BIOL3611 FA1

**Includes questions from Quiz 3: On Ch.1.3 and 1.4

If a solution has a proton concentration of 10^-11 M, what is the hydroxide ion concentration? Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

10-11 M

3 M

0.001 M

0.01 M

0.001 M

The measure of randomness is called: Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices:

the hydrophobic effect

the spontaneous effect

enthalpy

entropy

entropy

Complete the following statement: Microorganisms and _____ appeared before the oxygen-containing atmosphere formed.Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

There is no correct answer because microorganisms did not appear until after the oxygen-containing atmosphere formed.

plants

human beings

cells with nuclei

dinosaurs

cells with nuclei

If an acid has a pK_a of 4, then which one of the following BEST indicates the pH at which the acid will be 90% protonated?Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

5

10

4

3

3

What is the charge of DNA at each phosphate?Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

−1

−2

1

0

-1

What might be an effect if DNA nucleotide bases in a double helix were held together by covalent bonds rather than hydrogen bonds?Please choose the correct answer from the following choices, and then select the submit answer button.

Group of answer choices

Replication of DNA, which requires separation of the two strands, would require a larger input of energy.

Purified helices would require very low temperatures to melt apart the two DNA strands.

Transcription of DNA, which requires separation of the two strands, would require a lower input of energy.

The helix would be less stable.

Replication of DNA, which requires separation of the two strands, would require a larger input of energy.

Water is a versatile solvent because of its hydrogen-bonding properties. Which of the following will be the LEAST soluble in water?Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

molecules with hydrogen bond acceptors

hydrophobic compounds

polar molecules

charged compounds

hydrophobic compounds

What property of the DNA structure proposed by Watson and Crick is one of the MOST important to the role of DNA as the genetic material?Please choose the correct answer from the following choices, and then select the submit answer button.

 

Group of answer choices

With the sugar–phosphate backbone on the outside of the helix, the positive charges help make the DNA molecule more soluble in an aqueous environment.

Because the two strands of a DNA molecule are held together by covalent bonds, they can be easily separated and rebound when necessary for replication.

The structure is compatible with any sequence of bases.

Because of base-pairing, the sequence of bases on one strand is identical to the other strand.

The structure is compatible with any sequence of bases.

If I used the appropriate tool in an application to visualize molecular structures, I expect that I could measure and confirm that the H-bonds that stabilize the protein structure are approximately 2 Angstroms in length.

2 Angstroms is equal to _______ nm.

Group of answer choices

20

0.2

200

0.02

none of the other options are suitable because it is actually a smaller value than 0.2 nm

0.2

Considering the following sequence:

5'- C A G G T G G T -3'

 

Write out the opposite strand for use in the question below.

Which one of the following is true regarding this short 8-base-pair segment of sequence? 

This double-stranded molecule:

 

Group of answer choices

has 4 adenines.

would have an increased Tm if you could replace two of the G's shown with A's (i.e. new sequence 5'-CAAATGGT-3' and you had a new appropriate opposite strand sequence that fully paired with this new one)

is stabilized by 21 H-bonds.

has 16 purines.

absorbs light at 260nm more efficiently while in double-stranded form than the corresponding single strands would.

is stabilized by 21 H-bonds.

What might be an effect if DNA nucleotide bases in a double helix were held together by covalent bonds rather than hydrogen bonds?Please choose the correct answer from the following choices.

Group of answer choices

Replication of DNA, which requires separation of the two strands, would require a larger input of energy.

Purified helices would require very low temperatures to melt apart the two DNA strands.

Transcription of DNA, which requires separation of the two strands, would require a lower input of energy.

The helix would be less stable.

Replication of DNA, which requires separation of the two strands, would require a larger input of energy.

DNA has multiple pKa's, but we looked at only one example site. Which one of the following is true according to our discussions of this site in particular and/or of DNA's pH-sensitivity in general?

Group of answer choices

DNA's 'most susceptible site for deprotonation' (i.e. the one that has the pKa that we discussed) is the 2'C of the sugar.

DNA's A, C, G, and T are referred to as nitrogenous 'bases' because they contain many -OH groups.

DNA's phosphates tend to have positive charge at high pH.

