DNA and Protein Synthesis

Question 1

What biological role is played by nucleic acids?

Answer 1

Nucleic acids store genetic material in the form of DNA, allowing it to be inherited. They also direct the formation of protein through translation from mRNA transcripts.

Nucleic acids include DNA, or deoxyribonucleic acid, and RNA, or ribonucleic acid.

Question 2

How do DNA and RNA differ in their function?

Assume that RNA refers to mRNA, not either of the other RNA types.

Answer 2

• DNA stores genetic information in the form of chromosomes. It directs the formation of protein through transcription to RNA and subsequent translation. DNA is self-replicating.
• mRNA is the product of DNA transcription. It is short-lived in the cell, as its function is to be translated into protein. It cannot replicate itself and must be transcribed from DNA.

Question 3

How do DNA and RNA differ in their structure?

Answer 3

• DNA is generally double-stranded, while RNA is single-stranded.
• DNA contains the sugar deoxyribose, while RNA contains ribose. Deoxyribose is similar in structure to ribose, but is missing the hydroxyl group at the 2’ carbon.
• Both DNA and RNA contain adenine, guanine, and cytosine, but the fourth base of DNA is thymine while RNA contains uracil instead.

Question 4

Name the three main types of ribonucleic acid (RNA).

Answer 4

The three types of RNA are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

mRNA is directly translated into protein, while tRNA is involved in carrying the amino acids required for translation. rRNA serves as a main structural component of ribosomes.

Question 5

Define:

nitrogenous base

Answer 5

Nitrogenous bases are molecules that serve as main components of DNA and RNA. As their name implies, all contain nitrogen and display basic properties.

The nitrogenous bases used in normal nucleic acids are guanine, cytosine, adenine, thymine, and uracil.

Question 6

Define:

nucleotide

Answer 6

A nucleotide is a molecule that consists of a nitrogenous base, a sugar, and at least one phosphate group.

The nucleotides that function as nucleic acid subunits contain only a single phosphate, but others, such as ATP, have several.

Question 7

Give two examples of nucleotides that are not components of DNA or RNA.

Answer 7

Nucleotides with non-genetic functions include:

• adenosine triphosphate (ATP), a source of energy produced in cellular metabolism
• cyclic AMP (cAMP), a signaling molecule involved in second messenger cascades

A variety of other examples exist, including GTP and modified nucleotides like NADH and FADH₂.

Question 8

How does a nucleoside differ from a nucleotide?

Answer 8

A nucleoside is simply a nucleotide without any phosphate groups. In other words, a nucleoside contains a nitrogenous base and a sugar molecule.

Technically, the nucleotides used in DNA and RNA can also be called nucleoside monophosphates.

Question 9

Which four bases are present in DNA?

Answer 9

DNA contains adenine, guanine, cytosine, and thymine.

Guanine is complementary to cytosine, while adenine is complementary to thymine. This means that those two pairs of bases always hydrogen bond together in double-stranded DNA.

Question 10

Which four bases are present in RNA?

Answer 10

RNA contains adenine, guanine, cytosine, and uracil.

Guanine is complementary to cytosine, while adenine is complementary to uracil. When RNA is transcribed from DNA, the new RNA strand will contain bases that are complementary to the template DNA.

Question 11

Nitrogenous bases are categorized into which two major groups?

Answer 11

The two major groups of nitrogenous bases are purines and pyrimidines.

Adenine and guanine are purines, while cytosine, thymine, and uracil are pyrimidines.

Question 12

How are purines similar to pyrimidines, and how are they different?

Answer 12

Both purines and pyrimidines contain one or more nitrogen-containing heterocyclic rings, and both are major components of DNA and RNA.

However, pyrimidines consist of a single six-membered ring that contains two nitrogens. Purines consist of two fused rings: one pyrimidine ring and one five-membered imidazole ring.

Question 13

What type of nitrogenous base is the structure below?

Answer 13

This structure is a purine (specifically, adenine). Purines are notable because they contain two fused rings.

Question 14

What term is given to the characteristic structure of double-stranded DNA (dsDNA)?

Answer 14

Double-stranded DNA forms a double helix. Two complementary strands are held together in a twisting, or helical, shape.

The strands are composed of nucleotides, or nitrogenous bases held in place by a sugar-phosphate backbone.

