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DNA and RNA

  • Introductory Definitions

    • Nucleotide- The monomer of nucleic acids (RNA and DNA)

    • Composed of:

    • (1) a sugar molecule (ribose in RNA or deoxyribose in DNA)

    • (2) a phosphate group

    • (3) a nitrogen-containing base

    • Genetic code- The sequence of nucleotides in DNA and RNA that determines the amino acid sequence of proteins

    • Relationships among codons and anticodons

    • Triplet code on DNA is complementary to Codons on mRNA

    • Codons on mRNA are complementary to Anticodons on tRNA

    • Notes- The genetic code table connects DNA, RNA, codons, and amino acids

Section 3

  • DNA structure and cellular location

    • Location of DNA in a cell-

    • Bacterial DNA

      • Plasmid: a small circular DNA molecule

      • Plasmids are used as vectors for foreign DNA in recombinant DNA technology

      • Plasmids contribute to antibiotic resistance characteristics in bacterial strains

    • Animal cell DNA

      • Nuclear DNA exists as dense chromatin (DNA + Histone proteins)

      • Condenses to form chromosomes during cell division (mitosis/meiosis)

      • Mitochondrial DNA (mtDNA) can be inherited from the mother and can be used to trace maternal relations

    • Plant cell DNA

      • Chloroplast DNA (cpDNA) is important in biotechnology for modifying plants to improve yield, disease resistance, and environmental growth, and for studying plant evolution and photosynthesis

    • Key concepts-

    • Chromatin vs. chromosomes during division

    • Maternal inheritance through mtDNA

    • Chloroplast DNA's role in biotechnology and plant biology

Section 4

  • The nucleotides, bases, and the genetic code

    • Simple structure of nucleotides-

    • Purines: two-ring structures (Adenine A and Guanine G)

    • Pyrimidines: one-ring structures (Cytosine C, Thymine T, Uracil U)

    • In RNA, Thymine is replaced by Uracil

    • Bases and complementary pairing-

    • DNA bases: A, T, C, G

    • RNA bases: A, U, C, G

    • Complementary pairs in DNA: A-T and C-G

    • In RNA, base pairing with transcription/translation involves A-U instead of A-T

    • Sugars-

    • Deoxyribose in DNA

    • Ribose in RNA

Section 5

  • Differences Between DNA and RNA; Central Dogma

    • Localization- DNA primarily found in the nucleus; RNA primarily found in the cytoplasm

    • Central dogma- Explains how DNA codes for proteins through three processes: replication, transcription, translation

    • Summary of differences- DNA replication vs transcription differences (see Section 7) and RNA roles in protein synthesis

Section 6

  • DNA replication

    • Definition- DNA replication is the process of creating two identical copies of DNA from a single original DNA molecule

    • Occurrence- Occurs during interphase as a cell prepares to divide

    • Key idea- Two identical DNA molecules are formed, enabling genetic continuity across cell generations

Section 7

  • Protein synthesis

    • Overall idea- A gene is expressed as a protein (part of the phenotype) through two main steps: Transcription and Translation

    • Transcription- The gene’s message is copied from DNA to produce mRNA

    • Steps described:

    1. The double helix DNA unwinds

    2. Hydrogen bonds unzip the DNA strands

    3. One DNA strand acts as a template to form mRNA

    4. Free complementary RNA nucleotides attach to the template strand

    5. Adjacent nucleotides join to form an mRNA strand

    6. mRNA exits the nucleus

    7. DNA recoils back into a double helix

    • Partners - RNA polymerase with transcription factors

    • Translation- mRNA is used to code for a protein/polypeptide

    • Key players

    • tRNA: anticodon, carries specific amino acid

    • Ribosomes: site of protein synthesis in the cytoplasm

    • Translation steps- Step-by-step process:

    1. The ribosome reads mRNA

    2. The anticodon on the tRNA pairs with the codon on the mRNA

    3. tRNA delivers the appropriate amino acid

    4. Amino acids are linked by peptide bonds to form the growing polypeptide

    • Important numbers and concepts-

    • There are 20 amino acids used to build proteins

    • A polypeptide chain can have up to about 50 amino acids; a full protein may be longer

    • Applications and implications- Pharmacological drugs can interfere with protein synthesis to act as antibiotics

    • Mutations and their effects (overview)- Mutations are permanent changes to the DNA sequence of a gene

    • Causes include:

      • Errors in DNA replication

      • Exposure to chemicals or radiation

      • Viral infections

    • Consequences can include inherited disorders (examples cited: cystic fibrosis, sickle cell disease, Tay-Sachs disease)

Section 8

  • Mutations detailed

    • Point mutations- Affect only one or a very small number of nucleotides

    • Substitution: one base is swapped for another

    • Insertion: addition of nucleotides into a DNA segment

    • Deletion: loss of one or more nucleotides from a DNA segment

    • Frameshift mutations- Caused by deletion or insertion that shifts the reading frame

    • Effects on genetic code-

    • Can change the triplet code sequence

    • Can alter codon sequences on mRNA during transcription

    • Can change amino acids during translation

    • Often leads to a different, and possibly nonfunctional, protein

    • Silent mutations- A nucleotide change that does not alter the amino acid due to redundancy of the genetic code

    • Protein produced remains unchanged

Section 9

  • Application of DNA technology: DNA fingerprinting

    • Concept- Non-coding DNA is highly variable and used for fingerprinting

    • Steps in DNA fingerprinting

    1. Sample collection: biological samples like blood, semen, skin, or hair

    2. DNA extraction: isolate DNA from the sample

    3. Restriction endonuclease digestion: cut DNA into smaller fragments

    4. Amplify DNA sample: use polymerase chain reaction (PCR) to replicate DNA into multiple copies

    5. Fragment separation: use electrophoresis to separate fragments by size

    6. Analysis and data comparison: compare the DNA profile to identify matches

    • Applications-

    • Forensics: identifying suspects and linking evidence to crimes

    • Paternity: determining biological relationships

    • Medical research: identifying genes linked to diseases and developing cures

    • Population genetics: analyzing gene frequencies in populations

    • Note- The material includes a prompt about a fingerprinting exercise (conviction question) but no accompanying data; the key methods and uses are described above

Section 10

  • Additional notes and key ideas

    • The concept of complementary base pairing is foundational to DNA structure and function: A-T and C-G in DNA; in RNA, A-U replaces T

    • The double helix structure provides a mechanism for replication because each strand can serve as a template to create a new complementary strand

    • The genetic code links DNA sequences to proteins via transcription and translation, with mRNA codons and tRNA anticodons mediating amino acid assembly

    • The role of cellular compartments and organelles-

    • Nucleus and chromatin organization in eukaryotes

    • Mitochondrial DNA inheritance patterns

    • Chloroplast DNA in plants and its biotechnological applications

    • Practical implications of DNA technology-

    • Use of plasmids in genetic engineering and concerns about antibiotic resistance

    • DNA fingerprinting as a powerful tool across multiple fields

    • Ethical and real-world relevance- Biotechnology enables crop improvement and disease research but raises ethical considerations around manipulation of organisms, privacy in forensic contexts, and potential ecological impacts