Genetics: DNA and Genetic Material

• These notes cover key concepts in genetics, including experiments that identified DNA as genetic material, DNA structure and replication, transcription and translation, gene regulation, mutation, and cancer.

Griffith's Experiment

• Demonstrated bacterial transformation, where nonpathogenic bacteria become pathogenic.
• Heat-killed pathogenic bacteria were used to induce this transformation.

Avery's Experiment

• Identified DNA as the transforming substance.

Bacteriophages

• Viruses infecting bacteria, composed of DNA and protein.
• Phages T2 and T4 were used in genetic material studies.
• Bacteriophage infection involves phage DNA entering bacterial cells for replication.

Hershey and Chase Experiment

• Confirmed DNA as genetic material using radioactive labeling.
• Radioactivity detection indicated the presence of DNA inside bacteria.

Genetic Material

• Confirmed as DNA, which carries genetic information in living organisms.
• Proteins were initially considered candidates for carrying genetic information due to their variety.

DNA Monomers

• Nucleotides are the building blocks of DNA.
• Nucleoside triphosphates are building blocks for nucleic acid synthesis.
• Nucleotides contain a nitrogenous base, sugar, and phosphate group.
• Nucleotide bases are adenine (A), thymine (T), cytosine (C), and guanine (G).

Chargaff's Rules

• States that A=T and G=C in DNA structure, ensuring specific base pairing.

DNA Structure

• Consists of adenine, guanine, thymine, and cytosine.
• A double helix held together by hydrogen bonds.
• DNA consists of two complementary strands.
• DNA strands run in opposite directions (antiparallel strands).
• Information in DNA is determined by base order (nucleotide sequence).
• James Watson and Francis Crick proposed the DNA double helix model.
• Rosalind Franklin provided X-ray diffraction data essential for determining DNA structure.

Purines and Pyrimidines

• Purines (adenine and guanine) are two-ring nitrogenous bases.
• Pyrimidines (cytosine and thymine) are one-ring nitrogenous bases.

Base Pairing

• Adenine pairs with thymine using two hydrogen bonds.
• Guanine pairs with cytosine using three hydrogen bonds.
• Specific base pairing ensures accurate DNA replication and structure.
• Base-pairing rules are guidelines for nitrogenous base pairing in DNA.
• Example base sequence: 5′-ATAGGT-3′ pairs with 3′-TACCTA-5′.

DNA Backbone

• Formed by 5' deoxyribose and phosphate bonds.
• Phosphate groups are part of the DNA backbone, linking nucleotides.
• Covalent bonds provide strong bonds within DNA backbone structure and connect carbon atoms in deoxyribose sugar.

DNA Replication generally

• The process of copying DNA before cell division (mitosis).
• Involves template strands to guide the synthesis of new DNA strands.
• Each DNA strand serves as a template (semiconservative replication).
• Results in each new DNA molecule containing one old and one new strand (semiconservative replication).
• Requires an RNA primer to begin the elongation process, forming complementary strands.

Origins of Replication and Elongation

• Replication begins at a specific site (replication origin).
• Forms a replication bubble when DNA strands separate.
• Ends of the replication bubble are called replication forks.
• Proceeds bidirectionally from each origin.
• Prokaryotes have a single origin of replication on their chromosomes.
• Eukaryotes have multiple origins of replication on their chromosomes.
• Elongation rate in prokaryotes is about 500 nucleotides per second.
• Elongation rate in eukaryotes is about 50 nucleotides per second.

Enzymes in DNA replication

• DNA polymerases synthesize new DNA strands, adding nucleotides to the 3' end.
• Helicase unwinds the DNA double helix
• Primase synthesizes RNA primers for DNA synthesis.
• DNA ligase joins Okazaki fragments together.
• Topoisomerase relieves strain ahead of the replication fork.
• Nuclease removes RNA primers from DNA strands.
• Single-strand binding proteins stabilize unwound DNA strands during replication, preventing degradation.

Leading and Lagging Strands

• Strands run in opposite 5' to 3' directions (antiparallel strands).
• Follows complementary base pairing (A with T, G with C).
• The leading strand is synthesized continuously towards the replication fork.
• The lagging strand is synthesized in short segments called Okazaki fragments discontinuously away from the replication fork.
• DNA ligase joins Okazaki fragments on the lagging strand.

Proofreading and Repair

• Improves replication accuracy.
• Initial pairing errors during DNA replication occur at a rate of 1 in 100,000.
• Occurs via proofreading mechanisms during synthesis.
• The error rate in completed DNA is approximately 1 in 1,000,000.
• The mismatch repair system repairs incorrectly incorporated bases in DNA
• Nucleotide excision repair involves nucleases, DNA polymerase, and ligase.
• Helicase separates DNA strands to allow replication machinery access.
• Topoisomerase cuts DNA to alleviate twisting tension.

Consequences of Errors/Damage

• Errors in replication can occur during DNA copying.
• Initial paring errors occur at a rate of 1 in 100,000.
• Can lead to cell death.
• Uncorrected replication errors in bacteria are transmitted to offspring.
• Errors in sexual reproduction in eukaryotes are less likely transmitted.
• UV light exposure can cause thymine dimers leading to DNA damage.

