Wiley Qs: Flashcards by Gail I

which of the following statements concerning prokaryotes is FALSE?

prokaryotes are made up of two major groupings: the eubacteria and the archaea, which are as different from each other as from the eukaryotes

prokaryotes are generally much smaller than the eukaryotic cells

prokaryotes are one branch of the newer, more accurate phylogenic tree made up of prokarya, archaea, and eukarya

prokaryotes do not have organelles

none of the above is false

prokaryotes are one branch of the newer, more accurate phylogenic tree made up of prokarya, archaea, and eukarya

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which group of chemical compounds is thought to have been present in earth’s prebiotic atmosphere and was used by Miller and Urey in their spark-discharge experiment?

H2O, O2, and CO2
CH4, NH3, H2O, and H2
H20, N2, and O2
H2O, N2, and CO2

CH4, NH3, H2O, and H2

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which feature of eukaryotes is most common to prokaryotes?

an organized cytoplasm
multicellular organisms
a membrane-enclosed nucleus
mitochondria

an organized cytoplasm

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Which of the following statements is not accurate when considering water and biological molecules?

the hydrogen bonding pattern of water is disrupted by the presence of hydrophobic molecules

water is more likely to act as a hydrogen bond donor than a hydrogen bond acceptor

polar substances are soluble because of their interaction with water.

water is more likely to act as a hydrogen bond donor than a hydrogen bond acceptor

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which of the following statements is not accurate when considering water and biological molecules?

nonpolar substances associate with water to maximize their exposed surface area

water can act as a hydrogen bond acceptor

polar substances are soluble because of their interaction with water

water can act as a hydrogen bond donor

nonpolar substances associate with water to maximize their exposed surface area

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which of the following types of bonding interactions is NOT classified as noncovalent?

hydrogen bonding
electrostatic interactions
van der waals
dipole dipole interactions 
none of the above

none of the above

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an amphiphilic molecule:

has nonpolar groups
has both polar and nonpolar groups
has neither polar nor nonpolar groups
has polar groups

has both polar and nonpolar groups

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the 104.5 degree bond angle in the water molecule is the result of the … of electron orbitals around oxygen

tetrahedral arrangement

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the polarity of the OH bond is caused by the … of oxygen relative to that of hydrogen

higher electronegativity

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the strongest noncovalent interactions are:

van der waals forces
hydrogen bonds
dipole-dipole interactions
ionic interactions
London dispersion forces

ionic interactions

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in a hydrogen bond between a water molecule and another biomolecule:

a hydrogen ion on the water molecule forms an ionic bond with a hydride ion on the other molecule

a hydrogen on the water molecule forms a covalent bond with a hydrogen atom on the other molecule

the hydrogen bond will typically form between a hydrogen atom of the water molecule and either a nitrogen, sulfur, or oxygen atom of the other molecule

the hydrogen atom is located between an oxygen atom of the water and a carbon atom of the other molecule

the partial charge on a hydrogen of the water molecule interacts with the partial charge on a hydrogen of the other molecule

the hydrogen bond will typically form between a hydrogen atom of the water molecule and either a nitrogen, sulfur, or oxygen atom of the other molecule

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which of the following statements about water is incorrect?

water is an excellent solvent for polar molecules

pure water has a concentration of approximately 55.5 M

cations are solvated by shells of water molecules oriented with their hydrogen atoms pointed toward the ions

nonpolar molecules do not dissolve in water, but form a separate phase

amphiphilic detergents often form micelles with the polar groups on the outside exposed to water (solvent) and the nonpolar groups sequestered in the interior

cations are solvated by shells of water molecules oriented with their hydrogen atoms pointed toward the ions

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Ice:

is a crystal of water molecules packed in an open structure stabilized by hydrogen bonds

is less dense than liquid water

contains 15% more hydrogen bonds then water

all of the statements above are true

none of the statements above are true

all of the statements above are true

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the boiling point of water is 264 deg C. higher than the boiling point of methane because:

the molecular mass of methane is much lower than that of water

methane molecules tend to avoid contact with each other

water molecules are connected to each other by H-bonds

methane molecules do not undergo London dispersion forces

all of the above

water molecules are connected to each other by H-bonds

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physical properties that depend on the amounts of various species, rather than the identities of those species, are called:

aggregate properties
London dispersion forces
colligative properties
osmotic properties
hydrophobic properties

colligative properties

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Kw, the ionization constant of water is … at … deg. C

