylation by kinases, and what type of enzyme removes the phosphate to reverse the regulation? Both answers must be correct.

Tyrosine; phophatase

Which of the following are not standard DNA base pairs? Assess your answer based on traditional DNA Watson-Crick base pairing.

U-A, A-G, and C-T

A hydrogen bond can best be described as a weak hydrophobic effect. strong ionic interaction. weak covalent interaction. strong covalent interaction. weak non-covalent interaction.

Weak non-covalent interaction

Explain the difference between the coding strand and the template strand of DNA as it relates to RNA transcription.

When DNA is transcribed into RNA, the coding strand has the same base sequence as the RNA transcript. The template strand has a complementary sequence to the transcribed RNA.

Which form(s) of DNA exhibit(s) a zigzag arrangement?

Z-DNA

In plasmid transformation, DNA is transferred when

a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

In the following figure, what is the linkage between the two monosaccharide units and is this a reducing sugar?

a1-->b2, nonreducing

First messengers, but NOT second messengers

are located extracellularly

Acidic amino acids

aspartic acid, glutamic acid

If no NAD+ was available, the group 2 amino acid degradation pathway would experience a buildup of urea. buildup of glutamate. depletion of proline. depletion of histidine.

buildup of glutamate

pyruvate decarboxylase converts pyruvate into

carbon dioxide and acetaldehyde

Which molecule is used to transport fatty-acyl groups into the mitochondria? CoA-SH ATP biotin carnitine

carnitine

During eukaryotic DNA condensation, nucleosomes are packed together to form

chromatin

Which of the following is an energy conversion pathway?

citrate cycle

Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor?

covalent bond

Chymotrypsin is a serine protease requiring the formation of a covalent/noncovalent enzyme complex as a critical step in the reaction. The amino acid residue histidine has a central role in the reaction mechanism, which is described as a acid-based/metal-ion catalysis mechanism. The reaction sequence results in the release of the carboxyl/amino terminal fragment first as a result of the His 57 residue abstracting/donating a proton to the substrate. The chymotrypsin reaction relies on water to generate a nucleophile/electrophile that attacks the carbonyl carbond/amide nitrogen at the cleavage site. Both the Gly 193/Asp 102 and Serine 195 residues are essential to stabilization of the oxyanion intermediate

covalent, acid-base, carboxyl, donating, nucleophile, carbonyl carbond, Gly 193

edman degragation

cycnzation with TFA(trifluoracetic acid) breaks the scissile bond without hydrolyzing the remaining polypeptide. reaction stable and be be analyzed by HPLC n=1, repeat up to 50 AA residues adumation: 1 residue per hour sensitize: 5-10pmol

The nitrogen atoms of a purine originate from all of the following amino acids EXCEPT glycine. aspartate. cysteine. glutamine.

cysteine

In a single RNA transcript, polycistronic prokaryotic genes encode __________ protein(s). a. one b. two c. three d. multiple

d. multiple

proteins are workhorses of living cells and function as metabolic

enzymes

Which of the following metabolic conversions is considered to be the major control point of glycolysis?

fructose-6-phosphate --> fructose-1,6-bisphosphate

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments?

gel electrophoresis

The peptide bond

has a mix of single and double bond characters

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will

increase.

When ATP binds to myosin, the troponin binding sites are exposed. it cannot interact with actin. the actin nucleotide binding sites are exposed. the power stroke occurs.

it cannot interact with actin.

Which of the following is true of the induced-fit model of enzyme catalysis but NOT of the lock and key model of enzyme catalysis?

it involves a conformational change of the enzyme

Choose the ONE best response to complete this sentence: "A protein in solution is more likely to maintain its native conformation when

it s hydrophobic residues are largely buried in the protein interior

Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor?

none of these interactions are likely.

anaplerotic rxn

oxalate-->pyruvate

on a titration curve the midpoint represents

pH=pKa (pKa)

The complete complex that contains the enzymes and proteins required to replicate DNA is called the primase. polymerase. replisome. DNA gyrase.

replisome

Hutchinson-Gilford progeria syndrome (HGPS)

the most common in a group of fatal disorders that cause rapid aging in children as a result of DNA damage. (p. 122)

RNA only contains which of the bases?

uracil

A hydrogen bond can best be described as a

weak noncovalent interaction

How are changes in enthalpy (H) and entropy (S), related to changes in free energy (G)?

ΔG=ΔH−TΔS

In which case will a reaction be spontaneous only above a certain temperature according to the Gibbs free energy equation?

ΔH > 0; ΔS > 0

What is the approximate net charge of the molecule shown below at pH 7? mc018-1.jpg

−1

Which of the following biochemical relationships are CORRECT statements illustrating the hierarchical organization of molecular life? Choose the THREE best answers.

(1) Carbon, hydrogen and oxygen are the most abundant elements in biomolecules. (2) Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems (3) Insects degrade organic materials on the forest floor and generate nitrogen compounds used by the tree seedlings as nutrients

Although most protein sequencing is now done by mass spectrometry (MS), Edman degradation (ED) is useful if large amounts of a protein can be obtained even if from an uncharacterized species. Answer the True/False questions regarding methods used to sequence a polypeptide fragment and choose the set of all correct answers. 1. True / False - The N-terminal residue removed by acid treatment in ED is always a methionine. 2. True / False - Trypsin and chymotrypsin treatment often provides identical peptide fragments for ED. 3. True / False - Genomic sequences are needed to predict protein sequences by the MS method. 4. True / False - Trypsin treatment provides useful sequence information when analyzing data from MS. 5. True / False - Protein sequencing by ED does not require purified protein but sequencing by MS does.

(1) False (2) False (3) True (4) True (5) False

Name the four noncovalent interactions that occur within and between biomolecules that facilitate life processes at the molecular level. Which of these noncovalent interactions directly or indirectly involve H2O molecules? (ch.2)

(1) Hydrogen bonds, (2) ionic interactions, (3) van der Waals interactions, and (4) hydrophobic effects. Hydrogen bonds form directly between H2O and biomolecules and between H2O molecules themselves, whereas hydrophobic effects are indirectly caused by H2O due to "water-avoiding" interactions between nonpolar molecules.

Many different genetic variations can be found when comparing the gene sequence of two individuals. Explain three causes of the variations.

(1) Single nucleotide polymorphisms are when nucleotides change as a result of an unrepaired error during DNA replication. A short tandem repeat can also occur where a nucleotide is deleted (2) from the sequence or inserted (3) into the sequence.

On a gene microchip assay that has been prepared to measure gene expression, a ___________ level of green fluorescence corresponds to more transcripts present upon cell lysis.

(in the blank) greater

Km is equal to

(k-1+k2)/k1

tertiary protein structure definition

(monomer) *connection of secondary motifs that form in a single polypeptide

Predict the structure of a fatty acid that is trans 16:1 (delta^9).

(there's another option where the double bond is on the other side, don't pick that one)

christian anfunsin

*1957 1. RNase treated with urea and pME resulted in primary structure(single chain of AAs) 2. then added O2 which reestablished disulfide bridges but not activity. 3. after adding O2 then dialysis of urea it resulted in 90% of activity regained.

alpha helical stability

*25% of globular proteins contain alpha-helices 3 components: 1.H-bonding between j and j+4 2. R groups point away from helical axis 3. electrostatic interactions between R groups

tetromer

*4 subunits *noncovalently assembled

Hemoglobin

*Hb *Hb~4Mb *both Hb and Mb contain an iron 2+ heme *Hb has 2 different protomers, *Hb consist of a homodiner and heterodimer

for molecular weight determination, use SDS page

*SDS- sodium dodeacylsulfate CH3-(CH2)11-O-SO3- *sulfur binds to charged groups. *hydrophobic end - causes the protein to denature-unfold. *unfolded protein binds SFS ~1.4 gsds/g of protein *SO3- gives overal negative to the denatured protein *SDS destroys tertiary and quaternary structures.

sequencing proteins

*Why: sequence >> function (folding) *x-ray could be used for sequencing *some proteins don't form crystals *there are regions of disorder(N.C terminus) *a single site mutation (SNP) can cause disease.

sequencing by edman

*a limited hydrolysis/dragging that gives that N-term residue, N+1 residue >> N 1. form an edman reagent adduct (+ag) 2. cleavage of N-term +agged AA

beers law relations

*a small change (decrease) in I takes place over a small path length, dL, at given concentration. log(I0/I) =ecl = A (unitless)

beta-sheet structures

*allows for adjacent amino acid residues (backbones) to Hbond *pleated sheet is held together by Hb between residues (across) *residues up/down in staggard fashion

classification (R or S)

*cann-Ingoid preiog system 1. prioritize substituents off the chiral carbon. >>> molecular weight(high to low) 2.assign them w,x,y,z 3. z goes in background 4. if it goes to the left(CCW) its S 5. if it goes to the right (CW) its R S - sinestra R- rectus

endopeptidace

*cuts peptide bond inside to the C+N termini

electrophoresis

*electric field used to separate proteins (DNA/RNA) based on their molecular weight. *The force on anion due to an electric field. *F= qE

chyinstrysin

*endopeptide *cuts only at aromatic residues except when the proceeding AA is Pro.

chaperone proteins

*help protein under stress maintain its conformation *heat shock proteins *cold shock proteins *ATPases to bind a nacscient protein next to the ribosome, and help it fold to its adult shape away from destabilizing factors.

two kinds of interactions to form oligomers

*homologous>>>isologous *heterologous

molten globule

*inside forms first

protein source for protein purification

*large quantities of hearts, kidneys *crush tissue *break cells *large scale chemical extraction based on fundamental chemical characteristics.

primary protein structure definition

*linear sequence of AA that make of the protein monomer

column chromatography

*load resin into column... elute *wash non-binding proteins *SDS page to check punity.

beta sheet

*loop element: beta-hairpin

antiparallel beta sheet

*most common *2 stranded beta sheet *arrow always points toward C terminal *amino acid residues are much further apart.... less dense than alpha helix

peptide bond planar

*planar due to 40% charge transfer character in resonance. Rco = 1.24A Ralphac = 1.41A Rcn = 1.33A Rncalpha = 1.46A e resonance = 85 kj/mol rotational barrier = 7000K

SDS page

*polyacrylamide gel electrophoresis *acrylamide is polymorized using cross linking. *page only(no SDS detergent) -separation of amino acids

ion-exchange chromatography

*separates molecules by charge *the stationary phase may contain negatively or positively charged groups. *uses a mobile phase and a stationary phase to separate proteins.

statements describing SDS page

*sodium dodecyl sulfate denatures the proteins and adds negative charge, resulting in protein separation by size only. *sds page uses a polyacrylamide gel to separate proteins. *smaller proteins migrate farther than larger proteins.

lambert beer law of optical absorption

*the absorption of a particular wavelength of light by a molecule(in solution) depends on the concentration of the solution, the path length(l or b, units in cm) and E . *E=molar decaadic coefficient *E is a quantum mechanical property of the molecule. *E is the optical absorption spectrum *E=E(wavelength)

biomolecules that have color

*visible, UV, IR *bees see in UV (chromophore) *snakes can "see" in the infared IR (chromophore)

A transporter protein transports Ca2+ ions across a membrane at 37 °C in a cell in which the membrane potential is 100 mV (inside of the cell is negative relative to the outside) and the Ca2+ ion concentrations are 150 mM inside and 15 mM outside. What is the delta G when transporting 2 Ca2+ from the inside to the outside of the cell? +7.2 kJ/mol +19.0 kJ/mol +9.5 kJ/mol +5.9 kJ/mol +26.2 kJ/mol

+26.2 kJ/mol

draw the structure for the peptide bond below: +H3N-C(CH3)H-C(=O)-NH-CH2-COO-

+H3N-C(CH3)H-CO=N+H-CH2-COO-

identify the three conditions in the list below that best describe low energy charge in a cell

- low atp concentration -energy charge rate below 0.70 -high AMP concentrations

The standard reduction potential for the NAD+ reduction is -0.32 Volts as shwon on the front cover of the exam. What is the actual reduction potential of this reaction at 25 C if the concentration ratio of NAD+ to NADH int he mitochondrial matrix is 20:1?

-0.28 V

What is the approximate net charge of the molecule shown below at pH 7? −2 0 −1 +1

-1

What is the approximate net charge of the molecules shown below at pH 7?

-1

Based on the standard reduction potentials on the front page, calculate the overall change in standard free energy for the citrate cycle reaction catalyzed by the enzyme isocitrate dehydrogenase

-11.6 kJ/mol

at steady- state in cells at 37 degrees celsius [A] is 0.05 mM and [B] is 15 mM, calculate delta G for the A<->B reaction

-13.8 kj/mol

Calculate the deltaG value (actual change in free energy) at 25 ºC for the aldolase reaction, which converts fructose-1,6-bisphosphate (F-1,6-BP) to dihydroxyacetone-phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP), given the deltaGº' value of +23.8 kJ/mol and the concentrations of these metabolites at steady state; F-1,6-BP = 15 mM, DHAP = 4 x 10-5M, GAP = 0.04 mM. -2,702 kJ/mol -20.1 kJ/mol -15.8 kJ/mol +20.5 kJ/mol +1.2 kJ/mol

-15.8 kJ/mol

Using the actual reduction potential that you calculated in question #4, what is the new calculated overall change in standard free energy for the isocitrate dehydrogenase reaction from question #3 and is it more or less favorable under these actual conditions?

-19.3 kJ/mol, more favorable

calculate the G value at 37 C for the aldolase reaction, which converts fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone-phophate, given the G values on front page of exam and the concentrations of these metabolites at steady state; F-1,6-BP=10mM, GAP=0.02mM, DHAP=0.02mM

-20.1 kJ/mol

the diagram above shows the free energy G for several possible states of a chemical reaction. the black arrows represent possible transitions between these states and the brackets represent the corresponding free energy differences. select the option which most closely corresponds to each description

-C= free energy difference between standard conditions and equilibrium -C= delta G degrees -A= free energy difference between actual conditions and equilibrium -A= delta G -B= RTlnQ -B= free energy difference between actual conditions and standard conditions -Neither A, B, or C= Keq

Choose 3 reasons below why RNA is a dynamic biomolecule, and in that way, distinct from DNA

-RNA is degraded within the nucleus and the cytoplasm,, where as DNA is normally never degraded -RNA tertiary structure is altered by the binding of protein and small molecule ligands -RNA is able to participate in transitory functional base pairing interactions with RNA or DNA

from the list below choose three molecules that are examples of biological polymers

-alcohol dehydrogenase -DNA -glycogen

what characterizes secondary and tertiary protein structure

-alpha helices/beta sheets -zinc fingers

what characterizes primary and quaternary protein structure

-amino acid sequence -multisubunit complexes

Which 3 of the following biochemical relationships are corrects statements illustrating the hierarchical organization of molecular life?

-carbon, hydrogen, and oxygen are the most abundant elements in biomolecules -insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients -metabolic pathways are considered more complex than biomolecules but less complex than ecosystems

amino acids can be D or L

-depends on their specific rotation =[alpha]^25 D =[observed rotation(degrees)]/[(optical path(cm)*(cooncentration of sample(g/cm3)]

based on the chemical properties of the residues, which of the following sequences could form the following: -most likely an amphipathic alpha helix -most likely an amphipathic beta sheet -most likely a turn/loop -not amphipathic ala-phe-leu-val-ile-trp-phe-val-ala lys-gln-asn-glu-pro-arg-ala-asn-glu gln-ile-thr-phe-thr-leu-gln-val-ser asn-leu-ala-asp-ser-phe-arg-gln-ile

-most likely an amphipathic alpha helix: asn-leu-ala-asp-ser-phe-arg-gln-ile -most likely an amphipathic beta sheet: gln-ile-thr-phe-thr-leu-gln-val-ser -most likely a turn/loop: lys-gln-asn-glu-pro-arg-ala-asn-glu -not amphipathic: ala-phe-leu-val-ile-trp-phe-val-ala

what would happen if DNA contained uracil instead of thymine as the adenine base pair?

-naturally occurring uracil bases would not be distinguishable from cytosine deamination events

Select the four TRUE statements below describing the standard free energy change (delta G) and the equilibrium constant (Keq).

-the equilibrium constant is the ratio of the product and reactant concentrations at equilibrium -the value for the standard free energy change is constant for a given reaction -if the value of the equilibrium constant is known, the value for the standard free energy charge can be determined -the value for the equilibrium constant can be experimentally determined for a given reaction

the sequencing of the human genome has been instrumental towards

-the field of individualized/personalized drug development -our understanding of the genetic basis of disease -better genetic counseling of prospective parents -a more complete understanding of Homo sapiens molecular inheritance

which of the following statements are correct regarding the relationship of pH and pKa

-when pH < pKa, then the [A-]/[HA] ratio is less than 1 and [HA] > [A-] -when pH>pKa then the [A-]/[HA] ratio is greater than 1 and [A-] > [HA]

Which sequence is MOST likely to contain an O-linked oligosaccharide in the ER? (The ... represents additional amino acids N-terminal or C-terminal to those shown.) ...Phe-Leu-Cys-Gly-Leu-Ile... ...Gly-Leu-Phe-Ala-Ile-Gly... ...Tyr-Leu-Ala-Ile-Gly-Phe... ...Ala-Thr-Leu-Phe-Ser-Gly...

...Ala-Thr-Leu-Phe-Ser-Gly...

How many more passes through beta-oxidation does the saturated fat stearic acid (18:0) require, compared with the monounsaturated fat oleic acid (18:1)? 0 1 2 17

Consider a reaction consisting of 2 species D and M which interconvert according to the reaction D < == > 2M. Assume that at equilibrium, the concentrations are [D]eq = 4.8 x 10^-5 M and [M]eq = 4.0 x 10^-6 M . What is Keq for this reaction?

0.00000033M

[D]eq=4.8 x 10^-5M and [M]eq= 4.10 x 10^-6 M. What is Keq for this reaction

0.00000033M

Mutations in adenylate kinase have led to a hyperactive enzyme that ultimately ends up elevating ADP levels in a cell. Calculate the EC (energy charge) given the following atypical adenylate concentrations for the cell containing the mutant adenylate kinase: ATP = 0.5 𝑚𝑀mM, ADP = 12.2 𝑚𝑀mM, AMP = 80 𝜇𝑀μM.

0.52

Under steady-state conditions in a mammalian cell, the adenine nucleotide concentrations are [ATP] = 3.3 mM, [ADP] = 1.2 mM, and [AMP] = 0.2 mM. What is the energy charge of this cell?

0.83

Calculate the energy charge in a cultured cancer cell line found to have the following adenylate concentrations: 1.25 mM ATP, 0.35 mM ADP, and 0.12 mM AMP. Is this too high, too low, or normal?

0.83; normal

Starting from the oxidative phase of the pentose phosphate pathway, how many ATP and high-energy reduced molecules, respectively, are made in going from one glucose molecule to glyceraldehyde-3-phosphate and fructose-6-phosphate? 0; 0 0; 2 2; 0 2; 2

0; 2

How many of the nitrogens in orotidine-5'-monophosphate arise from glutamine? 0 1 2 3

Which is the step in glucagon signaling where adipose triglyceride lipase mediates a reaction? 1. A hydrolysis reaction cleaves a fatty acid from the stored triacylglycerols to generate diacylglycerol and a fatty acid. 2. Perilipin is phosphorylated on the surface of lipid droplets. 3. Albumin transports the free fatty acid. 4. A GDP-GTP exchange stimulates cyclic AMP production by the enzyme adenylate cyclase. 1 2 3 4

hydrogen bonding in tertiary protein

hierarchy of life

1 elements/functional groups 2 biomolecules 3 macromolecules 4 metabolism 5 cells 6 organisms 7 ecosystems

1 x 10-14 M2

A titratable group is in the active site of an enzyme and must be protonated for the enzyme to function. Assume that the group has a pKa of 6.5 and that the activity is proportional to the fraction of molecules in the protonated state. Which of the following are true?

