DNA Structure and Function

• DNA, or deoxyribonucleic acid, serves as the genetic material containing instructions for specific traits.
• Genes are short segments of DNA and are organized into chromosomes.
• In eukaryotic cells, DNA resides in the nucleus, with a small amount also in the mitochondria.
• DNA replicates, stores information, and undergoes mutation to provide genetic variability.

Structure of DNA

• DNA exists as a double helix composed of two strands spiraling around each other.
• Each strand consists of nucleotides built from phosphate, a pentose sugar (deoxyribose), and a nitrogen-containing base.
• The nitrogenous bases consist of adenine (A), cytosine (C), guanine (G), and thymine (T)
• Adenine and guanine are classified as purines, which contain two rings
• Cytosine and thymine are pyrimidines, characterized by a single ring structure.
• The phosphate and sugar molecules form the backbone of the DNA strand.
• Bases are joined by hydrogen bonds following complementary base pair rules: A pairs with T (two hydrogen bonds), and G pairs with C (three hydrogen bonds).

Replication of DNA

• DNA replication, which is the copying of DNA, transpires during the S phase of interphase.
• Each original strand acts as a template for creating a complementary new strand.
• DNA replication follows a semiconservative pattern where each new double helix has an original and a new strand.
• DNA helicase unwinds and "unzips" DNA by disrupting hydrogen bonds between bases.
• DNA polymerase incorporates new DNA nucleotides aligning with complementary base pairing rules.
• DNA synthesis occurs in opposite directions, the leading strand follows helicase, and the lagging strand develops short segments of DNA or Okazaki fragments.
• DNA ligase seals breaks in the sugar-phosphate backbone.
• Every new double-stranded helix consists of one new strand and one old strand.

The Structure and Function of RNA

• RNA, or ribonucleic acid, is composed of nucleotides with the sugar ribose.
• The four RNA nucleotides are adenine (A), uracil (U), cytosine (C), and guanine (G).
• In RNA, thymine is replaced with uracil.
• C pairs with G, and A pairs with U in RNA base pairing.
• RNA is usually single-stranded.
• There are three types of RNA: ribosomal RNA (rRNA), messenger RNA (mRNA), and transfer RNA (tRNA).
• Ribosomal RNA joins with proteins, producing the large and small subunits of ribosomes.
• Messenger RNA, made in the nucleus where DNA acts as a template, carries genetic information from DNA to ribosomes in the cytoplasm.
• Transfer RNA carries amino acids to the ribosome during protein synthesis.
• Each tRNA type carries a specific amino acid.
• There are 20 different tRNAs.

Comparing DNA and RNA

• Similarities: Both are nucleic acids, are composed of nucleotides, have sugar-phosphate backbones, and contain four types of bases.
• Differences: DNA is double-stranded, whereas RNA is single-stranded, DNA has thymine (T), while RNA has uracil (U).
• RNA is found in the cytoplasm and nucleus, while DNA is primarily in the nucleus.
• DNA undergoes transcription, and RNA undergoes translation.

Structure and Function of Proteins

• Proteins consist of amino acids subunits.
• There are 20 different amino acids.
• Protein variations arise from differences in the quantity and sequence of amino acids.
• The amino acid sequence determines a protein's particular shape.
• Proteins are synthesized at the ribosomes.
• Proteins are crucial for diverse functions in the body, including as hormones, enzymes, and for transport.
• Proteins are susceptible to denaturation, which results in a loss of function.

Steps of Gene Expression

• Transcription takes place first, where DNA is read to create mRNA in the nucleus.
• Translation, the second step, involves reading mRNA to create a protein in the cytoplasm.

The Genetic Code

• The genetic code-the bases in DNA and mRNA code for amino acids.
• Codon-a three-base sequence in mRNA.
• Each specified a specific amino acid.
• There are 64 possible codons.
• 61 codons correspond to a specific amino acid.
• The remaining three are stop codons signal polypeptide termination.
• One of the codons, AUG, codes for the methionine and signals the beginning of a polypeptide.

Transcription

• A segment of DNA strand that forms a template to make mRNA
• mRNA undergoes processing before exiting the nucleus.
• mRNA is transported to the ribosomes for reading.
• Every three bases on the mRNA form a codon, coding for a particular amino acid for translation.

Modifications of mRNA

• The new primary mRNA is changed to a mature mRNA
• One end of the RNA is capped.
• Introns, non-coding segments of DNA, are taken out.
• Exons, gene segments that code that result in a protein product
• A Poly-A tail is added.

Translation

• Transfer RNA brings the amino acids to the ribosomes
• The translation complex constitutes small and large ribosomal subunits bound to mRNA.
• Ribosomes contain binding sites labeled as A, P, and E, where tRNA binds with mRNA.
• tRNA is equipped with an area that binds an amino acid and another called an anticodon.
• The anticodon is a series of three bases complementary to mRNA codons.
• Every amino acid has a corresponding tRNA for the translation complex.

Translation Steps

• Initiation: mRNA binds to the small ribosomal subunit, prompting the association of both ribosomal units.
• Elongation: The polypeptide chain gets longer.
• tRNA collects an amino acid.
• tRNA contains an anticodon that matches with the mRNA codon.
• The tRNA anticodon binds the codon and releases its amino acid, adding to the growing polypeptide.
• Termination: A stop codon presents on the mRNA results in ribosome separating from the mRNA.