DNA is most likely to be 50% single-stranded and 50% double-stranded at pH 7.

DNA is more likely to be single-stranded than double-stranded at low pH (e.g. pH 4) due to over-protonation of what should normally be H-bond acceptors

DNA is more likely to be single-stranded than double-stranded at low pH (e.g. pH 4) due to over-protonation of what should normally be H-bond acceptors

A single stranded DNA molecule can

Group of answer choices

interact by homology only with its complement

interact by homologous sequences only with itself and fold

have partial homologous interactions with itself or a second DNA/RNA molecule if sequence allows

interact with only a second molecule of DNA if the sequence permits

have partial homologous interactions with itself or a second DNA/RNA molecule if sequence allows

Adenine, Guanine, Cytosine and Thymine 

Group of answer choices

are nitrogenous bases

together with sugar and phosphate constitute the building blocks of only DNA

Cytosine and Guanine are purines

Cytosine and thymine are purines

are nitrogenous bases

The length of covalent and non-covalent bonds is important to consider because  

Group of answer choices

covalent bonds such as those found in the nitrogenous bases are always constant

non-covalent bonds are critical for molecules to have a given shape

both covalent and non-covalent bonds restrict or allow for structure

Van der Walls are a covalent type of bonds critical for DNA strcuture stability

both covalent and non-covalent bonds restrict or allow for structure

Take a careful look at the relationships shown below. Where do they come from?

Group of answer choices

They are key for the equilibrium of water

They are well known

They come from Kw

The concentration of pure water in most conditions is 55.5M

They come from Kw

The Meselson and Stahl experiment (also known as pulse chase) showed that 

Group of answer choices

generation zero showed a heavy N15 band at the bottom of the tube

the first generation showed no heavy N15 DNA

the first generation showed an intermediate size band representing N15-N14(light) mix

the first generation showed a size band representing only N14(light)

The first three are true

The first three are true

Which of the following is NOT true of DNA?

Group of answer choices

DNA is antiparallel.

DNA has a backbone made of alternating sugars and phosphates

DNA is a linear polymer containing deoxyribose sugars

The sugars in single stranded DNA are all oriented in the same direction which means a single strand of DNA does NOT have directionality

Deoxyribose is the sugar in DNA.

The sugars in single stranded DNA are all oriented in the same direction which means a single strand of DNA does NOT have directionality

Which of the following best describes the structural backbone of nucleic acids

Group of answer choices

… – base – sugar – base – sugar – …

… – base – phosphate – base – phosphate – …

… – base – phosphate – sugar – base – phosphate – sugar – …

… – phosphate – sugar – phosphate – sugar – …

… – phosphate – phosphate – sugar – phosphate – phosphate – sugar – …

… – phosphate – sugar – phosphate – sugar – …

How does a nucleotide differ from a deoxynucleotide?

 

Group of answer choices

Nucleotides are found in DNA, whereas deoxynucleotides are found in RNA

Purines are only found in nucleotides.

Nucleotides contain a deoxyribose sugars.

pyrimidines are only found in DNA

deoxynucleotides are found only in DNA

deoxynucleotides are found only in DNA

Which of the following statements is NOT true for DNA polymerases?

Group of answer choices

Requires a primer.

uses an RNA template

Direction of synthesis is 5' -> 3'.

Uses a DNA template

uses an RNA template

What are the minimal components needed for DNA replication? 

Group of answer choices

DNA polymerase, DNA or RNA primers with a 3'OH

DNA polymerase, DNA or RNA primers with a 3'OH, nucleotides

magnesium ions

DNA polymerase, DNA or RNA primers with a 3'OH and deoxynucleotides

None of these

None of these

What is the pH of a solution with proton concentration 0.001M?

Group of answer choices

3

2

11

12

None of the others is correct

3

What is the log (base 10) of 100,000,000?

Group of answer choices

8

-8

10

4

None of the others is correct

8

What is the antilog (base 10) of -4?

Group of answer choices

.0001

4

10,000

0.4

None of the others is correct

10^x —> .0001

What is the antilog of 1?