Question 15

What type of bonds connect an adenine base with a thymine on the complementary strand?

Answer 15

Hydrogen bonds connect the bases of two distinct, complementary strands.

Though hydrogen bonds are strong for intermolecular interactions, they are much weaker than covalent bonds. For this reason, it is possible to pull apart, or denature, double-stranded DNA.

Question 16

What type of bonds connect a deoxyribose sugar with an adjacent phosphate on the same strand?

Answer 16

Covalent bonds connect the adjacent components of each strand’s backbone.

The strand begins with a free phosphate group at the 5’ carbon of the first sugar. From there, sugar and phosphate alternate; one phosphate is located on both sides of each sugar, bound to its 5’ and 3’ carbons. Finally, the sugar at the 3’ end contains a free hydroxyl group.

Question 17

What electrical charge, if any, exists on DNA molecules?

Answer 17

DNA molecules are negatively charged.

This charge comes from the sugar-phosphate backbone, not the nitrogenous bases themselves. Specifically, phosphate ion (PO₄^3-) carries a negative charge.

Question 18

In gel electrophoresis, the anode is positive while the cathode is negative. Toward which electrode will DNA migrate?

Answer 18

DNA will migrate toward the anode, or positive terminal.

Due to the presence of phosphate groups on its backbone, DNA is negatively charged. Since opposite charges experience attractive forces, it will move toward a positive electrode.

Question 19

Which two numbers are used to denote the ends of a DNA strand?

Answer 19

5’ and 3’ (pronounced “five prime” and “three prime”)

The 5’ end of a DNA strand contains an unbound phosphate group, while its 3’ end is marked by a free -OH.

Question 20

In double-stranded DNA, the 5’ end of one strand lines up with the 3’ end of the other. What term describes this structural relationship?

Answer 20

DNA strands are antiparallel. They are situated next to each other but point in opposite directions.

For this reason, be careful when finding the complementary sequence to a certain strand. The 3’ end must align with the 5’ end of its complement, and vice versa.

Question 21

Explain Chargaff’s rules for the DNA bases contained in double-stranded DNA.

Answer 21

Double-stranded DNA must contain:

• the same number of purines as pyrimidines
• the same number of guanine and cytosine bases
• the same number of adenine and thymine bases

These rules are true due to the complementarity of double-stranded DNA. Adenine (a purine), always pairs with thymine (a pyrimidine). Guanine (a purine) always pairs with cytosine (a pyrimidine).

Question 22

A single fragment of DNA has the sequence 5’-AGATTCG-3’. Give the complementary sequence, beginning from its 5’ end.

Answer 22

5’-CGAATCT-3’

When finding this sequence, remember that dsDNA strands are antiparallel; in other words, the 5’ end of one strand must contain complementary bases to the 3’ end of the other. Since this strand must begin with 5’, start at the 3’ end of the given fragment. C is complementary to G, and A is complementary to T.

Question 23

If a piece of single-stranded DNA contains 28 adenine nucleotides, how many thymine bases must it also contain?

Answer 23

This cannot be answered.

Chargaff’s rules dictate that adenine and thymine must be present in a 1:1 ratio; however, this applies to double-stranded DNA alone. Since this single DNA strand is not associated with a complementary partner, any number of thymines may be present.

Question 24

In a segment of double-stranded DNA, which base pair is stronger: A-T or G-C?

Answer 24

A G-C pair is stronger.

Guanine and cytosine are connected by three hydrogen bonds, while adenine and thymine are only bound by two. For this reason, a DNA strand rich in G and C bases will associate more strongly with its complement.

Question 25

Throughout a series of PCR reactions, it is noted that DNA Strand A denatures at a lower temperature than DNA Strand B. Which property of the two strands might determine this result?

Answer 25

Strand A likely has more adenine and thymine bases, while Strand B probably contains more guanines and cytosines.

This property is referred to as GC content. Strands with more G and C bases will denature at a higher temperature, as the three hydrogen bonds between guanine and cytosine form a stronger connection than the two between adenine and thymine.

Question 26

Which process allows a double-stranded DNA molecule to split apart and form two identical copies?

Answer 26

DNA replication

Replication involves a number of enzymes, including DNA polymerase, helicase, and topoisomerase. Note that RNA molecules, unlike DNA, are not self-replicating.

Question 27

When DNA is replicated, the parent strands separate so each copy contains one original and one new strand. What name is given to this process?

