What biological role is played by nucleic acids?
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.
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.
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.
How does a nucleoside differ from a nucleotide?
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.
Nitrogenous bases are categorized into which two major groups?
The two major groups of nitrogenous bases are purines and pyrimidines.
Adenine and guanine are purines, while cytosine, thymine, and uracil are pyrimidines.
How are purines similar to pyrimidines, and how are they different?
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.
What type of nitrogenous base is the structure below?
This structure is a purine (specifically, adenine). Purines are notable because they contain two fused rings.
Which four bases are present in DNA?
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.
Which four bases are present in RNA?
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.
Explain Chargaff's rules for the DNA bases contained in double-stranded DNA.
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).
In a segment of double-stranded DNA, which base pair is stronger: A-T or G-C?
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.
Researchers observe that DNA Strand A denatures at a lower temperature than DNA Strand B. Which property of the two strands might determine this result?
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.
How do DNA and mRNA differ in their function?
- 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.
How do DNA and RNA differ in their structure?
- 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.
Give two examples of nucleotides that are not components of DNA or RNA.
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.
What term is given to the characteristic structure of double-stranded DNA (dsDNA)?
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.
What type of bonds connect an adenine base with a thymine on the complementary strand?
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.
What type of bonds connect a deoxyribose sugar with an adjacent phosphate on the same strand?
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.
What electrical charge, if any, exists on DNA molecules?
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.
In gel electrophoresis, the anode is positive while the cathode is negative. Toward which electrode will DNA migrate?
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.
Which two numbers are used to denote the ends of a DNA strand?
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.
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?
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.
A single fragment of DNA has the sequence 5'-AGATTCG-3'. Give the complementary sequence, beginning from its 5' end.
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.
If a piece of single-stranded DNA contains 28 adenine nucleotides, how many thymine bases must it also contain?
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.
Which process allows a double-stranded DNA molecule to split apart and form two identical copies?
Replication involves a number of enzymes, including DNA polymerase, helicase, and topoisomerase. Note that RNA molecules, unlike DNA, are not self-replicating.
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?
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.
What broad name is given for enzymes that add nucleotides, one by one, onto a growing nucleic acid strand?
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.
In DNA replication, what function is performed by helicase?
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.
Which enzyme functions as an RNA polymerase but is involved in DNA replication?
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.
In DNA replication, what function is performed by single-stranded binding proteins?
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.
In DNA replication, what function is performed by topoisomerase?
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.
In which region of a eukaryotic cell would helicase be found?
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.
The diagram below shows the leading and lagging strands at a replication fork. What features distinguish these two structures?
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.
Name the short DNA segments that are synthesized discontinuously during replication of the lagging strand.
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.
Name the enzymes that are involved in the synthesis of the lagging strand.
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.
Which cell types would be expected to contain DNA ligase?
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).
Which replication enzyme is involved in DNA proofreading?
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.
Which DNA modification is involved in mismatch repair?
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.
Name the three main types of ribonucleic acid (RNA).
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.
In what direction is a new strand of mRNA synthesized?
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'.
Which process allows a single-stranded mRNA molecule to be synthesized from a DNA template?
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.
How do the terms sense strand, antisense strand, and template strand relate to the RNA strand initially produced during transcription?
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.
A certain mRNA sequence reads 5'-AUGCCAUGU-3'. In this context, what term describes AUG, CCA, and UGU?
Those three sequences are codons. A codon is a set of three nucleotides that corresponds to a particular amino acid.
Give the mRNA sequences of the start and stop codons.
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.
Between the start and stop codons in the sequence below, how many complete codons are present?
Do not include the start and stop codons themselves.
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'-GUAUG CUC AGU ACU UAG-3'
Degeneracy refers to the property of the genetic code that allows multiple codons to code for the same amino acid.
Specifically, there are 64 possible codons and only 20 relevant amino acids. Codons for the same amino acid often differ at the position of their third base.
Which genetic processes take place in the nucleus?
The main processes that take place in the nucleus are replication and transcription.
In contrast, translation occurs at ribosomes outside the nucleus. These organelles can either be bound to the ER or located in the cytoplasm.
In what part of the cell is rRNA transcribed?
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.
What is the difference between introns and exons?
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.
Which three main processes are involved in post-transcriptional modification of eukaryotic DNA?
- The 5' end is capped. Specifically, this cap consists of a 7-methylguanosine molecule.
- The 3' end is polyadenylated, forming the poly-A tail. This tail is simply a string of adenine nucleotides.
- 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.
How do post-transcriptional modifications differ in eukaryotes versus prokaryotes?
