Molecular Biology Concepts

Nucleic Acids

• Living things maintain species uniqueness and characteristics, passing survival abilities and genetic information to the next generation.
• Proteins are the cell's workhorses, vital for cell viability and species uniqueness.
• Proteins are very abundant and functionally versatile.
• A cells uniqueness relies on its proteins.
• Proteins have a short average lifespan making them poor candidates for genetic transmission.
• The problem with proteins include; they have short half lives and cannot synthesise themselves.
• The challenge is how to synthesize the right proteins regularly to maintain species uniqueness and pass this ability on.
• The solution is using a genetic code made of DNA, or deoxyribonucleic acid, which directs protein synthesis throughout a cell's lifetime.
• DNA is passed to the next generation, taking the place of the proteins.
• A cellular machinery involving various types of RNA, or ribonucleic acids is also used for protein synthesis.
• DNA and RNA are nucleic acids.
• The central dogma of genetics explains how DNA, through transcription and translation, leads to protein synthesis.

Nucleotides

• Nucleic acids like DNA and RNA are built from monomers called nucleotides.
• Each nucleotide has three parts: a pentose sugar (ribose or deoxyribose), a nitrogenous base (purine or pyrimidine), and a phosphate group.
• Nucleotides containing deoxyribose are called deoxyribonucleotides and are monomers of DNA.
• Nucleotides containing ribose are called ribonucleotides and are monomers of RNA.
• Deoxyribonucleotides contain; a phosphate group, a pentose sugar (deoxyribose) and one of the following nitrogenous bases; adenine, thymine, cytosine or guanine
• The polymer deoxyribonucleic acid is made of deoxyribonucleotides.
• Ribonucleotides contain; a phosphate group, a pentose sugar (ribose) and one of the following nitrogenous bases; adenine, uracil, cytosine or guanine.
• The polymer ribonucleic acid is made of ribonucleotides.

Pentose Sugar

• Deoxyribose and ribose sugars are aldopentoses.
• The -anomer is used in nucleotide formation.
• The difference between deoxyribose and ribose is that deoxyribose lacks an oxygen atom otherwise present in ribose.
• Nucleotides are formed through the use of -anomer.

Phosphate Group

• The phosphate group forms a phosphoester bond with the C5 of the pentose sugar.
• A phosphoester bond links the phosphorous atom of a phosphate group to an oxygen atom.
• Phosphate groups lose a hydrogen ion (H+) at cellular pH, becoming negatively charged and polar.

Nitrogenous Bases

• Nitrogenous bases are heterocyclic compounds containing carbon and nitrogen atoms.
• The nitrogenous bases in nucleic acids are purines or pyrimidines.
• Bases form a -N-glycosidic bond with the C1 of the sugar.
• Note that the concept of "base" is different from the "base" in acid/alkaline chemistry.

Purine Bases

• Adenine and guanine are purine bases found in both deoxyribonucleotides and ribonucleotides.
• Adenine and guanine are purines.

Pyrimidine Bases

• Cytosine is found in both deoxyribonucleotides and ribonucleotides.
• Thymine is found only in deoxyribonucleotides.
• Uracil is found only in ribonucleotides.
• Cytosine, thymine and uracil are pyrimidines.

Nucleotides and ATP

• Nucleotides are building blocks for nucleic acids.
• Adenosine triphosphate or ATP, a ribonucleotide, is a widely used nucleotide.
• ATP fuels biochemical reactions.
• Key nucleotides include adenosine triphosphate (ATP), adenosine diphosphate, and adenosine monophosphate.
• Dephosphorylation of ATP releases energy.

Nucleosides

• Removing the phosphate group from a nucleotide renders a nucleoside.
• A deoxyribonucleoside forms when the pentose sugar is deoxyribose.
• Nucleosides are nucleotides' precursors.
• Enzymes add a phosphate group to nucleosides to form nucleotides.

Naming of Nucleosides

• Purine derivatives include:
• Adenine's nucleoside is Adenosine.
• Deoxyadenosine is its deoxynucleoside.
• Guanine's nucleoside is Guanosine and its deoxynucleoside is Deoxyguanosine.
• Pyrimidine derivatives include:
• Uracil becomes Uridine.
• Thymine becomes Thymidine.
• Cytosine becomes Cytidine.
• Deoxycytidine becomes Deoxycytidine.

DNA and RNA overview

• Side+P=tide(poly)=acid is a summary of the building blocks of DNA and RNA
• Nucleic acids (DNA and RNA) are nucleotide polymers.
• Nucleotides consist of a pentose sugar, a nitrogenous base, and a phosphate group.

DNA and RNA overview

• There are four types of nucleotides for DNA and four types for RNA.
• DNA and RNA consist of polynucleotides.
• Monomers of nucleic acids such as DNA are structurally similar in their ability to polymerize, and their diversity supports information variability.

DNA structure

• Genetic material (DNA) remains throughout the lifetime of a cell.
• It must be stable, non-degrading, and non-reactive to other biomolecules, being also readily available for information retrieval.
• A DNA strand is formed by the reaction of a phosphate group on C5 with the 3'-OH group of another to form a phosphodiester bond.