Answer 27

This process is called semiconservative replication. The original molecule is partially conserved: though the parent strands separate, each of them is fully present in one of the two new copies.

Two other theories of replication, now shown to be incorrect, are the dispersive model and the conservative model.

Question 28

In DNA replication, what function is performed by helicase?

Answer 28

Helicase moves along double-stranded DNA molecules ahead of the replication fork, separating the two bound strands so replication can occur.

The enzymatic function of helicase requires ATP.

Question 29

In DNA replication, what function is performed by topoisomerase?

Answer 29

Topoisomerase relieves supercoiling, or strain caused by excess twisting of the DNA helix. It does this by breaking the sugar-phosphate backbone, unwinding, and reannealing.

This function is necessary because as helicase “unzips” the double-stranded molecule, the region ahead of the replication fork becomes supercoiled. Without topoisomerase, this would make replication progressively more difficult.

Question 30

In DNA replication, what function is performed by single-stranded binding proteins?

Answer 30

Single-stranded binding proteins attach to each of the two strands and keep them apart to facilitate replication.

In other words, these proteins prevent reannealing until the strands have been properly replicated by DNA polymerase.

Question 31

What broad name is given for enzymes that add nucleotides, one by one, onto a growing nucleic acid strand?

Answer 31

These enzymes are polymerases. While a variety of examples exist in both prokaryotes and eukaryotes, those that synthesize DNA are broadly known as DNA polymerases, while those that synthesize RNA are called RNA polymerases.

In bacteria, the main nucleotide-adding function is performed by DNA pol III.

Question 32

Which enzyme functions as an RNA polymerase but is involved in DNA replication?

Answer 32

Primase

Although replication serves to synthesize new strands of DNA, this process cannot be initiated without a short RNA sequence, or primer. Primase adds these sequences at the beginning of the area to be replicated. Later, primers are excised, replaced with DNA nucleotides, and connected by the enzyme DNA ligase.

Question 33

The diagram below shows the leading and lagging strands at a replication fork. What features distinguish these two structures?

Answer 33

The leading strand points toward the replication fork when read from 5’ to 3’. Since DNA polymerase can only add nucleotides to the 3’ end, the leading strand can be synthesized continuously as the fork opens in front of it.

The lagging strand points away from the replication fork when read from 5’ to 3’. It must be synthesized discontinuously in a series of short Okazaki fragments. Later, these fragments must be joined by DNA ligase.

Question 34

Name the short DNA segments that are synthesized discontinuously during replication of the lagging strand.

Answer 34

The short fragments synthesized by DNA polymerase are called Okazaki fragments.

Like all other segments, they are elongated from 5’ to 3’, but point away from the opening replication fork. The polymerase must constantly “jump back” and synthesize new fragments.

Question 35

Name the enzymes that are involved in the synthesis of the lagging strand.

Answer 35

Like that of the leading strand, synthesis of the lagging strand requires DNA polymerase, primase, and DNA ligase.

However, the lagging strand involves a larger amount of primase and ligase activity, since each Okazaki fragment must begin with a distinct RNA primer. These fragments must be ligated after RNA is excised and replaced with DNA.

Question 36

Which cell types would be expected to contain DNA ligase?

Answer 36

Nearly every cell type, in both eukaryotes and prokaryotes, must contain DNA ligase. It serves a vital function: to connect DNA fragments during replication, mainly those synthesized discontinuously on the lagging strand.

The only cells that could function without ligase would be those that do not contain DNA at all, like erythrocytes (red blood cells).

Question 37

Which replication enzyme is involved in DNA proofreading?

Answer 37

DNA polymerase, in addition to its main role of nucleotide addition, also monitors the growing strand for errors.

Mistakes in which the wrong base is paired with its complementary template are called mismatch errors. DNA polymerase senses the weak bonding associated with such errors, excises the incorrect base, and replaces it with the correct one.

Question 38

Which DNA modification is involved in mismatch repair?

Answer 38

Methylation, or the addition of a methyl group to a nucleotide, helps DNA polymerase distinguish between the parent strand and the newly synthesized one.

This role is important when an incorrect base has been incorporated. DNA polymerase must excise the mismatched base from the new strand, not the sequentially correct parent.

Question 39

In which region of a eukaryotic cell would helicase be found?