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.
How does the cellular location of translation differ from that of transcription and replication?
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.
Which genetic processes require the action of an RNA polymerase?
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.
Which process allows a polypeptide to be synthesized from an mRNA transcript?
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.
What are the three main steps involved in translation?
Initiation, elongation, and termination
Briefly describe the initiation step of translation.
- 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.
Briefly describe the elongation step of translation.
- 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.
Briefly describe the termination step of translation.
- 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.
In eukaryotes, one mRNA transcript codes for exactly one polypeptide molecule. What name is given to this characteristic, and what is its opposite?
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."
How many chromosomes do human cells contain?
Human cells contain 46 chromosomes.
Human chromosomes are organized into 23 homologous pairs, the members of which code for the same traits but are genetically different. Corresponding alleles are located on homologous chromosomes.
What is the relationship between a histone and a nucleosome?
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.
Name the two main types of chromatin found in eukaryotic cells.
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.
Which type of chromatin is likely to be more prevalent in genes that are actively being transcribed?
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.
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.
What is a mutation, and how does it arise?
A mutation is an alteration in DNA sequence. Mutations can arise spontaneously (often from errors in DNA replication) or be induced by mutagenic substances.
For the AP Biology exam, remember that mutations never arise in response to selective pressure. For example, a resistant strain of bacteria did not mutate to become resistant; the mutation arose spontaneously and persisted due to its evolutionary advantage.
In the replication of a DNA strand, an adenine base is included instead of a cytosine. The rest of the strand is replicated normally. What type of mutation occurred?
Since one base was replaced with another, a substitution mutation occurred.
Such a mutation can also be described as a point mutation, since only a single base was altered.
What is the result of a missense mutation?
A missense mutation replaces one amino acid with another.
For example, the codon AGU codes for the placement of a serine residue, while AGG codes for the placement of arginine. A simple substitution of G for U, then, can result in a missense mutation.
What is the result of a nonsense mutation?
A nonsense mutation transforms an amino acid into a stop codon, resulting in a shortened and often nonfunctional protein.
The three stop codons are UGA, UAA, and UAG. The start codon is AUG, which corresponds to methionine.
Some changes in DNA sequence, known as silent mutations, do not affect the organisms in which they occur. Describe two situations that could lead to a silent mutation.
A silent mutation could be caused by:
- A mutation in an intron, or noncoding, sequence
- A mutation that replaces one degenerate codon with another
With regard to mutations, what is an inversion?
An inversion is a chromosomal mutation in which a nucleotide sequence is completely reversed.
With regard to DNA, what is a translocation?
A translocation is a chromosomal mutation in which a nucleotide sequence moves to another position, either within the same or between different chromosomes.
Name two types of mutation that lead to a frameshift.
A frameshift mutation can be caused by:
- Insertion, or the addition of one or more nucleotides
- Deletion, or the removal of one or more nucleotides
Note that the insertion or deletion of a multiple of three nucleotides would not result in a frameshift.
Which is more likely to be harmful: a base substitution or a frameshift mutation?
A frameshift mutation is much more likely to adversely affect the organism.
While a single-base substitution only changes at most a single codon, a frameshift causes the entire reading frame to be moved. This alters many or even all of the amino acids after the aberration, resulting in a drastically different or nonfunctional protein.
Which is more likely to be harmful: a missense or a nonsense mutation?
A nonsense mutation is much more likely to adversely affect the organism.
While a missense mutation only changes a single amino acid to another, a nonsense mutation causes the entire process of translation to be prematurely stopped. This results in a shorter and often functionally useless protein.
A student argues that a species without mutations would be evolutionarily favorable, since its genetic code would be free of errors. Describe the major flaw in this student's reasoning.
Mutations provide genetic variation, which is evolutionarily vital.
In bacteria, for example, mutations can result in the survival advantage of antibiotic resistance. Without these mutations, the entire species would be equally susceptible to attack.
A mutagen is a chemical or other substance that can induce changes in DNA. In what related category are many mutagens included?
Mutagens are often classified as carcinogens, or cancer-causing substances.
Name and briefly describe the three steps involved in a polymerase chain reaction (PCR)?
Denaturation. Heating separates the two DNA strands, making them available for replication.
Annealing. Specific primers attach to the DNA strands, specifying the location to be replicated.
Extension. Free nucleotides are added to the growing strand by a polymerase, usually one acquired from a thermostable bacterium.
After several rounds of PCR replication, 16 molecules of DNA are present. How many molecules should exist after two more rounds?
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.
What laboratory function is performed by restriction enzymes?
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.