DNA and RNA Nucleic Acids

Nucleic Acids: DNA and RNA

• DNA and RNA both contain a sugar, a phosphate group, and a nitrogenous base
• These form nucleotide units connected by covalent bonds
• This creates a linear molecule with 5’ and 3’ ends
• Nitrogenous bases are perpendicular to the sugar-phosphate backbone
• DNA contains deoxyribose, while RNA contains ribose
• RNA contains uracil, while DNA contains thymine
• DNA is usually double-stranded, and RNA is usually single-stranded
• The two DNA strands in double-stranded DNA are antiparallel

Passing Hereditary Information

• DNA, and in some cases RNA, is the primary source of heritable information
• Genetic information is stored in and passed to subsequent generations through DNA or RNA molecules
• Prokaryotic organisms typically have circular chromosomes
• Eukaryotic organisms typically have multiple linear chromosomes
• Both prokaryotes and eukaryotes can contain plasmids
• Plasmids are small extrachromosomal, double-stranded, circular DNA molecules

DNA as Hereditary Material

• DNA, and sometimes RNA, exhibits specific nucleotide base pairing
• Adenine pairs with thymine or uracil (A-T or A-U)
• Cytosine pairs with guanine (C-G)
• Purines (G and A) have a double ring structure
• Pyrimidines (C, T, and U) have a single ring structure

Replication (DNA → DNA)

• DNA replication ensures continuity of hereditary information
• DNA is synthesized in the 5’ to 3’ direction
• Replication is a semiconservative process
• One strand of DNA serves as the template for a new strand of complementary DNA
• Helicase unwinds the DNA strands
• Topoisomerase relaxes supercoiling in front of the replication fork
• DNA polymerase requires RNA primers to initiate DNA synthesis
• DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand
• Ligase joins the Okazaki fragments on the lagging strand

Transcription (DNA → RNA) and RNA Processing (RNA → mRNA)

• The sequence of RNA bases and the structure of the RNA molecule determines RNA function
• Messenger RNA (mRNA) molecules carry information from DNA to the ribosome
• Transfer RNA (tRNA) molecules bind specific amino acids and have anticodon sequences that base pair with the mRNA
• tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence
• Ribosomal RNA (rRNA) molecules are functional building blocks of ribosomes
• Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein
• RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule, a process known as transcription
• The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand
• Selection of which DNA strand serves as the template strand depends on the gene being transcribed
• The enzyme RNA polymerase synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction
• In eukaryotic cells, the mRNA transcript undergoes a series of enzyme-regulated modifications
• These include the addition of a poly-A tail, and the addition of a GTP cap
• Excision of introns and splicing and retention of exons occurs
• Excision of introns and splicing and retention of exons can generate different versions of the resulting mRNA molecule; this is known as alternative splicing

Translation (mRNA → Protein)

• Translation of the mRNA to generate a polypeptide occurs on ribosomes
• Ribosomes are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the rough endoplasmic reticulum of eukaryotic cells
• In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed
• Translation involves energy and many sequential steps, including initiation, elongation, and termination
• Translation is initiated when the rRNA in the ribosome interacts with the mRNA at the start codon [AUG]
• The sequence of nucleotides on the mRNA is read in triplets called codons
• Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart
• Many amino acids are encoded by more than one codon
• Nearly all living organisms use the same genetic code
• This is evidence for the common ancestry of all living organisms
• tRNA brings the correct amino acid to the correct place specified by the codon on the mRNA
• The amino acid is transferred to the growing polypeptide chain
• The process continues along the mRNA until a stop codon is reached
• The process terminates by release of the newly synthesized polypeptide or protein
• Genetic information in retroviruses flows from RNA to DNA
• This is made possible by reverse transcriptase
• Reverse transcriptase is an enzyme that copies the viral RNA genome into DNA
• This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny

Regulation of Gene Expression

• Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription
• Epigenetic changes can affect gene expression through reversible modifications of DNA or histones
• The phenotype of a cell or organism is determined by the combination of genes that are expressed and the levels at which they are expressed
• Observable cell differentiation results from the expression of genes for tissue specific proteins
• Induction of transcription factors during development results in sequential gene expression
• Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated
• In prokaryotes, groups of genes called operons are transcribed in a single mRNA molecule, and the lac operon is an example of an inducible system
• In eukaryotes, groups of genes may be influenced by the same transcription factor to coordinately regulate expression
• Promoters are DNA sequences upstream of the transcription start site
• RNA polymerase and transcription factors bind here to initiate transcription
• Negative regulatory molecules inhibit gene expression by binding to DNA and blocking transcription
• Gene regulation results in differential gene expression and influences cell products and function
• Certain small RNA molecules have roles in regulating gene expression

Mutations

• Changes in genotype can result in changes in phenotype
• The function and amount of gene products determine the phenotype of organisms
• The normal function of the genes and gene products collectively comprises the normal function of organisms
• Disruptions in genes and gene products cause new phenotypes
• Alterations in a DNA sequence can lead to changes in the type or amount of protein produced and the consequent phenotype
• DNA mutations can be positive, negative, or neutral
• Whether a mutation is detrimental, beneficial, or neutral depends on the environmental context
• Mutations are the primary source of genetic variation
• Errors in mitosis or meiosis can result in changes in phenotype
• Changes in chromosome number often result in new phenotypes
• Some changes include sterility caused by triploidy, and increased vigor of other polyploids
• Changes in chromosome number often result in human disorders with developmental limitations
• These include Down syndrome/Trisomy 21 and Turner syndrome
• Changes in genotype may affect phenotypes that are subject to natural selection
• Genetic changes that enhance survival and reproduction can be selected for by environmental conditions
• Horizontal acquisition of genetic information in prokaryotes increases variation
• Transformation (uptake of naked DNA) is an example of this
• Transduction (viral transmission of genetic information) is also an example
• Conjugation (cell-to-cell transfer of DNA) is an example
• Transposition (movement of DNA segments within and between DNA molecules) is an example
• Related viruses can combine or recombine genetic information if they infect the same host cell
• Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms

Biotechnology

• Genetic engineering techniques can be used to analyze and manipulate DNA and RNA
• Electrophoresis separates molecules according to size and charge
• During polymerase chain reaction (PCR), DNA fragments are amplified
• Bacterial transformation introduces DNA into bacterial cells
• DNA sequencing determines the order of nucleotides in a DNA molecule