1) At pH 6.5, the enzyme is 50% active 2)At pH 9.0 close to 100% of the enzyme molecules are active.

Match each of the four building block biomolecules on the left with the ONE specific biomolecule on the right that best represents it. 1) Fatty Acid 2) Simple Sugars 3) Nucleotides 4) Amino Acids

1) Fatty Acid- palmitate 2) Simple Sugar- Ribose 3) Nucleotide- cytidine monophosphate 4) Amino Acid- aspartate

Which THREE of the following biochemical relationships are correct statements illustrating the hierarchical organization of molecular life?

1) Insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients. 2)Monomers are covalently linked together in biochemical reactions catalyzed by enzymes to generate polymers 3)Adenosine monophosphate contains all five of the most abundant elements found in a living cell

Select the four TRUE statements below describing the standard free energy change (delta G) and the equilibrium constant (Keq).

1) The value for the standard free energy change is constant for a given reaction 2) The value for the equilibrium constant can be experimentally determined for a given reaction 3)If the value of the equilibrium constant is known, the value for the standard free energy change can be determined 4) The equilibrium constant is the ratio of product and reactant concentrations at equilibrium

Energy conversion in living systems is required for what 3 types of work?

1) osmotic work 2) chemical work 3) mechanical work

Choose three reasons below why RNA is a dynamic biomolecule, and in that way, distinct from DNA and record your answer. 1. RNA is degraded within the nucleus and the cytoplasm, whereas DNA is normally never degraded. 2. RNA forms base pairs with complementary nucleotides and transmits information in a predictable way. 3. RNA tertiary structure is altered by the binding of protein and small molecule ligands. 4. RNA forms a double helical structure between anti-parallel strands with 5' - 3' and 3' - 5' polarity. 5. RNA is able to participate in transitory functional base pairing interactions with RNA or DNA. 6. RNA contains a ribose sugar, a nucleotide base attached to the ribose, and phosphate groups. 7. RNA can be degraded in the 5' to 3' direction or in the 3' to 5' direction, and it can be cleaved internally. 2, 4, 6 1, 4, 6 1, 3, 5 4, 5, 7 3, 5, 7

1, 3, 5

Which of the TWO statements below about myosin are true? Record your answers and choose the set below that is correct. 1. The interaction between myosin and actin converts chemical energy to mechanical work. 2. The myosin head has a binding site for actin, titin, troponin, tropomyosin, and ATP. 3. The myosin head functions like molecular lever during the power stroke of contraction. 4. Myosin-actin reaction cycle requires hydrolysis of 1 ATP per myosin head in each cycle. 5. The A band and I band belong to the Z club and meet up at the T tubule to disco nightly.

1, 4

pH range of a buffer is around ____ pH unit above and below the ___ of the acid base conjugate pair

1, pKa (pertains to the ionization of water)

Which are critical features or properties of nearly all protein enzymes? Choose all that apply

1,3,5 1. enzymes usually display high affinity and specificity for their susbstrates 3. enzyme activity is often highly regulated to provide maximum control of catalysis 5. conformational changes, both small and large, can occur after substrate binding

Which of the following compounds contains a "high-energy" bond and is used to produce ATP by substrate-level phosphorylation in glycolysis?

1,3-bisphosphoglycerate

Which of the following compounds contains a "high-energy" bond and is used to produce ATP by substrate-level phosphorylation in glycolysis? 1,3-bisphosphoglycerate 3-phosphoglycerate fructose-1,6-BP glucose

1,3-bisphosphoglycerate

Which three amino acids are most likely be found in the core of a soluble and globular protein?

1,4,8

Match the polymer with the monomer that can be one of its components. Correct Response __3__ Glycogen phosphorylase Correct Response __1__ Glycogen Correct Response __2__ DNA

1. Glucose 2. ATP 3. Glutamate

Match the generic enzyme name to the general type of reaction they catalyze __2__ removal of phosphoryl groups __3__ addition of methyl groups __4__ peptide cleavage __5__ rearrangements that don't change the molecular formula __1__ addition of phosphoryl groups

1. Kinase 2. Phosphatase 3. Methyltransferase 4. Protease 5. Isomerase

Match each protein with its functional class __4__ Cell signaling protein __1__ Metabolic enzyme __2__ Transport protein __3__ Structural protein __5__ Genomic caretaker protein

1. Malate dehydrogenase 2. Na+/K+ ATP ase 3. Tubulin 4. G-protein coupled receptors 5. RNA polymerase

__2__ Second messenger produced by __4__ Result __1__ Second messenger __3__ Kinase

1. cAMP 2. Adenylate cyclase 3. Protein kinase A (PKA) 4. Glucose mobilization 5. diacylglycerol (DAG) 6. phospholipase C (PLC) 7. protein kinase C (PKC) 8. Glucose storage (as glycogen)

answer with A. pepsin, B. cyanogen bromide, C. phenyl isothiocyanate, and D. chymotrypsin 1. is a protease(2) 2. cleaves N-terminal to leucine 3. cleaves adjacent to tyrosine residues(2) 4. can be used as part of an effort to sequence a protein (4) 5. always reacts with the N-terminal residue 6. is used repeatedly in cycles during peptide sequencing. 7. reacts with a sulfur-containing amino acid.

1. A,D 2. A 3. A, D 4. A, B, C, D 5. C 6. C 7. B

Use the titration curve for acetic acid shown to the right to answer the three questions and then choose the letter with all three correct answers

1. CH3COOH 2. pKa 3. CH3COO

Chosoe the five correct labels for the figure to the right

1. ES 2. TS 3. EP 4. E+P 5. substrate

21. What are the three phases of the Calvin Cycle?

1. Fixation 2. Reduction 3. Regeneration

1. Which of the following nucleotides are parts of these interacting molecular structures? (Nucleotides are represented by their single letter symbols.) 2.To break the base pair, energy needs to be invested than is required to break a base pair that consists of two-hydrogen bonds. 3. An organism that has evolved to grow at significantly high temperatures is most likely to have:

1. G-C 2. more 3. greater G/C content as compared to A/T.

Put the following enzymes in the order they appear in the pentose phosphate pathway, starting with glucose-6-P and ending with erythrose-4-P.

1. Glucose-6-phosphate dehydrogenase 2. Ribulose-5-P isomerase 3. Transketolase 4. Transaldolase

What are the three ways that RNA and DNA differ?

1. RNA has a hydroxyl group on the 2′ carbon on the ribose ring, whereas DNA lacks the hydroxyl group at this position. 2. RNA contains the base uracil and DNA contains the base thymine. 3. RNA can form the catalytic molecules (ribozymes), whereas DNA does not form catalytic molecules.

2 kinds of beta sheets

1. antiparallel 2.parallel *can be connected by a loop or a b-a-b motif

protein electrophoresis

1. denaturing page(SDS) 2. native page

chemical sequencing strategy

1. determine number of subunits (4structure) * SDS page + native page *size exclusion chromatography *separates units based on size. 2. Determine the number of free N-termini *benzyl chloride *6N HCl >> all peptide bonds hydrolyzed but only the N-terminal (AA) is labeled. *will work for monomers and multimers (4 structure) 3. determine amino acid composition *6N HCl used to hydrolyze all peptide bonds. *lable each AA with a flourescent dye molecule that attacks NH3 functionality of each AA.

christian anfunsin conclusion

1. internal residues drive folding 2. driving force is hydrophobicity, "hydrphobic collapse" 3. water must be excluded from protein interior *tested to see if disulfide bonds are driving force... they are not.

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell.

1. the energy charge ration below 0.70 2. low ATP concentrations 3. high AMP concentrations

separating the protein of interest from all other proteins in a complex lysate

1. use an affinity approach taking advantage of the POI's requirements for NADH, ATP, DNA binding. >make an affinity resin from sepharase (gelatinous sugar that can be chemically derived)

Calculate the mc017-1.jpg of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table below. mc017-2.jpg

1.25

Calculate the mc017-1.jpg of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table below. 0.39 1.25 −0.39 −1.25

1.25

steps in protein folding from linear peptide

1.hydrophobic collapse 2.molten globule. 3.2 degree structure/super 2 degree structure forms 4. 2 degree structure interacts to form tertiary(3 degree) structure. 5. protomers form in step 4>> multisubunit proteins(GADPH,Hb) *-S-S- can form in step 4 as well.

Which of the following membranes would have the greatest fluidity based on the following percentage of cholesterol in the membrane? 10% 25% 30% 40%

10%

How many base pairs per turn does B-DNA contain?

10.5

As 18 Na+ ions are exported out of the cell by the Na+-K+ ATPase membrane transport protein, __________ K+ ions are imported into the cell.

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is guanine?

15%

In two turns of the citrate cycle, how many electrons are transferred from the citrate cycle intermediates to NAD+ and FAD?

In two turns of the citrate cycle, how many electrons are transferred from the citrate cycle intermediates to NAD+ and FAD? 16 8 4 12

Use the table below to determine how many possible RNA sequences could code for the dipeptide Pro-Ala.

In 3 turns of the citrate cycle, how many electrons are transferred to NAD+, how many CO2 are produced and how many GTP are generated

18 electrons, 6 CO2, 3 GTP

Put the correct steps required for absorption of dietary fats into order:

1: emulsification of fats 2: lipase cleavage 3: intracellular synthesis of triglycerides 4: chylomicron assembly 5: export of lipoprotein 6: Entry into the circulatory system

In purines, __________ nitrogen atoms and __________ carbon atoms originate from glycine. 0; 2 1; 1 2; 1 1; 2

1; 2

From part 1, those main chemical components of the plasma membrane each contain fatty acids.

How many GTP are hydrolyzed during a single round of translation elongation in a eukaryote? 0 1 2 6

Starting from a molecule of glucose imported from the blood, what is the energy cost for adding that molecule of glucose to a growing glycogen chain?

2 ATP

Which of the following best explains why the fatty acyl-CoA synthetase reaction is considered to consume 2 ATP? Choose one: A. 2 ATP are required to regenerate the AMP product. B. 2 ATP are required to provide the free energy change necessary to make formation of the thioester bond favorable. C. PPi is hydrolyzed to 2 Pi. D. Each fatty acid must be activated in both the cytosol and mitochondrion, requiring an overall input of 2 ATP.

2 ATP are required to regenerate the AMP product.

Starting with glucose derived from the diet, how many ATP are required to incorporate this dietary glucose molecule into liver glycogen. Explain your reasoning A. 2 ATP; one ATP needed to generate Glucose-6-P (isomerized to G-1P), and another to regenerate UTP B. 1 ATP; one ATP equivalent is needed in AMP-dependent kinase reaction to regenerate UTP C. 3 ATP; one ATP needed to generate Glucose-6-P, and two ATP equivalents to convert UMP to UTP D. 2 ATP; one ATP needed to generate Fructose-6P, and another to convert G-6-P to G-1-P and UTP E. 1 ATP; one ATP is needed to generate UTP used in the UDP-glucose pyrophosphorylase reaction

2 ATP; one ATP needed to generate Glucose-6-P (isomerized to G-1P), and another to regenerate UTP

Which of the following statements are correct regarding the relationship of pH and pKa

2 and 5 2. When pH<pKa then the [A]/[HA] ratio is less than 1 and [HA]>[A] 5. When pH>pKa then the [A]/[HA] ratio is greater than 1 and [A]>[HA]

Which of the following process are driven by the hydrophobic effect? Four numbered processes are correct, choose the letter below that contains all four of the correct numbered processes. 1. Dissolving sodium chloride in water to brine chicken. 2. Separation of oil and vinegar in salad dressing. 3. Ice melting in a cooler at a UA football game tailgate party. 4. Formation of a protein dimer through leucine and valine residues. 5. The interaction between antifreeze protein and ice crystals. 6. Protein folding of a globular protein that transports fatty acids. 7. The solubility of glucose in a solution of simple syrup. 8. The formation of limonene droplets on the surface of a mixed drink. 9. Movement of H2O through a porin channel in a bacterial membrane. 3, 5, 7, 9 1, 2, 3, 8 2, 4, 6, 8 2, 5, 6, 7 2, 3, 6, 9

2, 4, 6, 8

Below is a figure of adult hemoglobin. The arrow points to where __________ binds.

2,3-biphosphoglycerate

What are the THREE key assumptions of Michaelis-Menten kinetics

2,4,6 2. the reaction is analyzed at a time int he reaction that negligible product is formed 4. the steady state condition is reached quickly under conditions where S>>E 6. product release is assumed to be a rapid step in the process

Approximately how many amino acids are identical in both myoglobin and the adult alpha-subunit of hemoglobin?

20%

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 mc005-1.jpg 102 mmol/sec and the catalyzed rate is 2.4 mc005-2.jpg 104 mmol/sec?

200

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 mc005-1.jpg 102 mmol/sec and the catalyzed rate is 2.4 mc005-2.jpg 104 mmol/sec? 2 0.005 200 2.88 mc005-3.jpg 106

200

What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 mc131-1.jpg 102 mmol/sec and the catalyzed rate is 2.4 mc131-2.jpg 104 mmol/sec?

200

How many possible protein primary structures are there for a tripeptide given the 20 amino acids? 20^(3) 3^(20) 400 1.27 x 10^(130)

20^(3)

How many possible protein primary structures are there for a tripeptide given the 20 amino acids?

20^3

How many possible protein primary structures are there for a tripeptide given the 20 amino acids? 400 3^20 1.27 x 10^130 20^3

20^3

4. Based on the overall reactions for photosynthetic electron transport and the Calvin cycle reactions, how many photons of light are required to generate enough ATP to produce glyceraldehyde-3-phosphate?

24 photons

Mammalian fatty acid synthase is composed of approximately 2,500 residues. This corresponds to approximately ___ kDa.

275.0

Noncanonical base pairings of A and I would contain __________ hydrogen bonds. The base pairing of C and I would contain __________ hydrogen bonds. 1; 3 1; 2 2; 2 2; 1

2; 2

Aspartate contains four carbons. If all are radioactively labeled, how many carbons of UMP will be radioactively labeled? 0 2 3 4

How many beta-turns or beta-loops are required to construct a beta-sheet composed of four antiparallel strands?

hydrophobic interaction in tertiary protein

During intense exercise, muscle ATP stores will be depleted in about 3 minutes. 5 minutes. 30 seconds. 3 seconds.

3 seconds

The Re group charged at pH 12, charged at pH 3, phosphorylated; hydrophilic

3,2,5,6

Order the five steps in the actin-myosin reaction cycle; which step is the power stroke?

3,5,2,4,1 Step 5

Which of the following reactions would depend only on susbtrate avilability?

3-phosphoglycerate->2-phosphoglycerate

Match the four amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A). 1. Tryptophan 2. Arginine 3. Valine 4. Threonine

3. Valine - Hydrophobic 4. Threonine - Hydrophilic 2. Arginine - Charged 1. Tryptophan - Aromatic

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein?

3.6 fold

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein? 3.6-fold 0.28-fold 1.3-fold 7.5-fold

3.6 fold

residues per turn

3.6 residues per tern

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein?

3.6-fold

Glycogen phosphorylase - What is the closest distance between pyridoxal phosphate and glucose-1-phosphate when interacting with glycogen phosphorylase in this molecular structure?

3.67 angstroms

What is the energy requirement to transport 2 moles of K+ from the outside to the inside?

3.7 kJ

A histidine residue is in a hydrophobic environment in the interior of a protein. If the pKa of the imidazole group of this histidine is 5.5, what would be the ratio of deprotonated imidazole sidechain to protonated imidazole sidechain at pH 7?

31.6/1

Calculate the ∆G'º of a redox reaction of pyruvate and hydrogen under standard conditions using the table below. 36.66 kJ/mol 18.33 kJ/mol 73.32 kJ/mol 54.99 kJ/mol

36.66

Calculate the delta g of a redox reaction of pyruvate and hydrogen under standard conditions using the table below. mc020-2.jpg

36.66 kJ/mol

Which sequence looks as if it could include a β turn (reverse turn)? 2. Which sequence looks as if it could form a β strand, with one surface facing the interior of the protein, and the other surface exposed to water? 3. Which sequence looks as if it could form an amphipathic α-helix? (Use a helical wheel to help)

3_ Ile-Gln-Ser-Ala-Leu-Asn-Glu-Ile-Glu-Asn-Phe-Met-Ser-Cys-Val __1__ Val-Asn-Tyr-Gly-Pro-Gln-Leu-Phe-Ala-Leu-Val-Arg-Gln-Cys-Val __2__ Ile-Asn-Leu-Glu-Met-Asp-Leu-Arg-Val-Gln-Leu-Glu-Phe-Lys-Val

How many different forms of pyridoxal phosphate are observed in the aminotransferase reaction? 7 6 5 4

What is the maximum number of covalent bonds a carbon atom can make? 2 6 8 4

What is the minimum number of amino acids needed to make one turn of an alpha-helix?

disulfide bond in tertiary protein segment

Which of the TWO following statements about myosin are true?

4 and 6 4: Myosin actin reaction cycle requires hydrolysis of 1 ATP per myosin head in each cycle 6. The interaction between myosin and actin converts chemical energy to mechanical work

Which of the following is the correct solar energy reaction that takes place on the sun?

4 hydrogen to helium 4 radioactive

a segment of a single chain in an antiparallel beta sheet has a length of 144A. how many residues are in this segment

ionic bonding in tertiary protein segment

32. The net change in stage 3 of the Calvin cycle can be represented as which of the following?

5 C3 → 3 C5

Predict the complementary strand of the following DNA sequence: 5'-ATCTGAATCT-3'

5' AGATTCAGAT 3'

Predict the complementary strand of the following DNA sequence: 5'-ATCTGAATCT-3'

5'-AGATTCAGAT-3'

Given a DNA sequence of 3'-CAT-5', what is the complementary sequence in mRNA?

5'-GUA-3'

When making cDNA from mRNA, what is the appropriate primer to use? Choose one: 5'-CCCCCCCCCCCCCCC-3' 5'-TTTTTTTTTTTTTTT-3' 5'-AAAAAAAAAAAAAAA-3' 5'-GGGGGGGGGGGGGGG-3' 5'-UUUUUUUUUUUUUUU-3'

5'-TTTTTTTTTTTTTTT-3'

average alpha helix length

5.4A per turn

If a typical person hydrolyzes 100.0 mol of ATP per day, how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol.)

50.7 kg .507g/mol x 100mol

If a typical person hydrolyzes 100.0 mol of ATP per day, how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol.)

50.7kg

alhpa helices are a type of secondary structure in proteins. what is the length of a 39-kDa single stranded alpha helical protein segment. assume the residue mass is 110Da

531.82 A

If there are six mRNA codons, none of which is a STOP codon, what is the greatest number of amino acids that they could encode in a sequence?

