DNA and RNA Structure

DNA Structure

• Nucleotides are the building blocks of DNA, consisting of deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base.
• Adenine (A) and Guanine (G) are double-ringed purines, while Cytosine (C) and Thymine (T) are single-ringed pyrimidines.
• Adjacent nucleotides are linked by a phosphate group, covalently bonded to the sugar molecules.
• The sugar-phosphate linkages form a "backbone" for each DNA strand.
• The sugar's carbon atoms are numbered 1', 2', 3', 4', and 5'.
• The phosphate group binds to the 5' carbon of one nucleotide and the 3' carbon of the next.
• Two DNA strands are held together via hydrogen bonds between the base pairs.
• DNA has 2 strands twisted together in a double helix.
• Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).
• Adenine and thymine share 2 hydrogen bonds while cytosine and guanine share 3.

RNA Structure

• Ribonucleic acid, or RNA, is a nucleic acid found in all cells
• RNA is a polymer of nucleotides.
• RNA contains the five-carbon sugar ribose, which has a hydroxyl group at the 2' carbon, whereas deoxyribose has only a hydrogen atom.
• RNA nucleotides include adenine, cytosine, and guanine, but not thymine.
• Uracil (U) takes the place of thymine in RNA.
• RNA exists as a single-stranded molecule, unlike DNA.
• RNA types vary in function, for example: mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA).
• These RNAs aid in producing proteins from the DNA code.

DNA Arrangement in the Cell

• DNA must replicate when a cell prepares to divide and produce molecules for cell functions.
• DNA can be 2 meters long in a human cell.
• Most prokaryotes contain a single, circular chromosome in the cytoplasm, called a nucleoid.
• Histones are proteins that DNA wraps around to make nucleosomes.
• The DNA is tightly wrapped around the histone core.
• Nucleosomes link via a short segment of DNA lacking histones.
• Nucleosomes group into a 30 nm wide fiber, which then coils further.
• Mitotic chromosomes are compact during metaphase, around 100nm wide, and attach to scaffold proteins.
• Interphase chromosomes are less compact and stain differently where darkly stained regions are tightly packed, contain inactive genes, and are near the centromere and telomeres.
• Lightly staining regions have lower density, active genes, and are loosely packaged around nucleosomes.

DNA Replication/Synthesis

• During cell division, each daughter cell gets an identical copy of the DNA through DNA replication in the S phase before mitosis.
• 2 strands are complementary
• An example is DNA strand AGTCATGA and complimentary strand TCAGTACT.
• The new strand is complimentary to the “old” or parental strand (called semiconservative replication).
• The two DNA copies have identical nucleotide sequences and are divided equally into daughter cells.
• Helicase breaks hydrogen bonds creating replication fork.
• Primase generates primers to attract DNA poly III.
• DNA Polymerase III bring builds the new strand of DNA in both leading and lagging strands.
• Exonuclease removes primers allowing DNA poly III to fill gaps.
• Ligase Creates bonds anywhere necessary.

DNA Replication in Eukaryotes

• DNA Replication occurs in three stages: Initiation, elongation, and termination.
• Direction of synthesis is from 5' to 3'
• DNA must be made accessible to enzymes for replication.
• Proteins bind to the origin, and helicase unwinds the DNA
• Y-shaped replication fork form, with two forks extending in both directions.
• DNA polymerase adds nucleotides to the 3' end of the template strand.
• A primer (made of RNA) is added to start the process.
• One strand is synthesized continuously towards the replication fork (Leading strand)
• The other strand (lagging strand) is made in short pieces called Okazaki fragments.
• RNA primers are removed, replaced by DNA, and the fragments are joined by DNA ligase.
• The replication process ends when the replication fork meets or reaches the end of the chromosome.
• DNA polymerase stops adding nucleotides when they reach a specific signal or sequence on the DNA.
• DNA unwinds at the origin of the cell.
• New bases are added: one strand is continuous (leading), the other is made in pieces (lagging)
• RNA primers are removed, replaced by DNA, and the backbone is sealed by DNA ligase.

Telomere Replication

• Eukaryotic chromosomes are liner, so DNA replication faces challenges at the ends.
• DNA polymerase can only add nucleotides in one direction.
• On the lagging strand, there is no place for a primer at the end of the chromosome, leaving the end unpaired
• Over time, as cells divide, these ends get shorter
• Telomeres are repetitive DNA sequences at the end of chromosomes that don't code for genes.
• In humans, the sequence TTAGGG repeats 100-1000 times at the chromosome end
• With each cell division, telomeres shorten instead of coding genes
• Telomerase is an enzyme that helps chromosome ends.
• The lagging strand is elongated, DNA polymerase can add nucleotides, allowing the chromosome ends to be fully replicated.
• It can be found to be active in germ cells, adult stem cells, and some cancer cells.