Gene Expression Regulation

• Transcriptional Control (nucleus): Regulates which genes are transcribed and the rate of transcription, using transcription factors.
• Posttranscriptional Control (nucleus): mRNA processing.
• Translational Control (cytoplasm): Differential ability of mRNA to bind ribosomes.
• Posttranslational Control (cytoplasm): Changes to the protein to make it functional

Participants in Gene Expression

• DNA contains genetic information for proteins.
• RNA polymerase is the enzyme copies DNA into mRNA.
• mRNA moves information from DNA to the ribosome.
• tRNA translates genetic information into amino acid sequences.
• rRNA helps from the structure of the ribosome.
• Amino acids are used to build a polypeptide chain.

The Human Genome

• Genomics is the study of genomes, or genes.
• In 2003, The Human Genome Project (HGP) mapped the human genome.
• The NIH funded the project, and many labs all over the country mapped and determined the base sequence of human genes.
• The human genome contains 3.4 billion bases, with 99.9% of these bases identical in all humans.
• The average functional gene contains 3,000 bases, with 23,000 functional genes in humans.
• Genome size is not related to the number of genes and does not correlate to a organism's complexity.
• Less than 2% of the human genome codes for functional proteins.
• The remaining 98% may produce RNA molecules, which regulate genes.
• Diagnosis of genetic disease.
• Functional genomics is aimed at understanding how the 23,000 human genes function and gene deserts.
• Comparative genomics, which involves comparing the human genome with those of animals.
• DNA sequences of chimpanzees and humans are 95 to 98% alike
• Aiding in understanding how species have evolved and identification of base sequences that cause human illness and regulation of genes.
• Proteomics is the study of the structure, function, and interactions of cell proteins, and bioinformatics studies the genome using a computer.
• Better drug discoveries using proteins and analyzing genomic data through computer analysis.

Modifying a Person's Genome

• Using gene therapy, genetic material into cells to treat a disorder
• Ex vivo therapy removes stem cells from a person and returning them to the patient.
• In vivo therapy - gene directly inserted through a vector or injected to replace mutated genes.
• Has had most success in the treatment of cancer.
• Adenosine deaminase (ADA) deficiency causes collapse of the immune system treated with gene therapy.
• Stem cells are extracted with blood samples, cultured, and genetically engineered with a good ADA gene using a vector.
• Cultured cells are then put back into the host circulation to make the ADA.

Biotechnology

• Gene therapy to treat human genetic diseases
• Determining the sequence of the human genome
• Immunotherapy for human diseases
• Detecting human diseases such as cancer
• Forensic (crime detection) applications
• Products of drugs, vaccines, enzymes, and chemicals for industry
• Crops and farm animals that are improved

DNA Technology Terms

• Genetic engineering: Modifying DNA in organisms, plants, and animal cells through recombinant DNA technology.
• Recombinant DNA: DNA from 2 or more different sources.
• Transgenic Organisms: Foreign gene.
• Biotechnology: Using biological systems to create a product for humans.

DNA Technology

• Gene cloning via recombinant DNA
• Polymerase Chain Reaction (PCR)
• DNA fingerprinting
• Biotechnology products from bacteria, plants, and animals

Gene Cloning

• Cloning-the production of genetically identical copies of DNA, cells, or organisms.
• Gene cloning-produces many copies of a gene.
• Recombinant DNA (rDNA)—contains DNA from more than one source.
• To create rDNA, a vector introduces the gene of interest into a host cell such as a bacterium.
• A common vector is a plasmid, which are small rings of DNA in bacteria that are not part of bacterial chromosomes.

Gene Cloning Example

• Isolating a gene of interest or making from nucleotides (PCR)
• Creating a restriction enzyme to cut vector
• Using the DNA ligase
• Inserting bacteria using plasmid

DNA Sequencing

• Determines the order of nucleotides in DNA.
• Allows researchers to identify alleles that are associated with a disease to so they can develop treatments.
• Aids forensic biology and contributes to understanding of evolutionary history.
• Used via polymerase chain reactions.

Polymerase Chain Reaction (PCR)

• Uses DNA polymerase to copy DNA.
• Creates millions of copies.
• Can amplify amounts from fossils and more.

PCR Steps

• Denaturation-DNA is heated to become single-stranded.
• Annealing-DNA cooled
• Primer attaches each strand.
• DNA adds bases and creates two new strands.

PCR and DNA Fingerprinting

• Used for DNA fingerprinting profiling
• PCR amplifies DNA fragments.
• Restriction enzymes cut DNA forming restriction depending on the alleles present.
• Separates fragments by size using gel electrophoresis.
• Shows restriction fragment polymorphism.
• Patterns match and source is determined using DNA fingerprinting.

DNA Fingerprinting Uses

• Testing viral infections and cancers
• Compares blood tissues from crime scenes
• Used in forensics or victims of disasters to identity the remains.
• Used for paternity.

DNA Editing

• Genome editing focuses on removal or replacement.

CRISPR

• Uses an enzyme that determines the nucleotides by a guide.
• The PAM bacteria from cas9 must be found next to the target for the DNA sequence.

Biotechnology Products

• Created by cells that are genetically engineered.
• DNA is altered to make certain products.

Genetically Engineered Bacteria

• Contains gene for things such as insulin.
• Acts a factor.
• Bacteria break down oil to clean beaches also has "suicide" genes.

Genetically Engineered Plants

• Can regenerate to be genetically engineered in one single plant.
• Soybeans, potatoes, and corn are engineered
• Can decrease food spoilage.
• Increases shelf life.
• Take in more carbon dioxide.
• Transgenic animals produce growth hormones, fish, sheep and mice.
• Gene is inserted to make transgencic animal and current pharmaceutical in animal milk.
• Increase meat, size, better size and growth rate and salmon.
• Concerns about BT crops, impact target test and genetic material.
• BT crops can also affect other species that are not target.
• Can affect plants in the wild.
• Has ethical and safety concerns against diseases and research.