10^-14; 25

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weak acids:

are of no value in a buffering system

are almost insoluble in water

do not provide hydronium ions

are only partially ionized in an aqueous solution

give solutions with a high pH

are only partially ionized in an aqueous solution

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To make a phosphate buffer at pH 6.82 starting with one liter of 10 mM phosphoric acid (pKs are 2.15, 6.82, and 12.38), you could add

5 millimoles of HCl
20 millimoles of K+ 
25 millimoles of HCl 
15 millimoles of KOH 
You can't make a buffer by adding HCl or KOH

15 millimoles of KOH

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You mix equal volumes of 0.05 M NaH2PO4 and 0.05 M Na2HPO4 (pK’s for phosphoric acid are 2.15, 6.82 and 12.38). Which of the following best describes the resulting solution?

pH 2.15 and poorly buffered
pH 6.82 and well buffered
pH 2.15 and well buffered
pH 12.38 and well buffered
pH 6.82 and poorly buffered

pH 6.82 and well buffered

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The pKs of succinic acid are 4.21 and 5.64. How many grams of monosodium succinate (FW = 140 g/mol) and disodium succinate (FW = 162 g/mol) must be added to 1 L of water to produce a solution with a pH 5.28 and a total solute concentration of 100 mM? (Assume the total volume remains 1 liter, answer in grams monosodium succinate, grams disodium succinate, respectively.)

9 g, 9.7 g
7 g, 4.9 g
9 g, 1.1 g
1 g, 14.9 g
3 g, 4.2 g

9.7 g, 4.9 g

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A graduate student at SDSU wants to measure the activity of a particular enzyme at pH 4.0. To buffer her reaction, she will use a buffer system based on one of the acids listed below, which acid is most appropriate for the experiment?

Tris (Ka 8.32 × 10-9)

PIPES (Ka 1.74 × 10-7)

Piperidine (Ka 7.58 × 10-12)

Formic acid (Ka 1.78 × 10-4)

MES (Ka 8.13 × 10-7)

Formic acid (Ka 1.78 × 10-4)

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The pH of blood is affected by:

the reaction of CO2 with H2O to form carbonic acid.

the ionization of aqueous carbonic acid to hydronium ions and the bicarbonate anions.

the decrease of the blood pH due to the production of hydronium ions.

the excretion of bicarbonate and ammonium ions from the kidneys.

all of the above.

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ribonucleotides are made of a sugar phosphate plus the pyrimidine bases cytosine or thymine. T or F

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adenine and guanine are common purines. T or F

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In the Watson-Crick model of DNA, the two strands are parallel, meaning that they run in the same 5' to 3' direction. T or F

According to Chargaff's rules for the base composition of DNA, %A = %T and %G = %C. T or F

the complementary base paired double helix structure of DNA is ideal for replicating genetic information because each DNA strand can act as a template for the synthesis of its complementary strand with the hereditary information encoded in the sequence of bases on either strand. T or F

site of protein synthesis:

ribosome

primary component of the ribosome:

ribosomal RNA

synthesis of a strand of RNA complementary to a strand of DNA:

transcription

synthesis of a polypeptide that is complementary to a strand of RNA:

translation

a small nucleic acid that covalently links to an amino acid, and base pairs with messenger RNA

transfer RNA

the RNA transcript of a gene:

messenger RNA

the synthesis of DNA in cells through the assembly of a complementary strand from a template strand:

replication

DNA is the carrier of genetic information in all cells and in many viruses. T or F

enzyme that cleaves a nucleotide by removing a terminal residue:

exonuclease

enzyme that participates in DNA replication:

DNA polymerase

nucleotide sequence with two fold symmetry:

palindrome

enzyme that cleaves DNA at sites that correspond to a particular sequence of nucleotides:

restriction endonuclease

modification enzyme that adds a methyl group to a nucleotide:

methylase

nucleotide that lacks both 2' and 3' OH groups

dideoxynucleoside triphosphate

the chain terminator method of sequencing DNA uses …-nucleoside triphosphates to terminate synthesis of the complementary strand

dideoxy

an … is an enzyme that cleaves a nucleic acid by removing terminal residues

exonuclease

phylogenetic relationships can be revealed by comparing the sequences of similar genes in different organisms. the number of nucleotide differences between the corresponding genes in two species roughly indicates the degree to which the species have diverged through evolution. T or F

which of the following statements is NOT true about restriction enzymes (restriction endonucleases or RE's): they are endonucleases they are a part of a bacteria's restriction-modification system - a system bacteria use to defend themselves against bacteriophages they recognize and cut palindromic DNA sequences they recognize and cut methylated DNA

they recognize and cut methylated DNA

modification of a nucleotide sequence to alter an amino acid sequence: ...

site directed mutagenesis

production of multiple identical organisms:

cloning

stable introduction of foreign DNA into a host cell:

transformation

amplification of a DNA sequence via multiple cycles of synthesis

polymerase chain reaction

covalent linking of two segments of DNA

ligation

recombinant DNA technology is also called molecular … or genetic engineering

cloning

a ... is a DNA molecule that contains the sequences necessary to direct DNA replication in a host cell

vector

using the techniques of molecular cloning, it is possible to isolate, amplify, and modify specific DNA sequences. T or F

``` Gene therapy (the transfer of new genetic material to the cells of an individual in order to produce a therapeutic effect) is a relatively new, yet commonly used medical treatment to overcome inherited deficiencies in humans T or F ```

tandemly repeated DNA sequences occur throughout the human genome and include short tandem repeats (STRs), which contain variable numbers of repeating segments of two to seven base pairs. the number of repeats at any one site on the DNA varies between individuals. It is thus possible to distinguish between individuals by amplifying particular STR regions of their DNA by PCR and comparing the lengths of the amplified STR regions via gel electrophoresis in a technique called DNA fingerprinting. T or F

What feature must an expression vector have that an ordinary plasmid might lack? sequences to direct replication sequences to control transcription and translation a gene encoding antibiotic resistance a circular structure

sequences to control transcription and translation

why does the polymerase chain reaction require a heat stable DNA polymerase? high temperatures are necessary to cause strand separation after each cycle of synthesis high temperatures are necessary for annealing the primers high temperatures are necessary for initiating DNA synthesis high temperatures are necessary for high fidelity in DNA synthesis

high temperatures are necessary to cause strand separation after each cycle of synthesis

What is the net charge of the predominant form of Arg at pH 1.0? … At pH 5.0? … At pH 10.5? … At pH 13.5? ….

+2 +1 0 -1

Three of the 20 amino acids that are incorporated into proteins are aromatic. They are: ``` valine, leucine, and isoleucine tyrosine, phenylalanine, and tryptophan tyrosine, phenylalanine, and proline arginine, lysine, and histidine tryptophan, phenylalanine, and proline ```

tyrosine, phenylalanine, and tryptophan

``` There are several amino acid side chains which are always charged at physiological pH. These are: Glu, Asp, Lys, and His Gln, Asn, Glu, and Asp Glu, Lys, Asp, His, and Arg Glu, Aspk, Lys, and Arg none of the above ```

Glu, Asp, Lys, and Arg

which one of the following sequences of five amino acids would most likely be located in the interior of a globular soluble protein? ``` Met-Cys-Pro-His-Tyr Val-Ala-Val-Glu-Val Met-Phe-Pro-Ile-Leu Tyr-Phe-Glu-Asn-Leu Glu-Asn-Ser-Thr-Gln ```

Met-Phe-Pro-Ile-Leu

which of the following statements regarding amino acids is/are true? Ala, Val, Leu, and Ile play an important role in establishing and maintaining the 3D structures of proteins Every amin oacid has at least two pKa values when the pH of a solution is below the pKa value of an ionizable group, the protonated form of that group predominates

all

which amino acid side chain can form a charged ion? lysine serine phenylalanine leucine

lysine

which amino acid side chain is NOT aromatic? methionine phenylalanine tryptophan tyrosine

met

Serine has pK values of 2.19 and 9.21. What is its estimated pI? 7. 00 9. 21 2. 19 5. 70

5.70

Lysine has pK values of 2.16, 9.06, and 10.54, for its carboxyl, a-amino, and E-amino groups, respectively. What is its estimated pI? 5. 66 9. 80 9. 06 6. 85