Group of answer choices

10

-1

0.1

1

Undefined

10

If a functional group has a pKa of 9, then what is the deprotonated:protonated ratio for this functional group at pH 4?

Group of answer choices

1:100,000

100,000:1

1:10,000

10,000:1

None of the others is correct

1:100,000

If a functional group has a pKa of 3, then what is the (approximate) likelihood that this functional group will be protonated at pH 5?

Group of answer choices

1%

10%

50%

90%

99%

1%

(The functional group might have been the terminal carboxyl group of a protein, and the environment might have been a slightly acidic organelle like the Golgi complex.) Hopefully you also gave your answer a logical test: does it make sense that a functional group would be mostly deprotonated when the pH is two units higher than the pKa? Yes! And although the actual mathematical answer given by the Henderson-Hasselbalch equation is a 1:100 ratio of deprotonated:protonated (which isn't precisely 1%), sometimes we find it more intuitive to think in percentages rather than ratios. So in this example, we could state approximately that at pH 5, carboxyl groups are about 99% deprotonated and 1% protonated and get a pretty good mental image of their likely protonation status

At what pH is a functional group expected to be ~90% deprotonated if its pKa is 4?

Group of answer choices

5

2

3

4

6

5

Smile! You are on the right track with Henderson-Hasselbalch questions! You found the pH where there is a 10:1 ratio of deprotonated:protonated functional group (which is almost mathematically the same as saying that there is 90% deprotonated and 10% protonated). Make sure to do a logical check – does it make sense to say that deprotonation is favored when the pH is higher than the pKa? Yes! This is always a good logical test of your answer to do on exams….

Which amino acid has the molecular formula C₃H₇NO₃?

Group of answer choices

Ser

Ala

Gln

Lys

Met

Ser

Of course we never memorize amino acid formulas! We are trying to make deductions using the following steps: (1) What atoms does every amino acid have, factoring in the central carbon, the alpha-amino group, and the alpha-carboxyl group? (2) Ignoring the hydrogens, what's left over, and what deductions does that allow us to make??

Which amino acid has an expected net charge of +1 at pH 7?

Group of answer choices

Lys

Asn

Glu

Trp

all four of the listed amino acids

Lys

Great! For side chain pKa’s, only consider those listed in Table 2.1 (remember, we are looking only at those truly classified as acidic/basic, and skipped Cys and Tyr), and group them generally as either being acidic (pKa ~3-4), highly basic (pKa ~11-12), or moderately basic (Histidine, with pKa of 6). For one that has positive charge at pH 7, we want one that's nitrogen-containing and has a high pKa. Also take note that your textbook, unless otherwise noted, aims to show molecules at their most likely charge at pH 7.

What is the most likely net charge of the dipeptide Asp-Glu at pH 10?

Group of answer choices

None of the others is correct

+1

0

-1

-2

None of the others is correct

First, remember that deprotonation is favored when the pH is above the pKa. Next think about the functional groups that any dipeptide has: one amino group (pKa ~8-9), and one carboxyl group (pKa ~3-4). Then note that both side chains contain carboxyl groups as well (each has pKa ~3-4). pH 10 is higher than every pKa under consideration, meaning that deprotonation is favored for all. This means that all three carboxyl groups will have -1 charges and the amino group will have no charge, for a net charge of -3. (-1-1-1 = -3)

What is the net charge of the tripeptide Ser-Arg-Gln at pH 2?

Group of answer choices

+2

+1

-1

0

None of the others is correct

+2

Strong finish! It looks like you’ve accounted for all of the functional groups, and noted that the alpha-carboxyl group will be protonated at such a low pH, and that the alpha-amino group and the Arg side chain will be protonated as well. The charges come only from the alpha-amino group (+1) and the Arg (+1).

The covalent link between a DNA base and the rest of the nucleotide always directly involves one of the base:

carbon atoms.

nitrogen atoms.

hydrogen atoms.

phosphorus atoms.

nitrogen atoms —> The covalent carbon–nitrogen bonds define the structures of the bases themselves.