Answer 39

Helicase, like all enzymes involved in DNA replication, would be found in the nucleus.

Both replication and transcription occur in the nucleus, while translation occurs on ribosomes in the cytosol or bound to the rough ER.

Question 40

How do the terms sense strand, antisense strand, and template strand relate to the RNA strand initially produced during transcription?

Answer 40

The sense strand is exactly the same as the RNA strand, except it contains thymine instead of uracil.

The antisense strand is directly transcribed into RNA. Because of this, it is complementary to the new RNA strand, except it contains thymine instead of uracil. The antisense strand is also called the template strand.

Question 41

Which process allows a single-stranded mRNA molecule to be synthesized from a DNA template?

Answer 41

Transcription

Like replication, transcription takes place in the nucleus. It produces a strand that is complementary and antiparallel to the original DNA, with uracil bases replacing thymine.

Question 42

In what direction is a new strand of mRNA synthesized?

Answer 42

Like DNA, mRNA is synthesized from 5’ to 3’. In other words, nucleotides are added to the 3’ end of the growing strand.

Due to its antiparallel nature, the DNA template is read in the opposite direction, from 3’ to 5’.

Question 43

In eukaryotes, one mRNA transcript codes for exactly one polypeptide molecule. What name is given to this characteristic, and what is its opposite?

Answer 43

Eukaryotic mRNA is monocistronic, while that of prokaryotes is polycistronic.

Eukaryotic, but not prokaryotic, DNA undergoes post-transcriptional modification. After this modification, the mature mRNA transcript contains the sequence for a single peptide. In contrast, a prokaryotic mRNA transcript can code for many proteins and includes multiple start and stop codons.

Polycistronic means “many genes.”

Question 44

Give the mRNA sequences of the start and stop codons.

Answer 44

The start codon is AUG. It codes for a methionine amino acid residue.

The stop codons are UGA, UAG, and UAA. They do not code for amino acids, but signal the termination of translation.

Question 45

Between the start and stop codons in the sequence below, how many complete codons are present?

5’-GUAUGCUCAGUACUUAG-3’

Do not include the start and stop codons themselves.

Answer 45

Three codons are present.

Below, the start and stop codons are bolded. Nine nucleotides are included between the two; since three nucleotides comprise a codon, exactly three codons are present.

5’-GUAUGCUCAGUACUUAG-3’

Question 46

What is the difference between introns and exons?

Answer 46

Only exons are eventually transcribed into protein. Introns are noncoding DNA sequences that are excised from mRNA as part of post-transcriptional modification.

The removal of introns and splicing of exons occurs in the nucleus as part of the production of mature mRNA.

Question 47

Name the three main post-transcriptional modifications that are made to eukaryotic DNA.

Answer 47

1. The 5’ end is capped. Specifically, this cap consists of a 7-methylguanosine molecule.
2. The 3’ end is polyadenylated, forming the poly-A tail. This tail is simply a string of adenine nucleotides.
3. Introns are removed from the sequence and exons, or coding sequences, are spliced together.

After these processes have concluded, the mRNA transcript is mature and can be exported from the nucleus.

Question 48

How do post-transcriptional modifications differ in eukaryotes versus prokaryotes?

Answer 48

Prokaryotic mRNA does not undergo post-transcriptional modification.

Unlike in eukaryotes, where transcription and translation are distinct processes and occur in different locations, prokaryotic transcription and translation are simultaneous. Also, prokaryotes do not have introns.

Question 49

Which process allows a polypeptide to be synthesized from an mRNA transcript?

Answer 49

Translation

Unlike replication and transcription, which take place in the nucleus, translation occurs on ribosomes. It involves the synthesis of a polypeptide chain where each amino acid residue corresponds to a three-base mRNA codon.

Question 50

How does the cellular location of translation differ from that of transcription and replication?

Answer 50

Translation occurs on a ribosome, whether free-floating in the cytosol or bound to the rough endoplasmic reticulum.

Transcription and replication occur in the nucleus.

Question 51

Which genetic processes require the action of an RNA polymerase?

Answer 51

Both replication and transcription need an RNA polymerase to occur properly.

Since transcription involves the synthesis of mRNA, it clearly requires RNA polymerase. However, even replication cannot be initiated without short RNA sequences called primers. Primase, an enzyme with RNA polymerase activity, functions in this process.