9.80

The pI of any amino acid can be estimated by the average of the pK values of the a-amino group and the a-carboxyl group. T or F

Glutamine has pK values of 2.17 and 9.13. What is its estimated pI? 5. 65 9. 13 7. 00 2. 17

5.65

glutamic acid has pK values of 2.10, 4.07, and 9.47 for its a-carboxyl group, gamma-carboxyl group, and a-amino group, respectively. What is its estimated pI? 6. 77 3. 085 4. 07 5. 785

3.085

many drugs are chemically synthesized as racemic mixtures, although only one enantiomer has biological activity. T or F

molecules that are nonsuperimposable mirror images are known as … of each other: diastereomers racemers enantiomers zwitterions

enantiomers

biological systems usually produce a single enantiomer, whereas chemical synthesis produces a ….

racemic mixture

which of the followings statements is true? amino acids can be derived from purines purines and pyrimidines can be derived from amino acids corn contains all 20 standard amino acids amino acids can be derived from pyrimidines none of the above

purines and pyrimidines can be derived from amino acids

zwitterions are: amino acids ionic molecules that are racemic ions that bear both negatively and positively charged groups side chain carboxylate anions delocalized ions

ions that bear both negatively and positively charged groups

the ionization of amino acids depends on the pH and the pKas of the ionizable groups. the pK1 and pK2 for the amino acid shown are below are 2.1 and 8..8, respectively. at what pH is the amino acid ionized predominantly as shown? ``` pH 1.0 pH 2.1 pH 5.5 pH 8.8 pH 10.0 ```

1.0

ribosomes use L amino acids to synthesize proteins. these amino acids are called "L" because: they are chiral they turn polarized light to the left they have a config of groups around the Ca that can be related to the configuration of groups around the asymmetric carbon in L-glyceraldehyde they are all (S)- amino acids they are all (R)-amino acids

they have a config...

the … character of most standard amino acids causes solutions of amino acids to rotate the plane of polarized light: ``` chiral zwitterionic polar hydrophobic none ```

chiral

which of the following tripeptides carries a net positive charge at pH 7.0? ``` Ala-Thr-Asn Gln-Val-Ser Arg-Glu-Met Pro-Ile-Leu Leu-Lys0Gly ```

Leu-Lys-Gly

The pK1, pK2, and pKR for the amino acid glutamate are 2.1, 9.5, and 4.1, respectively. At pH 11.0, glutamate would be charged predominantly as follows: a-carboxylate +1, -amino 0, gamma-carboxylate +1, net charge +2 a-carboxylate —1, -amino +1, gamma-carboxylate —1, net charge —1 a-carboxylate 0, -amino 0, gamma-carboxylate 0, net charge 0 a-carboxylate +1, -amino —1, gamma-carboxylate +1, net charge +1 a-carboxylate —1, -amino 0, gamma-carboxylate —1, net charge —2

a-carboxylate —1, -amino 0, gamma-carboxylate —1, net charge —2

The isoelectronic point of an amino acid is the point where the pKa of the -carboxylic acid is the same as the pKa of the -amino group. the -carboxylic acid is protonated and the -amino group is unprotonated. the solubility of the amino acid is maximized. the -carboxylic acid and the -amino group are both half protonated. the amino acid carries no net electrical charge.

the amino acid carries no net electrical charge.

All amino acids derived from proteins have the same stereochemical conformation as. L-glyceraldehyde. (R)-alanine. D-glucose. (S)-cysteine. glycine.

L-glyceraldehyde.

the … structure of a protein is the amino acid sequence of its polypeptide chain, or chains if the protein consists of more than one polypeptide

primary

ion-exchange chromatography: Separation on the basis of charge. Separation on the basis of binding specificity. Separation on the basis of size and shape. Separation on the basis of polarity.

Separation on the basis of charge.

Gel filtration chromatography: Separation on the basis of size and shape. Separation on the basis of binding specificity. Separation on the basis of charge. Separation on the basis of polarity.

Separation on the basis of size and shape.

Affinity chromatography: Separation on the basis of charge. Separation on the basis of binding specificity. Separation on the basis of size and shape. Separation on the basis of polarity.