How many hydrogen bond donors and acceptors are on cytosine that are participating in hydrogen bonds between guanine and cytosine?

one donor and two acceptors

two donors and one acceptor

two acceptors and two donors

one donor and one acceptor

one donor and two acceptors

What property of the DNA structure proposed by Watson and Crick is one of the MOST important to the role of DNA as the genetic material?

With the sugar–phosphate backbone on the outside of the helix, the positive charges help make the DNA molecule more soluble in an aqueous environment.

Because of base-pairing, the sequence of bases on one strand is identical to the other strand.

Because the two strands of a DNA molecule are held together by covalent bonds, they can be easily separated and rebound when necessary for replication.

The structure is compatible with any sequence of bases

The structure is compatible with any sequence of bases

Estimate the length of a carbon–carbon triple bond.

1.54 × 10⁻¹⁰ m

Estimate the length of a carbon–carbon triple bond.

1.54 × 10⁻¹⁰ m

1.2 × 10⁻¹⁰ m

1.35 × 10⁻⁸ m

1.34 Angstroms

1.8 Angstroms

1.35 × 10⁻⁸ m

1.34 Angstroms

1.8 Angstroms

1.2 × 10⁻¹⁰ m —> A typical single carbon–carbon covalent bond has a bond length of 1.54 Å, where 1 Å = 10⁻¹⁰ m. A double bond is 1.34 Å; a triple bond will be even shorter and stronger.

Why does a DNA strand have directionality?

The order of bases along a DNA strand consists of a repetition of the sequence GATC.

Each sugar is oriented in the same way in the sugar–phosphate backbone.

The phosphate groups attach only to one side of the base.

The bases all protrude from the sugar–phosphate backbone

Each sugar is oriented in the same way in the sugar–phosphate backbone.

pKa

The susceptibility of a proton to removal by reaction with a base

• When pH=pKa, the deprotonated and protonated concentrations are the same as the deprotonation process is halfway

pH > pKa

Deprotonation occurs when the pH of the solution is greater than the pKa of the molecule (acids with lower pKa values lose their protons more easily) —> the environment is basic relative to the compound so the compound would lose their proton

pH < pKa

Protonation occurs when the pH of the solution is lower than the pKa of the molecule, as the environment is acidic relative to the compound so the environment donates a proton to the compound

Biochemical similarities in key processes from bacteria to humans suggest:

that bacteria are very different to mammals

that there is a common ancestor to life on earth

the common ancestor is likely to have appeared after microorganisms were detected on earth

biochemical similarities do not mean anything

that there is a common ancestor to life on earth

Avery's experiment demonstrated that DNA was the carrier of the genetic information because:

 

Isolated DNA from one bacterium will transmit a trait to a bacterium that did not have it

Nucleases, DNA hydrolyzing enzymes, kill the transforming ability

Proteases, protein hydrolyzing enzymes, do NOT affect transforming ability

All answers are correct

All answers are correct

Adenine, Guanine, Cytosine and Thymine 

 

are bases found on DNA and RNA

together with deoxysugars and phosphate constitute the building blocks of nucleic acids

Cytosine and Guanine are purines

Cytosine and thymine are purines

all of them are incorrect

all of them are incorrect

The nitrogenous bases 

 

are covalently attached to sugar-phosphate in DNA

the sugar-phosphate are on the inside of the double helix

are the DNA backbone

base pair to each other on the inside of the DNA helix by covalent bonds

are covalently attached to sugar-phosphate in DNA

Water in biochemistry is important because 

 

contributes to the specificity of base pairing

it can make hydrogen bonds to produce highly ordered structures

it is the solvent of life

all answers are correct

all answers are correct

A single stranded DNA molecule can

 

interact by homology only with its complement

interact with homologous sequences only with itself and fold

have partial homologous interactions with itself or a second DNA/RNA molecule if sequence allows

interact with only a second molecule of DNA if the sequence permits

have partial homologous interactions with itself or a second DNA/RNA molecule if sequence allows

Take a look at the DNA image below. 

In the figure the 'W end' label represents 5'.  

If each end label (W, X, Y, Z), was replaced with a 5' or a  3' label, then Z would represent a _____ label. Inspection of the nitrogenous base closest to the W label also shows that it is a _____.