Telomeres and Telomerase

• Telomeres are protective ends of linear chromosomes that shorten with replication.
• Telomerase lengthens telomeres in certain cells, influencing cellular aging.
• Telomerase can increase the longevity of cancer cells.

Additional Techniques

• Electrophoresis separates DNA fragments by size.
• Radioactive labeling traces DNA molecules in experiments.
• Cloned DNA is copied from a specific organism.
• Transgenic animals are genetically modified to carry foreign DNA.

Nucleosomes and Chromatin

• Nucleosomes: DNA wrapped around histone proteins, forming "beads on a string".
• Chromatin structure: DNA and protein complex in the nucleus.
• Heterochromatin: tightly packed form of DNA, transcriptionally inactive.

One Gene-One Enzyme Hypothesis

• Proposed by George Beadle and Edward Tatum, it states that each gene codes for one enzyme.

Genetic Code

• Information is transferred from the nucleus to the cytoplasm via RNA.
• Each amino acids are coded by three DNA bases.
• Universal code for amino acids across organisms.
• The genetic code is nearly identical across organisms.
• Codon: three-nucleotide sequence coding for an amino acid.
• The start codon for protein synthesis is AUG.
• Polypeptide sequence: chain of amino acids formed during translation.
• Nucleotide bases are units of DNA and RNA coding information.
• 450 amino acids require at least 1,350 nucleotides to code.
• Redundancy: multiple codons can specify the same amino acid.

Transcription

• The process of synthesizing RNA from a DNA template.
• Requires transcription factors and occurs in the nucleus in eukaryotes.
• RNA polymerase binds to the promoter to start transcription (transcription initiation).
• Eukaryotic transcription requires transcription factors and occurs in the nucleus.
• In prokaryotes, the RNA transcript is immediately usable as mRNA.
• Transcription occurs in the nucleus of eukaryotic cells.
• Requires ribonucleotides.
• One DNA strand is used (template strand).

Translation

• Process of synthesizing proteins from mRNA.
• Amino acids are delivered during protein synthesis from the tRNA molecule.
• Polypeptides are synthesized at ribosomes from mRNA.

RNA Polymerase

• Synthesizes RNA from a DNA template.
• Binds to the promoter (recognition sequence) to start transcription (transcription initiation).

Promoters

• DNA region where transcription begins.
• Recognition sequence for RNA polymerase binding.

Transcription Factors

• Proteins enhancing RNA polymerase binding to promoters, required for eukaryotic transcription.

RNA Splicing

• Joins exons after intron removal during mRNA processing.
• Can produce different mRNAs from the same gene (alternative splicing).

Introns and Exons

• Intron: non-coding sequence removed during mRNA processing.
• Exon: coding sequence that remains in mature mRNA.
• In mRNA processing, introns are removed and exons are spliced together.

Ribosomes

• Site of protein synthesis in cells.
• Ribosomal RNA composes the core of ribosome structure.
• Composed of large and small subunits.
• Sub-units move through nuclear pores (Nuclear transport).
• Function to catalyze polymerization of amino acids into proteins.
• Groups of ribosomes translate the same mRNA (polysomes).

Ribozymes

• RNA molecules with catalytic activity.

tRNA

• Delivers amino acids during protein synthesis.
• tRNA molecules transfer RNA that carries amino acids to ribosomes.
• Molecule whose three-nucleotide sequence is complementary to the mRNA codon is the tRNA anticodon.

Aminoacyl-tRNA Synthetase

• Enzyme that attaches amino acids to tRNA.

Codons

• mRNA codons are triplet sequences that encode specific amino acids.

Translation Sites

• Holds tRNA with growing polypeptide chain (P site of ribosome).

Start and stop codons

• The first amino acid is typically methionine in eukaryotic polypeptides.
• Stop codon signals termination of amino acid chain elongation.

Polypeptide Properties and modification

• Hydrogen bonds stabilize the three-dimensional structure of tRNA.
• Primary Transcript: Initial RNA molecule before processing occurs.
• Undergoes post-translational modification (changes made to polypeptides after translation).

Synthesis

• mRNA is synthesized from DNA, then translated.
• Amino acid chain elongation continues until a stop codon is reached.
• Amino acid building blocks are added via codon-anticodon pairing in translation
• The processes of transcription and translation can be controlled (gene expression regulation).

Protein Destinations

• Proteins synthesized solely in the cytoplasm (cytoplasmic proteins).
• Proteins destined for secretion outside the cell (secreted proteins).
• Signal region directs ribosome to attach to ER.
• Translocation occurs to the Endoplasmic Reticulum (ER) lumen.
• Lysosome: Cell organelle containing digestive enzymes (Compartment-specific protein).

Mutation Types

• Frameshift (insertion or deletion altering the reading frame).
• Nonsense (introducing a premature stop codon).
• Silent: no effect on protein function.
• Missense: causing a different amino acid substitution.
• Base-pair substitution: single nucleotide change in DNA sequence.
• Mutation: permanent alteration in DNA sequence.