Separation on the basis of binding specificity.

in polyacrylamide gel electrophoresis, … is often used to denature the proteins and facilitate protein separation through gel filtration effects.

sodium dodecyl sulfate

… uses a stable pH gradient to separate proteins

isoelectric focusing

A protein is most soluble at its isoelectric point. T or F

In two-dimensional (2D) gel electrophoresis, a sample of proteins is first subjected to isoelectric focusing, and then to SDS-PAGE in a perpendicular direction. T or F

Which technique has allowed the purification of proteins of very low natural abundance? Enzyme-linked immunosorbent assay. Ion exchange chromatography. Molecular cloning. Electrophoresis.

Molecular cloning.

dansyl chloride is used for: amino-terminal determination polypeptide cleave on the C side of Lys or Arg. polypeptide cleavage on the C side of Glu polypeptide cleave on the C side of Met reduction of disulfide bonds between cysteine residues

amino-terminal determination

Endopeptidase V8 is used for: amino-terminal determination. polypeptide cleavage on the C side of Met. reduction of disulfide bonds between cysteine residues. polypeptide cleavage on the C side of Glu. polypeptide cleavage on the C side of Lys or Arg.

polypeptide cleavage on the C side of Glu.

2-Mercaptoethanol is used for: polypeptide cleavage on the C side of Lys or Arg. amino-terminal determination. polypeptide cleavage on the C side of Glu. reduction of disulfide bonds between cysteine residues. polypeptide cleavage on the C side of Met.

reduction of disulfide bonds between cysteine residues.

Chymotrypsin is used for: polypeptide cleavage on the C side of Met. amino-terminal determination. polypeptide cleavage on the C side of Glu. polypeptide cleavage on the C side of Trp, Tyr or Phe. reduction of disulfide bonds between cysteine residues. polypeptide cleavage on the C side of Lys or Arg.

polypeptide cleavage on the C side of Trp, Tyr or Phe.

enzymes that catalyze the hydrolysis of N- or C- terminal residues are known as...

exopeptidases

… are enzymes that catalyze the hydrolytic cleavage of internal peptide bonds in a polypeptide

endopeptidases

the amino acid sequence of a polypeptide can be determined through repetitive cycles of the ...

edman degradation

in protein sequencing, the protein is typically degraded into smaller peptides which are sequenced and the full-length protein sequence is then reconstructed by assembling the overlapping fragments. T or F

...: The torsion angles describing rotation about the C -N and C -C bonds in a polypeptide chain.

chi, psi Angles

... this bond lacks rotational freedom because of its 40% double-bond character.

Peptide Bond:

…: common, highly compact peptide segments that typically occur on the protein surface and may have important roles in biological recognition processes

omega loops

…: two alpha helices that twist around each other to form a left handed coil

coiled-coil

…: a regular secondary structure, proposed by Pauling and Corey, in which extended polypeptide chains form interstrand hydrogen bonds

beta sheet

…: a triple helix composed of three left handed helices that are wound around each other with a right hand twist

collagen helix

…: a plot of chi, psi values that indicates the sterically allowed conformations of a polypeptide

Ramachandran diagram

…: a regular secondary structure discovered by Linus Pauling in 1951, in which the C=O oxygen of the nth residue makes a hydrogen bond to the N-H hydrogen of the (n+4)th residue of a polypeptide chain

alpha helix

Which of statements in the following list pairing a biochemical term related to protein structure with its definition or a statement concerning it is INCORRECT

Reverse turns: usually composed of 3 successive residues that cause an abrupt change in the direction of the polypeptide.

In an -helix, which amino acid makes a hydrogen bond to the 2nd residue? 1st. 3rd. 5th. 6th

6th

Which is NOT a result of the existence of Cys residues in -keratin? Hair has the property of "springiness" when stretched slightly. Disulfide bonds cross-link adjacent polypeptide chains. Disulfide bonds help -keratin resist deformation. Hair can be set in a "permanent wave" by reduction and reoxidation of disulfide bonds.