In the production of one glyceraldehyde-3-phosphate as part of the net Calvin cycle, __________ are NOT required.

6 ATP

Calculate G for the conversion of 3-phosphoglycerate to phosphoenolpyruvate using the table of G values on the front page of the exam.

6.3 kJ/mol

A 20 bp duplex with __________ content at __________ will have the highest absorbance at 260 nm.

60% A-T 50 degrees C

Bioinformatics shows that 98% of human DNA is identical to that of chimpanzees. If human DNA contains 3.2 billion nucleotides, how many nucleotides are different between the two species?

64 million

The formation of one net glyceraldehyde-3-phosphate during the net Calvin cycle reactions requires __________ NADPH and __________ ATP. 3; 3 3; 6 6; 6 6; 9

6; 9

Refer to the reaction coordinate diagram at right that compares catalyzed and uncatalyzed reactions. Which of the following labels are correct?

6=AE for catalyzed rxn, 5= product, 1=G

How many passes through the fatty acid oxidation pathway are required to degrade palmitic acid? 1 7 8 16

Which amino acid is most unlikely to be in an alpha helix; most likely to be in a beta turns

7,9

Calculate the linking number for a B-DNA strand that contains 735 total base pairs

Calculate the linking number for a B-DNA strand that contains 735 total base pairs.

Calculate the net number of moles of NADH, FADH2, and acetyl-CoA from oxidation of 1 mole of the fatty acid shown to the right A. 6 moles NADH, 6 moles FADH2, 7 moles of acetyl-CoA. B. 9 moles NADH, 9 moles FADH2, 9 moles of acetyl-CoA. C. 7 moles NADH, 7 moles FADH2, 8 moles of acetyl-CoA. D. 5 moles NADH, 5 moles FADH2, 6 moles of acetyl-CoA. E. 8 moles NADH, 8 moles FADH2, 9 moles of acetyl-CoA.

8 moles NADH, 8 moles FADH2, 9 moles of acetyl-CoA.

Infants express the enzyme lactase in their intestines to metabolize lactose. How many ne tmoles of ATP can be generated from 2 moles of lactose under anaeorbic conditions by infants with high levels of lactase?

8 net ATP

3. For every four reduced plastoquinol molecules (PQBH2) that are oxidized in the PQ cycle, how many protons are translocated into the thylakoid lumen?

8 protons

The net fatty acid synthesis reaction for stearate (C18) is: __ Acetyl CoA + __ ATP + __ NADPH + __ H+ à stearate + __ CoA + __ ADP + __ Pi + __ NADP+ + __ H2O

9, 8, 16, 16; 9, 8, 8, 16, 7

Calculate the specific activity when 500 mg of protein has an activity of 18,000 units.

9000 units/mg protein

If the equilibrium constant (Keq) is greater than 1, what is the value of delta G?

A double helix that crosses itself in a left-handed twist is referred to as a a. positive supercoil. b. negative supercoil. c. topoisomer. d. linking number.

A double helix that crosses itself in a right-handed twist is referred to as a A) negative supercoil B) topoisomer C) linking number D) positive supercoil E) none of the above

A solution of which of the following would be a good buffer system? A) CH3COOH and NaCH3COO B) HCl and H2O C) NaOH and KOH D) none of the above E) HCl and NaOH

Deletions or insertions into the genome cause a polymorphism called a. short tandem repeats. b. variable number tandem repeats. c. long tandem repeats. d. single nucleotide polymorphism.

Given a biological system at 1 atm with 16kJ/g, what is the internal energy of the system? A) 16kJ/g B) not enough information is given to calculate the answer C) 15kJ/g D) 14 kJ/g

Given that the approximate bond length of O-H in water is roughly 1 Å, what is the approximate distance each proton "hops" between molecules? A. 1.5 Å (1 × 10-10 m) B. 15 nm (1.5 ×10-8 m) C. 1.5 fm (1.5 × 10-15 m) D. 1.5 µM (1.5 × 10-6 m) E. 15 pm (1 × 10-12 m)

Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true? A. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. B. Keratin in hair has more cysteines and therefore fewer disulfide bonds than keratin in fingernails. C. Keratin in hair has more cysteines and therefore more disulfide bonds than keratin in fingernails. D. Keratin in hair has fewer cysteines and therefore more disulfide bonds than keratin in fingernails.

How many beta turns or beta loops are required to construct a beta sheet composed of four antiparallel strands? A) 3 B) 4 C) 6 D) 0 E) 5

Identify the phase of PCR amplification where DNA is denatured and the strands are separated. *SEE #72* a. A b. B c. C d. D

Identify the products when Smal cleaves the following DNA sequence. *SEE #62* a. CCC-3′ 5′-GGG GGG-5′ 3′-CCC b. GG-3′ 5′-CC CC-3′ 5′-GG c. GGG-3′ 5′-CCC CCC-3′ 5′-GGG d. CC-5′ 3′-GG GG-5′ 3′-CC

If the concentration of aspartate in the cell decreased, what would be the predicted outcome? A) decreased concentration of fumarate B) increased concentration of arginine C) increased concentration of argininosuccinate D) decreased concentration of citrulline E) none of the above

In the eukaryotic cell, the coding sequences on a gene are referred to as a. exons. b. operons. c. introns. d. promoter.

In viral transduction DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

Increasing the ion concentration increases the Tm because the ions a. bind to the phosphate groups of the DNA backbone and increase stability. b. bind to the nucleic acids and disrupt the base pairs, decreasing stability. c. increase the base length of the DNA, increasing stability. d. associate with the ribose sugars, decreasing stability.

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure? A) framework model B) none of the above C) mutant globule D) nucleation model E) hydrophobic collapse model

Pyruvate decarboxylase converts pyruvate into A) Carbon dioxide and acetaldehyde B) Ethanol and carbon dioxide C) none of these answers are correct D) water and glucose E) carbon monoxide and acetaldehyde

The A-T content for several DNA strands is reported below. Which strand would have the highest Tm? a. 40% A-T b. 50% A-T c. 60% A-T d. 70% A-T

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is guanine? a. 15% b. 30% c. 35% d. 70%

The basic structure of DNA is a right-handed helix formed by two __________ strands of DNA. a. antiparallel b. parallel c. coding d. template

The exons of a single gene often encode for different functional domains of a protein, which can result in a. genetic recombination. b. gene regulation. c. untranslated regions. d. termination of transcription.

The interior stacking of the DNA bases in the double helix provides stability through a. hydrophobic and van der Waals interactions. b. hydrophilic and van der Waals interactions. c. hydrophilic and ion-dipole interactions. d. hydrophobic and ion-dipole interactions.

The linking number of a relaxed DNA strand whose axis is not coiling is 30. Predict the twist and writhe of the DNA stand. a. Wr=0,Tw=30 b. Wr=30,Tw=0 c. Wr=15,Tw=15 d. Wr=30,Tw=-30

The process of condensation reduced the size of DNA by A) 10,000 fold B) 1,000 fold C) 100 fold D) 1,000,000,000 E) 100,000 fold

The various chemical properties of the amino acid side chains determine the chemical properties and the three-dimensional structures of proteins. What are the four groups that amino acids can be divided into? A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic B. polar; nonpolar; aerobic; hydrophobic or aliphatic C. short-chain Polar; long-chain aliphatic; aromatic; unreactive D. charged; aromatic; lipophilic; sulfur-containing

What is the dominant secondary structure found in hair keratin? A) alpha helices B) disulfide bonds C) beta sheets D) loop structures

What mediates the binding of histone proteins to DNA? a. ionic attractions b. London dispersion forces c. hydrophilic interactions d. hydrophobic interactions

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? a. gel electrophoresis b. blue-white screening c. antibiotic resistance d. fluorescent labeling

When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme? A) reverse transcriptase B) DNA ligase C) restriction endonucleases D) DNA methylase E) telomerase

Which of the following gene expression assays requires that the sequence of genes be known in advance? A. gene microarray B. RNA-seq analysis C. both RNA-seq analysis and gene microarray D. neither RNA-seq analysis nor gene microarray

Which of the following is most likely to be found on the exterior of a protein? A. Ser B. Glu C. Pro D. Trp

Which of the following statements about Ramachandran plots is true? A) they show that beta sheets and alpha helices occupy different psy and sigma angles B) none of the above C) they are needed to determine the secondary structure of a protein D) they are good predictors of protein tertiary structure E) they show equal distributions of psy and sigma angles for alpha helical and beta sheet containing proteins

Which of the following steps is performed when preparing to do both an RNA-seq analysis and a gene microarray? A. Isolate mRNA from whole cell lysate. B. Convert RNA to complementary DNA called cDNA. C. Create high-throughput DNA sequencing. D. Generate fluorescently labeled RNA fragments.

__________ maintain the length a. Telomeres b. Centromeres c. Kinetochores d. Sister chromatids

Chargaff's rule is that the amount of

A = T and the amount of C = G.

Which form(s) of DNA exhibit(s) a right-handed helical structure?

A DNA and B DNA

Which of the following is/are functional groups contained in all amino acids? A. amino group B. carboxyl group C. methyl group D. phosphoryl group

A and B

A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.

An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Km does not change but that the kcat increases as the pH goes above 7. Which of the following is true? A chemical group with a pKa of around 7 must be deprotonated in order for substrate to bind. A covalent enzyme intermediate is likely formed. Protons are acting as positive heterotropic allosteric effectors of this enzyme. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism. A chemical group with a pKa of around 7 must be positively charged in order for the substrate to bind.

A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.

An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Km does not change but that the kcat increases as the pH goes above 7. Which of the following is true? A chemical group with a pKa of around 7 must be deprotonated in order for substrate to bind. A chemical group with a pKa of around 7 must be positively charged in order for the substrate to bind. A covalent enzyme intermediate is likely formed. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism. Protons are acting as positive heterotropic allosteric effectors of this enzyme

A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism.

Why does DNA contain thymine instead of uracil?

A common reaction in cells is for cytosine to spontaneously go through a deamination reaction to form uracil. Any cytosine deamination producing uracil that is not repaired before the next round of DNA replication will change a C-G base pair to a U-A base pair, which during the next round of DNA replication will become a T-A base pair. Therefore, by having only thymine present in DNA, the presence of uracil can be more easily detected, thereby maintaining the genetic information.

A ligand is bound to a single subunit and that subunit is in the T state.

Consider an allosteric protein that contains three identical subunits. Which of the following is true only if the protein follows the concerted model of allostery and NOT the sequential model of allostery? All three subunits exist in the R state simultaneously. No ligand is bound; two subunits are in the T state and one subunit is in the L state. All three subunits exist in the T state simultaneously. A ligand is bound to a single subunit and that subunit is in the T state.

A ligand is bound to a single subunit and that subunit is in the T state.

Consider an allosteric protein that contains three identical subunits. Which of the following is true only if the protein follows the concerted model of allostery and NOT the sequential model of allostery? All three subunits exist in the T state simultaneously. No ligand is bound; two subunits are in the T state and one subunit is in the L state. A ligand is bound to a single subunit and that subunit is in the T state. All three subunits exist in the R state simultaneously.

A ligand is bound to a single subunit and that subunit is in the T state.

Explain the difference between a negative supercoil and a positive supercoil.

A negative supercoil is when the direction of the twist is right handed. A positive supercoil is when the direction of the supercoil is left handed.

Which one of the statements below best describes the mechanism of proton translocation by the Electron Transport System using a redox loop mechanism exemplified by the Q cycle

A redox reaction separating protons and electrons within complex III of the electron transport system, with the protons translocated to the inter-membrane space and the electrons used to reduce Q

What would be the expected orientation of an amphipathic alpha helix occurring in a globular protein in aqueous solution?

A soluble protein will have lots of hydrophilic amino acids on its surface, so the helix will be arranged to have the hydrophilic side facing toward the outside of the protein.

Select the one TRUE statement below regarding X-ray crystallography

A structure determined at 2 Angstrom resolution has higher resolution (more detail can be seen in the model) than a structure determined at 3 Angstrom resolution

Select the one TRUE statement below regarding X-ray crystallography An individual protein has sufficient mass to scatter X-rays A structure determined at 2 Angstrom resolution has higher resolution (more detail can be seen in the model) than a structure determined at 3 Angstrom resolution The first structure of sperm whale myoglobin was determined from X-ray data from Rosalind Franklin. High concentrations of proteins are needed to make sure that higher resolution models can be obtained. None of these statements are correct.

A structure determined at 2 Angstrom resolution has higher resolution (more detail can be seen in the model) than a structure determined at 3 Angstrom resolution

A) ETS activity after DNP added compared to no DNP was higher B) ATP production after DNP added compared to no DNP was lower C) DNP first, then oligomycin, ATP production after oligomycin added compared to DNP alone was lower

Select the one best answer for each of A, B, and C to explain what happens in a mitochondrial suspension that contains succinate and ADP+Pi: A) When DNP is added, what happens to electron transport system activity compared to no DNP? B) When DNP is added, what happens to ATP production compared to no DNP? C) When DNP is added first and then oligomycin is added, what happens to ATP production after oligomycin compared to DNP alone? (DNP is dinitrophenol, a chemical uncoupler that allows proton flow across the mitochondrial membrane. Oligomycin is an inhibitor of ATP synthase.) A) ETS activity after DNP added compared to no DNP was higher A) ETS activity after DNP added compared to no DNP was lower A) ETS activity after DNP added compared to no DNP was unchanged. B) ATP production after DNP added compared to no DNP was higher B) ATP production after DNP added compared to no DNP was lower B) ATP production after DNP added compared to no DNP was unchanged. C) DNP first, then oligomycin, ATP production after oligomycin added compared to DNP alone was higher C) DNP first, then oligomycin, ATP production after oligomycin added compared to DNP alone was lower C) DNP first, then oligomycin, ATP production after oligomycin added compared to DNP alone was unchanged

A) coupled redox reactions B) the inner mitochondrial membrane C) NADH D) 10 H+

Choose one answer each for A, B, C and D to correctly complete the sentences. The chemiosmotic theory states that energy captured by (A) in the electron transport system is used to translocate protons across (B), creating a proton-motive force. Oxidation of (C) by the electron transport system leads to a translocation of (D) across the mitochondrial membrane. A) coupled redox reactions A) substrate-level phosphorylation B) the inner mitochondrial membrane B) the outer mitochondrial membrane C) NADH C) O2 D) 4 H+ D) 10 H+

A) coupled redox reactions B) the inner mitochondrial membrane C) NADH D) 10 H+

Which of the following are properties of water? A. Water is less dense as a solid than as a liquid. B. Water is liquid over a wide range of temperatures. C. Water is miscible with oil. D. Water is a strong acid at high temperatures. E. Water is polar and an excellent solvent because of its hydrogen-bonding properties. F. Water freezes more readily when ionic solutes are dissolved in it.

A, B, and E

What is the appropriate order of the following steps? A. Glutamine binding to uridylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase

A, C, B

Which of the following are mechanisms of horizontal gene transfer that can insert DNA into a bacterial cell? A. transformation B. transcription C. transduction D. conjugation

A, C, and D

Which of the following statements is correct?Choose one: A. An exergonic reaction drives an endergonic reaction in living systems. B. The overall free energy of a coupled reaction is the difference of the free energies for the individual reactions. C. ATP is rarely used in coupled reactions. D. An endergonic reaction drives an exergonic reaction in living systems.

A- An exergonic reaction drives and endergonic reaction in living systems

Which of the following is an example of a weak acid? Choose one: A. Vinegar, CH3COOH B. HCl C. Ammonia, NH3 D. NaOH

A- Vinegar, CH3COOH

The mobility of lipids in membranes is best described by Choose one: A. fast lateral diffusion and slow transverse diffusion. B. slow lateral diffusion and fast transverse diffusion. C. slow lateral diffusion and slow transverse diffusion. D. fast lateral diffusion and fast transverse diffusion.

A- fast lateral diffusion and slow transverse diffusion

Which of the following types of chromatin is usually associated with non-coding DNA? Choose one: A. heterochromatin B. euchromatin

A- heterochromatin

For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change?Choose one: A. The EC would increase. B. The EC would remain unchanged. C. There is no way to predict how the EC would change. D. The EC would decrease.

A- the EC would increase

Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur? Choose one or more: A. The unfavorable reaction is coupled to a favorable one. B. Energy is absorbed from the surroundings. C. A favorable enthalpy change overcomes entropic penalty. D. It is not possible.

A- the unfavorable reaction is coupled to a favorable one C- A favorable enthalpy change overcomes entropic penalty

If a cell is placed in a hypotonic solution, thenChoose one: A. water will flow into the cell. B. water will flow out of the cell. C. there will be no net change in flow of water into or out of the cell. D. solutes in the solution will enter the cell.

A- water will flow into the cell

Which form(s) of DNA exhibit(s) a right handed helical structure?

A-DNA and B-DNA

Which form(s) of DNA exhibit(s) a right-handed helical structure?

A-DNA and B-DNA

Which of the following three terms includes the other two? A) homologous B) orthologous C) paralogous

A-homologous

The partial sidechain of asparagine or glutamine is shown above. For the three atoms marked A, B, and C, indicate whether they serve as donors, acceptors, or neither for hydrogen bonds. (Choose THREE total answers (one each for A, B, C) from the list of nine possibilities) B-neither A-acceptor C-neither A- donor A-neither B-acceptor C-acceptor C-donor B-donor

A-neither B-acceptor C-donor

When a protein enzyme folds in an aqueous solution, which of the following is correct? Choose one: A. Non-polar amino acids are found in the interior of the protein. B. Polar amino acids are found in the interior of the protein. C. A mixture of polar and non-polar amino acids is found in the interior of the protein. D. Water is always excluded from the active site in the interior of the protein.

A-nonpolar amino acids are found in the interior of the protein

Which of the following is an example of a heterotroph?Choose one: A. Yeast B. Plants C. Cyanobacteria D. Single-cell algae

A-yeast

Two new microorganisms, labeled X and Y, were isolated from an oil spill during a search for organisms that will degrade petroleum products. DNA was isolated from each, and the percent adenine was measured. Assume each organism contains normal double-stranded DNA. Organism X: 18.7% adenine Organism Y: 29.9% adenine a.) What percentage of thymine does organism X have? b.) What percentage of cytosine does organism Y have? c.) Which organism will have the higher melting DNA (require a higher temperature to denature)?

A. 18.7% B. 20.1% C. organism X

Consider the following DNA: 5'-AGGCT-3'. If this were serving as the template strand for new polynucleotide polymerization, how would the new strand read? Choose one: A. 3'-TCCGA-5' B. 3'-AGGCT-5' C. 5'-TCCGA-3' D. 5'-AGGCT-3'

A. 3'-TCCGA-5'

A 20 bp duplex with __________ content at __________ will have the highest absorbance at 260 nm. A. 60 percent A-T; 50 degrees C B. 40 percent G-C; 50 degrees C and 50 mM NaCl C. 60 percent G-C; 50 degrees C and 50 mM NaCl D. 60 percent G-C; 50 degrees C

A. 60 percent A-T; 50 degrees C

DNA methylase enzymes transfer a methyl group to C-5 of a cytosine or to N-6 of an adenine within a DNA sequence recognized by the enzyme. What effect, if any, would this have on the establishment of the HindIII-DNA complex that is shown in this molecular structure? Choose one: A. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. B. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site. C. If the HindIII target DNA were methylated, then it would increase the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site. D. If the HindIII target DNA were methylated, then it would not alter the probability of binding between HindIII and DNA and would not alter the endonuclease activity at that methylated site. E. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would increase the endonuclease activity at that methylated site.

