AP BIO UNIT 6

Purines vs. Pyrimidines

1. Purines

   • Adenine (A) and Guanine (G)

   • Consist of two nitrogen rings

2. Pyrimidines

   • Thymine (T) and Cytosine (C)

   • Consist of one nitrogen ring

Frederick Griffith's Discovery

Performed experiments with two strains of Streptococcus pneumoniae (one harmless, one pathogenic) showing that DNA is the molecule of heredity and can transform bacteria.

DNA Nucleotide Composition

DNA is a double-stranded helical molecule composed of nucleotide monomers, each containing:

• A five-carbon sugar called deoxyribose

• A phosphate group

• One of four nitrogenous bases (A, T, C, or G)

Anti-parallel Strands

The two strands of DNA run in opposite directions relative to each other (5' to 3' and 3' to 5'), with covalently bonded sugar-phosphate backbones.

Helicase

The "unzipping" enzyme that breaks the hydrogen bonds holding the DNA bases together, separating the two strands to create a replication template.

SSB (Single-Strand Binding) Proteins

Proteins that bind to the separated DNA strands during replication to stabilize them and prevent them from rewinding.

Topoisomerase

An enzyme that prevents the DNA double helix from supercoiling (over-winding) ahead of the replication fork.

Semi-conservative Replication

The mechanism of DNA replication where each new molecule consists of one conserved original template strand and one newly synthesized strand.

Primase and DNA Polymerase

1. Primase: Lays down an RNA primer so DNA polymerase knows where to start.

2. DNA Polymerase: Replicates DNA by adding nucleotides to the 3' end of the new strand.

3. DNA Polymerase I: Removes RNA primers and replaces them with DNA.

Ligase

The enzyme that acts as "glue" to seal gaps between DNA fragments (such as Okazaki fragments) by forming sugar-phosphate bonds.

Leading vs. Lagging Strand

1. Leading Strand: DNA synthesis is continuous, following the direction of the replication fork.

2. Lagging Strand: DNA synthesis is discontinuous and moves away from the fork, creating short sequences called Okazaki fragments.

Prokaryotic vs. Eukaryotic DNA

1. Prokaryotes

   • Circular chromosomes in loops; usually "naked" (no histones)

   • Approximately 100,000 to 10,000,000 base pairs

2. Eukaryotes

   • Multiple linear chromosomes wrapped around histones

   • Human genome contains approximately 3.2 billion base pairs

Plasmids

Small extra-chromosomal loops of DNA found mostly in bacteria. They are involved in horizontal gene transfer (conjugation), often carry antibiotic resistance genes, and are used in genetic engineering.

Central Dogma of Molecular Biology

The process of information flow in cells: DNA is transcribed into RNA, which is then translated into Protein.

Types of RNA

1. mRNA: Messenger RNA that carries instructions from DNA to the ribosome.

2. rRNA: Ribosomal RNA that forms the catalytic part of ribosomes and binds amino acids.

3. tRNA: Transfer RNA that brings specific amino acids to the ribosome.

Transcription Process

1. Initiation: RNA polymerase binds to the promoter region.

2. Elongation: RNA polymerase reads DNA in the 3' to 5' direction and synthesizes RNA in the 5' to 3' direction.

3. Termination: The process ends when the enzyme reaches the terminator region.

Non-Coding vs. Coding Strand

1. Non-Coding Strand: The template strand that actually gets transcribed; also called the antisense or negative strand.

2. Coding Strand: The strand complementary to the template; it has the same sequence as the resulting RNA (with T instead of U) and is called the sense or positive strand.

Structure of the Ribosome (Translation)

Ribosomes are protein factories with a large and small subunit and three tRNA binding sites:\n- A site: Accepts the new amino acid.\n- P site: Holds the growing polypeptide chain.\n- E site: The exit site for empty tRNAs.