External Factors contributing to mutations

• Can be caused by Ultraviolet (UV) radiation, damaging cellular structures
• Can be induced by substances that cause in DNA (chemical mutagens).

trp Operon

• Gene regulation system for tryptophan synthesis in E. coli.

Tryptophan

• Essential amino acid for protein synthesis.
• Affects the lac operon activity.

Lac Operon

• Operon involved in lactose metabolism.
• Activity affected by Tryptophan.

Operons generally

• Group of related genes with shared regulation.
• Can be inhibited by Glycine (amino acid).

Activators and Repressors

• An inducible operon is one that's activated by the presence of a substrate.
• A repressible operon is one that's turned off by the end product.
• A corepressor enhances repressor activity.
• Repressor protein binds to DNA to inhibit gene expression.
• Transcriptional activators are proteins that increase the likelihood of transcription.
• Transcriptional repressors are proteins that decrease the likelihood of transcription.

Promoters and Operators

• Operator: region of DNA where repressor binds.
• Promoter: DNA sequence where RNA polymerase binds to start transcription.

Post-Transcriptional Control

• Regulates gene expression after mRNA synthesis.
• Involves alternate RNA splicing to produce multiple proteins from a single gene.
• mRNA stability determines mRNA lifespan in the cell (3' untranslated regionContains sequences affecting mRNA stability).

miRNAs

• Small RNAs that regulate gene expression post-transcriptionally.

Translational control

• Regulates the rate of protein synthesis.

E. coli

• Bacterium that uses Operons commonly used in genetic studies.

DNA Methylation

• Addition of methyl groups to DNA, affecting expression.
• Inhibits transcription by tightly packing DNA and is an epigenetic mechanism.

Histone acetylation

• Loosens chromatin structure, enhancing transcription.

Gene Packing

• Compaction of DNA, influencing accessibility for transcription.

Transcription Factors

• Proteins that regulate the transcription of genes.
• General transcription factors bind to the TATA box for transcription.
• Activators and repressors regulate transcription by binding to enhancer or silencer regions.

Coordinate Control and Differential expression

• Involves the Simultaneous regulation of genes across different chromosomes.
• Occurs in Nuclear sites where multiple genes are co-activated (transcription factory).
• Differential activation of genes leads to unique gene expression patterns in different cell types.

RNA degradation

• Regulation point achieved by breaking down mRNA to regulate translation.

Noncoding RNA

• RNA molecules that do not code for proteins but regulate genes (ncRNA).
• Include MicroRNAs (miRNAs); small RNA molecules that inhibit gene expression post-transcriptionally.
• Includes Small Interfering RNA (siRNAs): RNA fragments that silence genes by degrading mRNA
• Increased ncRNA diversity drives organismal structural evolution.

The 5 levels of regulation of gene expressions

• Chromatin Packing.
• Transcription factors.
• Post-transcription control.
• Translational control.
• Modification of protein.

Myoblast Determination

• Undifferentiated cells destined to become muscle cells.
• Promoted Transcription factor promoting muscle cell development (MyoD).

Maternal Effect Genes

• Maternal Effect Genes: Genes whose products influence embryonic development (cytoplasmic determinants, induction).

Differential gene expression

• Differential activation of key transcription factor genes is the reason; for instance transcription factor genes in all types of cells are transcribed but are present in different combinations in different types of cells.

Cell Differentiation

• Process where cells become specialized in function.

Cancer Cells

• Disregard normal division signals.
• Often evade apoptosis mechanisms.

Somatic vs Germline

• Somatic mutations: Mutations acquired during a person's lifetime.
• Germ cells: undergo meiosis to produce gametes.
• Somatic cells: body cells in multicellular organisms, not germ cells.

Proto-oncogenes

• Normal genes that can become oncogenes when mutated (Oncogenes: genes that stimulate cell division and growth).

Tumor-Suppressor Genes

• Genes that prevent uncontrolled cell growth.
• Examples include p53, BRCA1, and BRCA2 (tumor-suppressor genes linked to breast cancer).

Cell Adhesion

• Process by which cells stick to each other, and cancer cells lose this ability.

Metastasis

• Aberrant cell adhesion explains how tumor cells will detach from original tumor and potentially end up in the blood stream (called circulatory system, where tumor cell circulate).

Apoptosis

• Programmed cell death to eliminate damaged cells

Signals

• Cells respond to external signals through signal transduction pathways.
• Signal-transduction pathway: series of molecular events triggered by receptor activation.

Multistep mutations

• accumulation of mutations: process leading to cancer development over time.
• Inherited (hereditary cancer) as well as acquired mutations trigger the development of cancer.
• Cancer is more prevalent in older people due to accumulated mutations over time.

Hallmarks of Cancer

• Cell division disregarding the standard signal
• Inhibition of Apoptosis
• Cell-Cell Adhesion
• Signal Transduction- Cellular response to external signals through response pathways.