A. If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site.

Which conclusion is supported by the data in the figure? Choose one: A. Shorter-length nucleic acid has a lower melting temperature than that of longer-length DNA. B. Shorter-length nucleic acid cannot become completely denatured. C. Longer-length nucleic acid cannot become completely denatured. D. Longer-length nucleic acid has a lower melting temperature than that of shorter-length DNA.

A. Shorter-length nucleic acid has a lower melting temperature than that of longer-length DNA

Which of the following is expected for DNA that is exposed to increasingly elevated temperature? Choose one or more: A. The quantity of light absorbed at wavelength 260nm is expected to increase. B. The quantity of light absorbed at wavelength 260nm is expected to decrease. C. The quantity of light absorbed at wavelength 260nm is expected to remain constant. D. The sample is expected to behave more like DNA with intact base pairs. E. The sample is expected to behave more like DNA with disrupted base pairs.

A. The quantity of light absorbed at wavelength 260nm is expected to increase. E. The sample is expected to behave more like DNA with disrupted base pairs.

Cancer therapeutics are designed to impact the life of the replicative cell in some way. Some chemotherapy drugs target topoisomerase enzymes. Which of the following statements most accurately describes the effect of these types of anticancer drugs? A. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest. B. These drugs prevent the cell from producing plasma membrane lipids so that the cell cannot grow in size. C. These drugs decrease the ability of the cell to produce ribonucleotides, thereby preventing transcription. D. These drugs embed pores in the plasma membrane of cells so that cytoplasm leaks out and the cell apoptoses.

A. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest.

How much space along the longitudinal axis of DNA does the HindIII enzyme occupy when bound? Choose one: A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms B. approximately two major grooves and the two neighboring minor grooves, which in total is approximately 40 angstroms C. approximately three major grooves and the three neighboring minor grooves, which in total is approximately 20 angstroms D. approximately four major grooves and the four neighboring minor grooves, which in total is approximately 20 angstroms

A. approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms

A. gene microarray

Which of the following gene expression assays requires that the sequence of genes be known in advance? Choose one: A. gene microarray B. RNA-seq analysis C. both RNA-seq analysis and gene microarray D. neither RNA-seq analysis nor gene microarray

A. gene microarray

As DNA unwinds and denatures, absorbance is predicted to A. increase. B. vary unpredictably. C. decrease. D. remain the same.

A. increase.

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called A. operons. B. promoters. C. introns. D. enhancers. E. exons.

A. operons.

The excess sodium ions are most likely interacting with which chemical component of the nucleotides? Choose one: A. phosphate group B. nitrogenous base C. pentose sugar

A. phosphate group

the carbon nitrogen peptide bond is rigid. A.which of the following most likely describes part of an observed alpha helix B. which of the following would NOT likely occur in a beta sheet?

A. psi = -60degrees; psi=-47degrees, many ala residues B. psi=+60;psi=+60, many gly residues psi=-57;psi=-49, many ala residues psi=-51; psi=+153, many gly and pro residues.

The main activator molecule of the ATP synthesis and the electron transport system is

ADP

Within one of the homodimeric Fe protein components, shown in green, which ligand has a binding site within each part of the dimer? Choose one: A. ADP B. P cluster C. 4 Fe-4 S cluster D. FeMo cofactor

ADP

Which of the following molecules would activate phosphofructokinase 1 (PFK1)? NADH AMP ATP pyruvate

AMP

helix making, stabilizing

ARG+_______-GLU (salt bridge) pi-stacking

Which of the following statements are true?

ATCase is regulated by feedback inhibition

A high concentration of which molecule would inhibit citrate synthase in the citrate cycle?

ATP

To study the allosteric regulation of E. coli ribonucleotide reductase in a cell-free in vitro system, which of the following would be a good choice to add to the system? glucose ATP Ca2+ IP3

ATP

Which of the following molecules would inhibit the last reaction of glycolysis? ATP glucose AMP NAD+

ATP

20. Cyclic photophosphorylation produces __________, but does not produce __________.

ATP ; O2 or NADPH

What precursors are required for the breakdown of palmitate? 14 ATP and 14 NADH ATP and CoA acetyl-CoA NADH and FADH2

ATP and CoA

11. Among the Calvin cycle inputs, which ones are generated by the light reactions of photosynthesis?

ATP and NADPH

The Calvin cycle requires which species from the light reactions? ATP and NADPH reducing electrons CO2 and ATP NADH and FADH2

ATP and NADPH

Phosphorylation of serine residues is a common way to regulate the activity of proteins. The source of phosphate for phosphorylation is ATP. Here are the two reactions involved: phosphoserine + H20 <==> serine + Pi ΔG°' = -10.3 kJ/mol ATP + H2O <==> ADP + Pi ΔG°' = -30.5 kJ/mol Using the information in the reactions above, which of the following are correct?

ATP hydrolysis is exergonic

1. Which of the following steps used to convert solar energy to chemical energy does NOT involve the movement of electrons?

ATP synthesis by the chloroplast ATP synthase complex

ATP synthesis rates will decrease because of decrease of the proton-motive force. O2 consumption will decrease after the addition of carbon monoxide, because O2 will not be reduced by the ETS.

The citrate cycle is often called the metabolic engine in the cell. IN this analogy, what is considered the work, the fuel, and the exhaust?

ATP synthesis, acetyl CoA, CO2

What is the net reaction (1+2) shown below (???) and what is the delta G (???) for this net reaction?

ATP+Glutamate+NH4+ <-> Glutamine+ADP+Pi G=-16.3 kJ/mol

The step in solid-phase peptide synthesis that occurs at number 2 is

Activation of the Fmoc blocked residue

Associate each cellular condition or molecular state with its effect on the Calvin cycle.

Active Calvin Cycle NADP+ becomes limiting in the stroma. Ferredoxin continues to donate electrons to ferredoxin-thioredoxin reductase at night. Inhibited Calvin Cycle Chloroplast thioredoxin gene is unable to be expressed. Mutant version of ferredoxin-thioredoxin reductase irreversibly binds thioredoxin.

Below shows the cell survival pathway promoted by TNF-mc171-1.jpg. A complex is indicated with a question mark. What is this complex?

Active NFkB

Consider the pathway A → B → C → D → E. Reactions A → B, B → C, and D → E have a ΔG near equilibrium, while C → D has a ΔG << 0. Which of the following is true about this pathway if it were operating within a cell?

Adding more A to the system will increase the amount of B and C in the system.

Alanine

Ala, A, nonpolar, hyrdophobic

What reaction is occurring at step 4 of the rubisco reaction, as shown in the figure below?

Aldol cleavage

Which of the following enzymes from glycolysis does NOT have an equivalent enzyme involved in stage 2 of the Calvin cycle?

Aldolase

The sequencing of the human genome has been instrumental toward

All of these areas were enhanced by the sequencing of the human genome

Observe only the seven fatty acid ligands of serum albumin. Which of the following is correct for this specific example?

All seven of these ligands contain an unsaturated hydrocarbon chain.

Compare and contrast the arrangements of A-DNA, B-DNA, and Z-DNA.

All three forms have identical covalent bonds between the nucleotides. All three have antiparallel strands and exhibit Watson-Crick base pairing. A-DNA has the widest helix (23 A in diameter) with 11 base pairs per turn, whereas the Z form is the most narrow (18 A in diameter) with 12 base pairs per turn. B-DNA is 20 A in diameter with 10.5 base pairs per turn. Both A-DNA and B-DNA have right-handed helix structures, whereas Z-DNA has a left-handed helix resulting in a zigzag structure.

Which secondary structure elements are stabilized by hydrogen bonds?

Alpha helicesAntiparallel beta sheetsParallel beta sheets

Which two functional groups are involved in producing a peptide bond?

Amino and carboxyl

Which two functional groups are involved in producing a peptide bond? amino and thiol amino and carboxyl methyl and amino alcohol and amino

Amino and carboxyl

What two functional groups are found in producing a peptide bond?

Amino and carboxyl groups

Select the TWO true statements about amphipathic alpha helices from the statements below. For a membrane protein with a single membrane spanning alpha helix, this helix is often amphipathic. Amphipathic alpha helices are charged on one face and polar on the other. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. It is energetically favorable for an amphipathic alpha helix to be completely buried in the hydrophobic core of a protein. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. A polypeptide sequence with alternating polar and nonpolar residues (P-N-P-N-P-N etc) will form an amphipathic alpha helix. Amphipathic alpha helices are most often found transversing the plasma membrane as components of GPCRs.

Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein.

Select the THREE true statements about amphipathic alpha helices from the statements below. Amphipathic alpha helices are charged on one face and polar on the other. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. For a membrane protein with a single membrane spanning alpha helix, this helix is often amphipathic. An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. It is energetically favorable for an amphipathic alpha helix to be completely buried in the hydrophobic core of a protein. Amphipathic alpha helices are most often found transversing the plasma membrane as components of GPCRs. A polypeptide sequence with alternating polar and nonpolar residues (P-N-P-N-P-N etc) will form an amphipathic alpha helix.

Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face. An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein.

Again consider the pathway above. Under what conditions would adding more A to the system not lead to an increase in the flux of the pathway from A to E?

An allosteric inhibitor of the enzyme that catalyzes C → D is also present in the system. The enzyme that catalyzes C → D has already reached 100% of Vmax.

Describe the properties of an amphipathic alpha helix and identify numbered amino acids in a dodecamer polypeptide that contribute to the chemical properties of this secondary protein structure. Where are amphipathic alpha helices found in a globular cytosolic protein?

An amphipathic alpha helix has a hydrophobic face and a hydrophilic face owing to the arrangement of hydrophobic and hydrophilic side chains in the sequential amino acids. A dodecamer would have hydrophobic residues at positions 2, 3, 5, 6, 9, and hydrophilic residues at positions 1, 4, 7, 11, 12. Amphipathic alpha helices are found on the surface of globular cytosolic proteins

Select the THREE true statements about amphipathic alpha helices from the statements below.

An amphipathic alpha helix is stabilized by intrastrand hydrogen bonding between backbone amino and carbonyl groups. Amphipathic alpha helices are often found on the surface of a globular protein, packed against the rest of the protein. Amphipathic alpha helices are chemically polar on one face and nonpolar on the opposite face.

Which of the following would be an example of decreasing entropy?

An anabolic pathway

Evaluate which of the following statements is/are true about enzymes and the transition from reactants to products.

An enzyme does not change the energy of the reactants or product, nor does it change the equilibrium constant of a reaction. An enzyme lowers the activation energy of a reaction, which means the transition state is not as energetically unfavorable as it would be without the presence of an enzyme.

topoisomerase

An enzyme that catalyzes the cleavage of one or both DNA strands and relaxes positive supercoiled regions, allowing DNA to return to its relaxed state. (p. 103)

restriction endonuclease

An enzyme that cleaves DNA at specific sequences; isolated from bacteria that use restriction endonucleases to protect against invading bacteriophage. (p. 130)

An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG

Binding of the negatively charge allosteric effector 2,3-bisphosphoglycerate (2,3-BPG) stabilizes the T state of hemoglobin. A lysine residue in the central cavity of hemoglobin interacts with 2,3-BPG. In a hemoglobin variant, there is a substitution of this lysine by an asparagine. Relative to the wild-type hemoglobin, this variant would be expected to have. Choose the ONE most correct statement. An increased affinity for oxygen in the presence of 2,3-BPG, and a decreased affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG An equivalent affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG

An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG

Binding of the negatively charge allosteric effector 2,3-bisphosphoglycerate (2,3-BPG) stabilizes the T state of hemoglobin. A lysine residue in the central cavity of hemoglobin interacts with 2,3-BPG. In a hemoglobin variant, there is a substitution of this lysine by an asparagine. Relative to the wild-type hemoglobin, this variant would be expected to have. Choose the ONE most correct statement. An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG A decreased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG An increased affinity for oxygen in the presence of 2,3-BPG, and a decreased affinity in the absence of 2,3-BPG An equivalent affinity for oxygen in the presence of 2,3-BPG, and an increased affinity in the absence of 2,3-BPG

An increased affinity for oxygen in the presence of 2,3-BPG, and an equivalent affinity in the absence of 2,3-BPG

For the alanine titration curve shown below, which best describes point A?

An isoelectric point

nucleoside

An organic molecule consisting of a purine or pyrimidine base covalently linked to a five-membered sugar (ribose or deoxyribose). (p. 92)

Which of the following is true regarding apoenzymes and holoenzymes?

Apoenzymes do not have a non-amino, acid-based cofactor bound, whereas holoenzymes do.

Arginine

Arg R Polar Hydrophilic Positive basic pK = 12.5

What is the biochemical explanation for the observed toxic effects of arsenic contaminated well water in Bangladesh? There are TWO correct answers. Arsenic is converted to arsenite, which covalently modifies reduced lipoamide, thereby inhibiting activity of the pyruvate dehydrogenase complex and blocking conversion of pyruvate to acetyl-CoA. Cracked skin on the feet is caused by aresenic crystals deposited in the keratin granules of the lower extremities, and once they form, the only treatment is daily application of acai beri beri extract. TPP and arsenic form an inactive vitamin complex called B12 that scavenges acetyl-CoA from the citrate cycle causing low energy charge and eventual apoptosis. The aresenic contaminated well water caused inhibition of dihydrolipoyl transacetylase, which is an enzyme subunit required for metabolism of rice starch, the source of 70% of their daily caloric intake. Aresenite activates thiaminase in the small intestine, which decreases functional levels of thiamin required to produce TPP, resulting in dangerously low levels of vitamin D and riboflavin. Arsenite froms a bidentate adduct on oxidized dihydrolipoamide and this blocks conversion of pyruvate to oxaloacetate, thereby inhibiting flux through the citrate cycle. Two correct answers are not provided. Arsenic is an electron carrier that accepts electrons from thiamin pyrophosphate and thereby short circuits the dihydrolipoamide transacetylase reaction by donating electrons directly to FAD.

Arsenic is converted to arsenite, which covalently modifies reduced lipoamide, thereby inhibiting activity of the pyruvate dehydrogenase complex and blocking conversion of pyruvate to acetyl-CoA. the aresenic contaminated well water caused inhibition of dihydrolipoyl transacetylase, which is an enzyme subunit required for metabolism of rice starch, the source of 70% of their daily caloric intake.

Asparagine

Asn N polar hydrophilic uncharged/non-acidic

Aspartate

Asp D Polar Negatively charged Hydrophilic pK = 3.9

based on the table shown on the cover of the exam, which amino acids side chains in proteins carry a charge at pH 9 (positive or negative)?

Asp, Glu, Cys, Lys, Arg

The mutation that would lead to the most dramatic effect on Ca2+ transport is a mutation of

Asp351 in SERCA

Which of the THREE following statements about the charge on the pentapeptide AHDLV at pH 2, pH 7, and pH 10 are correct? Use the following table of pKa values to solve the problem. Chemical group: pKa terminal a-carboxyl: 3.1 sidechain carboxyl: 4.1 imidazole: 6.0 terminal a-amino: 8.0 thiol: 8.3 aromatic hydroxyl: 10.9 e-amino: 10.8 guanidino: 12.5 Possible Answers: At pH 7, the charge on the peptide is -2. At pH 2, the charge on the peptide is -1. At pH 7, the charge on the peptide is -1. At pH 10, the charge on the peptide is zero. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

At pH 7, the charge on the peptide is -1. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

Which of the THREE following statements about the charge on the pentapeptide AHDLV are correct? Use the following table of pKa values to solve the problem. At pH 5, the charge on the peptide is -1. At pH 7, the charge on the peptide is zero. At pH 7, the charge on the peptide is -2. At pH 7, the charge on the peptide is -1. At pH 10, the charge on the peptide is -2. At pH 2, the charge on the peptide is +2.

At pH 7, the charge on the peptide is -1. At pH 10, the charge on the peptide is -2. At pH 2, the charge on the peptide is +2.

Which of the THREE following statements about the charge on the pentapeptide AHDLV are correct? Use the following table of pKa values to solve the problem. Chemical group pKa terminal a-carboxyl 3.1 sidechain carboxyl 4.1 imidazole 6.0 terminal a-amino 8.0 thiol 8.3 aromatic hydroxyl 10.9 e-amino 10.8 guanidino 12.5

At pH 7, the charge on the peptide is -1. At pH 2, the charge on the peptide is +2. At pH 10, the charge on the peptide is -2.

A double helix that crosses itself in a right-handed twist is referred to as a a. positive supercoil. b. negative supercoil. c. topoisomer. d. linking number.

Below are the steps involved in cloning gene sequences using mRNA. Arrange the steps in the appropriate order. 1. The double-stranded cDNA is treated with a restriction endonuclease to generate compatible ends for annealing and ligation. 2. mRNA is isolated from the cell and converted back into double-stranded sequences using reverse transcriptase to generate complementary DNA. 3. The RNA-DNA hybrid is treated with a nuclease to cleave the RNA strand, producing RNA fragments. 4. Reverse transcriptase completes the single-stranded cDNA when it reaches the 5′ end of the mRNA transcript. 5. RNA fragments serve as primers for DNA synthesis of the second strand of cDNA using DNA polymerase. a. 4,2,1,5,3 b. 2,4,3,5,1 c. 2,3,5,4,1 d. 3,2,5,4,1

Calculate the pH of a solution containing 0.105 M HA and 0.146 M A-. The Ka for the weak acid is 1.8x10^-5 A) 7 B) 4.88 C) 9.11 D) 2.44 E) 4.74

DNA strands are considered to be antiparallel. This means the a. phosphodiester bonds run in the same direction. b. phosphodiester bonds run in different directions. c. base pairs form hydrogen bonds. d. phosphate backbone is on the outside of the helix.

During eukaryotic DNA condensation, nucleosomes are packed together to form a. histones. b. chromatin. c. chromosomes.

For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change? A. The EC would remain unchanged. B. The EC would increase. C. There is no way to predict how the EC would change. D. The EC would decrease.

Given the energy charge equation, if a biological system has an EC=0.8, what is true about the concentrations of ATP, ADP, and AMP in the system? A) the concentrations are all equal B) there is more ATP in the system than ADP or AMP C) There is more ADP in the system than ATP or AMP D) none of the above E) There is more AMP in the system than ATP and ADP

How are polar molecules like glucose transported across a membrane? A) polar molecules diffuse across the hydrophobic barrier B) There are proteins that allow the transportation of polar molecules across the membrane C) none of the above D) polar molecules cannot ever enter the cell E) there are holes in the membrane

How many base pairs per turn does B-DNA contain? a. 10.0 b. 10.5 c. 11.0 d. 12.0

Identify the phase of PCR amplification where the primer is annealed.

Identify the phase of PCR amplification where the primer is annealed. *SEE #71* a. A b. B c. C d. D

If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water? A. The protein would demonstrate no change in water binding. B. The protein would not bind water and would lose antifreeze properties. C. The protein would bind water more tightly. D. The protein would have increased affinity for the phosphate backbone of DNA.

Not all single nucleotide polymorphisms cause a phenotypic change because sometimes the changes occur in the a. coding region. b. noncoding region. c. promoter sequence. d. telomeres.