DNA Strand

• The sugar phosphate are alternating and attached by phosphodiester bonds which form the “backbone” within the strand.
• One strand has a 5' phosphate group while the other has a 3' OH.
• DNA exists as a double stranded molecule.
• James Watson and Francis Crick deduced the double helix of DNA.

DNA Properties and Properties

• Each DNA strand typically pairs with a complementary strand.
• The two DNA strands run antiparallel to each other.
• The antiparallel DNA strands run parallel to each other, with one strand going in the 5' PO4 to 3' OH direction and the other going in the 3'OH to 5' PO4 direction
• DNA Double helix structure are twisted together

Properties and Structure

• Hydrogen bonds hold the DNA strands together
• Complementary bases on the DNA strands always pair.
• A purine will only pair with a pyrimidine
• Adenine is a purine and will pair with thymine
• Guanine is a purine and will pair with Cytosine

Bases

• A purine base forms hydrogen bonds with a pyrimidine base
• Adenine forms 2 bonds with thymine.
• Guanine forms 3 bonds with cytosine.
• The backbone consists of alternating sugar and phosphate groups joined by phosphodiester bonds which are covalent and stable.
• Phosphate groups in the backbone are negatively charged forming ionic interactions.

DNA Bonds

• Interstrand hydrogen bonds are non-covalent.
• Non-covalent bonds break and reform easily.
• Breaking the non-covalent bonds occurs by high temperature, extreme pH, and high ion concentrations.
• "Melting" or "denaturing" occurs when hydrogen bonds break, separating the 2 strands.

DNA Packaging and Chromosomes

• Each human cells holds 6 billion nucleotides
• The human cell's nucleotides' total length amounts to 1.8 to 2 meters.
• 46 dsDNA molecules divide the genome.
• The 46 dsDNA molecules are tightly packed into a nucleus of about 6 uM diameter through proteins being known as histones.
• The proteins and nucleotides form chromatin.
• Each double stranded DNA is equivalent to 1 chromosome.

DNA Packaging Levels

• At the simplest level, chromatin is a double-stranded helical structure of DNA.
• DNA is complexed with histones to form nucleosomes.
• Each nucleosome consists of eight histone proteins around which the DNA wraps 1.65 times.
• A chromatosome consists of a nucleosome plus the H1 histone.
• Tight coiling of the 250-nm fiber produces the chromatid of a chromosome.

DNA and Protein Synthesis

• DNA contains the genetic code to make proteins.
• Specifically, a base sequence in DNA defines the amino acid sequence of a protein.
• DNA carries the code for making proteins, with each coding region being called a "gene."

Key Protein Steps

• The code must first be copied on DNA into RNA to form a Messenger RNA (mRNA).
• This process is called Transcription as well as occurs in the nucleus.
• In eukaryotes, the messenger RNA leaves the nucleus to ribosomes where it read to produce polypeptides.
• This process is called Translation.
• DNA also codes for functional RNA other than mRNA
• DNA is produced by transcription and are not translated.

DNA

• Deoxyribonucleotides polymerize to form a single DNA strand.
• DNA is double-stranded, with complementary strands held together by base-pairing through hydrogen bonds.
• Adenine pairs with Thymine.
• Cytosine pairs with Guanine.
• Tight packaging of DNA is needed to fit it into chromosomes.
• DNA carries codes for messenger RNA and functional RNAs.

Central Dogma of Genetics

• Synthesis of DNA can undergo replication
• Replication of DNA distributes into daughter cells and ensures that the correct proteins continue to be synthesized in future generations.

Summary of DNA Synthesis

• DNA includes the replication step
• DNA involves copying information of DNA into messenger RNA(transcription) and proteins can be synthesized using information in messenger RNA as a template (translation).

Transcription

• Protein Helicase begins to separate a double stranded DNA
• DNA must copy the information to RNA molecules in order for the cell functions
• Genes that code protein are transcribed into mRNA
• Genes that encode other functional RNA are transcribed into messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), micro RNA (miRNA) etc.
• Transcription converts a region of DNA into a specific RNA.
• Messenger RNA, transfer RNA and ribosomal RNA play a role in protein synthesis and regulated cellular activities.
• DNA can either regulate or control cell activities through RNA.
• The general structure of protein encoding genes includes promoter, transcribed region, terminator, and regulatory sequences that result in transcription.
• Transcription occurs in the regulatory sequence.
• RNA polymerase copies a DNA strand, producing a complementary RNA strand (mRNA)
• RNA polymerase uses only one template strand to produce mRNA
• The transcribed region contains a leader sequence, a coding region, and also the tail region.
• The unwound DNA region rewinds. (reanneled)
• Note that After transcription is complete, the helicase and RNA polymerase detaches from the DNA

Test your knowledge of molecular biology. This quiz covers the central dogma, gene regulation, RNA types, protein synthesis, and nucleotide composition. Learn about transcription factors, microRNAs, and the roles of ribosomes and RNA polymerase.