 

3'. Purine

3'. Pyrimidine

5'. Purine

5'. Pyrimidine

5'. Purine

Chargaff's experiments aided in the discovery of the DNA structure because:

 

Only guanines and adenines have a 1:1 ratio in all organisms

Only adenines and thymines have a 1:1 ratio in all organisms 

Guanines and thymines are always in the same proportion

all answers are incorrect

all answers are incorrect

The fact that there is biochemical unity is demonstrated by 

 

Protein diversity and uniqueness among living cells

Protein diversity but evolutionary conservation among living organisms

DNA and protein diversity

Only protein conservation among living organisms

Protein diversity but evolutionary conservation among living organisms

Which of the following domains includes all multicellular organisms?

 

bacteria

archaea

eukaryotes

prokaryotes

eukaryotes

What is the defining characteristic of eukaryotes?

 

Lack of a nucleus

Presence of a nucleus

Unicellular nature

Biochemical similarity to Bacteria

Presence of a nucleus

Carl Woese’s discovery in 1977 led to the recognition of which domain?

Bacteria

Eukarya

Archaea

Prokaryotes

Archaea

Prokaryotes belong to which domains?

 

Eukarya and Bacteria

Bacteria and Archaea

Archaea and Eukarya

Eukarya and Metabolites

Bacteria and Archaea

Why are certain species' biochemical pathways unique?

 

They have no common ancestor.

They evolved in specific biological niches.

They lack metabolic adaptation.

They belong to the same domain.

They evolved in specific biological niches.

Biochemical pathways help scientists understand:

 

Evolutionary history

Physical appearances

Unrelated cellular functions

 Genetic mutations

Evolutionary history

What kind of organisms are included in the domain Eukarya?

 

Only microscopic unicellular organisms

Both multicellular and unicellular organisms

Only plants and animals

Exclusively multicellular organisms

Both multicellular and unicellular organisms

Which statement is true about Archaea?

They include all animals and plants.

They are more biochemically like Eukarya than to Bacteria.

They have a well-defined nucleus.

They were the first domain of life

They are more biochemically like Eukarya than to Bacteria.

Blood contains a total concentration of phosphate of approximately 1 mM and typically has a pH of 7.4. Given that the pK_a of is 7.21, what is the ratio of  [HPO^-2₄] and [H2PO^-₄] in blood?

Tip: is there an equation that relating pH to pKa?

 

0.55

1.55

1

impossible to calculate

1.55

Think about why it is important for blood to maintain a stable pH. Choose the incorrect answer form below:

 

blood contains charged molecules

Blood contains charged molecules that will have altered function at differetn pHs

nothing in blood has the probablity to change its state or charge since it is sterile

Blood is sterile though this is not key for answering this question

nothing in blood has the probablity to change its state or charge since it is sterile

Multiple answers. What does a zwitterionic form of an amino acid mean? Multiple answers

 

The ionization state is altered by changes in pH

aminoacids in solution (in a test tube) exist at neutral pH as dipolar ions

In the dipolar form the amino group is protonated and the carboxyl form is deprotonated

the dipolar form is present at alkaline pHs

A, B, and C

Multiple answers. What are hydrophobic aminoacids?

 

these are a group of Aminoacids with nonpolar R groups 

these are a group of aminoacids with polar R group

these are a group of aminoacids with a single hydrogen

a group of aminoacids that are averse to water

A and D

Mutliple answers. Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine, Tryptophan, and Phenyalanine are 

 

aminoacids that have non-polar R groups

aminoacids that have hydrophilic R groups

aminoacids with a a hydrophobic R group

building blocks of proteins

A, C, and D

Multiple anaswers. Which of the following is true about the polar aminoacids Serine, Threonine, and Tyrosine?

 

The hydroxyl group makes them hydrophilic 

The hydroxyl group makes them more reactive than hydrophobic aminoacids

They are not building blocks of proteins

They are uncharged

A, B, and D

Multiple answers. Which of these statements are true about Lysine and Arginine?

