Biochem module 6: Nucleic Acids and Nucleotides

Nucleotide

The basic building block of nucleic acids, consisting of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

Nucleoside

A molecule composed of a nitrogenous base and a pentose sugar, without a phosphate group.

Phosphodiester Bond

A covalent bond that links successive nucleotides in DNA and RNA, formed between the 5′ phosphate of one nucleotide and the 3′ hydroxyl of another.

Base Pairing

The specific hydrogen bonding between complementary nitrogenous bases in DNA and RNA. Adenine pairs with thymine (or uracil in RNA), and guanine pairs with cytosine.

DNA (Deoxyribonucleic Acid)

A double-stranded nucleic acid that carries the genetic information of an organism.

RNA (Ribonucleic Acid)

A single-stranded nucleic acid involved in protein synthesis and other cellular functions.

Double Helix

The three-dimensional structure of DNA, characterized by two antiparallel strands wound around each other in a helical shape.

Antiparallel

Refers to the orientation of the two strands in a DNA double helix, running in opposite directions (5′ to 3′ and 3′ to 5′).

Denaturation

The separation of double-stranded DNA into single strands, often caused by heat or extreme pH.

Annealing

The process by which separated complementary strands of DNA or RNA re-associate to form a double helix.

Palindrome

A DNA sequence that reads the same backward and forward.

Hairpin

A secondary structure formed in single-stranded DNA or RNA when a palindromic sequence base-pairs with itself, creating a loop.

Mutation

A permanent change in the DNA sequence.

Replication

The process by which DNA makes a copy of itself.

Transcription

The process of synthesizing RNA from a DNA template.

Translation

The process of synthesizing a protein from an mRNA template.

mRNA (messenger RNA)

The type of RNA that carries genetic information from DNA to the ribosomes, where it serves as a template for protein synthesis.

rRNA (ribosomal RNA)

The type of RNA that is a structural component of ribosomes.

tRNA (transfer RNA)

The type of RNA that carries amino acids to the ribosome during protein synthesis.

PCR (polymerase chain reaction)

A technique used to amplify a specific DNA segment.

Sequencing

The process of determining the order of nucleotides in a DNA or RNA molecule.

Methylation

The addition of a methyl group to a molecule, often to DNA, which can affect gene expression.

a nitrogenous base, a pentose sugar (either ribose or deoxyribose), and a phosphate group

What are the three main components of a nucleotide?

Phosphodiester bond; forms when the phosphate group of one nucleotide attaches to the OH group on the 3' carbon of the sugar molecule in the adjacent nucleotide, essentially creating a "sugar-phosphate backbone" through a condensation reaction where a water molecule is removed.

What type of bond links successive nucleotides in nucleic acids, and how is it formed?

RNA contains a hydroxyl group at the 2' position of its ribose sugar, which acts as a nucleophile and readily attacks the phosphate backbone in alkaline environments

Why is RNA more susceptible to hydrolysis under alkaline conditions than DNA?

The Watson-Crick model describes DNA as a right-handed double helix with antiparallel strands. The two strands are held together by hydrogen bonds between complementary bases: adenine (A) pairs with thymine (T) via two hydrogen bonds, and guanine (G) pairs with cytosine (C) via three hydrogen bonds.

Briefly describe the Watson-Crick model of DNA structure, including details about basepairing

The DNA double helix is stabilized by: a) metal cations that neutralize the negative charges of the phosphate backbone, and b) base-stacking interactions between adjacent base pairs through van der Waals and dipole-dipole forces.

What forces stabilize the DNA double helix?

A palindrome is a DNA sequence that reads the same backward and forward. A hairpinstructure is a secondary structure formed in single-stranded DNA or RNA when apalindromic sequence base-pairs with itself, creating a loop.

Explain the terms "palindrome" and "hairpin" in the context of DNA structure.

The three forms of DNA are A-form, B-form, and Z-form. B-form is the most common formunder physiological conditions. A-form is favored in dehydrated conditions, while Z-formcan occur in sequences with alternating purines and pyrimidines.

What are the three forms of DNA, and what conditions favor each form?

Denaturation refers to the separation of double-stranded DNA into single strands, oftencaused by heat or extreme pH, which disrupts hydrogen bonds and base-stackinginteractions. Annealing is the reverse process where separated complementary strands re-associate to form a double helix upon returning to favorable conditions.

Define "denaturation" and "annealing" in relation to nucleic acids.

DNA methylation, typically at cytosine residues, plays a crucial role in regulating geneexpression and DNA replication. It can silence genes, protect DNA from restrictionenzymes, and distinguish between old and new DNA strands during replication.

What is the significance of methylation in DNA?