Of these three parameters regarding DNA twist, which is calculated by adding the other two parameters together? A. writhe (Wr) B. linking number (Lk) C. twist (Tw)

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called a. exons. b. operons. c. introns. d. promoters.

RNA-seq is considered to be complementary to gene expression microarrays because RBA-Seq A. probes mRNA, while gene expression microarrays probe DNA. B. is able to identify low-abundance, alternatively spliced transcripts. C. does not require the formation of cDNA. D. is based on a pre-determined set of DNA sequences.

Several histones can bind to one DNA molecule, forming a repeating unit called a a. ribozyme. b. nucleosome. c. topoisomerase. d. nucleoside.

The DNA double helix is considered to be a __________ structure. a. primary b. secondary c. tertiary d. quaternary

The amino acid with the neutral side chain at neutral pH is A) glutamate B) asparagine C) aspartate D) serine E) arginine

The mixing and matching of novel genes in eukaryotic cells occurs through a. operons. b. exon shuffling. c. promoter regions. d. untranslated regions.

Type I topoisomerase activity results in a region of __________ DNA. A) spliced B) none of the above C) unrepaired D) semiconservative E) negatively supercoiled DNA

Upon reception of a biochemical signal by a eukaryotic cell, which of the following would change first when the genetic expression pattern of the cell changes? A. The proteome would change first. B. The transcriptome would change first. C. The proteome and transcriptome would change simultaneously. D. The proteome and transcriptome would not change; they are not parts of genetic expression.

What is a current hypothesis that explains the infectious nature of prion diseases? A) The small molecule denaturants found in infected cells are passed on to healthy cells B) the presence of an improperly folded prion protein promotes the misfolding of normal prion proteins C) unfavorable environmental factors negatively influence healthy cells D) DNA encodes prion mutant proteins E) the virus responsible for prion diseases is transmissible

What is the melting temperature from the DNA absorbance shown in the figure below? *see #16* a. 80°C b. 85°C c. 90°C d. 95°C

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? A) fluorescent labeling B) gel electrophoresis C) polymerase chain reaction D) blue-white screening E) antibiotic resistance

When a protein enzyme folds in an aqueous solution, which of the following is correct? A. Water is always excluded from the active site in the interior of the protein. B. Non-polar amino acids are found in the interior of the protein. C. Polar amino acids are found in the interior of the protein. D. A mixture of polar and non-polar amino acids is found in the interior of the protein.

Which enzyme is used to cleave DNA at specific sequences during the production of recombinant DNA? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase

Which of the following binds to DNA using a specific sequence? a. histones b. Lac repressor protein c. double-stranded binding proteins d. single-stranded binding proteins

Which of the following is an intermediate in the conversion of AMP to uric acid but NOT an intermediate in the conversion of GMP to uric acid? A B C D

Which of the following is correct about biological membranes? A. Molecules freely pass through the membrane. B. Biological membranes are made up of a lipid monolayer. C. Phospholipid head groups are directed toward the aqueous environment. D. Phospholipid tails are directed toward the aqueous environment.

Which of the following is the correct solar energy reaction that take place on the sun? A) 4He-->^4He B) 4H-->^4He

Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur? A. Energy is absorbed from the surroundings. B. A favorable enthalpy change overcomes entropic penalty. C. It is not possible. D. The unfavorable reaction is coupled to a favorable one.

B and D

Biological membranes partition aqueous environments to permit life processes to maintain regions of low entropy within the high entropy state of the surrounding environment. What characteristic do molecules found in biological membranes have that allows this capability? Choose one: A. highly ordered and forming a physically rigid barrier B. amphipathic C. strictly hydrophobic D. strictly hydrophilic

B- amphipathic

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? Choose one or more: A. elevated excretion of HCO3- B. more CO2 exhaled (hyperventilation) C. no change in CO2 exhalation D. diminished HCO3- excretion E. less CO2 exhaled (decreased breathing rate) F. no change in HCO3- excretion

B- more CO2 exhaled (hyperventilation) D- diminished HCO3- excretion

Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf?Choose one: A. CO2 B. osmotic pressure C. air pressure D. dew point

B- osmotic pressure

Which of the following is correct about biological membranes?Choose one: A. Phospholipid tails are directed toward the aqueous environment. B. Phospholipid head groups are directed toward the aqueous environment. C. Biological membranes are made up of a lipid monolayer. D. Molecules freely pass through the membrane.

B- phospholipid head groups are directed toward the aqueous environment

A reaction is always spontaneous if Choose one: A. entropy is increased. B. the change in free energy, ΔG, is negative. C. the change in free energy, ΔG, is positive. D. the change in enthalpy is zero. E. enthalpy is reduced.

B- the change in free energy is negative

Which of the following are properties of water? Choose one or more: A. Water is miscible with oil. B. Water is liquid over a wide range of temperatures. C. Water is polar and an excellent solvent because of its hydrogen-bonding properties. D. Water freezes more readily when ionic solutes are dissolved in it. E. Water is a strong acid at high temperatures. F. Water is less dense as a solid than as a liquid.

B- water is liquid over a wide range of temperatures C- water is polar and an excellent solvent because of its hydrogen-bonding properties F- water is less dense as a solid than as a liquid

30. Which chromophore appears orange and absorbs in the blue range of the visible spectrum?

B-carotene

Which of the following types of chromatin is usually associated with the centromere of a chromosome? Choose one: A. euchromatin B. heterochromatin

B-heterochromatin

What is the concentration of [OH-] in a solution of 0.025 M HCl? Choose one: A. 4.1 × 10-13 M B. 4.0 × 10-13 M C. 1.0 × 10-14 M D. 2.5 × 10-2 M

B. 4.0 × 10-13 M

Choose the one best statement that completes this sentence: "Two amphipathic α helices in a dilute aqueous solution are likely to:" A. form a coiled coil structure with the polar amino acid side chains interacting with each other down the middle. B. form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle. C. repel each other and remain as individual helical molecules. D. rearrange into β sheets in order to stack against each other to bury hydrophobic side chains.

B. form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle.

RNA-seq is considered to be complementary to gene expression microarrays because RBA-Seq Choose one: A. does not require the formation of cDNA. B. is able to identify low-abundance, alternatively spliced transcripts. C. probes mRNA, while gene expression microarrays probe DNA. D. is based on a pre-determined set of DNA sequences.

B. is able to identify low-abundance, alternatively spliced transcripts.

Which of the following pairs contain terms that would be considered synonyms of one another regarding DNA integrity? A. denatured : annealed B. renatured : annealed C. annealed : melted D. melted : denatured E. denatured : renatured

B. renatured : annealed D. melted : denatured

In all of the aminotransferases that have been characterized, the catalytic mechanism involves a two-stage reaction in which the α amino group of the amino acid is first transferred to an enzyme-linked pyridoxal phosphate (PLP) group. Pyridoxal phosphate is a coenzyme derivative of vitamin ___

The cross linked nature of the acrylamide media in SDS-PAGE can limit migration through the polymer matrix. Based on the figure to the right put the SDS-PAGE gels in the correct order of lowest to highest acrylamide concentration using A,B, and C

B<C<A

How did the polymerase chain reaction (PCR) revolutionize DNA detection methodologies? Choose the TWO most correct statements below.

Because it is so sequence specific and easy to use, multiple confirmatory data points can be collected, and thereby rule out DNA matches by chance alone. PCR increases the sensitivity of DNA detection in a given sample by up to 1 million fold using a site-specific in vitro DNA synthesis reaction.

Why do inhibitors of Topoisomerase II cause cancer cell death more than neuronal cell death?

Because they inhibit DNA replication; since cancer cells divide frequently, they are preferentially killed

Why do inhibitors of Topoisomerase II cause cancer cell death more than neuronal cell death

Because they inhibit DNA replication;; since cancer cells divide frequently, they are preferentially killed

The effect of pH on O2 binding in the tissues is significant, whereas the effect of pH on O2 binding in the lungs is minimal (very little change in O2 binding as a function of pH in the lungs). Explain this observation Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect. Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the R state as described by the Bohr effect. Because tissues have higher CO2 concentrations than the lungs, which increases the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect. Because tissues have higher O2 concentrations than the lungs, which increases the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect.

Because tissues have higher CO2 concentrations than the lungs, which lowers the pH in the tissues and shifts the equilibrium to the T state as described by the Bohr effect.

Which of the following is a photosynthetic light harvesting pigment? FeS cluster NADPH plastoquinone Beta-carotene

Beta-carotene

Muscle glycogen phosphorylase is regulated by both allosteric effectors, such as AMP and ATP, and by hormonal signaling. Allosteric effectors bind to the phosphorylated and unphosphorylated forms of the enzyme and shift the equilibrium between the inactive T conformation and the active R conformation. In contrast, hormonal regulation involves activation of kinase and phosphatase enzymes, which modulate the phosphorylation status of glycogen phosphorylase. Which TWO statement(s) below best explain the metabolic logic of this dual regulatory mechanism?

Both forms of control are important because they work together to ensure maximum interconversion of glucose and glycogen so that liver cells can maintain safe blood glucose levels at all times. Allosteric regulation by AMP and ATP provides a way to quickly shift the activity of muscle glycogen phosphorylase between the active and inactive states before hormonal signaling is fully stimulated.

Compare the structure of an aldose to a ketose.

Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

Compare the structure of an aldose to a ketose. Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule. Both have a carbon backbone where ketose has a ketone group at the end of the molecule, and aldose also has an aldehyde group at the end of the molecule. Ketose has a carbon backbone with a ketone group at the end of the molecule, whereas aldose has an aldehyde group at the end of the molecule. Ketose has a carbon backbone with an aldehyde group at the end of the molecule, whereas aldose has a ketone group at the end of the molecule.

Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

If DNA is not cleaved, the total linking number will remain the same, even though the twist and writhe can change. Using one or two complete sentences, explain why the total linking number does not change

Both the twist and the writhe can change by stretching or bending. However, the linking number remains constant because of the relationship Lk = Tw + Wr. If the twist changes, the writhe will change in such a fashion that the linking number remains constant. Because these manipulations do not change the number of helical turns, the linking number remains constant.

Compare and contrast the steps used to induce a positive supercoil and a negative supercoil.

Breaking the phosphodiester bond between two adjacent bases and cleaving the DNA is the first step in generating positive or negative supercoils. If turns are removed by unwinding the cut strand before resealing, negative supercoils are formed. If turns are added before resealing the cut strand, positive supercoils are formed.

In plasmid conjugation, DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

In the eukaryotic cell, the NONcoding sequences on a gene are referred to as a. exons. b. operons. c. introns.

In the second temperature phase of PCR, why does the temperature vary from 55°C to 65°C? a. different ionic strengths b. different primer concentrations c. G-C content d. different amount of hydrogen bonds

Predict how type I topoisomerases change the supercoil region. a. Lk=2 b. Lk=1 c. Lk=-1 d. Lk=-2

RNA only contains which of the following bases? a. thymine b. adenine c. uracil d. guanine

Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution A) had a very high concentration of solvent B) none of these answers are correct C) had no solutes D) had a very high concentration of solutes E) was at equilibrium

The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine? a. 15% b. 30% c. 35% d. 70%

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will a. remain the same. b. decrease. c. increase. d. vary unpredictably.

The figure below shows part of the primary structure of DNA. Identify the nucleoside.

The figure below shows part of the primary structure of DNA. Identify the nucleoside. *see #1* a. A b. B c. C d. D

The most common purpose for cloning a gene sequence using mRNA is to a. disrupt antibiotic resistance. b. determine homologous genomic sequences. c. generate a library of actively transcribed genes. d. disrupt the lacZ gene, resulting in blue-white screening.

The process of condensation reduced the size of DNA by a. 100-fold. b. 1,000-fold. c. 10,000-fold. d. 100,000-fold.

The titration curve for the amino acid glutamate is shown above. Refer to this figure to answer the following question. The form of glutamate shown above predominates at what point on the titration curve? D C B F E A

The β-galactosidase gene that is inserted into plasmid cloning vectors is used to a. cleave the DNA in a sequence-specific fashion. b. disrupt the antibiotic-resistance gene, making it nonfunctional. c. determine if the cloning has been successful. d. protect the bacteria from bacteriophage infection.

This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences. A) viral transduction B) polymerase chain reaction C) gene expression microarrays D) plasmid cloning E) RNA seq

Type I topoisomerase activity results in a region of __________ DNA. a. semiconservative b. spliced c. relaxed d. unrepaired

Type II topoisomerase enzymes are important in replication and transcription because they a. prevent autocleavage. b. prevent DNA cleavage. c. relieve the positive supercoiling. d. stabilize the cleaved complex.

When DNA is transcribed into RNA, the __________ strand has the same base sequences as the RNA transcript. A) antiparallel B) parallel C) coding D) none of the above E) template

When DNA is transcribed into RNA, the __________ strand has the same base sequences as the RNA transcript. a. antiparallel b. parallel c. coding d. template

When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase

Which form(s) of DNA exhibit(s) a zigzag arrangement? a. A-DNA b. B-DNA c. Z-DNA d. A-DNA and B-DNA

Which method of analyzing RNA transcripts is considered to be an unbiased approach because it does not use a predetermined collection of complementary DNA sequence? a. plasmid cloning b. viral transduction c. RNA-seq d. gene-expression microarrays

Which protein is responsible for the proper separation of the chromosomes during cell division? a. telomeres b. centromeres c. kinetochores d. sister chromatids

Which two functional groups are involved in producing a peptide bond? A) none of these answers are correct B) alcohol and amino C) amino and carboxyl D) amino and thiol E) methyl and amino

C (look this up)

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? A. elevated excretion of HCO3- B. less CO2 exhaled (decreased breathing rate) C. more CO2 exhaled (hyperventilation) D. no change in CO2 exhalation E. diminished HCO3- excretion F. no change in HCO3- excretion

C and E

What responses are observed in a person experiencing acidosis, a condition defined by the pH of the blood falling below 7.4? A. no change in CO2 exhalation B. no change in HCO3- excretion C. more CO2 exhaled (hyperventilation) D. less CO2 exhaled (decreased breathing rate) E. elevated excretion of HCO3- F. diminished HCO3- excretion

C and F

Place the following steps in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins

C, A, D, B

Consider five proteins with the properties shown in the table above and answer the following four questions. Record your answers and choose the set of correct answers for questions a --> d. Note that some proteins may be used more than once and others may not be used at all. a) Which protein would elute last from a gel filtration chromatography column under non-denaturing conditions? b) Which protein would migrate the slowest in an SDS-PAGE gel? c) Which protein would elute last from a (-) charged cation exchange column in buffer at pH 4.0? d) Which protein would elute first from a (+) charged anion exchange column in buffer at pH 4.0?

C, E, A, A

If a sample of double-stranded DNA is determined to be 20% guanine, what percent adenine is the sample? Choose one: A. 10% B. 20% C. 30% D. 40% E. 50%

C- 30%

From the following list, which common substance that you encounter in your daily life has molecular properties similar to the molecules found in biological membranes? Choose one: A. water B. lemon juice C. detergent D. gasoline

C- detergent

Which of the following differentiates the biochemical standard state from the standard state when discussing standard free energy changes?Choose one: A. Constant pressure of 1 atm B. Temperature of 298 K C. pH of 7 D. 1 M concentrations for all reactants and products

C- pH of 7

In the elongation of glycogen, activated glucose units are attached to which hydroxyl of the terminal residue of the growing glycogen chain? C-1 C-3 C-4 C-6

C-4

What distance does proton A appear to travel through the water wire to reach the position marked F? Choose one: A. 10 fm B. 100 pm C. 1 nm D. 1 pm E. 1 µM

C. 1nm

Proton hopping allows for the rapid apparent movement of protons (H+) through aqueous solution. From first to last in the figure above, what is the correct chronological order of proton hopping events (B-E) that form the "water wire" between proton A and proton F? Choose one: A. E → D → C → B B. B → C → D → E C. C → E → B → D D. D → E → B → C

C. C,E,B,D

Which of the following steps is performed when preparing to do both an RNA-seq analysis and a gene microarray? A. Convert RNA to complementary DNA called cDNA. B. Generate fluorescently labeled RNA fragments. C. Isolate mRNA from whole cell lysate. D. Create high-throughput DNA sequencing.

C. Isolate mRNA from whole cell lysate.

Cancer therapeutics are designed to impact the life of the replicative cell in some way. Some chemotherapy drugs target topoisomerase enzymes. Which of the following statements most accurately describes the effect of these types of anticancer drugs? Choose one: A. These drugs prevent the cell from producing plasma membrane lipids so that the cell cannot grow in size. B. These drugs embed pores in the plasma membrane of cells so that cytoplasm leaks out and the cell apoptoses. C. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest. D. These drugs decrease the ability of the cell to produce ribonucleotides, thereby preventing transcription.

C. These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest.

If the same experiment were performed again for the 60 bp DNA, but this time in the presence of 1.5 M NaCl, in what direction would the new curve be positioned compared to the 60 bp DNA that is already in place in this figure? Choose one: A. directly on top of the current curve B. to the left of the current curve C. to the right of the current curve

C. to the right of the current curve

19. The __________ pathway is used by plants that thrive in high temperate conditions, such as sugarcane.

C4 The C4 pathway is found in tropical plants, such as sugarcane, and relies on two different cell types to prevent atmospheric O2 from binding rubisco. The CAM pathway is used by desert succulents, such as cacti, to capture CO2 at night to again prevent atmospheric oxygen from binding rubisco.

27. C4 vs CAM plants

C4: - Malate transferred to bundle sheath cells - Use spatial separation of CO2 fixation and rubisco activity to decrease photorespiration rates - Stomata open during the day. - Sugarcane is an example. CAM: - Malate stored in vacuoles - Use temporal separation of CO2 fixation and rubisco activity to decrease photorespiration rates - Saguaro cactus is an example. - Stomata open only at night

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand

C; the curve furthest to the right

17. What is a major difference between the mechanisms used by C4 and CAM plants to minimize photorespiration and maximize fixation of CO2 by rubisco?

CAM plants allow CO2 to enter the mesophyll cells only at night. The CO2 is stored as malate and then malate is decarboxylated during the day. The CO2 then enters the Calvin cycle. C4 plants capture CO2 in mesophyll cells, convert the CO2 to malate, and transfer the malate to neighboring bundle sheath cells, where the Calvin cycle operates on the CO2 derived from decarboxylated malate.

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

CCNC

What side products of pyruvate are being converted into alcohol and carbon dioxide by yeast?

CO2 and NAD+

Which of the following is NOT a passive transporter protein?

Ca2+-ATPase transporter protein

10. Identify the inputs and outputs of the Calvin cycle.

Calvin Cycle Inputs: CO2, ATP, NADPH Outputs: NADP+, ADP + Pi, Triose phosphates

Which THREE of the following biochemical relationships are correct statements illustrating the hierarchical organization of molecular life?

Carbon, hydrogen, and oxygen are the most abundant elements in biomolecules.Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems.Insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients.

Which key protein in the TNF receptor pathway is shown int he protein structure below?

Caspase 3

Which separatioin technique exploits the density differences of biomoelcules and organelles?