Question 52

What are the three main steps involved in translation?

Answer 52

Initiation, elongation, and termination

Question 53

Briefly describe the initiation step of translation.

Answer 53

• The ribosomal subunits assemble, and the start codon of mRNA (AUG) binds to the ribosome.
• A tRNA molecule with the corresponding anticodon, carrying a methionine residue, enters the ribosome as well.

Question 54

Briefly describe the elongation step of translation.

Answer 54

• More tRNA molecules, each with an anticodon corresponding to the next codon on the mRNA chain, approach the ribosome one at a time.
• Their amino acids attach to the growing polypeptide chain, and peptide bonds are formed by the enzyme peptidyl transferase.

The new polypeptide chain is synthesized from its N (amino) terminal to its C (carboxy) terminal.

Question 55

Briefly describe the termination step of translation.

Answer 55

• The ribosome approaches the stop codon, terminating translation when it is read.
• The new polypeptide chain is released and the ribosomal subunits separate.

The mRNA stop codons are UGA, UAG, and UAA.

Question 56

In what part of the cell is rRNA transcribed?

Answer 56

Ribosomal RNA (rRNA) is transcribed in the nucleolus, a region within the nucleus. This area is also the site of ribosome assembly from protein and rRNA.

The nucleolus temporarily disappears during prophase of mitosis and meiosis.

Question 57

Name the two main types of chromatin found in eukaryotic cells.

Answer 57

Euchromatin and heterochromatin

Euchromatin is loosely packed and appears light-colored when viewed under a microscope. Heterochromatin is more dense, or tightly-packed, and appears darker.

Question 58

Which type of chromatin is likely to be more prevalent in genes that are actively being transcribed?

Answer 58

Euchromatin

Euchromatin is the loosely-wound form of chromatin, which allows enzymes like RNA polymerase access to the nucleotide structure. In contrast, heterochromatin is dense and protects the DNA when it is not being transcribed.

Question 59

What is the relationship between a histone and a nucleosome?

Answer 59

Histones are small proteins that form core complexes, around which DNA wraps tightly. A nucleosome includes a histone core and its associated DNA.

These structures are present in chromatin, the tightly packed organizational structure that forms chromosomes.

Question 60

Define:

telomere

Answer 60

Telomeres are repetitive sequences of DNA that are positioned at the ends of chromosomes. They are thought to protect the DNA from degeneration.

Telomeres shorten over time, a process that may be connected to aging and the medical problems that come with it.

Question 61

What laboratory function is performed by restriction enzymes?

Answer 61

Restriction enzymes, also called endonucleases, cut DNA strands at specific sequences. In genetic research, restriction enzymes are used to cut DNA for later sequencing or manipulation.

These enzymes are generally isolated from bacteria, in which they serve a protective function by cleaving the DNA of foreign invaders.

Question 62

Describe the four types of restriction enzymes.

Answer 62

1. Type I enzymes cut DNA at distant positions from their recognition sequences. These enzymes are not generally used in research.
2. Type II enzymes cut DNA either inside or near their recognition sequences. These are the enzymes that serve a laboratory function.
3. Type III enzymes are large and cleave at fairly distant positions from their recognition sites, which must contain two inverted sequences.
4. Type IV enzymes recognize methylated DNA or that which has undergone other modifications.

Question 63

The restriction enzyme HindIII cleaves DNA at a short sequence within its recognition site. It is one of the most commonly used enzymes in laboratory research. Which type of restriction enzyme is HindIII most likely to be?

Answer 63

HindIII is a type II restriction enzyme.

Only type II enzymes cleave within or very close to their recognition sites; for this reason, they include most restriction enzymes typically used for research purposes.

Question 64

Name and briefly describe the three steps involved in a polymerase chain reaction (PCR)?

Answer 64

1. Denaturation. Heating separates the two DNA strands, making them available for replication.
2. Annealing. Specific primers attach to the DNA strands, specifying the location to be replicated.
3. Extension. Free nucleotides are added to the growing strand by a polymerase, usually one acquired from a thermostable bacterium.

Question 65

After several rounds of PCR replication, 16 molecules of DNA are present. How many molecules should exist after two more rounds?

Answer 65

64 molecules

Each additional round of PCR should double the existing number of DNA strands. The same math works when calculating the products of normal DNA replication: 2ⁿ strands will be present after n rounds of replication.