Nucleic Acids

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Questions and Answers

Which of the following is true about the glycosidic linkage in nucleosides?

It forms a bond between the C-1' carbon of the sugar and the N-1 nitrogen of purines.

It forms a bond between the C-1' carbon of the sugar and the N-1 nitrogen of pyrimidines. (correct)

It forms a bond between the C-1' carbon of the sugar and the N-9 nitrogen of purines.

It forms a bond between the C-1' carbon of the sugar and the N-9 nitrogen of pyrimidines.

What is the correct terminology for the process of phosphoric acid forming ester bonds with the hydroxyl groups of the sugar?

Esterification (correct)

Phosphorylation

Hydrolysis

Dehydrogenation

Which of the following is NOT a common naturally occurring nucleotide?

Deoxycytidine 5'-monophosphate

Adenosine 3'-monophosphate

Uridine 2'-monophosphate (correct)

Guanosine 5'-monophosphate

What type of bond is formed between the phosphate groups and the hydroxyl groups of adjacent sugar residues in nucleic acids?

Phosphodiester bond Signup and view all the answers

What is the standard notation for representing the sequence of an oligonucleotide?

Using only single letters to represent the order of the bases Signup and view all the answers

What is the primary difference between the sugar moieties in DNA and RNA?

The presence of a hydroxyl group on the 2' carbon in RNA Signup and view all the answers

What is the significance of Chargaff's rule in the discovery of the double-helical structure of DNA?

It showed that the amount of A was always equal to the amount of T Signup and view all the answers

What is the correct notation for representing a 5'-nucleotide?

pA Signup and view all the answers

What is the term for the process of forming nucleic acids from nucleotides?

Polymerization Signup and view all the answers

What is the primary function of the sugar-phosphate backbone in nucleic acids?

To provide a repeating structure for the attachment of bases Signup and view all the answers

What is the smallest unit of a polymer?

Monomer Signup and view all the answers

What is the difference between a nucleoside and a nucleotide?

A nucleotide has a phosphate group, while a nucleoside does not. Signup and view all the answers

Which type of nucleic acid base is thymine?

Pyrimidine Signup and view all the answers

What is the purpose of the order of bases in DNA?

To produce the correct amino acid sequence in proteins Signup and view all the answers

What is a glycosidic bond?

A bond between a sugar and a base Signup and view all the answers

What is the difference between a ribonucleoside and a deoxyribonucleoside?

The type of sugar present Signup and view all the answers

Which of the following bases is found only in RNA?

Uracil Signup and view all the answers

What is the purpose of methylation in nucleic acids?

To modify the structure of a base Signup and view all the answers

What is the primary determinant of the alignment of the helix in DNA?

Hydrogen bonds between bases on opposite chains Signup and view all the answers

What is the diameter of the sugar–phosphate backbone of the double helix?

11 Å (1.1 nm) Signup and view all the answers

What is the distance between the points of attachment of the bases to the two strands of the sugar–phosphate backbone?

11 Å (1.1 nm) Signup and view all the answers

What is the length of one complete turn of the helix along its axis?

34 Å (3.4 nm) Signup and view all the answers

What is the characteristic of the base pairs other than A!T and G!C?

They do not have the correct hydrogen bonding pattern or the right dimensions Signup and view all the answers

What is the form of DNA that is thought to be the principal form that occurs in nature?

B-DNA Signup and view all the answers

What is the characteristic of A-DNA?

Its base pairs are at an angle of about 20° to the perpendicular Signup and view all the answers

What is the characteristic of Z-DNA?

It is a left-handed helix Signup and view all the answers

What is the role of positively charged ions and polypeptides in DNA?

They neutralize the negative charges of the phosphate groups Signup and view all the answers

What is the characteristic of the grooves in the double helix?

They are sites at which drugs or polypeptides can bind to DNA Signup and view all the answers

What is the primary reason for the increase in absorption of light during heat denaturation of DNA?

Unstacking of the bases Signup and view all the answers

What is the characteristic temperature at which DNA from a distinct source melts?

Transition temperature Signup and view all the answers

What is the process by which the order of bases is passed from DNA to RNA?

Transcription Signup and view all the answers

What is the role of ribosomes in protein synthesis?

To translate RNA into protein Signup and view all the answers

What is the process by which single-stranded DNA is obtained?

Heat denaturation Signup and view all the answers

What is the term for the process of recombining separated strands of DNA?

Renaturation Signup and view all the answers

What is the role of transfer RNA (tRNA) in protein synthesis?

To bring amino acids to the assembly site Signup and view all the answers

What is the fundamental process of information transfer in cells?

Translation Signup and view all the answers

What is the sequence of three bases in mRNA that directs the incorporation of a particular amino acid into the growing protein chain?

Codon Signup and view all the answers

What is the primary function of mRNA in protein synthesis?

To specify the order of amino acids in the growing protein chain Signup and view all the answers

What is the primary role of cytosine methylation in DNA?

Regulating gene expression Signup and view all the answers

What is the characteristic of the Z form of DNA compared to the B form?

It has a zigzag look of the phosphodiester backbone Signup and view all the answers

What is the primary function of base stacking in DNA?

Increasing the stability of the double helix Signup and view all the answers

What is the result of the twist and slide of bases in DNA?

Optimal base stacking and reduced water exposure Signup and view all the answers

What is the primary unit of DNA structure used in research?

Dinucleotide Signup and view all the answers

What is the characteristic of a relaxed DNA molecule?

It has no twists in it, other than the helical twists Signup and view all the answers

What is the result of underwinding DNA?

Formation of negative supercoils Signup and view all the answers

What is the effect of negative supercoiling on DNA?

It compacts DNA, making it more torsionally stressed Signup and view all the answers

What is the function of enzymes that affect DNA supercoiling?

To compact DNA Signup and view all the answers

What is the characteristic of prokaryotic DNA?

It is circular and forms supercoils Signup and view all the answers

What is the main difference between prokaryotic and eukaryotic mRNA?

Eukaryotic mRNA undergoes considerable processing, including splicing, while prokaryotic mRNA is directly translated. Signup and view all the answers

What is the role of small nuclear RNAs in eukaryotic cells?

They are involved in the processing of initial mRNA transcription products. Signup and view all the answers

What is the role of micro RNAs in bacteria?

They are involved in the prevention of bacteriophage infection. Signup and view all the answers

What is the function of tRNA nucleotidyltransferase?

It adds the sequence CCA to the 3' end of tRNA. Signup and view all the answers

What is the structure of tRNA?

A single-stranded polynucleotide chain with a cloverleaf structure. Signup and view all the answers

What is the role of the L-shaped conformation of tRNA?

It is necessary for the binding of amino acids to tRNA. Signup and view all the answers

What is the function of RNA interference (RNAi)?

It is involved in the elimination of the effect of a gene. Signup and view all the answers

What is the role of siRNAs in RNA interference?

They are involved in the elimination of the effect of a gene. Signup and view all the answers

What is the purpose of the quality control mechanism in tRNA synthesis?

To prevent the synthesis of defective tRNA molecules. Signup and view all the answers

What is the consequence of a structural defect in tRNA?

The tRNA is degraded through a rapid decay pathway. Signup and view all the answers

What is the primary function of siRNA molecules in many species?

To eliminate expression of undesirable genes, such as those causing uncontrolled cell growth Signup and view all the answers

What is the significance of RNA interference in biotechnology?

It has enabled the development of designer siRNA to knock out specific genes Signup and view all the answers

What is the potential medical application of siRNA technology?

Protecting against viral infections by eliminating viral genes Signup and view all the answers

What is the length of the RNA molecules involved in RNA interference?

20-30 nucleotides Signup and view all the answers

What is the role of scientists in the context of RNA interference?

They are using siRNA to study gene expression Signup and view all the answers

What is the primary function of topoisomerase enzymes in DNA?

To introduce supercoils into DNA Signup and view all the answers

What is the characteristic of Class II topoisomerases?

They cut both strands of DNA and pass some of the remaining DNA helix between the cut ends Signup and view all the answers

What is the purpose of DNA gyrase in bacteria?

To introduce negative supercoils into DNA Signup and view all the answers

What is the method used to detect supercoiled DNA?

Ultracentrifugation Signup and view all the answers

What is the composition of the octamer in chromatin?

(H2A)2(H2B)2(H3)2(H4)2 Signup and view all the answers

What is the function of histones in chromatin?

To tightly bind to DNA and form nucleosomes Signup and view all the answers

What is the significance of the spacer region in chromatin?

It is the region where DNA is complexed to H1 histone and nonhistone proteins Signup and view all the answers

What is the effect of acetylation on histones?

It decreases the positive charge of histones Signup and view all the answers

What is the function of ubiquitin in chromatin?

It is involved in the degradation of other proteins Signup and view all the answers

What is the significance of the absorption of ultraviolet light by DNA?

It is used to measure the concentration of DNA Signup and view all the answers

What is the primary function of ribosomal RNA?

Combining with proteins to form ribosomes Signup and view all the answers

What percentage of the total weight of a ribosome is accounted for by RNA?

60%–65% Signup and view all the answers

What is the sedimentation coefficient of a typical E. coli ribosome?

70S Signup and view all the answers

What is the molecular mass of a typical 5S rRNA?

40,000 Da Signup and view all the answers

How many different proteins are present in the 50S subunit of a prokaryotic ribosome?

34 Signup and view all the answers

What is the purpose of analytical ultracentrifugation in the study of ribosomes?

To monitor the dissociation and reassociation of ribosomes Signup and view all the answers

What is the difference between the sedimentation coefficients of the small and large subunits of a prokaryotic ribosome?

50S Signup and view all the answers

What is the function of messenger RNA in protein synthesis?

Directing amino acid sequence of proteins Signup and view all the answers

What is the sedimentation coefficient of a typical eukaryotic ribosome?

80S Signup and view all the answers

What is the function of small nuclear RNA in eukaryotes?

Processing initial mRNA to its mature form Signup and view all the answers

What is the approximate molecular mass of 16S rRNA?

500,000 Da Signup and view all the answers

What is the primary function of small nuclear RNA (snRNA)?

To help with the processing of the initial mRNA transcribed from DNA Signup and view all the answers

What is the approximate percentage of total cellular RNA comprised of mRNA?

5-10% Signup and view all the answers

What is the name of the larger precursor molecule of mRNA in eukaryotes?

Heterogeneous nuclear RNA (hnRNA) Signup and view all the answers

What is the approximate length of small nuclear RNA (snRNA)?

100-200 nucleotides Signup and view all the answers

What is the primary difference between the turnover of mRNA and other types of RNA?

mRNA is less stable than other types of RNA Signup and view all the answers

What is the sedimentation coefficient of small nuclear ribonucleoprotein particles (snRNPs)?

10S Signup and view all the answers

What is the primary location of mRNA synthesis in eukaryotic cells?

Nucleus Signup and view all the answers

What is the role of the 5'-cap and 3' poly(A) tails in mRNA processing?

To add protective units to the mRNA Signup and view all the answers

What is the significance of the discovery that ribosomal RNA catalyzes the formation of peptide bonds in bacteria?

It highlights the importance of ribosomal RNA in protein synthesis Signup and view all the answers

Study Notes

Structure of Nucleic Acids

Nucleic acids can be broken down into smaller units called monomers, also known as nucleotides.
A nucleotide consists of three parts: a nitrogenous base, a sugar, and a phosphoric acid residue, all covalently bonded together.
The order of bases in the nucleic acids of DNA contains the information necessary to produce the correct amino acid sequence in the cell’s proteins.

Types of Nitrogenous Bases

There are two types of nitrogenous bases: pyrimidines and purines.
The pyrimidine bases are cytosine, thymine, and uracil, which are single-ring aromatic compounds.
The purine bases are adenine and guanine, which are double-ring aromatic compounds.

Nucleosides and Nucleotides

A nucleoside is a compound that consists of a base and a sugar covalently linked together.
When a sugar is linked to a base, a glycosidic bond is formed between the C-1' carbon of the sugar and the N-1 nitrogen of pyrimidines or the N-9 nitrogen of purines.
A nucleotide is formed when phosphoric acid is esterified to one of the hydroxyl groups of the sugar portion of a nucleoside.

Polymerization of Nucleotides

The polymerization of nucleotides gives rise to nucleic acids.
The linkage between monomers in nucleic acids involves the formation of two ester bonds by phosphoric acid.
The resulting repeated linkage is a 3', 5'-phosphodiester bond.

Structure of DNA

DNA consists of two polynucleotide chains wrapped around each other to form a helix.
Hydrogen bonds between bases on opposite chains determine the alignment of the helix, with the paired bases lying in planes perpendicular to the helix axis.
The sugar-phosphate backbone is the outer part of the helix.
The chains run in antiparallel directions, one 3' to 5' and the other 5' to 3'.

Base Pairing

Adenine pairs with thymine and guanine pairs with cytosine.
A-T base pairs have two hydrogen bonds, while G-C base pairs have three hydrogen bonds.

Double Helix Structure

The diameter of the double helix is about 20 Å (2 nm).
The length of one complete turn of the helix along its axis is 34 Å (3.4 nm) and contains 10 base pairs.
There are two grooves in the double helix, a large major groove and a smaller minor groove.

Variations in DNA Structure

There are other forms of DNA, such as A-DNA, which has 11 base pairs for each turn of the helix, and Z-DNA, which is a left-handed helix.
A-DNA is known to occur in dehydrated DNA samples and in DNA:RNA hybrids.
Z-DNA is known to occur in nature, often with sequences of alternating purine-pyrimidine.

Supercoiling

Supercoiling is a twisting or untwisting of the double helix, which can introduce a torsional stress.
There are two types of supercoiling: negative supercoiling, which introduces a torsional stress that favors unwinding of the right-handed B-DNA double helix, and positive supercoiling, which overwinds such a helix.
Enzymes called topoisomerases can change the supercoiling state of DNA.

Chromatin Structure

Eukaryotic DNA is complexed with a number of proteins, especially with basic proteins that have abundant positively charged side chains at physiological pH.
The resulting material is called chromatin.
The principal proteins in chromatin are the histones, of which there are five main types.

Melting of DNA

Heat denaturation is a way to obtain single-stranded DNA.
The melting temperature (Tm) of DNA is dependent on the base composition, with higher percentages of G-C base pairs resulting in higher melting temperatures.

Renaturation of DNA

Renaturation of denatured DNA is possible on slow cooling.
The separated strands can recombine and form the same base pairs responsible for maintaining the double helix.### Replication and Transcription
DNA replication yields two identical DNA molecules, ensuring the transmission of genetic information to daughter cells with high fidelity.
The sequence of bases in DNA is recorded as a sequence of complementary bases in a single-stranded mRNA molecule.

Translation

Three-base codons on the mRNA direct the sequence of amino acids in a protein.
These codons are recognized by tRNAs carrying the appropriate amino acids.
Ribosomes are the "machinery" for protein synthesis.

Information Transfer

The fundamental process of information transfer in cells involves transcribing DNA into RNA, which is then translated into a protein.
This process is encapsulated in the dogma: DNA → RNA → protein.
The details of the process differ between prokaryotes and eukaryotes.

Types of RNA

Transfer RNA (tRNA): transports amino acids to the site of protein synthesis.
Ribosomal RNA (rRNA): combines with proteins to form ribosomes, the site of protein synthesis.
Messenger RNA (mRNA): directs the amino acid sequence of proteins.
Small nuclear RNA (snRNA): involved in the processing of initial mRNA transcripts in eukaryotes.
Small interfering RNA (siRNA): affects gene expression; used to knock out a gene being studied.
MicroRNA (miRNA): affects gene expression; important in growth and development.

tRNA Structure and Function

tRNA is a single-stranded polynucleotide chain with a molecular mass of about 25,000 Da.
Intrachain hydrogen bonding occurs in tRNA, forming A-U and G-C base pairs.
tRNA has a cloverleaf structure, with hydrogen-bonded stems and non-hydrogen-bonded loops.
Modified bases are present in some loops.
tRNA folds into an L-shaped conformation to interact with the enzyme that covalently attaches an amino acid.

rRNA Structure and Function

rRNA molecules are larger than tRNA molecules.
rRNA combines with proteins to form ribosomes.
Ribosomes consist of two subunits: one larger and one smaller.
The smaller subunit consists of one large RNA molecule and about 20 different proteins.
The larger subunit consists of two RNA molecules (in prokaryotes) or three RNA molecules (in eukaryotes) and about 35-50 different proteins.

mRNA Structure and Function

mRNA is the least abundant of the main types of RNA.
mRNA sequences specify the order of amino acids in proteins.
mRNA is formed when it is needed and is degraded shortly after.
mRNA molecules are heterogeneous in size.

snRNA Structure and Function

snRNA is found in the nucleus of eukaryotic cells.
snRNA is small, about 100-200 nucleotides long.
snRNA is complexed with proteins to form small nuclear ribonucleoprotein particles (snRNPs).
snRNPs help with the processing of initial mRNA transcripts into a mature form.

RNA Interference

RNA interference is a process that allows for the control of gene expression.
Short stretches of RNA (siRNAs) can be used to eliminate the expression of a specific gene.
siRNAs are used to protect cells from viruses and to study gene expression.
siRNA has medical applications, such as protecting liver cells from hepatitis.

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Description

Test your knowledge of nucleic acids, including nucleosides, phosphoric acid, and nucleotides. Learn about the bonds and processes involved in their structure and formation.