Centrifugation using centrifuge tubes in a rotor placed in a centrifuge

In the closely packed interior of the tertiary structure of an enzyme, an alanine residue was changed by mutation to a valine, leading to a loss of enzyme activity, although that residue was not directly involved in the catalytic function of the enzyme. However, activity was partially regained when an additional mutation at a different position in the primary structure changed an isoleucine residue to a glycine. Based on the structure of the amino acid side chains of alanine, valine, isoleucine, and glycine, explain how the first mutation Ala→Val likely caused a loss of activity, and the second mutation in another region of the protein, Ile→Gly, resulted in a partial recovery of enzyme activity.

Changing an Ala to a Val would introduce a bulkier side chain, taking up more volume in the protein interior; the resulting structural adjustments in the tertiary structure must be serious enough to cause the enzyme to lose activity. The replacement of an Ile residue with a Gly allows a tertiary structure close enough to the original structure for partial enzyme activity.

9. Photons first enter the Z scheme via which molecule?

Chlorophyll P680

22. Which of the following cellular structures is NOT involved in the glyoxylate cycle?

Chloroplast

Molecular O2 competes with CO2 for the active site of rubisco. When this happens, one of the reaction products is of little metabolic use to the plant. That product is then metabolized by the glycolate pathway, which uses enzymes located in three cellular compartments. Sort the glycolate pathway reactions into their proper cellular compartment.

Chloroplast Oxygenation of RuBP to form 2-phosphoglycolate Transfer of a phosphate group from ATP to glycerate to form 3-phosphoglycerate Peroxisome Conversion of serine to glycerate Transamination of glyoxylate to form glycine Oxidation of glycolate to glyoxylate and release of hydrogen peroxide Mitochondrion Deamination and decarboxylation of glycine to form serine

B. Genes in the A group are initially expressed at the same level as the control genes, but have increased expression later in the time course. C. Genes in the D group are initially expressed at the same level as the control genes, but have decreased expression later in the time course. H. Genes in the B and C groups are differentially expressed at about the same time, but the pattern of expression is reciprocal.

Choose the THREE most correct statements regarding interpretation of the gene expression microarray data shown above. The color code is represented by the following using a reference gene as the control; RED means higher level of gene expression, GREEN means lower level of gene expression, and YELLOW would mean that the expression is unchanged. A. Genes in the A, B, C, and D groups are all on the same chromosome and show a differential pattern of expression over time because of differences in the location of each gene relative to the centromere. B. Genes in the A group are initially expressed at the same level as the control genes, but have increased expression later in the time course. C. Genes in the D group are initially expressed at the same level as the control genes, but have decreased expression later in the time course. D. Genes in the B group are the only genes that display differential gene expression as a function of time, the other gene groups show differential gene expression as a function of the evolutionary tree. E. Genes in the D group are initially expressed at the same level as the control genes, but have increased expression later in the time course. F. Genes in the A and D groups are differentially expressed at the same level as the control genes during the early time course, but have equivalent expression later in the time course. G. Genes in the C group are coordinately controlled and display a so-called down-up-down pattern similar to insulin regulation of glucokinase gene expression in pancreatic cells. H. Genes in the B and C groups are differentially expressed at about the same time, but the pattern of expression is reciprocal.

During eukaryotic DNA condensation, nucleosomes are packed together to form genes. histones. genomes. chromatin. chromosomes.

Chromatin

During eukaryotic DNA condensation, nucleosomes are packed together to form Question options: A. genes. B. genomes. C. histones. D. chromatin. E. chromosomes.

Chromatin

Which metabolite is an allosteric activator of the enzyme acetyl-CoA carboxylase? A. Glucose B. Glycerol-3-phosphate C. Acetyl-CoA D. Citrate E. NADH

Citrate

Which enzyme requires acetyl COA

Citrate synthase

Five coenzymes are needed for the pyruvate dehydrogenase reaction, of which three are covalently linked to proteins int he PDH complex. Name the two coenzymes that are diffusible within the matrix.

CoA and NAD+

Identify the correct order of electron transfers in the electron transport system starting with NADH. Answer are shown to the right.

Complex I->Ubiquionone->Complex III->Complex IV

How would someone that has a G6P dehydrogenase deficiency attempt to mitigate the symptoms of the genetic disease?

Consume more five carbon-containing foods.

For the cAMP-mediated pathway, identify the following components: Second messenger produced by Second messenger Kinase Result 1. cAMP 2. Adenylate cyclase 3. Protein kinase A (PKA) 4. Glucose mobilization 5. diacylglycerol (DAG) 6. phospholipase C (PLC) 7. protein kinase C (PKC) 8. Glucose storage (as glycogen)

Correct Response __2__ Second messenger produced by Correct Response __1__ Second messenger Correct Response __3__ Kinase Correct Response __4__ Result

Why is less ATP obtained from the average carbon in a sugar molecule than from a carbon in a fat molecule?

Correct answer is not given. Find the right answer!

Which of the following interactions it NOT likely to be found between the lac repressor protein and its DNA binding partner? Choose one: A. Ionic interactions B. Covalent linkages C. Hydrogen bonding D. van der Waals interactions

Covalent Linkages The interactions between proteins and DNA are dynamic and rely on weak interactions, including hydrogen bonding, ionic interactions, and van der Waals interactions. Covalent linkages are stronger and would prevent release of the binding partners, which could lead to inactive proteins and could inactivate genes. A combination of these weak interactions leads to the specific interaction between a DNA sequence and a protein, such as that between the lac repressor and its DNA binding site.

The importance of stable free radicals in the mechanism of E. coli ribonucleotide reductase was identified in the early 1970s. The existence of stable radicals in a protein had not been previously observed. Which of the following amino acids can exist as a stable radical in ribonucleotide reductase? Cys His Ser Glu

Cys

Cysteine

Cys C No charge/non-acidic Nonpolar hydrophilic

15. Which of the following is responsible for transporting protons across the thylakoid membrane?

Cytochrome b6f

Which of the following enzymes is NOT necessary for producing the monounsaturated oleoyl-CoA? Choose one: A. Stearoyl-CoA 9-desaturase B. Cytochrome b5 reductase C. Cytochrome b5 D. Cytochrome c

Cytochrome c

A common database tool used to determine homologous genomic sequences is called a. the National Center for Biotechnology Information. b. the National Human Genome Research Institute. c. Computational Analysis. d. Basic Local Alignment Search Tool.

A polypeptide has a high pI value. Which amino acids might comprise it? A) a mixture of aspartate and arginine residues B) aspartate and glutamate residues C) none of the above D) arginine and lysine residues E) the large nonpolar amino acids

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located? mc031-1.jpg

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located? A C D B

Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA?

Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA? C A B none of these answers are correct. D

Energy conversion in living systems is required for what three types of work? A) none of the above B) osmotic work, photosynthetic work, mechanical work C) kinetic work, chemical work, mechanical work D) osmotic work, chemical work, mechanical work E) osmotic work, chemical work, potential work

Fatty acids are amphipathic, meaning that within the molecular structure, A. both ends repel from water; they are both hydrophobic. B. both ends interact with water; they are both hydrophilic. C. one end is negatively charged and the other end is positively charged. D. one end is polar and the other end is nonpolar.

How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment? A) semipermeable cell walls B) photosynthesis C) flexible cells walls D) none of these answers are correct E) they lack cell walls

How many possible unique triplet codons could there be in a genome? A) 72 B) 3 C) 36 D) none of the above E) 20

Identify the kinetochore in the following figure. *SEE #41* a. A b. B c. C d. D

In a single RNA transcript, polycistronic prokaryotic genes encode __________ protein(s). a. one b. two c. three d. multiple

In plasmid transformation, DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

In the production of recombinant DNA, which enzyme links matching cohesive ends using covalent interactions? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase

Individual nucleotide changes to the genome cause a polymorphism called a. short tandem repeats. b. variable number tandem repeats. c. long tandem repeats. d. single nucleotide polymorphism.

Limonene is a nonpolar molecule. The water molecules around it forms A) none of the above B) covalent bonds with limonene and entropy increases C) ionic bonds with itself and the entropy decreases D) hydrogen bonds with itself and entropy decreases E) hydrogen bonds with limonene and the entropy increases

Predict how type II topoisomerases change the supercoil region. a. Lk=2 b. Lk=1 c. Lk=-1 d. Lk=-2

Predict the complementary strand of the following DNA sequence: 5′-ATCTGAATCT-3′ a. 5′-TCTAAGTCTA-3′ b. 5′-TAGACTTAGA-3′ c. 5′-ATCTGAATCT-3′ d. 5′-AGATTCAGAT-3′

The figure below shows part of the primary structure of DNA. Identify the nucleotide. *see #2* a. A b. B c. C d. D

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first? Peptide Molecular Weight (g/mol) Charge A 360 -2 B 1080 -1 C 1800 0 D 1440 +1

The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first? Peptide, Molecular Weight (g/mol), Charge A, 360, -2 B, 1080, -1 C, 1800, 0 D, 1440, +1

This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences. a. plasmid cloning b. viral transduction c. RNA-seq d. gene-expression microarrays

Two identical copies of replicated DNA that remain attached until cell division are referred to as a. telomeres. b. centromeres. c. kinetochores. d. sister chromatids.

What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group, and 10.5 for the side chain amino group? A. 6.3 B. 5.9 C. 7.0 D. 10.1

What mediates the binding of histone proteins to DNA? A) hydrophilic interactions B) hydrophobic interactions C) London dispersion forces D) ionic attractions E) none of the above

When DNA is transcribed into RNA, the __________ strand has the complementary sequence to the transcribed RNA. a. antiparallel b. parallel c. coding d. template

When DNA molecules from multiple sources have been connected in the laboratory, the result is referred to as a. promoters. b. cloning vectors. c. cloning sites. d. recombinant DNA.

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase

When a protein enzyme folds in an aqueous solution, which of the following is correct? A. Water is always excluded from the active site in the interior of the protein. B. A mixture of polar and non-polar amino acids is found in the interior of the protein. C. Polar amino acids are found in the interior of the protein. D. Non-polar amino acids are found in the interior of the protein.

Which form(s) of DNA exhibit(s) a right-handed helical structure? a. A-DNA b. B-DNA c. Z-DNA d. A-DNA and B-DNA

Which of the following expresses the relationship among the linking number, twist, and writhe? a. Tw=Lk+Wr b. Lk=Tw−Wr c. Lk=Wr−Tw d. Lk=Tw+Wr

Which of the following is correct about biological membranes? A. Phospholipid tails are directed toward the aqueous environment. B. Molecules freely pass through the membrane. C. Biological membranes are made up of a lipid monolayer. D. Phospholipid head groups are directed toward the aqueous environment.

D 1440 +1

The Sanger method of DNA sequencing requires which of the following to be in the reaction tube? Choose one: A. template DNA B. deoxyribonucleotides C. dideoxyribonucleotides D. A, B, and C are correct. E. Only A and B are correct. F. Only A and C are correct.

D -- A, B, and C are correct

Which of the following pairs contain terms that would be considered synonyms of one another regarding DNA integrity? A. annealed : melted B. denatured : annealed C. denatured : renatured D. melted : denatured E. renatured : annealed

D and E

The genetic anomaly that leads to Hutchinson-Gilford Progeria Syndrome (HGPS) causes Choose one: A. an elongated version of a certain nuclear protein to be synthesized by the cell. B. too much of a certain nuclear protein to be synthesized by the cell. C. too little of a certain nuclear protein to be synthesized by the cell. D. a shortened version of a certain nuclear protein to be synthesized by the cell.

D- a shortened version of a certain nuclear protein to be synthesized by the cell

The genetic anomaly that leads to HGPS is a cytosine Choose one: A. amination. B. carboxylation. C. decarboxylation. D. deamination.

D- deamination

Placed in a hypertonic solution, a living cell will Choose one: A. absorb water and get larger. B. remain unchanged. C. decrease the pH of the cytoplasm to stop water movement. D. shrink as water leaves the cell.

D- shrink as water leaves the cell

What is the isoelectric point (pI) of lysine, which has pKa values of 2.1 for the α-carboxyl group, 9.7 for the α-amino group, and 10.5 for the side chain amino group? A. 6.3 B. 5.9 C. 7.0 D. 10.1

D. 10.1

Predict the complementary strand of the following DNA sequence: 5'-ATCTGAATCT-3' A. 5'-ATCTGAATCT-3' B. 5'-TCTAAGTCTA-3' C. 5'-TAGACTTAGA-3' D. 5'-AGATTCAGAT-3'

D. 5'-AGATTCAGAT-3'

Calculate the linking number for a B-DNA strand that contains 735 total base pairs A. 67 B. 61 C. 50 D. 70

D. 70

Identify the products when SmaI cleaves the following DNA sequence: 5' - CCCGGG GGGCCC - 5' A. GGG-3' 5'-CCC CCC-3' 5'-GGG B. CC-5'. 3'-GG GG-5'. 3'-CC C. GG-3'. 5'-CC CC-3'. 5'-GG D. CCC-3'. 5'-GGG GGG-5'. 3'-CCC

D. CCC-3'. 5'-GGG GGG-5'. 3'-CCC

Which of the following steps is performed when preparing to do both an RNA-seq analysis and a gene microarray? Choose one: A. Generate fluorescently labeled RNA fragments. B. Convert RNA to complementary DNA called cDNA. C. Create high-throughput DNA sequencing. D. Isolate mRNA from whole cell lysate.

D. Isolate mRNA from whole cell lysate.

RNA-seq is considered to be complementary to gene expression microarrays because RBA-Seq A. probes mRNA, while gene expression microarrays probe DNA. B. does not require the formation of cDNA. C. is based on a pre-determined set of DNA sequences. D. is able to identify low-abundance, alternatively spliced transcripts.

D. is able to identify low-abundance, alternatively spliced transcripts.

What coenzyme shown at the right is required for the glycogen phosphorylase reaction? A. lipoamide B. nicotinamide dinucleotide C. thiamin pyrophosphate D. pyridoxal phosphate. E. dihydroxyacetone phosphate

D. pyridoxal phosphate.

Type II topoisomerase enzymes are important in replication and transcription because they A. prevent DNA cleavage B. prevent autocleavage C. stabilize the cleaved complex D. relieve the positive supercoiling

D. relieve the positive supercoiling

Which of the following biochemical reactions are endergonic?Choose one or more: A.ATP ⇒ ADP + Pi ; Δ𝐺∘ΔG∘ = −30.5 kJ/mol B.Acetyl-CoA + Oxaloacetate + H2O ⇒ Citrate + CoASH + H+ ; Δ𝐺∘ΔG∘ = -32.2 kJ/mol C.Glutamate + NH4+ + ATP ⇒ Glutamine + ADP + Pi ; Δ𝐺∘ΔG∘ = −16.3 kJ/mol D.L-Malate + NAD+ ⇒ Oxaloacetate + NADH + H+ ; Δ𝐺∘ΔG∘ = +29.7 kJ/mol E.Glutamate + NH4+ ⇒ Glutamine; Δ𝐺∘ΔG∘ = +14.2 kJ/mol

D.L-Malate + NAD+ ⇒ Oxaloacetate + NADH + H+ ; Δ𝐺∘ΔG∘ = +29.7 kJ/mol E.Glutamate + NH4+ ⇒ Glutamine; Δ𝐺∘ΔG∘ = +14.2 kJ/mol

Place the following steps of the apoptotic pathway in their proper order. A. CASP3 cleavage of cellular proteins B. Cleavage of procaspase 8 C. Cleavage of procaspase 3 D. Assembly of DD and DED protein complexes

DBCA

Succinate dehydrogenase is the citrate cycle enzyme that catalyzes the conversion of succinate into fumarate, and in the process converts FAD to FADH2. Use the standard reduction potentials given below for the reduction reactions to calculate the standard free energy change for the reaction. (Note that the value for FAD given here estimates the reduction potential for FAD when bound to succinate dehydrogenase.) FAD + 2H+ + 2e- ---> FADH2 Eo' = 0.035 V Fumarate + 2H+ + 2e- ---> Succinate Eo' = 0.031 V DGo' = -0.77 kJ/mol DGo' = 12.7 kJ/mol DGo' = 0.77 kJ/mol DGo' = 0.38 kJ/mol DGo' = -12.7 kJ/mol DGo' = -0.38 kJ/mol

DGo' = -0.77 kJ/mol

gene segments of ___ are functional units defined by nucleic acid products they produce

DNA

Match the polymer with the monomer that can be one of its components. DNA Glycogen phosphorylase Glycogen 1. Glucose 2. ATP 3. Glutamate

DNA - 2. ATP Glycogen phosphorylase - 3. Glutamate Glycogen - 1. Glucose

Compare the three different ways that DNA can be transferred between organisms using plasmids.

DNA can be transferred between organisms by conjugation, transformation, or transduction. Plasmid conjugation occurs during the bacterial mating process when the donor bacterium transfers a copy of the plasmid to a recipient bacterium. Plasmid transformation occurs when a bacterium dies and the plasmid is transferred to another bacterium via a process involving the cell wall. Viral transduction occurs when a virus known as a bacteriophage infects the bacterium.

Which of the following would cause a genetic mutation? DNA makes too many copies in the cell. DNA synthesis does not occur. DNA damage is not corrected. Death of a cell occurs.

DNA damage is not corrected

In the production of recombinant DNA, which enzyme links matching cohesive ends using covalent interactions?

DNA ligase

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?

DNA ligase

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?

DNA ligase

Which of the following is not a transport protein?

DNA polymerase

What do o factors bind to in RNA synthesis? DNA promoters and RNA polymerase RNA promoters and DNA DNA and RNA transcription factors

DNA promoters and RNA polymerase

Enzymes function as reaction catalysts in cells. If the enzymes were removed from a cell, the rate of biochemical reactions would It is impossible to know. remain the same. increase. decrease.

Decrease

You are preparing for a debate about climate change. Which of the following statements would support the idea that preservation of forests, or even expanding the world's forests, would help stabilize the greenhouse effect?

Decreasing global production of CO2 by burning fewer fossil fuels, for example, would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms. Expanding the amount of the Earth covered by forests and other photosynthesizing organisms would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms.

If the equilibrium constant (Keq) is greater than 1, what is the value of delta Gº? Delta Gº=1 Delta Gº>0 Delta Gº>1 Delta Gº<0

Delta Gº<0

If a reaction has a DeltaH > 0 and a DeltaS < 0, then __________ and the reaction is __________ at all temperatures.

DeltaG > 0 and nonspontaneous

If the equilibrium constant (Keq) is greater than 1, what is the value of DeltaG o? DeltaG o>1 DeltaG o>0 DeltaG o=0 DeltaG o<0

DeltaG o<0

When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase, the final mixture contains twice as much glucose 6-phosphate as fructose 6-phosphate. Which one of the following statements is MOST correct, when applied to the reaction below (R = 8.315 J/mol·K and T = 298 K)? Glucose 6-phosphate ↔ fructose 6-phosphate

DeltaG'o is +1.7 kJ/mol

DeltaG`º is +1.7 kJ/mol.

Which of the experimental steps listed at the right is considered the most challenging in X-ray crystallography

Determining the phases of the diffracted X-rays

Outline the steps involved in DNA condensation.

Double-stranded DNA wraps around histones to form nucleosome particles. These particles pack together to form chromatin fiber. Beyond these two steps, the condensation process depends on the type of DNA and the phase of the cell.

As DNA unwinds and denatures, absorbance is predicted to A) reamain the same B) decrease C) none of the above D) vary unpredictably E) increase

In the following structure, which carbon is the anomeric carbon?

