DNA, RNA, and Protein Flashcards
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.
Define:
nitrogenous base
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.
Define:
nucleotide
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.
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.
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?
DNA replication
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?
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.
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.
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.
Define:
degeneracy
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.
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 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
- Heterochromatin
Euchromatin is loosely packed and appears light-colored when viewed under a microscope. Heterochromatin is more dense, or tightly-packed, and appears darker.
Define:
telomere
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.
With regard to mutations, what is an inversion?
A chromosomal mutation in which a nucleotide sequence is completely reversed.
With regard to DNA, what is a translocation?
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.
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.
