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MCAT > MCAT Biology > DNA and Protein Synthesis > Flashcards

DNA and Protein Synthesis Flashcards

DNA, RNA, and protein synthesis is a major topic in both biology and biochemistry. With these cards, you can master the content knowledge required to attack a complicated question or understand a dense experiment-based passage.

1
Q

What biological role is played by nucleic acids?

A

They 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.

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2
Q

How do DNA and RNA differ in their function?

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

A
  • 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.
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3
Q

How do DNA and RNA differ in their structure?

A
  • 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.
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4
Q

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

A
  1. messenger RNA (mRNA)
  2. transfer RNA (tRNA)
  3. 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.

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5
Q

Define:

nitrogenous base

A

They 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.

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6
Q

Define:

nucleotide

A

It 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.

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7
Q

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

A
  1. adenosine triphosphate (ATP)
  2. cyclic AMP (cAMP)

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.

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8
Q

How does a nucleoside differ from a nucleotide?

A

It 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.

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9
Q

Which four bases are present in DNA?

A
  1. adenine
  2. guanine
  3. cytosine
  4. 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.

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10
Q

Which four bases are present in RNA?

A
  1. adenine
  2. guanine
  3. cytosine
  4. 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.

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11
Q

Nitrogenous bases are categorized into which two major groups?

A
  1. purines
  2. pyrimidines

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

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12
Q

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

A
  • 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.
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13
Q

What type of nitrogenous base is the structure below?

A

It is a purine (specifically, adenine).

Purines are notable because they contain two fused rings.

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14
Q

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

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.

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15
Q

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

A

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.

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16
Q

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

A

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.

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17
Q

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

A

DNA molecules are negatively charged.

This charge comes from the sugar-phosphate backbone, not the nitrogenous bases themselves. Specifically, phosphate ion (PO43-) carries a negative charge.

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18
Q

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

A

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.

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19
Q

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

A

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.

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20
Q

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?

A

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.

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21
Q

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

A

It 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).

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22
Q

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

A

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.

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23
Q

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

A

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.

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24
Q

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

A

G-C pair

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.

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25
Q

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?

A

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.

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26
Q

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

A

DNA replication

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

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27
Q

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?

A

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.

28
Q

In DNA replication, what function is performed by helicase?

A

It 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.

29
Q

In DNA replication, what function is performed by topoisomerase?

A

It 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.

30
Q

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

A

They 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.

31
Q

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

A

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.

32
Q

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

A

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.

33
Q

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

A
  • 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.
34
Q

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

A

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.

35
Q

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

A

Like that of the leading strand, synthesis of the lagging strand requires:

  • DNA polymerase
  • primase
  • 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.

36
Q

Which cell types would be expected to contain DNA ligase?

A

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).

37
Q

Which replication enzyme is involved in DNA proofreading?

A

DNA polymerase

In addition to its main role of nucleotide addition, it 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.

38
Q

Which DNA modification is involved in mismatch repair?

A

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.

39
Q

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

A

Like all enzymes involved in DNA replication, it 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.

40
Q

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

A

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.

41
Q

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

A

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.

42
Q

In what direction is a new strand of mRNA synthesized?

A

Like DNA, it 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’.

43
Q

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

A

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.”

44
Q

Give the mRNA sequences of the start and stop codons.

A

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.

45
Q

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.

A

Three

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’

46
Q

What is the difference between introns and exons?

A
  • 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.

47
Q

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

A
  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.

48
Q

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

A

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.

49
Q

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

A

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.

50
Q

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

A
  • 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.
51
Q

Which genetic processes require the action of an RNA polymerase?

A

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.

52
Q

What are the three main steps involved in translation?

A
  1. initiation
  2. elongation
  3. termination
53
Q

Briefly describe the initiation step of translation.

A
  • 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.
54
Q

Briefly describe the elongation step of translation.

A
  • 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.

55
Q

Briefly describe the termination step of translation.

A
  • 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.

56
Q

In what part of the cell is rRNA transcribed?

A

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.

57
Q

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

A
  1. Euchromatin
  2. Heterochromatin

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

58
Q

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

A

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.

59
Q

What is the relationship between a histone and a nucleosome?

A
  • 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.

60
Q

Define:

telomere

A

They 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.

61
Q

What laboratory function is performed by restriction enzymes?

A

Also called endonucleases, they 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.

62
Q

Describe the four types of restriction enzymes.

A
  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.
63
Q

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?

A

type II

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.

64
Q

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

A
  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.
65
Q

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

A

64

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.

MCAT Biology (14 decks)

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