Hair has the property of "springiness" when stretched slightly. (springiness due to coiled coil conformation, which has a tendency to recover its original conformation after being untwisted by stretching)

the amino acid sequence of a polypeptide is also called its .. structure

primary

the local spatial arrangement of a protein's backbone atoms without regard to the conformations of its substituent side chains is called its … structure

secondary

…: two anti-parallel beta strands connected by a tight turn

beta hairpin motif

beta sheets that are rolled up to form a continuous, circular sheet, with the first strand adjacent to the last strand:

beta barrels

..: two successive antiparallel alpha helices packed against each other with their axes slightly inclined

alpha-alpha motif

…: an alpha helix connecting two parallel strands of a beta sheet

beta-alpha-beta motif

… involves two beta-alpha-beta-alpha-beta units that combine to form a dinucleotide binding site.

rossman fold

an … involves a large proportion of beta sheets and is devoid of alpha helices

immunoglobulin fold

… residues occur mostly in the interior of proteins

nonpolar

… residues occur mostly on the surfaces of proteins

charged polar

the entire three-dimensional structure of a single-chain protein, including that of its side chains is called its … structure

tertiary

the beta strands in a beta-alpha-beta motif are parallel. T or F

which of the following statements about domains found in multi-domain proteins is false? they are often structurally independent they contain 20-50 amino acids they resemble small, globular proteins. they often have specialized functions

they contain 20-50 amino acids

… denatures proteins by increasing the solubility of nonpolar groups in water

chaotropic agent

… have an opposite effect as chaotropic agents and preserve protein structure against denaturation caused by heating

cosmotropic

….: electrostatic interactions that usually occur on the surfaces of proteins

ion pairs

..: interferes with the hydrophobic interactions responsible for a protein's native structure

detergent

…: in proteins, the tendency of nonpolar side chains to minimize their contacts with water

hydrophobic effect

…: a protein that can rapidly renature spontaneously

hydrophobic effect

…: a protein that can rapidly renature spontaneously

ribonuclease A

…: they fine-tune tertiary structure by selecting a unique conformation among many hydrophobically-stabilized ones

hydrogen bonds

…: can stabilize folded proteins, e.g. by the tetrahedral coordination of Zn2+

metal ion

…: a measure of the combined hydrophobicity and hydrophilicity of an amino acid residue

hydropathy value

Which statement about disulfide bonds is false? Disulfide bonds help stabilize extracellular proteins. Disulfide bonds can occur between two different polypeptide chains. Can be reductively cleaved by 2-mercaptoethanol. Disulfide bonds are rare in intracellular proteins because the cytoplasm is a reducing environment. Disulfide bonds are not essential for stabilizing a folded protein. Disulfide bonds can occur within a polypeptide chain. Disulfide bonds can occur between either Cys or Met residues.

Disulfide bonds can occur between either Cys or Met residues.

which pairs of amino acid side chains could interact in the interior of a protein only via van der Waals interactions? Gln, His Arg, Thr Val, Leu Ser, Ser

Val, Leu

Which statement about the structure of collagen is FALSE? Collagen includes nonstandard residues like 4-hydroxyproline (Hyp) and 3-hydroxyproline. Collagen include the nonstandard residue 3-hydroxylysine (Hyl). The introduction of vitamin C containing limes to the diet of the British navy alleviated scurvy and led to the nickname “limey” for the British sailor. The modified prolines found in collagen are synthesized from proline post-translationally by an enzyme called prolyl hydroxylase. Scurvy is a disease caused by vitamin C deficiency that results in weak collagen Prolyl hydroxylase requires ascorbic acid (vitamin C) to maintain its activity.

Collagen include the nonstandard residue 3-hydroxylysine (Hyl).

Proteins fold to their native conformations via directed pathways rather than stumbling on them through random conformational searches. Thus, proteins appear to fold in a hierarchical manner, with small local elements of structure forming and then coalescing to yield larger elements, which coalesce with other such elements to form yet larger elements. T or F

Prions are transmitted as follows: Prion P (PrP) is the product of a normal cellular gene that has no known function. Infection of cells by prions somehow alters the PrP protein. Various methods have demonstrated that the harmful, scrapie form of PrP (PrPSc) is identical to normal cellular PrP (PrPC) in sequence but differs in secondary and/or tertiary structure. This suggests that PrPSc induces PrPC to adopt the conformation of PrPSc, that is, a small amount of PrPSc triggers the formation of additional PrPSc from PrPC, which triggers more PrPSc to form, and so on. T or F

Structure Comparisons Reveal Evolutionary Relationships: Most proteins have a related sequence to other proteins, since evolution tends to conserve the sequences of proteins rather than their structures. T or F

Wiley Qs: Flashcards

(138 cards)