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called A) enhancers B) promoters C) introns D) exons E) operons

The fluidity of a membrane depends on A) osmotic pressure B) the size of the polar head group C) the number of phospholipids in the membrane D) the protein composition E) the degree of saturation of the phospholipids

The sequencing of the human genome has been instrumental toward A. the field of individualized/personalized drug development. B. our understanding of the genetic basis of disease. C. better genetic counseling to prospective parents. D. a more complete understanding of Homo sapiens' molecular inheritance. E. All of these areas were enhanced by the sequencing of the human genome.

Type II topoisomerase enzymes are important in replication and transcription because they A) prevent DNA cleavage B) stabilize the cleaved complex C) none of the above D) prevent autocleavage E) relieve the positive supercoiling

Which of the following are negatively charged amino acids at pH = 7? A) Cys, Asn B) Thr, Tyr C) Gln, Asn D) none of the above E) Glu, Asp

Which of the following statements regarding protein domains is true? A) a domain is a region absent of alpha helices and beta sheets B) each protein has one unique domain C) multiple domains require multiple subunits and quaternary structure D) a motif can be composed of smaller structural units called domains E) none of the above

Which stabilizing force in protein tertiary structures is a covalent bonding force? A) van der Waals B) ionic C) none of the above D) hydrophobic E) disulfide bonding

The sequencing of the human genome has been instrumental toward: A. the field of individualized/personalized drug development. B. our understanding of the genetic basis of disease. C. better genetic counseling to prospective parents. D. a more complete understanding of Homo sapiens' molecular inheritance. E. All of these areas were enhanced by the sequencing of the human genome.

E- all of the above

During eukaryotic DNA condensation, nucleosomes are packed together to form A. chromosomes. B. histones. C. genes. D. genomes. E. chromatin.

E. chromatin.

To purify glutathione reductase to carry out a kinetics analysis, which organism would be the best source of the enzyme? cod fish chimpanzee E. coli turtle

E. coli

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? A. polymerase chain reaction B. blue-white screening C. fluorescent labeling D. antibiotic resistance E. gel electrophoresis

E. gel electrophoresis

Calculate the energy charge of the cell assuming that the concentration of ATP, ADP, and AMP were all equal. Why is this value not a good representation of actual energy charge in a healthy cell? EC = 0.5; because ATP levels are normally higher and AMP levels are normally lower. EC = 0.5; because ATP levels are normally lower and AMP levels are normally higher. EC = 0.7; because ATP levels are normally lower and AMP levels are normally lower. EC = 1.0; because ATP levels are normally higher and AMP levels are normally lower. EC = 0.9; because ATP levels are normally lower and AMP levels are normally higher.

EC = 0.5; because ATP levels are normally higher and AMP levels are normally lower.

Calculate the energy charge of the cell assuming that the concentration of ATP, ADP, and AMP were all equal. Why is this value not a good representation of actual energy charge in a healthy cell

EC = 0.5;; because ATP levels are normally higher and AMP levels are normally lower.

After the initiation complex is complete, what occurs next in the process of translation? peptide bond formation EF-G•GTP binding EF-Tu•GTP^AA-tRNAAA binding RF2 binding

EF-Tu•GTP^AA-tRNAAA binding

Which technique ionizes polypeptides by releasing them from a small metallic capillary at high voltage?

ESI

Which of the following statements best supports the idea that photon absorption by chlorophyll is an all-or-none phenomenon?

Each delocalized electron above and below the porphyrin ring possesses an energy difference with its adjacent orbital that corresponds to the energy of a photon within the visible light range.

Choose the one TRUE statement from the choices below regarding peptide synthesis

Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide.

Choose the one TRUE statement from the choices below regarding peptide synthesis None of these answers are correct. Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide. Peptide synthesis in the lab cannot incorporate proline residues due to the ring structure of this amino acid. Peptide synthesis in the lab can only be done for short peptides due to the high cost of the reagents involved. Peptide synthesis in the lab requires that the side chain are deprotected prior to their addition to the growing peptide chain.

Each round of peptide synthesis in the lab a new amino acid to the N-terminal end of the peptide.

energy charge

Ec= ATP +.5(ADP)/ ATP +ADP +ATP

8. Which of the following statements is correct about the flow of electrons in photosystem I?

Electrons enter PSI from electron carriers in the thylakoid lumen and exit PSI via electron carriers in the stroma. All electron carriers in PSI are embedded in the thylakoid membrane.

Within a eukaryotic cell, is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis:

Endoplasmic Reticulum

Within a eukaryotic cell, the _________ is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis.

Endoplasmic reticulum

Enzymes that showed altered activity (higher or lower) were phosphorylated.

Liver cells were monitored for changes in metabolic enzymatic activity after exposure to glucagon. The enzymes that showed changes in activity were then analyzed to assess if they had been covalently modified. Which of the following results were likely observed? None of these answers are correct. Enzymes that showed altered activity (higher or lower) were phosphorylated. Enzymes that showed lower activity were not phosphorylated. Enzymes that showed higher activity were methylated. Enzymes that showed altered activity (higher or lower) were methylated.

Enzymes that showed altered activity (higher or lower) were phosphorylated.

Compare and contrast the structure of euchromatin and heterochromatin. Explain how their structure relates to biological function.

Euchromatin is less condensed and more gene rich than heterochromatin. This is because gene-rich chromatin would need to be less condensed to allow access by DNA binding proteins that regulate transcription.

according to the hierarchal levels organize the following: a. bird b. cytoplasm c. glycolysis d. simple sugar e. carbs f. oxygen g. forest

F,D,E,C,B,A,G

Which one of the following amino acid residues would most likely be buried in the interior of a water-soluble protein? A. Ser B. Lys C. Asp D. Gly E. Arg F. Trp

F. Trp

Which of the following is a coenzyme that is derived from ATP? coenzyme Q FAD heme Fe4-S4 cluster

FAD

Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?

FADD

The drug oligomycin inhibits ATP synthase by preventing protons from flowing through the enzyme. Oligomycin must bind to the __________ of ATP synthase.

Fo subunit of

What is the "cost" of using the glycerol-3-phosphate shuttle instead of the malate-aspartate shuttle in terms of proton-motive force and ATP synthesis? (choose one correct answer). For the glycerol-3-phosphate shuttle, electrons are transferred to NAD to form NADH, resulting in 4 more translocated H+, and more ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to NAD to form NADH, resulting in 4 fewer translocated H+, and less ATP synthesis For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to form FADH2, resulting in 4 more translocated H+, and more ATP synthesis.

For the glycerol-3-phosphate shuttle, electrons are transferred to FAD to make FADH2, resulting in 4 fewer translocated H+, and less ATP synthesis

Explain the two methods used to determine that plasmid cloning has been successful.

Foreign DNA can be inserted to disrupt the antibiotic resistance gene of bacteria, making it nonfunctional. Antibiotic susceptibility can be used to screen to determine if DNA insertion has been successful. Plasmid cloning vectors also contain the β-galactosidase gene (lacZ), which produces the β-galactosidase enzyme that cleaves a substrate into a blue product. If foreign DNA has been inserted into lacZ, the enzyme function is lost and the bacteria with successful DNA insertion are white.

Two amphipathic α helices in a dilute aqueous solution are likely to: None of these answers are correct. rearrange into β sheets in order to stack against each other to bury hydrophobic side chains. repel each other and remain as individual helical molecules. form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle. form a coiled coil structure with the polar amino acid side chains interacting with each other down the middle.

Form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle.

Which FOUR statements are true regarding β sheets?

Found in globular proteins Stabilized by H-bonds between -NH and -CO groups An extended conformation of the polypeptide chain The stability is affected by amino acid sequence

The same four reactions that are central to the beta-oxidation pathway are also present in the fatty acid synthesis pathway, except they are reversed. What is a key difference between the four reactions in these two pathways? One set of reactions synthesizes an ATP, whereas the other set uses an ATP. One set occurs in the muscle, whereas the second pathway occurs in the liver. One pathway adds three carbon atoms at a time, whereas the other removes two carbons. Four enzymes are used in one, whereas one enzyme is used in the other.

Four enzymes are used in one, whereas one enzyme is used in the other.

In comparison with glycerophospholipids and sphingolipids, cholesterol contains: A. Four steroid rings B. Glycerol moiety C. Phosphate group D. Three steroid rings E. Choline head group

Four steroid rings

25. Which of the following are common features of glycoconjugates?

Frequently contain the hexosamine N-acetylgalactosamine Are covalently attached to lipids and proteins Contain both modified and unmodified monosaccharides

12. Where does the CO2 come from that is used in the Calvin cycle?

From the air

Why does the Tm increase as the G-C content increases?

G-C base pairs have more favorable base stacking interactions than A-T base pairs. Therefore, it takes more heat energy to disrupt the base stacking interactions of the G-C base pairs.

In the second temperature phase of PCR, why does the temperature vary from 55°C to 65°C?

G-C content

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer).

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer). More DNA binding proteins bind to G-C rich regions, and therefore stabilize these structures. None of these answers are correct. Counterions (like Mg2+) bind preferentially to G-C rich regions, enhancing their stability. G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions The primary reason G-C rich regions are more stable is that G-C base pairs have three hydrogen bonds, and A-T base pairs have only two hydrogen bonds.

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA are more stable to denaturation than A-T rich regions. Why? (choose one correct answer). The primary reason G-C rich regions are more stable is that G-C base pairs have three hydrogen bonds, and A-T base pairs have only two hydrogen bonds. Counterions (like Mg2+) bind preferentially to G-C rich regions, enhancing their stability. More DNA binding proteins bind to G-C rich regions, and therefore stabilize these structures. G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

G-C rich regions of DNA have more favorable base stacking energy than A-T rich regions

How are changes in enthalpy (H) and entropy (S), related to changes in free energy (G)? Given the following common reactions, which are entropically favored?

G=H-T delta S ATP ⇒ ADP + Pi

An inhibitor of __________ would specifically prohibit the release of Ran from importin. GTP-GDP exchange in Ran exportin the signal peptide peptidase GAP

GAP

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA GLMKTY PDSTA GLMK TYPDSTA GLM KTYPDSTA GLMKTYPD STA

GLMK TYPDSTA

Predict the fragments of the following peptide after cleavage by trypsin. GLMKTYPDSTA GLMKTY PDSTA GLMKTYPD STA GLMK TYPDSTA GLM KTYPDSTA

GLMK TYPDSTA

helix breaking, destabilizing

GLU-_________-GLU (repulsive) ILE_________ILE (steric)

creutzfeld and jakob disease

GOF

huntington's disease is caused by a

GOF mutation

After inhalation of the asthma drug fluticasone, what two signaling mechanisms mediated by the glucocorticoid receptor lead to a decrease in airway inflammation and relief of asthma symptoms?

GR blocks NFkB induction of Cox2 gene expression and GR activates expression of the annexin gene

Which amino acid side chain from the list below is the most polar?

Gln

Which amino acid side chain from the list below is the most polar? Leu Gln Ala Phe

Gln

Glutamine

Gln Q Polar Hydrophilic no charge

Glutamate

Glu E Negatively charged/acidic polar hydrophilic pK = 4.2

Which of the following are negatively charged amino acids at pH = 7?

Glu, Asp

Based on the structures of D-glucose and D-galactose (shown below), which of the following statements is true?

Glucose and galactose are epimers of each other.

Based on the structures of D-glucose and D-galactose (shown below), which of the following statements is true? Glucose and galactose are tetroses. Glucose and galactose are epimers of each other. Glucose and galactose are ketoses. none of these statements are correct. Glucose and galactose are anomers of each other.

Glucose and galactose are epimers of each other.

Which of the following occurs after activation of the PI-3K signaling pathway?

Glucose uptake increases.

Which of the following occurs after activation of the PI-3K signaling pathway? Glycogen synthesis rates decrease. PTEN protein dimerizes. GLUT-1 levels decrease. Glucose uptake increases. GRB2 is activated.

Glucose uptake increases.

Which of the reactions below is the balance reaction for the catabolism of glucose to lactate?

Glucose+2ADP+2Pi->2ATP+2H2O

For the yeast biochemical pathway, identify fermentative reactants and products by dragging the chemical names to their respective structures Within the biochemical pathway in Part 1, which chemical contains completely oxidized carbon atoms?

Glucose, Ethanol, Carbon dioxide Carbon dioxide

Glycine

Gly G Nonpolar Hydrophilic No charge/non-acidic

14. Which of the following is an example of a polysaccharide?

Glycogen

If protein kinase A is activated in a liver cell in response to glucagon binding to the beta2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on.

order the following according to hierarchal placement a desert b lizard c hexokinase d muscle cell F fructose g glycolysis h hydroxyl group i earth

H, F, C, G, D, B, A, I

Which of the following is a reactant in the net reaction of the citrate cycle?

H2O

Nonprimate mammals convert uric acid to allantoin. This reaction, catalyzed by urate oxidase, also generates which of the following products? H2O H2O2 O2 NH4+

H2O2

What molecules are missing from boxes in the gluconeogenesis reaction shown below? Ser-Pi; Ser-Pi H2O; Pi ADP; ATP ATP; ADP

H2O; Pi

given a solution with pH > pKa, what are the relative concentrations of H and HA

HA < A

Weak acids have a high pka because

HA concentration is high

In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support?

An enzyme panel analysis of a patient reveals a lack of __________, which is an indication of Lesch-Nyhan syndrome. PRPP synthetase adenosine deaminase HGPRT xanthine oxidase

HGPRT

If a Glu sidechain is in a hydrophobic environment, would you expect that the pKa of this sidechain would be higher or lower than the pKa for the sidechain in aqueous solution? (choose one correct answer).

HIGHER

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin? His57 Ser195 Asp102 Gly193

HIs57

Glycan arrays can be coupled with __________ to qualitatively compare fractionated cell extracts from different sources. MALDI-TOF HPLC size exclusion chromatography mass spectrometry

HPLC

Which statement most accurately describes the structure and function of O2 transport proteins? Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG. Leghemoglobin, myoglobin, and hemoglobin all have one thing in common; they bind CO2 very tightly. Myoglobin is found in skeletal muscle, red blood cells, and adipose tissue; hemoglobin is in heart muscle. None of the above statements is correct. Hemoglobin and myoglobin are identical in structure with the only difference being the color of the heme.

Hemoglobin is a tetramer that can bind BPG and O2 whereas myoglobin binds O2 but cannot bind BPG.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are true?

Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration.The majority of autotrophs on Earth require aerobic respiration in order to survive.Heterotrophs depend on autotrophs for conversion of light energy to chemical energy.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE?

Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. The majority of autotrophs on Earth require aerobic respiration in order to survive.

Which THREE of the following statements about autotrophs and heterotrophs on Earth are TRUE? Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. Autotrophs depend on heterotrophs to oxidize sugar and release CO2 into the atmosphere. Heterotrophs evolved on Earth before autotrophs. There are no metabolic differences between autotrophs and heterotrophs. Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. Heterotrophs that do not eat autotrophs every day will die in a short time. The majority of autotrophs on Earth require aerobic respiration in order to survive. The majority of heterotrophs on Earth do not use aerobic respiration as a form of energy conversion.

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell.

High AMP, low ATP, EC below 0.7

Which of the following is true regarding the roles of adenylylation and uridylylation in the control of glutamine synthetase?

High levels of ATP and α-ketoglutarate result in more deadenylylated glutamine synthetase.

Higher

Histidine

His H Polar Hydrophilic Positively charged/basic pK = 6.0

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin?

His57

Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin? Gly193 His57 Asp102 Ser195

His57

Which of the following pairs of amino acids need glutamine to be generated, but are also both allosteric regulators of glutamine synthetase? Choose one: A. Alanine, serine B. Serine, tryptophan C. Glycine, histidine D. Histidine, tryptophan

Histidine, tryptophan

A scientist can use a variety of bioinformatic tools to compare the DNA of individuals suffering from a genetic disease to the DNA of unaffected individuals. Why, then, do scientists try to identify the gene involved in the disease before searching for a specific mutation?

Human genomes contain many random mutations that have little to no effect on protein expression or function. Some are spontaneous, whereas SNPs and STRs are inherited. Simply comparing the DNA of two individuals would result in the identification of hundreds to thousands of differences. If the affected gene is known, then the sequence of that gene from an affected individual can be compared to unaffected individuals, including parents or siblings, in order to help eliminate inherited variations as potential disease-causing mutations.

Why does hydrogen bonding between base pairs contribute little to overall helix stability?

Hydrogen bonding occurs between bases within a DNA double helix, but when DNA strands are denatured, the hydrogen bonds are replaced by hydrogen bonds between bases and water that are similar in strength.

Hydrolysis of ATP is an exergonic reaction

Match the 4 amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A). Chemical groups: hydrophobic, hydrophilic, aromatic, charged Amino acids: Serine, Phenylalanine, Aspartate, Isoleucine

Hydrophobic - Isoleucine Hydrophilic - Serine Aromatic - Phenylalanine Charged - Aspartate

Match the four amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A).

Hydrophobic-Valine Charged- Arginine Hydrophilic- Threonine Aromatic- Tryptophan

Enzyme deficiencies that affect the fatty acid β-oxidation pathway are often diagnosed by examining the different metabolic intermediates in the bloodstream. An individual with a deficiency in an enzyme required for β oxidation would have which of the following results if the ketone bodies and glucose concentration of their blood were tested after fasting? Choose one: A. Ketotic hypoglycemia B. Hypoketotic hypoglycemia C. Hyperketotic hypoglycemia D. Ketotic hyperglycemia

Hypoketotic hypoglycemia

Use the table below to answer the question. In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc018-5.jpg O2 + NADH II. FADH2 + H2O mc018-6.jpg O2 + FAD III. NADH + O2 mc018-7.jpg H2O + NAD+ I and III I, II, and III II only II and III III only I and II I only

III only

Use the table below to answer the question. Standard Reduction Potentials (mc018-1.jpg) for Half Reactions NAD+ + H+ + 2 e− mc018-2.jpg NADH −0.32 V FAD + 2 H+ + 2 e− mc018-3.jpg FADH2 −0.22 V O2 + 4 H+ + 4 e− mc018-4.jpg 2 H2O +0.82 V In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc018-5.jpg O2 + NADH II. FADH2 + H2O mc018-6.jpg O2 + FAD III. NADH + O2 mc018-7.jpg H2O + NAD+

III only

Use the table below to answer the question. In the direction indicated, which of the following reactions are thermodynamically favored? I. NAD+ + H2O mc227-5.jpg O2 + NADH II. FADH2 + H2O mc227-6.jpg O2 + FAD III. NADH + O2 mc227-7.jpg H2O + NAD+

III only

Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes?

IKK

Activation of __________ in __________ leads to downregulation of adiponectin. IKK; adipocytes p38 MAP kinase; adipocytes p38 MAP kinase; liver cells JNK; adipocytes

IKK; adipocytes

Select the TWO true statements below describing the standard free energy change (delta G) and the equilibrium constant (Keq). The equilibrium constant is equal to ratio of the concentration of reactants over products at equilibrium. If the value of the equilibrium constant is known, the value for the standard free energy change can be determined. The value for the standard free energy change is constant for a given reaction. The standard free energy change is a function of enzyme concentration in the reaction. A reaction is spontaneous when the standard free energy change and the equilibrium constant are both negative values.

If the value of the equilibrium constant is known, the value for the standard free energy change can be determined. The value for the standard free energy change is constant for a given reaction.