DNA Repair

• DNA polymerase proofreads each newly added base and corrects mistakes by removing and replacing incorrect bases.
• Mismatch repair: if proof reading fails, mismatch repair enzymes recognize and remove incorrectly incorporated bases, replacing the with the correct ones.
• Nucleotide excision repair, involves unwinding the DNA, removing incorrect base along with some adjacent bases (5' to 3' ends), and replacing them using the template and DNA polymerase
• The importance of nucleotide excision repair is essential for correcting thymine dimers to prevent mutations.
• Thymine dimers is when exposure to UV light where two adjacent thymine nucleotides bond covalently, disrupting normal base pairing.
• Individuals who have faulty nucleotide excision repair genes are highly sensitive to sunlight and have a higher risk of developing skin cancers early in life.

Transcription

• First function of DNA: Replication (duplication of genetic material).
• Second function of DNA: provides information to construct proteins for cell functions.
• Transcription: DNA is “read” and transcribed to mRNA.
• Translation: mRNA provides the code to form a protein.
• Protein synthesis: a protein is built with a specific sequence of amino acids encoded in the DNA.
• In eukaryotes, transcription occurs in the nucleus, and the mRNA transcript is transported to the cytoplasm for translation.
• In prokaryotes, transcription occurs directly in the cytoplasm since they lack a membrane-bound nuclei and other organelles.
• Stages in transcription: Initiation, Elongation, and Termination.

Initiation

• Process starts, the DNA double helix partially unwinds in the region where mRNA synthesis occurs, forming what is called a transcription bubble.
• Promoter is the specific DNA sequence where proteins and enzymes involved in transcription bind to initiate the process.
• Promoters are usually located upstream (before) the gene they regulate.
• The specific sequence of the promoter is crucial as it determines the level of gene transcription, whether a gene is transcribed continuously, occasionally, or very rarely.
• Direction of transcription is 5' to 3'

Elongation

• Transcription always proceeds from one of two strands, known as the template strand (antisense strand).
• The mRNA product is complementary to the template strand and resembles the nontemplate strand, except that RNA uses uracil (U) instead of thymine (T).
• During elongation, RNA polymerase moves along the DNA template, adding nucleotides by base pairing with DNA template, similar to DNA replication, but the RNA strand is not bound to the DNA template.
• As elongation continues, the DNA is unwound ahead of the RNA polymerase and rewound behind it.

Termination

• After Transcription, prokaryotic RNA polymerase dissociates from the DNA template and release newly made mRNA.
• Two types of termination signals, both involving repeated nucleotide sequences that cause RNA polymerase to stall, detach from template, and release the mRNA transcript.
• Transcription completes when termination occurs.
• Transcription and translation can happen simultaneously in prokaryotic cells, allowing the mRNA to be used to synthesize multiple copies of the encoded protein right after it's transcribed.
• The nucleus in eukaryotic cells separates transcription and translation, so they cannot occur simultaneously.

Eukaryotic RNA Processing

• Newly transcribed eukaryotic mRNAs undergo several processing steps before being exported form the nucleus to the cytoplasm for translation.
• Eukaryotic mRNA lasts several hours compared to prokaryotic cells which lasts 5 seconds.
• The mRNA transcript is coated with stabilizing proteins to prevent degradation during processing and export form the nucleus.
• 5' Cap is added to the 5' end of the growing mRNA transcript, protecting it from degradation and helping initiate translation by ribosomes.
• Poly-A tail: a modification protects the mRNA form degradation and signals it to be exported to the cytoplasm.
• Exons are coding sequences while Introns are non-coding sequences.
• Introns are removed during mRNA processing, while exons are joined together to form the final mRNA sequence.
• The process of removing introns and connecting all exons is called splicing. This process must ensure that correct sequence of exons is joined to form an mRNA that codes for the right protein.
• Accurate removal of introns and correct exon joining in crucial, as even a single nucleotide error can result in a nonfunctional protein.
• After removal, introns are degraded while the pre-mRNA is still in the nucleus.

Translation

• The synthesis of proteins is one of the most energy-consuming processes in a cell.
• Translation is the process of decoding an mRNA message into a polypeptide product.
• Polypeptides are made covalently linking amino acids, with lengths ranging from about 50 to more than 1000 amino acids.