The Process of Translation

1. Initiation: Small subunit binds mRNA at the AUG start codon; tRNA-Met binds the P site.\n2. Elongation: New tRNA enters the A site; ribosome catalyzes a peptide bond and translocates.\n3. Termination: Release Factor binds the stop codon, causing the ribosome to dissociate.

Trp vs. Lac Operons

1. Trp Operon: A repressible system; high Tryptophan levels (co-repressor) cause the repressor to bind the operator, turning synthesis \"off.\"\n2. Lac Operon: An inducible system; the presence of an inducer (lactose) removes the repressor, turning transcription \"on.\"

Epigenetics: Acetylation and Methylation

1. Acetylation: Loosens DNA/histone binding, enabling transcription (turning genes \"on\").\n2. Methylation: Tightens DNA/histone binding, preventing transcription (turning genes \"off\").

Eukaryotic Gene Regulation Features

• Enhancers: Remote DNA sequences that interact with regulatory proteins to increase transcription probability.\n- Transcription Factors: Proteins that enable RNA polymerase to bind to the promoter.

mRNA Processing: Cap, Tail, and Splicing

1. 5' GTP Cap: Protects mRNA from breakdown and assists in nuclear export.\n2. 3' Poly A Tail: Stabilizes mRNA in the cytoplasm.\n3. Splicing: Introns (non-coding) are removed, and Exons (coding) are joined.

Alternative Splicing

The process where exons are joined in different combinations from one pre-mRNA, allowing for multiple protein versions from a single gene.

Point Mutations

1. Silent: Changes a nucleotide but results in the same amino acid.\n2. Nonsense: Changes a codon to a stop codon.\n3. Missense: Changes a codon to a different amino acid (e.g., Sickle Cell).

Frameshift Mutations

Mutations where nucleotides are inserted or deleted, changing the reading frame of codons (groups of 3) and resulting in extensive nonsense or missense.

Horizontal Gene Transfer

1. Transformation: Uptake of DNA from the environment.\n2. Conjugation: Transfer of plasmids via a pilus extension.\n3. Transduction: DNA transfer mediated by viruses.

Restriction Enzymes and Recombinant DNA

• Restriction Enzymes: Cut DNA at specific sites, often leaving sticky ends.\n- DNA Ligase: \"Glues\" fragments together via sugar-phosphate bonds to create recombinant DNA.

Reverse Transcriptase and cDNA

Used to clone eukaryotic genes into bacteria by creating cDNA (complementary DNA) from mRNA, effectively removing introns.

Gel Electrophoresis (DNA Fingerprinting)

Molecules are sorted by size and charge in a gel; negatively charged DNA moves toward the positive end, with smaller fragments moving faster and further.

Polymerase Chain Reaction (PCR)

A cell-free technique using repeated cycles of heating (separating strands) and cooling (primer binding/polymerase synthesis) to double DNA samples.

DNA Stability and Mutation

The double helix structure is highly stable and protects the base sequence, yet it remains capable of undergoing random changes known as mutations.

Genomic Equivalence

The principle that all cells in a multicellular organism (excluding gametes) contain identical DNA because they all originate from the same zygote.

Positive, Negative, and Neutral Mutations

The effect of a mutation depends on the environment: positive mutations increase evolutionary fitness, negative mutations decrease it, and neutral mutations have no effect on phenotype.

Germ Line vs. Somatic Mutations

Germ line mutations occur in cells that produce gametes and can be passed to offspring; somatic mutations occur in body cells, affecting only the individual organism.

Micro-RNAs and RNA Silencing

Small RNA molecules involved in post-transcriptional control that can lead to the destruction of mRNA, preventing it from being translated.

Tissue-Specific Gene Regulation

Different tissues may share common regulatory sequences (like hormone receptors) but activate different genes based on their specialized purpose within the organism.

Viral Recombination

The process where DNA from a host cell recombines with viral DNA, often resulting in the emergence of new viral strains that the immune system cannot recognize.

Applications of DNA Sequencing

A technique used to determine an organism's protein-coding potential, resolve paternity disputes, and exonerate suspects through forensic analysis.