 

They have R groups made of repetitive CH2

The Arginine R group has more NH2s than Lysine

They are highly hydrophobic

They are highly hydrophylic

A, B, and D

These aminoacids have short R groups compared to methionine. Choose the best answer

 

Glycine

Alanine

Lysine

Valine

Glycine

In which one of the following conditions would the dipeptide Pro-Lys be most likely to have a net charge of +2?

 

pH 13

pH 10

pH 6

pH 1

pH 4

pH 1

I was reading recently about a new amino acid that has a pKa of 5

This amino acid  will have an overall ______ net charge at pH 7 and would be attracted to a_______________ charged pole 

 

negative; negative

negative; positive

positive; negative

positive; negative

negative; positive

As you have no doubt encountered, internet images/sources can contain errors! Here is one that I just came across:

Of course we are not memorizing chemical formulas! However we can inspect this one, and compare it to our overall amino acid knowledge in order to determine the impact of the error. 

Which one of the following best describes a  problem with this chemical formula for glutamine, based on what we were supposed to remember about this amino acid (and amino acids in general)?

Knowing what we know about amino acids in general and glutamine in particular, the error in this chemical formula ________.

 

either impacts the side chain or the alpha-carboxyl group (but there is no way to narrow it down further).

either impacts the side chain or the alpha-amino group (but there is no way to narrow it down further).

must definitely impact the alpha-amino group (none of the other answer options are suitable).

must definitely impact the alpha-carboxyl group (none of the other answer options are suitable).

must definitely impact the side chain (none of the other answer options are suitable).

either impacts the side chain or the alpha-carboxyl group (but there is no way to narrow it down further).

Which one of the following molecules (not side chains) has a most likely net charge of +1 at the indicated pH, according to our coverage?

 

Glu at pH 12

Trp at pH 2

Tyr at pH 10

Val at pH 6

His at pH 5

Trp at pH 2

Anfinsen experiment demonstrated that protein......... is encoded in a protein's ...............................structure and was dependent on the ................................of Ribonuclease A

 

structure/secondary/folding

folding/secondary/performance

folding/primary/activity

structure/tertiary/activity

folding/primary/activity

The role of betamercaptoethanol and urea in Anfinsen's experiment is respectively 

 

denaturation of all types of bonds/no role

denaturation of non-covalent bonds/denaturation of covalent bonds

dentaturation of covalent bonds/denaturation of non-covalent bonds

denaturation of hydrogen bonds/denaturation of disulfide bonds

dentaturation of covalent bonds/denaturation of non-covalent bonds

This image is from your book, and we discussed it in class. This image represents 

 

two proteins encoded by two genes

two activities encoded by the same gene

different activities based on the same structure

two activities with the same secondary structures but different tertiary structure

two activities encoded by the same gene

The graph above depicts the interaction of a transcription factor EppR and its cognate binding site on the DNA. The dissociation constant is shown. Choose the incorrect answer

 

The transcription factor extracellular concentration is independent of the KD

The transcription factor intracellular concentration is represented by the KD

The transcription factor intracellular concentration is at least the value of the KD

The transcription factor intracellular concentration is lower than the KD

The transcription factor intracellular concentration is lower than the KD

A protein X was shown to interact with itself, and with additional different proteins, all of them with a different tertiary structure while the KD measured with the different interacting proteins were in similar ranges. Choose below the best explanation for the data.

 

Protein X is encoded by a gene able to form different structures and thus to have multiple interacting partners

Protein X is likely an IDP or has ID regions

There is an error in the measurements and

None of the answer is true

Protein X is likely an IDP or has ID regions

Intrisically disordered proteins or proteins with intrinsically disordered regions

 

All proteins in the proteome contain these regions

adopt a given structure upon interaction with a partner

adopt always an alpha helix structure upon interaction with a partner

adopt always a beta sheet structure upon interaction with a partner

adopt a given structure upon interaction with a partner

The table represents probability of a given aminoacid to be part of an alpha helix, beta sheet or a turn. Choose the incorrect answer 

 

Leu and Ala have similar probabilities to be in alpha helices

Glu is equally likely to be in an alpha helix or in a turn

Alanine is equally likely to be in an alpha helix or a beta sheet

met can be in alpha helices or beta sheets

Alanine is equally likely to be in an alpha helix or a beta sheet