Protein Synthesis Machinery

• Translation requires the input of mRNA, ribosomes, tRNA, and various enzymatic factors.
• In prokaryotes, ribosomes are located in the cytoplasm, while in eukaryotes, they are found in the cytoplasm and the endoplasmic reticulum.
• Ribosomes consist of a large and small subunit that come together for translation.
• Small subunit binds the mRNA template.
• Large subunit binds tRNAs, which bring amino acids to the growing polypeptide chain.
• Many ribosomes translate a single mRNA molecule at the same time, all synthesizing the protein in the same direction.
• Depending on the species, there are 40 to 60 types of tRNA in the cytoplasm.
• tRNA acts as adaptors by binding to a specific sequence on the mRNA template and adding correct amino acid to the polypeptide chain (translates RNA to protein).
• tRNAs must be “charged" by bonding to its specific amino acid through a process called tRNA charging.

The Genetic Code

• Proteins are made up of 20 commonly occurring amino acids, so the protein alphabet consists of 20 letters.
• Each amino acid is defined by a three-nucleotide sequence called a codon.
• The relationship between a nucleotide codon and its corresponding amino acids is referred to as the genetic code.
• With 64 possible codon combinations, multiple codons can encode the same amino acids, meaning the code is redundant.
• Three of the 64 codons are stop codons, which terminate protein synthesis and release the polypeptide from the translation from the machinery.
• The codon AUG specifies the amino acid methionine and also acts as the start codon to initiate translation.
• The genetic code is nearly universal across all species, with only a few exceptions.

The Mechanism of Protein Synthesis

• Translation occurs in three phases: Initiation, Elongation, and Termination.
• In E. coli, the initiation complex consists of a small ribosome subunit, the mRNA template, three initiation factors, and a special initiator tRNA.
• The initiator tRNA binds to the AUG start codon and carries a special methionine, which is typically removed from the polypeptide after translation.
• The large ribosomal subunit in E. coli has three compartments.
• A Site binds charged tRNA with their attached amino acids.
• P sites binds tRNAs carrying amino acids.
• E Site releases uncharged tRNA
• The ribosome shifts codon by codon. With each step, a charged tRNA enters, the polypeptide chain grows by one amino acid, and an uncharged tRNA departs.
• The energy source for forming each peptide bond comes from GPT, a molecule similar to ATP.
• Translation terminates when a stop codon (UAA, UAG, or UGA) is encountered.
• Upon encountering the stop codon, the ribosome releases the growing polypeptide, and the ribosomal subunits dissociate from the mRNA.
• After translation is completed by multiple ribosomes, the mRNA is degraded, allowing its nucleotides to be reused in future transcription reactions.

How Genes are Regulated

• The process of turning on a gene to produce RNA and protein is called gene expression. This process regulates when and how genes are expressed in a cell.
• Different cells express many genes that others do not, allowing for specialized functions. Cells also turn genes on and off in response to environmental changes or during different stages of organism development.
• Unicellular organisms, both eukaryotic and prokaryotic, also regulate gene expression in response to environmental demands, adapting to special conditions.

Eukaryotic Gene Expression

• In eukaryotic cells, transcription occurs in the nucleus, and translation occurs in the centre puzzle. These two processes are physically separated by the nuclear membrane.
• Gene expression in eukaryotes is regulated at various stages: epigenetic level, transcriptional level, post transcriptional level, translation level and post translation level.

Mutations

• Produced through errors in replication, exposure to environmental chemicals, radiation or viruses.
• Mutations can be detrimental, beneficial, or silent.
• A point mutation involves a change in a single nucleotide of the DNA sequence.
• Point mutations include: Missense, Silent and Nonsense.
• A missense mutation replaces one nucleotide with another, resulting in a different amino acid.
• Genetic disorders range in severity, for example, Inability to bind oxygen to hemoglobin of red blood cells called Sickle cell anemia.
• A silent mutation changes a nucleotide but does not harm the organism.
• Nonsense Mutation can produce nonfunctional protein
• Genetic afflictions are caused by nonsense mutations.
• When there is a nonsense mutation it is considered Autosomal recessive.
• Cystic Fibrosis is caused by Mutation of the CFTR gene where the CFTR protein regulates salt and other fluids inside and out of the cell.
• Duchenne Muscular Dystrophy is caused by Mutated gene dystrophin on the X chromosome and it helps repair muscles cells and keep them intact with Symptoms as early as 2 years old.
• Insertions are when 2 or more nucleotides are added to the DNA sequence.
• Deletions where Removing 1 or more nucleotides to the DNA sequence.
• Adding/deletion of nucleotides changes the reading frame.
• Reading frame consists of nucleotides.
• Insertion and deletion can all be frameshift mutation depending on the number of nucleotide changes.
• If the number of insertions/deletions is not divided by 3, then a frameshift will occur.