Isoleucine

Ile I nonpolar hydrophobic

Describe and explain what occurs at the three temperature phases in PCR.

In the first temperature phase, the DNA is heated to denature and separate the strands. In the second phase, the temperature is lowered to facilitate annealing of the primer to each strand (normally in the temperature range of 55°C-65°C). The annealing temperature depends on the Tm of the primer, which is based on length and G-C content. In the third phase the temperature is raised to 72°C to allow extension of the primer and DNA synthesis.

As DNA unwinds and denatures, absorbance is predicted to

Increase

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tmwill Question options: A: remain the same. B: decrease. C: increase D: vary unpredictably.

Increase

How does the ionic strength of DNA affect the Tm? Explain.

Increasing the ionic strength of the solution increases the Tm. The ions bind to the phosphate groups of the DNA backbone, stabilizing the helix. Because the helix is more stable with increasing ion concentration, it takes more heat energy to denature the helix and the Tm increases.

Beriberi is a nutritional deficiency disorder that causes debilitating neurological symptoms. Why do individuals with beriberi have a large amount of pyruvate in their blood following a high-carbohydrate meal? (choose one correct answer). Individuals with beriberi cannot readily metabolize pyruvate to phosphoenolpyruvate because succinyl-CoA synthase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to phosphoenolpyruvate because pyruvate dehydrogenase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because pyruvate dehydrogenase is inactive without thiamine pyrophosphate. Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because succinyl-CoA synthase is inactive without thiamine pyrophosphate.

Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because pyruvate dehydrogenase is inactive without thiamine pyrophosphate

Individuals with beriberi cannot readily metabolize pyruvate to acetyl-CoA because pyruvate dehydrogenase is inactive without thiamine pyrophosphate.

beers law image

Io light bulb >>> monochrometer>>> Sample>>>> I(intensity of transmitted light) ^c=conc. length of sample=l

What mediates the binding of histone proteins to DNA?

Ionic interactions

How do we deal with the double bonds during the degradation of unsaturated fatty acids? Convert the three-carbon propionyl-CoA to succinyl-CoA and feed it into the TCA cycle. Converge them with the TCA cycle to produce acetyl-CoAs. Isomerize the position of the double bonds to converge them with the beta-oxidation pathway. Reduce them to single bonds and feed the saturated fatty acid into the beta-oxidation pathway.

Isomerize the position of the double bonds to converge them with the beta-oxidation pathway.

To study red blood cells without damaging them through osmotic shock, they should be kept in a solution which is... (choose one correct answer).

Isoonic

To study red blood cells without damaging them through osmotic shock, they should be kept in a solution which is... (choose one correct answer). Hypertonic Hypotonic Allosteric Isotonic At the pI

Isotonic

Which of the following is true of the glyoxylate cycle? It allows plants to produce glucose from fats and two-carbon molecules like acetate. It occurs in plant cells as an alternative to photosynthesis. It bypasses all regulated steps of the TCA cycle. It results in a net production of ATP and NADH without proceeding through the TCA cycle.

It allows plants to produce glucose from fats and two-carbon molecules like acetate.

Which of the following is true of procaspase 8?

It can be activated by proteolysis.

Which of the following is true of procaspase 8? It is a kinase. It is proteolytically active. It can cleave caspase 3. It can be activated by proteolysis.

It can be activated by proteolysis.

18. What is a oligosaccharide?

It contains more than two monosaccharide residues connected by a glycodisic bond. Oligosaccharides generally contain between three and twenty residues.

16. Having PSII and PSI complexes unevenly distributed in the thylakoid membrane offers several advantages for the light reactions of photosynthesis. Among the reasons below, which is not correct?

It ensures that plastocyanin and ferredoxin, soluble electron carriers associated with PSII and PSI, respectively, are able to come into close contact and transfer electrons with each other during cyclic photophosphorylation. Plastocyanin is in the thylakoid lumen, and ferredoxin is in the stroma. The thylakoid membrane prevents them from contacting each other.

Which of the following is true of the induced-fit model of enzyme catalysis but NOT of the lock and key model of enzyme catalysis?

It involves a conformational change of the enzyme

Which of the following is NOT a reason why glycolysis is considered one of the core metabolic pathways in nature?

It is a primary pathway for nitrogen generation.

Which of the following is correct concerning methicillin?

It is produced by synthetic antibiotic.

How does phosphoglycerate kinase make glycolysis energy neutral at this step?

It produces 2 ATP along with 3-phosphoglycerate

Suppose the alpha amino group of a protein has a pKa of about 8 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8 if the alpha amino group were buried in the hydrophobic interior of the protein and why?

It would be lower because the alpha amino group would be uncharged at neutral pH, which is favorable.

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha-amino group of a protein has a pKa of about 8.0 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8.0 if the alpha-amino group were buried in the hydrophobic interior of the protein and why? It would be the same because the hydrophobic environment would have no effect on the pKa. It would be lower because the hydrophobic environment has more water and less hydroxyl groups. It would be higher because the hydrophobic environment would provide stability to the proton. It would be higher because the alpha-amino group would be uncharged at neutral pH, which is favorable. It would be lower because the alpha-amino group would be uncharged at neutral pH, which is favorable.

It would be lower because the alpha-amino group would be uncharged at neutral pH, which is favorable.

For the reaction: Fructose 1,6-bisphosphate (F-1,6-BP) ↔ DHAP + GAP ΔG°' = +23.9 kJ/mol at 37 °C. What is Keq?

K eq= 9.4 x 10^-5

For the reaction: A + B ↔ C + D, which of the following is correct?

Keq = [C][D]/[A][B]

For the reaction: A + B ↔ C + D, which of the following is correct? Keq = [A][B]/[C][D] ΔG° = RT ln Keq Keq = [C][D]/[A][B] ΔG° = -RT log Keq

Keq = [C][D]/[A][B]

for the reaction A+B<-> C+D which of the following is correct

Keq= [C][D]/[A][B]

The chirality of naturally occurring amino acids in proteins is

counter clockwise rotation

L Left (levorotary)

cysteine is the only

L amino acid with an absolute configuration of R

Which lipid is thought to give rise to the plaques that can clog arteries? HDL LDL VLDL chylomicrons

LDL

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

LMYKWDERMGFCE

cystic fibrosis mutation

LOF

The human gut microbiome is a collection of microbes that are necessary for proper function of the digestive system and that contribute to the overall health of the individual. Infants are colonized with these microbes at birth and their nutrition in the early days of life is important for supporting growth of these microbes. Milk sugars are important in development of the microbiome. Which of the following best explains how both lacto-N-tetraose and lacto-N-fucopentaose could contribute to proper development of an infant's microbiome?

Lacto-N-fucopentaose binds to surface receptors on pathogenic bacteria and prevents them from entering epithelial cells in the intestine. Lacto-N-tetraose is a food source for bacteria that aid in digestion of this and other oligosaccharides.

29. Which of the following is an example of a disaccharide?

Lactose

complexity of life

Least complex: elements & functional groups (C,N,O,H,P) biomolecules (amino acids, nucleotides, simple sugars fatty acids) macromolecules (proteins, DNA/RNA, carbohydrates, lipids) Metabolism (glycolysis, citrate cycle, beta oxidation, urea cycle) cells (cell wall, plasma membranes, organelles) organisms (trees, mammals, fish, birds, insects) Most complex: ecosystems (rivers, islands, forests, deserts)

Leucine

Leeu L nonpolar hydrophobic

Which of the of four amino acids residues listed in the choices below are all most likely to be buried in the interior of a water soluble protein? Ala, Asp, Cys, Lys Glu, Thr, Phe, Arg Glu, Trp, Tyr, His Cys, Thr, Ser, Glu Leu, Ile, Val, Ala

Leu, Ile, Val, Ala

which of the four amino acids residues are most likely to be buried in the interior of a water soluble protein

Leu, Ile, Val, Ala

The Biosphere 2 project, in Tucson, Arizona, was an experiment involving a large sealed terrarium with humans and photosynthetic plants living in balance. Why did the project have to be interrupted after only a few months? Levels of CO2 rose to dangerous levels. The humans ran out of food. The plants stopped producing oxygen. The rate of photosynthesis was too high.

Levels of CO2 rose to dangerous levels.

Choose the four TRUE statements below regarding receptor tyrosine kinases. Ligand binding is required for autophosphorylation (cross-phosphorylation) The structure includes a transmembrane helix The alpha subunit contains seven alpha helices that span the membrane RTKs are dimeric in the presence of ligand The ligand binds to the extracellular domain The intracellular domian has phosphatase domains

Ligand binding is required for autophosphorylation (cross-phosphorylation) The structure includes a transmembrane helix RTKs are dimeric in the presence of ligand The ligand binds to the extracellular domain

In addition to a ligand binding site, PPARgamma/RXRalpha complexes also contain coregulator binding sites that bind LXXLL peptides. Select the one TRUE statement below.

Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins.

In addition to a ligand binding site, PPARgamma/RXRalpha complexes also contain coregulator binding sites that bind LXXLL peptides. Select the one TRUE statement below. The coregulator binding site selects for phosphorylated LXXLL peptides, so that ligand binding can be modulated by phosphorylation. Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins. The coregulator binding site is located on the face of PPAR/RXR that binds DNA, to prevent DNA binding when the coregulator is bound. Only RXRalpha binds the coregulator, which enhances ligand binding by PPARgamma.

Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins.

In the opening sequence of the video, a protein is "unraveled" down to an extended linear conformation. Which of the following statements accurately captures what is happening in this process?

Linearizing the polypeptide destroys the spatial relationships that define secondary and tertiary structure.

Of these three parameters regarding DNA twist, which is calculated by adding the other two parameters together

Linking number (Lk)

How does glycogen metabolism differ between muscle and liver cells? A. Glycogen degradation is stimulated by glucagon in liver cells but insulin in muscle cells. B. Glycogen particles in muscle cells has fewer a-1,6-glycosidic bonds than glycogen in liver cells. C. Liver cells contain glucose-6-phosphatase, which dephosphorylates glucose-6P to release glucose. D. The glycogen phosphorylase enzyme in liver cells is activated acetyl-CoA rather than ATP. E. Glycogen metabolism in muscle cells produces palmitate from acetyl-CoA, but myristate in liver cells

Liver cells contain glucose-6-phosphatase, which dephosphorylates glucose-6P to release glucose.

Predict how type I topoisomerases change the supercoil region.

Lk = -1

Predict how type II topoisomerases change the supercoil region

Lk = -2

Predict how type II topoisomerases change the supercoil region.

Lk = -2

Which of the following express the relationship among the linking number, twist, and writhe?

Lk = Tw + Wr

In one type of hemoglobin mutant the amino acid change eliminates a hydrogen bond that normally stabilizes the R state. Would you expect this mutant hemoglobin to have a higher or lower O2 affinity compared to the normal protein and why? Lower O2 affinity because the R-T equilibrium would be mostly shifted to the T state. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the R state Lower O2 affinity because the R-T equilibrium would be mostly shifted to the R state. Higher O2 affinity because the R-T equilibrium would be mostly shifted to the T state.

Lower O2 affinity because the R-T equilibrium would be mostly shifted to the T state.

Lysine

Lys K polar hydrophilic positively charged/basic pK = 10.5

Which of the following sequences is most likely a nuclear localization signal? Lys-Lys-Arg-Gly-Arg Glu-Asp-Asp-Gly-Glu Ile-Leu-Phe-Leu-Gly Lys-Asp-Arg-Glu-Glu

Lys-Lys-Arg-Gly-Arg

A mutation in the beta subunit of hemoglobin is discovered that reduces the affinity of 2,3-BPG binding. Which of the following mutations is most likely to have this consequence?

Lys82 -> Asp82

Which technique ionizes polypeptides by embedding the tryptic fragments into a light-absorbing matrix and exposing it to a laser?

MALDI

31. Which of the following is an example of a monosaccharide?

Mannose

Which of the statements below best describes the mechanism of proton translocation via a redox-driven conformational change?

Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane.

Which of the statements below best describes the mechanism of proton translocation via a redox-driven conformational change? When the e- binds to cytochrome c, it results in dissociation of cytochrome c from complex III, which stimulates release of H+ from complex III. Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane. A redox reaction results in a H+ and e- that are separated within the transmembrane electron transport system and deposited on opposite sides of the inner mitochondrial membrane. The e- is used to reduce an oxidant, and the H+ is released into the intermembrane space. The flow of coenzyme Q between complex I and complex III alters membrane fluidity, which makes the membrane briefly permeable to protons.

Matrix-derived protons are translocated across the mitochondrial membrane by altering pKa values of functional groups located on the inner and outer faces of the membrane.

- Flippases are enzymes that catalyze the flip-flop movement of phospholipids in a membrane bilayer. What property of membranes contributes to the energy barrier that flippases lower in order to increase the rate of phospholipid flipping?

Membranes consist of a phospholipid bilayer, which means that it has a polar surface on both sides and a hydrophobic center layer. For a phospholipid to flip, the polar head group has to pass through the hydrophobic layer and that is an energy barrier that is lowered by the flippase enzyme, most likely by shielding the head group

C4 plants inhibit photorespiration and increase CO2 fixation efficiency by separating the capture of CO2 and the Calvin cycle into two adjacent cell types. Sort the following reactions based on whether they occur in mesophyll cells or bundle sheath cells.

Mesophyll Cells: Reduction of oxaloacetate to malate Pyruvate + ATP → PEP HCO3- + PEP → oxaloacetate Bundle Sheath Cells: Malate + NADP+ → Pyruvate + NADPH + CO2 Calvin cycle Glyceraldehyde-3-P → Starch and Sucrose

Which of the following is NOT a component that is released from the ribosome on translation termination? RF2 nascent polypeptide tRNA Met-tRNA^fMet

Met-tRNA^fMet

Which of the following common functional groups in biomolecules is NOT capable of multiple protonation states?

Methyl

Using the table below, determine the kind of gene mutation illustrated ATG_AAT_CAC --> ATG_AAG_CAC

Missense mutation

Using the table below, determine the kind of gene mutation illustrated. ATG_AAT_CAC -> ATG_AAG_CAC frameshift mutation silent mutation nonsense mutation missense mutation

Missense mutation

Compare and contrast a monocistronic gene and a polycistronic gene

Monocistronic genes contain a promoter and a single protein-coding sequence. Polycistronic genes also contain a promoter but have multiple coding regions. Therefore, monocistronic genes only encode for one protein, whereas polycistronic genes encode for multiple proteins in a single RNA transcript.

Rank the following cellular features and/or activities in terms of their decreasing complexity compared to one another. The most complex should be positioned on top, and the least complex should be positioned on the bottom.

Most Complex: Ecosystem Cells Metabolism Macromolecules Least Complex: Elements and functional groups

The Second Law of Thermodynamics states that all spontaneous processes in the universe tend toward the dispersal of energy in the absence of energy input, which leads to death for a living organism. What are the two sources of energy for an autotroph over a 24 hour period and what are the chemical processes involved in each?

Most all autotrophs on Earth use photosynthetic processes to convert light energy into chemical energy (ATP and NADPH), which is then used to synthesize carbohydrates in the form of sucrose, starch, and cellulose. In the absence of light (at night), photosynthetic autotrophs metaboliz sucrose in the glycolytic pathway, citrate cycle, and oxidative phosphorylation to maintain homeostasis

Why is it important that muscle cells are unresponsive to glucagon? Muscle cells store glycogen for its own energy needs and not the needs of other tissues. The muscles do not store glycogen. The muscles release glucose to other tissues in need. Muscle cells respond to insulin instead.

Muscle cells store glycogen for its own energy needs and not the needs of other tissues.

If SERCA is not functioning in a myoblast, which of the processes described at the right is most likely to occur?

Muscle contraction occurs but not muscle relaxation

The DNA alkylation of guanine is possible because the __________ of guanine is __________ and reacts rapidly with __________ alkylating agents. N-7; nucleophilic; electrophilic N-5; nucleophilic; electrophilic N-7; electrophilic; nucleophilic N-5; electrophilic; nucleophilic

N-7; nucleophilic; electrophilic

Which of these modifications best describes the CD2 glycoprotein?

N-linked glycosylation that is covalent in nature

The coenzyme _________ is the oxidizing agent in glycolysis.

NAD+

What is the fate of NADH after it donates its electrons to the electron transport system?

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

What is the fate of NADH after it donates its electrons to the electron transport system? NAD+ is fed into the TCA cycle for oxidation of CO2. none of these answers are correct. NAD+ is excreted from the cell and sent to the liver for final degradation. NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated. NADH is used for cellular biosynthesis.

NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated.

Fill in the blanks showing the moles of reactants and products int he net reaction of the citrate cycle

NAD+, GDP, FADH2

Which molecule in the net reaction of the citrate cycle contributes to the inhibition of pyruvate dehydrogenase?

NADH

Which reaction does the concept of oxidative phosphorylation refer to?

NADH + 1/2 O2 + H+ + ADP + Pi --> NAD+ + ATP + H2O

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?

NCCNCC

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace? NCCNCC CNCCNC None of these answers are correct. NCONCO NCCONCCO

NCCNCC

Which of the following is the net reaction of the urea cycle? Urea + Fumerate + 2 ADP + 2Pi + AMP + PPi --> NH+ + HCO3- + aspartate + 3ATP NH+ + HCO3mc123-2.jpg + aspartate + 3ATP --> urea + fumerate + 2 ADP + 2Pi + AMP + PPi NH+ + HCO3mc123-4.jpg + fumerate + 3ATP --> urea + aspartate + 2 ADP + 2Pi + AMP + PPi NH+ + HCO3mc123-6.jpg + aspartate + 2 ADP + 2Pi + AMP + PPi --> urea + fumerate + 3ATP

NH+ + HCO3mc123-2.jpg + aspartate + 3ATP --> urea + fumerate + 2 ADP + 2Pi + AMP + PPi

What would happen if DNA contained uracil isntead of thymine as the adenine base pair?

Naturally ocuring uracil bases would not be distinguishable from cytosine deamination events

helices notation

Nm N=number of turns m=number of atoms

28. Which of the following is FALSE concerning cyclic photophosphorylation?

No NADP+ is produced

Does hydrogen bonding between base pairs account for the overall stability of the DNA helix

No, because hydrogen bonding between bases in the DNA helix is replaced by hydrogen bonding with water in single strand DNA, therefore hydrogen bonding is in sufficient to explain why DNA helix is stable

Does hydrogen bonding between base pairs account for the overall stability of the DNA helix?

The points in the Ramachandran plot are derived by None of these answers are correct. calculating the mc030-2.jpg and mc030-3.jpg angles using a computer modeling program based on estimating peptide bond lengths between adjacent amino acids. experimentally measuring the optical rotation of polarized light. counting the number of amino acids and placing points in allowed regions. placing each amino acid in regions commonly occupied by that amino acid.

None of these answer are correct

Two-dimensional polyacrylamide gel electrophoresis separates proteins based on shape and ligand affinity. ligand affinity and molecular weight. subunit composition and molecular weight. none of these answers are correct. pI and shape.

None of these answers are correct

Which class of protein structures does the protein shown below fit into?

None of these answers are correct

Which of the following statements about association and dissociation constants describing the binding of Ligands X and Y to Protein Z is the most correct?

None of these answers are correct

Choose the best answer below describing why the metabolic cycle discovered by Hans Krebs should be called the citrate cycle is: