Biochemistry 314: Nucleic Acids

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Questions and Answers

What are the two main types of nucleic acids?

Lipids and Hormones

Amino acids and Nucleotides

Proteins and Carbohydrates

Ribonucleic acid (RNA) and Deoxyribonucleic acid (DNA) (correct)

What is the primary role of DNA in the cell?

To provide structural support to cells

To store genetic information and guide RNA synthesis (correct)

To transport nutrients across cell membranes

To catalyze biochemical reactions

What are nucleotides composed of?

A sugar, a phosphate group, and a nitrogenous base (correct)

An amino group, a carboxyl group, and a side chain

A fatty acid, a glycerol, and a carbohydrate

A glucose molecule and a ribosome

Which process involves the synthesis of mRNA from DNA?

Transcription Signup and view all the answers

What is a key feature of gene function?

Gene function is controlled by gene products and signaling pathways Signup and view all the answers

How many types of monomeric units make up nucleic acids?

Four types Signup and view all the answers

Which of the following correctly describes the pathway of genetic information?

DNA -> RNA -> Protein Signup and view all the answers

What is not a function of nucleic acids?

Catalyzing metabolic reactions Signup and view all the answers

What significant conclusion was drawn from the experiments by Avery, MacLeod, and McCarty in 1944?

DNA contains the genetic information. Signup and view all the answers

Which scientist is credited with the discovery of the DNA double helix structure?

James Watson and Francis Crick Signup and view all the answers

What structural feature distinguishes purines from pyrimidines?

Purines have a two-ring system while pyrimidines have a single ring. Signup and view all the answers

Who made significant contributions to understanding the molecular structure of DNA aside from Watson and Crick?

Rosalind Franklin Signup and view all the answers

How do purines and pyrimidines stabilize double-stranded DNA?

Through their planar character facilitating stacking. Signup and view all the answers

What is the primary sugar component found in RNA?

Ribose Signup and view all the answers

What is a common misconception regarding the sizes of purines and pyrimidines?

Pyrimidines are larger with a more complex structure. Signup and view all the answers

In physiological conditions, which forms of purines and pyrimidines are favored?

Amino and oxo forms Signup and view all the answers

What distinguishes the sugar atoms in nucleosides from the heterocyclic base atoms?

The numbering system with primes Signup and view all the answers

Which sugar is found in ribonucleosides?

D-ribose Signup and view all the answers

How are the sugar and heterocyclic base linked in nucleosides?

Through a -N-glycosidic bond Signup and view all the answers

What type of conformers predominates in nature for nucleosides?

Anti conformers Signup and view all the answers

What is the significance of the 5′- and 3′-nucleotides?

They indicate the location of the phosphoryl group on the sugar Signup and view all the answers

What typically happens to the prefix '5′-' in nucleotide naming?

It is omitted in most cases Signup and view all the answers

What type of bond connects additional phosphoryl groups in nucleotides to form diphosphates or triphosphates?

Acid anhydride bonds Signup and view all the answers

Which base pairing occurs in RNA?

A-U Signup and view all the answers

What differentiates RNA from DNA in terms of structure?

RNA contains ribose sugar. Signup and view all the answers

What is the primary structure of RNA based on?

The sequence of nucleotides in the polymer. Signup and view all the answers

What happens to RNA in mammalian cells?

It is degraded within the nucleus. Signup and view all the answers

Which type of RNA is involved in protein synthesis, carrying amino acids to ribosomes?

Transfer RNA (tRNA) Signup and view all the answers

What structure can RNA adopt that includes intramolecular base pairing?

Stem-loop Signup and view all the answers

What is not a class of RNA molecules existing in prokaryotic and eukaryotic organisms?

Cytoplasmic RNA (cRNA) Signup and view all the answers

Which statement accurately describes the relationship between RNA and its template strand?

RNA is transcribed from the template strand. Signup and view all the answers

What type of acid arises from the rearrangement of UMP in preformed tRNA?

Pseudouridylic acid Signup and view all the answers

Which process leads to the formation of thymidine monophosphate (TMP) from UMP?

Methylation by S-adenosylmethionine Signup and view all the answers

What is the significance of the 3′ and 5′ ends in polynucleotides?

They represent the positions of phosphate groups Signup and view all the answers

How do synthetic nucleotide analogs affect nucleic acid synthesis?

They inhibit enzymes responsible for nucleic acid synthesis Signup and view all the answers

Which analog is specifically known for treating hyperuricemia and gout?

Allopurinol Signup and view all the answers

What type of bond links mononucleotides to form polynucleotides?

3′ → 5′-phosphodiester bonds Signup and view all the answers

What is the consequence of incorporating synthetic nucleotide analogs into nucleic acids?

Altered base-pairing and disruptive effects Signup and view all the answers

Which of the following is NOT considered an additional nucleic acid base?

Dihydrouracil Signup and view all the answers

What does hyperchromicity of denaturation refer to?

An increase in the optical absorbance of purine and pyrimidine bases Signup and view all the answers

What is the effect of a tenfold increase in monovalent cation concentration on Tm?

Increases Tm by 16.6 °C Signup and view all the answers

Which base pairing in DNA is more resistant to denaturation?

C–G pairs Signup and view all the answers

How does formamide affect the Tm of DNA?

It decreases Tm by destabilizing hydrogen bonds Signup and view all the answers

What sugar moiety is present in RNA?

Ribose Signup and view all the answers

What is the primary structural difference between DNA and RNA?

RNA contains ribonucleotides, while DNA contains deoxyribonucleotides Signup and view all the answers

What happens to the viscosity of DNA during denaturation?

Decreases upon denaturation Signup and view all the answers

What structural characteristic does RNA possess that allows it to acquire double-stranded features?

It forms hairpin loops Signup and view all the answers

What is the approximate distance spanned by one turn of B-DNA?

3.4 nm Signup and view all the answers

Which strand in a DNA double helix is referred to as the coding strand?

The strand that matches the RNA transcript Signup and view all the answers

Which form of DNA is typically found under physiological conditions?

B-DNA Signup and view all the answers

How many base pairs are typically found in a single turn of B-DNA?

10 base pairs Signup and view all the answers

What is the helical diameter of the double helix in B-DNA?

2.0 nm Signup and view all the answers

Which of the following statements about DNA base pairing is correct?

A pairs with T and G pairs with C. Signup and view all the answers

What does the notation 'pGpGpApTpCpA' primarily represent?

A compact representation of DNA with indicated phosphodiester bonds. Signup and view all the answers

In terms of nucleotide sequence, which of the following statements is incorrect?

Phosphorylated groups are always explicitly shown in the sequence. Signup and view all the answers

Which of the following best describes the structure of DNA?

A double helix with alternating purines and pyrimidines. Signup and view all the answers

What is the function of the phosphodiester bond in DNA?

To link sugar and phosphate groups of different nucleotides. Signup and view all the answers

How many chromosomes in humans contain the 3 billion base pairs of DNA?

23 chromosomes. Signup and view all the answers

Which of the following best explains the uniqueness of each individual based on DNA?

The specific sequence of base pairs. Signup and view all the answers

What is the significance of the 3′ and 5′ positions in DNA?

They determine the replication direction. Signup and view all the answers

What distinguishes nucleosides from nucleotides?

Nucleosides contain a sugar linked to a nitrogenous base. Signup and view all the answers

Which of the following statements is true about the sugar in deoxyribonucleosides?

It lacks the hydroxyl group at the 2' position. Signup and view all the answers

What occurs due to steric hindrance in nucleosides and nucleotides?

Restriction of rotation around the β-N-glycosidic bond. Signup and view all the answers

Which of the following best describes 5'-nucleotides?

They are nucleotides resulting from nucleotide polymerization. Signup and view all the answers

What is the typical naming convention for nucleotides?

The prefix '5'- can usually be omitted in naming nucleotides. Signup and view all the answers

Which nitrogen atoms are most commonly involved in glycosidic bonds in nucleosides?

N-1 of pyrimidines and N-9 of purines. Signup and view all the answers

What establishes the structural differences between ribonucleosides and deoxyribonucleosides?

The presence of a 2'-hydroxyl group in deoxyribonucleosides. Signup and view all the answers

What structural feature is typical of mononucleotides?

They contain a phosphoryl group esterified to a hydroxyl group of the sugar. Signup and view all the answers

What phenomenon describes the increase in optical absorbance of purine and pyrimidine bases during DNA denaturation?

Hyperchromicity Signup and view all the answers

What is the effect of a tenfold increase in monovalent cation concentration on the melting temperature of DNA?

Increases Tm by 16.6 °C Signup and view all the answers

Which of the following statements about G–C pairs and A–T pairs in DNA is true?

G–C pairs melt at a higher temperature due to their triple bonds. Signup and view all the answers

What role does formamide play in recombinant DNA experiments?

Destabilizes hydrogen bonding between bases Signup and view all the answers

Which sugar component is found in DNA as opposed to RNA?

Deoxyribose Signup and view all the answers

How does the structure of RNA differ from that of DNA?

RNA contains uracil and DNA contains thymine. Signup and view all the answers

Which of the following statements is true regarding the melting temperature (Tm) of DNA?

Tm is influenced by the base composition of DNA. Signup and view all the answers

What characteristic allows a single strand of RNA to exhibit double-stranded features?

Ability to fold back on itself forming hairpin structures Signup and view all the answers

Which component is essential for the optimal functioning of the PCR process?

Heat-stable DNA polymerase Signup and view all the answers

Which stage of transcription involves the addition of nucleotides to form a growing RNA strand?

Elongation Signup and view all the answers

Which type of PCR is specifically used for measuring the quantity of target nucleic acid in real-time?

Real-Time PCR Signup and view all the answers

What is the role of Mg(II) ions in the PCR process?

To catalyze the polymerase enzyme activity Signup and view all the answers

What type of RNA is directly involved in decoding mRNA during translation?

tRNA Signup and view all the answers

Which of the following accurately describes the function of RNA polymerases during transcription?

They connect nucleotides to synthesize RNA Signup and view all the answers

Which of the following is NOT a common type of PCR?

Amplified Sequence PCR Signup and view all the answers

Which stage of transcription is marked by the release of the RNA strand from the DNA template?

Termination Signup and view all the answers

What role do nucleotides play concerning coenzymes?

They function as donors of phosphoryl groups, sugars, or lipids. Signup and view all the answers

Which of the following best describes the function of methylated bases in DNA and RNA?

They participate in oligonucleotide recognition and regulate RNA half-lives. Signup and view all the answers

What is the significance of adenine and guanine derivatives such as hypoxanthine and xanthine in nucleic acid metabolism?

They serve as intermediates in the catabolism of adenine and guanine. Signup and view all the answers

How do synthetic purine and pyrimidine analogs contribute to cancer treatment?

They inhibit nucleotide synthesis and impair cell division. Signup and view all the answers

What type of bond is involved in posttranslational modifications of nucleotides, such as pseudouridine formation?

A carbon-to-carbon bond. Signup and view all the answers

What is a consequence of the presence of regulatory nucleotides like cAMP in cellular processes?

They participate in allosteric regulation of enzyme activity. Signup and view all the answers

Which of the following best describes the relationship between mononucleotides and polynucleotides?

Mononucleotides are linked by covalent bonds to form polynucleotides. Signup and view all the answers

What is a distinct function of coenzymes that incorporate nucleotide derivatives like ATP and GTP?

They donate phosphoryl groups, sugars, or lipids for critical reactions. Signup and view all the answers

Study Notes

Course Information

Course name: Biochemistry I
Course number: 314
Level: 3rd Year Pharmacy, 1st Semester
Credit hours: 3 (Theory) + 1 (Practical)
Textbook: Harper's Illustrated Biochemistry, 26th Edition
Lecturer: Dr. Zeyad Hasan A. Nafaee
Lecture topic: Nucleic acids

Nucleic Acid Introduction

Nucleic acids are polynucleotide molecules.
A polymeric molecule made of four types of monomeric units called nucleotides.
Genetic information is coded throughout the polymer's length.
Nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
DNA directs RNA synthesis and in turn proteins are synthesized from RNA.

Nucleic Acid Objectives

Integrate core Biochemistry topics: structure and metabolism.
Understand the chemical structure and function of all biomolecules in living organisms.

Nucleic Acid Structure and Functions

Chemical properties
- Polarity, having a 5' terminal hydroxyl or phosphate and 3' terminal hydroxyl or phosphate.
Structures
- Phosphodiester bonds connect nucleotides.
- DNA and RNA form a backbone of alternating sugars and phosphates.
Functions
- Building blocks
- Replication
- Transcription
- Translation.

Nucleic Acid Importance

Essential for understanding genetics, pathology, and disease mechanisms.
In many cases, double-stranded DNA transcripts integrate into the host genome and serve as genetic templates for gene expression.
Plays a role in viral replication mechanisms (some RNA viruses may not transcribe into DNA or even have a DNA stage).
Retroviruses (e.g. HIV) employ RNA-dependent DNA polymerase (Reverse Transcriptase) to produce a double-stranded DNA copy from RNA.
Synthetic analogs are used for cancer therapies or to suppress the immune response.

Antibiotic Target Sites

Drugs target cell wall synthesis, folic acid metabolism, cytoplasmic membrane, etc.
Table showing Antibiotic classes and target sites in Nucleic Acid.

Nucleic Acid History

In 1871, Miescher isolated phosphorus-containing material (nuclein) from the cell nucleus.
Researchers proposed that nuclein was vital for cell division and that understanding nucleus interactions would reveal cellular processes.
Avery, MacLeod, and McCarty demonstrated DNA contained genetic information in 1944.
Watson and Crick elucidated the DNA double helix structure in 1953.
Rosalind Franklin contributed to the understanding of DNA, RNA, and other structures.

Purines and Pyrimidines

Purines (Adenine, Guanine) and pyrimidines (Cytosine, Uracil, Thymine) are nitrogen-containing heterocycles.
They are cyclic compounds containing both carbon atoms and other heteroatoms, or "additional atoms".
Their six-atom rings are numbered in opposite directions.
Planar character facilitates close association (stacking) and stabilizes double-stranded nucleic acids.

Nucleosides & Nucleotides

Nucleosides: Purines or pyrimidines linked to a sugar molecule
Nucleotides: Nucleosides with one or more phosphate groups attached to the sugar
Sugar in ribonucleosides is D-ribose, and deoxyribonucleosides: 2-deoxy-D-ribose.
Sugar and base are connected with N-glycosidic bond.
Syn or Anti conformers, with anti predominating.

Chemical Properties of Nucleic Acids

Polar molecules with a 5' and 3' end, typically a phosphate at the 5' end and hydroxyl group at the 3' end
Nucleosides/pyrimidine bases are uncharged at physiological pH.
Primary and secondary phosphoridyl groups contribute to a negative charge of nucleic acids.
Can act as proton donors/acceptors.
Conjugated double bonds absorb ultraviolet light.
Absorption (Abs) spectra are pH dependent, absorb at 260 nm, commonly used to measure concentrations.

DNA Replication

The process in which a cell generates a copy of its DNA.
It involves four main stages: initiation, unwinding, primer synthesis, and elongation.

PCR (Polymerase Chain Reaction)

A technique for rapidly amplifying DNA segments.
Involves cycles of DNA separation, primer hybridization, and DNA synthesis.
Requires specific primers, DNA template, DNA polymerase, dNTPs and buffer to complete the cycle.

Transcription

The process of creating RNA from DNA.
RNA polymerase enzymes synthesize RNA by pairing nucleotides to DNA template.
The process is divided into three stages: initiation, elongation, and termination.

Translation

The process of using mRNA to synthesize proteins.
Ribosomes process the mRNA to create amino acid sequences and synthesize polypeptide chains.
Codon tables are used to determine amino acids and protein products.

RNA structure

RNA molecules exist in various single-stranded structures
RNA molecules are composed of A, G, C, and U nucleotides; ribose is the sugar.
RNA typically comes in single stranded forms, but can form secondary structures (e.g. hairpins).

Types of RNAs

Messenger RNA (mRNA): carries instructions from DNA to ribosome.
Transfer RNA (tRNA): carries specific amino acids to ribosomes.
Ribosomal RNA (rRNA): Structural component of ribosomes
Small nuclear RNAs (snRNA): Involved in RNA processing.

Denaturation (Melting) of DNA

Process of separating double-stranded DNA into single strands.
Heat or decreasing salt concentration can induce denaturation
The base composition and salt concentration effect the melting temperature (Tm).
G-C pairs, which have three bonds, melt at higher temperatures than A-T pairs.
Hyperchromicity is observed as increased light absorption during denaturation.

Differences between DNA and RNA

The sugar composing DNA is 2′-deoxyribose, and the sugar in RNA is ribose.
DNA is typically double-stranded, while RNA is single-stranded; some can form complex structures.
RNA contains uracil, while DNA contains thymine.
RNA can be hydrolyzed by alkali, and DNA cannot.

Additional Purines and Pyrimidines

Unusual purines and pyrimidines occur in small amounts in DNA and RNA.
Examples of these additions include: 5-methylcytosine, 5-hydroxymethylcytosine, mono- and di-N-methylated adenine, and guanine, hypoxanthine, xanthine, and uric acid.
Methylated bases come from plants, including caffeine, theophylline, and theobromine.

Synthetic Nucleotide Analogs in Chemotherapy

Synthetic analogs of purines, pyrimidines, nucleosides, and nucleotides are used to treat diseases.
The mechanisms of these drugs may involve inhibiting enzyme function or being incorporated into DNA during cell division.
Examples include: 5-fluoro- or 5-iodouracil, 3-deoxyuridine, 6-thioguanine, 6-mercaptopurine, 5- or 6-azauridine, 5- or 6-azacytidine, and 8-azaguanine.

Nucleosides and Nucleotides Serve Diverse Physiological Functions

Nucleotides participate in various biological processes.
They serve as components of many coenzymes.
They serve as donors of phosphate groups (e.g., ATP, GTP).
They serve as components of lipid derivatives.
They act as second messengers (e.g., cAMP, cGMP).

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Description

This quiz covers the foundational concepts of nucleic acids, including their structure, function, and significance in genetic coding. You'll explore the chemical properties of DNA and RNA, as well as their roles in protein synthesis and metabolism. Prepare to assess your understanding of these essential biomolecules.